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Sample records for barcoded yeast deletion

  1. The Yeast Deletion Collection: A Decade of Functional Genomics

    Science.gov (United States)

    Giaever, Guri; Nislow, Corey

    2014-01-01

    The yeast deletion collections comprise >21,000 mutant strains that carry precise start-to-stop deletions of ∼6000 open reading frames. This collection includes heterozygous and homozygous diploids, and haploids of both MATa and MATα mating types. The yeast deletion collection, or yeast knockout (YKO) set, represents the first and only complete, systematically constructed deletion collection available for any organism. Conceived during the Saccharomyces cerevisiae sequencing project, work on the project began in 1998 and was completed in 2002. The YKO strains have been used in numerous laboratories in >1000 genome-wide screens. This landmark genome project has inspired development of numerous genome-wide technologies in organisms from yeast to man. Notable spinoff technologies include synthetic genetic array and HIPHOP chemogenomics. In this retrospective, we briefly describe the yeast deletion project and some of its most noteworthy biological contributions and the impact that these collections have had on the yeast research community and on genomics in general. PMID:24939991

  2. DNA barcoding analysis of more than 9 000 yeast isolates contributes to quantitative thresholds for yeast species and genera delimitation

    NARCIS (Netherlands)

    Vu, D; Groenewald, M; Szöke, S; Cardinali, G; Eberhardt, U; Stielow, B; de Vries, M; Verkleij, G J M; Crous, P W; Boekhout, T; Robert, V

    DNA barcoding is a global initiative for species identification through sequencing of short DNA sequence markers. Sequences of two loci, ITS and LSU, were generated as barcode data for all (ca. 9k) yeast strains included in the CBS collection, originally assigned to ca. 2 000 species. Taxonomic

  3. The smt-0 mutation which abolishes mating-type switching in fission yeast is a deletion

    DEFF Research Database (Denmark)

    Styrkársdóttir, U; Egel, R; Nielsen, O

    1993-01-01

    Mating-type switching in the fission yeast, S. pombe, is initiated by a DNA double-strand break (DSB) between the mat1 cassette and the H1 homology box. The mat1-cis-acting mutant, smt-0, abolishes mating-type switching and is shown here to be a 263-bp deletion. This deletion starts in the middle...

  4. An extensive deletion causing overproduction of yeast iso-2-cytochrome c

    International Nuclear Information System (INIS)

    McKnight, G.L.; Cardillo, T.S.; Sherman, F.

    1981-01-01

    CYC7-H3 is a cis-dominant regulatory mutation that causes a 20-fold overproduction of yeast iso-2-cytochrome c. The CYC7-H3 mutation is an approximately 5 kb deletion with one breakpoint located in the 5' noncoding region of the CYC7 gene, approximately 200 base from the ATG initiation codon. The deletion apparently fuses a new regulatory region to the structural portion of the CYC7 locus. The CYC7-H3 deletion encompasses the RAD23 locus, which controls UV sensitivity and the ANP1 locus, which controls osmotic sensitivity. The gene cluster CYC7-RAD23-ANP1 displays striking similarity to the gene cluster CYC1-OSM1-RAD7, which controls, respectively, iso-1-cytochrome c, osmotic sensitivity and UV sensitivity. We suggest that these gene clusters are related by an ancient transpositional event

  5. Cellular localization of human p53 expressed in the yeast Saccharomyces cerevisiae: effect of NLSI deletion.

    Science.gov (United States)

    Abdelmoula-Souissi, Salma; Delahodde, Agnès; Bolotin-Fukuhara, Monique; Gargouri, Ali; Mokdad-Gargouri, Raja

    2011-07-01

    The tumor suppressor p53 plays a central role in the regulation of cellular growth and apoptosis. In Saccharomyces cerevisiae, over-expression of the human wtp53 leads to growth inhibition and cell death on minimal medium. In the present work, we showed that deletion of the nuclear localization signal (NLSI) of p53 restores the yeast growth. In this heterologous context, the level of p53∆NLSI was low and the protein mainly located in the cytoplasm while the wtp53 was observed in both the cytoplasmic and nuclear compartments. Interestingly, the wtp53 protein was observed in the mitochondria, whereas the p53∆NLSI protein failed to localize in mitochondria. Moreover, mitochondrial morphology defect and release of cytochrome c in the cytosol were noticed only in the yeast strain expressing the wtp53. In conclusion, our results provide evidence that the human wtp53 is active in S. cerevisiae probably through dependent and independent transcriptional mechanisms leading to cell death. The deletion of the NLSI sequence decreases p53 nuclear translocation as well as its mitochondrial localization and consequently its effect on yeast growth.

  6. A Yeast Mutant Deleted of GPH1 Bears Defects in Lipid Metabolism.

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    Martina Gsell

    Full Text Available In a previous study we demonstrated up-regulation of the yeast GPH1 gene under conditions of phosphatidylethanolamine (PE depletion caused by deletion of the mitochondrial (M phosphatidylserine decarboxylase 1 (PSD1 (Gsell et al., 2013, PLoS One. 8(10:e77380. doi: 10.1371/journal.pone.0077380. Gph1p has originally been identified as a glycogen phosphorylase catalyzing degradation of glycogen to glucose in the stationary growth phase of the yeast. Here we show that deletion of this gene also causes decreased levels of phosphatidylcholine (PC, triacylglycerols and steryl esters. Depletion of the two non-polar lipids in a Δgph1 strain leads to lack of lipid droplets, and decrease of the PC level results in instability of the plasma membrane. In vivo labeling experiments revealed that formation of PC via both pathways of biosynthesis, the cytidine diphosphate (CDP-choline and the methylation route, is negatively affected by a Δgph1 mutation, although expression of genes involved is not down regulated. Altogether, Gph1p besides its function as a glycogen mobilizing enzyme appears to play a regulatory role in yeast lipid metabolism.

  7. The high-throughput yeast deletion fitness data and the theories of dominance.

    Science.gov (United States)

    Manna, F; Gallet, R; Martin, G; Lenormand, T

    2012-05-01

    The development of high-throughput fitness measurement methods provides unprecedented power to test evolutionary theories. However, with this comes new challenges regarding data quality and data analysis. We illustrate this by reanalysing the fitness distribution in several environments of yeast mutants (homo- and heterozygous) from the yeast deletion project. Originally created to study functional properties of genes, evolutionary biologists took advantage of this database to study evolutionary questions, such as dominance for fitness of mutations. We uncover several problems in this data set strongly affecting these questions that have remained unnoticed despite the numerous studies based on it. High-throughput methodologies are necessarily challenging, both experimentally and for data analysis: our point is not to criticize these approaches, but to pinpoint these challenges and to propose several improvements that may help avoid several shortcomings. Further, in the light of this finding, we question the conclusions regarding theories of dominance that have been made using this data set. We show that the data on deletion of small effects are not sufficiently reliable to be informative on this question. On the other hand, deletions of large effect exhibit no correlation between homo- and heterozygous fitness effects, a pattern that sheds new light on the h-s correlation issue, with several consequences for the debate over the different theories of dominance. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  8. Use of a wine yeast deletion collection reveals genes that influence fermentation performance under low-nitrogen conditions.

    Science.gov (United States)

    Peter, Josephine J; Watson, Tommaso L; Walker, Michelle E; Gardner, Jennifer M; Lang, Tom A; Borneman, Anthony; Forgan, Angus; Tran, Tina; Jiranek, Vladimir

    2018-05-01

    A deficiency of nitrogenous nutrients in grape juice can cause stuck and sluggish alcoholic fermentation, which has long been a problem in winemaking. Nitrogen requirements vary between wine yeast strains, and the ability of yeast to assimilate nitrogen depends on the nature and concentration of nitrogen present in the medium. In this study, a wine yeast gene deletion collection (1844 deletants in the haploid AWRI1631 background) was screened to identify genes whose deletion resulted in a reduction in the time taken to utilise all sugars when grown in a chemically defined grape juice medium supplemented with limited nitrogen (75 mg L-1 as a free amino acid mixture). Through micro-scale and laboratory-scale fermentations, 15 deletants were identified that completed fermentation in a shorter time than the wildtype (c.a. 15%-59% time reduction). This group of genes was annotated to biological processes including protein modification, transport, metabolism and ubiquitination (UBC13, MMS2, UBP7, UBI4, BRO1, TPK2, EAR1, MRP17, MFA2 and MVB12), signalling (MFA2) and amino acid metabolism (AAT2). Deletion of MFA2, encoding mating factor-a, resulted in a 55% decrease in fermentation duration. Mfa2Δ was chosen for further investigation to understand how this gene deletion conferred fermentation efficiency in limited nitrogen conditions.

  9. Genome-wide screening for genes whose deletions confer sensitivity to mutagenic purine base analogs in yeast

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    Kozmin Stanislav G

    2005-06-01

    Full Text Available Abstract Background N-hydroxylated base analogs, such as 6-hydroxylaminopurine (HAP and 2-amino-6-hydroxylaminopurine (AHA, are strong mutagens in various organisms due to their ambiguous base-pairing properties. The systems protecting cells from HAP and related noncanonical purines in Escherichia coli include specialized deoxyribonucleoside triphosphatase RdgB, DNA repair endonuclease V, and a molybdenum cofactor-dependent system. Fewer HAP-detoxification systems have been identified in yeast Saccharomyces cerevisiae and other eukaryotes. Cellular systems protecting from AHA are unknown. In the present study, we performed a genome-wide search for genes whose deletions confer sensitivity to HAP and AHA in yeast. Results We screened the library of yeast deletion mutants for sensitivity to the toxic and mutagenic action of HAP and AHA. We identified novel genes involved in the genetic control of base analogs sensitivity, including genes controlling purine metabolism, cytoskeleton organization, and amino acid metabolism. Conclusion We developed a method for screening the yeast deletion library for sensitivity to the mutagenic and toxic action of base analogs and identified 16 novel genes controlling pathways of protection from HAP. Three of them also protect from AHA.

  10. Comparison of a coq7 deletion mutant with other respiration-defective mutants in fission yeast.

    Science.gov (United States)

    Miki, Risa; Saiki, Ryoichi; Ozoe, Yoshihisa; Kawamukai, Makoto

    2008-11-01

    Among the steps in ubiquinone biosynthesis, that catalyzed by the product of the clk-1/coq7 gene has received considerable attention because of its relevance to life span in Caenorhabditis elegans. We analyzed the coq7 ortholog (denoted coq7) in Schizosaccharomyces pombe, to determine whether coq7 has specific roles that differ from those of other coq genes. We first confirmed that coq7 is necessary for the penultimate step in ubiquinone biosynthesis, from the observation that the deletion mutant accumulated the ubiquinone precursor demethoxyubiquinone-10 instead of ubiquinone-10. The coq7 mutant displayed phenotypes characteristic of other ubiquinone-deficient Sc. pombe mutants, namely, hypersensitivity to hydrogen peroxide, a requirement for antioxidants for growth on minimal medium, and an elevated production of sulfide. To compare these phenotypes with those of other respiration-deficient mutants, we constructed cytochrome c (cyc1) and coq3 deletion mutants. We also assessed accumulation of oxidative stress in various ubiquinone-deficient strains and in the cyc1 mutant by measuring mRNA levels of stress-inducible genes and the phosphorylation level of the Spc1 MAP kinase. Induction of ctt1, encoding catalase, and apt1, encoding a 25 kDa protein, but not that of gpx1, encoding glutathione peroxidase, was indistinguishable in four ubiquinone-deficient mutants, indicating that the oxidative stress response operates at similar levels in the tested strains. One new phenotype was observed, namely, loss of viability in stationary phase (chronological life span) in both the ubiquinone-deficient mutant and in the cyc1 mutant. Finally, Coq7 was found to localize in mitochondria, consistent with the possibility that ubiquinone biosynthesis occurs in mitochondria in yeasts. In summary, our results indicate that coq7 is required for ubiquinone biosynthesis and the coq7 mutant is not distinguishable from other ubiquinone-deficient mutants, except that its phenotypes are more

  11. Systematic hybrid LOH: a new method to reduce false positives and negatives during screening of yeast gene deletion libraries

    DEFF Research Database (Denmark)

    Alvaro, D.; Sunjevaric, I.; Reid, R. J.

    2006-01-01

    We have developed a new method, systematic hybrid loss of heterozygosity, to facilitate genomic screens utilizing the yeast gene deletion library. Screening is performed using hybrid diploid strains produced through mating the library haploids with strains from a different genetic background...... complementation of any spurious recessive mutations in the library strain, facilitating attribution of the observed phenotype to the documented gene deletion and dramatically reducing false positive results commonly obtained in library screens. The systematic hybrid LOH method can be applied to virtually any...

  12. Effect of deletion and overexpression of tryptophan metabolism genes on growth and fermentation capacity at low temperature in wine yeast.

    Science.gov (United States)

    López-Malo, María; García-Rios, Estefani; Chiva, Rosana; Guillamon, José Manuel; Martí-Raga, María

    2014-01-01

    Low-temperature fermentations produce wines with greater aromatic complexity, but the success of these fermentations greatly depends on the adaptation of yeast cells to cold. Tryptophan has been previously reported to be a limiting amino acid during Saccharomyces cerevisiae growth at low temperature. The objective of this study was to determine the influence of the tryptophan metabolism on growth and fermentation performance during low-temperature wine fermentation. To this end, we constructed the deletion mutants of the TRP1 and TAT2 genes in a derivative haploid of a commercial wine strain, and the TAT2 gene was overexpressed in the prototroph and auxotroph (Δtrp1) backgrounds. Then we characterized growth and fermentation activity during wine fermentation at low and optimum temperatures. Our results partially support the role of this amino acid in cold yeast growth. Although deletion of TRP1 impaired amino acid uptake and the growth rate at low temperature in synthetic must, this growth impairment did not affect the fermentation rate. Deletion of TAT2 endorsed this strain with the highest nitrogen consumption capacity and the greatest fermentation activity at low temperature. Our results also evidenced reduced ammonium consumption in all the strains at low temperature. © 2014 American Institute of Chemical Engineers.

  13. Deletions, duplications and transpositions of the COR segment that encompasses the structural gene of yeast iso-1-cytochrome c

    Energy Technology Data Exchange (ETDEWEB)

    Stiles, J.I.; Friedman, L.R.; Sherman, F.

    1980-01-01

    It has been recently found that a specific chromosomal segment, in certain but not all laboratory strains of Saccharomyces cerevisiae, is deleted and transposed at high frequencies. This segment, denoted COR, encompasses the three closely linked loci CYC1, OSM1 and RAD7 which control iso-1-cytochrome c, osmotic sensitivity and UV-sensitivity, respectively. Two types of apparently normal laboratory strains of yeast designated COR1 and COR2, were uncovered after the examination of the frequencies and types of mutations causing either deficiencies or overproduction of iso-1-cytochrome c; in contrast to COR1 strains which give predominantly point mutations causing deficiencies of iso-1-cytochrome c, COR2 strains give rise to deletions and transpositions of the COR segment. We have undertaken a systematic investigation of the physical structure and genetic properties of the COR region and of the aberrations arising in COR2 strains.

  14. Deletion of Genes Encoding Arginase Improves Use of "Heavy" Isotope-Labeled Arginine for Mass Spectrometry in Fission Yeast.

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    Weronika E Borek

    Full Text Available The use of "heavy" isotope-labeled arginine for stable isotope labeling by amino acids in cell culture (SILAC mass spectrometry in the fission yeast Schizosaccharomyces pombe is hindered by the fact that under normal conditions, arginine is extensively catabolized in vivo, resulting in the appearance of "heavy"-isotope label in several other amino acids, most notably proline, but also glutamate, glutamine and lysine. This "arginine conversion problem" significantly impairs quantification of mass spectra. Previously, we developed a method to prevent arginine conversion in fission yeast SILAC, based on deletion of genes involved in arginine catabolism. Here we show that although this method is indeed successful when (13C6-arginine (Arg-6 is used for labeling, it is less successful when (13C6(15N4-arginine (Arg-10, a theoretically preferable label, is used. In particular, we find that with this method, "heavy"-isotope label derived from Arg-10 is observed in amino acids other than arginine, indicating metabolic conversion of Arg-10. Arg-10 conversion, which severely complicates both MS and MS/MS analysis, is further confirmed by the presence of (13C5(15N2-arginine (Arg-7 in arginine-containing peptides from Arg-10-labeled cells. We describe how all of the problems associated with the use of Arg-10 can be overcome by a simple modification of our original method. We show that simultaneous deletion of the fission yeast arginase genes car1+ and aru1+ prevents virtually all of the arginine conversion that would otherwise result from the use of Arg-10. This solution should enable a wider use of heavy isotope-labeled amino acids in fission yeast SILAC.

  15. Acetic acid inhibits nutrient uptake in Saccharomyces cerevisiae: auxotrophy confounds the use of yeast deletion libraries for strain improvement.

    Science.gov (United States)

    Ding, Jun; Bierma, Jan; Smith, Mark R; Poliner, Eric; Wolfe, Carole; Hadduck, Alex N; Zara, Severino; Jirikovic, Mallori; van Zee, Kari; Penner, Michael H; Patton-Vogt, Jana; Bakalinsky, Alan T

    2013-08-01

    Acetic acid inhibition of yeast fermentation has a negative impact in several industrial processes. As an initial step in the construction of a Saccharomyces cerevisiae strain with increased tolerance for acetic acid, mutations conferring resistance were identified by screening a library of deletion mutants in a multiply auxotrophic genetic background. Of the 23 identified mutations, 11 were then introduced into a prototrophic laboratory strain for further evaluation. Because none of the 11 mutations was found to increase resistance in the prototrophic strain, potential interference by the auxotrophic mutations themselves was investigated. Mutants carrying single auxotrophic mutations were constructed and found to be more sensitive to growth inhibition by acetic acid than an otherwise isogenic prototrophic strain. At a concentration of 80 mM acetic acid at pH 4.8, the initial uptake of uracil, leucine, lysine, histidine, tryptophan, phosphate, and glucose was lower in the prototrophic strain than in a non-acetic acid-treated control. These findings are consistent with two mechanisms by which nutrient uptake may be inhibited. Intracellular adenosine triphosphate (ATP) levels were severely decreased upon acetic acid treatment, which likely slowed ATP-dependent proton symport, the major form of transport in yeast for nutrients other than glucose. In addition, the expression of genes encoding some nutrient transporters was repressed by acetic acid, including HXT1 and HXT3 that encode glucose transporters that operate by facilitated diffusion. These results illustrate how commonly used genetic markers in yeast deletion libraries complicate the effort to isolate strains with increased acetic acid resistance.

  16. Genetic barcodes

    Science.gov (United States)

    Weier, Heinz -Ulrich G

    2015-08-04

    Herein are described multicolor FISH probe sets termed "genetic barcodes" targeting several cancer or disease-related loci to assess gene rearrangements and copy number changes in tumor cells. Two, three or more different fluorophores are used to detect the genetic barcode sections thus permitting unique labeling and multilocus analysis in individual cell nuclei. Gene specific barcodes can be generated and combined to provide both numerical and structural genetic information for these and other pertinent disease associated genes.

  17. 9,10-Phenanthrenequinone induces DNA deletions and forward mutations via oxidative mechanisms in the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Rodriguez, Chester E; Sobol, Zhanna; Schiestl, Robert H

    2008-03-01

    The estimated cancer risk from diesel exhaust particles (DEP) in the air is approximately 70% of the cancer risk from all air pollutants. DEP is comprised of a complex mixture of chemicals whose carcinogenic potential has not been adequately assessed. The polycyclic aromatic hydrocarbon quinone 9,10-phenanthrenequinone (9,10 PQ) is a major component of DEP and a suspect genotoxic agent for DEP induced DNA damage. 9,10 PQ undergoes redox cycling to produce reactive oxygen species that can lead to oxidative DNA damage. We used two systems in the yeast Saccharomyces cerevisiae to examine possible differential genotoxicity of 9,10 PQ. The DEL assay measures intra-chromosomal homologous recombination leading to DNA deletions and the CAN assay measures forward mutations leading to canavanine resistance. Cells were exposed to 9,10 PQ aerobically and anaerobically followed by DNA damage assessment. The results indicate that 9,10 PQ induces DNA deletions and point mutations in the presence of oxygen while exhibiting negligible effects anaerobically. In contrast to the cytotoxicity observed aerobically, the anaerobic effects of 9,10 PQ seem to be cytostatic in nature, reducing growth without affecting cell viability. Thus, 9,10 PQ requires oxygen for genotoxicity while different toxicities exhibited aerobically and anaerobically suggest multiple mechanisms of action.

  18. Microarray data analyses of yeast RNA Pol I subunit RPA12 deletion strain

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    Kamlesh Kumar Yadav

    2016-06-01

    Full Text Available The ribosomal RNA (rRNA biosynthesis is the most energy consuming process in all living cells and the majority of total transcription activity is dedicated for synthesizing rRNA. The cells may adjust the synthesis of rRNA with the availability of resources. rRNA is mainly synthesized by RNA polymerase I that is composed of 14 subunits. Deletion of RPA12, 14, 39 and 49 are viable. RPA12 is a very small protein (13.6 kDa, and the amount of protein in the cells is very high (12,000 molecules per cell, but the role of this protein is unknown in other cellular metabolic processes (Kulak et al., 2014 [1]. RPA12 consists of two zinc-binding domains and it is required for the termination of rRNA synthesis (Mullem et al., 2002 [2]. Deletions of RPA12 in Saccharomyces cerevisiae and Schizosaccharomyces pombe cause a conditional growth defect (Nogi et al., 1993 [3]. In S. pombe, C-terminal deletion behaves like wild-type (Imazawa et al., 2001 [4]. This prompted us to investigate in detail the physiological role of RPA12 in S. cerevisiae, we performed the microarray of rpa12∆ strain and deposited into Gene Expression Omnibus under GSE68731. The analysis of microarray data revealed that the expression of major cellular metabolism genes is high. The amino acid biosynthesis, nonpolar lipid biosynthesis and glucose metabolic genes are highly expressed. The analyses also revealed that the rpa12∆ cells have an uncontrolled synthesis of cell metabolites, so RPA12 could be a master regulator for whole cellular metabolism.

  19. CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

    Science.gov (United States)

    Lemos, Brenda R; Kaplan, Adam C; Bae, Ji Eun; Ferrazzoli, Alexander E; Kuo, James; Anand, Ranjith P; Waterman, David P; Haber, James E

    2018-02-13

    Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

  20. Different roles of eukaryotic MutS and MutL complexes in repair of small insertion and deletion loops in yeast.

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    Nina V Romanova

    2013-10-01

    Full Text Available DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors. In order to understand how this fidelity is maintained, it is important to uncover the relative specificities of the different components of mismatch repair. There are two major mispair recognition complexes in eukaryotes that are homologues of bacterial MutS proteins, MutSα and MutSβ, with MutSα recognizing base-base mismatches and small loop mispairs and MutSβ recognizing larger loop mispairs. Upon recognition of a mispair, the MutS complexes then interact with homologues of the bacterial MutL protein. Loops formed on the primer strand during replication lead to insertion mutations, whereas loops on the template strand lead to deletions. We show here in yeast, using oligonucleotide transformation, that MutSα has a strong bias toward repair of insertion loops, while MutSβ has an even stronger bias toward repair of deletion loops. Our results suggest that this bias in repair is due to the different interactions of the MutS complexes with the MutL complexes. Two mutants of MutLα, pms1-G882E and pms1-H888R, repair deletion mispairs but not insertion mispairs. Moreover, we find that a different MutL complex, MutLγ, is extremely important, but not sufficient, for deletion repair in the presence of either MutLα mutation. MutSβ is present in many eukaryotic organisms, but not in prokaryotes. We suggest that the biased repair of deletion mispairs may reflect a critical eukaryotic function of MutSβ in mismatch repair.

  1. Transcriptome analysis of acetic-acid-treated yeast cells identifies a large set of genes whose overexpression or deletion enhances acetic acid tolerance.

    Science.gov (United States)

    Lee, Yeji; Nasution, Olviyani; Choi, Eunyong; Choi, In-Geol; Kim, Wankee; Choi, Wonja

    2015-08-01

    Acetic acid inhibits the metabolic activities of Saccharomyces cerevisiae. Therefore, a better understanding of how S. cerevisiae cells acquire the tolerance to acetic acid is of importance to develop robust yeast strains to be used in industry. To do this, we examined the transcriptional changes that occur at 12 h post-exposure to acetic acid, revealing that 56 and 58 genes were upregulated and downregulated, respectively. Functional categorization of them revealed that 22 protein synthesis genes and 14 stress response genes constituted the largest portion of the upregulated and downregulated genes, respectively. To evaluate the association of the regulated genes with acetic acid tolerance, 3 upregulated genes (DBP2, ASC1, and GND1) were selected among 34 non-protein synthesis genes, and 54 viable mutants individually deleted for the downregulated genes were retrieved from the non-essential haploid deletion library. Strains overexpressing ASC1 and GND1 displayed enhanced tolerance to acetic acid, whereas a strain overexpressing DBP2 was sensitive. Fifty of 54 deletion mutants displayed enhanced acetic acid tolerance. Three chosen deletion mutants (hsps82Δ, ato2Δ, and ssa3Δ) were also tolerant to benzoic acid but not propionic and sorbic acids. Moreover, all those five (two overexpressing and three deleted) strains were more efficient in proton efflux and lower in membrane permeability and internal hydrogen peroxide content than controls. Individually or in combination, those physiological changes are likely to contribute at least in part to enhanced acetic acid tolerance. Overall, information of our transcriptional profile was very useful to identify molecular factors associated with acetic acid tolerance.

  2. Unicolor woven barcode; Unicolor nuno barcode

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    Development was made on a woven barcode system of single and inconspicuous color of thermal light emission infrared ray detecting system. This is a new barcode system to detect characteristic infrared ray of 4.5 {mu}m from polyacrylonitrile fiber constituting the barcode when it is heated to 70 degrees C. Codes can normally be read in 0.7 second. Differing from transparent barcode made with fluorescent color, the new barcode can be made into a thread, which resulted in realizing a woven barcode. This woven barcode could be applied in different and new ways utilizing its inconspicuousness, in addition to applicability to simplification of control in uniform rental and linen supply operations subject to repeated washing. (translated by NEDO)

  3. Tol1, a Fission Yeast Phosphomonoesterase, Is an In Vivo Target of Lithium, and Its Deletion Leads to Sulfite Auxotrophy

    Science.gov (United States)

    Miyamoto, Rumi; Sugiura, Reiko; Kamitani, Shinya; Yada, Tomoko; Lu, Yabin; Sio, Susie O.; Asakura, Masahiro; Matsuhisa, Akio; Shuntoh, Hisato; Kuno, Takayoshi

    2000-01-01

    Lithium is the drug of choice for the treatment of bipolar affective disorder. The identification of an in vivo target of lithium in fission yeast as a model organism may help in the understanding of lithium therapy. For this purpose, we have isolated genes whose overexpression improved cell growth under high LiCl concentrations. Overexpression of tol1+, one of the isolated genes, increased the tolerance of wild-type yeast cells for LiCl but not for NaCl. tol1+ encodes a member of the lithium-sensitive phosphomonoesterase protein family, and it exerts dual enzymatic activities, 3′(2′),5′-bisphosphate nucleotidase and inositol polyphosphate 1-phosphatase. tol1+ gene-disrupted cells required high concentrations of sulfite in the medium for growth. Consistently, sulfite repressed the sulfate assimilation pathway in fission yeast. However, tol1+ gene-disrupted cells could not fully recover from their growth defect and abnormal morphology even when the medium was supplemented with sulfite, suggesting the possible implication of inositol polyphosphate 1-phosphatase activity for cell growth and morphology. Given the remarkable functional conservation of the lithium-sensitive dual-specificity phosphomonoesterase between fission yeast and higher-eukaryotic cells during evolution, it may represent a likely in vivo target of lithium action across many species. PMID:10850973

  4. A resource for functional profiling of noncoding RNA in the yeastSaccharomyces cerevisiae.

    Science.gov (United States)

    Parker, Steven; Fraczek, Marcin G; Wu, Jian; Shamsah, Sara; Manousaki, Alkisti; Dungrattanalert, Kobchai; de Almeida, Rogerio Alves; Estrada-Rivadeneyra, Diego; Omara, Walid; Delneri, Daniela; O'Keefe, Raymond T

    2017-08-01

    Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research. © 2017 Parker et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  5. Effect of deletion and overexpression of tryptophan metabolism genes on growth and fermentation capacity at low temperature in wine yeast

    OpenAIRE

    Martí-Raga, M.; Guillamon, J.M.; Chiva, R.; García-Rios, E.; López-Malo, M.

    2014-01-01

    10.1002/btpr.1915 Low-temperature fermentations produce wines with greater aromatic complexity, but the success of these fermentations greatly depends on the adaptation of yeast cells to cold. Tryptophan has been previously reported to be a limiting amino acid during Saccharomyces cerevisiae growth at low temperature. The objective of this study was to determine the influence of the tryptophan metabolism on growth and fermentation performance during low-temperature wine fermentation. To t...

  6. Fungal DNA barcoding.

    Science.gov (United States)

    Xu, Jianping

    2016-11-01

    Fungi are ubiquitous in both natural and human-made environments. They play important roles in the health of plants, animals, and humans, and in broad ecosystem functions. Thus, having an efficient species-level identification system could significantly enhance our ability to treat fungal diseases and to monitor the spatial and temporal patterns of fungal distributions and migrations. DNA barcoding is a potent approach for rapid identification of fungal specimens, generating novel species hypothesis, and guiding biodiversity and ecological studies. In this mini-review, I briefly summarize (i) the history of DNA sequence-based fungal identification; (ii) the emergence of the ITS region as the consensus primary fungal barcode; (iii) the use of the ITS barcodes to address a variety of issues on fungal diversity from local to global scales, including generating a large number of species hypothesis; and (iv) the problems with the ITS barcode region and the approaches to overcome these problems. Similar to DNA barcoding research on plants and animals, significant progress has been achieved over the last few years in terms of both the questions being addressed and the foundations being laid for future research endeavors. However, significant challenges remain. I suggest three broad areas of research to enhance the usefulness of fungal DNA barcoding to meet the current and future challenges: (i) develop a common set of primers and technologies that allow the amplification and sequencing of all fungi at both the primary and secondary barcode loci; (ii) compile a centralized reference database that includes all recognized fungal species as well as species hypothesis, and allows regular updates from the research community; and (iii) establish a consensus set of new species recognition criteria based on barcode DNA sequences that can be applied across the fungal kingdom.

  7. The low-temperature- and salt-induced RCI2A gene of Arabidopsis complements the sodium sensitivity caused by a deletion of the homologous yeast gene SNA1.

    Science.gov (United States)

    Nylander, M; Heino, P; Helenius, E; Palva, E T; Ronne, H; Welin, B V

    2001-02-01

    Two closely related, tandemly arranged, low-temperature- and salt-induced Arabidopsis genes, corresponding to the previously isolated cDNAs RCI2A and RCI2B, were isolated and characterized. The RCI2A transcript accumulated primarily in response to low temperature or high salinity, and to a lesser extent in response to ABA treatment or water deficit stress. The RCI2B transcript was present at much lower levels than RCI2A, and could only be detected by reverse transcription-PCR amplification. The predicted 6 kDa RCI2 proteins are highly hydrophobic and contain two putative membrane-spanning regions. The polypeptides exhibit extensive similarity to deduced low-temperature- and/or salt-induced proteins from barley, wheat grass and strawberry, and to predicted proteins from bacteria, fungi, nematodes and yeast. Interestingly, we found that a deletion of the RCI2 homologous gene, SNA1 (YRD276c), in yeast causes a salt-sensitive phenotype. This effect is specific for sodium, since no growth defect was observed for the sna1 mutant on 1.7 M sorbitol, 1 M KCl or 0.6 M LiCl. Finally, we found that the Arabidopsis RCI2A cDNA can complement the sna1 mutant when expressed in yeast, indicating that the plant and yeast proteins have similar functions during high salt stress.

  8. Unsaturated fatty acids-dependent linkage between respiration and fermentation revealed by deletion of hypoxic regulatory KlMGA2 gene in the facultative anaerobe-respiratory yeast Kluyveromyces lactis.

    Science.gov (United States)

    Ottaviano, Daniela; Montanari, Arianna; De Angelis, Lorenzo; Santomartino, Rosa; Visca, Andrea; Brambilla, Luca; Rinaldi, Teresa; Bello, Cristiano; Reverberi, Massimo; Bianchi, Michele M

    2015-08-01

    In the yeast Kluyveromyces lactis, the inactivation of structural or regulatory glycolytic and fermentative genes generates obligate respiratory mutants which can be characterized by sensitivity to the mitochondrial drug antimycin A on glucose medium (Rag(-) phenotype). Rag(-) mutations can occasionally be generated by the inactivation of genes not evidently related to glycolysis or fermentation. One such gene is the hypoxic regulatory gene KlMGA2. In this work, we report a study of the many defects, in addition to the Rag(-) phenotype, generated by KlMGA2 deletion. We analyzed the fermentative and respiratory metabolism, mitochondrial functioning and morphology in the Klmga2Δ strain. We also examined alterations in the regulation of the expression of lipid biosynthetic genes, in particular fatty acids, ergosterol and cardiolipin, under hypoxic and cold stress and the phenotypic suppression by unsaturated fatty acids of the deleted strain. Results indicate that, despite the fact that the deleted mutant strain had a typical glycolytic/fermentative phenotype and KlMGA2 is a hypoxic regulatory gene, the deletion of this gene generated defects linked to mitochondrial functions suggesting new roles of this protein in the general regulation and cellular fitness of K. lactis. Supplementation of unsaturated fatty acids suppressed or modified these defects suggesting that KlMga2 modulates membrane functioning or membrane-associated functions, both cytoplasmic and mitochondrial. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Barcode uses and abuses

    Energy Technology Data Exchange (ETDEWEB)

    KEENEN,MARTHA JANE; NUSBAUM,ANNA W.

    2000-05-18

    Barcodes are something that everybody sees every day; so common as to be taken for granted and normally unnoticed. Readable, no one reads them. They are used to allow machines to identify a wide variety of non-electronic, real life objects. Barcode is one of the earliest types of what is now called ``Automatic Identification and Data Capture'' (AIDC), meaning ``data was transmitted into whatever system by something other than typing or hand-writing.'' There are 18 technologies, broken down into six categories--biometrics, electromagnetic, magnetic, optical, Smart Cards, Touch--included in the AIDC concept. Many are used jointly with or as adjuncts to a basic barcode system of some type. All are based on assignment of a unique identifier to the object, usually a number. The uniqueness presumption makes barcode systems very applicable and appropriate to the nuclear information management venue as they inherently comply with the Nuclear Quality Assurance (NQA-1) requirements. Barcode systems belong to the optical category of AIDC. It is very old in usage as these technologies go, having first been patented in 1949. It astonished me, in researching this paper, to find that there are over 250 types of barcode (symbologies), each with its own specialized attributes, though only a few dozen are in active use. The initial uses were in the early 1950s and diversity of use is ever increasing as people find new ways to make this versatile old technology work. To what else could it be applied, in the future? This paper attempts to answer this.

  10. Toxicity of CuO nanoparticles to yeast Saccharomyces cerevisiae BY4741 wild-type and its nine isogenic single-gene deletion mutants.

    Science.gov (United States)

    Kasemets, Kaja; Suppi, Sandra; Künnis-Beres, Kai; Kahru, Anne

    2013-03-18

    A suite of eight tentatively oxidative stress response-deficient Saccharomyces cerevisiae BY4741 single-gene mutants (sod1Δ, sod2Δ, yap1Δ, cta1Δ, ctt1Δ, gsh1Δ, glr1Δ, and ccs1Δ) and one copper-vulnerable mutant (cup2Δ) was used to elucidate weather the toxicity of CuO nanoparticles to S. cerevisiae is mediated by oxidative stress (OS). Specifically, sensitivity profiles of mutants' phenotypes and wild-type (wt) upon exposure to nano-CuO were compared. As controls, CuSO4 (solubility), bulk-CuO (size), H2O2, and menadione (OS) were used. Growth inhibition of wt and mutant strains was studied in rich YPD medium and cell viability in deionized water (DI). Dissolved Cu-ions were quantified by recombinant metal-sensing bacteria and chemical analysis. To wt strain nano-CuO was 32-fold more toxic than bulk-CuO: 24-h IC50 4.8 and 155 mg/L in DI and 643 and >20000 mg/L in YPD, respectively. In toxicant-free YPD medium, all mutants had practically similar growth patterns as wt. However, the mutant strains sod1Δ, sod2Δ, ccs1Δ, and yap1Δ showed up to 12-fold elevated sensitivity toward OS standard chemicals menadione and H2O2 but not to nano-CuO, indicating that CuO nanoparticles exerted toxicity to yeast cells via different mechanisms. The most vulnerable strain to all studied Cu compounds was the copper stress response-deficient strain cup2Δ (∼16-fold difference with wt), indicating that the toxic effect of CuO (nano)particles proceeds via dissolved Cu-ions. The dissolved copper solely explained the toxicity of nano-CuO in DI but not in YPD. Assumingly, in YPD nano-CuO acquired a coating of peptides/proteins and sorbed onto the yeast's outer surface, resulting in their increased solubility in the close vicinity of yeast cells and increased uptake of Cu-ions that was not registered by the assays used for the analysis of dissolved Cu-ions in the test medium. Lastly, as yeast retained its viability in DI even by 24th hour of incubation, the profiling of the acute

  11. Deletion of mitochondrial ATPase inhibitor in the yeast Saccharomyces cerevisiae decreased cellular and mitochondrial ATP levels under non-nutritional conditions and induced a respiration-deficient cell-type.

    Science.gov (United States)

    Lu, Y M; Miyazawa, K; Yamaguchi, K; Nowaki, K; Iwatsuki, H; Wakamatsu, Y; Ichikawa, N; Hashimoto, T

    2001-12-01

    T(1), a mutant yeast lacking three regulatory proteins of F(1)F(o)ATPase, namely ATPase inhibitor, 9K protein and 15K protein, grew on non-fermentable carbon source at the same rate as normal cells but was less viable when incubated in water. During the incubation, the cellular ATP content decreased rapidly in the T(1) cells but not in normal cells, and respiration-deficient cells appeared among the T(1) cells. The same mutation was also induced in D26 cells lacking only the ATPase inhibitor. Overexpression of the ATPase inhibitor in YC63 cells, which were derived from the D26 strain harboring an expression vector containing the gene of the ATPase inhibitor, prevented the decrease of cellular ATP level and the mutation. Isolated T(1) mitochondria exhibited ATP hydrolysis for maintenance of membrane potential when antimycin A was added to the mitochondrial suspension, while normal and YC63 mitochondria continued to show low hydrolytic activity and low membrane potential. Thus, it is likely that deletion of the ATPase inhibitor induces ATPase activity of F(1)F(o)ATPase to create a dispensable membrane potential under the non-nutritional conditions and that this depletes mitochondrial and cellular ATP. The depletion of mitochondrial ATP in turn leads to occurrence of aberrant DNA in mitochondria.

  12. Barcoding Queensland Fruit Flies (Bactrocera tryoni): impediments and improvements.

    Science.gov (United States)

    Blacket, Mark J; Semeraro, Linda; Malipatil, Mallik B

    2012-05-01

    Identification of adult fruit flies primarily involves microscopic examination of diagnostic morphological characters, while immature stages, such as larvae, can be more problematic. One of the Australia's most serious horticultural pests, the Queensland Fruit Fly (Bactrocera tryoni: Tephritidae), is of particular biosecurity/quarantine concern as the immature life stages occur within food produce and can be difficult to identify using morphological characteristics. DNA barcoding of the mitochondrial Cytochrome Oxidase I (COI) gene could be employed to increase the accuracy of fruit fly species identifications. In our study, we tested the utility of standard DNA barcoding techniques and found them to be problematic for Queensland Fruit Flies, which (i) possess a nuclear copy (a numt pseudogene) of the barcoding region of COI that can be co-amplified; and (ii) as in previous COI phylogenetic analyses closely related B. tryoni complex species appear polyphyletic. We found that the presence of a large deletion in the numt copy of COI allowed an alternative primer to be designed to only amplify the mitochondrial COI locus in tephritid fruit flies. Comparisons of alternative commonly utilized mitochondrial genes, Cytochrome Oxidase II and Cytochrome b, revealed a similar level of variation to COI; however, COI is the most informative for DNA barcoding, given the large number of sequences from other tephritid fruit fly species available for comparison. Adopting DNA barcoding for the identification of problematic fly specimens provides a powerful tool to distinguish serious quarantine fruit fly pests (Tephritidae) from endemic fly species of lesser concern. © 2012 Blackwell Publishing Ltd.

  13. Levenshtein error-correcting barcodes for multiplexed DNA sequencing.

    Science.gov (United States)

    Buschmann, Tilo; Bystrykh, Leonid V

    2013-09-11

    High-throughput sequencing technologies are improving in quality, capacity and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag or barcode that is attached to the sequencing or amplification primer and hence appears at the beginning of the sequence in every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence.Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and Levenshtein codes. Levenshtein codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this paper we demonstrate the decreased error correction capability of Levenshtein codes in a DNA context and suggest an adaptation of Levenshtein codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaption we take the DNA context into account and redefine the word length whenever an insertion or deletion is revealed. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. We present an adaptation of Levenshtein codes to DNA contexts capable of correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable

  14. 76 FR 34871 - Mobile Barcode Promotion

    Science.gov (United States)

    2011-06-15

    .... The mobile barcodes must be used for marketing, promotional or educational purposes. They may not be... POSTAL SERVICE 39 CFR Part 111 Mobile Barcode Promotion AGENCY: Postal Service TM . ACTION: Final... and flats, and Standard Mail[reg] letters and flats bearing two-dimensional mobile barcodes. DATES...

  15. Improvement in two-dimensional barcode

    Indian Academy of Sciences (India)

    A lot of work has been already done to deal with such variations but acceptable results have not yet been achieved. The objective behind colour barcode is to increase the capacity to 3 fold as compared with 2D monochrome barcode. In this paper we proposed a novel approach that will increase the capacity of barcode ...

  16. Profiling of the toxicity mechanisms of coated and uncoated silver nanoparticles to yeast Saccharomyces cerevisiae BY4741 using a set of its 9 single-gene deletion mutants defective in oxidative stress response, cell wall or membrane integrity and endocytosis.

    Science.gov (United States)

    Käosaar, Sandra; Kahru, Anne; Mantecca, Paride; Kasemets, Kaja

    2016-09-01

    The widespread use of nanosilver in various antibacterial, antifungal, and antiviral products warrants the studies of the toxicity pathways of nanosilver-enabled materials toward microbes and viruses. We profiled the toxicity mechanisms of uncoated, casein-coated, and polyvinylpyrrolidone-coated silver nanoparticles (AgNPs) using Saccharomyces cerevisiae wild-type (wt) and its 9 single-gene deletion mutants defective in oxidative stress (OS) defense, cell wall/membrane integrity, and endocytosis. The 48-h growth inhibition assay in organic-rich growth medium and 24-h cell viability assay in deionized (DI) water were applied whereas AgNO3, H2O2, and SDS served as positive controls. Both coated AgNPs (primary size 8-12nm) were significantly more toxic than the uncoated (~85nm) AgNPs. All studied AgNPs were ~30 times more toxic if exposed to yeast cells in DI water than in the rich growth medium: the IC50 based on nominal concentration of AgNPs in the growth inhibition test ranged from 77 to 576mg Ag/L and in the cell viability test from 2.7 to 18.7mg Ag/L, respectively. Confocal microscopy showed that wt but not endocytosis mutant (end3Δ) internalized AgNPs. Comparison of toxicity patterns of wt and mutant strains defective in OS defense and membrane integrity revealed that the toxicity of the studied AgNPs to S. cerevisiae was not caused by the OS or cell wall/membrane permeabilization. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Statistical Approaches for DNA Barcoding

    DEFF Research Database (Denmark)

    Nielsen, Rasmus; Matz, M.

    2006-01-01

    The use of DNA as a tool for species identification has become known as "DNA barcoding" (Floyd et al., 2002; Hebert et al., 2003; Remigio and Hebert, 2003). The basic idea is straightforward: a small amount of DNA is extracted from the specimen, amplified and sequenced. The gene region sequenced...... is chosen so that it is nearly identical among individuals of the same species, but different between species, and therefore its sequence, can serve as an identification tag for the species ("DNA barcode"). By matching the sequence obtained from an unidentified specimen ("query" sequence) to the database...

  18. A microarray-based genetic screen for yeast chronological aging factors.

    Directory of Open Access Journals (Sweden)

    Mirela Matecic

    2010-04-01

    Full Text Available Model organisms have played an important role in the elucidation of multiple genes and cellular processes that regulate aging. In this study we utilized the budding yeast, Saccharomyces cerevisiae, in a large-scale screen for genes that function in the regulation of chronological lifespan, which is defined by the number of days that non-dividing cells remain viable. A pooled collection of viable haploid gene deletion mutants, each tagged with unique identifying DNA "bar-code" sequences was chronologically aged in liquid culture. Viable mutants in the aging population were selected at several time points and then detected using a microarray DNA hybridization technique that quantifies abundance of the barcode tags. Multiple short- and long-lived mutants were identified using this approach. Among the confirmed short-lived mutants were those defective for autophagy, indicating a key requirement for the recycling of cellular organelles in longevity. Defects in autophagy also prevented lifespan extension induced by limitation of amino acids in the growth media. Among the confirmed long-lived mutants were those defective in the highly conserved de novo purine biosynthesis pathway (the ADE genes, which ultimately produces IMP and AMP. Blocking this pathway extended lifespan to the same degree as calorie (glucose restriction. A recently discovered cell-extrinsic mechanism of chronological aging involving acetic acid secretion and toxicity was suppressed in a long-lived ade4Delta mutant and exacerbated by a short-lived atg16Delta autophagy mutant. The identification of multiple novel effectors of yeast chronological lifespan will greatly aid in the elucidation of mechanisms that cells and organisms utilize in slowing down the aging process.

  19. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

    Science.gov (United States)

    Schoch, Conrad L; Seifert, Keith A; Huhndorf, Sabine; Robert, Vincent; Spouge, John L; Levesque, C André; Chen, Wen

    2012-04-17

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

  20. Self-registering spread-spectrum barcode method

    Science.gov (United States)

    Cummings, Eric B.; Even Jr., William R.

    2004-11-09

    A novel spread spectrum barcode methodology is disclosed that allows a barcode to be read in its entirety even when a significant fraction or majority of the barcode is obscured. The barcode methodology makes use of registration or clocking information that is distributed along with the encoded user data across the barcode image. This registration information allows for the barcode image to be corrected for imaging distortion such as zoom, rotation, tilt, curvature, and perspective.

  1. Barcoding poplars (Populus L. from western China.

    Directory of Open Access Journals (Sweden)

    Jianju Feng

    Full Text Available BACKGROUND: Populus is an ecologically and economically important genus of trees, but distinguishing between wild species is relatively difficult due to extensive interspecific hybridization and introgression, and the high level of intraspecific morphological variation. The DNA barcoding approach is a potential solution to this problem. METHODOLOGY/PRINCIPAL FINDINGS: Here, we tested the discrimination power of five chloroplast barcodes and one nuclear barcode (ITS among 95 trees that represent 21 Populus species from western China. Among all single barcode candidates, the discrimination power is highest for the nuclear ITS, progressively lower for chloroplast barcodes matK (M, trnG-psbK (G and psbK-psbI (P, and trnH-psbA (H and rbcL (R; the discrimination efficiency of the nuclear ITS (I is also higher than any two-, three-, or even the five-locus combination of chloroplast barcodes. Among the five combinations of a single chloroplast barcode plus the nuclear ITS, H+I and P+I differentiated the highest and lowest portion of species, respectively. The highest discrimination rate for the barcodes or barcode combinations examined here is 55.0% (H+I, and usually discrimination failures occurred among species from sympatric or parapatric areas. CONCLUSIONS/SIGNIFICANCE: In this case study, we showed that when discriminating Populus species from western China, the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions. Meanwhile, combining the ITS region with chloroplast regions may improve the barcoding success rate and assist in detecting recent interspecific hybridizations. Failure to discriminate among several groups of Populus species from sympatric or parapatric areas may have been the result of incomplete lineage sorting, frequent interspecific hybridizations and introgressions. We agree with a previous proposal for constructing a tiered barcoding system in

  2. DNA barcodes of Philippine accipitrids.

    Science.gov (United States)

    Ong, Perry S; Luczon, Adrian U; Quilang, Jonas P; Sumaya, Anna Mae T; Ibañez, Jayson C; Salvador, Dennis J; Fontanilla, Ian Kendrich C

    2011-03-01

    DNA barcoding is a molecular method that rapidly identifies an individual to a known taxon or its closest relative based on a 650-bp fragment of the cytochrome c oxidase subunit I (COI). In this study, DNA barcodes of members of the family Accipitridae, including Haliastur indus (brahminy kite), Haliaeetus leucogaster (white-bellied sea eagle), Ichthyophaga ichthyaetus (grey-headed fish eagle), Spilornis holospilus (crested serpent-eagle), Spizaetus philippensis (Philippine hawk-eagle), and Pithecophaga jefferyi (Philippine eagle), are reported for the first time. All individuals sampled are kept at the Philippine Eagle Center in Davao City, Philippines. Basic local alignment search tool results demonstrated that the COI sequences for these species were unique. The COI gene trees constructed using the maximum-likelihood and neighbour-joining (NJ) methods supported the monophyly of the booted eagles of the Aquilinae and the sea eagles of the Haliaeetinae but not the kites of the Milvinae. © 2010 Blackwell Publishing Ltd.

  3. Improvement in two-dimensional barcode

    Indian Academy of Sciences (India)

    SONAM WASULE

    ing devices uses red, green and blue sensing channels. This causes problem of intensity and depth variation during printing and scanning. The problem of colour ... and data security and compression, over the traditional black and white barcodes. The development of colour barcodes is still challenging since the intensity ...

  4. Microcoding: the second step in DNA barcoding

    NARCIS (Netherlands)

    Summerbell, R.C.; Lévesque, C.A.; Seifert, K.A.; Bovers, M.; Fell, J.W.; Diaz, M.R.; Boekhout, T.; Hoog, de G.S.; Stalpers, J.A.; Crous, P.W.

    2005-01-01

    After the process of DNA barcoding has become well advanced in a group of organisms, as it has in the economically important fungi, the question then arises as to whether shorter and literally more barcode-like DNA segments should be utilized to facilitate rapid identification and, where applicable,

  5. DNA Barcoding Investigations Bring Biology to Life

    Science.gov (United States)

    Musante, Susan

    2010-01-01

    This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

  6. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  7. Improvement in two-dimensional barcode

    Indian Academy of Sciences (India)

    SONAM WASULE

    chrome counterpart to allow error recovery for data extracted from the barcode. Note that the proposed frame- work is applicable to any monochrome barcode; the encoding rate of the monochrome counterpart can be increased utilizing imaginary bit planes using grey levels. The independent input data are converted into a ...

  8. 77 FR 12764 - POSTNET Barcode Discontinuation

    Science.gov (United States)

    2012-03-02

    ... inspect and photocopy all written comments at USPS[supreg] Headquarters Library, 475 L'Enfant Plaza SW... POSTNET barcodes and allowing only Intelligent Mail[supreg] barcodes (IMb TM ) for automation price... are committed to providing information to and working with individual mailers and software providers...

  9. Genetically modified yeast species, and fermentation processes using genetically modified yeast

    Energy Technology Data Exchange (ETDEWEB)

    Rajgarhia, Vineet; Koivuranta, Kari; Penttila, Merja; Ilmen, Marja; Suominen, Pirkko; Aristidou, Aristos; Miller, Christopher Kenneth; Olson, Stacey; Ruohonen, Laura

    2017-09-12

    Yeast cells are transformed with an exogenous xylose isomerase gene. Additional genetic modifications enhance the ability of the transformed cells to ferment xylose to ethanol or other desired fermentation products. Those modifications include deletion of non-specific or specific aldose reductase gene(s), deletion of xylitol dehydrogenase gene(s) and/or overexpression of xylulokinase.

  10. Genetically modified yeast species, and fermentation processes using genetically modified yeast

    Energy Technology Data Exchange (ETDEWEB)

    Rajgarhia, Vineet; Koivuranta, Kari; Penttila, Merja; Ilmen, Marja; Suominen, Pirkko; Aristidou, Aristos; Miller, Christopher Kenneth; Olson, Stacey; Ruohonen, Laura

    2016-08-09

    Yeast cells are transformed with an exogenous xylose isomerase gene. Additional genetic modifications enhance the ability of the transformed cells to ferment xylose to ethanol or other desired fermentation products. Those modifications include deletion of non-specific or specific aldose reductase gene(s), deletion of xylitol dehydrogenase gene(s) and/or overexpression of xylulokinase.

  11. Genetically modified yeast species and fermentation processes using genetically modified yeast

    Energy Technology Data Exchange (ETDEWEB)

    Rajgarhia, Vineet [Kingsport, TN; Koivuranta, Kari [Helsinki, FI; Penttila, Merja [Helsinki, FI; Ilmen, Marja [Helsinki, FI; Suominen, Pirkko [Maple Grove, MN; Aristidou, Aristos [Maple Grove, MN; Miller, Christopher Kenneth [Cottage Grove, MN; Olson, Stacey [St. Bonifacius, MN; Ruohonen, Laura [Helsinki, FI

    2011-05-17

    Yeast cells are transformed with an exogenous xylose isomerase gene. Additional genetic modifications enhance the ability of the transformed cells to ferment xylose to ethanol or other desired fermentation products. Those modifications', include deletion of non-specific or specific aldose reductase gene(s), deletion of xylitol dehydrogenase gene(s) and/or overexpression of xylulokinase.

  12. Genetically modified yeast species, and fermentation processes using genetically modified yeast

    Energy Technology Data Exchange (ETDEWEB)

    Rajgarhia, Vineet [Kingsport, TN; Koivuranta, Kari [Helsinki, FI; Penttila, Merja [Helsinki, FI; Ilmen, Marja [Helsinki, FI; Suominen, Pirkko [Maple Grove, MN; Aristidou, Aristos [Maple Grove, MN; Miller, Christopher Kenneth [Cottage Grove, MN; Olson, Stacey [St. Bonifacius, MN; Ruohonen, Laura [Helsinki, FI

    2014-01-07

    Yeast cells are transformed with an exogenous xylose isomerase gene. Additional genetic modifications enhance the ability of the transformed cells to ferment xylose to ethanol or other desired fermentation products. Those modifications include deletion of non-specific aldose reductase gene(s), deletion of xylitol dehydrogenase gene(s) and/or overexpression of xylulokinase.

  13. Genetically modified yeast species, and fermentation processes using genetically modified yeast

    Energy Technology Data Exchange (ETDEWEB)

    Rajgarhia, Vineet; Koivuranta, Kari; Penttila, Merja; Ilmen, Marja; Suominen, Pirkko; Aristidou, Aristos; Miller, Christopher Kenneth; Olson, Stacey; Ruohonen, Laura

    2013-05-14

    Yeast cells are transformed with an exogenous xylose isomerase gene. Additional genetic modifications enhance the ability of the transformed cells to ferment xylose to ethanol or other desired fermentation products. Those modifications include deletion of non-specific or specific aldose reductase gene(s), deletion of xylitol dehydrogenase gene(s) and/or overexpression of xylulokinase.

  14. A yeast artificial chromosome contig that spans the RB1-D13S31 interval on human chromosome 13 and encompasses the frequently deleted region in B-cell chronic lymphocytic leukemia

    NARCIS (Netherlands)

    Hawthorn, L; Roberts, T; Verlind, E; Kooy, RF; Cowell, JK

    1995-01-01

    Abnormalities involving chromosome 13 have been reported as the only cytogenetic change in B-cell chronic lymphocytic leukemia (BCLL). Deletions are the most common cytogenetic abnormality and always involve 13q14, but when translocations are seen, the consistent breakpoint is always in 13q14. It is

  15. DNA barcode of Chaetognatha from Indian waters

    Digital Repository Service at National Institute of Oceanography (India)

    Nair, V.R.; Kidangan, F.X.; Prabhu, R.G.; Bucklin, A.; Nair, S.

    Chaetognatha are the second most abundant zooplankton group in the Indian waters Precise identification of the species is critical for biogeographical studies DNA barcodes using mitochondrial cytochrome c oxidase (COI) of seven dominant...

  16. Recommendations for Using Barcode in Hospital Process.

    Science.gov (United States)

    Hachesu, Peyman Rezaei; Zyaei, Leila; Hassankhani, Hadi

    2016-06-01

    Lack of attention to the proper barcode using leads to lack of use or misuse in the hospitals. The present research aimed to investigate the requirements and barrier for using barcode technology and presenting suggestions to use it. The research is observational-descriptive. The data was collected using the designed checklist which its validity was assessed. This check list consists of two parts: "Requirements" and "barrier" of using the barcodes. Research community included 10 teaching hospitals and a class of 65 participants included people in the hospitals. The collected data was analyzed using descriptive statistics. Required changes of workflow processes in the hospital and compliance them with the hospital policy are such requirements that had been infringed in the 90 % of hospitals. Prioritization of some hospital processes for barcoding, system integration with Hospital Information system (HIS), training of staff and budgeting are requirements for the successful implementation which had been infringed in the 80% of hospitals. Dissatisfaction with the quality of barcode labels and lacks of adequate scanners both whit the rate of 100 %, and the lack of understanding of the necessary requirements for implementation of barcodes as 80% were the most important barrier. Integrate bar code system with clinical workflow should be considered. Lack of knowledge and understanding toward the infrastructure, inadequate staff training and technologic problems are considered as the greatest barriers.

  17. DNA barcoding insect-host plant associations.

    Science.gov (United States)

    Jurado-Rivera, José A; Vogler, Alfried P; Reid, Chris A M; Petitpierre, Eduard; Gómez-Zurita, Jesús

    2009-02-22

    Short-sequence fragments ('DNA barcodes') used widely for plant identification and inventorying remain to be applied to complex biological problems. Host-herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcodes amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included-more than 10 per cent of the known Australian fauna-feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions.

  18. DNA Barcoding through Quaternary LDPC Codes.

    Directory of Open Access Journals (Sweden)

    Elizabeth Tapia

    Full Text Available For many parallel applications of Next-Generation Sequencing (NGS technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH or have intrinsic poor error correcting abilities (Hamming. Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9 at the expense of a rate of read losses just in the order of 10(-6.

  19. Characterization of yeast mutants lacking alkaline ceramidases YPC1 and YDC1

    DEFF Research Database (Denmark)

    Voynova, Natalia S; Mallela, Shamroop K; Vazquez, Hector M

    2014-01-01

    Humans and yeast possess alkaline ceramidases located in the early secretory pathway. Single deletions of the highly homologous yeast alkaline ceramidases YPC1 and YDC1 have very little genetic interactions or phenotypes. Here, we performed chemical-genetic screens to find deletions...

  20. Ribosomal DNA polymorphisms in the yeast Geotrichum candidum.

    Science.gov (United States)

    Alper, Iraz; Frenette, Michel; Labrie, Steve

    2011-12-01

    The dimorphic yeast Geotrichum candidum (teleomorph: Galactomyces candidus) is commonly used to inoculate washed-rind and bloomy-rind cheeses. However, little is known about the phylogenetic lineage of this microorganism. We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 regions (5126 nucleotides) from 18 G. candidum strains from various environmental niches, with a focus on dairy strains. Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA) within a given species because of the concerted evolution mechanism. This mechanism drives genetic homogenization to prevent the divergent evolution of rDNA copies within individuals. While the polymorphisms observed were mainly substitutions, one insertion/deletion (indel) polymorphism was detected in ITS1. No polymorphic sites were detected downstream from this indel site, that is, in 5.8S and ITS2. More surprisingly, many sequence electrophoregrams generated during the sequencing of the rDNA had dual peaks, suggesting that many individuals exhibited intragenomic rDNA variability. The ITS1-5.8S-ITS2 regions of four strains were cloned. The sequence analysis of 68 clones revealed 32 different ITS1-5.8S-ITS2 variants within these four strains. Depending on the strain, from four to twelve variants were detected, indicating that multiple rDNA copies were present in the genomes of these G. candidum strains. These results contribute to the debate concerning the use of the ITS region for barcoding fungi and suggest that community profiling techniques based on rDNA should be used with caution. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  1. DNA barcoding of Canada's skates.

    Science.gov (United States)

    Coulson, M W; Denti, D; Van Guelpen, L; Miri, C; Kenchington, E; Bentzen, P

    2011-11-01

    DNA-based identifications have been employed across broad taxonomic ranges and provide an especially useful tool in cases where external identification may be problematic. This study explored the utility of DNA barcoding in resolving skate species found in Atlantic Canadian waters. Most species were clearly resolved, expanding the utility for such identification on a taxonomically problematic group. Notably, one genus (Amblyraja) contained three of four species whose distributions do not overlap that could not be readily identified with this method. On the other hand, two common and partially sympatric species (Little and Winter skates) were readily identifiable. There were several instances of inconsistency between the voucher identification and the DNA sequence data. In some cases, these were at the intrageneric level among species acknowledged to be prone to misidentification. However, several instances of intergeneric discrepancies were also identified, suggesting either evidence of past introgressive hybridization or misidentification of vouchered specimens across broader taxonomic ranges. Such occurrences highlight the importance of retaining vouchered specimens for subsequent re-examination in the light of conflicting DNA evidence. © 2011 Blackwell Publishing Ltd.

  2. International Barcode of Life Project : Engaging Developing Nations ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    DNA barcoding is a new tool for taxonomic research. The DNA barcode is a very short standardized DNA sequence in a well-known gene. It provides a secure and less complicated way of identifying the species to which an animal, plant or fungus belongs than traditional observation. The barcoding tool was developed by ...

  3. QR Codes in the Library: "It's Not Your Mother's Barcode!"

    Science.gov (United States)

    Dobbs, Cheri

    2011-01-01

    Barcode scanning has become more than just fun. Now libraries and businesses are leveraging barcode technology as an innovative tool to market their products and ideas. Developed and popularized in Japan, these Quick Response (QR) or two-dimensional barcodes allow marketers to provide interactive content in an otherwise static environment. In this…

  4. VIP Barcoding: composition vector-based software for rapid species identification based on DNA barcoding.

    Science.gov (United States)

    Fan, Long; Hui, Jerome H L; Yu, Zu Guo; Chu, Ka Hou

    2014-07-01

    Species identification based on short sequences of DNA markers, that is, DNA barcoding, has emerged as an integral part of modern taxonomy. However, software for the analysis of large and multilocus barcoding data sets is scarce. The Basic Local Alignment Search Tool (BLAST) is currently the fastest tool capable of handling large databases (e.g. >5000 sequences), but its accuracy is a concern and has been criticized for its local optimization. However, current more accurate software requires sequence alignment or complex calculations, which are time-consuming when dealing with large data sets during data preprocessing or during the search stage. Therefore, it is imperative to develop a practical program for both accurate and scalable species identification for DNA barcoding. In this context, we present VIP Barcoding: a user-friendly software in graphical user interface for rapid DNA barcoding. It adopts a hybrid, two-stage algorithm. First, an alignment-free composition vector (CV) method is utilized to reduce searching space by screening a reference database. The alignment-based K2P distance nearest-neighbour method is then employed to analyse the smaller data set generated in the first stage. In comparison with other software, we demonstrate that VIP Barcoding has (i) higher accuracy than Blastn and several alignment-free methods and (ii) higher scalability than alignment-based distance methods and character-based methods. These results suggest that this platform is able to deal with both large-scale and multilocus barcoding data with accuracy and can contribute to DNA barcoding for modern taxonomy. VIP Barcoding is free and available at http://msl.sls.cuhk.edu.hk/vipbarcoding/. © 2014 John Wiley & Sons Ltd.

  5. Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics.

    Science.gov (United States)

    Maclean, Calum J; Metzger, Brian P H; Yang, Jian-Rong; Ho, Wei-Chin; Moyers, Bryan; Zhang, Jianzhi

    2017-10-01

    The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome. Many of these nonreference genes are expressed and we functionally confirmed that two of these genes confer increased resistance to antifungals. Next, we simultaneously measured the growth rates of over 4,500 laboratory strains, each of which lacks a nonessential gene, and 81 natural strains across multiple environments using unique DNA barcode present in each strain. By combining the genome-wide reverse genetic information gained from the gene deletion strains with a genome-wide association analysis from the natural strains, we identified genomic regions associated with fitness variation in natural populations. To experimentally validate a subset of these associations, we used reciprocal hemizygosity tests, finding that while the combined forward and reverse genetic approaches can identify a single causal gene, the phenotypic consequences of natural genetic variation often follow a complicated pattern. The resources and approach provided outline an efficient and reliable route to association mapping in yeast and significantly enhance its value as a model for understanding the genetic mechanisms underlying phenotypic variation and evolution in natural populations. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. DNA barcodes for ecology, evolution, and conservation.

    Science.gov (United States)

    Kress, W John; García-Robledo, Carlos; Uriarte, Maria; Erickson, David L

    2015-01-01

    The use of DNA barcodes, which are short gene sequences taken from a standardized portion of the genome and used to identify species, is entering a new phase of application as more and more investigations employ these genetic markers to address questions relating to the ecology and evolution of natural systems. The suite of DNA barcode markers now applied to specific taxonomic groups of organisms are proving invaluable for understanding species boundaries, community ecology, functional trait evolution, trophic interactions, and the conservation of biodiversity. The application of next-generation sequencing (NGS) technology will greatly expand the versatility of DNA barcodes across the Tree of Life, habitats, and geographies as new methodologies are explored and developed. Published by Elsevier Ltd.

  7. Functional differences in yeast protein disulfide isomerases

    DEFF Research Database (Denmark)

    Nørgaard, P; Westphal, V; Tachibana, C

    2001-01-01

    PDI1 is the essential gene encoding protein disulfide isomerase in yeast. The Saccharomyces cerevisiae genome, however, contains four other nonessential genes with homology to PDI1: MPD1, MPD2, EUG1, and EPS1. We have investigated the effects of simultaneous deletions of these genes. In several...

  8. DNA Barcoding on Bacteria: A Review

    Directory of Open Access Journals (Sweden)

    D. E. Lebonah

    2014-01-01

    Full Text Available Bacteria are omnipotent and they can be found everywhere. The study of bacterial pathogens has been happening from olden days to prevent epidemics, food spoilage, losses in agricultural production, and loss of lives. Modern techniques in DNA based species identification are considered. So, there is a need to acquire simple and quick identification technique. Hence, this review article covers the efficacy of DNA barcoding of bacteria. Routine DNA barcoding involves the production of PCR amplicons from particular regions to sequence them and these sequence data are used to identify or “barcode” that organism to make a distinction from other species.

  9. DNA BARCODING IKAN HIAS INTRODUKSI

    Directory of Open Access Journals (Sweden)

    Melta Rini Fahmi

    2017-05-01

    Full Text Available Identifikasi spesies menjadi tantangan dalam pengelolaan ikan hias introduksi baik untuk tujuan budidaya maupun konservasi. Penelitian ini bertujuan untuk melakukan identifikasi molekuler ikan hias introduksi yang beredar di pembudidaya dan pasar ikan hias Indonesia dengan menggunakan barcode DNA gen COI. Sampel ikan diperoleh dari pembudidaya dan importir ikan hias di kawasan Bandung dan Jakarta. Total DNA diekstraksi dari jaringan sirip ekor dengan menggunakan metode kolom. Amplifikasi gen target dilakukan dengan menggunakan primer FishF1, FishF2, FishR1, dan FishR2. Hasil pembacaan untai DNA disejajarkan dengan sekuen yang terdapat pada genbank melalui program BLAST. Identifikasi dilakukan melalui kekerabatan pohon filogenetik dan presentasi indeks kesamaan dengan sekuen genbank. Hasil identifikasi menunjukkan sampel yang diuji terbagi menjadi lima grup, yaitu: Synodontis terdiri atas lima spesies, Corydoras: empat spesies, Phseudoplatystoma: tiga spesies, Botia: tiga spesies, dan Leporinus: tiga spesies dengan nilai boostrap 99-100. Indeks kesamaan sekuen menunjukkan sebanyak 11 spesies memiliki indeks kesamaan 99%-100% dengan data genbank yaitu Synodontis decorus, Synodontis eupterus, Synodontis greshoffi, Botia kubotai, Botia lohachata, Rasbora erythromicron, Corydoras aeneus, Gyrinocheilus aymonieri, Eigenmannia virescens, Leporinus affinis, Phractocephalus hemioliopterus. Dua spesies teridentifikasi sebagai hasil hibridisasi (kawin silang yaitu Leopard catfish (100% identik dengan Pseudoplatystoma faciatum dan Synodontis leopard (100% identik dengan Synodontis notatus. Hasil analisis nukleotida penciri diperoleh tujuh nukleotida untuk Synodontis decora, 10 nukleotida untuk Synodontis tanganyicae, 13 nukleotida untuk Synodontis euterus, empat nukleotida untuk Synodontis notatus, dan 14 untuk Synodontis grashoffi. Kejelasan identifikasi spesies ikan menjadi kunci utama dalam budidaya, perdagangan, manajemen, konservasi, dan pengembangan

  10. Partial deletion 11q

    DEFF Research Database (Denmark)

    Hertz, Jens Michael; Tommerup, N; Sørensen, F B

    1995-01-01

    We describe the cytogenetic findings and the dysmorphic features in a stillborn girl with a large de novo terminal deletion of the long arm of chromosome 11. The karyotype was 46,XX,del(11)(q21qter). By reviewing previous reports of deletion 11q, we found that cleft lip and palate are most...... frequently seen in proximal 11q deletions involving 11q21. Telomeric staining using the PRINS technique demonstrated normal telomeric sequences in the deleted chromosome 11....

  11. Universal COI primers for DNA barcoding amphibians.

    Science.gov (United States)

    Che, Jing; Chen, Hong-Man; Yang, Jun-Xiao; Jin, Jie-Qiong; Jiang, Ke; Yuan, Zhi-Yong; Murphy, Robert W; Zhang, Ya-Ping

    2012-03-01

    DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians. © 2011 Blackwell Publishing Ltd.

  12. DNA Barcoding of Philippine Herbal Medicinal Products.

    Science.gov (United States)

    Pedales, Ronniel D; Damatac, Amor M; Limbo, Carlo A; Marquez, Cielo Mae D; Navarro, Anna Isabel B; Molina, Jeanmaire

    2016-11-01

    The Philippine government established the Traditional and Alternative Medicine Act in 1997 to promote traditionally used herbal products and to provide an effective yet affordable alternative to conventional medicines. However, government regulation of herbal medicinal products (HMPs) is not stringent, relying only on submitted quality data from the manufacturer. In this study we validated the taxonomic identity of 26 plant samples contained within 22 HMPs, each produced by different local manufacturers, through DNA barcoding of the nuclear internal transcribed spacer-2 (ITS2) region. We recovered 19 ITS2 barcodes from 26 samples. These were compared to sequences in GenBank using MEGABLAST, but ambiguous results (similar max scores for different species) were phylogenetically analyzed. Twelve of the 19 samples matched the indicated species on the product label, three were equivocal in specific identity but were placed in the expected genus, and four other samples from three manufacturers contained contamination and/or substitution. GenBank's reference database was at times problematic because some sequences were lacking or were misidentified, but the database was still useful. Overall, ITS2 barcoding was successful in authenticating the HMPs, and it is recommended during the premarket evaluation process so as to obtain a certificate of registration from the government. The government should also develop a comprehensive database of barcodes for Philippine plants, and should prioritize the development of the traditional pharmacopeia because many locally produced HMPs are not indigenous.

  13. DNA barcoding in Mexico: an introduction.

    Science.gov (United States)

    Elías-Gutiérrez, M; León-Regagnon, V

    2013-11-01

    DNA barcoding has become an important current scientific trend to the understanding of the world biodiversity. In the case of mega-diverse hot spots like Mexico, this technique represents an important tool for taxonomists, allowing them to concentrate in highlighted species by the barcodes instead of analyzing entire sets of specimens. This tendency resulted in the creation of a national network named Mexican Barcode of Life (MEXBOL) which main goals are to train students, and to promote the interaction and collective work among researchers interested in this topic. As a result, the number of records in the Barcode of Life Database (BOLD) for some groups, such as the Mammalia, Actinopterygii, Polychaeta, Branchiopoda, Ostracoda, Maxillopoda, Nematoda, Pinophyta, Ascomycota and Basidiomycota place Mexico among the top ten countries in the generation of these data. This special number presents only few of the many interesting findings in this region of the world, after the use of this technique and its integration with other methodologies. © 2013 John Wiley & Sons Ltd.

  14. DNA barcoding Bromeliaceae: achievements and pitfalls.

    Directory of Open Access Journals (Sweden)

    Vitor Hugo Maia

    Full Text Available BACKGROUND: DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. METHODOLOGY/PRINCIPAL FINDINGS: It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%. Species paraphyly was a common feature in our sampling. CONCLUSIONS/SIGNIFICANCE: Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to

  15. DNA barcoding Bromeliaceae: achievements and pitfalls.

    Science.gov (United States)

    Maia, Vitor Hugo; Mata, Camila Souza da; Franco, Luciana Ozório; Cardoso, Mônica Aires; Cardoso, Sérgio Ricardo Sodré; Hemerly, Adriana Silva; Ferreira, Paulo Cavalcanti Gomes

    2012-01-01

    DNA barcoding has been successfully established in animals as a tool for organismal identification and taxonomic clarification. Slower nucleotide substitution rates in plant genomes have made the selection of a DNA barcode for land plants a much more difficult task. The Plant Working Group of the Consortium for the Barcode of Life (CBOL) recommended the two-marker combination rbcL/matK as a pragmatic solution to a complex trade-off between universality, sequence quality, discrimination, and cost. It is expected that a system based on any one, or a small number of plastid genes will fail within certain taxonomic groups with low amounts of plastid variation, while performing well in others. We tested the effectiveness of the proposed CBOL Plant Working Group barcoding markers for land plants in identifying 46 bromeliad species, a group rich in endemic species from the endangered Brazilian Atlantic Rainforest. Although we obtained high quality sequences with the suggested primers, species discrimination in our data set was only 43.48%. Addition of a third marker, trnH-psbA, did not show significant improvement. This species identification failure in Bromeliaceaecould also be seen in the analysis of the GenBank's matK data set. Bromeliaceae's sequence divergence was almost three times lower than the observed for Asteraceae and Orchidaceae. This low variation rate also resulted in poorly resolved tree topologies. Among the three Bromeliaceae subfamilies sampled, Tillandsioideae was the only one recovered as a monophyletic group with high bootstrap value (98.6%). Species paraphyly was a common feature in our sampling. Our results show that although DNA barcoding is an important tool for biodiversity assessment, it tends to fail in taxonomy complicated and recently diverged plant groups, such as Bromeliaceae. Additional research might be needed to develop markers capable to discriminate species in these complex botanical groups.

  16. Barcode server: a visualization-based genome analysis system.

    Directory of Open Access Journals (Sweden)

    Fenglou Mao

    Full Text Available We have previously developed a computational method for representing a genome as a barcode image, which makes various genomic features visually apparent. We have demonstrated that this visual capability has made some challenging genome analysis problems relatively easy to solve. We have applied this capability to a number of challenging problems, including (a identification of horizontally transferred genes, (b identification of genomic islands with special properties and (c binning of metagenomic sequences, and achieved highly encouraging results. These application results inspired us to develop this barcode-based genome analysis server for public service, which supports the following capabilities: (a calculation of the k-mer based barcode image for a provided DNA sequence; (b detection of sequence fragments in a given genome with distinct barcodes from those of the majority of the genome, (c clustering of provided DNA sequences into groups having similar barcodes; and (d homology-based search using Blast against a genome database for any selected genomic regions deemed to have interesting barcodes. The barcode server provides a job management capability, allowing processing of a large number of analysis jobs for barcode-based comparative genome analyses. The barcode server is accessible at http://csbl1.bmb.uga.edu/Barcode.

  17. DSN1 deletion is deleterious to the Saccharomyces cerevisiae while ...

    African Journals Online (AJOL)

    insufficiency and segregational errors in yeast diploid single deletants. Expression of Dsn1p in CHO has been achieved using the pcDNA 3.1/HIS A expression vector. Analysis by DNA sequencing showed no changes in the DSN1 DNA sequence.

  18. Exploring Canadian Echinoderm Diversity through DNA Barcodes.

    Science.gov (United States)

    Layton, Kara K S; Corstorphine, Erin A; Hebert, Paul D N

    2016-01-01

    DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

  19. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  20. [Nurses' Innovation Acceptance of Barcode Technology].

    Science.gov (United States)

    Cheng, Hui-Ping; Lee, Ting-Ting; Liu, Chieh-Yu; Hou, I-Ching

    2016-04-01

    Healthcare organizations have increasingly adopted barcode technology to improve care quality and work efficiency. Barcode technology is simple to use, so it is frequently used in patient identification, medication administration, and specimen collection processes. This study used a technology acceptance model and innovation diffusion theory to explore the innovation acceptance of barcode technology by nurses. The data were collected using a structured questionnaire with open-ended questions that was based on the technology acceptance model and innovation diffusion theory. The questionnaire was distributed to and collected from 200 nurses from March to May 2014. Data on laboratory reporting times and specimen rejection rates were collected as well. Variables that were found to have a significant relationship (pinnovation acceptance included (in order of importance): perceived usefulness (r=.722), perceived ease of use (r=.720), observability (r=.579), compatibility (r=.364), and trialability (r=.344). N-level nurses demonstrated higher acceptance than their N1 and N2 level peers (F=3.95, ptechnology has been accepted by nurses and that this technology effectively decreases both laboratory reporting times and specimen rejection rates. However, network speed and workflow should be further improved in order to benefit clinical practice.

  1. Highlighting Astyanax Species Diversity through DNA Barcoding

    Science.gov (United States)

    Oliveira, Carlos Alexandre Miranda; de Melo, Filipe Augusto Gonçalves; Bertaco, Vinicius de Araújo; de Astarloa, Juan M. Díaz; Rosso, Juan J.; Foresti, Fausto; Oliveira, Claudio

    2016-01-01

    DNA barcoding has been used extensively to solve taxonomic questions and identify new species. Neotropical fishes are found in a wide variety of shapes and sizes, with a large number of species yet to be described, many of which are very difficult to identify. Characidae is the most species-rich family of the Characiformes, and many of its genera are affected by taxonomic uncertainties, including the widely-distributed, species-rich genus Astyanax. In this study, we present an extensive analysis of Astyanax covering almost its entire area of occurrence, based on DNA barcoding. The use of different approaches (ABGD, GMYC and BIN) to the clustering of the sequences revealed ample consistency in the results obtained by the initial cutoff value of 2% divergence for putative species in the Neighbor-Joining analysis using the Kimura-2-parameter model. The results indicate the existence of five Astyanax lineages. Some groups, such as that composed by the trans-Andean forms, are mostly composed of well-defined species, and in others a number of nominal species are clustered together, hampering the delimitation of species, which in many cases proved impossible. The results confirm the extreme complexity of the systematics of the genus Astyanax and show that DNA barcoding can be an useful tool to address these complexes questions. PMID:27992537

  2. Partial deletion 11q

    DEFF Research Database (Denmark)

    Hertz, Jens Michael; Tommerup, N; Sørensen, F B

    1995-01-01

    We describe the cytogenetic findings and the dysmorphic features in a stillborn girl with a large de novo terminal deletion of the long arm of chromosome 11. The karyotype was 46,XX,del(11)(q21qter). By reviewing previous reports of deletion 11q, we found that cleft lip and palate are most...

  3. Schizophrenia and chromosomal deletions

    Energy Technology Data Exchange (ETDEWEB)

    Lindsay, E.A.; Baldini, A. [Baylor College of Medicine, Houston, TX (United States); Morris, M. A. [Univ. of Geneva School of Medicine, NY (United States)] [and others

    1995-06-01

    Recent genetic linkage analysis studies have suggested the presence of a schizophrenia locus on the chromosomal region 22q11-q13. Schizophrenia has also been frequently observed in patients affected with velo-cardio-facial syndrome (VCFS), a disorder frequently associated with deletions within 22q11.1. It has been hypothesized that psychosis in VCFS may be due to deletion of the catechol-o-methyl transferase gene. Prompted by these observations, we screened for 22q11 deletions in a population of 100 schizophrenics selected from the Maryland Epidemiological Sample. Our results show that there are schizophrenic patients carrying a deletion of 22q11.1 and a mild VCFS phenotype that might remain unrecognized. These findings should encourage a search for a schizophrenia-susceptibility gene within the deleted region and alert those in clinical practice to the possible presence of a mild VCFS phenotype associated with schizophrenia. 9 refs.

  4. Targeted gene deletion in Zygosaccharomyces bailii.

    Science.gov (United States)

    Mollapour, M; Piper, P

    2001-01-30

    Yeasts of the genus Zygosaccharomyces are notable agents of large-scale food spoilage. Despite the economic importance of these organisms, little is known about the stress adaptations whereby they adapt to many of the more severe conditions of food preservation. In this study it was shown that genes of Z. bailii, a yeast notable for its high resistances to food preservatives and ethanol, can be isolated by complementation of the corresponding mutant strains of Saccharomyces cerevisiae. It was also discovered that the acquisition by S. cerevisiae of a single small Z. bailii gene (ZbYME2) was sufficient for the former yeast to acquire the ability to degrade two major food preservatives, benzoic acid and sorbic acid. Using DNA cassettes containing dominant selectable markers and methods originally developed for performing gene deletions in S. cerevisiae, the two copies of ZbYME2 in the Z. bailii genome were sequentially deleted. The resulting Zbyme2/Zbyme2 homozygous deletant strain had lost any ability to utilize benzoate as sole carbon source and was more sensitive to weak acid preservatives during growth on glucose. Thus, ZbYME2, probably the nuclear gene for a mitochondrial mono-oxygenase function, is essential for Z. bailii to degrade food preservatives. This ability to catabolize weak acid preservatives is a significant factor contributing to the preservative resistance of Z. bailii under aerobic conditions. This study is the first to demonstrate that it is possible to delete in Z. bailii genes that are suspected as being important for growth of this organism in preserved foods and beverages. With the construction of further mutant of Z. bailii strains, a clearer picture should emerge of how this yeast adapts to the conditions of food preservation. This information will, in turn, allow the design of new preservation strategies. GenBank Accession Nos: ZbURA3 (AF279259), ZbTIM9 (AF279260), ZbYME2 (AF279261), ZbTRP1 (AF279262), ZbHHT1(AF296170). Copyright 2000 John

  5. Quantum deletion: Beyond the no-deletion principle

    International Nuclear Information System (INIS)

    Adhikari, Satyabrata

    2005-01-01

    Suppose we are given two identical copies of an unknown quantum state and we wish to delete one copy from among the given two copies. The quantum no-deletion principle restricts us from perfectly deleting a copy but it does not prohibit us from deleting a copy approximately. Here we construct two types of a 'universal quantum deletion machine' which approximately deletes a copy such that the fidelity of deletion does not depend on the input state. The two types of universal quantum deletion machines are (1) a conventional deletion machine described by one unitary operator and (2) a modified deletion machine described by two unitary operators. Here it is shown that the modified deletion machine deletes a qubit with fidelity 3/4, which is the maximum limit for deleting an unknown quantum state. In addition to this we also show that the modified deletion machine retains the qubit in the first mode with average fidelity 0.77 (approx.) which is slightly greater than the fidelity of measurement for two given identical states, showing how precisely one can determine its state [S. Massar and S. Popescu, Phys. Rev. Lett. 74, 1259 (1995)]. We also show that the deletion machine itself is input state independent, i.e., the information is not hidden in the deleting machine, and hence we can delete the information completely from the deletion machine

  6. Internal Transcribed Spacer (ITS), an ideal DNA barcode for species ...

    African Journals Online (AJOL)

    Background: DNA barcoding is a technique used to identify species based on species-specific differences in short regions of their DNA. It is widely used in species discrimination of medicinal plants and traditional medicines. Materials and Methods: In the present study, four potential DNA barcodes, namely rbcL, matK, ...

  7. Dissecting host-associated communities with DNA barcodes

    Science.gov (United States)

    Pierce, Naomi E.

    2016-01-01

    DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481780

  8. Real-Time Barcode Detection and Classification Using Deep Learning

    DEFF Research Database (Denmark)

    Hansen, Daniel Kold; Nasrollahi, Kamal; Rasmussen, Christoffer Bøgelund

    2017-01-01

    Barcodes, in their different forms, can be found on almost any packages available in the market. Detecting and then decoding of barcodes have therefore great applications. We describe how to adapt the state-of-the- art deep learning-based detector of You Only Look Once (YOLO) for the purpose...

  9. Developing DNA barcoding (matK) primers for marama bean ...

    African Journals Online (AJOL)

    DNA barcoding is based on the premise that a short standardized DNA barcoding sequence can distinguish individuals of a species because the genetic variation between species exceeds that within species. Information on genetic variation of breeding materials helps to maintain genetic diversity and sustains long term ...

  10. Contribution towards the development of a DNA barcode reference ...

    African Journals Online (AJOL)

    DNA barcoding is a widely used molecular approach for species cataloging for unambiguous identification and conservation. In the present study, DNA barcoding of some West African mammals were performed with six new mitochondrial CO1 sequences for Civettictis civetta, Tadarida nigeriae, Orycteropus afer, ...

  11. DNA Barcoding and PBL in an Australian Postsecondary College

    Science.gov (United States)

    Cross, Joseph; Garard, Helen; Currie, Tina

    2018-01-01

    DNA barcoding is increasingly being introduced into biological science educational curricula worldwide. The technique has a number of features that make it ideal for science curricula and particularly for Project-Based Learning (PBL). This report outlines the development of a DNA barcoding project in an Australian TAFE college, which also combined…

  12. Systematic identification of African Sapindaceae using DNA barcoding

    African Journals Online (AJOL)

    This research aimed at exploring the diversity of Sapindaceae in West and Central Africa with particular emphasis on identification of the plant samples as well as generation of DNA barcodes with a view to sharing the DNA barcode sequence(s) in a public database. These were achieved following standard protocols.

  13. DNA barcoding of South Africa's ornamental freshwater fish – are ...

    African Journals Online (AJOL)

    DNA barcoding of South Africa's ornamental freshwater fish – are the names reliable? ... African Journal of Aquatic Science ... Because its effective implementation requires accurate identification, the aim of the present study was to test whether DNA barcoding is a useful tool to identify freshwater fishes in the South African ...

  14. A comparison of DNA barcode clustering methods applied to ...

    Indian Academy of Sciences (India)

    2012-10-15

    Oct 15, 2012 ... ABGD; biodiversity inventory; cluster analysis; cryptic species; cytochrome oxidase subunit I; DNA barcode of life; Fuzzy. Identification; GMYC; SAP .... set of phylogenetic trees is sampled using Bayesian Markov chain Monte Carlo ..... Critical factors for assembling a high volume of DNA barcodes. Philos.

  15. DNA barcoding of catfish: species authentication and phylogenetic assessment.

    Directory of Open Access Journals (Sweden)

    Li Lian Wong

    Full Text Available As the global market for fisheries and aquaculture products expands, mislabeling of these products has become a growing concern in the food safety arena. Molecular species identification techniques hold the potential for rapid, accurate assessment of proper labeling. Here we developed and evaluated DNA barcodes for use in differentiating United States domestic and imported catfish species. First, we sequenced 651 base-pair barcodes from the cytochrome oxidase I (COI gene from individuals of 9 species (and an Ictalurid hybrid of domestic and imported catfish in accordance with standard DNA barcoding protocols. These included domestic Ictalurid catfish, and representative imported species from the families of Clariidae and Pangasiidae. Alignment of individual sequences from within a given species revealed highly consistent barcodes (98% similarity on average. These alignments allowed the development and analyses of consensus barcode sequences for each species and comparison with limited sequences in public databases (GenBank and Barcode of Life Data Systems. Validation tests carried out in blinded studies and with commercially purchased catfish samples (both frozen and fresh revealed the reliability of DNA barcoding for differentiating between these catfish species. The developed protocols and consensus barcodes are valuable resources as increasing market and governmental scrutiny is placed on catfish and other fisheries and aquaculture products labeling in the United States.

  16. A laboratory information management system for DNA barcoding workflows

    NARCIS (Netherlands)

    Vu, D.; Eberhardt, U.; Szöke, S.; Groenewald, M.; Robert, V.

    2012-01-01

    This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA

  17. International Barcode of Life Project : Engaging Developing Nations ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Barcoding has numerous potential applications in, for example, resources conservation, disease prevention, detection of invasive species, water quality control, monitoring disease vectors, identification of illegally traded plants or animals, and the elimination of weed seeds in seed collections. To date, most of the barcoding ...

  18. [Molecular identification in genus of Lilium based on DNA barcoding].

    Science.gov (United States)

    Zheng, Si-Hao; Li, Ya-Kang; Ren, Wei-Guang; Huang, Lin-Fang

    2014-12-01

    To establish a new method for identifying genus of Lilium by DNA barcoding technology, ITS, ITS2, psbA-trnH, matK and rbcL sequences were analyzed in term of variation of inter- and intra-species, barcoding gap, neighbor-joining tree to distinguish genus of Lilium based on 978 sequences from experimental and GenBank database, and identification efficiency was evaluated by Nearest distance and BLAST1 methods. The results showed that DNA barcoding could identify different species in genus of Lilium. ITS sequence performed higher identification efficiency, and had significant difference between intra- and inter-species. And NJ tree could also divide species into different clades. Results indicate that DNA barcoding can identify genus of Lilium accurately. ITS sequence can be the optimal barcode to identify species of Lilium.

  19. Identifying Chinese species of Gammarus (Crustacea: Amphipoda using DNA barcoding

    Directory of Open Access Journals (Sweden)

    HOU Zhong-E

    2009-04-01

    Full Text Available Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection.

  20. [Hydrophidae identification through analysis on Cyt b gene barcode].

    Science.gov (United States)

    Liao, Li-xi; Zeng, Ke-wu; Tu, Peng-fei

    2015-08-01

    Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid the problem. The gene barcodes of the 6 species of Hydrophidae like Lapemis hardwickii were aquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficency by BLAST. Our results revealed that the barcode sequences performed high identification efficiency, and had obvious difference between intra- and inter-species. These all indicated that Cyt b DNA barcoding can confirm the Hydrophidae identification.

  1. DNA Barcoding for Identification of "Candidatus Phytoplasmas" Using a Fragment of the Elongation Factor Tu Gene

    DEFF Research Database (Denmark)

    Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta

    2012-01-01

    barcoding gap. The use of the tuf barcode allowed separation of main ribosomal groups and most of their subgroups. Phytoplasma tuf barcodes were deposited in the NCBI GenBank and Q-bank databases. Conclusions/Significance This study demonstrates that DNA barcoding principles can be applied...... by plant health services and researchers for online phytoplasma identification....

  2. Novel DNA barcodes for detection, idenfication and tracking of stachybotrys and chaetomium species

    DEFF Research Database (Denmark)

    Lewinska, Anna Malgorzata; Hoof, Jakob Blæsbjerg; Peuhkuri, Ruut Hannele

    2014-01-01

    and Stachybotrys. The existing DNA barcodes: ITS, SSU, LSU, B-TUB, CMD, RP and TEF-1α do not give satisfying species resolution to be considered as DNA barcodes for the two genera. Therefore, novel barcodes for them are needed. Barcode potentials, such as HOG1 a NAHA, were identified using bioinformatics...

  3. Identifying Fishes through DNA Barcodes and Microarrays.

    Science.gov (United States)

    Kochzius, Marc; Seidel, Christian; Antoniou, Aglaia; Botla, Sandeep Kumar; Campo, Daniel; Cariani, Alessia; Vazquez, Eva Garcia; Hauschild, Janet; Hervet, Caroline; Hjörleifsdottir, Sigridur; Hreggvidsson, Gudmundur; Kappel, Kristina; Landi, Monica; Magoulas, Antonios; Marteinsson, Viggo; Nölte, Manfred; Planes, Serge; Tinti, Fausto; Turan, Cemal; Venugopal, Moleyur N; Weber, Hannes; Blohm, Dietmar

    2010-09-07

    International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90%) renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  4. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    Full Text Available BACKGROUND: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. METHODOLOGY/PRINCIPAL FINDINGS: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology. CONCLUSIONS/SIGNIFICANCE: Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  5. Digital biomagnetism: Electrodeposited multilayer magnetic barcodes

    Energy Technology Data Exchange (ETDEWEB)

    Palfreyman, Justin J. [Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE (United Kingdom)], E-mail: jjp38@cam.ac.uk; Cooper, Joshaniel F.K.; Belle, Frieda van; Hong Bingyan; Hayward, Tom J. [Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE (United Kingdom); Lopalco, Maria; Bradley, Mark [School of Chemistry, University of Edinburgh, King' s Buildings, Edinburgh, EH9 3JJ (United Kingdom); Mitrelias, Thanos; Bland, J. Anthony C. [Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, CB3 0HE (United Kingdom)

    2009-05-15

    A novel magnetic encoding technique for performing high-throughput biological assays is presented. Electrodeposited Ni/Cu and Co/Cu multilayer pillar structures with a diameter of 15 {mu}m and a thickness up to 10 {mu}m are presented as 'magnetic barcodes', where the number of unique codes possible increases exponentially with a linear increase in length. A gold cap facilitates the growth of self-assembled monolayers (SAMs), while microdrop printing allows efficient generation of large libraries of tagged probes. Coercivity-tuning techniques are used to exploit a non-proximity encoding methodology compatible with microfluidic flow.

  6. Methods and materials for the production of L-lactic acid in yeast

    Science.gov (United States)

    Hause, Ben [Jordan, MN; Rajgarhia, Vineet [Minnetonka, MN; Suominen, Pirkko [Maple Grove, MN

    2009-05-19

    Recombinant yeast are provided having, in one aspect, multiple exogenous LDH genes integrated into the genome, while leaving native PDC genes intact. In a second aspect, recombinant yeast are provided having an exogenous LDH gene integrated into its genome at the locus of a native PDC gene, with deletion of the native PDC gene. The recombinant yeast are useful in fermentation process for producing lactic acid.

  7. Exploring Canadian Echinoderm Diversity through DNA Barcodes.

    Directory of Open Access Journals (Sweden)

    Kara K S Layton

    Full Text Available DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold between mean intra- (0.48% and inter- (12.0% specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

  8. Chemical genomic guided engineering of gamma-valerolactone tolerant yeast.

    Science.gov (United States)

    Bottoms, Scott; Dickinson, Quinn; McGee, Mick; Hinchman, Li; Higbee, Alan; Hebert, Alex; Serate, Jose; Xie, Dan; Zhang, Yaoping; Coon, Joshua J; Myers, Chad L; Landick, Robert; Piotrowski, Jeff S

    2018-01-12

    Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in the presence of GVL, we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast. Chemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate cinnamic acid and its derivatives to vinyl forms, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain. We found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol accumulation in aerobically grown cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain

  9. Environmental barcoding reveals massive dinoflagellate diversity in marine environments.

    Directory of Open Access Journals (Sweden)

    Rowena F Stern

    2010-11-01

    Full Text Available Dinoflagellates are an ecologically important group of protists with important functions as primary producers, coral symbionts and in toxic red tides. Although widely studied, the natural diversity of dinoflagellates is not well known. DNA barcoding has been utilized successfully for many protist groups. We used this approach to systematically sample known "species", as a reference to measure the natural diversity in three marine environments.In this study, we assembled a large cytochrome c oxidase 1 (COI barcode database from 8 public algal culture collections plus 3 private collections worldwide resulting in 336 individual barcodes linked to specific cultures. We demonstrate that COI can identify to the species level in 15 dinoflagellate genera, generally in agreement with existing species names. Exceptions were found in species belonging to genera that were generally already known to be taxonomically challenging, such as Alexandrium or Symbiodinium. Using this barcode database as a baseline for cultured dinoflagellate diversity, we investigated the natural diversity in three diverse marine environments (Northeast Pacific, Northwest Atlantic, and Caribbean, including an evaluation of single-cell barcoding to identify uncultivated groups. From all three environments, the great majority of barcodes were not represented by any known cultured dinoflagellate, and we also observed an explosion in the diversity of genera that previously contained a modest number of known species, belonging to Kareniaceae. In total, 91.5% of non-identical environmental barcodes represent distinct species, but only 51 out of 603 unique environmental barcodes could be linked to cultured species using a conservative cut-off based on distances between cultured species.COI barcoding was successful in identifying species from 70% of cultured genera. When applied to environmental samples, it revealed a massive amount of natural diversity in dinoflagellates. This highlights

  10. DNA Barcoding Identifies Argentine Fishes from Marine and Brackish Waters

    Science.gov (United States)

    Mabragaña, Ezequiel; Díaz de Astarloa, Juan Martín; Hanner, Robert; Zhang, Junbin; González Castro, Mariano

    2011-01-01

    Background DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. Methodology/Principal Findings Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species), and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org). Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125) examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. Conclusions/Significance This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha taxonomy, barcodes provide

  11. DNA barcoding identifies Argentine fishes from marine and brackish waters.

    Directory of Open Access Journals (Sweden)

    Ezequiel Mabragaña

    Full Text Available BACKGROUND: DNA barcoding has been advanced as a promising tool to aid species identification and discovery through the use of short, standardized gene targets. Despite extensive taxonomic studies, for a variety of reasons the identification of fishes can be problematic, even for experts. DNA barcoding is proving to be a useful tool in this context. However, its broad application is impeded by the need to construct a comprehensive reference sequence library for all fish species. Here, we make a regional contribution to this grand challenge by calibrating the species discrimination efficiency of barcoding among 125 Argentine fish species, representing nearly one third of the known fauna, and examine the utility of these data to address several key taxonomic uncertainties pertaining to species in this region. METHODOLOGY/PRINCIPAL FINDINGS: Specimens were collected and morphologically identified during crusies conducted between 2005 and 2008. The standard BARCODE fragment of COI was amplified and bi-directionally sequenced from 577 specimens (mean of 5 specimens/species, and all specimens and sequence data were archived and interrogated using analytical tools available on the Barcode of Life Data System (BOLD; www.barcodinglife.org. Nearly all species exhibited discrete clusters of closely related haplogroups which permitted the discrimination of 95% of the species (i.e. 119/125 examined while cases of shared haplotypes were detected among just three species-pairs. Notably, barcoding aided the identification of a new species of skate, Dipturus argentinensis, permitted the recognition of Genypterus brasiliensis as a valid species and questions the generic assignment of Paralichthys isosceles. CONCLUSIONS/SIGNIFICANCE: This study constitutes a significant contribution to the global barcode reference sequence library for fishes and demonstrates the utility of barcoding for regional species identification. As an independent assessment of alpha

  12. Study of the role of the covalently linked cell wall protein (Ccw14p) and yeast glycoprotein (Ygp1p) within biofilm formation in a flor yeast strain.

    Science.gov (United States)

    Moreno-García, J; Coi, A L; Zara, G; García-Martínez, T; Mauricio, J C; Budroni, M

    2018-03-01

    Flor yeasts are Saccharomyces cerevisiae strains noted by their ability to create a type of biofilm in the air-liquid interface of some wines, known as 'flor' or 'velum', for which certain proteins play an essential role. Following a proteomic study of a flor yeast strain, we deleted the CCW14 (covalently linked cell wall protein) and YGP1 (yeast glycoprotein) genes-codifying for two cell surface glycoproteins-in a haploid flor yeast strain and we reported that both influence the weight of the biofilm as well as cell adherence (CCW14).

  13. Topological mapping and navigation in indoor environment with invisible barcode

    International Nuclear Information System (INIS)

    Huh, Jin Wook; Chung, Woong Sik; Chung, Wan Kyun

    2006-01-01

    This paper addresses the localization and navigation problem using invisible two dimensional barcodes on the floor. Compared with other methods using natural/artificial landmark, the proposed localization method has great advantages in cost and appearance, since the location of the robot is perfectly known using the barcode information after the mapping is finished. We also propose a navigation algorithm which uses the topological structure. For the topological information, we define nodes and edges which are suitable for indoor navigation, especially for large area having multiple rooms, many walls and many static obstacles. The proposed algorithm also has an advantage that errors occurred in each node are mutually independent and can be compensated exactly after some navigation using barcode. Simulation and experimental results were performed to verify the algorithm in the barcode environment, and the result showed an excellent performance. After mapping, it is also possible to solve the kidnapped case and generate paths using topological information

  14. Application Research of QRCode Barcode in Validation of Express Delivery

    Science.gov (United States)

    Liu, Zhihai; Zeng, Qingliang; Wang, Chenglong; Lu, Qing

    The barcode technology has become an important way in the field of information input and identify automatically. With the outstanding features of big storage capacity, secure, rich encoding character set and fast decoding, the two-dimensional(2D) QRcode(Quick Response Barcode) has become an important choice of commerce barcode. The development of wireless communications technology and the popularization and application of mobile device has set the foundation of 2D barcode used in business. In this paper, the characteristics and the compositions of 2D QRcode are described, the secure validation workflows and contents of QRcode in goods express delivery are discussed, the encoding process of QRcode is showed, and the system framework is analyzed and established. At last, the system compositions and functions of each part are discussed.

  15. Keeping track. Barcodes and RFID tags make inroads in hospitals.

    Science.gov (United States)

    Degaspari, John

    2011-03-01

    Barcodes are a proven technology for reducing medication administration errors, while RFID tags show promise for tracking of assets as well as personnel and patients. Yet implementation has been slow, as hospitals struggle with cost and complexity issues.

  16. The approximability of the String Barcoding problem

    Directory of Open Access Journals (Sweden)

    Rizzi Romeo

    2006-08-01

    Full Text Available Abstract The String Barcoding (SBC problem, introduced by Rash and Gusfield (RECOMB, 2002, consists in finding a minimum set of substrings that can be used to distinguish between all members of a set of given strings. In a computational biology context, the given strings represent a set of known viruses, while the substrings can be used as probes for an hybridization experiment via microarray. Eventually, one aims at the classification of new strings (unknown viruses through the result of the hybridization experiment. In this paper we show that SBC is as hard to approximate as Set Cover. Furthermore, we show that the constrained version of SBC (with probes of bounded length is also hard to approximate. These negative results are tight.

  17. Graded core/shell semiconductor nanorods and nanorod barcodes

    Science.gov (United States)

    Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

    2010-12-14

    Graded core/shell semiconductor nanorods and shaped nanorods are disclosed comprising Group II-VI, Group III-V and Group IV semiconductors and methods of making the same. Also disclosed are nanorod barcodes using core/shell nanorods where the core is a semiconductor or metal material, and with or without a shell. Methods of labeling analytes using the nanorod barcodes are also disclosed.

  18. Reading 1-D Barcodes with Mobile Phones Using Deformable Templates

    Science.gov (United States)

    Gallo, Orazio; Manduchi, Roberto

    2011-01-01

    Camera cellphones have become ubiquitous, thus opening a plethora of opportunities for mobile vision applications. For instance, they can enable users to access reviews or price comparisons for a product from a picture of its barcode while still in the store. Barcode reading needs to be robust to challenging conditions such as blur, noise, low resolution, or low quality camera lenses, all of which are extremely common. Surprisingly, even state-of-the-art barcode reading algorithms fail when some of these factors come into play. One reason resides in the early-commitment strategy that virtually all existing algorithms adopt: the image is first binarized and then only the binary data is processed. We propose a new approach to barcode decoding that bypasses binarization. Our technique relies on deformable templates and exploits all the gray level information of each pixel. Due to our parametrization of these templates, we can efficiently perform maximum likelihood estimation independently on each digit and enforce spatial coherence in a subsequent step. We show by way of experiments on challenging UPC-A barcode images from five different databases that our approach outperforms competing algorithms. Implemented on a Nokia N95 phone, our algorithm can localize and decode a barcode on a VGA image (640×480, JPEG compressed) in an average time of 400–500 ms. PMID:21173448

  19. Reading 1D Barcodes with Mobile Phones Using Deformable Templates.

    Science.gov (United States)

    Gallo, Orazio; Manduchi, Roberto

    2011-09-01

    Camera cellphones have become ubiquitous, thus opening a plethora of opportunities for mobile vision applications. For instance, they can enable users to access reviews or price comparisons for a product from a picture of its barcode while still in the store. Barcode reading needs to be robust to challenging conditions such as blur, noise, low resolution, or low-quality camera lenses, all of which are extremely common. Surprisingly, even state-of-the-art barcode reading algorithms fail when some of these factors come into play. One reason resides in the early commitment strategy that virtually all existing algorithms adopt: The image is first binarized and then only the binary data are processed. We propose a new approach to barcode decoding that bypasses binarization. Our technique relies on deformable templates and exploits all of the gray-level information of each pixel. Due to our parameterization of these templates, we can efficiently perform maximum likelihood estimation independently on each digit and enforce spatial coherence in a subsequent step. We show by way of experiments on challenging UPC-A barcode images from five different databases that our approach outperforms competing algorithms. Implemented on a Nokia N95 phone, our algorithm can localize and decode a barcode on a VGA image (640 × 480, JPEG compressed) in an average time of 400-500 ms.

  20. Barcode System for Genetic Identification of Soybean [Glycine max(L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks.

    Science.gov (United States)

    Sohn, Hwang-Bae; Kim, Su-Jeong; Hwang, Tae-Young; Park, Hyang-Mi; Lee, Yu-Young; Markkandan, Kesavan; Lee, Dongwoo; Lee, Sunghoon; Hong, Su-Young; Song, Yun-Ho; Koo, Bon-Cheol; Kim, Yul-Ho

    2017-01-01

    For genetic identification of soybean [ Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, "Singang" and a recurrent parent, "Sowon" were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.

  1. (AJST) GENERALISED DELETION DESIGNS

    African Journals Online (AJOL)

    th row if the t-th level is deleted from factor Fj in the preliminary design d-p to obtain d and xss j is an s x s permutation matrix with 1 in the aj - th column of the o-th row. We shall also write j j a j j. * a. cDPDc d j j. ′. ′= (3.2) where cj is a contrast ...

  2. Wolbachia and DNA barcoding insects: patterns, potential, and problems.

    Directory of Open Access Journals (Sweden)

    M Alex Smith

    Full Text Available Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp, and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

  3. Wolbachia and DNA Barcoding Insects: Patterns, Potential, and Problems

    Science.gov (United States)

    Smith, M. Alex; Bertrand, Claudia; Crosby, Kate; Eveleigh, Eldon S.; Fernandez-Triana, Jose; Fisher, Brian L.; Gibbs, Jason; Hajibabaei, Mehrdad; Hallwachs, Winnie; Hind, Katharine; Hrcek, Jan; Huang, Da-Wei; Janda, Milan; Janzen, Daniel H.; Li, Yanwei; Miller, Scott E.; Packer, Laurence; Quicke, Donald; Ratnasingham, Sujeevan; Rodriguez, Josephine; Rougerie, Rodolphe; Shaw, Mark R.; Sheffield, Cory; Stahlhut, Julie K.; Steinke, Dirk; Whitfield, James; Wood, Monty; Zhou, Xin

    2012-01-01

    Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region. PMID:22567162

  4. Patterns of DNA barcode variation in Canadian marine molluscs.

    Science.gov (United States)

    Layton, Kara K S; Martel, André L; Hebert, Paul D N

    2014-01-01

    Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area. This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0-26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%-46.5%), and showed a significant positive correlation with nearest neighbour distances. DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.

  5. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species

    Science.gov (United States)

    Min Yu; Lichao Jiao; Juan Guo; Alex C. Wiedenhoeft; Tuo He; Xiaomei Jiang; Yafang Yin

    2017-01-01

    ITS2+trnH-psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens.

  6. Locating and decoding barcodes in fuzzy images captured by smart phones

    Science.gov (United States)

    Deng, Wupeng; Hu, Jiwei; Liu, Quan; Lou, Ping

    2017-07-01

    With the development of barcodes for commercial use, people's requirements for detecting barcodes by smart phone become increasingly pressing. The low quality of barcode image captured by mobile phone always affects the decoding and recognition rates. This paper focuses on locating and decoding EAN-13 barcodes in fuzzy images. We present a more accurate locating algorithm based on segment length and high fault-tolerant rate algorithm for decoding barcodes. Unlike existing approaches, location algorithm is based on the edge segment length of EAN -13 barcodes, while our decoding algorithm allows the appearance of fuzzy region in barcode image. Experimental results are performed on damaged, contaminated and scratched digital images, and provide a quite promising result for EAN -13 barcode location and decoding.

  7. DNA barcoding in the media: does coverage of cool science reflect its social context?

    Science.gov (United States)

    Geary, Janis; Camicioli, Emma; Bubela, Tania

    2016-09-01

    Paul Hebert and colleagues first described DNA barcoding in 2003, which led to international efforts to promote and coordinate its use. Since its inception, DNA barcoding has generated considerable media coverage. We analysed whether this coverage reflected both the scientific and social mandates of international barcoding organizations. We searched newspaper databases to identify 900 English-language articles from 2003 to 2013. Coverage of the science of DNA barcoding was highly positive but lacked context for key topics. Coverage omissions pose challenges for public understanding of the science and applications of DNA barcoding; these included coverage of governance structures and issues related to the sharing of genetic resources across national borders. Our analysis provided insight into how barcoding communication efforts have translated into media coverage; more targeted communication efforts may focus media attention on previously omitted, but important topics. Our analysis is timely as the DNA barcoding community works to establish the International Society for the Barcode of Life.

  8. DNA barcoding of the vegetable leafminer Liriomyza sativae Blanchard (Diptera: Agromyzidae) in Bangladesh

    Science.gov (United States)

    DNA barcoding revealed the presence of the polyphagous leafminer pest Liriomyza sativae Blanchard in Bangladesh. DNA barcode sequences for mitochondrial COI were generated for Agromyzidae larvae, pupae and adults collected from field populations across Bangladesh. BLAST sequence similarity searches ...

  9. DNA barcoding of Japanese click beetles (Coleoptera, Elateridae).

    Science.gov (United States)

    Oba, Yuichi; Ôhira, Hitoo; Murase, Yukio; Moriyama, Akihiko; Kumazawa, Yoshinori

    2015-01-01

    Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa.

  10. DNA barcoding of Japanese click beetles (Coleoptera, Elateridae.

    Directory of Open Access Journals (Sweden)

    Yuichi Oba

    Full Text Available Click beetles (Coleoptera: Elateridae represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation. These findings urge taxonomic reinvestigation of these mismatched taxa.

  11. Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae).

    Science.gov (United States)

    Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

    2015-04-01

    DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using "best match" and "best close match" methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  12. Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae

    Directory of Open Access Journals (Sweden)

    Giovanna Câmara Giudicelli

    2015-04-01

    Full Text Available DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1 region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.

  13. Automation and workflow considerations for embedding Digimarc Barcodes at scale

    Science.gov (United States)

    Rodriguez, Tony; Haaga, Don; Calhoon, Sean

    2015-03-01

    The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

  14. DNA Barcoding of Japanese Click Beetles (Coleoptera, Elateridae)

    Science.gov (United States)

    Oba, Yuichi; Ôhira, Hitoo; Murase, Yukio; Moriyama, Akihiko; Kumazawa, Yoshinori

    2015-01-01

    Click beetles (Coleoptera: Elateridae) represent one of the largest groups of beetle insects. Some click beetles in larval form, known as wireworms, are destructive agricultural pests. Morphological identification of click beetles is generally difficult and requires taxonomic expertise. This study reports on the DNA barcoding of Japanese click beetles to enable their rapid and accurate identification. We collected and assembled 762 cytochrome oxidase subunit I barcode sequences from 275 species, which cover approximately 75% of the common species found on the Japanese main island, Honshu. This barcode library also contains 20 out of the 21 potential pest species recorded in Japan. Our analysis shows that most morphologically identified species form distinct phylogenetic clusters separated from each other by large molecular distances. This supports the general usefulness of the DNA barcoding approach for quick and reliable identification of Japanese elaterid species for environmental impact assessment, agricultural pest control, and biodiversity analysis. On the other hand, the taxonomic boundary in dozens of species did not agree with the boundary of barcode index numbers (a criterion for sequence-based species delimitation). These findings urge taxonomic reinvestigation of these mismatched taxa. PMID:25636000

  15. A survey on barcode RFID and NFC

    Science.gov (United States)

    Thanapal, P.; Prabhu, J.; Jakhar, Mridula

    2017-11-01

    Over the recent years, many industries have started implementing new technologies for tracing and tracking their products. These technologies are a kind of blessing to their management system. The technology and management system has to work in parallel to avoid loopholes in the system. We can see so many technologies around us and the most difficult and important part is to choose best out of all these new technologies. The important point which we need to take care while choosing a technology for the system is to make sure the technology can integrate properly with the other parameters in the management system. The industry management system consists of many levels such as initial level, intermediate level, final level and tracking. Nowadays tracking a product from its initial stage is becoming a trend. To cope up with this upcoming trend and also with the company demand, integrating the product with Barcode, RFID tags, NFC tag or any other traceable technology. Many supply chain Management system are also adopting this techniques.

  16. 76 FR 23749 - Intelligent Mail Package Barcode (IMpb) Implementation for Commercial Parcels

    Science.gov (United States)

    2011-04-28

    ... POSTAL SERVICE 39 CFR Part 111 Intelligent Mail Package Barcode (IMpb) Implementation for... scanning of Intelligent Mail[supreg] package barcodes (IMpb) and other extra services barcodes via automated processing equipment and Intelligent Mail scanning devices. Once fully implemented, tracking data...

  17. 76 FR 59504 - Intelligent Mail Package Barcode (IMpb) Implementation for Commercial Parcels

    Science.gov (United States)

    2011-09-27

    ... POSTAL SERVICE 39 CFR Part 111 Intelligent Mail Package Barcode (IMpb) Implementation for... various sections to require the use of an Intelligent Mail unique tracking barcode on all commercial... extra services barcodes with automated processing equipment and Intelligent Mail scanning devices. Once...

  18. 78 FR 13006 - New Intelligent Mail Package Barcode Standards To Enhance Package Visibility; Opportunity for...

    Science.gov (United States)

    2013-02-26

    ... POSTAL SERVICE 39 CFR Part 111 New Intelligent Mail Package Barcode Standards To Enhance Package... comments. SUMMARY: The Postal Service is exploring the advisability of requiring the use of Intelligent Mail[supreg] package barcodes (IMpb) or unique tracking Intelligent Mail barcodes (IMb TM ) on all...

  19. |SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization--application to species and environmental barcoding.

    Science.gov (United States)

    Piry, S; Guivier, E; Realini, A; Martin, J-F

    2012-11-01

    Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| Barcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations (in silico and previously published, respectively). |SE|S|AM|E| Barcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/. © 2012 Blackwell Publishing Ltd.

  20. DNA Barcoding the Heliothinae (Lepidoptera: Noctuidae) of Australia and Utility of DNA Barcodes for Pest Identification in Helicoverpa and Relatives.

    Science.gov (United States)

    Mitchell, Andrew; Gopurenko, David

    2016-01-01

    Helicoverpa and Heliothis species include some of the world's most significant crop pests, causing billions of dollars of losses globally. As such, a number are regulated quarantine species. For quarantine agencies, the most crucial issue is distinguishing native species from exotics, yet even this task is often not feasible because of poorly known local faunas and the difficulties of identifying closely related species, especially the immature stages. DNA barcoding is a scalable molecular diagnostic method that could provide the solution to this problem, however there has been no large-scale test of the efficacy of DNA barcodes for identifying the Heliothinae of any region of the world to date. This study fills that gap by DNA barcoding the entire heliothine moth fauna of Australia, bar one rare species, and comparing results with existing public domain resources. We find that DNA barcodes provide robust discrimination of all of the major pest species sampled, but poor discrimination of Australian Heliocheilus species, and we discuss ways to improve the use of DNA barcodes for identification of pests.

  1. DNA Barcoding the Heliothinae (Lepidoptera: Noctuidae of Australia and Utility of DNA Barcodes for Pest Identification in Helicoverpa and Relatives.

    Directory of Open Access Journals (Sweden)

    Andrew Mitchell

    Full Text Available Helicoverpa and Heliothis species include some of the world's most significant crop pests, causing billions of dollars of losses globally. As such, a number are regulated quarantine species. For quarantine agencies, the most crucial issue is distinguishing native species from exotics, yet even this task is often not feasible because of poorly known local faunas and the difficulties of identifying closely related species, especially the immature stages. DNA barcoding is a scalable molecular diagnostic method that could provide the solution to this problem, however there has been no large-scale test of the efficacy of DNA barcodes for identifying the Heliothinae of any region of the world to date. This study fills that gap by DNA barcoding the entire heliothine moth fauna of Australia, bar one rare species, and comparing results with existing public domain resources. We find that DNA barcodes provide robust discrimination of all of the major pest species sampled, but poor discrimination of Australian Heliocheilus species, and we discuss ways to improve the use of DNA barcodes for identification of pests.

  2. VDAC regulates AAC-mediated apoptosis and cytochromecrelease in yeast.

    Science.gov (United States)

    Trindade, Dário; Pereira, Clara; Chaves, Susana R; Manon, Stéphen; Côrte-Real, Manuela; Sousa, Maria J

    2016-08-25

    Mitochondrial outer membrane permeabilization is a key event in apoptosis processes leading to the release of lethal factors. We have previously shown that absence of the ADP/ATP carrier (AAC) proteins (yeast orthologues of mammalian ANT proteins) increased the resistance of yeast cells to acetic acid, preventing MOMP and the release of cytochrome c from mitochondria during acetic acid - induced apoptosis. On the other hand, deletion of POR1 (yeast voltage-dependent anion channel - VDAC) increased the sensitivity of yeast cells to acetic acid. In the present work, we aimed to further characterize the role of yeast VDAC in acetic acid - induced apoptosis and assess if it functionally interacts with AAC proteins. We found that the sensitivity to acetic acid resulting from POR1 deletion is completely abrogated by the absence of AAC proteins, and propose that Por1p acts as a negative regulator of acetic acid - induced cell death by a mechanism dependent of AAC proteins, by acting on AAC - dependent cytochrome c release. Moreover, we show that Por1p has a role in mitochondrial fusion that, contrary to its role in apoptosis, is not affected by the absence of AAC, and demonstrate that mitochondrial network fragmentation is not sufficient to induce release of cytochrome c or sensitivity to acetic acid - induced apoptosis. This work enhances our understanding on cytochrome c release during cell death, which may be relevant in pathological scenarios where MOMP is compromised.

  3. Currency verification by a 2D infrared barcode

    International Nuclear Information System (INIS)

    Schirripa Spagnolo, Giuseppe; Cozzella, Lorenzo; Simonetti, Carla

    2010-01-01

    Nowadays all the National Central Banks are continuously studying innovative anti-counterfeiting systems for banknotes. In this note, an innovative solution is proposed, which combines the potentiality of a hylemetric approach (methodology conceptually similar to biometry), based on notes' intrinsic characteristics, with a well-known and consolidated 2D barcode identification system. In particular, in this note we propose to extract from the banknotes a univocal binary control sequence (template) and insert an encrypted version of it in a barcode printed on the same banknote. For a more acceptable look and feel of a banknote, the superposed barcode can be stamped using IR ink that is visible to near-IR image sensors. This makes the banknote verification simpler. (technical design note)

  4. A laboratory information management system for DNA barcoding workflows.

    Science.gov (United States)

    Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

    2012-07-01

    This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

  5. Red Yeast Rice: An Introduction

    Science.gov (United States)

    ... Yeast Rice For More Information Key References Acknowledgments © asian-ingredients Red yeast rice is a traditional Chinese ... products varies depending on the yeast strains and culture conditions used to manufacture them. The strains and ...

  6. Motor racing, tobacco company sponsorship, barcodes and alibi marketing.

    Science.gov (United States)

    Grant-Braham, Bruce; Britton, John

    2012-11-01

    Sponsorship of Formula One (F1) motor racing, which has been used as an indirect medium of tobacco advertising for several decades, was prohibited by the 2005 European Union Tobacco Advertising Directive. Most F1 tobacco sponsorship of motor racing in the EU has since ceased, with the exception of the Scuderia Ferrari team, which continues to be funded by Philip Morris. In 2007, the Marlboro logo on Ferrari cars and other race regalia was replaced by an evolving 'barcode' design, which Ferrari later claimed was part of the livery of the car, and not a Marlboro advertisement. To determine whether the 'barcode' graphics used by Ferrari represent 'alibi' Marlboro advertising. Academic and grey literature, and online tobacco industry document archives, were searched using terms relevant to tobacco marketing and motorsport. Tobacco sponsorship of F1 motor racing began in 1968, and Philip Morris has sponsored F1 teams since 1972. Phillip Morris first used a 'barcode' design, comprising red vertical parallel lines below the word Marlboro on the British Racing Motors F1 car in 1972. Vertical or horizontal 'barcode' designs have been used in this way, latterly without the word Marlboro, ever since. The modern 'barcode' logos occupied the same position on cars and drivers' clothing as conventional Marlboro logos in the past. The shared use of red colour by Marlboro and Ferrari is also recognised by Philip Morris as a means of promoting brand association between Marlboro and Ferrari. The Ferrari 'barcode' designs are alibi Marlboro logos and hence constitute advertising prohibited by the 2005 EU Tobacco Advertising Directive.

  7. Genetic Barcodes Facilitate Competitive Clonal Analyses In Vivo.

    Science.gov (United States)

    Aranyossy, Tim; Thielecke, Lars; Glauche, Ingmar; Fehse, Boris; Cornils, Kerstin

    2017-10-01

    Monitoring the fate of individual cell clones is an important task to better understand normal tissue regeneration, for example after hematopoietic stem cell (HSC) transplantation, but also cancerogenesis. Based on their integration into the host cell's genome, retroviral vectors are commonly used to stably mark target cells and their progeny. The development of genetic barcoding techniques has opened new possibilities to determine clonal composition and dynamics in great detail. A modular genetic barcode was recently introduced consisting of 32 variable positions (BC32) with a customized backbone, and its advantages were demonstrated with regard to barcode calling and quantification. The study presented applied the BC32 system in a complex in vivo situation, namely to analyze clonal reconstitution dynamics for HSC grafts consisting of up to three cell populations with distinguishable barcodes using different alpha- and lentiviral vectors. In a competitive transplantation setup, it was possible to follow the differently marked cell populations within individual animals. This enabled the clonal contribution of the different BC32 constructs during reconstitution and long-term hematopoiesis in the peripheral blood and the spatial distribution in bone marrow and spleen to be identified. Thus, it was demonstrated that the system allows the output of individually marked cells to be tracked in vivo and their influence on clonal dynamics to be analyzed. Successful application of the BC32 system in a complex, competitive in vivo situation provided proof-of-principle that its high complexity and the large Hamming distance between individual barcodes, combined with the easy customization, facilitate efficient and precise quantification, even without prior knowledge of individual barcode sequences. Importantly, simultaneous high-sensitivity analyses of different cell populations in single animals may significantly reduce numbers of animals required to investigate specific

  8. Barcoding Atlantic Canada's mesopelagic and upper bathypelagic marine fishes.

    Directory of Open Access Journals (Sweden)

    Ellen L Kenchington

    Full Text Available DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD. Most of the 118 species conformed to expectations of monophyly and the presence of a "barcode gap", though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean's sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that "resident" populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation

  9. Polylox barcoding reveals haematopoietic stem cell fates realized in vivo.

    Science.gov (United States)

    Pei, Weike; Feyerabend, Thorsten B; Rössler, Jens; Wang, Xi; Postrach, Daniel; Busch, Katrin; Rode, Immanuel; Klapproth, Kay; Dietlein, Nikolaus; Quedenau, Claudia; Chen, Wei; Sauer, Sascha; Wolf, Stephan; Höfer, Thomas; Rodewald, Hans-Reimer

    2017-08-24

    Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system. Polylox recombination in situ reaches a practical diversity of several hundred thousand barcodes, allowing tagging of single cells. We have used this experimental system, combined with fate mapping, to assess haematopoietic stem cell (HSC) fates in vivo. Classical models of haematopoietic lineage specification assume a tree with few major branches. More recently, driven in part by the development of more efficient single-cell assays and improved transplantation efficiencies, different models have been proposed, in which unilineage priming may occur in mice and humans at the level of HSCs. We have introduced barcodes into HSC progenitors in embryonic mice, and found that the adult HSC compartment is a mosaic of embryo-derived HSC clones, some of which are unexpectedly large. Most HSC clones gave rise to multilineage or oligolineage fates, arguing against unilineage priming, and suggesting coherent usage of the potential of cells in a clone. The spreading of barcodes, both after induction in embryos and in adult mice, revealed a basic split between common myeloid-erythroid development and common lymphocyte development, supporting the long-held but contested view of a tree-like haematopoietic structure.

  10. DNA barcoding as a screening tool for cryptic diversity

    DEFF Research Database (Denmark)

    Huemer, Peter; Karsholt, Ole; Mutanen, Marko

    2014-01-01

    oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy...... of these taxa has to be re-assessed in the future. We investigated one such deep split in Caryocolum amaurella (Hering, 1924) and found it in congruence with yet unrecognized diagnostic morphological characters and specific host-plants. The integrative species delineation leads to the description of Caryocolum...

  11. DNA barcoding as a means for identifying medicinal plants of Pakistan

    International Nuclear Information System (INIS)

    Schori, M.; Showalter, A.M.

    2011-01-01

    DNA barcoding involves the generation of DNA sequencing data from particular genetic regions in an organism and the use of these sequence data to identify or 'barcode' that organism and distinguish it from other species. Here, DNA barcoding is being used to identify several medicinal plants found in Pakistan and distinguished them from other similar species. Several challenges to the successful implementation of plant DNA barcoding are presented and discussed. Despite these challenges, DNA barcoding has the potential to uniquely identify medicinal plants and provide quality control and standardization of the plant material supplied to the pharmaceutical industry. (author)

  12. DNA barcoding reveals a cryptic nemertean invasion in Atlantic and Mediterranean waters

    Science.gov (United States)

    Fernández-Álvarez, Fernando Ángel; Machordom, Annie

    2013-09-01

    For several groups, like nemerteans, morphology-based identification is a hard discipline, but DNA barcoding may help non-experts in the identification process. In this study, DNA barcoding is used to reveal the cryptic invasion of Pacific Cephalothrix cf. simula into Atlantic and Mediterranean coasts. Although DNA barcoding is a promising method for the identification of Nemertea, only 6 % of the known number of nemertean species is currently associated with a correct DNA barcode. Therefore, additional morphological and molecular studies are necessary to advance the utility of DNA barcoding in the characterisation of possible nemertean alien invasions.

  13. Standard symbols for books, journals, and newspapers through the use of barcode

    Directory of Open Access Journals (Sweden)

    T. A. Titiova

    2014-01-01

    Full Text Available Barcode is serves for automatic identification. Barcode information is provided by dark and light strips of different weight. Recently, barcode has been mostly used in different industries e.g. in distributive trade to accelerate the paper-flow and keep or seek the objects in stores, as well as in medical, credit and other cards, and in libraries. Printing matter has another barcode. Like all goods it passes through the cash registers. Therefore, ISBN and SSN international standards ought to be changed for EAN standards. For the first three positions of barcode the indicia 978 for books and 977 for journals are introduced.

  14. DNA Barcoding Identifies Illegal Parrot Trade.

    Science.gov (United States)

    Gonçalves, Priscila F M; Oliveira-Marques, Adriana R; Matsumoto, Tania E; Miyaki, Cristina Y

    2015-01-01

    Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. Reliable DNA barcoding performance proved for species and island populations of comoran squamate reptiles.

    Directory of Open Access Journals (Sweden)

    Oliver Hawlitschek

    Full Text Available In the past decade, DNA barcoding became increasingly common as a method for species identification in biodiversity inventories and related studies. However, mainly due to technical obstacles, squamate reptiles have been the target of few barcoding studies. In this article, we present the results of a DNA barcoding study of squamates of the Comoros archipelago, a poorly studied group of oceanic islands close to and mostly colonized from Madagascar. The barcoding dataset presented here includes 27 of the 29 currently recognized squamate species of the Comoros, including 17 of the 18 endemic species. Some species considered endemic to the Comoros according to current taxonomy were found to cluster with non-Comoran lineages, probably due to poorly resolved taxonomy. All other species for which more than one barcode was obtained corresponded to distinct clusters useful for species identification by barcoding. In most species, even island populations could be distinguished using barcoding. Two cryptic species were identified using the DNA barcoding approach. The obtained barcoding topology, a Bayesian tree based on COI sequences of 5 genera, was compared with available multigene topologies, and in 3 cases, major incongruences between the two topologies became evident. Three of the multigene studies were initiated after initial screening of a preliminary version of the barcoding dataset presented here. We conclude that in the case of the squamates of the Comoros Islands, DNA barcoding has proven a very useful and efficient way of detecting isolated populations and promising starting points for subsequent research.

  16. DNA barcoding in the cycadales: testing the potential of proposed barcoding markers for species identification of cycads.

    Directory of Open Access Journals (Sweden)

    Chodon Sass

    Full Text Available Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL, and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS, were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

  17. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  18. Feasibility and Limitations of Vaccine Two-Dimensional Barcoding Using Mobile Devices.

    Science.gov (United States)

    Bell, Cameron; Guerinet, Julien; Atkinson, Katherine M; Wilson, Kumanan

    2016-06-23

    Two-dimensional (2D) barcoding has the potential to enhance documentation of vaccine encounters at the point of care. However, this is currently limited to environments equipped with dedicated barcode scanners and compatible record systems. Mobile devices may present a cost-effective alternative to leverage 2D vaccine vial barcodes and improve vaccine product-specific information residing in digital health records. Mobile devices have the potential to capture product-specific information from 2D vaccine vial barcodes. We sought to examine the feasibility, performance, and potential limitations of scanning 2D barcodes on vaccine vials using 4 different mobile phones. A unique barcode scanning app was developed for Android and iOS operating systems. The impact of 4 variables on the scan success rate, data accuracy, and time to scan were examined: barcode size, curvature, fading, and ambient lighting conditions. Two experimenters performed 4 trials 10 times each, amounting to a total of 2160 barcode scan attempts. Of the 1832 successful scans performed in this evaluation, zero produced incorrect data. Five-millimeter barcodes were the slowest to scan, although only by 0.5 seconds on average. Barcodes with up to 50% fading had a 100% success rate, but success rate deteriorated beyond 60% fading. Curved barcodes took longer to scan compared with flat, but success rate deterioration was only observed at a vial diameter of 10 mm. Light conditions did not affect success rate or scan time between 500 lux and 20 lux. Conditions below 20 lux impeded the device's ability to scan successfully. Variability in scan time was observed across devices in all trials performed. 2D vaccine barcoding is possible using mobile devices and is successful under the majority of conditions examined. Manufacturers utilizing 2D barcodes should take into consideration the impact of factors that limit scan success rates. Future studies should evaluate the effect of mobile barcoding on workflow and

  19. High-throughput knockout screen in fission yeast.

    Science.gov (United States)

    Gregan, Juraj; Rabitsch, Peter K; Rumpf, Cornelia; Novatchkova, Maria; Schleiffer, Alexander; Nasmyth, Kim

    2006-01-01

    We have designed the most efficient strategy to knock out genes in fission yeast Schizosaccharomyces pombe on a large scale. Our technique is based on knockout constructs that contain regions homologous to the target gene cloned into vectors carrying dominant drug-resistance markers. Most of the steps are carried out in a 96-well format, allowing simultaneous deletion of 96 genes in one batch. Based on our knockout technique, we designed a strategy for cloning knockout constructs for all predicted fission yeast genes, which is available in a form of a searchable database http://mendel.imp.ac.at/Pombe_deletion/. We validated this technique in a screen where we identified novel genes required for chromosome segregation during meiosis. Here, we present our protocol with detailed instructions. Using this protocol, one person can knock out 96 S. pombe genes in 8 days.

  20. Haploid deletion strains of Saccharomyces cerevisiae that determine survival during space flight

    Science.gov (United States)

    Johanson, Kelly; Allen, Patricia L.; Gonzalez-Villalobos, Romer A.; Nesbit, Jacqueline; Nickerson, Cheryl A.; Höner zu Bentrup, Kerstin; Wilson, James W.; Ramamurthy, Rajee; D'Elia, Riccardo; Muse, Kenneth E.; Hammond, Jeffrey; Freeman, Jake; Stodieck, Louis S.; Hammond, Timothy G.

    2007-02-01

    This study identifies genes that determine survival during a space flight, using the model eukaryotic organism, Saccharomyces cerevisiae. Select strains of a haploid yeast deletion series grew during storage in distilled water in space, but not in ground based static or clinorotation controls. The survival advantages in space in distilled water include a 133-fold advantage for the deletion of PEX19, a chaperone and import receptor for newly- synthesized class I peroxisomal membrane proteins, to 77-40 fold for deletion strains lacking elements of aerobic respiration, isocitrate metabolism, and mitochondrial electron transport. Following automated addition of rich growth media, the space flight was associated with a marked survival advantage of strains with deletions in catalytically active genes including hydrolases, oxidoreductases and transferases. When compared to static controls, space flight was associated with a marked survival disadvantage of deletion strains lacking transporter, antioxidant and catalytic activity. This study identifies yeast deletion strains with a survival advantage during storage in distilled water and space flight, and amplifies our understanding of the genes critical for survival in space.

  1. A retrospective approach to testing the DNA barcoding method.

    Directory of Open Access Journals (Sweden)

    David G Chapple

    Full Text Available A decade ago, DNA barcoding was proposed as a standardised method for identifying existing species and speeding the discovery of new species. Yet, despite its numerous successes across a range of taxa, its frequent failures have brought into question its accuracy as a short-cut taxonomic method. We use a retrospective approach, applying the method to the classification of New Zealand skinks as it stood in 1977 (primarily based upon morphological characters, and compare it to the current taxonomy reached using both morphological and molecular approaches. For the 1977 dataset, DNA barcoding had moderate-high success in identifying specimens (78-98%, and correctly flagging specimens that have since been confirmed as distinct taxa (77-100%. But most matching methods failed to detect the species complexes that were present in 1977. For the current dataset, there was moderate-high success in identifying specimens (53-99%. For both datasets, the capacity to discover new species was dependent on the methodological approach used. Species delimitation in New Zealand skinks was hindered by the absence of either a local or global barcoding gap, a result of recent speciation events and hybridisation. Whilst DNA barcoding is potentially useful for specimen identification and species discovery in New Zealand skinks, its error rate could hinder the progress of documenting biodiversity in this group. We suggest that integrated taxonomic approaches are more effective at discovering and describing biodiversity.

  2. Identification of Meconopsis species by a DNA barcode sequence ...

    African Journals Online (AJOL)

    Deoxyribonucleic acid (DNA) barcoding is a novel technology that uses a standard DNA sequence to facilitate species identification. Species identification is necessary for the authentication of traditional plant based medicines. Although a consensus has not been agreed regarding which DNA sequences can be used as ...

  3. DNA Barcodes of Lepidoptera Reared from Yawan, Papua New Guinea

    Czech Academy of Sciences Publication Activity Database

    Miller, S. E.; Rosati, M. E.; Gewa, B.; Novotný, Vojtěch; Weiblen, G. D.; Herbert, P. D. N.

    2015-01-01

    Roč. 117, č. 2 (2015), s. 247-250 ISSN 0013-8797 R&D Projects: GA ČR(CZ) GA14-04258S Institutional support: RVO:60077344 Keywords : DNA barcodes * Lepidoptera * Papua New Guinea Subject RIV: EH - Ecology, Behaviour Impact factor: 0.593, year: 2015

  4. Identification of rays through DNA barcoding: an application for ecologists.

    Directory of Open Access Journals (Sweden)

    Florencia Cerutti-Pereyra

    Full Text Available DNA barcoding potentially offers scientists who are not expert taxonomists a powerful tool to support the accuracy of field studies involving taxa that are diverse and difficult to identify. The taxonomy of rays has received reasonable attention in Australia, although the fauna in remote locations such as Ningaloo Reef, Western Australia is poorly studied and the identification of some species in the field is problematic. Here, we report an application of DNA-barcoding to the identification of 16 species (from 10 genera of tropical rays as part of an ecological study. Analysis of the dataset combined across all samples grouped sequences into clearly defined operational taxonomic units, with two conspicuous exceptions: the Neotrygon kuhlii species complex and the Aetobatus species complex. In the field, the group that presented the most difficulties for identification was the spotted whiptail rays, referred to as the 'uarnak' complex. Two sets of problems limited the successful application of DNA barcoding: (1 the presence of cryptic species, species complexes with unresolved taxonomic status and intra-specific geographical variation, and (2 insufficient numbers of entries in online databases that have been verified taxonomically, and the presence of lodged sequences in databases with inconsistent names. Nevertheless, we demonstrate the potential of the DNA barcoding approach to confirm field identifications and to highlight species complexes where taxonomic uncertainty might confound ecological data.

  5. 75 FR 56922 - Implementation of the Intelligent Mail Package Barcode

    Science.gov (United States)

    2010-09-17

    ... in planning for future mailings and preparing for system changes necessary to adopt the new IMpb... absence of information associating the piece with its specific payment method; and have limited...) and 3-digit Service Type Code. The data construction of the IMpb barcode will be different from that...

  6. Indigenous species barcode database improves the identification of zooplankton.

    Directory of Open Access Journals (Sweden)

    Jianghua Yang

    Full Text Available Incompleteness and inaccuracy of DNA barcode databases is considered an important hindrance to the use of metabarcoding in biodiversity analysis of zooplankton at the species-level. Species barcoding by Sanger sequencing is inefficient for organisms with small body sizes, such as zooplankton. Here mitochondrial cytochrome c oxidase I (COI fragment barcodes from 910 freshwater zooplankton specimens (87 morphospecies were recovered by a high-throughput sequencing platform, Ion Torrent PGM. Intraspecific divergence of most zooplanktons was < 5%, except Branchionus leydign (Rotifer, 14.3%, Trichocerca elongate (Rotifer, 11.5%, Lecane bulla (Rotifer, 15.9%, Synchaeta oblonga (Rotifer, 5.95% and Schmackeria forbesi (Copepod, 6.5%. Metabarcoding data of 28 environmental samples from Lake Tai were annotated by both an indigenous database and NCBI Genbank database. The indigenous database improved the taxonomic assignment of metabarcoding of zooplankton. Most zooplankton (81% with barcode sequences in the indigenous database were identified by metabarcoding monitoring. Furthermore, the frequency and distribution of zooplankton were also consistent between metabarcoding and morphology identification. Overall, the indigenous database improved the taxonomic assignment of zooplankton.

  7. Are mini DNA-barcodes sufficiently informative to resolve species ...

    Indian Academy of Sciences (India)

    Since then, the COI has been effec- tively used as 'universal DNA barcode' in several animal groups such as birds, butterflies, amphibians and fishes. ∗. For correspondence. E-mail: gravikanth@atree.org. (Hebert et al. 2003; Gu et al. 2011). However, in plants, the. COI was found to be ineffective in discriminating the taxa,.

  8. High-throughput knockout screen in fission yeast

    OpenAIRE

    Gregan, Juraj; Rabitsch, Peter K; Rumpf, Cornelia; Novatchkova, Maria; Schleiffer, Alexander; Nasmyth, Kim

    2006-01-01

    We have designed the most efficient strategy to knock out genes in fission yeast Schizosaccharomyces pombe on a large scale. Our technique is based on knockout constructs that contain regions homologous to the target gene cloned into vectors carrying dominant drug-resistance markers. Most of the steps are carried out in a 96-well format, allowing simultaneous deletion of 96 genes in one batch. Based on our knockout technique, we designed a strategy for cloning knockout constructs for all pred...

  9. Analyzing mosquito (Diptera: culicidae diversity in Pakistan by DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Muhammad Ashfaq

    Full Text Available Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications.Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection. The genus Aedes (Stegomyia comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments.As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

  10. Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan.

    Science.gov (United States)

    Ashfaq, Muhammad; Akhtar, Saleem; Rafi, Muhammad Athar; Mansoor, Shahid; Hebert, Paul D N

    2017-01-01

    Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species.

  11. Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding.

    Science.gov (United States)

    Ashfaq, Muhammad; Hebert, Paul D N; Mirza, Jawwad H; Khan, Arif M; Zafar, Yusuf; Mirza, M Sajjad

    2014-01-01

    Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

  12. Analyzing Mosquito (Diptera: Culicidae) Diversity in Pakistan by DNA Barcoding

    Science.gov (United States)

    Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, Jawwad H.; Khan, Arif M.; Zafar, Yusuf; Mirza, M. Sajjad

    2014-01-01

    Background Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. Methodology/Principal Findings Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010–2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0–2.4%, while congeneric species showed from 2.3–17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. Conclusions As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations. PMID:24827460

  13. DNA barcoding of sigmodontine rodents: identifying wildlife reservoirs of zoonoses.

    Science.gov (United States)

    Müller, Lívia; Gonçalves, Gislene L; Cordeiro-Estrela, Pedro; Marinho, Jorge R; Althoff, Sérgio L; Testoni, André F; González, Enrique M; Freitas, Thales R O

    2013-01-01

    Species identification through DNA barcoding is a tool to be added to taxonomic procedures, once it has been validated. Applying barcoding techniques in public health would aid in the identification and correct delimitation of the distribution of rodents from the subfamily Sigmodontinae. These rodents are reservoirs of etiological agents of zoonoses including arenaviruses, hantaviruses, Chagas disease and leishmaniasis. In this study we compared distance-based and probabilistic phylogenetic inference methods to evaluate the performance of cytochrome c oxidase subunit I (COI) in sigmodontine identification. A total of 130 sequences from 21 field-trapped species (13 genera), mainly from southern Brazil, were generated and analyzed, together with 58 GenBank sequences (24 species; 10 genera). Preliminary analysis revealed a 9.5% rate of misidentifications in the field, mainly of juveniles, which were reclassified after examination of external morphological characters and chromosome numbers. Distance and model-based methods of tree reconstruction retrieved similar topologies and monophyly for most species. Kernel density estimation of the distance distribution showed a clear barcoding gap with overlapping of intraspecific and interspecific densities < 1% and 21 species with mean intraspecific distance < 2%. Five species that are reservoirs of hantaviruses could be identified through DNA barcodes. Additionally, we provide information for the description of a putative new species, as well as the first COI sequence of the recently described genus Drymoreomys. The data also indicated an expansion of the distribution of Calomys tener. We emphasize that DNA barcoding should be used in combination with other taxonomic and systematic procedures in an integrative framework and based on properly identified museum collections, to improve identification procedures, especially in epidemiological surveillance and ecological assessments.

  14. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  15. Identification of North Sea molluscs with DNA barcoding.

    Science.gov (United States)

    Barco, Andrea; Raupach, Michael J; Laakmann, Silke; Neumann, Hermann; Knebelsberger, Thomas

    2016-01-01

    Sequence-based specimen identification, known as DNA barcoding, is a common method complementing traditional morphology-based taxonomic assignments. The fundamental resource in DNA barcoding is the availability of a taxonomically reliable sequence database to use as a reference for sequence comparisons. Here, we provide a reference library including 579 sequences of the mitochondrial cytochrome c oxidase subunit I for 113 North Sea mollusc species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match, Best Close Match (BCM) and All Species Barcode (ASB) criteria with three different threshold values. Each identification result was compared with our prior morphology-based taxonomic assignments. Our simulation resulted in 87.7% congruent identifications (93.8% when excluding singletons). The highest number of congruent identifications was obtained with BCM and ASB and a 0.05 threshold. We also compared identifications with genetic clustering (Barcode Index Numbers, BINs) computed by the Barcode of Life Datasystem (BOLD). About 68% of our morphological identifications were congruent with BINs created by BOLD. Forty-nine sequences were clustered in 16 discordant BINs, and these were divided in two classes: sequences from different species clustered in a single BIN and conspecific sequences divided in more BINs. Whereas former incongruences were probably caused by BOLD entries in need of a taxonomic update, the latter incongruences regarded taxa requiring further investigations. These include species with amphi-Atlantic distribution, whose genetic structure should be evaluated over their entire range to produce a reliable sequence-based identification system. © 2015 John Wiley & Sons Ltd.

  16. Identification of Species in Tripterygium (Celastraceae) Based on DNA Barcoding.

    Science.gov (United States)

    Zhang, Xiaomei; Li, Na; Yao, Yuanyuan; Liang, Xuming; Qu, Xianyou; Liu, Xiang; Zhu, Yingjie; Yang, Dajian; Sun, Wei

    2016-11-01

    Species of genus Tripterygium (Celastraceae) have attracted much attention owing to their excellent effect on treating autoimmune and inflammatory diseases. However, due to high market demand causing overexploitation, natural populations of genus Tripterygium have rapidly declined. Tripterygium medicinal materials are mainly collected from the wild, making the quality of medicinal materials unstable. Additionally, identification of herbal materials from Tripterygium species and their adulterants is difficult based on morphological characters. Therefore, an accurate, convenient, and stability method is urgently needed. In this wok, we developed a DNA barcoding technique to distinguish T. wilfordii HOOK. f., T. hypoglaucum (LÉVL.) HUTCH, and T. regelii SPRAGUE et TAKEDA and their adulterants based on four uniform and standard DNA regions (internal transcribed spacer 2 (ITS2), matK, rbcL, and psbA-trnH). DNA was extracted from 26 locations of fresh leaves. Phylogenetic tree was constructed with Neighbor-Joining (NJ) method, while barcoding gap was analyzed to assess identification efficiency. Compared with the other DNA barcodes applied individually or in combination, ITS2+psbA-trnH was demonstrated as the optimal barcode. T. hypoglaucum and T. wilfordii can be considered as conspecific, while T. regelii was recognized as a separate species. Furthermore, identification of commercial Tripterygium samples was conducted using BLAST against GenBank and Species Identification System for Traditional Chinese Medicine. Our results indicated that DNA barcoding is a convenient, effective, and stability method to identify and distinguish Tripterygium and its adulterants, and could be applied as the quality control for Tripterygium medicinal preparations and monitoring of the medicinal herb trade in markets.

  17. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.

    Science.gov (United States)

    Zhang, Wei; Fan, Xiaohong; Zhu, Shuifang; Zhao, Hong; Fu, Lianzhong

    2013-01-01

    Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.

  18. Building a DNA barcode library of Alaska's non-marine arthropods.

    Science.gov (United States)

    Sikes, Derek S; Bowser, Matthew; Morton, John M; Bickford, Casey; Meierotto, Sarah; Hildebrandt, Kyndall

    2017-03-01

    Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska - i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.

  19. Compounding & dispensing errors before and after implementing barcode technology in a nuclear pharmacy.

    Science.gov (United States)

    Galbraith, Wendy; Shadid, Jill

    2012-01-01

    The objective of this study was to determine whether the incidence of compounding and dispensing errors changed significantly in a nuclear pharmacy after the pharmacy adopted a barcode assistance system. Nuclear pharmacy dispensing errors are extremely low compared to that of busy traditional pharmacies, but there is no data available describing the use of bar-coding assistance on the rate of dispensing errors in nuclear pharmacy. A retrospective review of dispensing errors pre-barcode assistance system implementation (2001 through 2004) and post-barcode assistance system implementation (February 2005 through 2009) was conducted using data from a nuclear pharmacy that dispenses approximately 500 prescriptions per day to nuclear medicine clinics and hospitals. Data was obtained from pharmacy error logs filed by the pharmacy as reported by an end user receiving the compounded preparation or the pharmacist having recognized the error before it reached the end user. Dispensing errors were defined as any deviation in the dispensed preparation from the prescribed order. Categories identified as incorrect were: dosage, drug, volume, procedure, patient, and delivery destination. Implementation of the barcode assistance system included installation of computers, software, barcoding devices, and training of personnel. The barcode assistance system provided barcodes for each compounding component, final preparation, syringe label, prescription, and shipping material. The barcode assistant system communicated directly with the dose calibrator, enabling the dose calibrator settings to automatically change according to time of administration and isotope required. The average error rate pre- and post-barcode assistance system was 0.012% and 0.002%, respectively (Pdispensing errors: wrong dosage (60%) and wrong drug (28%). Post-barcode assistance system, the major category was delivery destination (90%). The results suggest that the barcode assistance system has been instrumental

  20. [Penicillium-inhibiting yeasts].

    Science.gov (United States)

    Benítez Ahrendts, M R; Carrillo, L

    2004-01-01

    The objective of this work was to establish the in vitro and in vivo inhibition of post-harvest pathogenic moulds by yeasts in order to make a biocontrol product. Post-harvest pathogenic moulds Penicillium digitatum, P. italicum, P. ulaiense, Phyllosticta sp., Galactomyces geotrichum and yeasts belonging to genera Brettanomyces, Candida, Cryptococcus, Kloeckera, Pichia, Rhodotorula were isolated from citrus fruits. Some yeasts strains were also isolated from other sources. The yeasts were identified by their macro and micro-morphology and physiological tests. The in vitro and in vivo activities against P. digitatum or P. ulaiense were different. Candida cantarellii and one strain of Pichia subpelliculosa produced a significant reduction of the lesion area caused by the pathogenic moulds P. digitatum and P. ulaiense, and could be used in a biocontrol product formulation.

  1. Deletions of the mitochondrial genome.

    Science.gov (United States)

    Harding, A E; Hammans, S R

    1992-01-01

    Single large deletions of mitochondrial DNA are found in the muscle of about 40% of patients with mitochondrial myopathies, and are detectable in both blood and muscle in Pearson syndrome. In mitochondrial myopathies, there is a close association between the presence of deletions and involvement of extra-ocular muscles, together with other features of the Kearns-Sayre syndrome. Deletions appear to arise as fresh mutations in the vast majority of patients and are often flanked by direct repeats up to 13 nucleotides in length. They should affect translation of all mitochondrially encoded components of the respiratory chain, but there is evidence to suggest that intramitochondrial complementation occurs in some cases.

  2. Forces in yeast flocculation

    Science.gov (United States)

    El-Kirat-Chatel, Sofiane; Beaussart, Audrey; Vincent, Stéphane P.; Abellán Flos, Marta; Hols, Pascal; Lipke, Peter N.; Dufrêne, Yves F.

    2015-01-01

    In the baker's yeast Saccharomyces cerevisiae, cell-cell adhesion (``flocculation'') is conferred by a family of lectin-like proteins known as the flocculin (Flo) proteins. Knowledge of the adhesive and mechanical properties of flocculins is important for understanding the mechanisms of yeast adhesion, and may help controlling yeast behaviour in biotechnology. We use single-molecule and single-cell atomic force microscopy (AFM) to explore the nanoscale forces engaged in yeast flocculation, focusing on the role of Flo1 as a prototype of flocculins. Using AFM tips labelled with mannose, we detect single flocculins on Flo1-expressing cells, showing they are widely exposed on the cell surface. When subjected to force, individual Flo1 proteins display two distinct force responses, i.e. weak lectin binding forces and strong unfolding forces reflecting the force-induced extension of hydrophobic tandem repeats. We demonstrate that cell-cell adhesion bonds also involve multiple weak lectin interactions together with strong unfolding forces, both associated with Flo1 molecules. Single-molecule and single-cell data correlate with microscale cell adhesion behaviour, suggesting strongly that Flo1 mechanics is critical for yeast flocculation. These results favour a model in which not only weak lectin-sugar interactions are involved in yeast flocculation but also strong hydrophobic interactions resulting from protein unfolding.

  3. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?

    Science.gov (United States)

    2013-01-01

    Background The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Results Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (2%), pointing to at least 23 strong candidates for new species. Conclusions Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic

  4. Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?

    Science.gov (United States)

    Pereira, Luiz H G; Hanner, Robert; Foresti, Fausto; Oliveira, Claudio

    2013-03-09

    The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region. Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (2%), pointing to at least 23 strong candidates for new species. Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of

  5. Enhancement of astaxanthin production in Xanthophyllomyces dendrorhous by efficient method for the complete deletion of genes.

    Science.gov (United States)

    Yamamoto, Keisuke; Hara, Kiyotaka Y; Morita, Toshihiko; Nishimura, Akira; Sasaki, Daisuke; Ishii, Jun; Ogino, Chiaki; Kizaki, Noriyuki; Kondo, Akihiko

    2016-09-13

    Red yeast, Xanthophyllomyces dendrorhous is the only yeast known to produce astaxanthin, an anti-oxidant isoprenoid (carotenoid) widely used in the aquaculture, food, pharmaceutical and cosmetic industries. The potential of this microorganism as a platform cell factory for isoprenoid production has been recognized because of high flux through its native terpene pathway. Recently, we developed a multiple gene expression system in X. dendrorhous and enhanced the mevalonate synthetic pathway to increase astaxanthin production. In contrast, the mevalonate synthetic pathway is suppressed by ergosterol through feedback inhibition. Therefore, releasing the mevalonate synthetic pathway from this inhibition through the deletion of genes involved in ergosterol synthesis is a promising strategy to improve isoprenoid production. An efficient method for deleting diploid genes in X. dendrorhous, however, has not yet been developed. Xanthophyllomyces dendrorhous was cultivated under gradually increasing concentrations of antibiotics following the introduction of antibiotic resistant genes to be replaced with target genes. Using this method, double CYP61 genes encoding C-22 sterol desaturases relating to ergosterol biosynthesis were deleted sequentially. This double CYP61 deleted strain showed decreased ergosterol biosynthesis compared with the parental strain and single CYP61 disrupted strain. Additionally, this double deletion of CYP61 genes showed increased astaxanthin production compared with the parental strain and the single CYP61 knockout strain. Finally, astaxanthin production was enhanced by 1.4-fold compared with the parental strain, although astaxanthin production was not affected in the single CYP61 knockout strain. In this study, we developed a system to completely delete target diploid genes in X. dendrorhous. Using this method, we deleted diploid CYP61 genes involved in the synthesis of ergosterol that inhibits the pathway for mevalonate, which is a common

  6. Independent and additive effects of glutamic acid and methionine on yeast longevity.

    Science.gov (United States)

    Wu, Ziyun; Song, Lixia; Liu, Shao Quan; Huang, Dejian

    2013-01-01

    It is established that glucose restriction extends yeast chronological and replicative lifespan, but little is known about the influence of amino acids on yeast lifespan, although some amino acids were reported to delay aging in rodents. Here we show that amino acid composition greatly alters yeast chronological lifespan. We found that non-essential amino acids (to yeast) methionine and glutamic acid had the most significant impact on yeast chronological lifespan extension, restriction of methionine and/or increase of glutamic acid led to longevity that was not the result of low acetic acid production and acidification in aging media. Remarkably, low methionine, high glutamic acid and glucose restriction additively and independently extended yeast lifespan, which could not be further extended by buffering the medium (pH 6.0). Our preliminary findings using yeasts with gene deletion demonstrate that glutamic acid addition, methionine and glucose restriction prompt yeast longevity through distinct mechanisms. This study may help to fill a gap in yeast model for the fast developing view that nutrient balance is a critical factor to extend lifespan.

  7. System Design Considerations In Bar-Code Laser Scanning

    Science.gov (United States)

    Barkan, Eric; Swartz, Jerome

    1984-08-01

    The unified transfer function approach to the design of laser barcode scanner signal acquisition hardware is considered. The treatment of seemingly disparate system areas such as the optical train, the scanning spot, the electrical filter circuits, the effects of noise, and printing errors is presented using linear systems theory. Such important issues as determination of depth of modulation, filter specification, tolerancing of optical components, and optimi-zation of system performance in the presence of noise are discussed. The concept of effective spot size to allow for impact of optical system and analog processing circuitry upon depth of modulation is introduced. Considerations are limited primarily to Gaussian spot profiles, but also apply to more general cases. Attention is paid to realistic bar-code symbol models and to implications with respect to printing tolerances.

  8. ISBN and QR Barcode Scanning Mobile App for Libraries

    Directory of Open Access Journals (Sweden)

    Graham McCarthy

    2011-04-01

    Full Text Available This article outlines the development of a mobile application for the Ryerson University Library. The application provides for ISBN barcode scanning that results in a lookup of library copies and services for the book scanned, as well as QR code scanning. Two versions of the application were developed, one for iOS and one for Android. The article includes some details on the free packages used for barcode scanning functionality. Source code for the Ryerson iOS and Android applications are freely available, and instructions are provided on customizing the Ryerson application for use in other library environments. Some statistics on the number of downloads of the Ryerson mobile app by users are included.

  9. DNA barcode goes two-dimensions: DNA QR code web server.

    Science.gov (United States)

    Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

    2012-01-01

    The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  10. DNA barcode goes two-dimensions: DNA QR code web server.

    Directory of Open Access Journals (Sweden)

    Chang Liu

    Full Text Available The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

  11. Evaluation of the DNA barcodes in Dendrobium (Orchidaceae from mainland Asia.

    Directory of Open Access Journals (Sweden)

    Songzhi Xu

    Full Text Available DNA barcoding has been proposed to be one of the most promising tools for accurate and rapid identification of taxa. However, few publications have evaluated the efficiency of DNA barcoding for the large genera of flowering plants. Dendrobium, one of the largest genera of flowering plants, contains many species that are important in horticulture, medicine and biodiversity conservation. Besides, Dendrobium is a notoriously difficult group to identify. DNA barcoding was expected to be a supplementary means for species identification, conservation and future studies in Dendrobium. We assessed the power of 11 candidate barcodes on the basis of 1,698 accessions of 184 Dendrobium species obtained primarily from mainland Asia. Our results indicated that five single barcodes, i.e., ITS, ITS2, matK, rbcL and trnH-psbA, can be easily amplified and sequenced with the currently established primers. Four barcodes, ITS, ITS2, ITS+matK, and ITS2+matK, have distinct barcoding gaps. ITS+matK was the optimal barcode based on all evaluation methods. Furthermore, the efficiency of ITS+matK was verified in four other large genera including Ficus, Lysimachia, Paphiopedilum, and Pedicularis in this study. Therefore, we tentatively recommend the combination of ITS+matK as a core DNA barcode for large flowering plant genera.

  12. DNA barcode of coastal alga ( Chlorella sorokiniana ) from Ago ...

    African Journals Online (AJOL)

    Five different loci 18S, UPA, rbcl, ITS and tufA were tested for their use as deoxyribonucleic acid (DNA) barcode in this study. Although the UPA primers were designed to amplify all phototrophic algae and cyanobacteria, UPA and 18S did not amplified at all for the genus Chlorella while ITS1, ITS2 rDNA and rbcL markers ...

  13. Countering criticisms of single mitochondrial DNA gene barcoding in birds.

    Science.gov (United States)

    Baker, Allan J; Tavares, Erika Sendra; Elbourne, Rebecca F

    2009-05-01

    General criticisms of a single mtDNA gene barcodes include failure to identify newly evolved species, use of species-delimitation thresholds, effects of selective sweeps and chance occurrence of reciprocal monophyly within species, inability to deal with hybridization and incomplete lineage sorting, and superiority of multiple genes in species identification. We address these criticisms in birds because most species are known and thus provide an ideal test data set, and we argue with selected examples that with the exception of thresholds these criticisms are not problematic for avian taxonomy. Even closely related sister species of birds have distinctive COI barcodes, but it is not possible to universally apply distance thresholds based on ratios of within-species and among-species variation. Instead, more rigorous methods of species delimitation should be favoured using coalescent-based techniques that include tests of chance reciprocal monophyly, and times of lineage separation and sequence divergence. Incomplete lineage sorting is also easily detected with DNA barcodes, and usually at a younger time frame than a more slowly evolving nuclear gene. Where DNA barcodes detect divergent reciprocally monophyletic lineages, the COI sequences can be combined with multiple nuclear genes to distinguish between speciation or population subdivision arising from high female philopatry or regional selective sweeps. Although selective sweeps are increasingly invoked to explain patterns of shallow within-species coalescences in COI gene trees, caution is warranted in this conjecture because of limited sampling of individuals and the reduced power to detect additional mtDNA haplotypes with one gene. © 2009 Blackwell Publishing Ltd.

  14. Decreasing mislabeled laboratory specimens using barcode technology and bedside printers.

    Science.gov (United States)

    Brown, Judy E; Smith, Nancy; Sherfy, Beth R

    2011-01-01

    Mislabeling of laboratory samples has been found to be a high-risk issue in acute care hospitals. The goal of this study was to decrease mislabeled blood specimens. In the first year after the implementation of a positive patient identification system using barcoding and computer technology, the number of labeling errors decreased from 103 to 8 per year. The outcome was clinically and statistically significant (P < .001).

  15. DNA Barcoding of Ichthyoplankton in Hampton Roads Bay Estuary

    Science.gov (United States)

    Wilkins, N.; Rodríguez, Á. E.

    2016-02-01

    Zooplankton is composed of animals that drift within the water column. The study of zooplankton biodiversity and distribution is crucial to understand oceanic ecosystems and anticipate the effects of climate change. In this study our focus is on ichthyoplankton (fish eggs and larvae). Our aim is to employ molecular genetic techniques such as DNA barcoding to begin a detailed characterization of ichthyoplankton diversity, abundance and community structure in the Hampton Roads Bay Estuary (HRBE). A sampling of zooplankton was performed on June 19, 2015. Samples were taken with a 0.5m, 200 µm mesh net in triplicates at two stations: inner shore in the mouth of Jones Creek and 5 miles off Hampton in the lower part of Chesapeake Bay. Physical parameters (dissolved oxygen, salinity, and temperature and water transparency) were measured simultaneously. Species were identified by DNA barcoding using the mitochondrial DNA (mtDNA) of the Cytochrome Oxidase 1 (CO1) gene. Fish eggs were identified from Opistonema oglinum (Atlantic Thread Herring) at the offshore stations while, Anchoa mitchilli was found at both stations. These species are common to the area and as observed, differences in species between stations were found. O. oglinum eggs were found in the offshore stations, which is their reported habitat. A. mitchilli eggs were found in both stations; both known to exhibit a wider salinity tolerance. This work indicates that using mtDNA-CO1 barcoding is suitable to identify ichthyoplankton to the species level and helped validate DNA barcoding as a faster taxonomic approach. The long term objective of this project is to provide taxonomic composition and biodiversity assessment of ichthyoplankton in HRBE. This data will be a reference for broad monitoring programs; for a better understanding and management of ecologically and commercially important species in the HRBE. Monthly samplings will be performed for a year beginning September 2015.

  16. Neotropical bats: estimating species diversity with DNA barcodes.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available DNA barcoding using the cytochrome c oxidase subunit 1 gene (COI is frequently employed as an efficient method of species identification in animal life and may also be used to estimate species richness, particularly in understudied faunas. Despite numerous past demonstrations of the efficiency of this technique, few studies have attempted to employ DNA barcoding methodologies on a large geographic scale, particularly within tropical regions. In this study we survey current and potential species diversity using DNA barcodes with a collection of more than 9000 individuals from 163 species of Neotropical bats (order Chiroptera. This represents one of the largest surveys to employ this strategy on any animal group and is certainly the largest to date for land vertebrates. Our analysis documents the utility of this tool over great geographic distances and across extraordinarily diverse habitats. Among the 163 included species 98.8% possessed distinct sets of COI haplotypes making them easily recognizable at this locus. We detected only a single case of shared haplotypes. Intraspecific diversity in the region was high among currently recognized species (mean of 1.38%, range 0-11.79% with respect to birds, though comparable to other bat assemblages. In 44 of 163 cases, well-supported, distinct intraspecific lineages were identified which may suggest the presence of cryptic species though mean and maximum intraspecific divergence were not good predictors of their presence. In all cases, intraspecific lineages require additional investigation using complementary molecular techniques and additional characters such as morphology and acoustic data. Our analysis provides strong support for the continued assembly of DNA barcoding libraries and ongoing taxonomic investigation of bats.

  17. Untangling taxonomy: a DNA barcode reference library for Canadian spiders.

    Science.gov (United States)

    Blagoev, Gergin A; deWaard, Jeremy R; Ratnasingham, Sujeevan; deWaard, Stephanie L; Lu, Liuqiong; Robertson, James; Telfer, Angela C; Hebert, Paul D N

    2016-01-01

    Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30,000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11-22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30-50% higher than currently recognized. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

  18. DNA barcodes for marine fungal identification and discovery

    Digital Repository Service at National Institute of Oceanography (India)

    Velmurugan, S.; Prasannakumar, C.; Manokaran, S.; AjithKumar, T.; Samkamaleson, A.; Palavesam, A.

    , monsoon, postmonsoon). DNA sequencing was performed in ABI high throughput DNA sequencer at Bioserve Biotechnologies Pvt Ltd (commercial company, India) and at Macrogen (commercial company, North Korea). DNA sequences, produced as chromatograms, were read.... The Fungi, 2nd edn. A Harcourt Science and Technology Company, p. 603. Dentinger BTM, Didukh MY, Moncalvo J, 2011. Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina). PLoS One 9: e25081. Domsch KH, Gams W, Anderson TH...

  19. Denture identification using unique identification authority of India barcode

    OpenAIRE

    Sudhindra Mahoorkar; Anoop Jain

    2013-01-01

    Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient's unique identification number and barcode printed in the patient's Aadhaar card issued by Unique Identification Authority of India (UIDAI) are used as denture markers. This article describes a simple, quick, and economical method for identification of individual.

  20. Denture identification using unique identification authority of India barcode.

    Science.gov (United States)

    Mahoorkar, Sudhindra; Jain, Anoop

    2013-01-01

    Over the years, various denture marking systems have been reported in the literature for personal identification. They have been broadly divided into surface marking and inclusion methods. In this technique, patient's unique identification number and barcode printed in the patient's Aadhaar card issued by Unique Identification Authority of India (UIDAI) are used as denture markers. This article describes a simple, quick, and economical method for identification of individual.

  1. Yeasts associated with Manteca.

    Science.gov (United States)

    Suzzi, Giovanna; Schirone, Maria; Martuscelli, Maria; Gatti, Monica; Fornasari, Maria Emanuela; Neviani, Erasmo

    2003-04-01

    Manteca is a traditional milk product of southern Italy produced from whey deriving from Caciocavallo Podolico cheese-making. This study was undertaken to obtain more information about the microbiological properties of this product and particularly about the presence, metabolic activities, and technological significance of the different yeast species naturally occurring in Manteca. High numbers of yeasts were counted after 7 days ripening (10(4)-10(5) cfu g(-1)) and then decreased to 10(2) at the end. A total of 179 isolates were identified and studied for their phenotypic and genotypic characteristics. The most frequently encountered species were Trichosporon asahii (45), Candida parapsilosis (33), Rhodotorula mucilaginosa (32), Candida inconspicua (29). Some of these yeasts showed lipolytic activity (32 strains) and proteolytic activity (29 strains), NaCl resistance up to 10% and growth up to 45 degrees C (42 strains). Biogenic amines were formed by proteolytic strains, in particular phenylethylamine, putrescine and spermidine. Spermidine was produced by all the yeasts tested in this work, but only Trichosporon produced a great quantity of this compound. Histamine was not detectable. Caseinolytic activity was common to almost all strains, corresponding to the ability to efficiently split off amino-terminal amino acids. The highest and most constant activity expressed by all species was X-prolyl-dipeptidyl aminopeptidase. The findings suggest that the presence of yeasts may play a significant role in justifying interactions with lactic acid bacteria, and consequently with their metabolic activity in the definition of the peculiar characteristics of Manteca cheese.

  2. Influence of killing method on Lepidoptera DNA barcode recovery.

    Science.gov (United States)

    Willows-Munro, Sandi; Schoeman, M Corrie

    2015-05-01

    The global DNA barcoding initiative has revolutionized the field of biodiversity research. Such large-scale sequencing projects require the collection of large numbers of specimens, which need to be killed and preserved in a way that is both DNA-friendly and which will keep voucher specimens in good condition for later study. Factors such as time since collection, correct storage (exposure to free water and heat) and DNA extraction protocol are known to play a role in the success of downstream molecular applications. Limited data are available on the most efficient, DNA-friendly protocol for killing. In this study, we evaluate the quality of DNA barcode (cytochrome oxidase I) sequences amplified from DNA extracted from specimens collected using three different killing methods (ethyl acetate, cyanide and freezing). Previous studies have suggested that chemicals, such as ethyl acetate and formaldehyde, degraded DNA and as such may not be appropriate for the collection of insects for DNA-based research. All Lepidoptera collected produced DNA barcodes of good quality, and our study found no clear difference in nucleotide signal strength, probability of incorrect base calling and phylogenetic utility among the three different treatment groups. Our findings suggest that ethyl acetate, cyanide and freezing can all be used to collect specimens for DNA analysis. © 2014 John Wiley & Sons Ltd.

  3. Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding.

    Science.gov (United States)

    Versteirt, V; Nagy, Z T; Roelants, P; Denis, L; Breman, F C; Damiens, D; Dekoninck, W; Backeljau, T; Coosemans, M; Van Bortel, W

    2015-03-01

    Since its introduction in 2003, DNA barcoding has proven to be a promising method for the identification of many taxa, including mosquitoes (Diptera: Culicidae). Many mosquito species are potential vectors of pathogens, and correct identification in all life stages is essential for effective mosquito monitoring and control. To use DNA barcoding for species identification, a reliable and comprehensive reference database of verified DNA sequences is required. Hence, DNA sequence diversity of mosquitoes in Belgium was assessed using a 658 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene, and a reference data set was established. Most species appeared as well-supported clusters. Intraspecific Kimura 2-parameter (K2P) distances averaged 0.7%, and the maximum observed K2P distance was 6.2% for Aedes koreicus. A small overlap between intra- and interspecific K2P distances for congeneric sequences was observed. Overall, the identification success using best match and the best close match criteria were high, that is above 98%. No clear genetic division was found between the closely related species Aedes annulipes and Aedes cantans, which can be confused using morphological identification only. The members of the Anopheles maculipennis complex, that is Anopheles maculipennis s.s. and An. messeae, were weakly supported as monophyletic taxa. This study showed that DNA barcoding offers a reliable framework for mosquito species identification in Belgium except for some closely related species. © 2014 John Wiley & Sons Ltd.

  4. A DNA barcoding approach to characterize pollen collected by honeybees.

    Directory of Open Access Journals (Sweden)

    Andrea Galimberti

    Full Text Available In the present study, we investigated DNA barcoding effectiveness to characterize honeybee pollen pellets, a food supplement largely used for human nutrition due to its therapeutic properties. We collected pollen pellets using modified beehives placed in three zones within an alpine protected area (Grigna Settentrionale Regional Park, Italy. A DNA barcoding reference database, including rbcL and trnH-psbA sequences from 693 plant species (104 sequenced in this study was assembled. The database was used to identify pollen collected from the hives. Fifty-two plant species were identified at the molecular level. Results suggested rbcL alone could not distinguish among congeneric plants; however, psbA-trnH identified most of the pollen samples at the species level. Substantial variability in pollen composition was observed between the highest elevation locality (Alpe Moconodeno, characterized by arid grasslands and a rocky substrate, and the other two sites (Cornisella and Ortanella at lower altitudes. Pollen from Ortanella and Cornisella showed the presence of typical deciduous forest species; however in samples collected at Ortanella, pollen of the invasive Lonicera japonica, and the ornamental Pelargonium x hortorum were observed. Our results indicated pollen composition was largely influenced by floristic local biodiversity, plant phenology, and the presence of alien flowering species. Therefore, pollen molecular characterization based on DNA barcoding might serve useful to beekeepers in obtaining honeybee products with specific nutritional or therapeutic characteristics desired by food market demands.

  5. DNA barcoding of the ichthyofauna of Taal Lake, Philippines.

    Science.gov (United States)

    Aquilino, Sean V L; Tango, Jazzlyn M; Fontanilla, Ian K C; Pagulayan, Roberto C; Basiao, Zubaida U; Ong, Perry S; Quilang, Jonas P

    2011-07-01

    This study represents the first molecular survey of the ichthyofauna of Taal Lake and the first DNA barcoding attempt in Philippine fishes. Taal Lake, the third largest lake in the Philippines, is considered a very important fisheries resource and is home to the world's only freshwater sardine, Sardinella tawilis. However, overexploitation and introduction of exotic fishes have caused a massive decline in the diversity of native species as well as in overall productivity of the lake. In this study, 118 individuals of 23 native, endemic and introduced fishes of Taal Lake were barcoded using the partial DNA sequence of the mitochondrial cytochrome c oxidase subunit I (COI) gene. These species belong to 21 genera, 17 families and 9 orders. Divergence of sequences within and between species was determined using Kimura 2-parameter (K2P) distance model, and a neighbour-joining tree was generated with 1000 bootstrap replications using the K2P model. All COI sequences for each of the 23 species were clearly discriminated among genera. The average within species, within genus, within family and within order percent genetic divergence was 0.60%, 11.07%, 17.67% and 24.08%, respectively. Our results provide evidence that COI DNA barcodes are effective for the rapid and accurate identification of fishes and for identifying certain species that need further taxonomic investigation. © 2011 Blackwell Publishing Ltd.

  6. DNA Barcoding for Minor Crops and Food Traceability

    Directory of Open Access Journals (Sweden)

    Andrea Galimberti

    2014-01-01

    Full Text Available This outlook paper addresses the problem of the traceability of minor crops. These kinds of cultivations consist in a large number of plants locally distributed with a modest production in terms of cultivated acreage and quantity of final product. Because of globalization, the diffusion of minor crops is increasing due to their benefit for human health or their use as food supplements. Such a phenomenon implies a major risk for species substitution or uncontrolled admixture of manufactured plant products with severe consequences for the health of consumers. The need for a reliable identification system is therefore essential to evaluate the quality and provenance of minor agricultural products. DNA-based techniques can help in achieving this mission. In particular, the DNA barcoding approach has gained a role of primary importance thanks to its universality and versatility. Here, we present the advantages in the use of DNA barcoding for the characterization and traceability of minor crops based on our previous or ongoing studies at the ZooPlantLab (Milan, Italy. We also discuss how DNA barcoding may potentially be transferred from the laboratory to the food supply chain, from field to table.

  7. Replacing Sanger with Next Generation Sequencing to improve coverage and quality of reference DNA barcodes for plants.

    Science.gov (United States)

    Wilkinson, Mike J; Szabo, Claudia; Ford, Caroline S; Yarom, Yuval; Croxford, Adam E; Camp, Amanda; Gooding, Paul

    2017-04-12

    We estimate the global BOLD Systems database holds core DNA barcodes (rbcL + matK) for about 15% of land plant species and that comprehensive species coverage is still many decades away. Interim performance of the resource is compromised by variable sequence overlap and modest information content within each barcode. Our model predicts that the proportion of species-unique barcodes reduces as the database grows and that 'false' species-unique barcodes remain >5% until the database is almost complete. We conclude the current rbcL + matK barcode is unfit for purpose. Genome skimming and supplementary barcodes could improve diagnostic power but would slow new barcode acquisition. We therefore present two novel Next Generation Sequencing protocols (with freeware) capable of accurate, massively parallel de novo assembly of high quality DNA barcodes of >1400 bp. We explore how these capabilities could enhance species diagnosis in the coming decades.

  8. Strategies for state-dependent quantum deleting

    International Nuclear Information System (INIS)

    Song Wei; Yang Ming; Cao Zhuoliang

    2004-01-01

    A quantum state-dependent quantum deleting machine is constructed. We obtain a upper bound of the global fidelity on N-to-M quantum deleting from a set of K non-orthogonal states. Quantum networks are constructed for the above state-dependent quantum deleting machine when K=2. Our deleting protocol only involves a unitary interaction among the initial copies, with no ancilla. We also present some analogies between quantum cloning and deleting

  9. Genetics of Yeasts

    Science.gov (United States)

    Querol, Amparo; Fernández-Espinar, M. Teresa; Belloch, Carmela

    The use of yeasts in biotechnology processes dates back to ancient days. Before 7000 BC, beer was produced in Sumeria. Wine was made in Assyria in 3500 BC, and ancient Rome had over 250 bakeries, which were making leavened bread by 100 BC. And milk has been made into Kefyr and Koumiss in Asia for many centuries (Demain, Phaff, & Kurtzman, 1999). However, the importance of yeast in the food and beverage industries was only realized about 1860, when their role in food manufacturing became evident.

  10. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species.

    Science.gov (United States)

    Yu, Min; Jiao, Lichao; Guo, Juan; Wiedenhoeft, Alex C; He, Tuo; Jiang, Xiaomei; Yin, Yafang

    2017-12-01

    ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.

  11. Proper microtubule structure is vital for timely progression through meiosis in fission yeast.

    Directory of Open Access Journals (Sweden)

    Akira Yamashita

    Full Text Available Cells of the fission yeast Schizosaccharomyces pombe normally reproduce by mitotic division in the haploid state. When subjected to nutrient starvation, two haploid cells fuse and undergo karyogamy, forming a diploid cell that initiates meiosis to form four haploid spores. Here, we show that deletion of the mal3 gene, which encodes a homolog of microtubule regulator EB1, produces aberrant asci carrying more than four spores. The mal3 deletion mutant cells have a disordered cytoplasmic microtubule structure during karyogamy and initiate meiosis before completion of karyogamy, resulting in twin haploid meiosis in the zygote. Treatment with anti-microtubule drugs mimics this phenotype. Mutants defective in karyogamy or mutants prone to initiate haploid meiosis exaggerate the phenotype of the mal3 deletion mutant. Our results indicate that proper microtubule structure is required for ordered progression through the meiotic cycle. Furthermore, the results of our study suggest that fission yeast do not monitor ploidy during meiosis.

  12. Polysome Profile Analysis - Yeast

    Czech Academy of Sciences Publication Activity Database

    Pospíšek, M.; Valášek, Leoš Shivaya

    2013-01-01

    Roč. 530, č. 2013 (2013), s. 173-181 ISSN 0076-6879 Institutional support: RVO:61388971 Keywords : grow yeast cultures * polysome profile analysis * sucrose density gradient centrifugation Subject RIV: CE - Biochemistry Impact factor: 2.194, year: 2013

  13. Barcode haplotype variation in North American agroecosystem ladybird beetles (Coleoptera: Coccinellidae

    Science.gov (United States)

    DNA barcodes have proven invaluable in identifying and distinguishing insect pests, for example for determining the provenance of exotic invasives, but relatively few insect natural enemies have been barcoded. We used Folmer et al.’s universal invertebrate primers (1994), and those designed by Heber...

  14. Potential DNA barcodes for Melilotus species based on five single loci and their combinations.

    Directory of Open Access Journals (Sweden)

    Fan Wu

    Full Text Available Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.

  15. A Mobile Phone Application Enabling Visually Impaired Users to Find and Read Product Barcodes.

    Science.gov (United States)

    Tekin, Ender; Coughlan, James M

    2010-07-01

    While there are many barcode readers available for identifying products in a supermarket or at home on mobile phones (e.g., Red Laser iPhone app), such readers are inaccessible to blind or visually impaired persons because of their reliance on visual feedback from the user to center the barcode in the camera's field of view. We describe a mobile phone application that guides a visually impaired user to the barcode on a package in real-time using the phone's built-in video camera. Once the barcode is located by the system, the user is prompted with audio signals to bring the camera closer to the barcode until it can be resolved by the camera, which is then decoded and the corresponding product information read aloud using text-to-speech. Experiments with a blind volunteer demonstrate proof of concept of our system, which allowed the volunteer to locate barcodes which were then translated to product information that was announced to the user. We successfully tested a series of common products, as well as user-generated barcodes labeling household items that may not come with barcodes.

  16. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    NARCIS (Netherlands)

    Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J.L.; Levesque, C.A.; Chen, W.; Fungal Barcoding Consortium, [No Value

    2012-01-01

    Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it

  17. The gene expression barcode 3.0: improved data processing and mining tools

    NARCIS (Netherlands)

    McCall, M.N.; Jaffee, H.A.; Zelisko, S.J.; Sinha, N.; Hooiveld, G.J.E.J.; Irizarry, R.A.; Zilliox, M.J.

    2014-01-01

    The Gene Expression Barcode project, http://barcode.luhs.org, seeks to determine the genes expressed for every tissue and cell type in humans and mice. Understanding the absolute expression of genes across tissues and cell types has applications in basic cell biology, hypothesis generation for gene

  18. Proteolytic activities in yeast.

    Science.gov (United States)

    Saheki, T; Holzer, H

    1975-03-28

    Studies on the mechanism and time course of the activation of proteinases A (EC 3.4.23.8), B (EC 3.4.22.9) and C (EC 3.4.12.--) in crude yeast extracts at pH 5.1 and 25 degrees C showed that the increase in proteinase B activity is paralleled with the disappearance of proteinase B inhibitor. Addition of purified proteinase A to fresh crude extracts accelerates the inactivation of the proteinase B inhibitor and the appearance of maximal activities of proteinases B and C. The decrease of proteinase B inhibitor activity and the increase of proteinase B activity are markedly retarded by the addition of pepstatin. Because 10-minus 7 M pepstatin completely inhibits proteinase A without affecting proteinase B activity, this is another indication for the role of proteinase A during the activation of proteinase B. Whereas extracts of yeast grown on minimal medium reached maximal activation of proteinases B and C after 20 h of incubation at pH 5.1 and 25 degrees C, extracts of yeast grown on complete medium had to be incubated for about 100 h. In the latter case, the addition of proteinas A results in maximal activation of proteinases B and C and disappearance of proteinase B inhibitor activity only after 10--20 h of incubation. With the optimal conditions, the maximal activities of proteinases A, B and C, as well as of the proteinase B inhibitor, were determined in crude extracts of yeast that had been grown batchwise for different lengths of time either on minimal or on complete medium. Upon incubation, all three proteinases were activated by several times their initial activity. This reflects the existence of proteolytically degradable inhibitors of the three proteinases and together with the above mentioned observations it demonstrates that the "activation" of yeast proteinases A, B and C upon incubation results from the proteolytic digestion of inhibitors rather than from activation of inactive zymogens by limited proteolysis.

  19. L-arabinose fermenting yeast

    Science.gov (United States)

    Zhang, Min; Singh, Arjun; Suominen, Pirkko; Knoshaug, Eric; Franden, Mary Ann; Jarvis, Eric

    2013-02-12

    An L-arabinose utilizing yeast strain is provided for the production of ethanol by introducing and expressing bacterial araA, araB and araD genes. L-arabinose transporters are also introduced into the yeast to enhance the uptake of arabinose. The yeast carries additional genomic mutations enabling it to consume L-arabinose, even as the only carbon source, and to produce ethanol. A yeast strain engineered to metabolize arabinose through a novel pathway is also disclosed. Methods of producing ethanol include utilizing these modified yeast strains.

  20. Functional analysis of transcribed spacers of yeast ribosomal DNA.

    Science.gov (United States)

    Musters, W; Boon, K; van der Sande, C A; van Heerikhuizen, H; Planta, R J

    1990-12-01

    Making use of an rDNA unit, containing oligonucleotide tags in both the 17S and 26S rRNA gene, we have analyzed the effect of various deletions in the External Transcribed Spacer (ETS) and in one of the Internal Transcribed Spacers 1 (ITS1) on the process of ribosome formation in yeast. By following the fate of the tagged transcripts of this rDNA unit in vivo by Northern hybridization we found that deleting various parts of the ETS prevents the accumulation of tagged 17S rRNA and its assembly into 40S subunits, but not the formation of 60S subunits. Deleting the central region of ITS1, including a processing site that is used in an early stage of the maturation process, was also found to prevent the accumulation of functional 49 S subunits, whereas no effect on the formation of 60S subunits was detected. The implications of these findings for yeast pre-rRNA processing are discussed.

  1. DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation.

    Directory of Open Access Journals (Sweden)

    Ricardo Koroiva

    Full Text Available We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2% and interspecific variation (15% and above in COI, and resulting separation of Barcode Index Numbers (BIN, allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.

  2. DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation.

    Science.gov (United States)

    Koroiva, Ricardo; Pepinelli, Mateus; Rodrigues, Marciel Elio; Roque, Fabio de Oliveira; Lorenz-Lemke, Aline Pedroso; Kvist, Sebastian

    2017-01-01

    We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.

  3. Yeast ecology of Kombucha fermentation.

    Science.gov (United States)

    Teoh, Ai Leng; Heard, Gillian; Cox, Julian

    2004-09-01

    Kombucha is a traditional fermentation of sweetened tea, involving a symbiosis of yeast species and acetic acid bacteria. Despite reports of different yeast species being associated with the fermentation, little is known of the quantitative ecology of yeasts in Kombucha. Using oxytetracycline-supplemented malt extract agar, yeasts were isolated from four commercially available Kombucha products and identified using conventional biochemical and physiological tests. During the fermentation of each of the four products, yeasts were enumerated from both the cellulosic pellicle and liquor of the Kombucha. The number and diversity of species varied between products, but included Brettanomyces bruxellensis, Candida stellata, Schizosaccharomyces pombe, Torulaspora delbrueckii and Zygosaccharomyces bailii. While these yeast species are known to occur in Kombucha, the enumeration of each species present throughout fermentation of each of the four Kombucha cultures demonstrated for the first time the dynamic nature of the yeast ecology. Kombucha fermentation is, in general, initiated by osmotolerant species, succeeded and ultimately dominated by acid-tolerant species.

  4. Flavour-active wine yeasts.

    Science.gov (United States)

    Cordente, Antonio G; Curtin, Christopher D; Varela, Cristian; Pretorius, Isak S

    2012-11-01

    The flavour of fermented beverages such as beer, cider, saké and wine owe much to the primary fermentation yeast used in their production, Saccharomyces cerevisiae. Where once the role of yeast in fermented beverage flavour was thought to be limited to a small number of volatile esters and higher alcohols, the discovery that wine yeast release highly potent sulfur compounds from non-volatile precursors found in grapes has driven researchers to look more closely at how choice of yeast can influence wine style. This review explores recent progress towards understanding the range of 'flavour phenotypes' that wine yeast exhibit, and how this knowledge has been used to develop novel flavour-active yeasts. In addition, emerging opportunities to augment these phenotypes by engineering yeast to produce so-called grape varietal compounds, such as monoterpenoids, will be discussed.

  5. The integration of barcode scanning technology into Canadian public health immunization settings.

    Science.gov (United States)

    Pereira, Jennifer A; Quach, Susan; Hamid, Jemila S; Quan, Sherman D; Diniz, Amanda Jane; Van Exan, Robert; Malawski, Jeffrey; Finkelstein, Michael; Samanani, Salim; Kwong, Jeffrey C

    2014-05-13

    As part of a series of feasibility studies following the development of Canadian vaccine barcode standards, we compared barcode scanning with manual methods for entering vaccine data into electronic client immunization records in public health settings. Two software vendors incorporated barcode scanning functionality into their systems so that Algoma Public Health (APH) in Ontario and four First Nations (FN) communities in Alberta could participate in our study. We compared the recording of client immunization data (vaccine name, lot number, expiry date) using barcode scanning of vaccine vials vs. pre-existing methods of entering vaccine information into the systems. We employed time and motion methodology to evaluate time required for data recording, record audits to assess data quality, and qualitative analysis of immunization staff interviews to gauge user perceptions. We conducted both studies between July and November 2012, with 628 (282 barcoded) vials processed for the APH study, and 749 (408 barcoded) vials for the study in FN communities. Barcode scanning led to significantly fewer immunization record errors than using drop-down menus (APH study: 0% vs. 1.7%; p=0.04) or typing in vaccine data (FN study: 0% vs. 5.6%; pnurses were interviewed; all noted improved record accuracy with scanning, but the majority felt that a more sensitive scanner was needed to reduce the occasional failures to read the 2D barcodes on some vaccines. Entering vaccine data into immunization records through barcode scanning led to improved data quality, and was generally well received. Further work is needed to improve barcode readability, particularly for unit-dose vials. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. DNA Barcoding for Species Assignment: The Case of Mediterranean Marine Fishes

    Science.gov (United States)

    Landi, Monica; Dimech, Mark; Arculeo, Marco; Biondo, Girolama; Martins, Rogelia; Carneiro, Miguel; Carvalho, Gary Robert; Brutto, Sabrina Lo; Costa, Filipe O.

    2014-01-01

    Background DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%–18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of

  7. A Ranking System for Reference Libraries of DNA Barcodes: Application to Marine Fish Species from Portugal

    Science.gov (United States)

    Costa, Filipe O.; Landi, Monica; Martins, Rogelia; Costa, Maria H.; Costa, Maria E.; Carneiro, Miguel; Alves, Maria J.; Steinke, Dirk; Carvalho, Gary R.

    2012-01-01

    Background The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. Methodology/Principal Findings Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A–E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). Conclusion/Significance We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the

  8. An Asiatic Chironomid in Brazil: morphology, DNA barcode and bionomics

    Directory of Open Access Journals (Sweden)

    Gizelle Amora

    2015-07-01

    Full Text Available In most freshwater ecosystems, aquatic insects are dominant in terms of diversity; however, there is a disproportionately low number of records of alien species when compared to other freshwater organisms. The Chironomidae is one aquatic insect family that includes some examples of alien species around the world. During a study on aquatic insects in Amazonas state (Brazil, we collected specimens of Chironomidae that are similar, at the morphological level, to Chironomus kiiensis Tokunaga and Chironomus striatipennis Kieffer, both with distributions restricted to Asia. The objectives of this study were to provide morphological information on this Chironomus population, to investigate its identity using DNA barcoding and, to provide bionomic information about this species. Chironomus DNA barcode data were obtained from GenBank and Barcode of Life Data Systems (BOLD and, together with our data, were analyzed using the neighbor-joining method with 1000 bootstrap replicates and the genetic distances were estimated using the Kimura-2-parameter. At the morphological level, the Brazilian population cannot be distinguished either from C. striatipennis or C. kiiensis, configuring a species complex but, at the molecular level our studied population is placed in a clade together with C. striatipennis, from South Korea. Bionomic characteristics of the Brazilian Chironomus population differ from the ones of C. kiiensis from Japan, the only species in this species complex with bionomic information available. The Brazilian Chironomus population has a smaller size, the double of the number of eggs and inhabits oligotrophic water, in artificial container. In the molecular analysis, populations of C. striatipennis and C. kiiensis are placed in a clade, formed by two groups: Group A (which includes populations from both named species, from different Asiatic regions and our Brazilian population and Group B (with populations of C. kiiensis from Japan and South Korea

  9. A simple protocol for venom peptide barcoding in scorpions

    Directory of Open Access Journals (Sweden)

    Stephan Schaffrath

    2014-06-01

    Full Text Available Scorpion venoms contain many species-specific peptides which target ion channels in cell membranes. Without harming the scorpions, these peptides can easily be extracted and detected by MALDI-TOF mass spectrometry. So far, only few studies compared the venom of different species solely for taxonomic purposes. Here, we describe a very simple protocol for venom extraction and mass fingerprinting that was developed for peptide barcoding (venom code for species identification and facilitates reproducibility if sample preparation is performed under field conditions. This approach may serve as suitable basis for a taxonomy-oriented scorpion toxin database that interacts with MALDI-TOF mass spectra.

  10. Deletion of ALS5, ALS6 or ALS7 increases adhesion of Candida albicans to human vascular endothelial and buccal epithelial cells

    OpenAIRE

    ZHAO, XIAOMIN; OH, SOON-HWAN; HOYER, LOIS L.

    2007-01-01

    C. albicans yeast forms deleted for ALS5, ALS6 or ALS7 are more adherent than a relevant control strain to human vascular endothelial cell monolayers and buccal epithelial cells. In the buccal and vaginal reconstituted human epithelium (RHE) disease models, however, mutant and control strains caused a similar degree of tissue destruction. Deletion of ALS5 or ALS6 significantly slowed growth of the mutant strain; this phenotype was not affected by addition of excess uridine to the culture medi...

  11. Physical mapping of chromosome 8p22 markers and their homozygous deletion in a metastatic prostate cancer

    Energy Technology Data Exchange (ETDEWEB)

    Bova, G.S.; Pin, S.S.; Isaacs, W.B. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)]|[Brady Urological Institute, Baltimore, MD (United States)] [and others

    1996-07-01

    Numerous studies have implicated the short arm of chromosome 8 as the site of one or more tumor suppressor genes inactivated in carcinogenesis of the prostate, colon, lung, and liver. Previously, we identified a homozygous deletion on chromosome 8p22 in a metastatic prostate cancer. To map this homozygous deletion physically, long-range restriction mapping was performed using yeast artificial chromosomes (YACs) spanning approximately 2 Mb of chromosome band 8p22. Subcloned genomic DNA and cDNA probes isolated by hybrid capture from these YACs were mapped in relation to one another, reinforcing map integrity. Mapped single-copy probes from the region were then applied to DNA isolated from a metastatic prostate cancer containing a chromosome 8p22 homozygous deletion and indicated that its deletion spans 730-970 kb. Candidate genes PRLTS (PDGF-receptor {beta}-like tumor suppressor) and CTSB (cathepsin B) are located outside the region of homozygous deletion. Genethon marker D8S549 is located approximately at the center of this region of homozygous deletion. Two new microsatellite polymorphisms, D8S1991 and D8S1992, also located within the region of homozygous deletion on chromosome 8p22, are described. Physical mapping places cosmid CI8-2644 telomeric to MSR (macrophage scavenger receptor), the reverse of a previously published map, altering the interpretation of published deletion studies. This work should prove helpful in the identification of candidate tumor suppressor genes in this region. 47 refs., 5 figs., 1 tab.

  12. Genetically engineered yeast

    DEFF Research Database (Denmark)

    2014-01-01

    A genetically modified Saccharomyces cerevisiae comprising an active fermentation pathway producing 3-HP expresses an exogenous gene expressing the aminotransferase YhxA from Bacillus cereus AH1272 catalysing a transamination reaction between beta-alanine and pyruvate to produce malonate semialde......A genetically modified Saccharomyces cerevisiae comprising an active fermentation pathway producing 3-HP expresses an exogenous gene expressing the aminotransferase YhxA from Bacillus cereus AH1272 catalysing a transamination reaction between beta-alanine and pyruvate to produce malonate...... semialdehyde. The yeast may also express a 3-hydroxyisobutyrate dehydrogenase (HIBADH) and a 3-hydroxypropanoate dehydrogenase (3-HPDH) and aspartate 1-decarboxylase. Additionally the yeast may express pyruvate carboxylase and aspartate aminotransferase....

  13. Yeast glycolipid biosurfactants.

    Science.gov (United States)

    Jezierska, Sylwia; Claus, Silke; Van Bogaert, Inge

    2017-10-25

    Various yeasts, both conventional and exotic ones, are known to produce compounds useful to mankind. Ethanol is the most known of these compounds, but more complex molecules such as amphiphilic biosurfactants can also be derived from eukaryotic microorganisms at an industrially and commercially relevant scale. Among them, glycolipids are the most promising, due to their attractive properties and high product titers. Many of these compounds can be considered as secondary metabolites with a specific function for the host. Hence, a dedicated biosynthetic process enables regulation and combines pathways delivering the lipidic moiety and the hydrophilic carbohydrate part of the glycolipid. In this Review, we will discuss the biosynthetic and regulatory aspects of the yeast-derived sophorolipids, mannosylerythritol lipids, and cellobiose lipids, with special emphasis on the relation between glycolipid synthesis and the general lipid metabolism. © 2017 Federation of European Biochemical Societies.

  14. Identification of food and beverage spoilage yeasts from DNA sequence analyses.

    Science.gov (United States)

    Kurtzman, Cletus P

    2015-11-20

    Detection, identification and classification of yeasts have undergone major changes in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences has resulted in a major revision of yeast systematics resulting in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, especially in the context of food and beverage spoilage yeasts. Published by Elsevier B.V.

  15. Building a DNA Barcode Reference Library for the True Butterflies (Lepidoptera) of Peninsula Malaysia: What about the Subspecies?

    Science.gov (United States)

    Wilson, John-James; Sing, Kong-Wah; Sofian-Azirun, Mohd

    2013-01-01

    The objective of this study was to build a DNA barcode reference library for the true butterflies of Peninsula Malaysia and assess the value of attaching subspecies names to DNA barcode records. A new DNA barcode library was constructed with butterflies from the Museum of Zoology, University of Malaya collection. The library was analysed in conjunction with publicly available DNA barcodes from other Asia-Pacific localities to test the ability of the DNA barcodes to discriminate species and subspecies. Analyses confirmed the capacity of the new DNA barcode reference library to distinguish the vast majority of species (92%) and revealed that most subspecies possessed unique DNA barcodes (84%). In some cases conspecific subspecies exhibited genetic distances between their DNA barcodes that are typically seen between species, and these were often taxa that have previously been regarded as full species. Subspecies designations as shorthand for geographically and morphologically differentiated groups provide a useful heuristic for assessing how such groups correlate with clustering patterns of DNA barcodes, especially as the number of DNA barcodes per species in reference libraries increases. Our study demonstrates the value in attaching subspecies names to DNA barcode records as they can reveal a history of taxonomic concepts and expose important units of biodiversity. PMID:24282514

  16. Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

    Science.gov (United States)

    Yue, Jia-Xing; Li, Jing; Aigrain, Louise; Hallin, Johan; Persson, Karl; Oliver, Karen; Bergström, Anders; Coupland, Paul; Warringer, Jonas; Lagomarsino, Marco Cosentino; Fischer, Gilles; Durbin, Richard; Liti, Gianni

    2017-06-01

    Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts are likely to reflect the influence of human activities on structural genome evolution.

  17. Contrasting evolutionary genome dynamics between domesticated and wild yeasts

    Science.gov (United States)

    Yue, Jia-Xing; Li, Jing; Aigrain, Louise; Hallin, Johan; Persson, Karl; Oliver, Karen; Bergström, Anders; Coupland, Paul; Warringer, Jonas; Lagomarsino, Marco Consentino; Fischer, Gilles; Durbin, Richard; Liti, Gianni

    2017-01-01

    Structural rearrangements have long been recognized as an important source of genetic variation with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here, we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation allow for the first time a precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus exhibits faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions) whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly. In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae. Such striking contrasts between wild and domesticated yeasts likely reflect the influence of human activities on structural genome evolution. PMID:28416820

  18. 76 FR 9555 - Procurement List; Proposed Deletions

    Science.gov (United States)

    2011-02-18

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Proposed Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed deletions from the Procurement...'Day Act (41 U.S.C. 46- 48c) in connection with the products proposed for deletion from the Procurement...

  19. 78 FR 56679 - Procurement List; Deletions

    Science.gov (United States)

    2013-09-13

    ... PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List; Deletions AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Deletions from the Procurement List. SUMMARY: This action deletes products from the Procurement List previously furnished by nonprofit agencies employing...

  20. Biogenesis of the yeast cytochrome bc1 complex.

    Science.gov (United States)

    Zara, Vincenzo; Conte, Laura; Trumpower, Bernard L

    2009-01-01

    The mitochondrial respiratory chain is composed of four different protein complexes that cooperate in electron transfer and proton pumping across the inner mitochondrial membrane. The cytochrome bc1 complex, or complex III, is a component of the mitochondrial respiratory chain. This review will focus on the biogenesis of the bc1 complex in the mitochondria of the yeast Saccharomyces cerevisiae. In wild type yeast mitochondrial membranes the major part of the cytochrome bc1 complex was found in association with one or two copies of the cytochrome c oxidase complex. The analysis of several yeast mutant strains in which single genes or pairs of genes encoding bc1 subunits had been deleted revealed the presence of a common set of bc1 sub-complexes. These sub-complexes are represented by the central core of the bc1 complex, consisting of cytochrome b bound to subunit 7 and subunit 8, by the two core proteins associated with each other, by the Rieske protein associated with subunit 9, and by those deriving from the unexpected interaction of each of the two core proteins with cytochrome c1. Furthermore, a higher molecular mass sub-complex is that composed of cytochrome b, cytochrome c1, core protein 1 and 2, subunit 6, subunit 7 and subunit 8. The identification and characterization of all these sub-complexes may help in defining the steps and the molecular events leading to bc1 assembly in yeast mitochondria.

  1. Layer-by-layer growth of superparamagnetic, fluorescent barcode nanospheres

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qiangbin [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Liu Yan [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States); Lin Chenxiang [Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287 (United States); Yan Hao [Biodesign Institute, Arizona State University, Tempe, AZ 85287 (United States)

    2007-10-10

    We report a novel stepwise layer-by-layer synthesis strategy to achieve multi-component barcode nanospheres that contain magnetic nanoparticles (MNPs) as the core and quantum dots (QDs) of different emission colors in spatially separated silica layers as the shells, with QD-free silica layers as the insulation layers. This strategy offers the following unique features: (1) the location of the MNPs and the QDs in the silica spheres are separated spatially, so that no interference of the QD photoluminescence (PL) by the magnetic particles is observed; (2) the PL spectra of barcode nanospheres can be easily tuned through the ratio of different QDs loaded in each layer; (3) the size of the silica nanospheres can range from submicron ({approx}100 nm) to micrometers depending on the number of layers and the thickness of each layer; (4) QD stability is preserved by embedding the QDs covalently in the silica matrix; (5) fluorescence resonance energy transfer (FRET) between different colored QDs is avoided by isolating them into separated layers with a silica spacer layer.

  2. Layer-by-layer growth of superparamagnetic, fluorescent barcode nanospheres

    International Nuclear Information System (INIS)

    Wang Qiangbin; Liu Yan; Lin Chenxiang; Yan Hao

    2007-01-01

    We report a novel stepwise layer-by-layer synthesis strategy to achieve multi-component barcode nanospheres that contain magnetic nanoparticles (MNPs) as the core and quantum dots (QDs) of different emission colors in spatially separated silica layers as the shells, with QD-free silica layers as the insulation layers. This strategy offers the following unique features: (1) the location of the MNPs and the QDs in the silica spheres are separated spatially, so that no interference of the QD photoluminescence (PL) by the magnetic particles is observed; (2) the PL spectra of barcode nanospheres can be easily tuned through the ratio of different QDs loaded in each layer; (3) the size of the silica nanospheres can range from submicron (∼100 nm) to micrometers depending on the number of layers and the thickness of each layer; (4) QD stability is preserved by embedding the QDs covalently in the silica matrix; (5) fluorescence resonance energy transfer (FRET) between different colored QDs is avoided by isolating them into separated layers with a silica spacer layer

  3. [Applying DNA barcoding technique to identify menthae haplocalycis herba].

    Science.gov (United States)

    Pang, Xiaohui; Xu, Haibin; Han, Jianping; Song, Jingyuan

    2012-04-01

    To identify Menthae Haplocalycis Herba and its closely related species using DNA barcoding technique. Total genomic DNA was isolated from Mentha canadensis and its closely related species. Nuclear DNA ITS2 sequences were amplified, and purified PCR products were sequenced. Sequence assembly and consensus sequence generation were performed using the CodonCode Aligner V3.0. The Kimura 2-Parameter (K2P) distances were calculated using software MEGA 5.0. Identification analyses were performed using BLAST1, Nearest Distance and neighbor-joining (NJ) methods. The intra-specific genetic distances of M. canadensis were ranged from 0 to 0.006, which were lower than inter-specific genetic distances between M. canadensis and its closely related species (0.071-0.231). All the three methods showed that ITS2 could discriminate M. canadensis from its closely related species correctly. The ITS2 region is an efficient barcode for identification of Menthae Haplocalycis Herba, which provides a scientific basis for fast and accurate identification of the herb.

  4. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes

    Directory of Open Access Journals (Sweden)

    Yvonne-Marie Linton

    2013-01-01

    Full Text Available Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase ( COI I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n = 179 is presented for the first time in 60 years.

  5. Mosquitoes of eastern Amazonian Ecuador: biodiversity, bionomics and barcodes.

    Science.gov (United States)

    Linton, Yvonne-Marie; Pecor, James E; Porter, Charles H; Mitchell, Luke Brett; Garzón-Moreno, Andrés; Foley, Desmond H; Pecor, David Brooks; Wilkerson, Richard C

    2013-01-01

    Two snapshot surveys to establish the diversity and ecological preferences of mosquitoes (Diptera: Culicidae) in the terra firme primary rain forest surrounding the Tiputini Biodiversity Station in the UNESCO Yasuní Biosphere Reserve of eastern Amazonian Ecuador were carried out in November 1998 and May 1999. The mosquito fauna of this region is poorly known; the focus of this study was to obtain high quality link-reared specimens that could be used to unequivocally confirm species level diversity through integrated systematic study of all life stages and DNA sequences. A total of 2,284 specimens were preserved; 1,671 specimens were link-reared with associated immature exuviae, all but 108 of which are slide mounted. This study identified 68 unique taxa belonging to 17 genera and 27 subgenera. Of these, 12 are new to science and 37 comprise new country records. DNA barcodes [658-bp of the mtDNA cytochrome c oxidase (COI) I gene] are presented for 58 individuals representing 20 species and nine genera. DNA barcoding proved useful in uncovering and confirming new species and we advocate an integrated systematics approach to biodiversity studies in future. Associated bionomics of all species collected are discussed. An updated systematic checklist of the mosquitoes of Ecuador (n=179) is presented for the first time in 60 years.

  6. Decreased production of higher alcohols by Saccharomyces cerevisiae for Chinese rice wine fermentation by deletion of Bat aminotransferases.

    Science.gov (United States)

    Zhang, Cui-Ying; Qi, Ya-Nan; Ma, Hong-Xia; Li, Wei; Dai, Long-Hai; Xiao, Dong-Guang

    2015-04-01

    An appropriate level of higher alcohols produced by yeast during the fermentation is one of the most important factors influencing Chinese rice wine quality. In this study, BAT1 and BAT2 single- and double-gene-deletion mutant strains were constructed from an industrial yeast strain RY1 to decrease higher alcohols during Chinese rice wine fermentation. The results showed that the BAT2 single-gene-deletion mutant strain produced best improvement in the production of higher alcohols while remaining showed normal growth and fermentation characteristics. Furthermore, a BAT2 single-gene-deletion diploid engineered strain RY1-Δbat2 was constructed and produced low levels of isobutanol and isoamylol (isoamyl alcohol and active amyl alcohol) in simulated fermentation of Chinese rice wine, 92.40 and 303.31 mg/L, respectively, which were 33.00 and 14.20 % lower than those of the parental strain RY1. The differences in fermentation performance between RY1-Δbat2 and RY1 were minor. Therefore, construction of this yeast strain is important in future development in Chinese wine industry and provides insights on generating yeast strains for other fermented alcoholic beverages.

  7. Potential use of DNA barcodes in regulatory science: applications of the Regulatory Fish Encyclopedia.

    Science.gov (United States)

    Yancy, Haile F; Zemlak, Tyler S; Mason, Jacquline A; Washington, Jewell D; Tenge, Bradley J; Nguyen, Ngoc-Lan T; Barnett, James D; Savary, Warren E; Hill, Walter E; Moore, Michelle M; Fry, Frederick S; Randolph, Spring C; Rogers, Patricia L; Hebert, Paul D N

    2008-01-01

    The use of a DNA-based identification system (DNA barcoding) founded on the mitochondrial gene cytochrome c oxidase subunit I (COI) was investigated for updating the U.S. Food and Drug Administration Regulatory Fish Encyclopedia (RFE; http://www.cfsan.fda.gov/-frf/rfe0.html). The RFE is a compilation of data used to identify fish species. It was compiled to help regulators identify species substitution that could result in potential adverse health consequences or could be a source of economic fraud. For each of many aquatic species commonly sold in the United States, the RFE includes high-resolution photographs of whole fish and their marketed product forms and species-specific biochemical patterns for authenticated fish species. These patterns currently include data from isoelectric focusing studies. In this article, we describe the generation of DNA barcodes for 172 individual authenticated fish representing 72 species from 27 families contained in the RFE. These barcode sequences can be used as an additional identification resource. In a blind study, 60 unknown fish muscle samples were barcoded, and the results were compared with the RFE barcode reference library. All 60 samples were correctly identified to species based on the barcoding data. Our study indicates that DNA barcoding can be a powerful tool for species identification and has broad potential applications.

  8. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

    Science.gov (United States)

    Frandsen, Paul B.; Holzenthal, Ralph W.; Beet, Clare R.; Bennett, Kristi R.; Blahnik, Roger J.; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V.; Collins, Gemma E.; deWaard, Jeremy; Dean, John; Flint, Oliver S.; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D.; Kondratieff, Boris C.; Malicky, Hans; Milton, Megan A.; Morinière, Jérôme; Morse, John C.; Mwangi, François Ngera; Pauls, Steffen U.; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L.; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A.; Zamora-Muñoz, Carmen; Ziesmann, Tanja

    2016-01-01

    DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481793

  9. A DNA barcode library for North American Ephemeroptera: progress and prospects.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Webb

    Full Text Available DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%, while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.

  10. A DNA barcode library for North American Ephemeroptera: progress and prospects.

    Science.gov (United States)

    Webb, Jeffrey M; Jacobus, Luke M; Funk, David H; Zhou, Xin; Kondratieff, Boris; Geraci, Christy J; DeWalt, R Edward; Baird, Donald J; Richard, Barton; Phillips, Iain; Hebert, Paul D N

    2012-01-01

    DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 nominal and 90 provisional species of mayflies (Insecta: Ephemeroptera) from Canada, Mexico, and the United States. No species shared barcode sequences and all can be identified with barcodes with the possible exception of some Caenis. Minimum interspecific distances ranged from 0.3-24.7% (mean: 12.5%), while the average intraspecific divergence was 1.97%. The latter value was inflated by the presence of very high divergences in some taxa. In fact, nearly 20% of the species included two or three haplotype clusters showing greater than 5.0% sequence divergence and some values are as high as 26.7%. Many of the species with high divergences are polyphyletic and likely represent species complexes. Indeed, many of these polyphyletic species have numerous synonyms and individuals in some barcode clusters show morphological attributes characteristic of the synonymized species. In light of our findings, it is imperative that type or topotype specimens be sequenced to correctly associate barcode clusters with morphological species concepts and to determine the status of currently synonymized species.

  11. The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life.

    Science.gov (United States)

    Zhou, Xin; Frandsen, Paul B; Holzenthal, Ralph W; Beet, Clare R; Bennett, Kristi R; Blahnik, Roger J; Bonada, Núria; Cartwright, David; Chuluunbat, Suvdtsetseg; Cocks, Graeme V; Collins, Gemma E; deWaard, Jeremy; Dean, John; Flint, Oliver S; Hausmann, Axel; Hendrich, Lars; Hess, Monika; Hogg, Ian D; Kondratieff, Boris C; Malicky, Hans; Milton, Megan A; Morinière, Jérôme; Morse, John C; Mwangi, François Ngera; Pauls, Steffen U; Gonzalez, María Razo; Rinne, Aki; Robinson, Jason L; Salokannel, Juha; Shackleton, Michael; Smith, Brian; Stamatakis, Alexandros; StClair, Ros; Thomas, Jessica A; Zamora-Muñoz, Carmen; Ziesmann, Tanja; Kjer, Karl M

    2016-09-05

    DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between 'Barcode Index Numbers' (BINs) and 'species' that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

  12. An integrated web medicinal materials DNA database: MMDBD (Medicinal Materials DNA Barcode Database

    Directory of Open Access Journals (Sweden)

    But Paul

    2010-06-01

    Full Text Available Abstract Background Thousands of plants and animals possess pharmacological properties and there is an increased interest in using these materials for therapy and health maintenance. Efficacies of the application is critically dependent on the use of genuine materials. For time to time, life-threatening poisoning is found because toxic adulterant or substitute is administered. DNA barcoding provides a definitive means of authentication and for conducting molecular systematics studies. Owing to the reduced cost in DNA authentication, the volume of the DNA barcodes produced for medicinal materials is on the rise and necessitates the development of an integrated DNA database. Description We have developed an integrated DNA barcode multimedia information platform- Medicinal Materials DNA Barcode Database (MMDBD for data retrieval and similarity search. MMDBD contains over 1000 species of medicinal materials listed in the Chinese Pharmacopoeia and American Herbal Pharmacopoeia. MMDBD also contains useful information of the medicinal material, including resources, adulterant information, medical parts, photographs, primers used for obtaining the barcodes and key references. MMDBD can be accessed at http://www.cuhk.edu.hk/icm/mmdbd.htm. Conclusions This work provides a centralized medicinal materials DNA barcode database and bioinformatics tools for data storage, analysis and exchange for promoting the identification of medicinal materials. MMDBD has the largest collection of DNA barcodes of medicinal materials and is a useful resource for researchers in conservation, systematic study, forensic and herbal industry.

  13. Yeasts in Hevea brasiliensis Latex.

    Science.gov (United States)

    Glushakova, A M; Kachalkin, A V; Maksimova, I A; Chernov, I Yu

    2016-07-01

    Yeast abundance and species diversity in the latex of caoutchouc tree Hevea brasiliensis (Willd. ex Juss.) M611. Arg., on its green leaves, and in soil below the plant Was studied. The yeasts present in the fresh latex in concentrations of up to 5.5 log(CFU/g) were almost exclusively represented by the species Candida heveicola, which was previously isolated from Hevea latex in China. In the course of natural modification of the latex yeast diversity increased, while yeast abundance decreased. The yeasts of thickened and solidified latex were represented by typical epiphytic and ubiquitous species: Kodamea ohmeri, Debaryomyces hansenii, Rhodotorula mucilaginosa, and synanthropic species Candida parapsilosis and Cutaneotrichosporon arbori- formis. The role of yeasts in latex modification at the initial stages of succession and their probable role in de- velopment of antifungal activity in the latex are discussed.

  14. Plant DNA barcodes can accurately estimate species richness in poorly known floras.

    Directory of Open Access Journals (Sweden)

    Craig Costion

    Full Text Available BACKGROUND: Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70% and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. METHODOLOGY/PRINCIPAL FINDINGS: Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. CONCLUSIONS/SIGNIFICANCE: We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.

  15. Plant DNA barcodes can accurately estimate species richness in poorly known floras.

    Science.gov (United States)

    Costion, Craig; Ford, Andrew; Cross, Hugh; Crayn, Darren; Harrington, Mark; Lowe, Andrew

    2011-01-01

    Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (∼70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.

  16. Sexual differentiation in fission yeast

    DEFF Research Database (Denmark)

    Egel, R; Nielsen, O; Weilguny, D

    1990-01-01

    The regulation of sexual reproduction in yeast constitutes the highest level of differentiation observed in these unicellular organisms. The various ramifications of this system involve DNA rearrangement, transcriptional control, post-translational modification (such as protein phosphorylation......) and receptor/signal processing. A few basic similarities are common to both fission and budding yeasts. The wiring of the regulatory circuitry, however, varies considerably between these divergent yeast groups....

  17. Flavour-active wine yeasts

    OpenAIRE

    Cordente, Antonio G.; Curtin, Christopher D.; Varela, Cristian; Pretorius, Isak S.

    2012-01-01

    The flavour of fermented beverages such as beer, cider, saké and wine owe much to the primary fermentation yeast used in their production, Saccharomyces cerevisiae. Where once the role of yeast in fermented beverage flavour was thought to be limited to a small number of volatile esters and higher alcohols, the discovery that wine yeast release highly potent sulfur compounds from non-volatile precursors found in grapes has driven researchers to look more closely at how choice of yeast can infl...

  18. Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia).

    Science.gov (United States)

    Marescaux, Jonathan; Van Doninck, Karine

    2013-12-30

    The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals.

  19. A bar-code reader for an alpha-beta automatic counting system - FAG

    International Nuclear Information System (INIS)

    Levinson, S.; Shemesh, Y.; Ankry, N.; Assido, H.; German, U.; Peled, O.

    1996-01-01

    A bar-code laser system for sample number reading was integrated into the FAG Alpha-Beta automatic counting system. The sample identification by means of an attached bar-code label enables unmistakable and reliable attribution of results to the counted sample. Installation of the bar-code reader system required several modifications: Mechanical changes in the automatic sample changer, design and production of new sample holders, modification of the sample planchettes, changes in the electronic system, update of the operating software of the system (authors)

  20. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

    Directory of Open Access Journals (Sweden)

    Jacob L. Steenwyk

    2018-02-01

    Full Text Available In recent years, copy number (CN variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.

  1. Current awareness on yeast.

    Science.gov (United States)

    2002-02-01

    In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on yeasts. Each bibliography is divided into 10 sections. 1 Books, Reviews & Symposia; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (3 weeks journals - search completed 5th. Dec. 2001)

  2. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species.

    Science.gov (United States)

    Singh, Hemant Kumar; Parveen, Iffat; Raghuvanshi, Saurabh; Babbar, Shashi B

    2012-01-19

    Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively) were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL) could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Any recommended barcode based on the loci tested so far, is not likely to provide 100% species identification

  3. The loci recommended as universal barcodes for plants on the basis of floristic studies may not work with congeneric species as exemplified by DNA barcoding of Dendrobium species

    Directory of Open Access Journals (Sweden)

    Singh Hemant

    2012-01-01

    Full Text Available Abstract Background Based on the testing of several loci, predominantly against floristic backgrounds, individual or different combinations of loci have been suggested as possible universal DNA barcodes for plants. The present investigation was undertaken to check the applicability of the recommended locus/loci for congeneric species with Dendrobium species as an illustrative example. Results Six loci, matK, rbcL, rpoB, rpoC1, trnH-psbA spacer from the chloroplast genome and ITS, from the nuclear genome, were compared for their amplification, sequencing and species discrimination success rates among multiple accessions of 36 Dendrobium species. The trnH-psbA spacer could not be considered for analysis as good quality sequences were not obtained with its forward primer. Among the tested loci, ITS, recommended by some as a possible barcode for plants, provided 100% species identification. Another locus, matK, also recommended as a universal barcode for plants, resolved 80.56% species. ITS remained the best even when sequences of investigated loci of additional Dendrobium species available on the NCBI GenBank (93, 33, 20, 18 and 17 of ITS, matK, rbcL, rpoB and rpoC1, respectively were also considered for calculating the percent species resolution capabilities. The species discrimination of various combinations of the loci was also compared based on the 36 investigated species and additional 16 for which sequences of all the five loci were available on GenBank. Two-locus combination of matK+rbcL recommended by the Plant Working Group of Consortium for Barcoding of Life (CBOL could discriminate 86.11% of 36 species. The species discriminating ability of this barcode was reduced to 80.77% when additional sequences available on NCBI were included in the analysis. Among the recommended combinations, the barcode based on three loci - matK, rpoB and rpoC1- resolved maximum number of species. Conclusions Any recommended barcode based on the loci tested so

  4. Effects of B vitamin deletion in chemically defined diets on brood development in Camponotus vicinus (Hymenoptera: Formicidae).

    Science.gov (United States)

    Mankowski, Mark E; Morrell, J J

    2014-08-01

    The potential contributions of B vitamins by a yeast associate to the nutrition of the carpenter ant Camponotus vicinus Mayr was examined as part of an effort to develop a chemically defined diet. This diet was used to test the effects of individual B vitamin and other nutrient deletions on larval development. The chemically defined diet contained amino acids, vitamins, minerals, and other growth factors in a liquid sucrose matrix. C. vicinus worker colonies with third- and fourth-instar larvae were fed a complete artificial diet or that diet with a component deleted for a 12-wk period. There was a significant effect of diet on larval growth and number of adult worker ants produced in the overall nutrient deletion test, but ant development was often better on incomplete diets with one B vitamin deleted compared with the complete holidic basal diet. Thiamine deletion resulted in significantly higher brood weights compared with the complete diet. Diets of sugar water plus all B vitamins, sugar water only, or a diet minus all B vitamins and cholesterol were associated with significantly lower brood weights. Significantly more adult worker ants were produced by worker colonies fed diets minus cholesterol, choline, thiamine, or riboflavin compared with the complete basal diet. The results suggest that the diet, while suitable for rearing, could benefit from further study to better define component levels. The potential relationship of C. vicinus with yeast associates is discussed in relation to further studies.

  5. A comparison of direct infusion MS and GC-MS for metabolic footprinting of yeast mutants

    DEFF Research Database (Denmark)

    Mass, S.; Villas-Bôas, Silas Granato; Hansen, Michael Adsetts Edberg

    2007-01-01

    -deletion mutants. Filtered fermentation broth samples were analyzed by GC-MS and direct infusion ESI-MS. The potential of both methods in producing specific and, therefore, discriminant metabolite profiles was evaluated using samples from several yeast deletion mutants grown in batch-culture conditions....... Thus, the GC-MS method is good for classification of mutants with altered nitrogen regulation as it primarily measures amino acids, whereas this method cannot classify mutants involved in regulation of phospholipids metabolism as well as the direct infusion MS (DI-MS) method. From the analysis, we find...

  6. Sociobiology of the budding yeast

    Indian Academy of Sciences (India)

    ... yeast Saccharomyces cerevisiae, for sociobiological research. I discuss the problems connected with clear classification of yeast behaviour based on the fitness-based Hamilton paradigm. Relevant traits include different types of communities, production of flocculins, invertase and toxins, and the presence of apoptosis.

  7. Direct Reading of Bona Fide Barcode Assays for Diagnostics with Smartphone Apps.

    Science.gov (United States)

    Wong, Jessica X H; Li, Xiaochun; Liu, Frank S F; Yu, Hua-Zhong

    2015-06-30

    The desire to develop new point-of-care (POC) diagnostic tools has led to the adaptation of smartphones to tackle limitations in state-of-the-art instrumentation and centralized laboratory facilities. Today's smartphones possess the computer-like ability to image and process data using mobile apps; barcode scanners are one such type of apps. We demonstrate herein that a diagnostic assay can be performed by patterning immunoassay strips in a bona fide barcode format such that after target binding and signal enhancement, the linear barcode can be read directly with a standard smartphone app. Quantitative analysis can then be performed based on the grayscale intensities with a customized mobile app. This novel diagnostic concept has been validated for a real-world application, i.e., the detection of human chorionic gonadotropin, a pregnancy hormone. With the possibility of multiplex detection, the barcode assay protocol promises to boost POC diagnosis research by the direct adaptation of mobile devices and apps.

  8. Barcode Medication Administration: Lessons Learned From an Intensive Care Unit Implementation

    National Research Council Canada - National Science Library

    Wideman, Mary V; Whittler, Michael E; Anderson, Timothy M

    2005-01-01

    An electronic barcode medication administration system was successfully implemented in the acute care and long-term care sections of a 118-bed Veterans Administration hospital beginning in February 2000...

  9. Towards writing the encyclopedia of life: an introduction to DNA barcoding.

    Science.gov (United States)

    Savolainen, Vincent; Cowan, Robyn S; Vogler, Alfried P; Roderick, George K; Lane, Richard

    2005-10-29

    An international consortium of major natural history museums, herbaria and other organizations has launched an ambitious project, the 'Barcode of Life Initiative', to promote a process enabling the rapid and inexpensive identification of the estimated 10 million species on Earth. DNA barcoding is a diagnostic technique in which short DNA sequence(s) can be used for species identification. The first international scientific conference on Barcoding of Life was held at the Natural History Museum in London in February 2005, and here we review the scientific challenges discussed during this conference and in previous publications. Although still controversial, the scientific benefits of DNA barcoding include: (i) enabling species identification, including any life stage or fragment, (ii) facilitating species discoveries based on cluster analyses of gene sequences (e.g. cox1 = CO1, in animals), (iii) promoting development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and (iv) providing insight into the diversity of life.

  10. Inheritance of the yeast mitochondrial genome

    DEFF Research Database (Denmark)

    Piskur, Jure

    1994-01-01

    Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast......Mitochondrion, extrachromosomal genetics, intergenic sequences, genome size, mitochondrial DNA, petite mutation, yeast...

  11. Mouse Rad1 deletion enhances susceptibility for skin tumor development

    Directory of Open Access Journals (Sweden)

    Wang Xiangyuan

    2010-03-01

    Full Text Available Abstract Background Cells are constantly exposed to stresses from cellular metabolites as well as environmental genotoxins. DNA damage caused by these genotoxins can be efficiently fixed by DNA repair in cooperation with cell cycle checkpoints. Unrepaired DNA lesions can lead to cell death, gene mutation and cancer. The Rad1 protein, evolutionarily conserved from yeast to humans, exists in cells as monomer as well as a component in the 9-1-1 protein complex. Rad1 plays crucial roles in DNA repair and cell cycle checkpoint control, but its contribution to carcinogenesis is unknown. Results To address this question, we constructed mice with a deletion of Mrad1. Matings between heterozygous Mrad1 mutant mice produced Mrad1+/+ and Mrad1+/- but no Mrad1-/- progeny, suggesting the Mrad1 null is embryonic lethal. Mrad1+/- mice demonstrated no overt abnormalities up to one and half years of age. DMBA-TPA combinational treatment was used to induce tumors on mouse skin. Tumors were larger, more numerous, and appeared earlier on the skin of Mrad1+/- mice compared to Mrad1+/+ animals. Keratinocytes isolated from Mrad1+/- mice had significantly more spontaneous DNA double strand breaks, proliferated slower and had slightly enhanced spontaneous apoptosis than Mrad1+/+ control cells. Conclusion These data suggest that Mrad1 is important for preventing tumor development, probably through maintaining genomic integrity. The effects of heterozygous deletion of Mrad1 on proliferation and apoptosis of keratinocytes is different from those resulted from Mrad9 heterozygous deletion (from our previous study, suggesting that Mrad1 also functions independent of Mrad9 besides its role in the Mrad9-Mrad1-Mhus1 complex in mouse cells.

  12. Genomic DNA extraction and barcoding of endophytic fungi.

    Science.gov (United States)

    Diaz, Patricia L; Hennell, James R; Sucher, Nikolaus J

    2012-01-01

    Endophytes live inter- and/or intracellularly inside healthy aboveground tissues of plants without causing disease. Endophytic fungi are found in virtually every vascular plant species examined. The origins of this symbiotic relationship between endophytes go back to the emergence of vascular plants. Endophytic fungi receive nutrition and protection from their hosts while the plants benefit from the production of fungal secondary metabolites, which enhance the host plants' resistance to herbivores, pathogens, and various abiotic stresses. Endophytic fungi have attracted increased interest as potential sources of secondary metabolites with agricultural, industrial, and medicinal use. This chapter provides detailed protocols for isolation of genomic DNA from fungal endophytes and its use in polymerase chain reaction-based amplification of the internal transcribed spacer region between the conserved flanking regions of the small and large subunit of ribosomal RNA for barcoding purposes.

  13. Barcode extension for analysis and reconstruction of structures

    Science.gov (United States)

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

    2017-03-01

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

  14. Identifying the ichthyoplankton of a coral reef using DNA barcodes.

    Science.gov (United States)

    Hubert, Nicolas; Espiau, Benoit; Meyer, Christopher; Planes, Serge

    2015-01-01

    Marine fishes exhibit spectacular phenotypic changes during their ontogeny, and the identification of their early stages is challenging due to the paucity of diagnostic morphological characters at the species level. Meanwhile, the importance of early life stages in dispersal and connectivity has recently experienced an increasing interest in conservation programmes for coral reef fishes. This study aims at assessing the effectiveness of DNA barcoding for the automated identification of coral reef fish larvae through large-scale ecosystemic sampling. Fish larvae were mainly collected using bongo nets and light traps around Moorea between September 2008 and August 2010 in 10 sites distributed in open waters. Fish larvae ranged from 2 to 100 mm of total length, with the most abundant individuals being fish larval ecology. © 2014 John Wiley & Sons Ltd.

  15. Synthesis, microstructure, and physical properties of metallic barcode nanowires

    Science.gov (United States)

    Park, Bum Chul; Kim, Young Keun

    2017-05-01

    With rapid progress in nanotechnology, nanostructured materials have come closer to our life. Single-component nanowires are actively investigated because of their novel properties, attributed to their nanoscale dimensions and adjustable aspect ratio, but their technical limitations cannot be resolved easily. Heterostructured nanomaterials gained attention as alternatives because they can improve the existing single-component structure or add new functions to it. Among them, barcode nanowires (BNWs), comprising at least two different functional segments, can perform multiple functions for use in biomedical sensors, information encoding and security, and catalysts. BNW applications require reliable response to the external field. Hence, researchers have been attempting to improve the reliability of synthesis and regulate the properties precisely. This article highlights the recent progress and prospects for the synthesis, properties, and applications of metallic BNWs with focus on the dependence of the magnetic, optical, and mechanical properties on material, composition, shape, and microstructure.

  16. Production of Food Grade Yeasts

    Directory of Open Access Journals (Sweden)

    Argyro Bekatorou

    2006-01-01

    Full Text Available Yeasts have been known to humans for thousands of years as they have been used in traditional fermentation processes like wine, beer and bread making. Today, yeasts are also used as alternative sources of high nutritional value proteins, enzymes and vitamins, and have numerous applications in the health food industry as food additives, conditioners and flavouring agents, for the production of microbiology media and extracts, as well as livestock feeds. Modern scientific advances allow the isolation, construction and industrial production of new yeast strains to satisfy the specific demands of the food industry. Types of commercial food grade yeasts, industrial production processes and raw materials are highlighted. Aspects of yeast metabolism, with respect to carbohydrate utilization, nutritional aspects and recent research advances are also discussed.

  17. Evolutionary History of Ascomyceteous Yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Riley, Robert; Salamov, Asaf; Goker, Markus; Klenk, Hans-Peter; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor; Jeffries, Thomas W.

    2014-06-06

    Yeasts are important for many industrial and biotechnological processes and show remarkable diversity despite morphological similarities. We have sequenced the genomes of 16 ascomycete yeasts of taxonomic and industrial importance including members of Saccharomycotina and Taphrinomycotina. A comparison of these with several other previously published yeast genomes have added increased confidence to the phylogenetic positions of previously poorly placed species including Saitoella complicata, Babjeviella inositovora and Metschnikowia bicuspidata. Phylogenetic analysis also showed that yeasts with alternative nuclear codon usage where CUG encodes serine instead of leucine are monophyletic within the Saccharomycotina. Most of the yeasts have compact genomes with a large fraction of single exon genes with Lipomyces starkeyi and the previously published Pneumocystis jirovecii being notable exceptions. Intron analysis suggests that early diverging species have more introns. We also observed a large number of unclassified lineage specific non-simple repeats in these genomes.

  18. Investigation of the Mesenchymal Stem Cell Compartment by Means of a Lentiviral Barcode Library.

    Science.gov (United States)

    Bigildeev, A E; Cornils, K; Aranyossy, T; Sats, N V; Petinati, N A; Shipounova, I N; Surin, V L; Pshenichnikova, O S; Riecken, K; Fehse, B; Drize, N I

    2016-04-01

    The hematopoietic bone marrow microenvironment is formed by proliferation and differentiation of mesenchymal stem cells (MSCs). The MSC compartment has been less studied than the hematopoietic stem cell compartment. To characterize the structure of the MSC compartment, it is necessary to trace the fate of distinct mesenchymal cells. To do so, mesenchymal progenitors need to be marked at the single-cell level. A method for individual marking of normal and cancer stem cells based on genetic "barcodes" has been developed for the last 10 years. Such approach has not yet been applied to MSCs. The aim of this study was to evaluate the possibility of using such barcoding strategy to mark MSCs and their descendants, colony-forming units of fibroblasts (CFU-Fs). Adherent cell layers (ACLs) of murine long-term bone marrow cultures (LTBMCs) were transduced with a lentiviral library with barcodes consisting of 32 + 3 degenerate nucleotides. Infected ACLs were suspended, and CFU-F derived clones were obtained. DNA was isolated from each individual colony, and barcodes were analyzed in marked CFU-F-derived colonies by means of conventional polymerase chain reaction and Sanger sequencing. Barcodes were identified in 154 marked colonies. All barcodes appeared to be unique: there were no two distinct colonies bearing the same barcode. It was shown that ACLs included CFU-Fs with different proliferative potential. MSCs are located higher in the hierarchy of mesenchymal progenitors than CFU-Fs, so the presented data indicate that MSCs proliferate rarely in LTBMCs. A method of stable individual marking and comparing the markers in mesenchymal progenitor cells has been developed in this work. We show for the first time that a barcoded library of lentiviruses is an effective tool for studying stromal progenitor cells.

  19. Assessing the potential of candidate DNA barcodes for identifying non-flowering seed plants.

    Science.gov (United States)

    Pang, X; Luo, H; Sun, C

    2012-09-01

    In plants, matK and rbcL have been selected as core barcodes by the Consortium for the Barcode of Life (CBOL) Plant Working Group (PWG), and ITS/ITS2 and psbA-trnH were suggested as supplementary loci. Yet, research on DNA barcoding of non-flowering seed plants has been less extensive, and the evaluation of DNA barcodes in this division has been limited thus far. Here, we evaluated seven markers (psbA-trnH, matK, rbcL, rpoB, rpoC1, ITS and ITS2) from non-flowering seed plants. The usefulness of each region was assessed using four criteria: the success rate of PCR amplification, the differential intra- and inter-specific divergences, the DNA barcoding gap and the ability to discriminate species. Among the seven loci tested, ITS2 produced the best results in the barcoding of non-flowering seed plants. In addition, we compared the abilities of the five most-recommended markers (psbA-trnH, matK, rbcL, ITS and ITS2) to identify additional species using a large database of gymnosperms from GenBank. ITS2 remained effective for species identification in a wide range of non-flowering seed plants: for the 1531 samples from 608 species of 80 diverse genera, ITS2 correctly authenticated 66% of them at the species level. In conclusion, the ITS2 region can serve as a useful barcode to discriminate non-flowering seed plants, and this study will contribute valuable information for the barcoding of plant species. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

  20. Single nucleotide polymorphism barcoding to evaluate oral cancer risk using odds ratio-based genetic algorithms

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    Cheng-Hong Yang

    2012-07-01

    Full Text Available Cancers often involve the synergistic effects of gene–gene interactions, but identifying these interactions remains challenging. Here, we present an odds ratio-based genetic algorithm (OR-GA that is able to solve the problems associated with the simultaneous analysis of multiple independent single nucleotide polymorphisms (SNPs that are associated with oral cancer. The SNP interactions between four SNPs—namely rs1799782, rs2040639, rs861539, rs2075685, and belonging to four genes (XRCC1, XRCC2, XRCC3, and XRCC4—were tested in this study, respectively. The GA decomposes the SNPs sets into different SNP combinations with their corresponding genotypes (called SNP barcodes. The GA can effectively identify a specific SNP barcode that has an optimized fitness value and uses this to calculate the difference between the case and control groups. The SNP barcodes with a low fitness value are naturally removed from the population. Using two to four SNPs, the best SNP barcodes with maximum differences in occurrence between the case and control groups were generated by GA algorithm. Subsequently, the OR provides a quantitative measure of the multiple SNP synergies between the oral cancer and control groups by calculating the risk related to the best SNP barcodes and others. When these were compared to their corresponding non-SNP barcodes, the estimated ORs for oral cancer were found to be great than 1 [approx. 1.72–2.23; confidence intervals (CIs: 0.94–5.30, p < 0.03–0.07] for various specific SNP barcodes with two to four SNPs. In conclusion, the proposed OR-GA method successfully generates SNP barcodes, which allow oral cancer risk to be evaluated and in the process the OR-GA method identifies possible SNP–SNP interactions.

  1. Assessing DNA Barcodes for Species Identification in North American Reptiles and Amphibians in Natural History Collections.

    Science.gov (United States)

    Chambers, E Anne; Hebert, Paul D N

    2016-01-01

    High rates of species discovery and loss have led to the urgent need for more rapid assessment of species diversity in the herpetofauna. DNA barcoding allows for the preliminary identification of species based on sequence divergence. Prior DNA barcoding work on reptiles and amphibians has revealed higher biodiversity counts than previously estimated due to cases of cryptic and undiscovered species. Past studies have provided DNA barcodes for just 14% of the North American herpetofauna, revealing the need for expanded coverage. This study extends the DNA barcode reference library for North American herpetofauna, assesses the utility of this approach in aiding species delimitation, and examines the correspondence between current species boundaries and sequence clusters designated by the BIN system. Sequences were obtained from 730 specimens, representing 274 species (43%) from the North American herpetofauna. Mean intraspecific divergences were 1% and 3%, while average congeneric sequence divergences were 16% and 14% in amphibians and reptiles, respectively. BIN assignments corresponded with current species boundaries in 79% of amphibians, 100% of turtles, and 60% of squamates. Deep divergences (>2%) were noted in 35% of squamate and 16% of amphibian species, and low divergences (reptiles and 23% of amphibians, patterns reflected in BIN assignments. Sequence recovery declined with specimen age, and variation in recovery success was noted among collections. Within collections, barcodes effectively flagged seven mislabeled tissues, and barcode fragments were recovered from five formalin-fixed specimens. This study demonstrates that DNA barcodes can effectively flag errors in museum collections, while BIN splits and merges reveal taxa belonging to deeply diverged or hybridizing lineages. This study is the first effort to compile a reference library of DNA barcodes for herpetofauna on a continental scale.

  2. Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade.

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    Rupert A Collins

    Full Text Available Poorly regulated international trade in ornamental fishes poses risks to both biodiversity and economic activity via invasive alien species and exotic pathogens. Border security officials need robust tools to confirm identifications, often requiring hard-to-obtain taxonomic literature and expertise. DNA barcoding offers a potentially attractive tool for quarantine inspection, but has yet to be scrutinised for aquarium fishes. Here, we present a barcoding approach for ornamental cyprinid fishes by: (1 expanding current barcode reference libraries; (2 assessing barcode congruence with morphological identifications under numerous scenarios (e.g. inclusion of GenBank data, presence of singleton species, choice of analytical method; and (3 providing supplementary information to identify difficult species.We sampled 172 ornamental cyprinid fish species from the international trade, and provide data for 91 species currently unrepresented in reference libraries (GenBank/Bold. DNA barcodes were found to be highly congruent with our morphological assignments, achieving success rates of 90-99%, depending on the method used (neighbour-joining monophyly, bootstrap, nearest neighbour, GMYC, percent threshold. Inclusion of data from GenBank (additional 157 spp. resulted in a more comprehensive library, but at a cost to success rate due to the increased number of singleton species. In addition to DNA barcodes, our study also provides supporting data in the form of specimen images, morphological characters, taxonomic bibliography, preserved vouchers, and nuclear rhodopsin sequences. Using this nuclear rhodopsin data we also uncovered evidence of interspecific hybridisation, and highlighted unrecognised diversity within popular aquarium species, including the endangered Indian barb Puntius denisonii.We demonstrate that DNA barcoding provides a highly effective biosecurity tool for rapidly identifying ornamental fishes. In cases where DNA barcodes are unable to

  3. Identification of processed Chinese medicinal materials using DNA mini-barcoding.

    Science.gov (United States)

    Song, Ming; Dong, Gang-Qiang; Zhang, Ya-Qin; Liu, Xia; Sun, Wei

    2017-07-01

    Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials. In the present study, six DNA barcode loci including ITS2, psbA-trnH, rbcL, matK, trnL (UAA) intron and its P6 loop, were employed for the authentication of 45 processed samples belonging to 15 species. We evaluated the amplification efficiency of each locus. We also examined the identification accuracy of the potential mini-barcode locus, of trnL (UAA) intron P6 loop. Our results showed that the five primary barcode loci were successfully amplified in only 8.89%-20% of the processed samples, while the amplification rates of the trnL (UAA) intron P6 loop were higher, at 75.56% successful amplification. We compared the mini-barcode sequences with Genbank using the Blast program. The analysis showed that 45.23% samples could be identified to genus level, while only one sample could be identified to the species level. We conclude that trnL (UAA) p6 loop is a candidate mini-barcode that has shown its potential and may become a universal mini-barcode as complementary barcode for authenticity testing and will play an important role in medicinal materials control. Copyright © 2017 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  4. DNA barcoding of feral tilapias in Philippine lakes.

    Science.gov (United States)

    Maranan, Justin Bryan D; Basiao, Zubaida U; Quilang, Jonas P

    2016-11-01

    Tilapia (Oreochromis mossambicus) was first introduced to the Philippines in 1950 for aquaculture. Since then, other species of tilapia have been introduced to the country and some of them (mainly Oreochromis niloticus) have become established in lakes and other water bodies. In this study, DNA barcoding using the mitochondrial cytochrome c oxidase subunit I (COI) gene was done to assess the reliability of morphological identification and the degree of introgression among feral tilapias (Oreochromis spp.) in seven major Philippine lakes, namely Laguna de Bay, Lake Lanao, Taal Lake, Lake Mainit, Lake Naujan, Lake Bato, and Lake Buhi. Specimens were also collected from a private hatchery in Sual, Pangasinan to serve as reference. Morphological traits, Nucleotide BLAST (BLASTn), and Translated BLAST (BLASTx) analyses were used to classify the specimens. A Neighbor-Joining tree was constructed using the Kimura 2-Parameter method, incorporating 66 COI sequences generated from the study and 20 additional reference sequences obtained from GenBank. Three Oreochromis clusters were obtained and were classified as the O. niloticus group, O. mossambicus group, and O. aureus group, with bootstrap support values of 99%, 74%, and 99%, respectively. The mean K2P genetic distances within each group were 0.008%, 0.959%, and 0.086%, respectively. The clustering of COI sequences generated from this study corresponded with the results of the BLASTn analysis. Oreochromis hybrids were also found in all the lakes. The study highlights the usefulness of DNA barcoding for molecular identification and detection of introgressed individuals, with potential applications in management of feral stocks.

  5. Applications of three DNA barcodes in assorting intertidal red macroalgal flora in Qingdao, China

    Science.gov (United States)

    Zhao, Xiaobo; Pang, Shaojun; Shan, Tifeng; Liu, Feng

    2013-03-01

    This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult solely depending on morphological characteristics. In recent years, DNA barcode technique has become a more and more effective tool to help solve some of the taxonomic difficulties. Some DNA markers such as COI (cytochrome oxidase subunit I) are proposed as standardized DNA barcodes for all seaweed species. In this study, COI, UPA (universal plastid amplicon, domain V of 23S rRNA), and ITS (nuclear internal transcribed spacer) were employed to analyze common species of intertidal red seaweeds in Qingdao (119.3°-121°E, 35.35°-37.09°N). The applicability of using one or a few combined barcodes to identify red seaweed species was tested. The results indicated that COI is a sensitive marker at species level. However, not all the tested species gave PCR amplification products due to lack of the universal primers. The second barcode UPA had effective universal primers but needed to be tested for the effectiveness of resolving closely related species. More than one ITS sequence types were found in some species in this investigation, which might lead to confusion in further analysis. Therefore ITS sequence is not recommended as a universal barcode for seaweeds identification.

  6. DNA barcoding detected improper labelling and supersession of crab food served by restaurants in India.

    Science.gov (United States)

    Vartak, Vivek Rohidas; Narasimmalu, Rajendran; Annam, Pavan Kumar; Singh, Dhirendra P; Lakra, Wazir S

    2015-01-01

    Detection of improper labelling of raw and processed seafood is of global importance for reducing commercial fraud and enhancing food safety. Crabs are crustaceans with intricate morphological as well as genetic divergence among species and are popular as seafood in restaurants. Owing to the high number of crab species available, it can be difficult to identify those included in particular food dishes, thus increasing the chance of supersession. DNA barcoding is an advanced technology for detecting improper food labelling and has been used successfully to authenticate seafood. This study identified 11 edible crab species from India by classical taxonomy and developed molecular barcodes with the cytochrome c oxidase I (COI) gene. These barcodes were used as reference barcodes for detecting any improper labelling of 50 restaurant crab samples. Neighbour-joining tree analysis with COI barcodes showed distinct clusters of restaurant samples with respective reference species. The study demonstrated 100% improper labelling of restaurant samples to cover up acts of inferior crab supersession. DNA barcoding successfully identified 11 edible crabs in accordance with classical taxonomy and discerned improper crab food labelling in restaurants of India. © 2014 Society of Chemical Industry.

  7. DNA barcoding of twelve shrimp species (Crustacea: Decapoda from Turkish seas reveals cryptic diversity

    Directory of Open Access Journals (Sweden)

    R. BILGIN

    2014-05-01

    Full Text Available DNA barcoding is a useful tool for the identification and potential discovery of new species. In this study, DNA barcoding was employed by sequencing the mitochondrial cytochrome oxidase subunit I gene (COI to characterize the genetic diversity of 12 shrimp species inhabiting Turkish coastal waters and, when possible, to compare with the genetic data available from different parts of the Mediterranean and eastern Atlantic. This study also comprises the first DNA barcoding study performed in the Turkish Seas using COI. A total of 40 shrimp specimens were collected and analyzed from 9 sites. Generally, the barcoding gap criterion was successful at identifying species; hence COI appeared to be a good marker of choice for DNA barcoding in this group. Out of the 12 species investigated, five were barcoded for the first time. In six species two intraspecific clades were retrieved after the analyses. The results suggest the presence of cryptic diversity in a genetically understudied marine area, Turkish coastal waters, and further investigation in these species using population genetics, taxonomic approaches and nuclear markers is likely to result in designation of new species.

  8. Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library.

    Directory of Open Access Journals (Sweden)

    Alessia Cariani

    Full Text Available Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera, including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions.

  9. Development of Attendance Database System Using Bar-coded Student Card

    Directory of Open Access Journals (Sweden)

    Abdul Fadlil

    2008-04-01

    Full Text Available The calculation of the level of attendance is very important, because one indicator of a person's credibility can be seen from the level of attendance. For example, at a university, data about the level of attendance of a student in a lecture is very important as one of components in the assessment. The manual presence system is considered less effective. This research presents the draft of presence system using bar codes (barcodes as input data representing the attendance. The presence system is supported by three main components, those are a bar code found on the student card (KTM, a CCD barcode scanner series and a CD-108E computer. Management of attendance list using this system allows for optimization of functions of KTM. The presence system has been tested with several KTM through a variety of distances and positions of the barcode scanner barcode. The test results is obtained at ideal position for reading a barcode when a barcode scanner is at 2 cm from the object with 90 degree. At this position the level of accuracy reach 100%.

  10. Integrative analysis of the mitochondrial proteome in yeast.

    Directory of Open Access Journals (Sweden)

    Holger Prokisch

    2004-06-01

    Full Text Available In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.

  11. Deletion of OSH3 gene confers resistance against ISP-1 in Saccharomyces cerevisiae.

    Science.gov (United States)

    Yano, Tatsuya; Inukai, Masatoshi; Isono, Fujio

    2004-02-27

    Sphingolipids have been reported to regulate the growth and death of mammalian and yeast cells, but their precise mechanisms are unknown. In this paper, it was shown that the deletion of the oxysterol binding protein homologue 3 (OSH3) gene confers hyper resistance against ISP-1, an inhibitor of sphingolipid biosynthesis, in the yeast Saccharomyces cerevisiae. Furthermore, the overexpression of the ROK1 gene, which directly binds to Osh3p, conferred resistance against ISP-1, and the deletion of the KEM1 gene, which regulates microtubule functions, exhibited ISP-1 hypersensitivity. And yet, an ISP-1 treatment caused an abnormal mitotic spindle formation, and the ISP-1-induced cell cycle arrest was rescued by the deletion of the OSH3 gene. Taken together, it is suggested that the expression levels of the OSH3 gene influence the ISP-1 sensitivity of S. cerevisiae, and the sphingolipids are necessary for normal mitotic spindle formation in which the Osh3p may play a pivotal role.

  12. Assessment of the Toxicity of CuO Nanoparticles by Using Saccharomyces cerevisiae Mutants with Multiple Genes Deleted

    Science.gov (United States)

    Bao, Shaopan; Lu, Qicong; Dai, Heping; Zhang, Chao

    2015-01-01

    To develop applicable and susceptible models to evaluate the toxicity of nanoparticles, the antimicrobial effects of CuO nanoparticles (CuO-NPs) on various Saccharomyces cerevisiae (S. cerevisiae) strains (wild type, single-gene-deleted mutants, and multiple-gene-deleted mutants) were determined and compared. Further experiments were also conducted to analyze the mechanisms associated with toxicity using copper salt, bulk CuO (bCuO), carbon-shelled copper nanoparticles (C/Cu-NPs), and carbon nanoparticles (C-NPs) for comparisons. The results indicated that the growth inhibition rates of CuO-NPs for the wild-type and the single-gene-deleted strains were comparable, while for the multiple-gene deletion mutant, significantly higher toxicity was observed (P CuO-NPs to yeast cells was compared with the toxicities of copper salt and bCuO, we concluded that the toxicity of CuO-NPs should be attributed to soluble copper rather than to the nanoparticles. The striking difference in adverse effects of C-NPs and C/Cu-NPs with equivalent surface areas also proved this. A toxicity assay revealed that the multiple-gene-deleted mutant was significantly more sensitive to CuO-NPs than the wild type. Specifically, compared with the wild-type strain, copper was readily taken up by mutant strains when cell permeability genes were knocked out, and the mutants with deletions of genes regulated under oxidative stress (OS) were likely producing more reactive oxygen species (ROS). Hence, as mechanism-based gene inactivation could increase the susceptibility of yeast, the multiple-gene-deleted mutants should be improved model organisms to investigate the toxicity of nanoparticles. PMID:26386067

  13. Genetic study on yeast

    International Nuclear Information System (INIS)

    Mortimer, R.K.

    1981-01-01

    Research during the past year has moved ahead on several fronts. A major compilation of all the genetic mapping data for the yeast Saccharomyces cerevisiae has been completed. The map describes the location of over 300 genes on 17 chromosomes. A report on this work will appear in Microbiological Reviews in December 1980. Recombinant DNA procedures have been introduced into the experiments and RAD52 (one of the genes involved in recombination and repair damage), has been successfully cloned. This clone will be used to determine the gene product. Diploid cells homozygous for RAD52 have exceptionally high frequencies of mitotic loss of chromosomes. This loss is stimulated by ionizing radiation. This effect is a very significant finding. The effect has also been seen with certain other RAD mutants

  14. Interaction Between Yeasts and Zinc

    Science.gov (United States)

    Nicola, Raffaele De; Walker, Graeme

    Zinc is an essential trace element in biological systems. For example, it acts as a cellular membrane stabiliser, plays a critical role in gene expression and genome modification and activates nearly 300 enzymes, including alcohol dehydrogenase. The present chapter will be focused on the influence of zinc on cell physiology of industrial yeast strains of Saccharomyces cerevisiae, with special regard to the uptake and subsequent utilisation of this metal. Zinc uptake by yeast is metabolism-dependent, with most of the available zinc translocated very quickly into the vacuole. At cell division, zinc is distributed from mother to daughter cells and this effectively lowers the individual cellular zinc concentration, which may become zinc depleted at the onset of the fermentation. Zinc influences yeast fermentative performance and examples will be provided relating to brewing and wine fermentations. Industrial yeasts are subjected to several stresses that may impair fermentation performance. Such stresses may also impact on yeast cell zinc homeostasis. This chapter will discuss the practical implications for the correct management of zinc bioavailability for yeast-based biotechnologies aimed at improving yeast growth, viability, fermentation performance and resistance to environmental stresses

  15. Lager Yeast Comes of Age

    Science.gov (United States)

    2014-01-01

    Alcoholic fermentations have accompanied human civilizations throughout our history. Lager yeasts have a several-century-long tradition of providing fresh beer with clean taste. The yeast strains used for lager beer fermentation have long been recognized as hybrids between two Saccharomyces species. We summarize the initial findings on this hybrid nature, the genomics/transcriptomics of lager yeasts, and established targets of strain improvements. Next-generation sequencing has provided fast access to yeast genomes. Its use in population genomics has uncovered many more hybridization events within Saccharomyces species, so that lager yeast hybrids are no longer the exception from the rule. These findings have led us to propose network evolution within Saccharomyces species. This “web of life” recognizes the ability of closely related species to exchange DNA and thus drain from a combined gene pool rather than be limited to a gene pool restricted by speciation. Within the domesticated lager yeasts, two groups, the Saaz and Frohberg groups, can be distinguished based on fermentation characteristics. Recent evidence suggests that these groups share an evolutionary history. We thus propose to refer to the Saaz group as Saccharomyces carlsbergensis and to the Frohberg group as Saccharomyces pastorianus based on their distinct genomes. New insight into the hybrid nature of lager yeast will provide novel directions for future strain improvement. PMID:25084862

  16. Yeasts: From genetics to biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Russo, S.; Poli, G. [Univ. of Milan (Italy); Siman-Tov, R.B. [Univ. of Jerusalem, Rehovot (Israel)

    1995-12-31

    Yeasts have been known and used in food and alcoholic fermentations ever since the Neolithic Age. In more recent times, on the basis of their peculiar features and history, yeasts have become very important experimental models in both microbiological and genetic research, as well as the main characters in many fermentative production processes. In the last 40 years, advances in molecular biology and genetic engineering have made possible not only the genetic selection of organisms, but also the genetic modification of some of them, especially the simplest of them, such as bacteria and yeasts. These discoveries have led to the availability of new yeast strains fit to fulfill requests of industrial production and fermentation. Moreover, genetically modified and transformed yeasts have been constructed that are able to produce large amounts of biologically active proteins and enzymes. Thus, recombinant yeasts make it easier to produce drugs, biologically active products, diagnostics, and vaccines, by inexpensive and relatively simple techniques. Yeasts are going to become more and more important in the {open_quotes}biotechnological revolution{close_quotes} by virtue of both their features and their very long and safe use in human nutrition and industry. 175 refs., 4 figs., 6 tabs.

  17. Caloric Restriction-Induced Extension of Chronological Lifespan Requires Intact Respiration in Budding Yeast

    OpenAIRE

    Kwon, Young-Yon; Lee, Sung-Keun; Lee, Cheol-Koo

    2017-01-01

    Caloric restriction (CR) has been shown to extend lifespan and prevent cellular senescence in various species ranging from yeast to humans. Many effects of CR may contribute to extend lifespan. Specifically, CR prevents oxidative damage from reactive oxygen species (ROS) by enhancing mitochondrial function. In this study, we characterized 33 single electron transport chain (ETC) gene-deletion strains to identify CR-induced chronological lifespan (CLS) extension mechanisms. Interestingly, defe...

  18. Deletion of intragenic tandem repeats in unit C of FLO1 of Saccharomyces cerevisiae increases the conformational stability of flocculin under acidic and alkaline conditions.

    Directory of Open Access Journals (Sweden)

    Ee Li

    Full Text Available Flocculation is an attractive property for Saccaromyces cerevisiae, which plays important roles in fermentation industry and environmental remediation. The process of flocculation is mediated by a family of cell surface flocculins. As one member of flocculins, Flo1 is characterized by four families of repeats (designated as repeat units A, B, C and D in the central domain. It is generally accepted that variation of repeat unit A in length in Flo1 influences the degree of flocculation or specificity for sugar recognization. However, no reports were observed for other repeat units. Here, we compared the flocculation ability and its sensitivity to environmental factors between yeast strain YSF1 carrying the intact FLO1 gene and yeast strains carrying the derived forms of FLO1 with partial or complete deletion of repeats in unit C. No obvious differences in flocculation ability and specificity of carbohydrate recognition were observed among these yeast strains, which indicates the truncated flocculins can stride across the cell wall and cluster the N-terminal domain on the surface of yeast cells as the intact Flo1 thereby improving intercellular binding. However, yeast strains with the truncated flocculins required more mannose to inhibit completely the flocculation, displayed broad tolerance of flocculation to pH fluctuation, and the fewer the repeats in unit C, the stronger adaptability of flocculation to pH change, which was not relevant to the position of deletion. This suggests that more stable active conformation is obtained for flocculin by deletion the repeat unit C in the central domain of Flo1, which was validated further by the higher hydrophobicity on the surface of cells of YSF1c with complete deletion of unit C under neutral and alkaline conditions and the stabilization of GFP conformation by fusion with flocculin with complete deletion of unit C in the central domain.

  19. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    International Nuclear Information System (INIS)

    Han, Sangjo; Lee, Minho; Chang, Hyeshik; Nam, Miyoung; Park, Han-Oh; Kwak, Youn-Sig; Ha, Hye-jeong; Kim, Dongsup; Hwang, Sung-Ook; Hoe, Kwang-Lae; Kim, Dong-Uk

    2013-01-01

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defect measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)

  20. Construction of the first compendium of chemical-genetic profiles in the fission yeast Schizosaccharomyces pombe and comparative compendium approach

    Energy Technology Data Exchange (ETDEWEB)

    Han, Sangjo [Bioinformatics Lab, Healthcare Group, SK Telecom, 9-1, Sunae-dong, Pundang-gu, Sungnam-si, Kyunggi-do 463-784 (Korea, Republic of); Lee, Minho [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Chang, Hyeshik [Department of Biological Science, Seoul National University, 599 Gwanakro, Gwanak-gu, Seoul 151-747 (Korea, Republic of); Nam, Miyoung [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Park, Han-Oh [Bioneer Corp., 8-11 Munpyeongseo-ro, Daedeok-gu, Daejeon 306-220 (Korea, Republic of); Kwak, Youn-Sig [Department of Applied Biology, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam 660-701 (Korea, Republic of); Ha, Hye-jeong [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of); Kim, Dongsup [Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Hwang, Sung-Ook [Department of Obstetrics and Gynecology, Inha University Hospital, 7-206 Sinheung-dong, Jung-gu, Incheon 400-711 (Korea, Republic of); Hoe, Kwang-Lae [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon, 305-764 (Korea, Republic of); Kim, Dong-Uk [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-Gu, Daejeon 305-806 (Korea, Republic of)

    2013-07-12

    Highlights: •The first compendium of chemical-genetic profiles form fission yeast was generated. •The first HTS of drug mode-of-action in fission yeast was performed. •The first comparative chemical genetic analysis between two yeasts was conducted. -- Abstract: Genome-wide chemical genetic profiles in Saccharomyces cerevisiae since the budding yeast deletion library construction have been successfully used to reveal unknown mode-of-actions of drugs. Here, we introduce comparative approach to infer drug target proteins more accurately using two compendiums of chemical-genetic profiles from the budding yeast S. cerevisiae and the fission yeast Schizosaccharomyces pombe. For the first time, we established DNA-chip based growth defect measurement of genome-wide deletion strains of S. pombe, and then applied 47 drugs to the pooled heterozygous deletion strains to generate chemical-genetic profiles in S. pombe. In our approach, putative drug targets were inferred from strains hypersensitive to given drugs by analyzing S. pombe and S. cerevisiae compendiums. Notably, many evidences in the literature revealed that the inferred target genes of fungicide and bactericide identified by such comparative approach are in fact the direct targets. Furthermore, by filtering out the genes with no essentiality, the multi-drug sensitivity genes, and the genes with less eukaryotic conservation, we created a set of drug target gene candidates that are expected to be directly affected by a given drug in human cells. Our study demonstrated that it is highly beneficial to construct the multiple compendiums of chemical genetic profiles using many different species. The fission yeast chemical-genetic compendium is available at (http://pombe.kaist.ac.kr/compendium)

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

    Directory of Open Access Journals (Sweden)

    Kazuhiro Hayashi

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

  2. A novel genetic screen implicates Elm1 in the inactivation of the yeast transcription factor SBF.

    Directory of Open Access Journals (Sweden)

    Emily N Manderson

    Full Text Available BACKGROUND: Despite extensive large scale analyses of expression and protein-protein interactions (PPI in the model organism Saccharomyces cerevisiae, over a thousand yeast genes remain uncharacterized. We have developed a novel strategy in yeast that directly combines genetics with proteomics in the same screen to assign function to proteins based on the observation of genetic perturbations of sentinel protein interactions (GePPI. As proof of principle of the GePPI screen, we applied it to identify proteins involved in the regulation of an important yeast cell cycle transcription factor, SBF that activates gene expression during G1 and S phase. METHODOLOGY/PRINCIPLE FINDINGS: The principle of GePPI is that if a protein is involved in a pathway of interest, deletion of the corresponding gene will result in perturbation of sentinel PPIs that report on the activity of the pathway. We created a fluorescent protein-fragment complementation assay (PCA to detect the interaction between Cdc28 and Swi4, which leads to the inactivation of SBF. The PCA signal was quantified by microscopy and image analysis in deletion strains corresponding to 25 candidate genes that are periodically expressed during the cell cycle and are substrates of Cdc28. We showed that the serine-threonine kinase Elm1 plays a role in the inactivation of SBF and that phosphorylation of Elm1 by Cdc28 may be a mechanism to inactivate Elm1 upon completion of mitosis. CONCLUSIONS/SIGNIFICANCE: Our findings demonstrate that GePPI is an effective strategy to directly link proteins of known or unknown function to a specific biological pathway of interest. The ease in generating PCA assays for any protein interaction and the availability of the yeast deletion strain collection allows GePPI to be applied to any cellular network. In addition, the high degree of conservation between yeast and mammalian proteins and pathways suggest GePPI could be used to generate insight into human disease.

  3. Human Adenine Nucleotide Translocase (ANT) Modulators Identified by High-Throughput Screening of Transgenic Yeast.

    Science.gov (United States)

    Zhang, Yujian; Tian, Defeng; Matsuyama, Hironori; Hamazaki, Takashi; Shiratsuchi, Takayuki; Terada, Naohiro; Hook, Derek J; Walters, Michael A; Georg, Gunda I; Hawkinson, Jon E

    2016-04-01

    Transport of ADP and ATP across mitochondria is one of the primary points of regulation to maintain cellular energy homeostasis. This process is mainly mediated by adenine nucleotide translocase (ANT) located on the mitochondrial inner membrane. There are four human ANT isoforms, each having a unique tissue-specific expression pattern and biological function, highlighting their potential as drug targets for diverse clinical indications, including male contraception and cancer. In this study, we present a novel yeast-based high-throughput screening (HTS) strategy to identify compounds inhibiting the function of ANT. Yeast strains generated by deletion of endogenous proteins with ANT activity followed by insertion of individual human ANT isoforms are sensitive to cell-permeable ANT inhibitors, which reduce proliferation. Screening hits identified in the yeast proliferation assay were characterized in ADP/ATP exchange assays employing recombinant ANT isoforms expressed in isolated yeast mitochondria and Lactococcus lactis as well as by oxygen consumption rate in mammalian cells. Using this approach, closantel and CD437 were identified as broad-spectrum ANT inhibitors, whereas leelamine was found to be a modulator of ANT function. This yeast "knock-out/knock-in" screening strategy is applicable to a broad range of essential molecular targets that are required for yeast survival. © 2016 Society for Laboratory Automation and Screening.

  4. Extension of Yeast Chronological Lifespan by Methylamine

    NARCIS (Netherlands)

    Kumar, Sanjeev; Lefevre, Sophie D.; Veenhuis, Marten; van der Klei, Ida J.

    2012-01-01

    Background: Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast

  5. Wine yeast sirtuins and Gcn5p control aging and metabolism in a natural growth medium.

    Science.gov (United States)

    Orozco, Helena; Matallana, Emilia; Aranda, Agustín

    2012-05-01

    Grape juice fermentation by wine yeast is an interesting model to understand aging under conditions closer to those in nature. Grape juice is rich in sugars and, unlike laboratory conditions, the limiting factor for yeast growth is nitrogen. We tested the effect of deleting sirtuins and several acetyltransferases to find that the role of many of these proteins during grape juice fermentation is the opposite to that under standard laboratory aging conditions using synthetic complete media. For instance, SIR2 deletion extends maximum chronological lifespan in wine yeasts grown under laboratory conditions, but shortens it in winemaking. Deletions of sirtuin HST2 and acetyltransferase GCN5 have the opposite effect to SIR2 mutation in both media. Acetic acid, a well known pro-aging compound in laboratory conditions, does not play a determinant role on aging during wine fermentation. We discovered that gcn5Δ mutant strain displays strongly increased aldehyde dehydrogenase Ald6p activity, caused by blocking of Ald6p degradation by autophagy under nitrogen limitation conditions, leading to acetic acid accumulation. We describe how nitrogen limitation and TOR inhibition extend the chronological lifespan under winemaking conditions and how the TOR-dependent control of aging partially depends on the Gcn5p function. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  6. Polyglutamine toxicity in yeast induces metabolic alterations and mitochondrial defects

    KAUST Repository

    Papsdorf, Katharina

    2015-09-03

    Background Protein aggregation and its pathological effects are the major cause of several neurodegenerative diseases. In Huntington’s disease an elongated stretch of polyglutamines within the protein Huntingtin leads to increased aggregation propensity. This induces cellular defects, culminating in neuronal loss, but the connection between aggregation and toxicity remains to be established. Results To uncover cellular pathways relevant for intoxication we used genome-wide analyses in a yeast model system and identify fourteen genes that, if deleted, result in higher polyglutamine toxicity. Several of these genes, like UGO1, ATP15 and NFU1 encode mitochondrial proteins, implying that a challenged mitochondrial system may become dysfunctional during polyglutamine intoxication. We further employed microarrays to decipher the transcriptional response upon polyglutamine intoxication, which exposes an upregulation of genes involved in sulfur and iron metabolism and mitochondrial Fe-S cluster formation. Indeed, we find that in vivo iron concentrations are misbalanced and observe a reduction in the activity of the prominent Fe-S cluster containing protein aconitase. Like in other yeast strains with impaired mitochondria, non-fermentative growth is impossible after intoxication with the polyglutamine protein. NMR-based metabolic analyses reveal that mitochondrial metabolism is reduced, leading to accumulation of metabolic intermediates in polyglutamine-intoxicated cells. Conclusion These data show that damages to the mitochondrial system occur in polyglutamine intoxicated yeast cells and suggest an intricate connection between polyglutamine-induced toxicity, mitochondrial functionality and iron homeostasis in this model system.

  7. The propeptide of yeast cathepsin D inhibits programmed necrosis.

    Science.gov (United States)

    Carmona-Gutiérrez, D; Bauer, M A; Ring, J; Knauer, H; Eisenberg, T; Büttner, S; Ruckenstuhl, C; Reisenbichler, A; Magnes, C; Rechberger, G N; Birner-Gruenberger, R; Jungwirth, H; Fröhlich, K-U; Sinner, F; Kroemer, G; Madeo, F

    2011-05-19

    The lysosomal endoprotease cathepsin D (CatD) is an essential player in general protein turnover and specific peptide processing. CatD-deficiency is associated with neurodegenerative diseases, whereas elevated CatD levels correlate with tumor malignancy and cancer cell survival. Here, we show that the CatD ortholog of the budding yeast Saccharomyces cerevisiae (Pep4p) harbors a dual cytoprotective function, composed of an anti-apoptotic part, conferred by its proteolytic capacity, and an anti-necrotic part, which resides in the protein's proteolytically inactive propeptide. Thus, deletion of PEP4 resulted in both apoptotic and necrotic cell death during chronological aging. Conversely, prolonged overexpression of Pep4p extended chronological lifespan specifically through the protein's anti-necrotic function. This function, which triggered histone hypoacetylation, was dependent on polyamine biosynthesis and was exerted via enhanced intracellular levels of putrescine, spermidine and its precursor S-adenosyl-methionine. Altogether, these data discriminate two pro-survival functions of yeast CatD and provide first insight into the physiological regulation of programmed necrosis in yeast.

  8. 1p36 deletion syndrome: an update

    Directory of Open Access Journals (Sweden)

    Jordan VK

    2015-08-01

    Full Text Available Valerie K Jordan,1 Hitisha P Zaveri,2 Daryl A Scott1,2 1Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA Abstract: Deletions of chromosome 1p36 affect approximately 1 in 5,000 newborns and are the most common terminal deletions in humans. Medical problems commonly caused by terminal deletions of 1p36 include developmental delay, intellectual disability, seizures, vision problems, hearing loss, short stature, distinctive facial features, brain anomalies, orofacial clefting, congenital heart defects, cardiomyopathy, and renal anomalies. Although 1p36 deletion syndrome is considered clinically recognizable, there is significant phenotypic variation among affected individuals. This variation is due, at least in part, to the genetic heterogeneity seen in 1p36 deletions which include terminal and interstitial deletions of varying lengths located throughout the 30 Mb of DNA that comprise chromosome 1p36. Array-based copy number variant analysis can easily identify genomic regions of 1p36 that are deleted in an affected individual. However, predicting the phenotype of an individual based solely on the location and extent of their 1p36 deletion remains a challenge since most of the genes that contribute to 1p36-related phenotypes have yet to be identified. In addition, haploinsufficiency of more than one gene may contribute to some phenotypes. In this article, we review recent successes in the effort to map and identify the genes and genomic regions that contribute to specific 1p36-related phenotypes. In particular, we highlight evidence implicating MMP23B, GABRD, SKI, PRDM16, KCNAB2, RERE, UBE4B, CASZ1, PDPN, SPEN, ECE1, HSPG2, and LUZP1 in various 1p36 deletion phenotypes. Keywords: chromosome 1p36, chromosome deletion, 1p36 deletion syndrome, monosomy 1p36

  9. Genetic basis of metabolome variation in yeast.

    Directory of Open Access Journals (Sweden)

    Jeffrey S Breunig

    2014-03-01

    Full Text Available Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

  10. Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN system.

    Directory of Open Access Journals (Sweden)

    Axel Hausmann

    Full Text Available BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN system of BOLD (Barcode of Life Datasystems, a method that supports automated, rapid species delineation and identification. METHODOLOGY/PRINCIPAL FINDINGS: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88% in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93% were found to possess diagnostic barcode sequences at the European level while only three species pairs (3% were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads shared BINs, while specimens from the remaining species (18% were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed

  11. Bartender: a fast and accurate clustering algorithm to count barcode reads.

    Science.gov (United States)

    Zhao, Lu; Liu, Zhimin; Levy, Sasha F; Wu, Song

    2017-10-23

    Barcode sequencing (bar-seq) is a high-throughput, and cost effective method to assay large numbers of cell lineages or genotypes in complex cell pools. Because of its advantages, applications for bar-seq are quickly growing - from using neutral random barcodes to study the evolution of microbes or cancer, to using pseudo-barcodes, such as shRNAs or sgRNAs to simultaneously screen large numbers of cell perturbations. However, the computational pipelines for bar-seq clustering are not well developed. Available methods often yield a high frequency of under-clustering artifacts that result in spurious barcodes, or over-clustering artifacts that group distinct barcodes together. Here, we developed Bartender, an accurate clustering algorithm to detect barcodes and their abundances from raw next-generation sequencing data. In contrast with existing methods that cluster based on sequence similarity alone, Bartender uses a modified two-sample proportion test that also considers cluster size. This modification results in higher accuracy and lower rates of under- and over-clustering artifacts. Additionally, Bartender includes unique molecular identifier (UMI) handling and a "multiple time point" mode that matches barcode clusters between different clustering runs for seamless handling of time course data. Bartender is a set of simple-to-use command line tools that can be performed on a laptop at comparable run times to existing methods. Bartender is available at no charge for non-commercial use at https://github.com/LaoZZZZZ/bartender-1.1. song.wu@stonybrook.edu, sasha.levy@stonybrook.edu. Supplementary data are available at Bioinformatics online.

  12. Identification of ungulates used in a traditional Chinese medicine with DNA barcoding technology.

    Science.gov (United States)

    Chen, Jing; Jiang, Zhigang; Li, Chunlin; Ping, Xiaoge; Cui, Shaopeng; Tang, Songhua; Chu, Hongjun; Liu, Binwan

    2015-05-01

    Horns of Saiga antelope (Saiga tatarica) have always been an ingredient of "Lingyangjiao", a traditional Chinese medicine (TCM). Persistent hunting for Saiga antelope has already threatened the survival of critical endangered populations in wild. To control the growing pressure, CITES and Chinese government have legislated for monitoring the trade of Saiga horns. However, similar ungulate horns are difficult to identify by their morphological characteristics, which has impeded the law enforcement. Besides Saiga antelope, other seven ungulate species which have similar horns are also sold and marked as "Lingyangjiao" in TCM markets to offset shortage of Saiga antelope horns. Such species are Gazella subgutturosa, Pantholops hodgsonii, Procapra picticaudata, Procapra gutturosa, Procapra przewalskii, Capra hircus, and Ovis aries. Our study aimed at implementing DNA barcoding technology to diagnose Saiga horns and the substitutes. We successfully extracted genomic DNA from horn samples. We recovered COI sequences of 644 bp with specific primers and 349 bp with nested PCR primers designed for degraded horn samples. The mean interspecific genetic distance of data set of the 644-bp full barcodes and the 349-bp mini-barcodes was 14.96% and 15.38%, respectively, and the mean intraspecific distance was 0.24% and 0.20%, respectively. Each species formed independent clades in neighbor-joining (NJ) phylogenetic tree of the two data sets with >99% supporting values, except P. gutturosa and P. przewalskii. The deep genetic distances gap and clear species clades in NJ tree of either full barcodes or mini-barcodes suggest that barcoding technology is an effective tool to diagnose Saiga horns and their substitutes. Barcoding diagnosis protocol developed here will simplify diagnosis of "Lingyangjiao" species and will facilitate conservation of endangered ungulates involved in TCM "Lingyangjiao" markets, especially the Saiga antelope.

  13. An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

    Science.gov (United States)

    Chuang, Li-Yeh; Lin, Yu-Da; Chang, Hsueh-Wei; Yang, Cheng-Hong

    2012-01-01

    Possible single nucleotide polymorphism (SNP) interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO) method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions. In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls) associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR) values (1.268 to 0.848; pPSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; pPSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n = 3∼10) are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification. Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.

  14. The Effects of Bar-coding Technology on Medication Errors: A Systematic Literature Review.

    Science.gov (United States)

    Hutton, Kevin; Ding, Qian; Wellman, Gregory

    2017-02-24

    The bar-coding technology adoptions have risen drastically in U.S. health systems in the past decade. However, few studies have addressed the impact of bar-coding technology with strong prospective methodologies and the research, which has been conducted from both in-pharmacy and bedside implementations. This systematic literature review is to examine the effectiveness of bar-coding technology on preventing medication errors and what types of medication errors may be prevented in the hospital setting. A systematic search of databases was performed from 1998 to December 2016. Studies measuring the effect of bar-coding technology on medication errors were included in a full-text review. Studies with the outcomes other than medication errors such as efficiency or workarounds were excluded. The outcomes were measured and findings were summarized for each retained study. A total of 2603 articles were initially identified and 10 studies, which used prospective before-and-after study design, were fully reviewed in this article. Of the 10 included studies, 9 took place in the United States, whereas the remaining was conducted in the United Kingdom. One research article focused on bar-coding implementation in a pharmacy setting, whereas the other 9 focused on bar coding within patient care areas. All 10 studies showed overall positive effects associated with bar-coding implementation. The results of this review show that bar-coding technology may reduce medication errors in hospital settings, particularly on preventing targeted wrong dose, wrong drug, wrong patient, unauthorized drug, and wrong route errors.

  15. The unfolded protein response has a protective role in yeast models of classic galactosemia

    Directory of Open Access Journals (Sweden)

    Evandro A. De-Souza

    2014-01-01

    Full Text Available Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast, which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.

  16. Biotechnical Microbiology, yeast and bacteria

    DEFF Research Database (Denmark)

    Villadsen, Ingrid Stampe

    1999-01-01

    This section contains the following single lecture notes: Eukaryotic Cell Biology. Kingdom Fungi. Cell Division. Meiosis and Recombination. Genetics of Yeast. Organisation of the Chromosome. Organization and genetics of the mitochondrial Geneme. Regulatio of Gene Expression. Intracellular Compart...

  17. Probiotic Yeasts and Their Properties

    Directory of Open Access Journals (Sweden)

    Hatice Yıldıran

    2017-10-01

    Full Text Available Probiotics are a group of organism those confer health benefit to consumers. There are lots of studies about health benefits of probiotic treatments. The more commonly used probiotic bacteria are bifidobacteria and lactic acid bacteria, such as lactobacilli, lactococci and streptococci. Microorganisms that are probiotic to humans also include yeasts, bacilli and enterococci. Probiotic yeasts have become a field of interest to scientists in recent years. Several previous studies showed that members of Saccharomyces genus can possess anti-bacterial and probiotic properties. Saccharomyces boulardii is non-pathogenic yeast used for many years as a probiotic agent to prevent or treat a variety of human gastrointestinal disorders. S. boulardii is commonly used in lyophilized form especially in the pharmaceutical industry. In this review, information about the probiotics, properties of probiotic yeasts, their usage fields is provided and the results of researches in this area has been presented.

  18. 78 FR 68823 - Procurement List Deletions

    Science.gov (United States)

    2013-11-15

    ...'Day Act (41 U.S.C. 8501-8506) in connection with the products and services deleted from the... Center, Chicago, IL. Service Type/Location: Janitorial/Custodial Service, Gamelin USARC, 10 Asylum Road... COMMITTEE FOR PURCHASE FROM PEOPLE WHO ARE BLIND OR SEVERELY DISABLED Procurement List Deletions...

  19. DNA barcode data accurately assign higher spider taxa

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    Jonathan A. Coddington

    2016-07-01

    Full Text Available The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%. Accurate assignment of higher taxa (PIdent above which errors totaled less than 5% occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However

  20. Single nucleotide polymorphism barcoding of cytochrome c oxidase I sequences for discriminating 17 species of Columbidae by decision tree algorithm.

    Science.gov (United States)

    Yang, Cheng-Hong; Wu, Kuo-Chuan; Dahms, Hans-Uwe; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2017-07-01

    DNA barcodes are widely used in taxonomy, systematics, species identification, food safety, and forensic science. Most of the conventional DNA barcode sequences contain the whole information of a given barcoding gene. Most of the sequence information does not vary and is uninformative for a given group of taxa within a monophylum. We suggest here a method that reduces the amount of noninformative nucleotides in a given barcoding sequence of a major taxon, like the prokaryotes, or eukaryotic animals, plants, or fungi. The actual differences in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, provide a tool for developing a rapid, reliable, and high-throughput assay for the discrimination between known species. Here, we investigated SNPs as robust markers of genetic variation for identifying different pigeon species based on available cytochrome c oxidase I (COI) data. We propose here a decision tree-based SNP barcoding (DTSB) algorithm where SNP patterns are selected from the DNA barcoding sequence of several evolutionarily related species in order to identify a single species with pigeons as an example. This approach can make use of any established barcoding system. We here firstly used as an example the mitochondrial gene COI information of 17 pigeon species (Columbidae, Aves) using DTSB after sequence trimming and alignment. SNPs were chosen which followed the rule of decision tree and species-specific SNP barcodes. The shortest barcode of about 11 bp was then generated for discriminating 17 pigeon species using the DTSB method. This method provides a sequence alignment and tree decision approach to parsimoniously assign a unique and shortest SNP barcode for any known species of a chosen monophyletic taxon where a barcoding sequence is available.

  1. Seven gene deletions in seven days

    DEFF Research Database (Denmark)

    Ingemann Jensen, Sheila; Lennen, Rebecca; Herrgard, Markus

    2015-01-01

    genes and a rhamnose inducible flippase recombinase was constructed to facilitate fast marker-free deletions. To further speed up the procedure, we integrated the arabinose inducible lambda Red recombineering genes and the rhamnose inducible FLP into the genome of E. coli K-12 MG1655. This system...... in which four to seven genes were deleted in E. coli W and E. coli K-12. The growth rate of an E. coli K-12 quintuple deletion strain was significantly improved in the presence of high concentrations of acetate and NaCl. In conclusion, we have generated a method that enables efficient and simultaneous...... deletion of multiple genes in several E. coli variants. The method enables deletion of up to seven genes in as little as seven days....

  2. Probabilistic cloning and deleting of quantum states

    International Nuclear Information System (INIS)

    Feng Yuan; Zhang Shengyu; Ying Mingsheng

    2002-01-01

    We construct a probabilistic cloning and deleting machine which, taking several copies of an input quantum state, can output a linear superposition of multiple cloning and deleting states. Since the machine can perform cloning and deleting in a single unitary evolution, the probabilistic cloning and other cloning machines proposed in the previous literature can be thought of as special cases of our machine. A sufficient and necessary condition for successful cloning and deleting is presented, and it requires that the copies of an arbitrarily presumed number of the input states are linearly independent. This simply generalizes some results for cloning. We also derive an upper bound for the success probability of the cloning and deleting machine

  3. Identification and characterization of major lipid particle proteins of the yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Athenstaedt, K; Zweytick, D; Jandrositz, A; Kohlwein, S D; Daum, G

    1999-10-01

    Lipid particles of the yeast Saccharomyces cerevisiae were isolated at high purity, and their proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Major lipid particle proteins were identified by mass spectrometric analysis, and the corresponding open reading frames (ORFs) were deduced. In silicio analysis revealed that all lipid particle proteins contain several hydrophobic domains but none or only few (hypothetical) transmembrane spanning regions. All lipid particle proteins identified by function so far, such as Erg1p, Erg6p, and Erg7p (ergosterol biosynthesis) and Faa1p, Faa4p, and Fat1p (fatty acid metabolism), are involved in lipid metabolism. Based on sequence homology, another group of three lipid particle proteins may be involved in lipid degradation. To examine whether lipid particle proteins of unknown function are also involved in lipid synthesis, mutants with deletions of the respective ORFs were constructed and subjected to systematic lipid analysis. Deletion of YDL193w resulted in a lethal phenotype which could not be suppressed by supplementation with ergosterol or fatty acids. Other deletion mutants were viable under standard conditions. Strains with YBR177c, YMR313c, and YKL140w deleted exhibited phospholipid and/or neutral lipid patterns that were different from the wild-type strain and thus may be further candidate ORFs involved in yeast lipid metabolism.

  4. Modeling Huntington disease in yeast

    Science.gov (United States)

    Mason, Robert P

    2011-01-01

    Yeast have been extensively used to model aspects of protein folding diseases, yielding novel mechanistic insights and identifying promising candidate therapeutic targets. In particular, the neurodegenerative disorder Huntington disease (HD), which is caused by the abnormal expansion of a polyglutamine tract in the huntingtin (htt) protein, has been widely studied in yeast. This work has led to the identification of several promising therapeutic targets and compounds that have been validated in mammalian cells, Drosophila and rodent models of HD. Here we discuss the development of yeast models of mutant htt toxicity and misfolding, as well as the mechanistic insights gleaned from this simple model. The role of yeast prions in the toxicity/misfolding of mutant htt is also highlighted. Furthermore, we provide an overview of the application of HD yeast models in both genetic and chemical screens, and the fruitful results obtained from these approaches. Finally, we discuss the future of yeast in neurodegenerative research, in the context of HD and other diseases. PMID:22052350

  5. Oral yeast colonization throughout pregnancy.

    Science.gov (United States)

    Rio, R; Simões-Silva, L; Garro, S; Silva, M-J; Azevedo, Á; Sampaio-Maia, B

    2017-03-01

    Recent studies suggest that placenta may harbour a unique microbiome that may have origin in maternal oral microbiome. Although the major physiological and hormonal adjustments observed in pregnant women lead to biochemical and microbiological modifications of the oral environment, very few studies evaluated the changes suffered by the oral microbiota throughout pregnancy. So, the aim of our study was to evaluate oral yeast colonization throughout pregnancy and to compare it with non-pregnant women. The oral yeast colonization was assessed in saliva of 30 pregnant and non-pregnant women longitudinally over a 6-months period. Demographic information was collected, a non-invasive intra-oral examination was performed and saliva flow and pH were determined. Pregnant and non-pregnant groups were similar regarding age and level of education. Saliva flow rate did not differ, but saliva pH was lower in pregnant than in non-pregnant women. Oral yeast prevalence was higher in pregnant than in non-pregnant women, either in the first or in the third trimester, but did not attain statistical significance. In individuals colonized with yeast, the total yeast quantification (Log10CFU/mL) increase from the 1st to the 3rd trimester in pregnant women, but not in non-pregnant women. Pregnancy may favour oral yeast growth that may be associated with an acidic oral environment.

  6. Cis and trans interactions between genes encoding PAF1 complex and ESCRT machinery components in yeast.

    Science.gov (United States)

    Rodrigues, Joana; Lydall, David

    2018-03-22

    Saccharomyces cerevisiae is a commonly used model organism for understanding eukaryotic gene function. However, the close proximity between yeast genes can complicate the interpretation of yeast genetic data, particularly high-throughput data. In this study, we examined the interplay between genes encoding components of the PAF1 complex and VPS36, the gene located next to CDC73 on chromosome XII. The PAF1 complex (Cdc73, Paf1, Ctr9, Leo1, and Rtf1, in yeast) affects RNA levels by affecting transcription, histone modifications, and post-transcriptional RNA processing. The human PAF1 complex is linked to cancer, and in yeast, it has been reported to play a role in telomere biology. Vps36, part of the ESCRT-II complex, is involved in sorting proteins for vacuolar/lysosomal degradation. We document a complex set of genetic interactions, which include an adjacent gene effect between CDC73 and VPS36 and synthetic sickness between vps36Δ and cdc73Δ, paf1Δ, or ctr9Δ. Importantly, paf1Δ and ctr9Δ are synthetically lethal with deletions of other components of the ESCRT-II (SNF8 and VPS25), ESCRT-I (STP22), or ESCRT-III (SNF7) complexes. We found that RNA levels of VPS36, but not other ESCRT components, are positively regulated by all components of the PAF1 complex. Finally, we show that deletion of ESCRT components decreases the telomere length in the S288C yeast genetic background, but not in the W303 background. Together, our results outline complex interactions, in cis and in trans, between genes encoding PAF1 and ESCRT-II complex components that affect telomere function and cell viability in yeast.

  7. Deletion of the mitochondrial superoxide dismutase sod-2 extends lifespan in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Jeremy M Van Raamsdonk

    2009-02-01

    Full Text Available The oxidative stress theory of aging postulates that aging results from the accumulation of molecular damage caused by reactive oxygen species (ROS generated during normal metabolism. Superoxide dismutases (SODs counteract this process by detoxifying superoxide. It has previously been shown that elimination of either cytoplasmic or mitochondrial SOD in yeast, flies, and mice results in decreased lifespan. In this experiment, we examine the effect of eliminating each of the five individual sod genes present in Caenorhabditis elegans. In contrast to what is observed in other model organisms, none of the sod deletion mutants shows decreased lifespan compared to wild-type worms, despite a clear increase in sensitivity to paraquat- and juglone-induced oxidative stress. In fact, even mutants lacking combinations of two or three sod genes survive at least as long as wild-type worms. Examination of gene expression in these mutants reveals mild compensatory up-regulation of other sod genes. Interestingly, we find that sod-2 mutants are long-lived despite a significant increase in oxidatively damaged proteins. Testing the effect of sod-2 deletion on known pathways of lifespan extension reveals a clear interaction with genes that affect mitochondrial function: sod-2 deletion markedly increases lifespan in clk-1 worms while clearly decreasing the lifespan of isp-1 worms. Combined with the mitochondrial localization of SOD-2 and the fact that sod-2 mutant worms exhibit phenotypes that are characteristic of long-lived mitochondrial mutants-including slow development, low brood size, and slow defecation-this suggests that deletion of sod-2 extends lifespan through a similar mechanism. This conclusion is supported by our demonstration of decreased oxygen consumption in sod-2 mutant worms. Overall, we show that increased oxidative stress caused by deletion of sod genes does not result in decreased lifespan in C. elegans and that deletion of sod-2 extends worm

  8. Metabolic regulation of yeast

    Science.gov (United States)

    Fiechter, A.

    1982-12-01

    Metabolic regulation which is based on endogeneous and exogeneous process variables which may act constantly or time dependently on the living cell is discussed. The observed phenomena of the regulation are the result of physical, chemical, and biological parameters. These parameters are identified. Ethanol is accumulated as an intermediate product and the synthesis of biomass is reduced. This regulatory effect of glucose is used for the aerobic production of ethanol. Very high production rates are thereby obtained. Understanding of the regulation mechanism of the glucose effect has improved. In addition to catabolite repression, several other mechanisms of enzyme regulation have been described, that are mostly governed by exogeneous factors. Glucose also affects the control of respiration in a third class of yeasts which are unable to make use of ethanol as a substrate for growth. This is due to the lack of any anaplerotic activity. As a consequence, diauxic growth behavior is reduced to a one-stage growth with a drastically reduced cell yield. The pulse chemostat technique, a systematic approach for medium design is developed and medium supplements that are essential for metabolic control are identified.

  9. An improved PSO algorithm for generating protective SNP barcodes in breast cancer.

    Directory of Open Access Journals (Sweden)

    Li-Yeh Chuang

    Full Text Available BACKGROUND: Possible single nucleotide polymorphism (SNP interactions in breast cancer are usually not investigated in genome-wide association studies. Previously, we proposed a particle swarm optimization (PSO method to compute these kinds of SNP interactions. However, this PSO does not guarantee to find the best result in every implement, especially when high-dimensional data is investigated for SNP-SNP interactions. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we propose IPSO algorithm to improve the reliability of PSO for the identification of the best protective SNP barcodes (SNP combinations and genotypes with maximum difference between cases and controls associated with breast cancer. SNP barcodes containing different numbers of SNPs were computed. The top five SNP barcode results are retained for computing the next SNP barcode with a one-SNP-increase for each processing step. Based on the simulated data for 23 SNPs of six steroid hormone metabolisms and signalling-related genes, the performance of our proposed IPSO algorithm is evaluated. Among 23 SNPs, 13 SNPs displayed significant odds ratio (OR values (1.268 to 0.848; p<0.05 for breast cancer. Based on IPSO algorithm, the jointed effect in terms of SNP barcodes with two to seven SNPs show significantly decreasing OR values (0.84 to 0.57; p<0.05 to 0.001. Using PSO algorithm, two to four SNPs show significantly decreasing OR values (0.84 to 0.77; p<0.05 to 0.001. Based on the results of 20 simulations, medians of the maximum differences for each SNP barcode generated by IPSO are higher than by PSO. The interquartile ranges of the boxplot, as well as the upper and lower hinges for each n-SNP barcode (n = 3∼10 are more narrow in IPSO than in PSO, suggesting that IPSO is highly reliable for SNP barcode identification. CONCLUSIONS/SIGNIFICANCE: Overall, the proposed IPSO algorithm is robust to provide exact identification of the best protective SNP barcodes for breast cancer.

  10. Application of DNA barcodes in wildlife conservation in Tropical East Asia.

    Science.gov (United States)

    Wilson, John-James; Sing, Kong-Wah; Lee, Ping-Shin; Wee, Alison K S

    2016-10-01

    Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced. © 2016 Society for Conservation Biology.

  11. Genetic algorithm-generated SNP barcodes of the mitochondrial D-loop for chronic dialysis susceptibility.

    Science.gov (United States)

    Chen, Jin-Bor; Chuang, Li-Yeh; Lin, Yu-Da; Liou, Chia-Wei; Lin, Tsu-Kung; Lee, Wen-Chin; Cheng, Ben-Chung; Chang, Hsueh-Wei; Yang, Cheng-Hong

    2014-06-01

    Single nucleotide polymorphism (SNP) interaction analysis can simultaneously evaluate the complex SNP interactions present in complex diseases. However, it is less commonly applied to evaluate the predisposition of chronic dialysis and its computational analysis remains challenging. In this study, we aimed to improve the analysis of SNP-SNP interactions within the mitochondrial D-loop in chronic dialysis. The SNP-SNP interactions between 77 reported SNPs within the mitochondrial D-loop in chronic dialysis study were evaluated in terms of SNP barcodes (different SNP combinations with their corresponding genotypes). We propose a genetic algorithm (GA) to generate SNP barcodes. The χ(2) values were then calculated by the occurrences of the specific SNP barcodes and their non-specific combinations between cases and controls. Each SNP barcode (2- to 7-SNP) with the highest value in the χ(2) test was regarded as the best SNP barcode (11.304 to 23.310; p algorithm to address the SNP-SNP interactions and demonstrated that many non-significant SNPs within the mitochondrial D-loop may play a role in jointed effects to chronic dialysis susceptibility.

  12. Barcoding of biting midges in the genus Culicoides: a tool for species determination.

    Science.gov (United States)

    Ander, M; Troell, K; Chirico, J

    2013-09-01

    Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) are insect vectors of economically important veterinary diseases such as African horse sickness virus and bluetongue virus. However, the identification of Culicoides based on morphological features is difficult. The sequencing of mitochondrial cytochrome oxidase subunit I (COI), referred to as DNA barcoding, has been proposed as a tool for rapid identification to species. Hence, a study was undertaken to establish DNA barcodes for all morphologically determined Culicoides species in Swedish collections. In total, 237 specimens of Culicoides representing 37 morphologically distinct species were used. The barcoding generated 37 supported clusters, 31 of which were in agreement with the morphological determination. However, two pairs of closely related species could not be separated using the DNA barcode approach. Moreover, Culicoides obsoletus Meigen and Culicoides newsteadi Austen showed relatively deep intraspecific divergence (more than 10 times the average), which led to the creation of two cryptic species within each of C. obsoletus and C. newsteadi. The use of COI barcodes as a tool for the species identification of biting midges can differentiate 95% of species studied. Identification of some closely related species should employ a less conserved region, such as a ribosomal internal transcribed spacer. © 2012 The Royal Entomological Society.

  13. Machine Learned Replacement of N-Labels for Basecalled Sequences in DNA Barcoding.

    Science.gov (United States)

    Ma, Eddie Y T; Ratnasingham, Sujeevan; Kremer, Stefan C

    2018-01-01

    This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label. KB must also rate the replacement with quality value of in the additional read. Corrections are only available during system training. Developing the system, nearly 850,000 N-labels are obtained from Barcode of Life Datasystems, the premier database of genetic markers called DNA Barcodes. Increasing the number of correct bases improves reference sequence reliability, increases sequence identification accuracy, and assures analysis correctness. Keeping with barcoding standards, our system maintains an error rate of percent. Our system only applies corrections when it estimates low rate of error. Tested on this data, our automation selects and recovers: 79 percent of N-labels from COI (animal barcode); 80 percent from matK and rbcL (plant barcodes); and 58 percent from non-protein-coding sequences (across eukaryotes).

  14. Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters.

    Directory of Open Access Journals (Sweden)

    Nikos Andreakis

    Full Text Available Marine fungi are an understudied group of eukaryotic microorganisms characterized by unresolved genealogies and unstable classification. Whereas DNA barcoding via the nuclear ribosomal internal transcribed spacer (ITS provides a robust and rapid tool for fungal species delineation, accurate classification of fungi is often arduous given the large number of partial or unknown barcodes and misidentified isolates deposited in public databases. This situation is perpetuated by a paucity of cultivable fungal strains available for phylogenetic research linked to these data sets. We analyze ITS barcodes produced from a subsample (290 of 1781 cultured isolates of marine-derived fungi in the Bioresources Library located at the Australian Institute of Marine Science (AIMS. Our analysis revealed high levels of under-explored fungal diversity. The majority of isolates were ascomycetes including representatives of the subclasses Eurotiomycetidae, Hypocreomycetidae, Sordariomycetidae, Pleosporomycetidae, Dothideomycetidae, Xylariomycetidae and Saccharomycetidae. The phylum Basidiomycota was represented by isolates affiliated with the genera Tritirachium and Tilletiopsis. BLAST searches revealed 26 unknown OTUs and 50 isolates corresponding to previously uncultured, unidentified fungal clones. This study makes a significant addition to the availability of barcoded, culturable marine-derived fungi for detailed future genomic and physiological studies. We also demonstrate the influence of commonly used alignment algorithms and genetic distance measures on the accuracy and comparability of estimating Operational Taxonomic Units (OTUs by the automatic barcode gap finder (ABGD method. Large scale biodiversity screening programs that combine datasets using algorithmic OTU delineation pipelines need to ensure compatible algorithms have been used because the algorithm matters.

  15. The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia.

    Directory of Open Access Journals (Sweden)

    Charles M Francis

    Full Text Available BACKGROUND: Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning. METHODOLOGY AND PRINCIPAL FINDINGS: DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized. CONCLUSIONS: DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning.

  16. A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library.

    Science.gov (United States)

    Lim, Voon-Ching; Ramli, Rosli; Bhassu, Subha; Wilson, John-James

    2017-01-01

    Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.

  17. Detection of tyrosine hydroxylase in dopaminergic neuron cell using gold nanoparticles-based barcode DNA.

    Science.gov (United States)

    An, Jeung Hee; Oh, Byung-Keun; Choi, Jeong Woo

    2013-04-01

    Tyrosine hydroxylase, the rate-limiting enzyme of catecholamine biosysthesis, is predominantly expressed in several cell groups within the brain, including the dopaminergic neurons of the substantia nigra and ventral tegmental area. We evaluated the efficacy of this protein-detection method in detecting tyrosine hydroxylase in normal and oxidative stress damaged dopaminergic cells. In this study, a coupling of DNA barcode and bead-based immnunoassay for detecting tyrosine hydroxylaser with PCR-like sensitivity is reported. The method relies on magnetic nanoparticles with antibodies and nanoparticles that are encoded with DNA and antibodies that can sandwich the target protein captured by the nanoparticle-bound antibodies. The aggregate sandwich structures are magnetically separated from solution, and treated to remove the conjugated barcode DNA. The DNA barcodes were identified by PCR analysis. The concentration of tyrosine hydroxylase in dopaminergic cell can be easily and rapidly detected using bio-barcode assay. The bio-barcode assay is a rapid and high-throughput screening tool to detect of neurotransmitter such as dopamine.

  18. Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

    Science.gov (United States)

    Dentinger, Bryn T. M.; Didukh, Maryna Y.; Moncalvo, Jean-Marc

    2011-01-01

    DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms. PMID:21966418

  19. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China.

    Science.gov (United States)

    Chen, Juan; Zhao, Jietang; Erickson, David L; Xia, Nianhe; Kress, W John

    2015-03-01

    The genus Curcuma L. is commonly used as spices, medicines, dyes and ornamentals. Owing to its economic significance and lack of clear-cut morphological differences between species, this genus is an ideal case for developing DNA barcodes. In this study, four chloroplast DNA regions (matK, rbcL, trnH-psbA and trnL-F) and one nuclear region (ITS2) were generated for 44 Curcuma species and five species from closely related genera, represented by 96 samples. PCR amplification success rate, intra- and inter-specific genetic distance variation and the correct identification percentage were taken into account to assess candidate barcode regions. PCR and sequence success rate were high in matK (89.7%), rbcL (100%), trnH-psbA (100%), trnL-F (95.7%) and ITS2 (82.6%) regions. The results further showed that four candidate chloroplast barcoding regions (matK, rbcL, trnH-psbA and trnL-F) yield no barcode gaps, indicating that the genus Curcuma represents a challenging group for DNA barcoding. The ITS2 region presented large interspecific variation and provided the highest correct identification rates (46.7%) based on BLASTClust method among the five regions. However, the ITS2 only provided 7.9% based on NJ tree method. An increase in discriminatory power needs the development of more variable markers. © 2014 John Wiley & Sons Ltd.

  20. DNA Barcode Analysis of Thrips (Thysanoptera Diversity in Pakistan Reveals Cryptic Species Complexes.

    Directory of Open Access Journals (Sweden)

    Romana Iftikhar

    Full Text Available Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27% at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%. BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci, and one predatory thrips (Aeolothrips intermedius showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

  1. Highlights of DNA Barcoding in identification of salient microorganisms like fungi.

    Science.gov (United States)

    Dulla, E L; Kathera, C; Gurijala, H K; Mallakuntla, T R; Srinivasan, P; Prasad, V; Mopati, R D; Jasti, P K

    2016-12-01

    Fungi, the second largest kingdom of eukaryotic life, are diverse and widespread. Fungi play a distinctive role in the production of different products on industrial scale, like fungal enzymes, antibiotics, fermented foods, etc., to give storage stability and improved health to meet major global challenges. To utilize algae perfectly for human needs, and to pave the way for getting a healthy relationship with fungi, it is important to identify them in a quick and robust manner with molecular-based identification system. So, there is a technique that aims to provide a well-organized method for species level identifications and to contribute powerfully to taxonomic and biodiversity research is DNA Barcoding. DNA Barcoding is generally achieved by the retrieval of a short DNA sequence - the 'barcode' - from a standard part of the genome and that barcode is then compared with a library of reference barcode sequences derived from individuals of known identity for identification. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  2. Experience and Compliance With Scanning Vaccines' Two-Dimensional Barcodes to Record Data.

    Science.gov (United States)

    Evanson, Heather V; Rodgers, Loren; Reed, Jenica; Daily, Ashley; Gerlach, Kenneth; Greene, Michael; Koeppl, Patrick; Cox, Regina; Williams, Warren

    2018-01-01

    Automated population of data into health information system fields offers the potential to increase efficiencies and save time. Increasingly, as two-dimensional barcoded vaccine products and barcode scanning technology become more widely available, manual recording of vaccine data can be reduced. This evaluation explores how often two-dimensional barcodes on vaccine vials and syringes were scanned and the perceived benefits and challenges reported by vaccine providers. Eighty-two facilities that administer vaccines completed the evaluation. Twenty-seven of those facilities provided records from vaccines administered between July 2014 and January 2015. Among the 63 179 two-dimensional barcoded vaccine administrations recorded, 12 408 (19%) were scanned. We received 116 user surveys from 63 facilities; using content analysis, we identified perceived benefits of scanning, workflow challenges, scanning challenges, and other challenges. The findings of this evaluation can guide health information system developers, vaccine manufacturers, and vaccine providers on how to remove potential barriers to using two-dimensional barcode scanning.

  3. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs

    Science.gov (United States)

    Sun, Shao’e; Li, Qi; Kong, Lingfeng; Yu, Hong; Zheng, Xiaodong; Yu, Ruihai; Dai, Lina; Sun, Yan; Chen, Jun; Liu, Jun; Ni, Lehai; Feng, Yanwei; Yu, Zhenzhen; Zou, Shanmei; Lin, Jiping

    2016-01-01

    This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes. PMID:27640675

  4. DNA Barcoding and Species Boundary Delimitation of Selected Species of Chinese Acridoidea (Orthoptera: Caelifera)

    Science.gov (United States)

    Huang, Jianhua; Zhang, Aibing; Mao, Shaoli; Huang, Yuan

    2013-01-01

    We tested the performance of DNA barcoding in Acridoidea and attempted to solve species boundary delimitation problems in selected groups using COI barcodes. Three analysis methods were applied to reconstruct the phylogeny. K2P distances were used to assess the overlap range between intraspecific variation and interspecific divergence. “Best match (BM)”, “best close match (BCM)”, “all species barcodes (ASB)” and “back-propagation neural networks (BP-based method)” were utilized to test the success rate of species identification. Phylogenetic species concept and network analysis were employed to delimitate the species boundary in eight selected species groups. The results demonstrated that the COI barcode region performed better in phylogenetic reconstruction at genus and species levels than at higher-levels, but showed a little improvement in resolving the higher-level relationships when the third base data or both first and third base data were excluded. Most overlaps and incorrect identifications may be due to imperfect taxonomy, indicating the critical role of taxonomic revision in DNA barcoding study. Species boundary delimitation confirmed the presence of oversplitting in six species groups and suggested that each group should be treated as a single species. PMID:24376533

  5. BOKP: A DNA Barcode Reference Library for Monitoring Herbal Drugs in the Korean Pharmacopeia

    Directory of Open Access Journals (Sweden)

    Jinxin Liu

    2017-12-01

    Full Text Available Herbal drug authentication is an important task in traditional medicine; however, it is challenged by the limitations of traditional authentication methods and the lack of trained experts. DNA barcoding is conspicuous in almost all areas of the biological sciences and has already been added to the British pharmacopeia and Chinese pharmacopeia for routine herbal drug authentication. However, DNA barcoding for the Korean pharmacopeia still requires significant improvements. Here, we present a DNA barcode reference library for herbal drugs in the Korean pharmacopeia and developed a species identification engine named KP-IDE to facilitate the adoption of this DNA reference library for the herbal drug authentication. Using taxonomy records, specimen records, sequence records, and reference records, KP-IDE can identify an unknown specimen. Currently, there are 6,777 taxonomy records, 1,054 specimen records, 30,744 sequence records (ITS2 and psbA-trnH and 285 reference records. Moreover, 27 herbal drug materials were collected from the Seoul Yangnyeongsi herbal medicine market to give an example for real herbal drugs authentications. Our study demonstrates the prospects of the DNA barcode reference library for the Korean pharmacopeia and provides future directions for the use of DNA barcoding for authenticating herbal drugs listed in other modern pharmacopeias.

  6. Authentication of Ginkgo biloba herbal dietary supplements using DNA barcoding.

    Science.gov (United States)

    Little, Damon P

    2014-09-01

    Ginkgo biloba L. (known as ginkgo or maidenhair tree) is a phylogenetically isolated, charismatic, gymnosperm tree. Herbal dietary supplements, prepared from G. biloba leaves, are consumed to boost cognitive capacity via improved blood perfusion and mitochondrial function. A novel DNA mini-barcode assay was designed and validated for the authentication of G. biloba in herbal dietary supplements (n = 22; sensitivity = 1.00, 95% CI = 0.59-1.00; specificity = 1.00, 95% CI = 0.64-1.00). This assay was further used to estimate the frequency of mislabeled ginkgo herbal dietary supplements on the market in the United States of America: DNA amenable to PCR could not be extracted from three (7.5%) of the 40 supplements sampled, 31 of 37 (83.8%) assayable supplements contained identifiable G. biloba DNA, and six supplements (16.2%) contained fillers without any detectable G. biloba DNA. It is hoped that this assay will be used by supplement manufacturers to ensure that their supplements contain G. biloba.

  7. Sushi barcoding in the UK: another kettle of fish

    Directory of Open Access Journals (Sweden)

    Sara G. Vandamme

    2016-03-01

    Full Text Available Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70% of fish species substitution. Based on indications that the European seafood retail sector may currently be under better control than its North American counterpart, here we investigated levels of seafood labelling accuracy in sushi bars and restaurants across England. We used the COI barcoding gene to screen samples of tuna, eel, and a variety of other products characterised by less visually distinctive ‘white flesh’. Moderate levels of substitution were found (10%, significantly lower than observed in North America, which lends support to the argument that public awareness, policy and governance of seafood labels is more effective in the European Union. Nevertheless, the results highlight that current labelling practice in UK restaurants lags behind the level of detail implemented in the retail sector, which hinders consumer choice, with potentially damaging economic, health and environmental consequences. Specifically, critically endangered species of tuna and eel continue to be sold without adequate information to consumers.

  8. Sushi barcoding in the UK: another kettle of fish.

    Science.gov (United States)

    Vandamme, Sara G; Griffiths, Andrew M; Taylor, Sasha-Ann; Di Muri, Cristina; Hankard, Elizabeth A; Towne, Jessica A; Watson, Mhairi; Mariani, Stefano

    2016-01-01

    Although the spread of sushi restaurants in the European Union and United States is a relatively new phenomenon, they have rapidly become among the most popular food services globally. Recent studies indicate that they can be associated with very high levels (>70%) of fish species substitution. Based on indications that the European seafood retail sector may currently be under better control than its North American counterpart, here we investigated levels of seafood labelling accuracy in sushi bars and restaurants across England. We used the COI barcoding gene to screen samples of tuna, eel, and a variety of other products characterised by less visually distinctive 'white flesh'. Moderate levels of substitution were found (10%), significantly lower than observed in North America, which lends support to the argument that public awareness, policy and governance of seafood labels is more effective in the European Union. Nevertheless, the results highlight that current labelling practice in UK restaurants lags behind the level of detail implemented in the retail sector, which hinders consumer choice, with potentially damaging economic, health and environmental consequences. Specifically, critically endangered species of tuna and eel continue to be sold without adequate information to consumers.

  9. A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

    KAUST Repository

    Coll, Francesc

    2014-09-01

    Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ∼92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ∼7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type. © 2014 Macmillan Publishers Limited.

  10. Multiresonator-Based Chipless RFID Barcode of the Future

    CERN Document Server

    Preradovic, Stevan

    2012-01-01

    This vital new resource offers engineers and researchers a window on important new technology that will supersede the barcode and is destined to change the face of logistics and product data handling. In the last two decades, radio-frequency identification has grown fast, with accelerated take-up of RFID into the mainstream through its adoption by key users such as Wal-Mart, K-Mart and the US Department of Defense. RFID has many potential applications due to its flexibility, capability to operate out of line of sight, and its high data-carrying capacity. Yet despite optimistic projections of a market worth $25 billion by 2018, potential users are concerned about costs and investment returns. Clearly demonstrating the need for a fully printable chipless RFID tag as well as a powerful and efficient reader to assimilate the tag’s data, this book moves on to describe both. Introducing the general concepts in the field including technical data, it then describes how a chipless RFID tag can be made using a planar...

  11. BLOG 2.0: a software system for character-based species classification with DNA Barcode sequences. What it does, how to use it

    NARCIS (Netherlands)

    Weitschek, E.; Velzen, van R.; Felici, G.; Bertolazzi, P.

    2013-01-01

    BLOG (Barcoding with LOGic) is a diagnostic and character-based DNA Barcode analysis method. Its aim is to classify specimens to species based on DNA Barcode sequences and on a supervised machine learning approach, using classification rules that compactly characterize species in terms of DNA

  12. The role of the Parkinson's disease gene PARK9 in essential cellular pathways and the manganese homeostasis network in yeast.

    Directory of Open Access Journals (Sweden)

    Alessandra Chesi

    Full Text Available YPK9 (Yeast PARK9; also known as YOR291W is a non-essential yeast gene predicted by sequence to encode a transmembrane P-type transport ATPase. However, its substrate specificity is unknown. Mutations in the human homolog of YPK9, ATP13A2/PARK9, have been linked to genetic forms of early onset parkinsonism. We previously described a strong genetic interaction between Ypk9 and another Parkinson's disease (PD protein α-synuclein in multiple model systems, and a role for Ypk9 in manganese detoxification in yeast. In humans, environmental exposure to toxic levels of manganese causes a syndrome similar to PD and is thus an environmental risk factor for the disease. How manganese contributes to neurodegeneration is poorly understood. Here we describe multiple genome-wide screens in yeast aimed at defining the cellular function of Ypk9 and the mechanisms by which it protects cells from manganese toxicity. In physiological conditions, we found that Ypk9 genetically interacts with essential genes involved in cellular trafficking and the cell cycle. Deletion of Ypk9 sensitizes yeast cells to exposure to excess manganese. Using a library of non-essential gene deletions, we screened for additional genes involved in tolerance to excess manganese exposure, discovering several novel pathways involved in manganese homeostasis. We defined the dependence of the deletion strain phenotypes in the presence of manganese on Ypk9, and found that Ypk9 deletion modifies the manganese tolerance of only a subset of strains. These results confirm a role for Ypk9 in manganese homeostasis and illuminates cellular pathways and biological processes in which Ypk9 likely functions.

  13. Genetics Home Reference: distal 18q deletion syndrome

    Science.gov (United States)

    ... Health Conditions Distal 18q deletion syndrome Distal 18q deletion syndrome Printable PDF Open All Close All Enable ... view the expand/collapse boxes. Description Distal 18q deletion syndrome is a chromosomal condition that occurs when ...

  14. Genetics Home Reference: proximal 18q deletion syndrome

    Science.gov (United States)

    ... Health Conditions Proximal 18q deletion syndrome Proximal 18q deletion syndrome Printable PDF Open All Close All Enable ... view the expand/collapse boxes. Description Proximal 18q deletion syndrome is a chromosomal condition that occurs when ...

  15. Detection of Avian Influenza Virus by Fluorescent DNA Barcode-based Immunoassay with Sensitivity Comparable to PCR

    DEFF Research Database (Denmark)

    Cao, Cuong; Dhumpa, Raghuram; Bang, Dang Duong

    2010-01-01

    In this paper, a coupling of fluorophore-DNA barcode and bead-based immunoassay for detecting avian influenza virus (AIV) with PCR-like sensitivity is reported. The assay is based on the use of sandwich immunoassay and fluorophore-tagged oligonucleotides as representative barcodes. The detection...

  16. DNA barcodes and citizen science provoke a diversity reappraisal for the "ring" butterflies of Peninsular Malaysia (Ypthima: Satyrinae: Nymphalidae: Lepidoptera).

    Science.gov (United States)

    Jisming-See, Shi-Wei; Sing, Kong-Wah; Wilson, John-James

    2016-10-01

    The "rings" belonging to the genus Ypthima are amongst the most common butterflies in Peninsular Malaysia. However, the species can be difficult to tell apart, with keys relying on minor and often non-discrete ring characters found on the hindwing. Seven species have been reported from Peninsular Malaysia, but this is thought to be an underestimate of diversity. DNA barcodes of 165 individuals, and wing and genital morphology, were examined to reappraise species diversity of this genus in Peninsular Malaysia. DNA barcodes collected during citizen science projects-School Butterfly Project and Peninsular Malaysia Butterfly Count-recently conducted in Peninsular Malaysia were included. The new DNA barcodes formed six groups with different Barcode Index Numbers (BINs) representing four species reported in Peninsular Malaysia. When combined with public DNA barcodes from the Barcode Of Life Datasystems, several taxonomic issues arose. We consider the taxon Y. newboldi, formerly treated as a subspecies of Y. baldus, as a distinct species. DNA barcodes also supported an earlier suggestion that Y. nebulosa is a synonym under Y. horsfieldii humei. Two BINs of the genus Ypthima comprising DNA barcodes collected during citizen science projects did not correspond to any species previously reported in Peninsular Malaysia.

  17. The HAL3-PPZ1 dependent regulation of nonsense suppression efficiency in yeast and its influence on manifestation of the yeast prion-like determinant [ISP(+)].

    Science.gov (United States)

    Aksenova, Anna; Muñoz, Iván; Volkov, Kirill; Ariño, Joaquín; Mironova, Ludmila

    2007-04-01

    The efficiency of stop codons read-through in yeast is controlled by multiple interactions of genetic and epigenetic factors. In this study, we demonstrate the participation of the Hal3-Ppz1 protein complex in regulation of read-through efficiency and manifestation of non-Mendelian anti-suppressor determinant [ISP(+)]. Over-expression of HAL3 in [ISP(+)] strain causes nonsense suppression, whereas its inactivation displays as anti-suppression of sup35 mutation in [isp(-)] strain. [ISP(+)] strains carrying hal3Delta deletion cannot be cured from [ISP(+)] in the presence of GuHCl. Since Hal3p is a negative regulatory subunit of Ppz1 protein phosphatase, consequences of PPZ1 over-expression and deletion are opposite to those of HAL3. The observed effects are mediated by the catalytic function of Ppz1 and are probably related to the participation of Ppz1 in regulation of eEF1Balpha elongation factor activity. Importantly, [ISP(+)] status of yeast strains is determined by fluctuation in Hal3p level, since [ISP(+)] strains have less Hal3p than their [isp(-)] derivatives obtained by GuHCl treatment. A model considering epigenetic (possibly prion) regulation of Hal3p amount as a mechanism underlying [ISP(+)] status of yeast cell is suggested.

  18. Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

    Energy Technology Data Exchange (ETDEWEB)

    Barajas, Daniel; Xu, Kai; Sharma, Monika; Wu, Cheng-Yu; Nagy, Peter D., E-mail: pdnagy2@uky.edu

    2014-12-15

    Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis.

  19. Improvement of fermentation ability under baking-associated stress conditions by altering the POG1 gene expression in baker's yeast.

    Science.gov (United States)

    Sasano, Yu; Haitani, Yutaka; Hashida, Keisuke; Oshiro, Satoshi; Shima, Jun; Takagi, Hiroshi

    2013-08-01

    During the bread-making process, yeast cells are exposed to many types of baking-associated stress. There is thus a demand within the baking industry for yeast strains with high fermentation abilities under these stress conditions. The POG1 gene, encoding a putative transcription factor involved in cell cycle regulation, is a multicopy suppressor of the yeast Saccharomyces cerevisiae E3 ubiquitin ligase Rsp5 mutant. The pog1 mutant is sensitive to various stresses. Our results suggested that the POG1 gene is involved in stress tolerance in yeast cells. In this study, we showed that overexpression of the POG1 gene in baker's yeast conferred increased fermentation ability in high-sucrose-containing dough, which is used for sweet dough baking. Furthermore, deletion of the POG1 gene drastically increased the fermentation ability in bread dough after freeze-thaw stress, which would be a useful characteristic for frozen dough baking. Thus, the engineering of yeast strains to control the POG1 gene expression level would be a novel method for molecular breeding of baker's yeast. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Deletion of acetate transporter gene ADY2 improved tolerance of Saccharomyces cerevisiae against multiple stresses and enhanced ethanol production in the presence of acetic acid.

    Science.gov (United States)

    Zhang, Mingming; Zhang, Keyu; Mehmood, Muhammad Aamer; Zhao, Zongbao Kent; Bai, Fengwu; Zhao, Xinqing

    2017-12-01

    The aim of this work was to study the effects of deleting acetate transporter gene ADY2 on growth and fermentation of Saccharomyces cerevisiae in the presence of inhibitors. Comparative transcriptome analysis revealed that three genes encoding plasma membrane carboxylic acid transporters, especially ADY2, were significantly downregulated under the zinc sulfate addition condition in the presence of acetic acid stress, and the deletion of ADY2 improved growth of S. cerevisiae under acetic acid, ethanol and hydrogen peroxide stresses. Consistently, a concomitant increase in ethanol production by 14.7% in the presence of 3.6g/L acetic acid was observed in the ADY2 deletion mutant of S. cerevisiae BY4741. Decreased intracellular acetic acid, ROS accumulation, and plasma membrane permeability were observed in the ADY2 deletion mutant. These findings would be useful for developing robust yeast strains for efficient ethanol production. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia

    Directory of Open Access Journals (Sweden)

    Jonathan Marescaux

    2013-12-01

    Full Text Available The zebra mussel (Dreissena polymorpha and the quagga mussel (Dreissena rostriformis bugensis are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit 1 mitochondrial gene (COI is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals.

  2. Barcoding bias in high-throughput multiplex sequencing of miRNA.

    Science.gov (United States)

    Alon, Shahar; Vigneault, Francois; Eminaga, Seda; Christodoulou, Danos C; Seidman, Jonathan G; Church, George M; Eisenberg, Eli

    2011-09-01

    Second-generation sequencing is gradually becoming the method of choice for miRNA detection and expression profiling. Given the relatively small number of miRNAs and improvements in DNA sequencing technology, studying miRNA expression profiles of multiple samples in a single flow cell lane becomes feasible. Multiplexing strategies require marking each miRNA library with a DNA barcode. Here we report that barcodes introduced through adapter ligation confer significant bias on miRNA expression profiles. This bias is much higher than the expected Poisson noise and masks significant expression differences between miRNA libraries. This bias can be eliminated by adding barcodes during PCR amplification of libraries. The accuracy of miRNA expression measurement in multiplexed experiments becomes a function of sample number.

  3. Towards monitoring the sandflies (Diptera: Psychodidae) of Thailand: DNA barcoding the sandflies of Wihan Cave, Uttaradit.

    Science.gov (United States)

    Polseela, Raxsina; Jaturas, Narong; Thanwisai, Aunchalee; Sing, Kong-Wah; Wilson, John-James

    2016-09-01

    Sandflies vary in their distributions and role in pathogen transmission. Attempts to record distributions of sandflies in Thailand have faced difficulties due to their high abundance and diversity. We aim to provide an insight into the diversity of sandflies in Thailand by (i) conducting a literature review, and (ii) DNA barcoding sandflies collected from Wihan Cave where eight morphologically characterized species were recorded. DNA barcodes generated for 193 sandflies fell into 13 distinct species clusters under four genera (Chinius, Idiophlebotomus, Phlebotomus and Sergentomyia). Five of these species could be assigned Linnaean species names unambiguously and two others corresponded to characterized morphospecies. Two species represented a complex under the name Sergentomyia barraudi while the remaining four had not been recognized before in any form. The resulting species checklist and DNA barcode library contribute to a growing set of records for sandflies which is useful for monitoring and vector control.

  4. Spectral signature barcodes based on S-shaped Split Ring Resonators (S-SRRs

    Directory of Open Access Journals (Sweden)

    Herrojo Cristian

    2016-01-01

    Full Text Available In this paper, it is shown that S-shaped split ring resonators (S-SRRs are useful particles for the implementation of spectral signature (i.e., a class of radiofrequency barcodes based on coplanar waveguide (CPW transmission lines loaded with such resonant elements. By virtue of its S shape, these resonators are electrically small. Hence S-SRRs are of interest for the miniaturization of the barcodes, since multiple resonators, each tuned at a different frequency, are used for encoding purposes. In particular, a 10-bit barcode occupying 1 GHz spectral bandwidth centered at 2.5 GHz, with dimensions of 9 cm2, is presented in this paper.

  5. High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.

    Science.gov (United States)

    Kebschull, Justus M; Garcia da Silva, Pedro; Reid, Ashlan P; Peikon, Ian D; Albeanu, Dinu F; Zador, Anthony M

    2016-09-07

    Neurons transmit information to distant brain regions via long-range axonal projections. In the mouse, area-to-area connections have only been systematically mapped using bulk labeling techniques, which obscure the diverse projections of intermingled single neurons. Here we describe MAPseq (Multiplexed Analysis of Projections by Sequencing), a technique that can map the projections of thousands or even millions of single neurons by labeling large sets of neurons with random RNA sequences ("barcodes"). Axons are filled with barcode mRNA, each putative projection area is dissected, and the barcode mRNA is extracted and sequenced. Applying MAPseq to the locus coeruleus (LC), we find that individual LC neurons have preferred cortical targets. By recasting neuroanatomy, which is traditionally viewed as a problem of microscopy, as a problem of sequencing, MAPseq harnesses advances in sequencing technology to permit high-throughput interrogation of brain circuits. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. TECHNICAL DESIGN NOTE: Currency verification by a 2D infrared barcode

    Science.gov (United States)

    Schirripa Spagnolo, Giuseppe; Cozzella, Lorenzo; Simonetti, Carla

    2010-10-01

    Nowadays all the National Central Banks are continuously studying innovative anti-counterfeiting systems for banknotes. In this note, an innovative solution is proposed, which combines the potentiality of a hylemetric approach (methodology conceptually similar to biometry), based on notes' intrinsic characteristics, with a well-known and consolidated 2D barcode identification system. In particular, in this note we propose to extract from the banknotes a univocal binary control sequence (template) and insert an encrypted version of it in a barcode printed on the same banknote. For a more acceptable look and feel of a banknote, the superposed barcode can be stamped using IR ink that is visible to near-IR image sensors. This makes the banknote verification simpler.

  7. Barcoding the food chain: from Sanger to high-throughput sequencing.

    Science.gov (United States)

    Littlefair, Joanne E; Clare, Elizabeth L

    2016-11-01

    Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace "environmental DNA", and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.

  8. [Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence].

    Science.gov (United States)

    Liao, Jing; Chao, Zhi; Zhang, Liang

    2013-11-01

    To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility. The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0. The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%. DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.

  9. Nuclear Transport of Yeast Proteasomes

    Directory of Open Access Journals (Sweden)

    Cordula Enenkel

    2014-10-01

    Full Text Available Proteasomes are conserved protease complexes enriched in the nuclei of dividing yeast cells, a major site for protein degradation. If yeast cells do not proliferate and transit to quiescence, metabolic changes result in the dissociation of proteasomes into proteolytic core and regulatory complexes and their sequestration into motile cytosolic proteasome storage granuli. These granuli rapidly clear with the resumption of growth, releasing the stored proteasomes, which relocalize back to the nucleus to promote cell cycle progression. Here, I report on three models of how proteasomes are transported from the cytoplasm into the nucleus of yeast cells. The first model applies for dividing yeast and is based on the canonical pathway using classical nuclear localization sequences of proteasomal subcomplexes and the classical import receptor importin/karyopherin αβ. The second model applies for quiescent yeast cells, which resume growth and use Blm10, a HEAT-like repeat protein structurally related to karyopherin β, for nuclear import of proteasome core particles. In the third model, the fully-assembled proteasome is imported into the nucleus. Our still marginal knowledge about proteasome dynamics will inspire the discussion on how protein degradation by proteasomes may be regulated in different cellular compartments of dividing and quiescent eukaryotic cells.

  10. Assessment of four molecular markers as potential DNA barcodes for red algae Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta).

    Science.gov (United States)

    Tan, Ji; Lim, Phaik-Eem; Phang, Siew-Moi; Hong, Dang Diem; Sunarpi, H; Hurtado, Anicia Q

    2012-01-01

    DNA barcoding has been a major advancement in the field of taxonomy, seeing much effort put into the barcoding of wide taxa of organisms, macro and microalgae included. The mitochondrial-encoded cox1 and plastid-encoded rbcL has been proposed as potential DNA barcodes for rhodophytes, but are yet to be tested on the commercially important carrageenophytes Kappaphycus and Eucheuma. This study gauges the effectiveness of four markers, namely the mitochondrial cox1, cox2, cox2-3 spacer and the plastid rbcL in DNA barcoding on selected Kappaphycus and Eucheuma from Southeast Asia. Marker assessments were performed using established distance and tree-based identification criteria from earlier studies. Barcoding patterns on a larger scale were simulated by empirically testing on the commonly used cox2-3 spacer. The phylogeny of these rhodophytes was also briefly described. In this study, the cox2 marker which satisfies the prerequisites of DNA barcodes was found to exhibit moderately high interspecific divergences with no intraspecific variations, thus a promising marker for the DNA barcoding of Kappaphycus and Eucheuma. However, the already extensively used cox2-3 spacer was deemed to be in overall more appropriate as a DNA barcode for these two genera. On a wider scale, cox1 and rbcL were still better DNA barcodes across the rhodophyte taxa when practicality and cost-efficiency were taken into account. The phylogeny of Kappaphycus and Eucheuma were generally similar to those earlier reported. Still, the application of DNA barcoding has demonstrated our relatively poor taxonomic comprehension of these seaweeds, thus suggesting more in-depth efforts in taxonomic restructuring as well as establishment.

  11. Barcode Technology Acceptance and Utilization in Health Information Management Department at Academic Hospitals According to Technology Acceptance Model.

    Science.gov (United States)

    Ehteshami, Asghar

    2017-03-01

    Nowdays, due to the increasing importance of quality care, organizations focuse on the improving provision, management and distribution of health. On one hand, incremental costs of the new technologies and on the other hand, increased knowledge of health care recipients and their expectations for high quality services have doubled the need to make changes in order to respond to resource constraints (financial, human, material). For this purpose, several technologies, such as barcode, have been used in hospitals to improve services and staff productivity; but various factors effect on the adoption of new technologies and despite good implementation of a technology and its benefits, sometimes personnel don't accept and don't use it. This is an applied descriptive cross-sectional study in which all the barcode users in health information management department of the three academic hospitals (Feiz, Al-Zahra, Ayatollah Kashani) affiliated to Isfahan University of Medical Sciences were surveyed by the barcode technology acceptance questionnaire, in six areas as following: barcode ease of learning, capabilities, perception of its usefulness and its ease of use, users attitudes towards its using, and users intention. The finding showed that barcode technology total acceptance was relatively desirable (%76.9); the most compliance with TAM model was related to the user perceptions about the ease of use of barcode technology and the least compliance was related to the ease of learning barcode technology (respectively %83.7 and %71.5). Ease of learning and barcode capability effect of usefulness and perceived ease of barcode technology. Users perceptions effect their attitudes toward greater use of technology and their attitudes have an effect on their intention to use the technology and finally, their intention makes actual use of the technology (acceptance). Therefore, considering the six elements related to technology implementation can be important in the barcode

  12. DNA barcoding of recently diverged species: relative performance of matching methods.

    Directory of Open Access Journals (Sweden)

    Robin van Velzen

    Full Text Available Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based, nearest neighbor and BLAST (similarity-based, and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75% than for older species (∼97% (P<0.00001. Similarity-based and diagnostic methods significantly outperform tree-based methods, when applied to simulated DNA barcode data (P<0.00001. The diagnostic method BLOG had highest correct query identification rate based on simulated (86.2% as well as empirical data (93.1%, indicating that it is a consistently better method overall. Another advantage of BLOG is that it offers species-level information that can be used outside the realm of DNA barcoding, for instance in species description or molecular detection assays. Even though we can confirm that identification success based on DNA barcoding is generally high in our data, recently diverged species remain difficult to identify. Nevertheless, our results contribute to improved solutions for their accurate identification.

  13. A multi-locus approach to barcoding in the Anopheles strodei subgroup (Diptera: Culicidae).

    Science.gov (United States)

    Bourke, Brian Patrick; Oliveira, Tatiane Porangaba; Suesdek, Lincoln; Bergo, Eduardo Sterlino; Sallum, Maria Anice Mureb

    2013-04-19

    The ability to successfully identify and incriminate pathogen vectors is fundamental to effective pathogen control and management. This task is confounded by the existence of cryptic species complexes. Molecular markers can offer a highly effective means of species identification in such complexes and are routinely employed in the study of medical entomology. Here we evaluate a multi-locus system for the identification of potential malaria vectors in the Anopheles strodei subgroup. Larvae, pupae and adult mosquitoes (n = 61) from the An. strodei subgroup were collected from 21 localities in nine Brazilian states and sequenced for the COI, ITS2 and white gene. A Bayesian phylogenetic approach was used to describe the relationships in the Strodei Subgroup and the utility of COI and ITS2 barcodes was assessed using the neighbor joining tree and "best close match" approaches. Bayesian phylogenetic analysis of the COI, ITS2 and white gene found support for seven clades in the An. strodei subgroup. The COI and ITS2 barcodes were individually unsuccessful at resolving and identifying some species in the Subgroup. The COI barcode failed to resolve An. albertoi and An. strodei but successfully identified approximately 92% of all species queries, while the ITS2 barcode failed to resolve An. arthuri and successfully identified approximately 60% of all species queries. A multi-locus COI-ITS2 barcode, however, resolved all species in a neighbor joining tree and successfully identified all species queries using the "best close match" approach. Our study corroborates the existence of An. albertoi, An. CP Form and An. strodei in the An. strodei subgroup and identifies four species under An. arthuri informally named A-D herein. The use of a multi-locus barcode is proposed for species identification, which has potentially important utility for vector incrimination. Individuals previously found naturally infected with Plasmodium vivax in the southern Amazon basin and reported as An

  14. DNA barcoding as a complementary tool for conservation and valorisation of forest resources.

    Science.gov (United States)

    Laiou, Angeliki; Mandolini, Luca Aconiti; Piredda, Roberta; Bellarosa, Rosanna; Simeone, Marco Cosimo

    2013-12-30

    Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources. The "core barcode" for land plants (rbcL, matK, and trnH-psbA) was tested on 68 tree specimens (24 taxa). Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intraspecific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%. This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.

  15. Two Mitochondrial Barcodes for one Biological Species: The Case of European Kuhl's Pipistrelles (Chiroptera).

    Science.gov (United States)

    Andriollo, Tommy; Naciri, Yamama; Ruedi, Manuel

    2015-01-01

    The Kuhl's pipistrelle (Pipistrellus kuhlii) is a Western Palaearctic species of bat that exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages occurring in Western Europe, and used both mitochondrial and nuclear markers to measure degrees of genetic isolation between bats carrying them. The sampling focused on an area of strict lineage sympatry in Switzerland but also included bats from further south, in North Africa. All individuals were barcoded for the COI gene to identify their mitochondrial lineages and five highly polymorphic microsatellite loci were used to cluster them according to their nuclear genotypes. Despite this low number of nuclear markers, all North African nuclear genotypes were grouped in a highly distinct subpopulation when compared with European samples sharing the same mitochondrial barcodes. The reverse situation prevailed in Switzerland where bats carrying distinct barcodes had similar nuclear genotypes. There was a weak east/west nuclear structure of populations, but this was independent of mitochondrial lineages as bats carrying either variant were completely admixed. Thus, the divergent mitochondrial barcodes present in Western Europe do not represent cryptic species, but are part of a single biological species. We argue that these distinct barcodes evolved in allopatry and came recently into secondary contact in an area of admixture north of the Alps. Historical records from this area and molecular dating support such a recent bipolar spatial expansion. These results also highlight the need for using appropriate markers before claiming the existence of cryptic species based on highly divergent barcodes.

  16. Pitfalls of establishing DNA barcoding systems in protists: the cryptophyceae as a test case.

    Directory of Open Access Journals (Sweden)

    Kerstin Hoef-Emden

    Full Text Available A DNA barcode is a preferrably short and highly variable region of DNA supposed to facilitate a rapid identification of species. In many protistan lineages, a lack of species-specific morphological characters hampers an identification of species by light or electron microscopy, and difficulties to perform mating experiments in laboratory cultures also do not allow for an identification of biological species. Thus, testing candidate barcode markers as well as establishment of accurately working species identification systems are more challenging than in multicellular organisms. In cryptic species complexes the performance of a potential barcode marker can not be monitored using morphological characters as a feedback, but an inappropriate choice of DNA region may result in artifactual species trees for several reasons. Therefore a priori knowledge of the systematics of a group is required. In addition to identification of known species, methods for an automatic delimitation of species with DNA barcodes have been proposed. The Cryptophyceae provide a mixture of systematically well characterized as well as badly characterized groups and are used in this study to test the suitability of some of the methods for protists. As species identification method the performance of blast in searches against badly to well-sampled reference databases has been tested with COI-5P and 5'-partial LSU rDNA (domains A to D of the nuclear LSU rRNA gene. In addition the performance of two different methods for automatic species delimitation, fixed thresholds of genetic divergence and the general mixed Yule-coalescent model (GMYC, have been examined. The study demonstrates some pitfalls of barcoding methods that have to be taken care of. Also a best-practice approach towards establishing a DNA barcode system in protists is proposed.

  17. Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics.

    Science.gov (United States)

    Aliota, Matthew T; Dudley, Dawn M; Newman, Christina M; Weger-Lucarelli, James; Stewart, Laurel M; Koenig, Michelle R; Breitbach, Meghan E; Weiler, Andrea M; Semler, Matthew R; Barry, Gabrielle L; Zarbock, Katie R; Haj, Amelia K; Moriarty, Ryan V; Mohns, Mariel S; Mohr, Emma L; Venturi, Vanessa; Schultz-Darken, Nancy; Peterson, Eric; Newton, Wendy; Schotzko, Michele L; Simmons, Heather A; Mejia, Andres; Hayes, Jennifer M; Capuano, Saverio; Davenport, Miles P; Friedrich, Thomas C; Ebel, Gregory D; O'Connor, Shelby L; O'Connor, David H

    2018-03-01

    Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a "synthetic swarm" whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcodes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 67 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.

  18. Barcoding success as a function of phylogenetic relatedness in Viburnum, a clade of woody angiosperms

    Directory of Open Access Journals (Sweden)

    Clement Wendy L

    2012-05-01

    Full Text Available Abstract Background The chloroplast genes matK and rbcL have been proposed as a “core” DNA barcode for identifying plant species. Published estimates of successful species identification using these loci (70-80% may be inflated because they may have involved comparisons among distantly related species within target genera. To assess the ability of the proposed two-locus barcode to discriminate closely related species, we carried out a hierarchically structured set of comparisons within Viburnum, a clade of woody angiosperms containing ca. 170 species (some 70 of which are currently used in horticulture. For 112 Viburnum species, we evaluated rbcL + matK, as well as the chloroplast regions rpl32-trnL, trnH-psbA, trnK, and the nuclear ribosomal internal transcribed spacer region (nrITS. Results At most, rbcL + matK could discriminate 53% of all Viburnum species, with only 18% of the comparisons having genetic distances >1%. When comparisons were progressively restricted to species within major Viburnum subclades, there was a significant decrease in both the discriminatory power and the genetic distances. trnH-psbA and nrITS show much higher levels of variation and potential discriminatory power, and their use in plant barcoding should be reconsidered. As barcoding has often been used to discriminate species within local areas, we also compared Viburnum species within two regions, Japan and Mexico and Central America. Greater success in discriminating among the Japanese species reflects the deeper evolutionary history of Viburnum in that area, as compared to the recent radiation of a single clade into the mountains of Latin America. Conclusions We found very low levels of discrimination among closely related species of Viburnum, and low levels of variation in the proposed barcoding loci may limit success within other clades of long-lived woody plants. Inclusion of the supplementary barcodes trnH-psbA and nrITS increased discrimination rates but

  19. A Festival-wide Social Network using 2D Barcodes, Mobile Phones and Situated Displays

    DEFF Research Database (Denmark)

    Larsen, Jakob Eg; Stopczynski, Arkadiusz

    2011-01-01

    In this paper we report our experiences with an exploratory prototype festival-wide social network applying unique 2D barcodes on wristbands and mobile phones to uniquely identify the festival participants. Experiments were carried out at the CO2PENHAGEN music festival in Denmark. We describe a set...... approach had potential to enable anyone at the festival to participate in the festival-wide social network, as participants did not need any special hardware or mobile client application to be involved. The 2D barcodes was found to be a feasible low-cost approach for unique participant identification...

  20. Discovery of new populations and DNA barcoding of the Arapahoe snowfly Arsapnia arapahoe (Plecoptera: Capniidae).

    Science.gov (United States)

    Heinold, Brian D; Gill, Brian A; Belcher, Thomas P; Verdone, Chris J

    2014-09-22

    The Arapahoe Snowfly, Arsapnia arapahoe (Nelson & Kondratieff)was recently discovered in six different first-order streams outside of the Cache la Poudre River Basin where it was previously considered endemic. Specimens of A. arapahoe were always collected in much lower relative abundance, 1.09% (±2.3SD), than other sympatric adult capniids. The first mitochondrial deoxyribonucleic acid (DNA) barcodes for A. arapahoe and A. coyote (Nelson & Baumann) are presented and compared with those of A. decepta. DNA barcoding was not able to differentiate between A. arapahoe and A. decepta Banks but it was able to indicate that A. coyote is specifically distinct.

  1. Improvement of aromatic thiol release through the selection of yeasts with increased β-lyase activity.

    Science.gov (United States)

    Belda, Ignacio; Ruiz, Javier; Navascués, Eva; Marquina, Domingo; Santos, Antonio

    2016-05-16

    The development of a selective medium for the rapid differentiation of yeast species with increased aromatic thiol release activity has been achieved. The selective medium was based on the addition of S-methyl-l-cysteine (SMC) as β-lyase substrate. In this study, a panel of 245 strains of Saccharomyces cerevisiae strains was tested for their ability to grow on YCB-SMC medium. Yeast strains with an increased β-lyase activity grew rapidly because of their ability to release ammonium from SMC in comparison to others, and allowed for the easy isolation and differentiation of yeasts with promising properties in oenology, or another field, for aromatic thiol release. The selective medium was also helpful for the discrimination between those S. cerevisiae strains, which present a common 38-bp deletion in the IRC7 sequence (present in around 88% of the wild strains tested and are likely to be less functional for 4-mercapto-4-methylpentan-2-one (4MMP) production), and those S. cerevisiae strains homozygous for the full-length IRC7 allele. The medium was also helpful for the selection of non-Saccharomyces yeasts with increased β-lyase activity. Based on the same medium, a highly sensitive, reproducible and non-expensive GC-MS method for the evaluation of the potential volatile thiol release by different yeast isolates was developed. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast.

    Directory of Open Access Journals (Sweden)

    Elke Ericson

    2008-08-01

    Full Text Available To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac interfered with establishment of cell polarity, cyproheptadine (Periactin targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol and pimozide (Orap. Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.

  3. Sorption of grape proanthocyanidins and wine polyphenols by yeasts, inactivated yeasts, and yeast cell walls.

    Science.gov (United States)

    Mekoue Nguela, J; Sieczkowski, N; Roi, S; Vernhet, A

    2015-01-21

    Inactivated yeast fractions (IYFs) can be used in enology to improve the stability and mouthfeel of red wines. However, information concerning the mechanisms involved and the impact of the IYF characteristics is scarce. Adsorption isotherms were used to investigate interactions between grape proanthocyanidin fractions (PAs) or wine polyphenols (WP) and a commercial yeast strain (Y), the inactivated yeast (IY), the yeast submitted to autolyzis and inactivation (A-IY), and the cell walls obtained by mechanical disruption (CW). High affinity isotherms and high adsorption capacities were observed for grape PAs and whole cells (Y, IY, and A-IY). Affinity and adsorbed amount were lower with wine PAs, due to chemical changes occurring during winemaking. By contrast to whole cells, grape PAs and WP adsorption on CW remained very low. This raises the issue of the part played by cell walls in the interactions between yeast and proanthocyanidins and suggests the passage of the latter through the wall pores and their interaction with the plasma membrane.

  4. Chromatin and Transcription in Yeast

    Science.gov (United States)

    Rando, Oliver J.; Winston, Fred

    2012-01-01

    Understanding the mechanisms by which chromatin structure controls eukaryotic transcription has been an intense area of investigation for the past 25 years. Many of the key discoveries that created the foundation for this field came from studies of Saccharomyces cerevisiae, including the discovery of the role of chromatin in transcriptional silencing, as well as the discovery of chromatin-remodeling factors and histone modification activities. Since that time, studies in yeast have continued to contribute in leading ways. This review article summarizes the large body of yeast studies in this field. PMID:22345607

  5. Emulsifying activity of hydrocarbonoclastic marine yeasts

    Digital Repository Service at National Institute of Oceanography (India)

    Gupta, R.

    Marine yeast growth on four petroleum hydrocarbons induced the production of extracellular emulsifying agents (biosurfactants). Out of the 17 marine yeast isolates tested, 7 isolates, i.e., Candida parapsilosis, C. cantarelli, C. membranae...

  6. Deletion of FPS1, encoding aquaglyceroporin Fps1p, improves xylose fermentation by engineered Saccharomyces cerevisiae.

    Science.gov (United States)

    Wei, Na; Xu, Haiqing; Kim, Soo Rin; Jin, Yong-Su

    2013-05-01

    Accumulation of xylitol in xylose fermentation with engineered Saccharomyces cerevisiae presents a major problem that hampers economically feasible production of biofuels from cellulosic plant biomass. In particular, substantial production of xylitol due to unbalanced redox cofactor usage by xylose reductase (XR) and xylitol dehydrogenase (XDH) leads to low yields of ethanol. While previous research focused on manipulating intracellular enzymatic reactions to improve xylose metabolism, this study demonstrated a new strategy to reduce xylitol formation and increase carbon flux toward target products by controlling the process of xylitol secretion. Using xylitol-producing S. cerevisiae strains expressing XR only, we determined the role of aquaglyceroporin Fps1p in xylitol export by characterizing extracellular and intracellular xylitol. In addition, when FPS1 was deleted in a poorly xylose-fermenting strain with unbalanced XR and XDH activities, the xylitol yield was decreased by 71% and the ethanol yield was substantially increased by nearly four times. Experiments with our optimized xylose-fermenting strain also showed that FPS1 deletion reduced xylitol production by 21% to 30% and increased ethanol yields by 3% to 10% under various fermentation conditions. Deletion of FPS1 decreased the xylose consumption rate under anaerobic conditions, but the effect was not significant in fermentation at high cell density. Deletion of FPS1 resulted in higher intracellular xylitol concentrations but did not significantly change the intracellular NAD(+)/NADH ratio in xylose-fermenting strains. The results demonstrate that Fps1p is involved in xylitol export in S. cerevisiae and present a new gene deletion target, FPS1, and a mechanism different from those previously reported to engineer yeast for improved xylose fermentation.

  7. X-ray survival characteristics and genetic analysis for nine saccharomyces deletion mutants that show altered radiation sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Game, John C.; Williamson, Marsha S.; Baccari, Clelia

    2004-01-07

    The availability of a genome-wide set of Saccharomyces deletion mutants provides a chance to identify all the yeast genes involved in DNA repair. Using X-rays, we are screening these mutants to identify additional genes that show increased sensitivity to the lethal effects of ionizing radiation. For each mutant identified as sensitive, we are confirming that the sensitivity phenotype co-segregates with the deletion allele and are obtaining multipoint survival-versus-dose assays in at least two haploid and one homozygous diploid strains. We present data for deletion mutants involving the genes DOT1, MDM20, NAT3, SPT7, SPT20, GCN5, HFI1, DCC1 and VID21/EAF1, and discuss their potential roles in repair. Eight of these genes have a clear radiation-sensitive phenotype when deleted, but the ninth, GCN5, has at most a borderline phenotype. None of the deletions confer substantial sensitivity to ultra-violet radiation, although one or two may confer marginal sensitivity. The DOT1 gene is of interest because its only known function is to methylate one lysine residue in the core of the histone H3 protein. We find that histone H3 mutants (supplied by K. Struhl) in which this residue is replaced by other amino-acids are also X-ray sensitive, seeming to confirm that methylation of the lysine-79 residue is required for effective repair of radiation damage.

  8. Identification of the Transcription Factor Znc1p, which Regulates the Yeast-to-Hypha Transition in the Dimorphic Yeast Yarrowia lipolytica

    Science.gov (United States)

    Martinez-Vazquez, Azul; Gonzalez-Hernandez, Angelica; Domínguez, Ángel; Rachubinski, Richard; Riquelme, Meritxell; Cuellar-Mata, Patricia; Guzman, Juan Carlos Torres

    2013-01-01

    The dimorphic yeast Yarrowia lipolytica is used as a model to study fungal differentiation because it grows as yeast-like cells or forms hyphal cells in response to changes in environmental conditions. Here, we report the isolation and characterization of a gene, ZNC1, involved in the dimorphic transition in Y. lipolytica. The ZNC1 gene encodes a 782 amino acid protein that contains a Zn(II)2C6 fungal-type zinc finger DNA-binding domain and a leucine zipper domain. ZNC1 transcription is elevated during yeast growth and decreases during the formation of mycelium. Cells in which ZNC1 has been deleted show increased hyphal cell formation. Znc1p-GFP localizes to the nucleus, but mutations within the leucine zipper domain of Znc1p, and to a lesser extent within the Zn(II)2C6 domain, result in a mislocalization of Znc1p to the cytoplasm. Microarrays comparing gene expression between znc1::URA3 and wild-type cells during both exponential growth and the induction of the yeast-to-hypha transition revealed 1,214 genes whose expression was changed by 2-fold or more under at least one of the conditions analyzed. Our results suggest that Znc1p acts as a transcription factor repressing hyphal cell formation and functions as part of a complex network regulating mycelial growth in Y. lipolytica. PMID:23826133

  9. 19 CFR 142.49 - Deletion of C-4 Code.

    Science.gov (United States)

    2010-04-01

    .... Entry filers may delete C-4 Codes from Line Release by notifying the port director in writing on a Deletion Data Loading Sheet. Such notification shall state the C-4 Code which is to be deleted, the port... TREASURY (CONTINUED) ENTRY PROCESS Line Release § 142.49 Deletion of C-4 Code. (a) By Customs. A port...

  10. 78 FR 17641 - Procurement List; Proposed Addition and Deletion

    Science.gov (United States)

    2013-03-22

    ... Addition and Deletion AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed Addition to and Deletion from the Procurement List. SUMMARY: The Committee is proposing to add a..., Washington, DC Deletion The following product is proposed for deletion from the Procurement List: Product...

  11. 46 CFR 67.171 - Deletion; requirement and procedure.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Deletion; requirement and procedure. 67.171 Section 67...; Requirement for Exchange, Replacement, Deletion, Cancellation § 67.171 Deletion; requirement and procedure. (a... provided in § 67.161, and the vessel is subject to deletion from the roll of actively documented vessels...

  12. 78 FR 54871 - Procurement List; Proposed Additions and Deletion

    Science.gov (United States)

    2013-09-06

    ... Additions and Deletion AGENCY: Committee for Purchase From People Who Are Blind or Severely Disabled. ACTION: Proposed additions to and deletions from the Procurement List. SUMMARY: The Committee is proposing to add... by the Defense Commissary Agency. Deletion The following product is proposed for deletion from the...

  13. Yeast as factory and factotum.

    Science.gov (United States)

    Dixon, B

    2000-02-01

    After centuries of vigorous activity in making fine wines, beers and breads, Saccharomyces cerevisiae is now acquiring a rich new portfolio of skills, bestowed by genetic manipulation. As shown in a recent shop-window of research supported by the European Commission, yeasts will soon be benefiting industries as diverse as fish farming, pharmaceuticals and laundering.

  14. Sociobiology of the budding yeast

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... media (figure 2). On solid substrates exposed to air, cells that do not produce flocculins will develop nonadhesive colonies, such as seen for the ..... Programmed cell death. Escherichia coli, protozoa, bacteria, slime moulds. Yeast apoptosis (Madeo et al. 1997; Honigberg 2011). Communication via.

  15. Surplus yeast tank failing catastrophically

    DEFF Research Database (Denmark)

    Hedlund, Frank Huess

    2016-01-01

    GOOD REASON FOR CAUTION I A large surplus yeast tank shot into the air leaving the floor plate and the contents behind. Although not designed for overpressure, the tank was kept at “very slight overpressure” to suppress nuisance foaming. The brewery was unaware of the hazards of compressed air...

  16. Yeast genomics on food flavours

    NARCIS (Netherlands)

    Schoondermark-Stolk, Sung Ah

    2005-01-01

    The appearance and concentration of the fusel alcohol 3-methyl-1-butanol is important for the flavour of fermented foods. 3-Methyl-1-butanol is formed by yeast during the conversion of L-leucine. Identification of the enzymes and genes involved in the formation of 3-methyl-1-butanol is a major

  17. Sociobiology of the budding yeast

    Indian Academy of Sciences (India)

    2014-03-15

    Mar 15, 2014 ... Social theory has provided a useful framework for research with microorganisms. Here I describe the advantages and possible risks of using a well-known model organism, the unicellular yeast Saccharomyces cerevisiae, for sociobio- logical research. I discuss the problems connected with clear ...

  18. 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

  19. DNA barcodes discriminate freshwater fishes from the Paraíba do Sul River Basin, São Paulo, Brazil.

    Science.gov (United States)

    Pereira, Luiz H G; Maia, Gláucia M G; Hanner, Robert; Foresti, Fausto; Oliveira, Claudio

    2011-10-01

    Considering the promising use of DNA barcoding for species identification, the importance of the freshwater fish fauna of the Paraíba do Sul River Basin, and its advanced stage of degradation, the present study evaluated the effectiveness of DNA barcoding to identify the fish species in this basin. A total of 295 specimens representing 58 species belonging to 40 genera, 17 families, and 5 orders were sequenced. The DNA barcodes discriminated all species analyzed without ambiguity. The results showed a pronounced difference between conspecific and congeneric pair-wise sequence comparisons, demonstrating the existence of a "barcode gap" for the species analyzed. The nearest-neighbor distance analysis showed only three cases with Kimura two-parameter values lower than a 2% divergence threshold. However, the patterns of divergence observed in each case remained sufficient to discriminate each species, revealing the accuracy of DNA barcoding even cases with relatively low genetic divergence. At the other extreme, three species displayed high genetic sequence divergence among conspecifics. For two cases, Characidium alipioi and Geophagus proximus, barcoding proved effective at flagging possible new species. For another case, Astyanax bimaculatus, the use of DNA barcoding of the comparison of shared freshwater fish fauna between different basins revealed itself as highly useful in disclosing that the previously identified A. bimaculatus "cluster A" probably represents the species Astyanax altiparanae. The present study is among the first to assess the efficiency of barcoding for the Brazilian freshwater fishes. The results demonstrate the utility of barcoding to identify the fauna from this basin, contribute to an enhanced understanding of the differentiation among species, and to help flag the presence of overlooked species.

  20. Barcoding nemo: DNA-based identifications for the ornamental fish trade.

    Directory of Open Access Journals (Sweden)

    Dirk Steinke

    Full Text Available BACKGROUND: Trade in ornamental fishes represents, by far, the largest route for the importation of exotic vertebrates. There is growing pressure to regulate this trade with the goal of ensuring that species are sustainably harvested and that their point of origin is accurately reported. One important element of such regulation involves easy access to specimen identifications, a task that is currently difficult for all but specialists because of the large number of species involved. The present study represents an important first step in making identifications more accessible by assembling a DNA barcode reference sequence library for nearly half of the ornamental fish species imported into North America. METHODOLOGY/PRINCIPAL FINDINGS: Analysis of the cytochrome c oxidase subunit I (COI gene from 391 species from 8 coral reef locations revealed that 98% of these species exhibit distinct barcode clusters, allowing their unambiguous identification. Most species showed little intra-specific variation (adjusted mean = 0.21%, but nine species included two or three lineages showing much more divergence (2.19-6.52% and likely represent overlooked species complexes. By contrast, three genera contained a species pair or triad that lacked barcode divergence, cases that may reflect hybridization, young taxa or taxonomic over-splitting. CONCLUSIONS/SIGNIFICANCE: Although incomplete, this barcode library already provides a new species identification tool for the ornamental fish industry, opening a realm of applications linked to collection practices, regulatory control and conservation.

  1. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae)

    Science.gov (United States)

    Larranaga, Nerea; Hormaza, José I.

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management. PMID:26284104

  2. Evaluating the efficacy of restoration plantings through DNA barcoding of frugivorous bird diets.

    Science.gov (United States)

    Galimberti, A; Spinelli, S; Bruno, A; Mezzasalma, V; De Mattia, F; Cortis, P; Labra, M

    2016-08-01

    Frugivores are critical components of restoration programs because they are seed dispersers. Thus, knowledge about bird-plant trophic relationships is essential in the evaluation of the efficacy of restoration processes. Traditionally, the diet of frugivores is characterized by microscopically identifying plant residues in droppings, which is time-consuming, requires botanical knowledge, and cannot be used for fragments lacking detectable morphological characteristics (e.g., fragmented seeds and skins). We examined whether DNA barcoding can be used as a universal tool to rapidly characterize the diet of a frugivorous bird, Eurasian blackcap (Sylvia atricapilla). We used the DNA barcoding results to assess restoration efforts and monitor the diversity of potentially dispersed plants in a protected area in northern Italy. We collected 642 Eurasian Blackcap droppings at the restored site during the autumn migration over 3 years. Intact seeds and fragmented plant material were analyzed at 2 plastidial barcode loci (rbcL and trnH-psbA), and the resulting plant identifications were validated by comparison with a reference molecular data set of local flora. At least 17 plant species, including 7 of the 11 newly transplanted taxa, were found. Our results demonstrate the potential for DNA barcoding to be used to monitor the effectiveness of restoration plantings and to obtain information about fruit consumption and dispersal of invasive or unexpected plant species. Such an approach provides valuable information that could be used to study local plant biodiversity and to survey its evolution over time. © 2016 Society for Conservation Biology.

  3. Identification of common horsetail (Equisetum arvense L.; Equisetaceae) using Thin Layer Chromatography versus DNA barcoding

    DEFF Research Database (Denmark)

    Saslis Lagoudakis, Haris; Bruun-Lund, Sam; Iwanycki, Natalie Eva

    2015-01-01

    : a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and a DNA barcoding approach, used in recent years to identify material in herbal products. We test the potential of these methods for distinguishing and identifying these species using material from herbarium...

  4. DNA barcodes to identify species and explore diversity in the Adelgidae (Insecta: Hemiptera: Aphidoidea)

    Science.gov (United States)

    R.G. Foottit; H.E.L. Maw; N.P. Havill; R.G. Ahern; M.E. Montgomery

    2009-01-01

    The Adelgidae are relatively small, cryptic insects, exhibiting complex life cycles with parthenogenetic reproduction. Due to these characteristics, the taxonomy of the group is problematic. Here, we test the effectiveness of the standard 658-bp barcode fragment from the 5'-end of the mitochondrial cytochrome c oxidase 1 gene (COI) in...

  5. The Use of DNA Barcoding in Identification of Genetic Diversity of ...

    African Journals Online (AJOL)

    In this study, for the first time, the use of DNA barcoding was used in identification of the genetic diversity of fish in Ugwu-omu Nike River, Enugu State, Nigeria. The fish were collected and placed in an aquarium and later transported to the Biotechnology laboratory of Godfrey Okoye University. The fish collection was ...

  6. DNA barcoding of a new record of epi-endophytic green algae ...

    Indian Academy of Sciences (India)

    2014-07-13

    Jul 13, 2014 ... ribosomal DNA Internal Transcribed Spacer 2 (ITS2) (Bown et al. 2003; Rinkel et al. 2012) and plastid DNA marker tufA. (Nielsen et al. 2013; Rinkel et al. 2012). While ITS1 is one of the widely used DNA barcode in plants and algae, its phylogenetic utility have not yet been assessed in Ulvella. Although it is ...

  7. Who Is in the Driver's Seat : Tracing Cancer Genes Using CRISPR-Barcoding

    NARCIS (Netherlands)

    Drost, Jarno; Clevers, Hans

    2016-01-01

    Intratumor heterogeneity is thought to be the driving force of tumor evolution and therapy resistance. Yet tools to study these processes are limited. In this issue, Guernet et al. (2016) devised clustered regularly interspaced short palindromic repeats (CRISPR)-barcoding to functionally annotate

  8. DNA barcoding of a colonial ascidian, Lissoclinum fragile (Van Name, 1902).

    Science.gov (United States)

    H Abdul, Jaffarali; Akram, Soban; Arshan, Kaleem M L

    2017-11-01

    Ascidians (tunicates) are marine benthic organisms possessing various pharmacological activities, including anti-oxidant, anti-tumour, antimicrobial, etc. They also play a key role as model organisms to study various neurobehavioral disorders. Ascidian diversity is reportedly less in India due to lack of taxonomists as well as the limitations in morphology based taxonomy. Molecular taxonomy, comprising the sequencing of cytochrome c oxidase 1 gene (barcode region) otherwise known as DNA barcoding reduces these bottlenecks. Since several species of the family Didemnidae closely resemble in morphology, the present study was aimed to develop DNA barcodes of a colonial ascidian, Lissoclinum fragile belonging to the family Didemnidae. CO1 gene of L. fragile from Thoothukudi, Mandapam, and Vizhinjam waters were sequenced and submitted in GenBank, NCBI through Barcode submission tool. BLAST results showed maximum identity (97-100%) for L. fragile collected from different stations. The pairwise genetic distances within species and genera were calculated using Kimura two parameter (K2P) and the phylogenetic tree was constructed using Neighbour-Joining Tree.

  9. DNA Barcoding reveals sexual dimorphism in Isotrias penedana Trematerra, 2013 (Lepidoptera: Tortricidae, Chlidanotinae).

    Science.gov (United States)

    Corley, Martin Francis Vanner; Ferreira, Sónia

    2017-01-20

    Isotrias penedana Trematerra, 2013 was described from north Portugal based on males alone. Unidentified females were associated with the males using DNA barcoding, revealing sexual dimorphism in the species. Males and females differ in forewing shape, markings, and size, with females significantly smaller than males. The female is described and illustrated for the first time. We also document the species' occurrence in northern Spain.

  10. Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes.

    Science.gov (United States)

    Oliveira, L M; Knebelsberger, T; Landi, M; Soares, P; Raupach, M J; Costa, F O

    2016-12-01

    A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re-evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended. © 2016 The Fisheries Society of the British Isles.

  11. QR-codes maken entree in de bibliotheek: barcode nieuwe stijl

    NARCIS (Netherlands)

    Braak, P.

    2010-01-01

    QR (Quick Response) codes zijn barcodes die je met een mobiele telefoon kunt lezen. Ze zijn steeds vaker te vinden op posters, advertenties en andere producten. Meestal bevat een QR-code een URL. Na het scannen opent op de telefoon direct een (mobiele) website met aanvullende informatie over hetgeen

  12. Spatial heterogeneity in the Mediterranean Biodiversity Hotspot affects barcoding accuracy of its freshwater fishes

    Czech Academy of Sciences Publication Activity Database

    Geiger, M. F.; Herder, F.; Monaghan, M. T.; Almada, V.; Barbieri, R.; Bariche, M.; Berrebi, P.; Bohlen, Jörg; Casal-Lopez, M.; Delmastro, G. B.; Denys, G. P. J.; Dettai, A.; Doadrio, I.; Kalogianni, E.; Kärst, H.; Kottelat, M.; Kovačič, M.; Laporte, M.; Lorenzoni, M.; Marčič, Z.; Özulug, M.; Percides, A.; Perea, S.; Persat, H.; Porcelotti, S.; Puzzi, C.; Robalo, J.; Šanda, R.; Schneider, M.; Šlechtová, Vendula; Stoumboudi, M.; Walter, S.; Freyhof, J.

    2014-01-01

    Roč. 14, č. 6 (2014), s. 1210-1221 ISSN 1755-098X Institutional support: RVO:67985904 Keywords : DNA barcoding * evolutionary distinct and globally endangered score * fish Subject RIV: EG - Zoology Impact factor: 3.712, year: 2014

  13. What do they eat? Using DNA barcoding to assess diet preferences of deer

    DEFF Research Database (Denmark)

    Fløjgaard, Camilla; Ejrnæs, Rasmus

    landscapes open. However, in order to use this tool properly, we need to know more about what the animals eat compared to what is available in different habitats and how access to supplementary fodder influences the grazing effect on the vegetation. Using DNA barcoding of feces, we are investigating the diet...

  14. Ultra-barcoding in cacao (Theobroma spp.; Malvaceae) using whole chloroplast genomes and nuclear ribosomal DNA.

    Science.gov (United States)

    Kane, Nolan; Sveinsson, Saemundur; Dempewolf, Hannes; Yang, Ji Yong; Zhang, Dapeng; Engels, Johannes M M; Cronk, Quentin

    2012-02-01

    To reliably identify lineages below the species level such as subspecies or varieties, we propose an extension to DNA-barcoding using next-generation sequencing to produce whole organellar genomes and substantial nuclear ribosomal sequence. Because this method uses much longer versions of the traditional DNA-barcoding loci in the plastid and ribosomal DNA, we call our approach ultra-barcoding (UBC). We used high-throughput next-generation sequencing to scan the genome and generate reliable sequence of high copy number regions. Using this method, we examined whole plastid genomes as well as nearly 6000 bases of nuclear ribosomal DNA sequences for nine genotypes of Theobroma cacao and an individual of the related species T. grandiflorum, as well as an additional publicly available whole plastid genome of T. cacao. All individuals of T. cacao examined were uniquely distinguished, and evidence of reticulation and gene flow was observed. Sequence variation was observed in some of the canonical barcoding regions between species, but other regions of the chloroplast were more variable both within species and between species, as were ribosomal spacers. Furthermore, no single region provides the level of data available using the complete plastid genome and rDNA. Our data demonstrate that UBC is a viable, increasingly cost-effective approach for reliably distinguishing varieties and even individual genotypes of T. cacao. This approach shows great promise for applications where very closely related or interbreeding taxa must be distinguished.

  15. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae

    Directory of Open Access Journals (Sweden)

    Nerea eLarranaga

    2015-07-01

    Full Text Available The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra and A. purpurea and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia and in an interspecific hybrid (A. cherimola x A. squamosa. The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.

  16. DNA barcoding of perennial fruit tree species of agronomic interest in the genus Annona (Annonaceae).

    Science.gov (United States)

    Larranaga, Nerea; Hormaza, José I

    2015-01-01

    The DNA barcode initiative aims to establish a universal protocol using short genetic sequences to discriminate among animal and plant species. Although many markers have been proposed to become the barcode of plants, the Consortium for the Barcode of Life (CBOL) Plant Working Group recommended using as a core the combination of two portions of plastid coding region, rbcL and matK. In this paper, specific markers based on matK sequences were developed for 7 closely related Annona species of agronomic interest (Annona cherimola, A. reticulata, A. squamosa, A. muricata, A. macroprophyllata, A. glabra, and A. purpurea) and the discrimination power of both rbcL and matK was tested using also sequences of the genus Annona available in the Barcode of Life Database (BOLD) data systems. The specific sequences developed allowed the discrimination among all those species tested. Moreover, the primers generated were validated in six additional species of the genus (A. liebmanniana, A. longiflora, A. montana, A. senegalensis, A. emarginata and A. neosalicifolia) and in an interspecific hybrid (A. cherimola x A. squamosa). The development of a fast, reliable and economic approach for species identification in these underutilized subtropical fruit crops in a very initial state of domestication is of great importance in order to optimize genetic resource management.

  17. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

    Czech Academy of Sciences Publication Activity Database

    Schoch, C.L.; Seifert, K.A.; Huhndorf, S.; Robert, V.; Spouge, J.L.; Levesque, C.A.; Chen, W.; Bolchacova, E.; Voigt, K.; Crous, P.W.; Miller, A.N.; Wingfield, M. J.; Aime, M.C.; An, K.D.; Bai, F.Y.; Barreto, R.W.; Bergeron, M.J.; Blackwell, M.; Boekhout, T.; Bogale, M.; Boonyuen, N.; Burgaz, A.R.; Buyck, B.; Cai, L.; Cai, Q.; Cardinali, G.; Chaverri, P.; Coppins, B.J.; Crespo, A.; Cubas, P.; Cummings, C.; Damm, U.; de Beer, Z.W.; de Hoog, G.S.; Del-Prado, R.; Dentinger, B.; Dieguez-Uribeondo, J.; Divakar, P.K.; Douglas, B.; Duenas, M.; Duong, T.A.; Eberhardt, U.; Edwards, J.E.; Elshahed, M.S.; Fliegerová, Kateřina; Furtado, M.; Garcia, M.A.; Ge, Z.W.; Griffith, G.W.; Griffiths, K.; Groenewald, J.Z.; Groenewald, M.; Grube, M.; Gryzenhout, M.; Guo, L.D.; Hagen, F.; Hambleton, S.; Hamelin, R.C.; Hansen, K.; Harrold, P.; Heller, G.; Herrera, C.; Hirayama, K.; Hirooka, Y.; Ho, H.M.; Hoffmann, K.; Hofstetter, V.; Hognabba, F.; Hollingsworth, P.M.; Hong, S.B.; Hosaka, K.; Houbraken, J.; Hughes, K.; Huhtinen, S.; Hyde, K.D.; James, T.; Johnson, E.M.; Johnson, J.E.; Johnston, P.R.; Jones, E.B.; Kelly, L.J.; Kirk, P.M.; Knapp, D.G.; Koljalg, U.; Kovacs, G.M.; Kurtzman, C.P.; Landvik, S.; Leavitt, S.D.; Liggenstoffer, A.S.; Liimatainen, K.; Lombard, L.; Luangsa-Ard, J.J.; Lumbsch, H.T.; Maganti, H.; Maharachchikumbura, S.S.; Martin, M.P.; May, T.W.; McTaggart, A.R.; Methven, A.S.; Meyer, W.; Moncalvo, J.M.; Mongkolsamrit, S.; Nagy, L.G.; Nilsson, R.H.; Niskanen, T.; Nyilasi, I.; Okada, G.; Okane, I.; Olariaga, I.; Otte, J.; Papp, T.; Park, D.; Petkovits, T.; Pino-Bodas, R.; Quaedvlieg, W.; Raja, H.A.; Redecker, D.; Rintoul, T.; Ruibal, C.; Sarmiento-Ramirez, J.M.; Schmitt, I.; Schussler, A.; Shearer, C.; Sotome, K.; Stefani, F.O.; Stenroos, S.; Stielow, B.; Stockinger, H.; Suetrong, S.; Suh, S.O.; Sung, G.H.; Suzuki, M.; Tanaka, K.; Tedersoo, L.; Telleria, M.T.; Tretter, E.; Untereiner, W.A.; Urbina, H.; Vagvolgyi, C.; Vialle, A.; Vu, T.D.; Walther, G.; Wang, Q.M.; Wang, Y.; Weir, B.S.; Weiss, M.; White, M.M.; Xu, J.; Yahr, R.; Yang, Z.L.; Yurkov, A.; Zamora, J.C.; Zhang, N.; Zhuang, W.Y.; Schindel, D.

    Roč. 109, č. 16 ( 2012 ), s. 6241-6246 ISSN 0027-8424 Institutional research plan: CEZ:AV0Z50450515 Keywords : DNA barcoding * fungal biodiversity Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.737, year: 2012

  18. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

    Science.gov (United States)

    Yahr, Rebecca; Schoch, Conrad L; Dentinger, Bryn T M

    2016-09-05

    The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

  19. Towards a global barcode library for Lymantria (Lepidoptera: Lymantriinae) tussock moths of biosecurity concern

    Science.gov (United States)

    Jeremy R. deWaard; Andrew Mitchell; Melody A. Keena; David Gopurenko; Laura M. Boykin; Karen F. Armstrong; Michael G. Pogue; Joao Lima; Robin Floyd; Robert H. Hanner; Leland M. Humble

    2010-01-01

    This study demonstrates the efficacy of DNA barcodes for diagnosing species of Lymantria and reinforces the view that the approach is an under-utilized resource with substantial potential for biosecurity and surveillance. Biomonitoring agencies currently employing the NB restriction digest system would gather more information by transitioning to the...

  20. Establishing a community-wide DNA barcode library as a new tool for arctic research

    DEFF Research Database (Denmark)

    Wirta, Helena; Várkonyi, Gergely; Rasmussen, Claus

    2016-01-01

    DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied a...

  1. Review and future prospects for DNA barcoding methods in forensic palynology.

    Science.gov (United States)

    Bell, Karen L; Burgess, Kevin S; Okamoto, Kazufusa C; Aranda, Roman; Brosi, Berry J

    2016-03-01

    Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. However, its use has previously been limited by the need for a high level of specialization by expert palynologists, slow speeds of identification, and relatively poor taxonomic resolution (typically to the plant family or genus level). By contrast, identification of pollen through DNA barcoding has the potential to overcome all three of these limitations, and it may seem surprising that the method has not been widely implemented. Despite what might seem a straightforward application of DNA barcoding to pollen, there are technical issues that have delayed progress. However, recent developments of standard methods for DNA barcoding of pollen, along with improvements in high-throughput sequencing technology, have overcome most of these technical issues. Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Sound Synthesis and Bar-Code Technology to Develop Learning Environments for Blind Children.

    Science.gov (United States)

    Burger, D.; And Others

    1990-01-01

    An interactive, computerized sound machine was designed, incorporating bar-code technology in the user interface. The system was used in a classroom of nine blind elementary level children to teach sound awareness, logic, metalinguistics, and technological literacy and was found to have pedagogical relevance. (Author/JDD)

  3. Developing an Apicomplexan DNA Barcoding System to Detect Blood Parasites of Small Coral Reef Fishes.

    Science.gov (United States)

    Renoux, Lance P; Dolan, Maureen C; Cook, Courtney A; Smit, Nico J; Sikkel, Paul C

    2017-08-01

    Apicomplexan parasites are obligate parasites of many species of vertebrates. To date, there is very limited understanding of these parasites in the most-diverse group of vertebrates, actinopterygian fishes. While DNA barcoding targeting the eukaryotic 18S small subunit rRNA gene sequence has been useful in identifying apicomplexans in tetrapods, identification of apicomplexans infecting fishes has relied solely on morphological identification by microscopy. In this study, a DNA barcoding method was developed that targets the 18S rRNA gene primers for identifying apicomplexans parasitizing certain actinopterygian fishes. A lead primer set was selected showing no cross-reactivity to the overwhelming abundant host DNA and successfully confirmed 37 of the 41 (90.2%) microscopically verified parasitized fish blood samples analyzed in this study. Furthermore, this DNA barcoding method identified 4 additional samples that screened negative for parasitemia, suggesting this molecular method may provide improved sensitivity over morphological characterization by microscopy. In addition, this PCR screening method for fish apicomplexans, using Whatman FTA preserved DNA, was tested in efforts leading to a more simplified field collection, transport, and sample storage method as well as a streamlining sample processing important for DNA barcoding of large sample sets.

  4. Taxonomic reference libraries for environmental barcoding: a best practice example from diatom research.

    Directory of Open Access Journals (Sweden)

    Jonas Zimmermann

    Full Text Available DNA barcoding uses a short fragment of a DNA sequence to identify a taxon. After obtaining the target sequence it is compared to reference sequences stored in a database to assign an organism name to it. The quality of data in the reference database is the key to the success of the analysis. In the here presented study, multiple types of data have been combined and critically examined in order to create best practice guidelines for taxonomic reference libraries for environmental barcoding. 70 unialgal diatom strains from Berlin waters have been established and cultured to obtain morphological and molecular data. The strains were sequenced for 18S V4 rDNA (the pre-Barcode for protists as well as rbcL data, and identified by microscopy. LM and for some strains also SEM pictures were taken and physical vouchers deposited at the BGBM. 37 freshwater taxa from 15 naviculoid diatom genera were identified. Four taxa from the genera Amphora, Mayamaea, Planothidium and Stauroneis are described here as new. Names, molecular, morphological and habitat data as well as additional images of living cells are also available electronically in the AlgaTerra Information System. All reference sequences (or reference barcodes presented here are linked to voucher specimens in order to provide a complete chain of evidence back to the formal taxonomic literature.

  5. The Use of DNA Barcoding in Identification of Genetic Diversity of ...

    African Journals Online (AJOL)

    Prof. Ogunji

    Fish species revealed similar and different polymorphism and genomic classification during the experiment. ..... Zoology. McGraw-Hill Publishing Co. 23. Savolainen, V., Cowan, R. S., Vogler, A. P. (2005). Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philos Trans. Ser. B. 360: 1850 – 1811.

  6. A DNA barcoding approach to identify plant species in multiflower honey.

    Science.gov (United States)

    Bruni, I; Galimberti, A; Caridi, L; Scaccabarozzi, D; De Mattia, F; Casiraghi, M; Labra, M

    2015-03-01

    The purpose of this study was to test the ability of DNA barcoding to identify the plant origins of processed honey. Four multifloral honeys produced at different sites in a floristically rich area in the northern Italian Alps were examined by using the rbcL and trnH-psbA plastid regions as barcode markers. An extensive reference database of barcode sequences was generated for the local flora to determine the taxonomic composition of honey. Thirty-nine plant species were identified in the four honey samples, each of which originated from a mix of common plants belonging to Castanea, Quercus, Fagus and several herbaceous taxa. Interestingly, at least one endemic plant was found in all four honey samples, providing a clear signature for the geographic identity of these products. DNA of the toxic plant Atropa belladonna was detected in one sample, illustrating the usefulness of DNA barcoding for evaluating the safety of honey. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. [DNA barcoding and its utility in commonly-used medicinal snakes].

    Science.gov (United States)

    Huang, Yong; Zhang, Yue-yun; Zhao, Cheng-jian; Xu, Yong-li; Gu, Ying-le; Huang, Wen-qi; Lin, Kui; Li, Li

    2015-03-01

    Identification accuracy of traditional Chinese medicine is crucial for the traditional Chinese medicine research, production and application. DNA barcoding based on the mitochondrial gene coding for cytochrome c oxidase subunit I (COI), are more and more used for identification of traditional Chinese medicine. Using universal barcoding primers to sequence, we discussed the feasibility of DNA barcoding method for identification commonly-used medicinal snakes (a total of 109 samples belonging to 19 species 15 genera 6 families). The phylogenetic trees using Neighbor-joining were constructed. The results indicated that the mean content of G + C(46.5%) was lower than that of A + T (53.5%). As calculated by Kimera-2-parameter model, the mean intraspecies genetic distance of Trimeresurus albolabris, Ptyas dhumnades and Lycodon rufozonatus was greater than 2%. Further phylogenetic relationship results suggested that identification of one sample of T. albolabris was erroneous. The identification of some samples of P. dhumnades was also not correct, namely originally P. korros was identified as P. dhumnades. Factors influence on intraspecific genetic distance difference of L. rufozonatus need to be studied further. Therefore, DNA barcoding for identification of medicinal snakes is feasible, and greatly complements the morphological classification method. It is necessary to further study in identification of traditional Chinese medicine.

  8. Internal transcribed spacer 2 barcode: A good tool for identifying Acanthopanacis cortex

    Directory of Open Access Journals (Sweden)

    Sha eZhao

    2015-10-01

    Full Text Available Acanthopanacis cortex has been used in clinical applications for a long time. Considering some historical and geographical factors, Acanthopanacis cortex is easily confused with other herbs in medicine markets, thereby causing potential safety issues. In this study, we used the internal transcribed spacer 2 (ITS2 barcode to identify 69 samples belonging to six species, including Acanthopanacis cortex and its adulterants. The nearest distance, single-nucleotide polymorphisms (SNPs, and neighbor-joining (NJ tree methods were used to evaluate the identification ability of the ITS2 barcode. According to the kimura-2-parameter model, the intraspecific distance of Eleutherococcus nodiflorus ITS2 sequences ranged from 0 to 0.0132. The minimum interspecific distance between E. nodiflorus and E. giraldii was 0.0221, which was larger than the maximum intraspecific distance of E. nodiflorus. Three stable SNPs in ITS2 can be used to distinguish Acanthopanacis cortex and its closely related species. The NJ tree indicated that the Acanthopanacis cortex samples clustered into one clade, which can be distinguished clearly from the adulterants of this herb. A secondary structure of ITS2 provided another dimensionality to identify species. In conclusion, the ITS2 barcode effectively identifies Acanthopanacis cortex, and DNA barcoding is a convenient tool for medicine market supervision.

  9. DNA barcoding evaluation and implications for phylogenetic relationships in ladybird beetles (Coleoptera: Coccinellidae).

    Science.gov (United States)

    Wang, Zheng-Liang; Wang, Tian-Zhao; Zhu, Hang-Feng; Wang, Zi-Ye; Yu, Xiao-Ping

    2018-03-08

    Ladybird beetles (Coleoptera: Coccinellidae), with broad morphological diversity, wide geographic distribution and substantial agricultural significance, are a challenging group for taxonomists and phylogenetics. As a promising tool to identify and discover new species, DNA barcoding might offer significant potential for identification, taxonomy and phylogeny of ladybird beetles. In the present study, a total of 1364 COI (cytochrome C oxidase subunit I) sequences representing 128 species from 52 genera of ladybird beetles were screened for barcoding evaluation and phylogenetic analysis. Our results from the barcoding analysis revealed that COI displays a similar level of species identification efficiency (nearly 90%) either based on Kimura two-parameter (K2P) distances calculation or on simplified neighbour-joining (NJ) tree construction. The phylogenetic relationships within the family Coccinellidae was analyzed by Bayesian-inference (BI) method. The phylogenetic results confirmed the monophyly of the subfamilies Microweisinae and Coccinellinae sensu Ślipiński (2007), and suggested that the subfamilies Coccidulinae, Chilocorinae and Scymninae are paraphyletic. However, the phylogenetic relationships among different subfamilies are not clearly defined and thus remain to be thoroughly studied. Overall, our study confirmed the usefulness of DNA barcoding for coccinellid species identification and phylogenetic inference.

  10. DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae).

    Science.gov (United States)

    Hernández-Triana, Luis M; Montes De Oca, Fernanda; Prosser, Sean W J; Hebert, Paul D N; Gregory, T Ryan; McMurtrie, Shelley

    2017-04-01

    In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%-4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

  11. Characterization of a Plasmodium falciparum Orthologue of the Yeast Ubiquinone-Binding Protein, Coq10p.

    Directory of Open Access Journals (Sweden)

    Bethany J Jenkins

    Full Text Available Coenzyme Q (CoQ, ubiquinone is a central electron carrier in mitochondrial respiration. CoQ is synthesized through multiple steps involving a number of different enzymes. The prevailing view that the CoQ used in respiration exists as a free pool that diffuses throughout the mitochondrial inner membrane bilayer has recently been challenged. In the yeast Saccharomyces cerevisiae, deletion of the gene encoding Coq10p results in respiration deficiency without inhibiting the synthesis of CoQ, suggesting that the Coq10 protein is critical for the delivery of CoQ to the site(s of respiration. The precise mechanism by which this is achieved remains unknown at present. We have identified a Plasmodium orthologue of Coq10 (PfCoq10, which is predominantly expressed in trophozoite-stage parasites, and localizes to the parasite mitochondrion. Expression of PfCoq10 in the S. cerevisiae coq10 deletion strain restored the capability of the yeast to grow on respiratory substrates, suggesting a remarkable functional conservation of this protein over a vast evolutionary distance, and despite a relatively low level of amino acid sequence identity. As the antimalarial drug atovaquone acts as a competitive inhibitor of CoQ, we assessed whether over-expression of PfCoq10 altered the atovaquone sensitivity in parasites and in yeast mitochondria, but found no alteration of its activity.

  12. ABC protein transport of MRI contrast agents in canalicular rat liver plasma vesicles and yeast vacuoles

    International Nuclear Information System (INIS)

    Pascolo, Lorella; Petrovic, Sinisa; Cupelli, Felicia; Bruschi, Carlo V.; Anelli, Pier Lucio; Lorusso, Vito; Visigalli, Massimo; Uggeri, Fulvio; Tiribelli, Claudio

    2001-01-01

    The mechanism of excretion into bile of hepatospecific magnetic resonance imaging (MRI) contrast media employed labeled Gd-reagents EOB.DTPA, BOPTA, B 20790 (iopanoate-linked), and B 21690 (glycocholate-linked) for measurement in rat liver canalicular plasma membrane vesicles and yeast vacuoles. The presence of ATP gave threefold greater transport of B 20790 and B 21690 than of EOB.DTPA and BOPTA. In yeast vacuoles the ATP stimulatory effect was eightfold with B 20790 and fivefold greater for B 21690, whereas in YCF1- or YLLO115w-deleted yeast cells the transport was significantly reduced and absent from double mutants, YCF1 and YLLO15w. The transport was similar in wild-type and deletant cells for B 21690; taurocholate gave 85% inhibition. These data suggest that bilary secretion of structurally related MRI agents depend on molecular structure. The findings are suggestive as of possible value for clinical diagnosis of inherited hyperbilirubinemias and other liver disorders

  13. DNA barcoding: a tool for standardization of herbal medicinal products (HMPS) of lamiaceae from pakistan

    International Nuclear Information System (INIS)

    Zahra, N.B.; Shinwari, Z.K.

    2016-01-01

    There has been a considerable interest worldwide in traditional and alternative medicine, particularly herbal products over the past few decades but the adulteration or contamination of herbal medicinal products (HMPs) is a potential threat to consumer safety. The fact highlights the importance of an effective and accurate science integrated method for taxonomic identification of the medicinal plants and their HMPs. DNA barcoding is a molecular technique which has made it possible to identify the herbs and to find the adulterants in HMPs. The current study was designed on DNA barcoding of medicinal plants of family Lamiaceae for their correct identification and to fix the problem of adulteration for protecting consumers from health risks associated with product substitution and contamination. Many Lamiaceae species are used as traditional medicines, as culinary herbs, spices and as source of essential oils. HMPs representing 32 Lamiaceae plant samples were purchased/collected from three herbal stores (Pansar stores) in Islamabad and a herbal pharmaceutical industry. We selected three plastid loci rbcL, matK and psbA-trnH to barcode these HMPs. MEGABLAST sequence comparison was performed to verify the taxonomic identity of the samples. We found four mislabeled samples and two product substitutions. The overall amplification success for rbcL and matK was 87% and 81% while psbA-trnH showed 69%. matK and psbA-trnH were able to distinguish the species relatively better with 40% success rate than rbcL (16%). On the whole we generated a total of 22 genus-level barcodes (78%) and 12 species-level barcodes (44%). The species-level identification was considerably low due to insufficient reference data and selection of plastid markers. Therefore, it is recommended to develop herbal barcode library for adequate availability of reference sequence data and addition of nuclear markers. DNA barcoding can help the regulatory authorities to devise a mechanism for quality control and

  14. Deletion of a Chitin Synthase Gene in a Citric Acid Producing Strain of Aspergillus niger

    Energy Technology Data Exchange (ETDEWEB)

    Rinker, Torri E.; Baker, Scott E.

    2007-01-29

    Citric acid production by the filamentous fungus Aspergillus niger is carried out in a process that causes the organism to drastically alter its morphology. This altered morphology includes hyphal swelling and highly limited polar growth resulting in clumps of swollen cells that eventually aggregate into pellets of approximately 100 microns in diameter. In this pelleted form, A. niger has increased citric acid production as compared to growth in filamentous form. Chitin is a crucial component of the cell wall of filamentous fungi. Alterations in the deposition or production of chitin may have profound effects on the morphology of the organism. In order to study the role of chitin synthesis in pellet formation we have deleted a chitin synthase gene (csmA) in Aspergillus niger strain ATCC 11414 using a PCR based deletion construct. This class of chitin synthases is only found in filamentous fungi and is not present in yeasts. The csmA genes contain a myosin motor domain at the N-terminus and a chitin synthesis domain at the C-terminus. They are believed to contribute to the specialized polar growth observed in filamentous fungi that is lacking in yeasts. The csmA deletion strain (csmAΔ) was subjected to minimal media with and without osmotic stabilizers as well as tested in citric acid production media. Without osmotic stabilizers, the mutant germlings were abnormally swollen, primarily in the subapical regions, and contained large vacuoles. However, this swelling is ultimately not inhibitory to growth as the germlings are able to recover and undergo polar growth. Colony formation was largely unaffected in the absence of osmotic stabilizers. In citric acid production media csmAΔ was observed to have a 2.5 fold increase in citric acid production. The controlled expression of this class of chitin synthases may be useful for improving production of organic acids in filamentous fungi.

  15. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis.

    Science.gov (United States)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta; Mikkelsen, Martin; Johansen, Peter; Børsting, Claus; Morling, Niels

    2014-08-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72 individuals using only 24 barcoded libraries.

  16. Rapid deletion production in fungi via Agrobacterium mediated transformation of OSCAR deletion contructs.

    Science.gov (United States)

    Precise deletion of gene(s) of interest, while leaving the rest of the genome unchanged, provides the ideal product to determine that particular gene’s function in the living organism. In this protocol we describe the OSCAR method of precise and rapid deletion plasmid construction. OSCAR relies on t...

  17. Yeast Cells Lacking the CIT1-encoded Mitochondrial Citrate Synthase Are Hypersusceptible to Heat- or Aging-induced Apoptosis

    OpenAIRE

    Lee, Yong Joo; Hoe, Kwang Lae; Maeng, Pil Jae

    2007-01-01

    In Saccharomyces cerevisiae, the initial reaction of the tricarboxylic acid cycle is catalyzed by the mitochondrial citrate synthase Cit1. The function of Cit1 has previously been studied mainly in terms of acetate utilization and metabolon construction. Here, we report the relationship between the function of Cit1 and apoptosis. Yeast cells with cit1 deletion showed a temperature-sensitive growth phenotype, and they displayed a rapid loss in viability associated with typical apoptotic hallma...

  18. The ATPase and protease domains of yeast mitochondrial Lon: Roles in proteolysis and respiration-dependent growth

    OpenAIRE

    van Dijl, Jan Maarten; Kutejová, Eva; Suda, Kitaru; Perečko, Dušan; Schatz, Gottfried; Suzuki, Carolyn K.

    1998-01-01

    The ATP-dependent Lon protease of Saccharomyces cerevisiae mitochondria is required for selective proteolysis in the matrix, maintenance of mitochondrial DNA, and respiration-dependent growth. Lon may also possess a chaperone-like function that facilitates protein degradation and protein-complex assembly. To understand the influence of Lon’s ATPase and protease activities on these functions, we examined several Lon mutants for their ability to complement defects of Lon-deleted yeast cells. We...

  19. Somatic mosaicism for a DMD gene deletion

    Energy Technology Data Exchange (ETDEWEB)

    Saito, Kayoko; Ikeya, Kiyoko; Kondo, Eri [Tokyo Women`s Medical College (Japan)] [and others

    1995-03-13

    Mosaicism is a mixed state, with two cell populations of different genetic origins caused by a cell mutation occurring after fertilization. In the present case, DNA analysis of lymphocytes led to a DMD diagnosis before death. Postmortem immunocytochemical and DNA analysis showed somatic mosaicism. At age 18 years, blood lymphocyte DNA analysis showed a DMD gene deletion, upstream from exon 7 to the 5{prime} end containing both muscle and brain promoters. As the patient`s mother and elder sister had no deletions, he was considered to have a new mutation. Immunocytochemical studies of postmortem tissues showed that dystrophin was absent from the tongue, deltoid, intercostal, psoas and rectus femoris muscles, but there was a mix of dystrophin-positive and negative fibers in the rectus abdominis, cardiac, temporalis and sternocleidomastoid muscles. All diaphragm cells were dystrophin positive. Polymerase chain reaction (PCR) amplification from all tissues except the temporalis and sternocleidomastoid muscles, diaphragm and kidney, in which no deletion was found, showed the deletion from at least exon 6 to the 5{prime} end containing both muscle and brain promoters. In this case, a genomic deletion of the DMD gene contributed to the formation of tissues derived from both ectoderm and endoderm, and cells of mesodermal origin showed genotypic and phenotypic heterogeneity. Our results indicate a mutation of the present case may have occurred just before the period of germ layer formation. 34 refs., 7 figs.

  20. Pictorial AR Tag with Hidden Multi-Level Bar-Code and Its Potential Applications

    Directory of Open Access Journals (Sweden)

    Huy Le

    2017-09-01

    Full Text Available For decades, researchers have been trying to create intuitive virtual environments by blending reality and virtual reality, thus enabling general users to interact with the digital domain as easily as with the real world. The result is “augmented reality” (AR. AR seamlessly superimposes virtual objects on to a real environment in three dimensions (3D and in real time. One of the most important parts that helps close the gap between virtuality and reality is the marker used in the AR system. While pictorial marker and bar-code marker are the two most commonly used marker types in the market, they have some disadvantages in visual and processing performance. In this paper, we present a novelty method that combines the bar-code with the original feature of a colour picture (e.g., photos, trading cards, advertisement’s figure. Our method decorates on top of the original pictorial images additional features with a single stereogram image that optically conceals a multi-level (3D bar-code. Thus, it has a larger capability of storing data compared to the general 1D barcode. This new type of marker has the potential of addressing the issues that the current types of marker are facing. It not only keeps the original information of the picture but also contains encoded numeric information. In our limited evaluation, this pictorial bar-code shows a relatively robust performance under various conditions and scaling; thus, it provides a promising AR approach to be used in many applications such as trading card games, educations, and advertisements.

  1. Character-based, population-level DNA barcoding in Mexican species of Zamia L. (Zamiaceae: Cycadales).

    Science.gov (United States)

    Nicolalde-Morejón, Fernando; Vergara-Silva, Francisco; González-Astorga, Jorge; Stevenson, Dennis W

    2010-12-01

    With the recent proposal of matK and rbcL as core plant DNA barcoding regions by the Consortium for the Barcoding of Life Plant Working Group, the construction of reference libraries in the botanical DNA barcoding initiative has entered a new phase. However, in a recent DNA barcoding study in the three Mexican genera of the gymnosperm order Cycadales, we found that neither matK nor rbcL allow high levels of molecular identification of previously established species. Our data analysis in that study rested on the "Characteristic Attributes Organization System" (CAOS), a character-based algorithm for the definition of "DNA diagnostics." Here, we use CAOS to analyze a population-level molecular data set in Zamia, one of the three cycad genera occurring in Mexico, whose populations display contrasting biogeographic patterns. Our population-level study, which includes all species in the region formally known as Megamexico, is restricted to the genome region, which showed the best single-locus molecular identification performance in our previous study-namely, the noncoding intergenic chloroplast spacer psbK-I. Our comparison of single-individual vs. population-level psbK-I datasets in Zamia indicates that CAOS analyses are sensitive to slight alignment changes, which in turn derive from the different amounts of molecular variation present in each matrix type. We, therefore, suggest that character-based studies that involve population-level data should contemplate this type of comparison between data matrices, before a set of DNA diagnostics in a given DNA barcoding reference library is considered definitive.

  2. Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker

    Science.gov (United States)

    Stern, Rowena F.; Andersen, Robert A.; Jameson, Ian; Küpper, Frithjof C.; Coffroth, Mary-Alice; Vaulot, Daniel; Le Gall, Florence; Véron, Benoît; Brand, Jerry J.; Skelton, Hayley; Kasai, Fumai; Lilly, Emily L.; Keeling, Patrick J.

    2012-01-01

    Background DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. Methodology/Principal Findings The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. Conclusions/Significance The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would

  3. Benefits and Limitations of DNA Barcoding and Metabarcoding in Herbal Product Authentication

    Science.gov (United States)

    Raclariu, Ancuta Cristina; Heinrich, Michael; Ichim, Mihael Cristin

    2017-01-01

    Abstract Introduction Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono‐substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry‐based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients. Objective To review the benefits and limitations of DNA barcoding and metabarcoding in complementing current herbal product authentication. Method Recent literature relating to DNA based authentication of medicinal plants, herbal medicines and products are summarised to provide a basic understanding of how DNA barcoding and metabarcoding can be applied to this field. Results Different methods of quality control and authentication have varying resolution and usefulness along the value chain of these products. DNA barcoding can be used for authenticating products based on single herbal ingredients and DNA metabarcoding for assessment of species diversity in processed products, and both methods should be used in combination with appropriate hyphenated chemical methods for quality control. Conclusions DNA barcoding and metabarcoding have potential in the context of quality control of both well and poorly regulated supply systems. Standardisation of protocols for DNA barcoding and DNA sequence‐based identification are necessary before DNA‐based biological methods can be implemented as routine analytical approaches and approved by the competent authorities for use in regulated procedures. © 2017 The Authors. Phytochemical Analysis Published by John Wiley & Sons Ltd. PMID:28906059

  4. DNA Barcoding to Improve the Taxonomy of the Afrotropical Hoverflies (Insecta: Diptera: Syrphidae.

    Directory of Open Access Journals (Sweden)

    Kurt Jordaens

    Full Text Available The identification of Afrotropical hoverflies is very difficult because of limited recent taxonomic revisions and the lack of comprehensive identification keys. In order to assist in their identification, and to improve the taxonomy of this group, we constructed a reference dataset of 513 COI barcodes of 90 of the more common nominal species from Ghana, Togo, Benin and Nigeria (W Africa and added ten publically available COI barcodes from nine nominal Afrotropical species to this (total: 523 COI barcodes; 98 nominal species; 26 genera. The identification accuracy of this dataset was evaluated with three methods (K2P distance-based, Neighbor-Joining (NJ / Maximum Likelihood (ML analysis, and using SpeciesIdentifier. Results of the three methods were highly congruent and showed a high identification success. Nine species pairs showed a low ( 0.03 maximum intraspecific K2P distance was observed in eight species and barcodes of these species not always formed single clusters in the NJ / ML analayses which may indicate the occurrence of cryptic species. Optimal K2P thresholds to differentiate intra- from interspecific K2P divergence were highly different among the three subfamilies (Eristalinae: 0.037, Syrphinae: 0.06, Microdontinae: 0.007-0.02, and among the different general suggesting that optimal thresholds are better defined at the genus level. In addition to providing an alternative identification tool, our study indicates that DNA barcoding improves the taxonomy of Afrotropical hoverflies by selecting (groups of taxa that deserve further taxonomic study, and by attributing the unknown sex to species for which only one of the sexes is known.

  5. DNA barcoding as a complementary tool for conservation and valorisation of forest resources

    Directory of Open Access Journals (Sweden)

    Angeliki Laiou

    2013-12-01

    Full Text Available Since the pre-historic era, humans have been using forests as a food, drugs and handcraft reservoir. Today, the use of botanical raw material to produce pharmaceuticals, herbal remedies, teas, spirits, cosmetics, sweets, dietary supplements, special industrial compounds and crude materials constitute an important global resource in terms of healthcare and economy. In recent years, DNA barcoding has been suggested as a useful molecular technique to complement traditional taxonomic expertise for fast species identification and biodiversity inventories. In this study, in situ application of DNA barcodes was tested on a selected group of forest tree species with the aim of contributing to the identification, conservation and trade control of these valuable plant resources.The “core barcode” for land plants (rbcL, matK, and trnH-psbA was tested on 68 tree specimens (24 taxa. Universality of the method, ease of data retrieval and correct species assignment using sequence character states, presence of DNA barcoding gaps and GenBank discrimination assessment were evaluated. The markers showed different prospects of reliable applicability. RbcL and trnH-psbA displayed 100% amplification and sequencing success, while matK did not amplify in some plant groups. The majority of species had a single haplotype. The trnH-psbA region showed the highest genetic variability, but in most cases the high intra-specific sequence divergence revealed the absence of a clear DNA barcoding gap. We also faced an important limitation because the taxonomic coverage of the public reference database is incomplete. Overall, species identification success was 66.7%.This work illustrates current limitations in the applicability of DNA barcoding to taxonomic forest surveys. These difficulties urge for an improvement of technical protocols and an increase of the number of sequences and taxa in public databases.

  6. Extent and divergence of heteroplasmy of the DNA barcoding region in Anapodisma miramae (Orthoptera: Acrididae).

    Science.gov (United States)

    Kang, Ah Rang; Kim, Min Jee; Park, In Ah; Kim, Kee Young; Kim, Iksoo

    2016-09-01

    A partial sequence of the mitochondrial cytochrome oxidase subunit I (COI) gene is widely used as a molecular marker for species identification in animals, also termed a DNA barcode. However, the presence of more than one sequence type in a single individual, also known as heteroplasmy, is one of the shortcomings of barcode identification. In this study, we examined the extent and divergence of COI heteroplasmy, including nuclear-encoded mitochondrial pseudogenes (NUMTs), at the genomic-DNA level from 13 insect species including orthopteran Anapodisma miramae, and a long fragment of mitochondrial DNA and cDNA from A. miramae as templates. When multiple numbers of clones originated from genomic DNA were sequenced, heteroplasmy was prevalent in all species and NUMTs were observed in five species. Long fragment DNA (∼13.5 kb) also is a source of heteroplasmic amplification, but the divergent haplotypes and NUMTs obtained from genomic DNA were not detected in A. miramae. On the other hand, cDNA was relatively heteroplasmy-free. Consistently, one dominant haplotype was always obtained from the genomic DNA-origin clones in all species and also from the long fragment- and cDNA-origin clones in the two tested individuals of A. miramae. Furthermore, the dominant haplotype was identical in sequence, regardless of the DNA source in A. miramae. Thus, one possible solution to avoid the barcoding problem in relationship to heteroplasmy could be the acquisition of multiple numbers of barcoding sequences to determine a dominant haplotype that can be assigned as barcoding sequence for a given species.

  7. Application of the ITS2 Region for Barcoding Medicinal Plants of Selaginellaceae in Pteridophyta.

    Science.gov (United States)

    Gu, Wei; Song, Jingyuan; Cao, Yuan; Sun, Qingwen; Yao, Hui; Wu, Qinan; Chao, Jianguo; Zhou, Juanjuan; Xue, Wenda; Duan, Jinao

    2013-01-01

    Selaginellaceae is a family of nonseed plants with special evolutionary significance. Plants of the family Selaginellaceae are similarly shaped and easily confused, complicating identification via traditional methods. This study explored, for the first time, the use of the DNA barcode ITS2 to identify medicinal plants of the Selaginellaceae family. In our study, 103 samples were collected from the main distribution areas in China; these samples represented 34 species and contained almost all of the medicinal plants of Selaginellaceae. The ITS2 region of the genome was amplified from these samples and sequenced using universal primers and reaction conditions. The success rates of the PCR amplification and sequencing were 100%. There was significant divergence between the interspecific and intraspecific genetic distances of the ITS2 regions, while the presence of a barcoding gap was obvious. Using the BLAST1 and nearest distance methods, our results proved that the ITS2 regions could successfully identify the species of all Selaginellaceae samples examined. In addition, the secondary structures of ITS2 in the helical regions displayed clear differences in stem loop number, size, position, and screw angle among the medicinal plants of Selaginellaceae. Furthermore, cluster analysis using the ITS2 barcode supported the relationship between the species of Selaginellaceae established by traditional morphological methods. The ITS2 barcode can effectively identify medicinal plants of Selaginellaceae. The results provide a scientific basis for the precise identification of plants of the family Selaginellaceae and the reasonable development of these resources. This study may broaden the application of DNA barcoding in the medicinal plant field and benefit phylogenetic investigations.

  8. Application of the ITS2 Region for Barcoding Medicinal Plants of Selaginellaceae in Pteridophyta.

    Directory of Open Access Journals (Sweden)

    Wei Gu

    Full Text Available Selaginellaceae is a family of nonseed plants with special evolutionary significance. Plants of the family Selaginellaceae are similarly shaped and easily confused, complicating identification via traditional methods. This study explored, for the first time, the use of the DNA barcode ITS2 to identify medicinal plants of the Selaginellaceae family.In our study, 103 samples were collected from the main distribution areas in China; these samples represented 34 species and contained almost all of the medicinal plants of Selaginellaceae. The ITS2 region of the genome was amplified from these samples and sequenced using universal primers and reaction conditions. The success rates of the PCR amplification and sequencing were 100%. There was significant divergence between the interspecific and intraspecific genetic distances of the ITS2 regions, while the presence of a barcoding gap was obvious. Using the BLAST1 and nearest distance methods, our results proved that the ITS2 regions could successfully identify the species of all Selaginellaceae samples examined. In addition, the secondary structures of ITS2 in the helical regions displayed clear differences in stem loop number, size, position, and screw angle among the medicinal plants of Selaginellaceae. Furthermore, cluster analysis using the ITS2 barcode supported the relationship between the species of Selaginellaceae established by traditional morphological methods.The ITS2 barcode can effectively identify medicinal plants of Selaginellaceae. The results provide a scientific basis for the precise identification of plants of the family Selaginellaceae and the reasonable development of these resources. This study may broaden the application of DNA barcoding in the medicinal plant field and benefit phylogenetic investigations.

  9. Endoplasmic reticulum involvement in yeast cell death

    International Nuclear Information System (INIS)

    Nicanor Austriaco, O.

    2012-01-01

    Yeast cells undergo programed cell death (PCD) with characteristic markers associated with apoptosis in mammalian cells including chromatin breakage, nuclear fragmentation, reactive oxygen species generation, and metacaspase activation. Though significant research has focused on mitochondrial involvement in this phenomenon, more recent work with both Saccharomyces cerevisiae and Schizosaccharomyces pombe has also implicated the endoplasmic reticulum (ER) in yeast PCD. This minireview provides an overview of ER stress-associated cell death (ER-SAD) in yeast. It begins with a description of ER structure and function in yeast before moving to a discussion of ER-SAD in both mammalian and yeast cells. Three examples of yeast cell death associated with the ER will be highlighted here including inositol starvation, lipid toxicity, and the inhibition of N-glycosylation. It closes by suggesting ways to further examine the involvement of the ER in yeast cell death.

  10. A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation.

    Directory of Open Access Journals (Sweden)

    Camille Duc

    Full Text Available Yeast cell death can occur during wine alcoholic fermentation. It is generally considered to result from ethanol stress that impacts membrane integrity. This cell death mainly occurs when grape musts processing reduces lipid availability, resulting in weaker membrane resistance to ethanol. However the mechanisms underlying cell death in these conditions remain unclear. We examined cell death occurrence considering yeast cells ability to elicit an appropriate response to a given nutrient limitation and thus survive starvation. We show here that a set of micronutrients (oleic acid, ergosterol, pantothenic acid and nicotinic acid in low, growth-restricting concentrations trigger cell death in alcoholic fermentation when nitrogen level is high. We provide evidence that nitrogen signaling is involved in cell death and that either SCH9 deletion or Tor inhibition prevent cell death in several types of micronutrient limitation. Under such limitations, yeast cells fail to acquire any stress resistance and are unable to store glycogen. Unexpectedly, transcriptome analyses did not reveal any major changes in stress genes expression, suggesting that post-transcriptional events critical for stress response were not triggered by micronutrient starvation. Our data point to the fact that yeast cell death results from yeast inability to trigger an appropriate stress response under some conditions of nutrient limitations most likely not encountered by yeast in the wild. Our conclusions provide a novel frame for considering both cell death and the management of nutrients during alcoholic fermentation.

  11. A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation.

    Science.gov (United States)

    Duc, Camille; Pradal, Martine; Sanchez, Isabelle; Noble, Jessica; Tesnière, Catherine; Blondin, Bruno

    2017-01-01

    Yeast cell death can occur during wine alcoholic fermentation. It is generally considered to result from ethanol stress that impacts membrane integrity. This cell death mainly occurs when grape musts processing reduces lipid availability, resulting in weaker membrane resistance to ethanol. However the mechanisms underlying cell death in these conditions remain unclear. We examined cell death occurrence considering yeast cells ability to elicit an appropriate response to a given nutrient limitation and thus survive starvation. We show here that a set of micronutrients (oleic acid, ergosterol, pantothenic acid and nicotinic acid) in low, growth-restricting concentrations trigger cell death in alcoholic fermentation when nitrogen level is high. We provide evidence that nitrogen signaling is involved in cell death and that either SCH9 deletion or Tor inhibition prevent cell death in several types of micronutrient limitation. Under such limitations, yeast cells fail to acquire any stress resistance and are unable to store glycogen. Unexpectedly, transcriptome analyses did not reveal any major changes in stress genes expression, suggesting that post-transcriptional events critical for stress response were not triggered by micronutrient starvation. Our data point to the fact that yeast cell death results from yeast inability to trigger an appropriate stress response under some conditions of nutrient limitations most likely not encountered by yeast in the wild. Our conclusions provide a novel frame for considering both cell death and the management of nutrients during alcoholic fermentation.

  12. Identification of Rbd2 as a candidate protease for sterol regulatory element binding protein (SREBP) cleavage in fission yeast

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jinsil; Ha, Hye-Jeong [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141 (Korea, Republic of); Kim, Sujin [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141 (Korea, Republic of); Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34113 (Korea, Republic of); Choi, Ah-Reum [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141 (Korea, Republic of); Lee, Sook-Jeong [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 (Korea, Republic of); Hoe, Kwang-Lae, E-mail: kwanghoe@cnu.ac.kr [Department of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 (Korea, Republic of); Kim, Dong-Uk, E-mail: kimdongu@kribb.re.kr [Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141 (Korea, Republic of)

    2015-12-25

    Lipid homeostasis in mammalian cells is regulated by sterol regulatory element-binding protein (SREBP) transcription factors that are activated through sequential cleavage by Golgi Site-1 and Site-2 proteases. Fission yeast SREBP, Sre1, engages a different mechanism involving the Golgi Dsc E3 ligase complex, but it is not clearly understood exactly how Sre1 is proteolytically cleaved and activated. In this study, we screened the Schizosaccharomyces pombe non-essential haploid deletion collection to identify missing components of the Sre1 cleavage machinery. Our screen identified an additional component of the SREBP pathway required for Sre1 proteolysis named rhomboid protein 2 (Rbd2). We show that an rbd2 deletion mutant fails to grow under hypoxic and hypoxia-mimetic conditions due to lack of Sre1 activity and that this growth phenotype is rescued by Sre1N, a cleaved active form of Sre1. We found that the growth inhibition phenotype under low oxygen conditions is specific to the strain with deletion of rbd2, not any other fission yeast rhomboid-encoding genes. Our study also identified conserved residues of Rbd2 that are required for Sre1 proteolytic cleavage. All together, our results suggest that Rbd2 is a functional SREBP protease with conserved residues required for Sre1 cleavage and provide an important piece of the puzzle to understand the mechanisms for Sre1 activation and the regulation of various biological and pathological processes involving SREBPs. - Highlights: • An rbd2-deleted yeast strain shows defects in growth in response to low oxygen levels. • rbd2-deficient cells fail to generate cleaved Sre1 (Sre1N) under hypoxic conditions. • Expression of Sre1N rescues the rbd2 deletion mutant growth phenotype. • Rbd2 contains conserved residues potentially critical for catalytic activity. • Mutation of the conserved Rbd2 catalytic residues leads to defects in Sre1 cleavage.

  13. The ATPase and protease domains of yeast mitochondrial Lon: roles in proteolysis and respiration-dependent growth.

    Science.gov (United States)

    van Dijl, J M; Kutejová, E; Suda, K; Perecko, D; Schatz, G; Suzuki, C K

    1998-09-01

    The ATP-dependent Lon protease of Saccharomyces cerevisiae mitochondria is required for selective proteolysis in the matrix, maintenance of mitochondrial DNA, and respiration-dependent growth. Lon may also possess a chaperone-like function that facilitates protein degradation and protein-complex assembly. To understand the influence of Lon's ATPase and protease activities on these functions, we examined several Lon mutants for their ability to complement defects of Lon-deleted yeast cells. We also developed a rapid procedure for purifying yeast Lon to homogeneity to study the enzyme's activities and oligomeric state. A point mutation in either the ATPase or the protease site strongly inhibited the corresponding activity of the pure protein but did not alter the protein's oligomerization; when expressed at normal low levels neither of these mutant enzymes supported respiration-dependent growth of Lon-deleted cells. When the ATPase- or the protease-containing regions of Lon were expressed as separate truncated proteins, neither could support respiration-dependent growth of Lon-deleted cells; however, coexpression of these two separated regions sustained wild-type growth. These results suggest that yeast Lon contains two catalytic domains that can interact with one another even as separate proteins, and that both are essential for the different functions of Lon.

  14. 9q22 Deletion - First Familial Case

    Directory of Open Access Journals (Sweden)

    Yamamoto Toshiyuki

    2011-06-01

    Full Text Available Abstract Background Only 29 cases of constitutional 9q22 deletions have been published and all have been sporadic. Most associate with Gorlin syndrome or nevoid basal cell carcinoma syndrome (NBCCS, MIM #109400 due to haploinsufficiency of the PTCH1 gene (MIM *601309. Methods and Results We report two mentally retarded female siblings and their cognitively normal father, all carrying a similar 5.3 Mb microdeletion at 9q22.2q22.32, detected by array CGH (244 K. The deletion does not involve the PTCH1 gene, but instead 30 other gene,s including the ROR2 gene (MIM *602337 which causing both brachydactyly type 1 (MIM #113000 and Robinow syndrome (MIM #268310, and the immunologically active SYK gene (MIM *600085. The deletion in the father was de novo and FISH analysis of blood lymphocytes did not suggest mosaicism. All three patients share similar mild dysmorphic features with downslanting palpebral fissures, narrow, high bridged nose with small nares, long, deeply grooved philtrum, ears with broad helix and uplifted lobuli, and small toenails. All have significant dysarthria and suffer from continuous middle ear and upper respiratory infections. The father also has a funnel chest and unilateral hypoplastic kidney but the daughters have no malformations. Conclusions This is the first report of a familial constitutional 9q22 deletion and the first deletion studied by array-CGH which does not involve the PTCH1 gene. The phenotype and penetrance are variable and the deletion found in the cognitively normal normal father poses a challenge in genetic counseling.

  15. Deletion 22q13.3 syndrome

    Directory of Open Access Journals (Sweden)

    Phelan Mary C

    2008-05-01

    Full Text Available Abstract The deletion 22q13.3 syndrome (deletion 22q13 syndrome or Phelan-McDermid syndrome is a chromosome microdeletion syndrome characterized by neonatal hypotonia, global developmental delay, normal to accelerated growth, absent to severely delayed speech, and minor dysmorphic features. The deletion occurs with equal frequency in males and females and has been reported in mosaic and non-mosaic forms. Due to lack of clinical recognition and often insufficient laboratory testing, the syndrome is under-diagnosed and its true incidence remains unknown. Common physical traits include long eye lashes, large or unusual ears, relatively large hands, dysplastic toenails, full brow, dolicocephaly, full cheeks, bulbous nose, and pointed chin. Behavior is autistic-like with decreased perception of pain and habitual chewing or mouthing. The loss of 22q13.3 can result from simple deletion, translocation, ring chromosome formation and less common structural changes affecting the long arm of chromosome 22, specifically the region containing the SHANK3 gene. The diagnosis of deletion 22q13 syndrome should be considered in all cases of hypotonia of unknown etiology and in individuals with absent speech. Although the deletion can sometimes be detected by high resolution chromosome analysis, fluorescence in situ hybridization (FISH or array comparative genomic hybridization (CGH is recommended for confirmation. Differential diagnosis includes syndromes associated with hypotonia, developmental delay, speech delay and/or autistic-like affect (Prader-Willi, Angelman, Williams, Smith-Magenis, Fragile X, Sotos, FG, trichorhinophalangeal and velocardiofacial syndromes, autism spectrum disorders, cerebral palsy. Genetic counseling is recommended and parental laboratory studies should be considered to identify cryptic rearrangements and detect parental mosaicism. Prenatal diagnosis should be offered for future pregnancies in those families with inherited rearrangements

  16. A serendipitous discovery that in situ proteolysis is essential for the crystallization of yeast CPSF-100 (Ydh1p)

    International Nuclear Information System (INIS)

    Mandel, Corey R.; Gebauer, Damara; Zhang, Hailong; Tong, Liang

    2006-01-01

    Proteolysis in situ by a protease secreted by a contaminating fungus is essential for the crystallization of yeast CPSF-100. The cleavage and polyadenylation specificity factor (CPSF) complex is required for the cleavage and polyadenylation of the 3′-end of messenger RNA precursors in eukaryotes. During structural studies of the 100 kDa subunit (CPSF-100, Ydh1p) of the yeast CPSF complex, it was serendipitously discovered that a solution that is infected by a fungus (subsequently identified as Penicillium) is crucial for the crystallization of this protein. Further analyses suggest that the protein has undergone partial proteolysis during crystallization, resulting in the deletion of an internal segment of about 200 highly charged and hydrophilic residues, very likely catalyzed by a protease secreted by the fungus. With the removal of this segment, yeast CPSF-100 (Ydh1p) has greatly reduced solubility and can be crystallized in the presence of a minute amount of precipitant

  17. Some analogies between quantum cloning and quantum deleting

    International Nuclear Information System (INIS)

    Qiu Daowen

    2002-01-01

    We further verify the impossibility of deleting an arbitrary unknown quantum state, and also show it is impossible to delete two nonorthogonal quantum states as a consequence of unitarity of quantum mechanics. A quantum approximate (deterministic) deleting machine and a probabilistic (exact) deleting machine are constructed. The estimation for the global fidelity characterizing the efficiency of the quantum approximate deleting is given. We then demonstrate that unknown nonorthogonal states chosen from a set with their multiple copies can evolve into a linear superposition of multiple deletions and failure branches by a unitary process if and only if the states are linearly independent. It is notable that the proof for necessity is somewhat different from Pati's [Phys. Rev. Lett. 83, 2849 (1999)]. Another deleting machine for the input states that are unnecessarily linearly independent is also presented. The bounds on the success probabilities of these deleting machines are derived. So we expound some preliminary analogies between quantum cloning and deleting

  18. [Hydrophidae identification through analysis on cytochrome c oxydase I(COI) and ribosome 16s rDNA gene barcode].

    Science.gov (United States)

    Liao, Li-Xi; Zeng, Ke-Wu; Tu, Peng-Fei

    2016-05-01

    Hydrophidae, one of the precious traditional Chinese medicines, is generally drily preserved to prevent corruption, but it is hard to identify the species of Hydrophidae through the appearance because of the change due to the drying process. The identification through analysis on gene barcode, a new technique in species identification, can avoid this problem. The gene barcodes of the 5 species of Hydrophidae, Lapemis hardwickii, Hydrophis fasciatus, Aipysurus eydouxii, Hydrophis belcher and Hydrophis lamberti, were acquired through DNA extraction and gene sequencing. These barcodes were then in sequence alignment and test the identification efficiency by BLAST. Our results showed that the 16S rDNA sequences identified Hydrophidae briefly and the COI sequenceshad obvious difference between intra-and inter-species, indicating that DNA bar-coding was an efficiency method of Hydrophidae identification. Copyright© by the Chinese Pharmaceutical Association.

  19. The utility of rbcl and matk regions for dna barcoding analysis of the genus suaeda (amaranthaceae) species

    International Nuclear Information System (INIS)

    Munir, U.; Perveen, A.; Qamarunnisa, S.

    2015-01-01

    The genus Suaeda (Forssk.) belongs to the family Chenopodiaceae. Identification of Suaeda species based on morphological data is quite difficult due to high phenotypic plasticity, few distinguishable and many overlapping characters. In current research, the efficiency of rbcL and matK (plants core barcode regions) for species identification of the genus Suaeda was assessed. The determination of intraspecific and interspecific divergence, assessment of barcoding gap, reconstruction of phylogenetic trees and evaluation of barcode regions for species identification (based on best match and best close match) were carried out. The results revealed that rbcL showed comparatively less overlapping for the distribution of interspecific and intraspecific divergence. In addition, the highest discriminating ability for correct species identification was also observed in this region. Therefore, rbcL was found to be a significant barcode region for the identification of Suaeda species. (author)

  20. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity.

    Science.gov (United States)

    Cristescu, Melania E

    2014-10-01

    DNA-based species identification, known as barcoding, transformed the traditional approach to the study of biodiversity science. The field is transitioning from barcoding individuals to metabarcoding communities. This revolution involves new sequencing technologies, bioinformatics pipelines, computational infrastructure, and experimental designs. In this dynamic genomics landscape, metabarcoding studies remain insular and biodiversity estimates depend on the particular methods used. In this opinion article, I discuss the need for a coordinated advancement of DNA-based species identification that integrates taxonomic and barcoding information. Such an approach would facilitate access to almost 3 centuries of taxonomic knowledge and 1 decade of building repository barcodes. Conservation projects are time sensitive, research funding is becoming restricted, and informed decisions depend on our ability to embrace integrative approaches to biodiversity science. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates.

    Directory of Open Access Journals (Sweden)

    Alexandre Angers-Loustau

    Full Text Available Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.

  2. Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: An Example from Queensland, Australia

    Directory of Open Access Journals (Sweden)

    Craig M. Costion

    2016-02-01

    Full Text Available A foundation for a DNA barcode reference library for the tropical plants of Australia is presented here. A total of 1572 DNA barcode sequences are compiled from 848 tropical Queensland species. The dataset represents 35% of the total flora of Queensland’s Wet Tropics Bioregion, 57% of its tree species and 28% of the shrub species. For approximately half of the sampled species, we investigated the occurrence of infraspecific molecular variation in DNA barcode loci rbcLa, matK, and the trnH-psbA intergenic spacer region across previously recognized biogeographic barriers. We found preliminary support for the notion that DNA barcode reference libraries can be used as a tool for inferring biogeographic patterns at regional scales. It is expected that this dataset will find applications in taxonomic, ecological, and applied conservation research.

  3. Next-generation detection of antigen-responsive T cells using DNA barcode-labeled peptidemajor histocompatibility complex I multimers

    DEFF Research Database (Denmark)

    Bentzen, Amalie Kai; Marquard, Andrea Marion; Lyngaa, Rikke Birgitte

    2016-01-01

    diversity of T cell recognition in humans. Consequently it has been impossible to comprehensively analyze T cell responsiveness in cancer, infectious and autoimmune diseases. We present and validate a novel technology that enables parallel detection of numerous different peptide-MHC responsive T cells...... in asingle sample using >1000 different peptide-MHC multimers labeled with individual DNA barcodes. After isolation of MHC multimer binding T cells their recognition are revealed by amplification and sequencing of the MHC multimer-associated DNA barcodes. The relative frequency of the sequenced DNA barcodes...... originating from a given peptide-MHC motif relates to the size of the antigenresponsive T cell population. We have demonstrated the use of large panels of >1000 DNA barcoded MHC multimers for detection of rare T cell populations of virus and cancer-restricted origin in various tissues and compared...

  4. Yeast Isolation for Bioethanol Production

    Directory of Open Access Journals (Sweden)

    EKA RURIANI

    2012-09-01

    Full Text Available We have isolated 12 yeast isolates from five different rotten fruits by using a yeast glucose chloramphenicol agar (YGCA medium supplemented with tetracycline. From pre-screening assay, four isolates exhibited higher substrate (glucose-xylose consumption efficiency in the reaction tube fermentation compared to Saccharomyces cerevisiae dan Saccharomyces ellipsoids as the reference strains. Based on the fermentation process in gooseneck flasks, we observed that two isolates (K and SB showed high fermentation efficiency both in sole glucose and mixed glucose-xylose substrate. Moreover, isolates K and SB produced relatively identical level of ethanol concentration compared to the reference strains. Isolates H and MP could only produce high levels of ethanol in glucose fermentation, while only half of that amount of ethanol was detected in glucose-xylose fermentation. Isolate K and SB were identified as Pichia kudriavzeevii (100% based on large sub unit (LSU ribosomal DNA D1/D2 region.

  5. Variable immune deficiency related to deletion size in chromosome 22q11.2 deletion syndrome.

    Science.gov (United States)

    Crowley, Blaine; Ruffner, Melanie; McDonald McGinn, Donna M; Sullivan, Kathleen E

    2018-01-17

    The clinical features of 22q11.2 deletion syndrome include virtually every organ of the body. This review will focus on the immune system and the differences related to deletion breakpoints. A hypoplastic thymus was one of the first features described in this syndrome and low T cell counts, as a consequence of thymic hypoplasia, are the most commonly described immunologic feature. These are most prominently seen in early childhood and can be associated with increased persistence of viruses. Later in life, evidence of T cell exhaustion may be seen and secondary deficiencies of antibody function have been described. The relationship of the immunodeficiency to the deletion breakpoints has been understudied due to the infrequent analysis of people carrying smaller deletions. This manuscript will review the immune deficiency in 22q11.2 deletion syndrome and describe differences in the T cell counts related to the deletion breakpoints. Distal, non-TBX1 inclusive deletions, were found to be associated with better T cell counts. Another new finding is the relative preservation of T cell counts in those patients with a 22q11.2 duplication. © 2018 Wiley Periodicals, Inc.

  6. R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring.

    Science.gov (United States)

    Rimet, Frédéric; Chaumeil, Philippe; Keck, François; Kermarrec, Lenaïg; Vasselon, Valentin; Kahlert, Maria; Franc, Alain; Bouchez, Agnès

    2016-01-01

    Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the

  7. Phenotypic variability in Angelman syndrome: comparison among different deletion classes and between deletion and UPD subjects.

    Science.gov (United States)

    Varela, Monica Castro; Kok, Fernando; Otto, Paulo Alberto; Koiffmann, Celia Priszkulnik

    2004-12-01

    Angelman syndrome (AS) can result from either a 15q11-q13 deletion (del), paternal uniparental disomy (UPD), imprinting, or UBE3A mutations. Here, we describe the phenotypic and behavioral variability detected in 49 patients with different classes of deletions and nine patients with UPD. Diagnosis was made by methylation pattern analysis of exon 1 of the SNRPN-SNURF gene and by microsatellite profiling of loci within and outside the 15q11-q13 region. There were no major phenotypic differences between the two main classes (BP1-BP3; BP2-BP3) of AS deletion patients, except for the absence of vocalization, more prevalent in patients with BP1-BP3 deletions, and for the age of sitting without support, which was lower in patients with BP2-BP3 deletions. Our data suggest that gene deletions (NIPA1, NIPA2, CYF1P1, GCP5) mapped to the region between breakpoints BP1 and BP2 may be involved in the severity of speech impairment, since all BP1-BP3 deletion patients showed complete absence of vocalization, while 38.1% of the BP2-BP3 deletion patients were able to pronounce syllabic sounds, with doubtful meaning. Compared to UPD patients, deletion patients presented a higher incidence of swallowing disorders (73.9% del x 22.2% UPD) and hypotonia (73.3% del x 28.57% UPD). In addition, children with UPD showed better physical growth, fewer or no seizures, a lower incidence of microcephaly, less ataxia and higher cognitive skills. As a consequence of their milder or less typical phenotype, AS may remain undiagnosed, leading to an overall underdiagnosis of the disease.

  8. Yeast: A new oil producer?

    Directory of Open Access Journals (Sweden)

    Beopoulos Athanasios

    2012-01-01

    Full Text Available The increasing demand of plant oils or animal fat for biodiesel and specific lipid derivatives for the oleochemical field (such as lubricants, adhesives or plastics have created price imbalance in both the alimentary and energy field. Moreover, the lack of non-edible oil feedstock has given rise to concerns on land-use practices and on oil production strategies. Recently, much attention has been paid to the exploitation of microbial oils. Most of them present lipid profiles similar in type and composition to plants and could therefore have many advantages as are no competitive with food, have short process cycles and their cultivation is independent of climate factors. Among microorganisms, yeasts seem to be very promising as they can be easily genetically enhanced, are suitable for large-scale fermentation and are devoid of endotoxins. This review will focus on the recent understanding of yeasts lipid metabolism, the succeeding genetic engineering of the lipid pathways and the recent developments on fermentation techniques that pointed out yeasts as promising alternative producers for oil or plastic.

  9. DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

    OpenAIRE

    Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, M. Sajjad; Khan, Arif M.; Mansoor, Shahid; Shah, Ghulam S.; Zafar, Yusuf

    2014-01-01

    Background Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Methods/Principal Findings Sequence diversity in the DNA barcode region (mtCOI-5′) ...

  10. Molecular Authentication of the Traditional Medicinal Plant "Lakshman Booti" (Smithia conferta Sm.) and Its Adulterants through DNA Barcoding.

    Science.gov (United States)

    Umdale, Suraj D; Kshirsagar, Parthraj R; Lekhak, Manoj M; Gaikwad, Nikhil B

    2017-07-01

    Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton . leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine. This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique. Genomic DNA extracted from S. conferta and its adulterants was used as templates for polymerase chain reaction amplification of the barcoding regions. The amplicons were directed for sequencing, and species identification was conducted using BLASTn and unweighted pair-group method with arithmetic mean trees. In addition, the secondary structures of internal transcribed spacer (ITS) 2 region were predicted. The nucleotide sequence of ITS provides species-specific single nucleotide polymorphisms and sequence divergence (22%) than psb A- trn H (10.9%) and rbc L (3.1%) sequences. The ITS barcode indicates that S. conferta and Smithia sensitiva are closely related compared to other species. ITS is the most applicable barcode for molecular authentication of S. conferta , and further chloroplast barcodes should be tested for phylogenetic analysis of genus Smithia. The present investigation is the first effort of utilization of DNA barcode for molecular authentication of S. conferta and its adulterants. Also, this study expanded the application of the ITS2 sequence data in the authentication. The ITS has been proved as a potential and reliable candidate barcode for the authentication of S. conferta . Abbreviations used: BLASTn: Basic Local Alignment Search Tool for Nucleotide; MEGA: Molecular Evolutionary Genetic Analysis; EMBL: European Molecular Biology Laboratory; psb A- trn H: Photosystem II protein D1- stuctural RNA: His tRNA gene; rbcL: Ribulose 1,5 bi-phosphate carboxylase

  11. Spider hosts (Arachnida, Araneae) and wasp parasitoids (Insecta, Hymenoptera, Ichneumonidae, Ephialtini) matched using DNA barcodes

    OpenAIRE

    Miller, Jeremy; Belgers, J. Dick; Beentjes, Kevin; Zwakhals, Kees; van Helsdingen, Peter

    2013-01-01

    Abstract The study of parasitoids and their hosts suffers from a lack of reliable taxonomic data. We use a combination of morphological characters and DNA sequences to produce taxonomic determinations that can be verified with reference to specimens in an accessible collection and DNA barcode sequences posted to the Barcode of Life database (BOLD). We demonstrate that DNA can be successfully extracted from consumed host spiders and the shed pupal case of a wasp using non-destructive methods. ...

  12. Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.

    Directory of Open Access Journals (Sweden)

    Eric D Stein

    Full Text Available Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI. On average, we obtained successful COI sequences (i.e. either full or partial barcodes for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.

  13. Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.

    Science.gov (United States)

    Stein, Eric D; White, Bryan P; Mazor, Raphael D; Miller, Peter E; Pilgrim, Erik M

    2013-01-01

    Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.

  14. Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

    Directory of Open Access Journals (Sweden)

    Aron J Fazekas

    Full Text Available A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s. We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples. The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA to 59% (trnH-psbA of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci, with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs. Several loci (matK, psbK-psbI, trnH-psbA were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations. This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the

  15. Forensic botany II, DNA barcode for land plants: Which markers after the international agreement?

    Science.gov (United States)

    Ferri, G; Corradini, B; Ferrari, F; Santunione, A L; Palazzoli, F; Alu', M

    2015-03-01

    The ambitious idea of using a short piece of DNA for large-scale species identification (DNA barcoding) is already a powerful tool for scientists and the application of this standard technique seems promising in a range of fields including forensic genetics. While DNA barcoding enjoyed a remarkable success for animal identification through cytochrome c oxidase I (COI) analysis, the attempts to identify a single barcode for plants remained a vain hope for a longtime. From the beginning, the Consortium for the Barcode of Life (CBOL) showed a lack of agreement on a core plant barcode, reflecting the diversity of viewpoints. Different research groups advocated various markers with divergent set of criteria until the recent publication by the CBOL-Plant Working Group. After a four-year effort, in 2009 the International Team concluded to agree on standard markers promoting a multilocus solution (rbcL and matK), with 70-75% of discrimination to the species level. In 2009 our group firstly proposed the broad application of DNA barcoding principles as a tool for identification of trace botanical evidence through the analysis of two chloroplast loci (trnH-psbA and trnL-trnF) in plant species belonging to local flora. Difficulties and drawbacks that were encountered included a poor coverage of species in specific databases and the lack of authenticated reference sequences for the selected markers. Successful preliminary results were obtained providing an approach to progressively identify unknown plant specimens to a given taxonomic rank, usable by any non-specialist botanist or in case of a shortage of taxonomic expertise. Now we considered mandatory to update and to compare our previous findings with the new selected plastid markers (matK+rbcL), taking into account forensic requirements. Features of all the four loci (the two previously analyzed trnH-psbA+trnL-trnF and matK+rbcL) were compared singly and in multilocus solutions to assess the most suitable combination for

  16. Identification of sites required for repression of a silent mating type locus in yeast.

    Science.gov (United States)

    Feldman, J B; Hicks, J B; Broach, J R

    1984-10-05

    There are three loci in the yeast Saccharomyces, each containing one of two possible genetic elements that can determine cell type. At one of these loci, MAT, this information is expressed to establish the mating type of the cell. At the other two loci, HML and HMR, this same information is phenotypically and transcriptionally silent, even though a large amount of identical sequence flanks MAT, HML and HMR coding regions. Transcriptional repression of HML and HMR requires the trans active gene products of four loci, designated variously as MAR or SIR, that are unlinked to each other or to MAT, HML or HMR. We have examined the phenotypic expression of a cloned, plasmid-borne copy of HML and of various deletion and insertion derivatives of this plasmid following their reintroduction into Mar+/Sir+ yeast strains. From these data, we have identified two sites flanking the locus, both of which are required for MAR/SIR repression of the locus. In addition, we demonstrate that each of these sites promotes autonomous replication in yeast. Abraham et al. (1984) have presented evidence demonstrating that a similar regulatory structure exists at the other silent locus, HMR. From an analysis of the sequences of these four regulatory sites, we have identified several specific sequences that may be involved in mediating repression of these loci and in promoting replication in yeast. These results are discussed in the context of potential models for the mechanism of regulation of the silent mating type loci.

  17. Effects of SNF1 on Maltose Metabolism and Leavening Ability of Baker's Yeast in Lean Dough.

    Science.gov (United States)

    Zhang, Cui-Ying; Bai, Xiao-Wen; Lin, Xue; Liu, Xiao-Er; Xiao, Dong-Guang

    2015-12-01

    Maltose metabolism of baker's yeast (Saccharomyces cerevisiae) in lean dough is negatively influenced by glucose repression, thereby delaying the dough fermentation. To improve maltose metabolism and leavening ability, it is necessary to alleviate glucose repression. The Snf1 protein kinase is well known to be essential for the response to glucose repression and required for transcription of glucose-repressed genes including the maltose-utilization genes (MAL). In this study, the SNF1 overexpression and deletion industrial baker's yeast strains were constructed and characterized in terms of maltose utilization, growth and fermentation characteristics, mRNA levels of MAL genes (MAL62 encoding the maltase and MAL61 encoding the maltose permease) and maltase and maltose permease activities. Our results suggest that overexpression of SNF1 was effective to glucose derepression for enhancing MAL expression levels and enzymes (maltase and maltose permease) activities. These enhancements could result in an 18% increase in maltose metabolism of industrial baker's yeast in LSMLD medium (the low sugar model liquid dough fermentation medium) containing glucose and maltose and a 15% increase in leavening ability in lean dough. These findings provide a valuable insight of breeding industrial baker's yeast for rapid fermentation. © 2015 Institute of Food Technologists®

  18. Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering

    Directory of Open Access Journals (Sweden)

    Khaled A. Selim

    2018-03-01

    Full Text Available Scarcity of the non-renewable energy sources, global warming, environmental pollution, and raising the cost of petroleum are the motive for the development of renewable, eco-friendly fuels production with low costs. Bioethanol production is one of the promising materials that can subrogate the petroleum oil, and it is considered recently as a clean liquid fuel or a neutral carbon. Diverse microorganisms such as yeasts and bacteria are able to produce bioethanol on a large scale, which can satisfy our daily needs with cheap and applicable methods. Saccharomyces cerevisiae and Pichia stipitis are two of the pioneer yeasts in ethanol production due to their abilities to produce a high amount of ethanol. The recent focus is directed towards lignocellulosic biomass that contains 30–50% cellulose and 20–40% hemicellulose, and can be transformed into glucose and fundamentally xylose after enzymatic hydrolysis. For this purpose, a number of various approaches have been used to engineer different pathways for improving the bioethanol production with simultaneous fermentation of pentose and hexoses sugars in the yeasts. These approaches include metabolic and flux analysis, modeling and expression analysis, followed by targeted deletions or the overexpression of key genes. In this review, we highlight and discuss the current status of yeasts genetic engineering for enhancing bioethanol production, and the conditions that influence bioethanol production.

  19. Nature of frequent deletions in CEBPA.

    Science.gov (United States)

    Fuchs, Ota; Kostecka, Arnost; Provaznikova, Dana; Krasna, Blazena; Brezinova, Jana; Filkukova, Jitka; Kotlin, Roman; Kouba, Michal; Kobylka, Petr; Neuwirtova, Radana; Jonasova, Anna; Caniga, Miroslav; Schwarz, Jiri; Markova, Jana; Maaloufova, Jacqueline; Sponerova, Dana; Novakova, Ludmila; Cermak, Jaroslav

    2009-01-01

    C/EBPalpha (CCAAT/enhancer binding protein alpha) belongs to the family of leucine zipper transcription factors and is necessary for transcriptional control of granulocyte, adipocyte and hepatocyte differentiation, glucose metabolism and lung development. C/EBPalpha is encoded by an intronless gene. CEBPA mutations cause a myeloid differentiation block and were detected in acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), multiple myeloma and non-Hodgkin's lymphoma (NHL) patients. In this study we identified in 41 individuals from 824 screened individuals (290 AML patients, 382 MDS patients, 56 NHL patients and 96 healthy individuals) a single class of 23 deletions in CEBPA gene which involved a direct repeat of at least 2 bp. These mutations are characterised by the loss of one of two same repeats at the ends of deleted sequence. Three most frequent repeats included in these deletions in CEBPA gene are CGCGAG (493-498_865-870), GCCAAGCAGC (508-517_907-916) and GG (486-487_885-886), all according to GenBank accession no. NM_004364.2. A mechanism for deletion formation between two repetitive sequences can be recombination events in the repair process. Double-stranded cut in DNA can initiate these recombination events of adjacent DNA sequences.

  20. Obtaining a Proportional Allocation by Deleting Items

    NARCIS (Netherlands)

    Dorn, B.; de Haan, R.; Schlotter, I.; Röthe, J.

    2017-01-01

    We consider the following control problem on fair allocation of indivisible goods. Given a set I of items and a set of agents, each having strict linear preference over the items, we ask for a minimum subset of the items whose deletion guarantees the existence of a proportional allocation in the

  1. 22q11.2 deletion syndrome

    NARCIS (Netherlands)

    McDonald-McGinn, Donna M.; Sullivan, Kathleen E.; Marino, Bruno; Philip, Nicole; Swillen, Ann; Vorstman, Jacob A S; Zackai, Elaine H.; Emanuel, Beverly S.; Vermeesch, Joris R.; Morrow, Bernice E.; Scambler, Peter J.; Bassett, Anne S.

    2015-01-01

    22q11.2 deletion syndrome (22q11.2DS) is the most common chromosomal microdeletion disorder, estimated to result mainly from de novo non-homologous meiotic recombination events occurring in approximately 1 in every 1,000 fetuses. The first description in the English language of the constellation of

  2. Sequence analysis of 17 NRXN1 deletions

    DEFF Research Database (Denmark)

    Hoeffding, Louise Kristine Enggaard; Hansen, Thomas; Ingason, Andrés

    2014-01-01

    into the molecular mechanisms governing such genomic rearrangements may increase our understanding of disease pathology and evolutionary processes. Here we analyse 17 carriers of non-recurrent deletions in the NRXN1 gene, which have been associated with neurodevelopmental disorders, e.g. schizophrenia, autism...

  3. Union-Find with Constant Time Deletions

    DEFF Research Database (Denmark)

    Alstrup, Stephen; Thorup, Mikkel; Gørtz, Inge Li

    2014-01-01

    operations performed, and α_M/N_(n) is a functional inverse of Ackermann’s function. They left open the question whether delete operations can be implemented more efficiently than find operations, for example, in o(log n) worst-case time. We resolve this open problem by presenting a relatively simple...

  4. DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica.

    Science.gov (United States)

    Janzen, Daniel H; Hallwachs, Winnie

    2016-09-01

    The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

  5. DNA barcode authentication of wood samples of threatened and commercial timber trees within the tropical dry evergreen forest of India.

    Science.gov (United States)

    Nithaniyal, Stalin; Newmaster, Steven G; Ragupathy, Subramanyam; Krishnamoorthy, Devanathan; Vassou, Sophie Lorraine; Parani, Madasamy

    2014-01-01

    India is rich with biodiversity, which includes a large number of endemic, rare and threatened plant species. Previous studies have used DNA barcoding to inventory species for applications in biodiversity monitoring, conservation impact assessment, monitoring of illegal trading, authentication of traded medicinal plants etc. This is the first tropical dry evergreen forest (TDEF) barcode study in the World and the first attempt to assemble a reference barcode library for the trees of India as part of a larger project initiated by this research group. We sampled 429 trees representing 143 tropical dry evergreen forest (TDEF) species, which included 16 threatened species. DNA barcoding was completed using rbcL and matK markers. The tiered approach (1st tier rbcL; 2nd tier matK) correctly identified 136 out of 143 species (95%). This high level of species resolution was largely due to the fact that the tree species were taxonomically diverse in the TDEF. Ability to resolve taxonomically diverse tree species of TDEF was comparable among the best match method, the phylogenetic method, and the characteristic attribute organization system method. We demonstrated the utility of the TDEF reference barcode library to authenticate wood samples from timber operations in the TDEF. This pilot research study will enable more comprehensive surveys of the illegal timber trade of threatened species in the TDEF. This TDEF reference barcode library also contains trees that have medicinal properties, which could be used to monitor unsustainable and indiscriminate collection of plants from the wild for their medicinal value.

  6. A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa.

    Science.gov (United States)

    Raupach, Michael J; Hannig, Karsten; Morinière, Jérome; Hendrich, Lars

    2016-01-01

    As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.

  7. Yeasts Diversity in Fermented Foods and Beverages

    Science.gov (United States)

    Tamang, Jyoti Prakash; Fleet, Graham H.

    People across the world have learnt to culture and use the essential microorganisms for production of fermented foods and alcoholic beverages. A fermented food is produced either spontaneously or by adding mixed/pure starter culture(s). Yeasts are among the essential functional microorganisms encountered in many fermented foods, and are commercially used in production of baker's yeast, breads, wine, beer, cheese, etc. In Asia, moulds are predominant followed by amylolytic and alcohol-producing yeasts in the fermentation processes, whereas in Africa, Europe, Australia and America, fermented products are prepared exclusively using bacteria or bacteria-yeasts mixed cultures. This chapter would focus on the varieties of fermented foods and alcoholic beverages produced by yeasts, their microbiology and role in food fermentation, widely used commercial starters (pilot production, molecular aspects), production technology of some common commercial fermented foods and alcoholic beverages, toxicity and food safety using yeasts cultures and socio-economy

  8. Biopharmaceutical discovery and production in yeast.

    Science.gov (United States)

    Meehl, Michael A; Stadheim, Terrance A

    2014-12-01

    The selection of an expression platform for recombinant biopharmaceuticals is often centered upon suitable product titers and critical quality attributes, including post-translational modifications. Although notable differences between microbial, yeast, plant, and mammalian host systems exist, recent advances have greatly mitigated any inherent liabilities of yeasts. Yeast expression platforms are important to both the supply of marketed biopharmaceuticals and the pipelines of novel therapeutics. In this review, recent advances in yeast-based expression of biopharmaceuticals will be discussed. The advantages of using glycoengineered yeast as a production host and in the discovery space will be illustrated. These advancements, in turn, are transforming yeast platforms from simple production systems to key technological assets in the discovery and selection of biopharmaceutical lead candidates. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Delayed chromosomal instability caused by large deletion

    International Nuclear Information System (INIS)

    Ojima, M.; Suzuki, K.; Kodama, S.; Watanabe, M.

    2003-01-01

    Full text: There is accumulating evidence that genomic instability, manifested by the expression of delayed phenotypes, is induced by X-irradiation but not by ultraviolet (UV) light. It is well known that ionizing radiation, such as X-rays, induces DNA double strand breaks, but UV-light mainly causes base damage like pyrimidine dimers and (6-4) photoproducts. Although the mechanism of radiation-induced genomic instability has not been thoroughly explained, it is suggested that DNA double strand breaks contribute the induction of genomic instability. We examined here whether X-ray induced gene deletion at the hprt locus induces delayed instability in chromosome X. SV40-immortalized normal human fibroblasts, GM638, were irradiated with X-rays (3, 6 Gy), and the hprt mutants were isolated in the presence of 6-thioguanine (6-TG). A 2-fold and a 60-fold increase in mutation frequency were found by 3 Gy and 6 Gy irradiation, respectively. The molecular structure of the hprt mutations was determined by multiplex polymerase chain reaction of nine exons. Approximately 60% of 3 Gy mutants lost a part or the entire hprt gene, and the other mutants showed point mutations like spontaneous mutants. All 6 Gy mutants show total gene deletion. The chromosomes of the hprt mutants were analyzed by Whole Human Chromosome X Paint FISH or Xq telomere FISH. None of the point or partial gene deletion mutants showed aberrations of X-chromosome, however total gene deletion mutants induced translocations and dicentrics involving chromosome X. These results suggest that large deletion caused by DNA double strand breaks destabilizes chromosome structure, which may be involved in an induction of radiation-induced genomic instability

  10. Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada 1

    OpenAIRE

    Kuzmina, Maria L.; Braukmann, Thomas W. A.; Fazekas, Aron J.; Graham, Sean W.; Dewaard, Stephanie L.; Rodrigues, Anuar; Bennett, Bruce A.; Dickinson, Timothy A.; Saarela, Jeffery M.; Catling, Paul M.; Newmaster, Steven G.; Percy, Diana M.; Fenneman, Erin; Lauron-Moreau, Aurélien; Ford, Bruce

    2017-01-01

    Premise of the study: Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada. Methods: Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recov...

  11. Revaluation of Waste Yeast from Beer Production

    OpenAIRE

    Nicoleta Suruceanu; Sonia Socaci; Teodora Coldea; Elena Mudura

    2013-01-01

    Brewing yeast is an important waste product from beer production. The valorification of slurry yeast mainly consists of separation of vitamins and important nitrogen compounds. The hops compounds, one of the most important raw materials in beer technology are removed beforehand valorification. The prenylflavonoids compounds from hops are important bioactive compounds that can be revaluation with proper technology. Revaluation of prenylflavonoids from waste yeast into dietary supplement, ident...

  12. QUALITY ANALYSIS OF THE YEAST SACCHAROMYCES CEREVISIAE

    OpenAIRE

    Adelya Marselovna Ermakova* , Elena Evgenievna Zinurova , Ramil Raisovich Levashov , Zamira Shamilovna Mingaleeva , Olga Alekseevna Reshetnik

    2017-01-01

    Yeast, as a part of the recipe mass, must have high fermentation activity, and also have the ability to expand under anaerobic conditions, and to adapt quickly to a changing nutrient medium, in order to obtain high-quality bakery products. Preliminary activation of the pressed bakery yeast allows to shorten the duration of the technological process for the production of bakery products, and to reduce the cost of the final product. The experiments on the preliminary activation of yeast were co...

  13. Need-based up-regulation of protein levels in response to deletion of their duplicate genes.

    Directory of Open Access Journals (Sweden)

    Alexander DeLuna

    2010-03-01

    Full Text Available Many duplicate genes maintain functional overlap despite divergence over long evolutionary time scales. Deleting one member of a paralogous pair often has no phenotypic effect, unless its paralog is also deleted. It has been suggested that this functional compensation might be mediated by active up-regulation of expression of a gene in response to deletion of its paralog. However, it is not clear how prevalent such paralog responsiveness is, nor whether it is hardwired or dependent on feedback from environmental conditions. Here, we address these questions at the genomic scale using high-throughput flow cytometry of single-cell protein levels in differentially labeled cocultures of wild-type and paralog-knockout Saccharomyces cerevisiae strains. We find that only a modest fraction of proteins (22 out of 202 show significant up-regulation to deletion of their duplicate genes. However, these paralog-responsive proteins match almost exclusively duplicate pairs whose overlapping function is required for growth. Moreover, media conditions that add or remove requirements for the function of a duplicate gene pair specifically eliminate or create paralog responsiveness. Together, our results suggest that paralog responsiveness in yeast is need-based: it appears only in conditions in which the gene function is required. Physiologically, such need-based responsiveness could provide an adaptive mechanism for compensation of genetic, environmental, or stochastic perturbations in protein abundance.

  14. [Molecular identification of Hibiscus syriacus and its adulterants using ITS2 barcode].

    Science.gov (United States)

    Liu, Yi-Mei; Jin, Li-Na; Xiong, Yong-Xin; Wu, Lan; Chen, Ke-Li

    2014-03-01

    To identify Hibiscus syriacus and its adulterants using DNA barcoding technique. Nine samples of five species were PCR amplified and sequenced, and twelve samples were downloaded from the GenBank. The intra-specific and interspecific K2P distances were calculated, and neighbor-joining( NJ) tree was constructed by MEGA 5.0. The results showed the intra-specific genetic distances of Hibiscus syriacus were ranged from 0.009 to 0.056, which were far lower than inter-specific genetic distances between Hibiscus syriacus and its adulterants (0.236 - 0.301). Variable sites within Hibiscus syriacus ranged from 2 to 9 which were far less than the adulterants (45 - 52); Different samples of Hibiscus syriacus were gathered together and could be distinguished from its adulterants by NJ tree. ITS2 can discriminate Hibiscus syriacus from its adulterants correctly. The ITS2 region is an efficient barcode for authentication of Hibiscus syriacus and its adulterants.

  15. Cryptic diversity in Australian stick insects (Insecta; Phasmida) uncovered by the DNA barcoding approach.

    Science.gov (United States)

    Velonà, A; Brock, P D; Hasenpusch, J; Mantovani, B

    2015-05-18

    The barcoding approach was applied to analyze 16 Australian morphospecies of the order Phasmida, with the aim to test if it could be suitable as a tool for phasmid species identification and if its discrimination power would allow uncovering of cryptic diversity. Both goals were reached. Eighty-two specimens representing twelve morphospecies (Sipyloidea sp. A, Candovia annulata, Candovia sp. A, Candovia sp. B, Candovia sp. C, Denhama austrocarinata, Xeroderus kirbii, Parapodacanthus hasenpuschorum, Tropidoderus childrenii, Cigarrophasma tessellatum, Acrophylla wuelfingi, Eurycantha calcarata) were correctly recovered as clades through the molecular approach, their sequences forming monophyletic and well-supported clusters. In four instances, Neighbor-Joining tree and barcoding gap analyses supported either a specific (Austrocarausius mercurius, Anchiale briareus) or a subspecific (Anchiale austrotessulata, Extatosoma tiaratum) level of divergence within the analyzed morphospecies. The lack of an appropriate database of homologous coxI sequences prevented more detailed identification of undescribed taxa.

  16. DNA fingerprinting, DNA barcoding, and next generation sequencing technology in plants.

    Science.gov (United States)

    Sucher, Nikolaus J; Hennell, James R; Carles, Maria C

    2012-01-01

    DNA fingerprinting of plants has become an invaluable tool in forensic, scientific, and industrial laboratories all over the world. PCR has become part of virtually every variation of the plethora of approaches used for DNA fingerprinting today. DNA sequencing is increasingly used either in combination with or as a replacement for traditional DNA fingerprinting techniques. A prime example is the use of short, standardized regions of the genome as taxon barcodes for biological identification of plants. Rapid advances in "next generation sequencing" (NGS) technology are driving down the cost of sequencing and bringing large-scale sequencing projects into the reach of individual investigators. We present an overview of recent publications that demonstrate the use of "NGS" technology for DNA fingerprinting and DNA barcoding applications.

  17. Identification of Mislabeled Samples and Sample Mix-ups in Genotype Data using Barcode Genotypes

    DEFF Research Database (Denmark)

    Have, Christian Theil; Appel, Emil Vincent Rosenbaum; Grarup, Niels

    2014-01-01

    Abstract—Undetected mislabeled samples may affect the results of genotype studies, particular when rare genetic variants are investigated. Mislabeled samples are often not detected during quality control and if they are detected, they are normally discarded due to a lack of a reliable method...... to recover the correct labels. Here we describe a statistical method which given a few extra independent genotypes (barcode genotypes) detects mislabeled samples and recovers the correct labels for sample mix-ups. We have implemented the method in a program (named Wunderbar) and we evaluate the reliability...... of the method on simulated data. We find that even with only a small number of barcode genotypes, Wunderbar is capable of identifying mislabeled samples and sample mix-ups with high sensitivity and specificity, even with a high genotyping error rate and even in the presence of dependency between the individual...

  18. DNA Barcoding as a Reliable Method for the Authentication of Commercial Seafood Products

    Directory of Open Access Journals (Sweden)

    Silvia Nicolè

    2012-01-01

    Full Text Available Animal DNA barcoding allows researchers to identify different species by analyzing a short nucleotide sequence, typically the mitochondrial gene cox1. In this paper, we use DNA barcoding to genetically identify seafood samples that were purchased from various locations throughout Italy. We adopted a multi-locus approach to analyze the cob, 16S-rDNA and cox1 genes, and compared our sequences to reference sequences in the BOLD and GenBank online databases. Our method is a rapid and robust technique that can be used to genetically identify crustaceans, mollusks and fishes. This approach could be applied in the future for conservation, particularly for monitoring illegal trade of protected and endangered species. Additionally, this method could be used for authentication in order to detect mislabeling of commercially processed seafood.

  19. Yeast screens for host factors in positive-strand RNA virus replication based on a library of temperature-sensitive mutants.

    Science.gov (United States)

    Nawaz-ul-Rehman, Muhammad Shah; Reddisiva Prasanth, K; Baker, Jannine; Nagy, Peter D

    2013-02-01

    RNA viruses exploit host cells by altering cellular pathways, recruiting host factors, remodeling intracellular membranes and escaping host antiviral responses. Model hosts, such as Saccharomyces cerevisiae (yeast), are valuable to identify host factors involved in viral RNA replication. The many advantages of using yeast include the availability of various yeast mutant libraries, such as (i) single gene-deletion library; (ii) the essential gene library (yTHC); and (iii) the yeast ORF over-expression library. Here, we have used a novel temperature-sensitive (ts) mutant library of essential yeast genes to identify 118 host proteins affecting replication of Tomato bushy stunt virus, in yeast model host. Testing 787 ts mutants led to the identification of host factors, of which 72 proteins facilitated TBSV replication in yeast and 46 proteins were inhibitory. Altogether, ~85% of the identified proteins are novel host factors affecting tombusvirus replication. The ts mutant library screen also led to the identification of 17 essential genes, which have been documented before, thus confirming the importance of these genomic screens. Overall, we show the power of ts mutant library in identification of host factors for RNA virus replication. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. DNA Barcoding and Genetic Structure Analysis of Deep-Sea Notacanthiform Fishes

    Directory of Open Access Journals (Sweden)

    David Barros-García

    2015-11-01

    Full Text Available Notacanthiformes Goodrich, 1909 is an order of deep-sea, benthopelagic or benthic fishes distributed from the continental slope to the abyssal plain, at a depth of between 125 and 4,900 m, but mostly occurring at depths of 450-2,500 m. They are characterized by an eel-like body, a snout projecting conspicuously beyond the mouth, large connective tissue nodules inserted between the pterygoid arch and maxilla and pelvic fin webs joined in the ventral midline. Fishes from this order were classified applying DNA barcoding. Cytochrome c oxidase subunit I (COI sequences belonging to new North Atlantic specimens and already deposited BOLD public records were used. The specimens from the two families of the order, Halosauridae (halosaurs and Notacanthidae (spiny eels, formed separated monophyletic clades in neighbor-joining trees and the sequences clustered as coherent species. Nine out of 16 species of Halosauridae and 9 out of 10 species of Notacanthidae were represented including 166 sequences of which 96% were successfully identified. The DNA barcode of the rare species Lipogenys gillii was obtained for the first time ever. The DNA barcode was further tested by exploring the genetic structure and historical demography of four species of notacanthiforms from five sample locations of the North Atlantic and South West Pacific. Neutrality tests, mismatch distribution and haplotype networks analyses pointed to a past bottleneck episode followed by a fast demographic expansion for all the samples. The genetic structure of the abyssal halosaur Halosauropsis macrochir showed no significant differences between the North Atlantic and South West Pacific samples. DNA barcoding was successful in validating field identifications and assigning species names to sequences of notacanthiforms worldwide. These results constitute a first example of high connectivity and gene flow in this group of deep-sea fish species. The historical demography suggests population