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Sample records for biological sequence comparison

  1. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, Thomas G.; Chang, William I-Wei

    1997-01-01

    A method and apparatus for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence.

  2. Method and apparatus for biological sequence comparison

    DOEpatents

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  3. Supercomputers and biological sequence comparison algorithms.

    PubMed

    Core, N G; Edmiston, E W; Saltz, J H; Smith, R M

    1989-12-01

    Comparison of biological (DNA or protein) sequences provides insight into molecular structure, function, and homology and is increasingly important as the available databases become larger and more numerous. One method of increasing the speed of the calculations is to perform them in parallel. We present the results of initial investigations using two dynamic programming algorithms on the Intel iPSC hypercube and the Connection Machine as well as an inexpensive, heuristically-based algorithm on the Encore Multimax.

  4. Geometric Aspects of Biological Sequence Comparison

    PubMed Central

    Stojmirović, Aleksandar

    2009-01-01

    Abstract We introduce a geometric framework suitable for studying the relationships among biological sequences. In contrast to previous works, our formulation allows asymmetric distances (quasi-metrics), originating from uneven weighting of strings, which may induce non-trivial partial orders on sets of biosequences. The distances considered are more general than traditional generalized string edit distances. In particular, our framework enables non-trivial conversion between sequence similarities, both local and global, and distances. Our constructions apply to a wide class of scoring schemes and require much less restrictive gap penalties than the ones regularly used. Numerous examples are provided to illustrate the concepts introduced and their potential applications. PMID:19361329

  5. Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison

    PubMed Central

    Li, Yushuang

    2016-01-01

    This paper constructed a novel injection from a DNA sequence to a 3D graph, named circular helix-like curve (CHC). The presented graphical representation is available for visualizing characterizations of a single DNA sequence and identifying similarities and differences among several DNAs. A 12-dimensional vector extracted from CHC, as a numerical characterization of CHC, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal RNAs, 48 Hepatitis E viruses, and 18 eutherian mammals, respectively. Successful experiments illustrated that CHC is an effective tool of biological sequence analysis and comparison. PMID:27403205

  6. Circular Helix-Like Curve: An Effective Tool of Biological Sequence Analysis and Comparison.

    PubMed

    Li, Yushuang; Xiao, Wenli

    2016-01-01

    This paper constructed a novel injection from a DNA sequence to a 3D graph, named circular helix-like curve (CHC). The presented graphical representation is available for visualizing characterizations of a single DNA sequence and identifying similarities and differences among several DNAs. A 12-dimensional vector extracted from CHC, as a numerical characterization of CHC, was applied to analyze phylogenetic relationships of 11 species, 74 ribosomal RNAs, 48 Hepatitis E viruses, and 18 eutherian mammals, respectively. Successful experiments illustrated that CHC is an effective tool of biological sequence analysis and comparison. PMID:27403205

  7. Comparison of biological and chemical phosphorus removals in continuous and sequencing batch reactors

    SciTech Connect

    Ketchum, L.H.; Irvine, R.L. Jr.; Breyfogle, R.E.; Manning, J.F. Jr.

    1987-01-01

    A full-scale study of phosphorus removal has been conducted at Culver using continuous-flow operation, SBR operation, and several different chemical treatment schemes. A full-scale demonstration of SBR biological phosphorus removal also has been shown to be effective. Four contributing groups of organisms and their roles in biological SBR phosphorus removal have been described: denitrifying organisms, fermentation product-manufacturing organisms, phosphorus- accumulating organisms, and aerobic autotrophs and heterotrophs. The SBR can provide the proper balance of anoxic, anaerobic, and aerobic conditions to allow these group of organisms to successfully remove phosphorus biologically, without chemical addition. Treatment results using various chemicals for phosphorus removal, both during conventional, continuous-flow operation and after the plant was converted for SBR operation, have also been provided for comparison. Effluent phosphorus concentrations were almost identical for each period, except for the period when phosphorus was removed biologically and without any chemical addition when effluent phosphorus concentrations were the lowest. These removals were made as a result of settling alone; no tertiary rapid stand filter was used or required.

  8. Zucchini yellow mosaic virus: biological properties, detection procedures and comparison of coat protein gene sequences.

    PubMed

    Coutts, B A; Kehoe, M A; Webster, C G; Wylie, S J; Jones, R A C

    2011-12-01

    Between 2006 and 2010, 5324 samples from at least 34 weed, two cultivated legume and 11 native species were collected from three cucurbit-growing areas in tropical or subtropical Western Australia. Two new alternative hosts of zucchini yellow mosaic virus (ZYMV) were identified, the Australian native cucurbit Cucumis maderaspatanus, and the naturalised legume species Rhyncosia minima. Low-level (0.7%) seed transmission of ZYMV was found in seedlings grown from seed collected from zucchini (Cucurbita pepo) fruit infected with isolate Cvn-1. Seed transmission was absent in >9500 pumpkin (C. maxima and C. moschata) seedlings from fruit infected with isolate Knx-1. Leaf samples from symptomatic cucurbit plants collected from fields in five cucurbit-growing areas in four Australian states were tested for the presence of ZYMV. When 42 complete coat protein (CP) nucleotide (nt) sequences from the new ZYMV isolates obtained were compared to those of 101 complete CP nt sequences from five other continents, phylogenetic analysis of the 143 ZYMV sequences revealed three distinct groups (A, B and C), with four subgroups in A (I-IV) and two in B (I-II). The new Australian sequences grouped according to collection location, fitting within A-I, A-II and B-II. The 16 new sequences from one isolated location in tropical northern Western Australia all grouped into subgroup B-II, which contained no other isolates. In contrast, the three sequences from the Northern Territory fitted into A-II with 94.6-99.0% nt identities with isolates from the United States, Iran, China and Japan. The 23 new sequences from the central west coast and two east coast locations all fitted into A-I, with 95.9-98.9% nt identities to sequences from Europe and Japan. These findings suggest that (i) there have been at least three separate ZYMV introductions into Australia and (ii) there are few changes to local isolate CP sequences following their establishment in remote growing areas. Isolates from A-I and B

  9. Bringing Next-Generation Sequencing into the Classroom through a Comparison of Molecular Biology Techniques

    ERIC Educational Resources Information Center

    Bowling, Bethany; Zimmer, Erin; Pyatt, Robert E.

    2014-01-01

    Although the development of next-generation (NextGen) sequencing technologies has revolutionized genomic research and medicine, the incorporation of these topics into the classroom is challenging, given an implied high degree of technical complexity. We developed an easy-to-implement, interactive classroom activity investigating the similarities…

  10. Nonlinear analysis of biological sequences

    SciTech Connect

    Torney, D.C.; Bruno, W.; Detours, V.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  11. Indigenous and introduced potyviruses of legumes and Passiflora spp. from Australia: biological properties and comparison of coat protein sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Coat protein sequences of 33 Potyvirus isolates from legume and Passiflora spp. were sequenced to determine the identity of infecting viruses. Phylogenetic analysis of the sequences revealed the presence of seven distinct virus species....

  12. Indigenous and introduced potyviruses of legumes and Passiflora spp. from Australia: biological properties and comparison of coat protein nucleotide sequences.

    PubMed

    Coutts, Brenda A; Kehoe, Monica A; Webster, Craig G; Wylie, Stephen J; Jones, Roger A C

    2011-10-01

    Five Australian potyviruses, passion fruit woodiness virus (PWV), passiflora mosaic virus (PaMV), passiflora virus Y, clitoria chlorosis virus (ClCV) and hardenbergia mosaic virus (HarMV), and two introduced potyviruses, bean common mosaic virus (BCMV) and cowpea aphid-borne mosaic virus (CAbMV), were detected in nine wild or cultivated Passiflora and legume species growing in tropical, subtropical or Mediterranean climatic regions of Western Australia. When ClCV (1), PaMV (1), PaVY (8) and PWV (5) isolates were inoculated to 15 plant species, PWV and two PaVY P. foetida isolates infected P. edulis and P. caerulea readily but legumes only occasionally. Another PaVY P. foetida isolate resembled five PaVY legume isolates in infecting legumes readily but not infecting P. edulis. PaMV resembled PaVY legume isolates in legumes but also infected P. edulis. ClCV did not infect P. edulis or P. caerulea and behaved differently from PaVY legume isolates and PaMV when inoculated to two legume species. When complete coat protein (CP) nucleotide (nt) sequences of 33 new isolates were compared with 41 others, PWV (8), HarMV (4), PaMV (1) and ClCV (1) were within a large group of Australian isolates, while PaVY (14), CAbMV (1) and BCMV (3) isolates were in three other groups. Variation among PWV and PaVY isolates was sufficient for division into four clades each (I-IV). A variable block of 56 amino acid residues at the N-terminal region of the CPs of PaMV and ClCV distinguished them from PWV. Comparison of PWV, PaMV and ClCV CP sequences showed that nt identities were both above and below the 76-77% potyvirus species threshold level. This research gives insights into invasion of new hosts by potyviruses at the natural vegetation and cultivated area interface, and illustrates the potential of indigenous viruses to emerge to infect introduced plants. PMID:21744001

  13. Information theory applications for biological sequence analysis.

    PubMed

    Vinga, Susana

    2014-05-01

    Information theory (IT) addresses the analysis of communication systems and has been widely applied in molecular biology. In particular, alignment-free sequence analysis and comparison greatly benefited from concepts derived from IT, such as entropy and mutual information. This review covers several aspects of IT applications, ranging from genome global analysis and comparison, including block-entropy estimation and resolution-free metrics based on iterative maps, to local analysis, comprising the classification of motifs, prediction of transcription factor binding sites and sequence characterization based on linguistic complexity and entropic profiles. IT has also been applied to high-level correlations that combine DNA, RNA or protein features with sequence-independent properties, such as gene mapping and phenotype analysis, and has also provided models based on communication systems theory to describe information transmission channels at the cell level and also during evolutionary processes. While not exhaustive, this review attempts to categorize existing methods and to indicate their relation with broader transversal topics such as genomic signatures, data compression and complexity, time series analysis and phylogenetic classification, providing a resource for future developments in this promising area.

  14. A relative Lempel-Ziv complexity: Application to comparing biological sequences

    NASA Astrophysics Data System (ADS)

    Liu, Liwei; Li, Dongbo; Bai, Fenglan

    2012-03-01

    One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relative Lempel-Ziv complexity to compare biological sequences. The vertebrate transferring genomes and the spike protein sequences are prepared and tested to evaluate the validity of the method. We use this method to build phylogenetic tree of two groups of the sequences. The result demonstrates that our method is powerful and efficient.

  15. Computational methods for protein sequence comparison and search.

    PubMed

    Xu, Dong

    2009-04-01

    Protein sequence comparison and search has become commonplace not only for bioinformatics researchers but also for experimentalists in many cases. Because of the exponential growth in sequence data, sequence comparison in particular has become an increasingly important tool. Relating a new gene sequence to other known sequences often reveals its function, structure, and evolution. Many sequence comparison and search tools are available through public Web servers, and biologists can use them easily with little knowledge of computers or bioinformatics. This unit provides some theoretical background and describes popular tools for dot plot, sequence search against a database, multiple sequence alignments, protein tree construction, and protein family and motif search. Step-by-step examples are provided to illustrate how to use some of the most well-known tools. Finally, some general advice is given on combining different sequence analysis tools for biological inference.

  16. Protein sequence comparison and protein evolution

    SciTech Connect

    Pearson, W.R.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  17. Function-Based Algorithms for Biological Sequences

    ERIC Educational Resources Information Center

    Mohanty, Pragyan Sheela P.

    2015-01-01

    Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

  18. Fungal genome sequencing: basic biology to biotechnology.

    PubMed

    Sharma, Krishna Kant

    2016-08-01

    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  19. Reading biological processes from nucleotide sequences

    NASA Astrophysics Data System (ADS)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  20. The computational linguistics of biological sequences

    SciTech Connect

    Searls, D.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Protein sequences are analogous in many respects, particularly their folding behavior. Proteins have a much richer variety of interactions, but in theory the same linguistic principles could come to bear in describing dependencies between distant residues that arise by virtue of three-dimensional structure. This tutorial will concentrate on nucleic acid sequences.

  1. A natural M RNA reassortant arising from two species of plant- and insect-infecting bunyaviruses and comparison of its sequence and biological properties to parental species.

    PubMed

    Webster, Craig G; Reitz, Stuart R; Perry, Keith L; Adkins, Scott

    2011-05-10

    Reassortment allows multicomponent viruses to exchange genome segments, a process well-documented in the vertebrate- and arthropod-infecting members of the family Bunyaviridae but not between distinct species of the plant- and insect-infecting members of the genus Tospovirus. Genome sequence comparisons of a virus causing severe tospovirus-like symptoms in Florida tomato with Groundnut ringspot virus (GRSV) and Tomato chlorotic spot virus (TCSV) demonstrated that reassortment has occurred, with the large (L) and small (S) RNAs coming from GRSV and the medium (M) RNA coming from TCSV (i.e. L(G)M(T)S(G)). Neither parental genotype is known to occur in the U.S. suggesting that L(G)M(T)S(G) was introduced as a reassortant. L(G)M(T)S(G) was transmitted by western flower thrips (Frankliniella occidentalis [Pergande]), and was not able to overcome the Sw5 resistance gene of tomato. Our demonstration of reassortment between GRSV and TCSV suggests caution in defining species within the family Bunyaviridae based on their ability to reassort.

  2. Sequence comparisons via algorithmic mutual information.

    PubMed

    Milosavljević, A

    1994-01-01

    One of the main problems in DNA and protein sequence comparisons is to decide whether observed similarity of two sequences should be explained by their relatedness or by mere presence of some shared internal structure, e.g., shared internal tandem repeats. The standard methods that are based on statistics or classical information theory can be used to discover either internal structure or mutual sequence similarity, but cannot take into account both. Consequently, currently used methods for sequence comparison employ "masking" techniques that simply eliminate sequences that exhibit internal repetitive structure prior to sequence comparisons. The "masking" approach precludes discovery of homologous sequences of moderate or low complexity, which abound at both DNA and protein levels. As a solution to this problem, we propose a general method that is based on algorithmic information theory and minimal length encoding. We show that algorithmic mutual information factors out the sequence similarity that is due to shared internal structure and thus enables discovery of truly related sequences. We extend that recently developed algorithmic significance method (Milosavljević & Jurka 1993) to show that significance depends exponentially on algorithmic mutual information.

  3. Frequent patterns mining in multiple biological sequences.

    PubMed

    Chen, Ling; Liu, Wei

    2013-10-01

    Existing algorithms for mining frequent patterns in multiple biosequences may generate multiple projected databases and short candidate patterns, which can increase computation time and memory requirement. In order to overcome such shortcomings, we propose a fast and efficient algorithm for mining frequent patterns in multiple biological sequences (MSPM). We first present the concept of a primary pattern, which can be extended to form larger patterns in the sequence. To detect frequent primary patterns, a prefix tree is constructed. Based on this prefix tree, a pattern-extending approach is also presented to mine frequent patterns without producing a large number of irrelevant candidate patterns. The experimental results show that the MSPM algorithm can achieve not only faster speed, but also higher quality results as compared with other methods. PMID:24034736

  4. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  5. Discovering New Biology through Sequencing of RNA.

    PubMed

    Weber, Andreas P M

    2015-11-01

    Sequencing of RNA (RNA-Seq) was invented approximately 1 decade ago and has since revolutionized biological research. This update provides a brief historic perspective on the development of RNA-Seq and then focuses on the application of RNA-Seq in qualitative and quantitative analyses of transcriptomes. Particular emphasis is given to aspects of data analysis. Since the wet-lab and data analysis aspects of RNA-Seq are still rapidly evolving and novel applications are continuously reported, a printed review will be rapidly outdated and can only serve to provide some examples and general guidelines for planning and conducting RNA-Seq studies. Hence, selected references to frequently update online resources are given.

  6. Comparison of metagenomic samples using sequence signatures

    PubMed Central

    2012-01-01

    Background Sequence signatures, as defined by the frequencies of k-tuples (or k-mers, k-grams), have been used extensively to compare genomic sequences of individual organisms, to identify cis-regulatory modules, and to study the evolution of regulatory sequences. Recently many next-generation sequencing (NGS) read data sets of metagenomic samples from a variety of different environments have been generated. The assembly of these reads can be difficult and analysis methods based on mapping reads to genes or pathways are also restricted by the availability and completeness of existing databases. Sequence-signature-based methods, however, do not need the complete genomes or existing databases and thus, can potentially be very useful for the comparison of metagenomic samples using NGS read data. Still, the applications of sequence signature methods for the comparison of metagenomic samples have not been well studied. Results We studied several dissimilarity measures, including d2, d2* and d2S recently developed from our group, a measure (hereinafter noted as Hao) used in CVTree developed from Hao’s group (Qi et al., 2004), measures based on relative di-, tri-, and tetra-nucleotide frequencies as in Willner et al. (2009), as well as standard lp measures between the frequency vectors, for the comparison of metagenomic samples using sequence signatures. We compared their performance using a series of extensive simulations and three real next-generation sequencing (NGS) metagenomic datasets: 39 fecal samples from 33 mammalian host species, 56 marine samples across the world, and 13 fecal samples from human individuals. Results showed that the dissimilarity measure d2S can achieve superior performance when comparing metagenomic samples by clustering them into different groups as well as recovering environmental gradients affecting microbial samples. New insights into the environmental factors affecting microbial compositions in metagenomic samples are obtained through

  7. Sequence analysis in partial genes of five isolates of Angiostrongylus cantonensis from Taiwan and biological comparison in infectivity and pathogenicity between two strains.

    PubMed

    Lee, June-Der; Chung, Li-Yu; Wang, Lian-Chen; Lin, Rong-Jyh; Wang, Jiun-Jye; Tu, Hung-Pin; Wu, Zhong-Dao; Yen, Chuan-Min

    2014-05-01

    Angiostrongylus cantonensis is the most common infectious agent causing eosinophilic meningitis and is present in Taiwan, Thailand and the Pacific islands. Clinical symptoms vary within different endemic regions, and their severity is probably dependent on the number of ingested parasites and the diversity among strains. The experimentally definitive host is the rat, and non-permissive hosts are certain mammals such as humans and mice. In this study, the partial gene sequences of two A. cantonensis strains isolated from five different regions in Taiwan were selected and molecularly analyzed. The internal transcribed spacer gene and cytochrome-c oxidase subunit I gene sequences of the Hualien (H) strain of A. cantonensis differed from those of the Pingtung (P) strain and the other three strains by 19% and 11%, respectively. We analyzed the infectivity, fecundity, and development of the H and P strain in rats and host pathogenicity in mice inoculated with both strains. The number of the emerged first-stage larvae, adult recovery, and average length of adults in Sprague-Dawley rats significantly differed between rats inoculated with the H and P strain. Young adult recovery, average length of young adults, eosinophil counts in the cerebrospinal fluid (CSF), glutathione peroxidase concentration, levels of reactive oxygen species as well as malondialdehyde concentration in the CSF, and the survival of mice significantly differed between BALB/c mice inoculated with the H and P strain. The H strain of A. cantonensis had lower infectivity, delayed fecundity, and poor development in rats, and caused milder pathology and lower mortality in mice than the P strain. These data clearly indicate that the H strain of A. cantonensis is a pathogenically distinct strain with lower infectivity to its definitive host, and causing mild pathogenic symptoms to its non-permissive host.

  8. The DNA sequence and biological annotation of human chromosome 1.

    PubMed

    Gregory, S G; Barlow, K F; McLay, K E; Kaul, R; Swarbreck, D; Dunham, A; Scott, C E; Howe, K L; Woodfine, K; Spencer, C C A; Jones, M C; Gillson, C; Searle, S; Zhou, Y; Kokocinski, F; McDonald, L; Evans, R; Phillips, K; Atkinson, A; Cooper, R; Jones, C; Hall, R E; Andrews, T D; Lloyd, C; Ainscough, R; Almeida, J P; Ambrose, K D; Anderson, F; Andrew, R W; Ashwell, R I S; Aubin, K; Babbage, A K; Bagguley, C L; Bailey, J; Beasley, H; Bethel, G; Bird, C P; Bray-Allen, S; Brown, J Y; Brown, A J; Buckley, D; Burton, J; Bye, J; Carder, C; Chapman, J C; Clark, S Y; Clarke, G; Clee, C; Cobley, V; Collier, R E; Corby, N; Coville, G J; Davies, J; Deadman, R; Dunn, M; Earthrowl, M; Ellington, A G; Errington, H; Frankish, A; Frankland, J; French, L; Garner, P; Garnett, J; Gay, L; Ghori, M R J; Gibson, R; Gilby, L M; Gillett, W; Glithero, R J; Grafham, D V; Griffiths, C; Griffiths-Jones, S; Grocock, R; Hammond, S; Harrison, E S I; Hart, E; Haugen, E; Heath, P D; Holmes, S; Holt, K; Howden, P J; Hunt, A R; Hunt, S E; Hunter, G; Isherwood, J; James, R; Johnson, C; Johnson, D; Joy, A; Kay, M; Kershaw, J K; Kibukawa, M; Kimberley, A M; King, A; Knights, A J; Lad, H; Laird, G; Lawlor, S; Leongamornlert, D A; Lloyd, D M; Loveland, J; Lovell, J; Lush, M J; Lyne, R; Martin, S; Mashreghi-Mohammadi, M; Matthews, L; Matthews, N S W; McLaren, S; Milne, S; Mistry, S; Moore, M J F; Nickerson, T; O'Dell, C N; Oliver, K; Palmeiri, A; Palmer, S A; Parker, A; Patel, D; Pearce, A V; Peck, A I; Pelan, S; Phelps, K; Phillimore, B J; Plumb, R; Rajan, J; Raymond, C; Rouse, G; Saenphimmachak, C; Sehra, H K; Sheridan, E; Shownkeen, R; Sims, S; Skuce, C D; Smith, M; Steward, C; Subramanian, S; Sycamore, N; Tracey, A; Tromans, A; Van Helmond, Z; Wall, M; Wallis, J M; White, S; Whitehead, S L; Wilkinson, J E; Willey, D L; Williams, H; Wilming, L; Wray, P W; Wu, Z; Coulson, A; Vaudin, M; Sulston, J E; Durbin, R; Hubbard, T; Wooster, R; Dunham, I; Carter, N P; McVean, G; Ross, M T; Harrow, J; Olson, M V; Beck, S; Rogers, J; Bentley, D R; Banerjee, R; Bryant, S P; Burford, D C; Burrill, W D H; Clegg, S M; Dhami, P; Dovey, O; Faulkner, L M; Gribble, S M; Langford, C F; Pandian, R D; Porter, K M; Prigmore, E

    2006-05-18

    The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.

  9. The technology and biology of single-cell RNA sequencing.

    PubMed

    Kolodziejczyk, Aleksandra A; Kim, Jong Kyoung; Svensson, Valentine; Marioni, John C; Teichmann, Sarah A

    2015-05-21

    The differences between individual cells can have profound functional consequences, in both unicellular and multicellular organisms. Recently developed single-cell mRNA-sequencing methods enable unbiased, high-throughput, and high-resolution transcriptomic analysis of individual cells. This provides an additional dimension to transcriptomic information relative to traditional methods that profile bulk populations of cells. Already, single-cell RNA-sequencing methods have revealed new biology in terms of the composition of tissues, the dynamics of transcription, and the regulatory relationships between genes. Rapid technological developments at the level of cell capture, phenotyping, molecular biology, and bioinformatics promise an exciting future with numerous biological and medical applications. PMID:26000846

  10. Bioinformatics comparison of sulfate-reducing metabolism nucleotide sequences

    NASA Astrophysics Data System (ADS)

    Tremberger, G.; Dehipawala, Sunil; Nguyen, A.; Cheung, E.; Sullivan, R.; Holden, T.; Lieberman, D.; Cheung, T.

    2015-09-01

    The sulfate-reducing bacteria can be traced back to 3.5 billion years ago. The thermodynamics details of the sulfur cycle have been well documented. A recent sulfate-reducing bacteria report (Robator, Jungbluth, et al , 2015 Jan, Front. Microbiol) with Genbank nucleotide data has been analyzed in terms of the sulfite reductase (dsrAB) via fractal dimension and entropy values. Comparison to oil field sulfate-reducing sequences was included. The AUCG translational mass fractal dimension versus ATCG transcriptional mass fractal dimension for the low temperature dsrB and dsrA sequences reported in Reference Thirteen shows correlation R-sq ~ 0.79 , with a probably of about 3% in simulation. A recent report of using Cystathionine gamma-lyase sequence to produce CdS quantum dot in a biological method, where the sulfur is reduced just like in the H2S production process, was included for comparison. The AUCG mass fractal dimension versus ATCG mass fractal dimension for the Cystathionine gamma-lyase sequences was found to have R-sq of 0.72, similar to the low temperature dissimilatory sulfite reductase dsr group with 3% probability, in contrary to the oil field group having R-sq ~ 0.94, a high probable outcome in the simulation. The other two simulation histograms, namely, fractal dimension versus entropy R-sq outcome values, and di-nucleotide entropy versus mono-nucleotide entropy R-sq outcome values are also discussed in the data analysis focusing on low probability outcomes.

  11. Performance comparison of Next Generation sequencing platforms.

    PubMed

    Erguner, Bekir; Ustek, Duran; Sagiroglu, Mahmut S

    2015-01-01

    Next Generation DNA Sequencing technologies offer ultra high sequencing throughput for very low prices. The increase in throughput and diminished costs open up new research areas. Moreover, number of clinicians utilizing DNA sequencing keeps growing. One of the main concern for researchers and clinicians who are adopting these platforms is their sequencing accuracy. We compared three of the most commonly used Next Generation Sequencing platforms; Ion Torrent from Life Technologies, GS FLX+ from Roche and HiSeq 2000 from Illumina.

  12. A comparative analysis of multiple sequence alignments for biological data.

    PubMed

    Manzoor, Umar; Shahid, Sarosh; Zafar, Bassam

    2015-01-01

    Multiple sequence alignment plays a key role in the computational analysis of biological data. Different programs are developed to analyze the sequence similarity. This paper highlights the algorithmic techniques of the most popular multiple sequence alignment programs. These programs are then evaluated on the basis of execution time and scalability. The overall performance of these programs is assessed to highlight their strengths and weaknesses with reference to their algorithmic techniques. In terms of overall alignment quality, T-Coffee and Mafft attain the highest average scores, whereas K-align has the minimum computation time. PMID:26405947

  13. Comparison of next-generation sequencing systems.

    PubMed

    Liu, Lin; Li, Yinhu; Li, Siliang; Hu, Ni; He, Yimin; Pong, Ray; Lin, Danni; Lu, Lihua; Law, Maggie

    2012-01-01

    With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.

  14. Identifying features in biological sequences: Sixth workshop report

    SciTech Connect

    Burks, C.; Myers, E.; Pearson, W.R.

    1995-12-31

    This report covers the sixth of an annual series of workshops held at the Aspen Center for Physics concentrating particularly on the identification of features in DNA sequence, and more broadly on related topics in computational molecular biology. The workshop series originally focused primarily on discussion of current needs and future strategies for identifying and predicting the presence of complex functional units on sequenced, but otherwise uncharacterized, genomic DNA. We addressed the need for computationally-based, automatic tools for synthesizing available data about individual consensus sequences and local compositional patterns into the composite objects (e.g., genes) that are -- as composite entities -- the true object of interest when scanning DNA sequences. The workshop was structured to promote sustained informal contact and exchange of expertise between molecular biologists, computer scientists, and mathematicians.

  15. Legume genomics: understanding biology through DNA and RNA sequencing

    PubMed Central

    O'Rourke, Jamie A.; Bolon, Yung-Tsi; Bucciarelli, Bruna; Vance, Carroll P.

    2014-01-01

    Background The legume family (Leguminosae) consists of approx. 17 000 species. A few of these species, including, but not limited to, Phaseolus vulgaris, Cicer arietinum and Cajanus cajan, are important dietary components, providing protein for approx. 300 million people worldwide. Additional species, including soybean (Glycine max) and alfalfa (Medicago sativa), are important crops utilized mainly in animal feed. In addition, legumes are important contributors to biological nitrogen, forming symbiotic relationships with rhizobia to fix atmospheric N2 and providing up to 30 % of available nitrogen for the next season of crops. The application of high-throughput genomic technologies including genome sequencing projects, genome re-sequencing (DNA-seq) and transcriptome sequencing (RNA-seq) by the legume research community has provided major insights into genome evolution, genomic architecture and domestication. Scope and Conclusions This review presents an overview of the current state of legume genomics and explores the role that next-generation sequencing technologies play in advancing legume genomics. The adoption of next-generation sequencing and implementation of associated bioinformatic tools has allowed researchers to turn each species of interest into their own model organism. To illustrate the power of next-generation sequencing, an in-depth overview of the transcriptomes of both soybean and white lupin (Lupinus albus) is provided. The soybean transcriptome focuses on analysing seed development in two near-isogenic lines, examining the role of transporters, oil biosynthesis and nitrogen utilization. The white lupin transcriptome analysis examines how phosphate deficiency alters gene expression patterns, inducing the formation of cluster roots. Such studies illustrate the power of next-generation sequencing and bioinformatic analyses in elucidating the gene networks underlying biological processes. PMID:24769535

  16. Bioclojure: a functional library for the manipulation of biological sequences

    PubMed Central

    Plieskatt, Jordan; Rinaldi, Gabriel; Brindley, Paul J.; Jia, Xinying; Potriquet, Jeremy; Bethony, Jeffrey; Mulvenna, Jason

    2014-01-01

    Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets. Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure’s functional style and emphasize laziness and composability, so that BioClojure, and user-defined, functions can be chained into simple pipelines that are thread-safe and seamlessly integrate lazy evaluation. Availability and implementation: BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence). Contact: jason.mulvenna@qimrberghofer.edu.au or jason.mulvenna@qimr.edu.au PMID:24794932

  17. Dynamite: a flexible code generating language for dynamic programming methods used in sequence comparison.

    PubMed

    Birney, E; Durbin, R

    1997-01-01

    We have developed a code generating language, called Dynamite, specialised for the production and subsequent manipulation of complex dynamic programming methods for biological sequence comparison. From a relatively simple text definition file Dynamite will produce a variety of implementations of a dynamic programming method, including database searches and linear space alignments. The speed of the generated code is comparable to hand written code, and the additional flexibility has proved invaluable in designing and testing new algorithms. An innovation is a flexible labelling system, which can be used to annotate the original sequences with biological information. We illustrate the Dynamite syntax and flexibility by showing definitions for dynamic programming routines (i) to align two protein sequences under the assumption that they are both poly-topic transmembrane proteins, with the simultaneous assignment of transmembrane helices and (ii) to align protein information to genomic DNA, allowing for introns and sequencing error.

  18. Biologic: Gene circuits and feedback in an introductory physics sequence for biology and premedical students

    NASA Astrophysics Data System (ADS)

    Cahn, S. B.; Mochrie, S. G. J.

    2014-05-01

    We describe an educational module on feedback and gene circuits that constitute the final topic in a new year-long introductory physics sequence aimed at biology and premedical students at Yale University. The overall goals of this sequence are threefold. First to demonstrate the application of physics and mathematics in the life sciences. Second to introduce biological science majors to mathematical and physical tools, principles, and experiences. Third to seed an enduring appreciation of quantitative approaches in biology and medicine. Here, we present a module on feedback and gene circuits that focuses on a genetic toggle switch and a repressilator. The genetic toggle switch consists of two genes, each of whose protein products represses the other's expression, while the repressilator consists of three genes, each of whose protein products represses the next gene's expression. Analytic, numerical, and electronic treatments of the genetic toggle switch show bistability. A similar treatment of the repressilator reveals sustained oscillations.

  19. Linear regression model of short k-word: a similarity distance suitable for biological sequences with various lengths.

    PubMed

    Yang, Xiwu; Wang, Tianming

    2013-11-21

    Originating from sequences' length difference, both k-word based methods and graphical representation approaches have uncovered biological information in their distinct ways. However, it is less likely that the mechanisms of information storage vary with sequences' length. A similarity distance suitable for sequences with various lengths will be much near to the mechanisms of information storage. In this paper, new sub-sequences of k-word were extracted from biological sequences under a one-to-one mapping. The new sub-sequences were evaluated by a linear regression model. Moreover, a new distance was defined on the invariants from the linear regression model. With comparison to other alignment-free distances, the results of four experiments demonstrated that our similarity distance was more efficient.

  20. COMPARISON OF BIOLOGICAL COMMUNITIES: THE PROBLEM OF SAMPLE REPRESENTATIVENESS

    EPA Science Inventory

    Obtaining an adequate, representative sample of biological communities or assemblages to make richness or compositional comparisons among sites is a continuing challenge. Traditionally, sample size is based on numbers of replicates or area collected or numbers of individuals enum...

  1. Biological nanopore MspA for DNA sequencing

    NASA Astrophysics Data System (ADS)

    Manrao, Elizabeth A.

    Unlocking the information hidden in the human genome provides insight into the inner workings of complex biological systems and can be used to greatly improve health-care. In order to allow for widespread sequencing, new technologies are required that provide fast and inexpensive readings of DNA. Nanopore sequencing is a third generation DNA sequencing technology that is currently being developed to fulfill this need. In nanopore sequencing, a voltage is applied across a small pore in an electrolyte solution and the resulting ionic current is recorded. When DNA passes through the channel, the ionic current is partially blocked. If the DNA bases uniquely modulate the ionic current flowing through the channel, the time trace of the current can be related to the sequence of DNA passing through the pore. There are two main challenges to realizing nanopore sequencing: identifying a pore with sensitivity to single nucleotides and controlling the translocation of DNA through the pore so that the small single nucleotide current signatures are distinguishable from background noise. In this dissertation, I explore the use of Mycobacterium smegmatis porin A (MspA) for nanopore sequencing. In order to determine MspA's sensitivity to single nucleotides, DNA strands of various compositions are held in the pore as the resulting ionic current is measured. DNA is immobilized in MspA by attaching it to a large molecule which acts as an anchor. This technique confirms the single nucleotide resolution of the pore and additionally shows that MspA is sensitive to epigenetic modifications and single nucleotide polymorphisms. The forces from the electric field within MspA, the effective charge of nucleotides, and elasticity of DNA are estimated using a Freely Jointed Chain model of single stranded DNA. These results offer insight into the interactions of DNA within the pore. With the nucleotide sensitivity of MspA confirmed, a method is introduced to controllably pass DNA through the pore

  2. Insights into cancer biology through next-generation sequencing.

    PubMed

    Nik-Zainal, Serena

    2014-12-01

    Cancer is the ultimate disorder of the genome, characterised not by just one or two mutations, but by hundreds to thousands of acquired mutations that have been accrued through the development of a tumour. Thanks to the recent increase in the speed of sequencing offered by modern sequencing technologies, we are no longer restricted to exploring tiny fragments of protein-coding portions of the human genome. We can now read all the genetic material in human cells. Here, the framework of a next-generation sequencing experiment is explained, giving insight into the advances and difficulties posed by processing the enormous datasets generated through these methods. Some of the recent insights into tumour biology, that exploit the extraordinary surge in scale and the digital nature of next-generation sequencing, are highlighted, including cancer gene discovery, the detection of mutation signatures and cancer evolution. Technological and intellectual developments are starting to shape the personalized cancer genomic profiles of tomorrow. Let's train the next-generation of clinicians to be able to read them from today.

  3. Insights into cancer biology through next-generation sequencing.

    PubMed

    Nik-Zainal, Serena

    2014-12-01

    Cancer is the ultimate disorder of the genome, characterised not by just one or two mutations, but by hundreds to thousands of acquired mutations that have been accrued through the development of a tumour. Thanks to the recent increase in the speed of sequencing offered by modern sequencing technologies, we are no longer restricted to exploring tiny fragments of protein-coding portions of the human genome. We can now read all the genetic material in human cells. Here, the framework of a next-generation sequencing experiment is explained, giving insight into the advances and difficulties posed by processing the enormous datasets generated through these methods. Some of the recent insights into tumour biology, that exploit the extraordinary surge in scale and the digital nature of next-generation sequencing, are highlighted, including cancer gene discovery, the detection of mutation signatures and cancer evolution. Technological and intellectual developments are starting to shape the personalized cancer genomic profiles of tomorrow. Let's train the next-generation of clinicians to be able to read them from today. PMID:25468925

  4. Experience using web services for biological sequence analysis

    PubMed Central

    Attwood, Teresa; Chohan, Shahid Nadeem; Côté, Richard; Cudré-Mauroux, Philippe; Falquet, Laurent; Fernandes, Pedro; Finn, Robert D.; Hupponen, Taavi; Korpelainen, Eija; Labarga, Alberto; Laugraud, Aurelie; Lima, Tania; Pafilis, Evangelos; Pagni, Marco; Pettifer, Steve; Phan, Isabelle; Rahman, Nazim

    2008-01-01

    Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed. PMID:18621748

  5. Experience using web services for biological sequence analysis.

    PubMed

    Stockinger, Heinz; Attwood, Teresa; Chohan, Shahid Nadeem; Côté, Richard; Cudré-Mauroux, Philippe; Falquet, Laurent; Fernandes, Pedro; Finn, Robert D; Hupponen, Taavi; Korpelainen, Eija; Labarga, Alberto; Laugraud, Aurelie; Lima, Tania; Pafilis, Evangelos; Pagni, Marco; Pettifer, Steve; Phan, Isabelle; Rahman, Nazim

    2008-11-01

    Programmatic access to data and tools through the web using so-called web services has an important role to play in bioinformatics. In this article, we discuss the most popular approaches based on SOAP/WS-I and REST and describe our, a cross section of the community, experiences with providing and using web services in the context of biological sequence analysis. We briefly review main technological approaches as well as best practice hints that are useful for both users and developers. Finally, syntactic and semantic data integration issues with multiple web services are discussed.

  6. Automated synthesis and sequence analysis of biological macromolecules

    SciTech Connect

    Smith, L.M.

    1988-03-15

    The traditional distinctions between the fields of physics, chemistry, and biology have blurred with time. As the important questions in biological research have become increasingly detailed and molecular in nature, the techniques needed to answer these questions have drawn increasingly on principles and methods usually ascribed to the fields of physics and chemistry. This fusion has resulted in the instruments and chemistries that constitute the technological foundations of modern biology and that are critical components in the new methods responsible for the explosive growth of modern biology during the last decade. Many of these instruments, such as microscopes, and spectrophotometers, have existed for decades; however, technological advances such as the user of imaging methods in NMR have greatly expanded their power and versatility. In the past several years, a new generation of instruments, whose everyday use has had revolutionary consequences, has come into existence. Central among these are the instruments concerned with the synthesis and sequence analysis of the two major biopolymers, protein and DNA. This article contains descriptions of these instruments, the chemistries on which they are based, and some of their manifold applications.

  7. A comparison of biological and cultural evolution.

    PubMed

    Portin, Petter

    2015-03-01

    This review begins with a definition of biological evolution and a description of its general principles. This is followed by a presentation of the biological basis of culture, specifically the concept of social selection. Further, conditions for cultural evolution are proposed, including a suggestion for language being the cultural replicator corresponding to the concept of the gene in biological evolution. Principles of cultural evolution are put forward and compared to the principles of biological evolution. Special emphasis is laid on the principle of selection in cultural evolution, including presentation of the concept of cultural fitness. The importance of language as a necessary condition for cultural evolution is stressed. Subsequently, prime differences between biological and cultural evolution are presented, followed by a discussion on interaction of our genome and our culture. The review aims at contributing to the present discussion concerning the modern development of the general theory of evolution, for example by giving a tentative formulation of the necessary and sufficient conditions for cultural evolution, and proposing that human creativity and mind reading or theory of mind are motors specific for it. The paper ends with the notion of the still ongoing coevolution of genes and culture.

  8. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    PubMed

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology. PMID:26886735

  9. Comparison of mitochondrial genome sequences of pangolins (Mammalia, Pholidota).

    PubMed

    Hassanin, Alexandre; Hugot, Jean-Pierre; van Vuuren, Bettine Jansen

    2015-04-01

    The complete mitochondrial genome was sequenced for three species of pangolins, Manis javanica, Phataginus tricuspis, and Smutsia temminckii, and comparisons were made with two other species, Manis pentadactyla and Phataginus tetradactyla. The genome of Manidae contains the 37 genes found in a typical mammalian genome, and the structure of the control region is highly conserved among species. In Manis, the overall base composition differs from that found in African genera. Phylogenetic analyses support the monophyly of the genera Manis, Phataginus, and Smutsia, as well as the basal division between Maninae and Smutsiinae. Comparisons with GenBank sequences reveal that the reference genomes of M. pentadactyla and P. tetradactyla (accession numbers NC_016008 and NC_004027) were sequenced from misidentified taxa, and that a new species of tree pangolin should be described in Gabon. PMID:25746396

  10. Comparison of mitochondrial genome sequences of pangolins (Mammalia, Pholidota).

    PubMed

    Hassanin, Alexandre; Hugot, Jean-Pierre; van Vuuren, Bettine Jansen

    2015-04-01

    The complete mitochondrial genome was sequenced for three species of pangolins, Manis javanica, Phataginus tricuspis, and Smutsia temminckii, and comparisons were made with two other species, Manis pentadactyla and Phataginus tetradactyla. The genome of Manidae contains the 37 genes found in a typical mammalian genome, and the structure of the control region is highly conserved among species. In Manis, the overall base composition differs from that found in African genera. Phylogenetic analyses support the monophyly of the genera Manis, Phataginus, and Smutsia, as well as the basal division between Maninae and Smutsiinae. Comparisons with GenBank sequences reveal that the reference genomes of M. pentadactyla and P. tetradactyla (accession numbers NC_016008 and NC_004027) were sequenced from misidentified taxa, and that a new species of tree pangolin should be described in Gabon.

  11. Comparison between optimized GRE and RARE sequences for 19F MRI studies

    NASA Astrophysics Data System (ADS)

    Soffientini, Chiara D.; Mastropietro, Alfonso; Caffini, Matteo; Cocco, Sara; Zucca, Ileana; Scotti, Alessandro; Baselli, Giuseppe; Bruzzone, Maria Grazia

    2014-03-01

    In 19F-MRI studies limiting factors are the presence of a low signal due to the low concentration of 19F-nuclei, necessary for biological applications, and the inherent low sensitivity of MRI. Hence, acquiring images using the pulse sequence with the best signal to noise ratio (SNR) by optimizing the acquisition parameters specifically to a 19F compound is a core issue. In 19F-MRI, multiple-spin-echo (RARE) and gradient-echo (GRE) are the two most frequently used pulse sequence families; therefore we performed an optimization study of GRE pulse sequences based on numerical simulations and experimental acquisitions on fluorinated compounds. We compared GRE performance to an optimized RARE sequence. Images were acquired on a 7T MRI preclinical scanner on phantoms containing different fluorinated compounds. Actual relaxation times (T1, T2, T2*) were evaluated in order to predict SNR dependence on sequence parameters. Experimental comparisons between spoiled GRE and RARE, obtained at a fixed acquisition time and in steady state condition, showed RARE sequence outperforming the spoiled GRE (up to 406% higher). Conversely, the use of the unbalanced-SSFP showed a significant increase in SNR compared to RARE (up to 28% higher). Moreover, this sequence (as GRE in general) was confirmed to be virtually insensitive to T1 and T2 relaxation times, after proper optimization, thus improving marker independence from the biological environment. These results confirm the efficacy of the proposed optimization tool and foster further investigation addressing in-vivo applicability.

  12. A Novel Method of Characterizing Genetic Sequences: Genome Space with Biological Distance and Applications

    PubMed Central

    Liang, Qian; He, Rong L.; Yau, Stephen S.-T.

    2011-01-01

    Background Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences. Methodology To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses. Conclusions Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve. PMID:21399690

  13. Molecular evolution of herpesviruses: genomic and protein sequence comparisons.

    PubMed Central

    Karlin, S; Mocarski, E S; Schachtel, G A

    1994-01-01

    Phylogenetic reconstruction of herpesvirus evolution is generally founded on amino acid sequence comparisons of specific proteins. These are relevant to the evolution of the specific gene (or set of genes), but the resulting phylogeny may vary depending on the particular sequence chosen for analysis (or comparison). In the first part of this report, we compare 13 herpesvirus genomes by using a new multidimensional methodology based on distance measures and partial orderings of dinucleotide relative abundances. The sequences were analyzed with respect to (i) genomic compositional extremes; (ii) total distances within and between genomes; (iii) partial orderings among genomes relative to a set of sequence standards; (iv) concordance correlations of genome distances; and (v) consistency with the alpha-, beta-, gammaherpesvirus classification. Distance assessments within individual herpesvirus genomes show each to be quite homogeneous relative to the comparisons between genomes. The gammaherpesviruses, Epstein-Barr virus (EBV), herpesvirus saimiri, and bovine herpesvirus 4 are both diverse and separate from other herpesvirus classes, whereas alpha- and betaherpesviruses overlap. The analysis revealed that the most central genome (closest to a consensus herpesvirus genome and most individual herpesvirus sequences of different classes) is that of human herpesvirus 6, suggesting that this genome is closest to a progenitor herpesvirus. The shorter DNA distances among alphaherpesviruses supports the hypothesis that the alpha class is of relatively recent ancestry. In our collection, equine herpesvirus 1 (EHV1) stands out as the most central alphaherpesvirus, suggesting it may approximate an ancestral alphaherpesvirus. Among all herpesviruses, the EBV genome is closest to human sequences. In the DNA partial orderings, the chicken sequence collection is invariably as close as or closer to all herpesvirus sequences than the human sequence collection is, which may imply that

  14. Sequence information signal processor for local and global string comparisons

    DOEpatents

    Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.

    1997-01-01

    A sequence information signal processing integrated circuit chip designed to perform high speed calculation of a dynamic programming algorithm based upon the algorithm defined by Waterman and Smith. The signal processing chip of the present invention is designed to be a building block of a linear systolic array, the performance of which can be increased by connecting additional sequence information signal processing chips to the array. The chip provides a high speed, low cost linear array processor that can locate highly similar global sequences or segments thereof such as contiguous subsequences from two different DNA or protein sequences. The chip is implemented in a preferred embodiment using CMOS VLSI technology to provide the equivalent of about 400,000 transistors or 100,000 gates. Each chip provides 16 processing elements, and is designed to provide 16 bit, two's compliment operation for maximum score precision of between -32,768 and +32,767. It is designed to provide a comparison between sequences as long as 4,194,304 elements without external software and between sequences of unlimited numbers of elements with the aid of external software. Each sequence can be assigned different deletion and insertion weight functions. Each processor is provided with a similarity measure device which is independently variable. Thus, each processor can contribute to maximum value score calculation using a different similarity measure.

  15. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology.

    PubMed

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right. PMID:26579190

  16. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology

    PubMed Central

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F.; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right. PMID:26579190

  17. Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology.

    PubMed

    Uddenberg, Daniel; Akhter, Shirin; Ramachandran, Prashanth; Sundström, Jens F; Carlsbecker, Annelie

    2015-01-01

    Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.

  18. It's more than stamp collecting: how genome sequencing can unify biological research.

    PubMed

    Richards, Stephen

    2015-07-01

    The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need.

  19. It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research

    PubMed Central

    Richards, Stephen

    2015-01-01

    The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. PMID:26003218

  20. Applications of next-generation sequencing techniques in plant biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing, allowing u...

  1. The DNA sequence and biology of human chromosome 19

    SciTech Connect

    Grimwood, J; Gordon, L A; Olsen, A; Terry, A; Schmutz, J; Lamerdin, J; Hellsten, U; Goodstein, D; Couronne, O; Tran-Gyamfi, M

    2004-04-06

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high GC content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in Mendelian disorders, including familial hypercholesterolemia and insulin-resistant diabetes. Nearly one quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

  2. The DNA sequence and biology of human chromosome 19

    SciTech Connect

    Grimwood, Jane; Gordon, Laurie A.; Olsen, Anne; Terry, Astrid; Schmutz, Jeremy; Lamerdin, Jane; Hellsten, Uffe; Goodstein, David; Couronne, Olivier; Tran-Gyamfi, Mary; Aerts, Andrea; Altherr, Michael; Ashworth, Linda; Bajorek, Eva; Black, Stacey; Branscomb, Elbert; Caenepeel, Sean; Carrano, Anthony; Caoile, Chenier; Chan, Yee Man; Christensen, Mari; Cleland, Catherine A.; Copeland, Alex; Dalin, Eileen; Dehal, Paramvir; Denys, Mirian; Detter, John C.; Escobar, Julio; Flowers, Dave; Fotopulos, Dea; Garcia, Carmen; Georgescu, Anca M.; Glavina, Tijana; Gomez, Maria; Gonzales, Eldelyn; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Ho, Issac; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Larionov, Vladimer; Leem, Sun-Hee; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Malfatti, Stephanie; Martinez, Diego; McCready, Paula; Medina, Catherine; Morgan, Jenna; Nelson, Kathryn; Nolan, Matt; Ovcharenko, Ivan; Pitluck, Sam; Pollard, Martin; Popkie, Anthony P.; Predki, Paul; Quan, Glenda; Ramirez, Lucia; Rash, Sam; Retterer, James; Rodriguez, Alex; Rogers, Stephanine; Salamov, Asaf; Salazar, Angelica; She, Xinwei; Smith, Doug; Slezak, Tom; Solovyev, Victor; Thayer, Nina; Tice, Hope; Tsai, Ming; Ustaszewska, Anna; Vo, Nu; Wagner, Mark; Wheeler, Jeremy; Wu, Kevin; Xie, Gary; Yang, Joan; Dubchak, Inna; Furey, Terrence S.; DeJong, Pieter; Dickson, Mark; Gordon, David; Eichler, Evan E.; Pennacchio, Len A.; Richardson, Paul; Stubbs, Lisa; Rokhsar, Daniel S.; Myers, Richard M.; Rubin, Edward M.; Lucas, Susan M.

    2003-09-15

    Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G1C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9 percent of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25 percent of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, a nd segments of coding and non-coding conservation with the distant fish species Takifugu.

  3. Effect of k-tuple length on sample-comparison with high-throughput sequencing data.

    PubMed

    Wang, Ying; Lei, Xiaoye; Wang, Shun; Wang, Zicheng; Song, Nianfeng; Zeng, Feng; Chen, Ting

    2016-01-22

    The high-throughput metagenomic sequencing offers a powerful technique to compare the microbial communities. Without requiring extra reference sequences, alignment-free models with short k-tuple (k = 2-10 bp) yielded promising results. Short k-tuples describe the overall statistical distribution, but is hard to capture the specific characteristics inside one microbial community. Longer k-tuple contains more abundant information. However, because the frequency vector of long k-tuple(k ≥ 30 bp) is sparse, the statistical measures designed for short k-tuples are not applicable. In our study, we considered each tuple as a meaningful word and then each sequencing data as a document composed of the words. Therefore, the comparison between two sequencing data is processed as "topic analysis of documents" in text mining. We designed a pipeline with long k-tuple features to compare metagenomic samples combined using algorithms from text mining and pattern recognition. The pipeline is available at http://culotuple.codeplex.com/. Experiments show that our pipeline with long k-tuple features: ①separates genomes with high similarity; ②outperforms short k-tuple models in all experiments. When k ≥ 12, the short k-tuple measures are not applicable anymore. When k is between 20 and 40, long k-tuple pipeline obtains much better grouping results; ③is free from the effect of sequencing platforms/protocols. ③We obtained meaningful and supported biological results on the 40-tuples selected for comparison.

  4. Toward in Silico Biology (from Sequences to Systems)

    NASA Astrophysics Data System (ADS)

    Yamato, Ichiro; Ando, Tadashi; Suzuki, Ayumi; Harada, Kazuo; Itoh, Seigo; Miyazaki, Satoru; Kobayashi, Naoki; Takeda, Masayuki

    2008-03-01

    Thanks to the many large-scale genome sequencing projects, thousands of primary sequences have been determined and the number of uncharacterized sequences will continue to grow. One of the major goals of genome science is to create a living system in a computer using such sequence information. To this goal, many researchers are developing several algorithms to predict folding structures of proteins from their amino acid sequences, to predict functions from sequence information or structures, and finally to simulate living systems in a computer. In this review, we describe our trials toward this goal.

  5. Protein sequence comparison based on K-string dictionary.

    PubMed

    Yu, Chenglong; He, Rong L; Yau, Stephen S-T

    2013-10-25

    The current K-string-based protein sequence comparisons require large amounts of computer memory because the dimension of the protein vector representation grows exponentially with K. In this paper, we propose a novel concept, the "K-string dictionary", to solve this high-dimensional problem. It allows us to use a much lower dimensional K-string-based frequency or probability vector to represent a protein, and thus significantly reduce the computer memory requirements for their implementation. Furthermore, based on this new concept, we use Singular Value Decomposition to analyze real protein datasets, and the improved protein vector representation allows us to obtain accurate gene trees.

  6. Statistical Comparison of Spatial Point Patterns in Biological Imaging

    PubMed Central

    Burguet, Jasmine; Andrey, Philippe

    2014-01-01

    In biological systems, functions and spatial organizations are closely related. Spatial data in biology frequently consist of, or can be assimilated to, sets of points. An important goal in the quantitative analysis of such data is the evaluation and localization of differences in spatial distributions between groups. Because of experimental replications, achieving this goal requires comparing collections of point sets, a noticeably challenging issue for which no method has been proposed to date. We introduce a strategy to address this problem, based on the comparison of point intensities throughout space. Our method is based on a statistical test that determines whether local point intensities, estimated using replicated data, are significantly different or not. Repeating this test at different positions provides an intensity comparison map and reveals domains showing significant intensity differences. Simulated data were used to characterize and validate this approach. The method was then applied to two different neuroanatomical systems to evaluate its ability to reveal spatial differences in biological data sets. Applied to two distinct neuronal populations within the rat spinal cord, the method generated an objective representation of the spatial segregation established previously on a subjective visual basis. The method was also applied to analyze the spatial distribution of locus coeruleus neurons in control and mutant mice. The results objectively consolidated previous conclusions obtained from visual comparisons. Remarkably, they also provided new insights into the maturation of the locus coeruleus in mutant and control animals. Overall, the method introduced here is a new contribution to the quantitative analysis of biological organizations that provides meaningful spatial representations which are easy to understand and to interpret. Finally, because our approach is generic and punctual structures are widespread at the cellular and histological scales, it

  7. Comparison of DNA Quantification Methods for Next Generation Sequencing

    PubMed Central

    Robin, Jérôme D.; Ludlow, Andrew T.; LaRanger, Ryan; Wright, Woodring E.; Shay, Jerry W.

    2016-01-01

    Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library’s heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality. PMID:27048884

  8. Aligning biological sequences on distributed bus networks: a divisible load scheduling approach.

    PubMed

    Min, Wong Han; Veeravalli, Bharadwaj

    2005-12-01

    In this paper, we design a multiprocessor strategy that exploits the computational characteristics of the algorithms used for biological sequence comparison proposed in the literature. We employ divisible load theory (DLT) that is suitable for handling large scale processing on network based systems. For the first time in the domain of DLT, the problem of aligning biological sequences is attempted. The objective is to minimize the total processing time of the alignment process. In designing our strategy, DLT facilitates a clever partitioning of the entire computation process involved in such a way that the overall time consumed for aligning the sequences is a minimum. The partitioning takes into account the computation speeds of the nodes and the underlying communication network. Since this is a real-life application, the post-processing phase becomes important, and hence we consider propagating the results back in order to generate an exact alignment. We consider several cases in our analysis such as deriving closed-form solutions for the processing time for heterogeneous, homogeneous, and networks with slow links. Further, we attempt to employ a multiinstallment strategy to distribute the tasks such that a higher degree of parallelism can be achieved. For slow networks, our strategy recommends near-optimal solutions. We derive an important condition to identify such cases and propose two heuristic strategies. Also, our strategy can be extended for multisequence alignment by utilizing a clustering strategy such as the Berger-Munson algorithm proposed in the literature. Finally, we use real-life DNA samples of house mouse mitochondrion (Mus Musculus Mitochondrion, NC_001569) consisting of 16,295 residues and the DNA of human mitochondrion (Homo Sapiens Mitochondrion, NC_001807) consisting of 16,571 residues, obtainable from the GenBank, in our rigorous simulation experiments to illustrate all the theoretical findings.

  9. De novo Sequencing, Characterization, and Comparison of Inflorescence Transcriptomes of Cornus canadensis and C. florida (Cornaceae)

    PubMed Central

    Zhang, Jian; Franks, Robert G.; Liu, Xiang; Kang, Ming; Keebler, Jonathan E. M.; Schaff, Jennifer E.; Huang, Hong-Wen; Xiang, Qiu-Yun (Jenny)

    2013-01-01

    Background Transcriptome sequencing analysis is a powerful tool in molecular genetics and evolutionary biology. Here we report the results of de novo 454 sequencing, characterization, and comparison of inflorescence transcriptomes of two closely related dogwood species, Cornus canadensis and C. florida (Cornaceae). Our goals were to build a preliminary source of genome sequence data, and to identify genes potentially expressed differentially between the inflorescence transcriptomes for these important horticultural species. Results The sequencing of cDNAs from inflorescence buds of C. canadensis (cc) and C. florida (cf), and normalized cDNAs from leaves of C. canadensis resulted in 251799 (ccBud), 96245 (ccLeaf) and 114648 (cfBud) raw reads, respectively. The de novo assembly of the high quality (HQ) reads resulted in 36088, 17802 and 21210 unigenes for ccBud, ccLeaf and cfBud. A reference transcriptome for C. canadensis was built by assembling HQ reads of ccBud and ccLeaf, containing 40884 unigenes. Reference mapping and comparative analyses found 10926 sequences were putatively specific to ccBud, and 6979 putatively specific to cfBud. Putative differentially expressed genes between ccBud and cfBud that are related to flower development and/or stress response were identified among 7718 shared sequences by ccBud and cfBud. Bi-directional BLAST found 87 (41.83% of 208) of Arabidopsis genes related to inflorescence development had putative orthologs in the dogwood transcriptomes. Comparisons of the shared sequences by ccBud and cfBud yielded 65931 high quality SNPs between two species. The twenty unigenes with the most SNPs are listed as potential genetic markers for evolutionary studies. Conclusions The data provide an important, although preliminary, information platform for functional genomics and evolutionary developmental biology in Cornus. The study identified putative candidates potentially involved in the genetic regulation of inflorescence evolution and

  10. Single-cell sequencing in stem cell biology.

    PubMed

    Wen, Lu; Tang, Fuchou

    2016-04-15

    Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of stem cell populations, but these differences are masked when bulk cells are used for omic analysis. Single-cell sequencing technologies serve as powerful tools to dissect cellular heterogeneity comprehensively and to identify distinct phenotypic cell types, even within a 'homogeneous' stem cell population. These technologies, including single-cell genome, epigenome, and transcriptome sequencing technologies, have been developing rapidly in recent years. The application of these methods to different types of stem cells, including pluripotent stem cells and tissue-specific stem cells, has led to exciting new findings in the stem cell field. In this review, we discuss the recent progress as well as future perspectives in the methodologies and applications of single-cell omic sequencing technologies.

  11. Effect of k-tuple length on sample-comparison with high-throughput sequencing data.

    PubMed

    Wang, Ying; Lei, Xiaoye; Wang, Shun; Wang, Zicheng; Song, Nianfeng; Zeng, Feng; Chen, Ting

    2016-01-22

    The high-throughput metagenomic sequencing offers a powerful technique to compare the microbial communities. Without requiring extra reference sequences, alignment-free models with short k-tuple (k = 2-10 bp) yielded promising results. Short k-tuples describe the overall statistical distribution, but is hard to capture the specific characteristics inside one microbial community. Longer k-tuple contains more abundant information. However, because the frequency vector of long k-tuple(k ≥ 30 bp) is sparse, the statistical measures designed for short k-tuples are not applicable. In our study, we considered each tuple as a meaningful word and then each sequencing data as a document composed of the words. Therefore, the comparison between two sequencing data is processed as "topic analysis of documents" in text mining. We designed a pipeline with long k-tuple features to compare metagenomic samples combined using algorithms from text mining and pattern recognition. The pipeline is available at http://culotuple.codeplex.com/. Experiments show that our pipeline with long k-tuple features: ①separates genomes with high similarity; ②outperforms short k-tuple models in all experiments. When k ≥ 12, the short k-tuple measures are not applicable anymore. When k is between 20 and 40, long k-tuple pipeline obtains much better grouping results; ③is free from the effect of sequencing platforms/protocols. ③We obtained meaningful and supported biological results on the 40-tuples selected for comparison. PMID:26721429

  12. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.

    PubMed

    Olson, Nathan D; Lund, Steven P; Zook, Justin M; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B

    2015-03-01

    This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing(®), or Ion Torrent PGM(®). The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies. PMID:27077030

  13. International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.

    PubMed

    Olson, Nathan D; Lund, Steven P; Zook, Justin M; Rojas-Cornejo, Fabiola; Beck, Brian; Foy, Carole; Huggett, Jim; Whale, Alexandra S; Sui, Zhiwei; Baoutina, Anna; Dobeson, Michael; Partis, Lina; Morrow, Jayne B

    2015-03-01

    This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing(®), or Ion Torrent PGM(®). The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

  14. Advancing small-molecule-based chemical biology with next-generation sequencing technologies.

    PubMed

    Anandhakumar, Chandran; Kizaki, Seiichiro; Bando, Toshikazu; Pandian, Ganesh N; Sugiyama, Hiroshi

    2015-01-01

    Next-generation-sequencing (NGS) technologies enable us to obtain extensive information by deciphering millions of individual DNA sequencing reactions simultaneously. The new DNA-sequencing strategies exceed their precursors in output by many orders of magnitude, resulting in a quantitative increase in valuable sequence information that could be harnessed for qualitative analysis. Sequencing on this scale has facilitated significant advances in diverse disciplines, ranging from the discovery, design, and evaluation of many small molecules and relevant biological mechanisms to maturation of personalized therapies. NGS technologies that have recently become affordable allow us to gain in-depth insight into small-molecule-triggered biological phenomena and empower researchers to develop advanced versions of small molecules. In this review we focus on the overlooked implications of NGS technologies in chemical biology, with a special emphasis on small-molecule development and screening.

  15. Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison

    PubMed Central

    2003-01-01

    Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA. PMID:12734555

  16. Evaluation of intra- and interspecific divergence of satellite DNA sequences by nucleotide frequency calculation and pairwise sequence comparison.

    PubMed

    Kato, Mikio

    2003-01-01

    Satellite DNA sequences are known to be highly variable and to have been subjected to concerted evolution that homogenizes member sequences within species. We have analyzed the mode of evolution of satellite DNA sequences in four fishes from the genus Diplodus by calculating the nucleotide frequency of the sequence array and the phylogenetic distances between member sequences. Calculation of nucleotide frequency and pairwise sequence comparison enabled us to characterize the divergence among member sequences in this satellite DNA family. The results suggest that the evolutionary rate of satellite DNA in D. bellottii is about two-fold greater than the average of the other three fishes, and that the sequence homogenization event occurred in D. puntazzo more recently than in the others. The procedures described here are effective to characterize mode of evolution of satellite DNA. PMID:12734555

  17. A versatile computer-controlled biological stimulus sequencer.

    PubMed

    Boyechko, G; Bose, D

    1984-08-01

    A computer-controlled stimulus sequencer has been developed. This device can be controlled by several commonly available, inexpensive 8-bit microcomputers in which the address, data, and control lines are externally accessible. Although the Apple implementation has been described, a similar interface has also been devised for the Radio Shack Color Computer. The hardware relies on the Rockwell Versatile Interface Adapter (VIA) chip (which has two 16-bit timers capable of functioning as frequency dividers, event counters, or one-shots) and a 12-bit digital-to-analog converter (DAC) chip. This hardware combination, along with software written in Basic and machine language (stored in an EPROM for turn-key operation), allows creation of a large number of unique trains that can be chained together in any sequence. This is aided by storing the train characteristics economically in the computer memory and chaining different train parameters in a link-list. Several train parameters can be incremented or decremented manually by a pair of keys. The amplitude of the train can be changed manually or under program control. Once created, the trains can be edited on the run or deleted from the sequence. The device also generates a trigger pulse that can be referenced to any pulse in a train and can be used to pretrigger an oscilloscope. The software has provision for detecting an external signal, and this information can be used to modify train parameters. The interface is interrupt driven and therefore does not require continuous use of the Basic interpreter.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Next-generation sequencing workflows in veterinary infection biology: towards validation and quality assurance.

    PubMed

    Van Borm, S; Wang, J; Granberg, F; Colling, A

    2016-04-01

    Recent advancements in DNA sequencing methodologies and sequence data analysis have revolutionised research in many areas of biology and medicine, including veterinary infection biology. New technology is poised to bridge the gap between the research and diagnostic laboratory. This paper defines the potential diagnostic value and purposes of next-generation sequencing (NGS) applications in veterinary infection biology and explores their compatibility with the existing validation principles and methods of the World Organisation for Animal Health. Critical parameters for validation and quality control (quality metrics) are suggested, with reference to established validation and quality assurance guidelines for NGS-based methods of diagnosing human heritable diseases. Although most currently described NGS applications in veterinary infection biology are not primary diagnostic tests that directly result in control measures, this critical reflection on the advantages and remaining challenges of NGS technology should stimulate discussion on its diagnostic value and on the potential to validate NGS methods and monitor their diagnostic performance.

  19. Sequence comparison on a cluster of workstations using the PVM system

    SciTech Connect

    Guan, X.; Mural, R.J.; Uberbacher, E.C.

    1995-02-01

    We have implemented a distributed sequence comparison algorithm on a cluster of workstations using the PVM paradigm. This implementation has achieved similar performance to the intel iPSC/860 Hypercube, a massively parallel computer. The distributed sequence comparison algorithm serves as a search tool for two Internet servers GRAIL and GENQUEST. This paper describes the implementation and the performance of the algorithm.

  20. The Transcriptome Sequence of Dientamoeba fragilis Offers New Biological Insights on its Metabolism, Kinome, Degradome and Potential Mechanisms of Pathogenicity.

    PubMed

    Barratt, Joel L N; Cao, Maisie; Stark, Damien J; Ellis, John T

    2015-09-01

    Dientamoeba fragilis is a human bowel parasite with a worldwide distribution. Dientamoeba was once described as a rare and harmless commensal though recent reports suggest it is common and potentially pathogenic. Molecular data on Dientamoeba is scarce which limits our understanding of this parasite. To address this, sequencing of the Dientamoeba transcriptome was performed. Messenger RNA was extracted from cultured Dientamoeba trophozoites originating from clinical stool specimens, and sequenced using Roche GS FLX and Illumina HiSeq technologies. In total 6,595 Dientamoeba transcripts were identified. These sequences were analysed using the BLAST2GO software suite and via BLAST comparisons to sequences available from TrichDB, GenBank, MEROPS and kinase.com. Several novel KEGG pathway maps were generated and gene ontology analysis was also performed. These results are thoroughly discussed guided by knowledge available for other related protozoa. Attention is paid to the novel biological insights afforded by this data including peptidases and kinases of Dientamoeba, as well as its metabolism, novel chemotherapeutics and possible mechanisms of pathogenicity. Currently, this work represents the largest contribution to our understanding of Dientamoeba molecular biology and also represents a major contribution to our understanding of the trichomonads generally, many of which are important pathogens of humans and animals.

  1. Strategies to improve usability and preserve accuracy in biological sequence databases.

    PubMed

    Bengtsson-Palme, Johan; Boulund, Fredrik; Edström, Robert; Feizi, Amir; Johnning, Anna; Jonsson, Viktor A; Karlsson, Fredrik H; Pal, Chandan; Pereira, Mariana Buongermino; Rehammar, Anna; Sanchez, José; Sanli, Kemal; Thorell, Kaisa

    2016-09-01

    Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence of inaccurately annotated or otherwise poorly described sequences introduces noise and bias to biological analyses. Accurate annotations are, for example, pivotal for correct identification of polypeptide fragments. However, standards for how sequence databases are organized and presented are currently insufficient. Here, we propose five strategies to address fundamental issues in the annotation of sequence databases: (i) to clearly separate experimentally verified and unverified sequence entries; (ii) to enable a system for tracing the origins of annotations; (iii) to separate entries with high-quality, informative annotation from less useful ones; (iv) to integrate automated quality-control software whenever such tools exist; and (v) to facilitate postsubmission editing of annotations and metadata associated with sequences. We believe that implementation of these strategies, for example as requirements for publication of database papers, would enable biology to better take advantage of large-scale data. PMID:27528420

  2. A novel statistical measure for sequence comparison on the basis of k-word counts.

    PubMed

    Yang, Xiwu; Wang, Tianming

    2013-02-01

    Numerous efficient methods based on word counts for sequence analysis have been proposed to characterize DNA sequences to help in comparison, retrieval from the databases and reconstructing evolutionary relations. However, most of them seem unrelated to any intrinsic characteristics of DNA. In this paper, we proposed a novel statistical measure for sequence comparison on the basis of k-word counts. This new measure removed the influence of sequences' lengths and uncovered bulk property of DNA sequences. The proposed measure was tested by similarity search and phylogenetic analysis. The experimental assessment demonstrated that our similarity measure was efficient.

  3. Correlation between MCAT biology content specifications and topic scope and sequence of general education college biology textbooks.

    PubMed

    Rissing, Steven W

    2013-01-01

    Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing general education (GE) graduation requirements. Biology textbooks for these three audiences present a topic scope and sequence that correlates with the topic scope and importance ratings of the biology content specifications for the MCAT regardless of the intended audience. Texts for "nonmajors," GE courses appear derived directly from their publisher's majors text. Topic scope and sequence of GE texts reflect those of "their" majors text and, indirectly, the MCAT. MCAT term density of GE texts equals or exceeds that of their corresponding majors text. Most American universities require a GE curriculum to promote a core level of academic understanding among their graduates. This includes civic scientific literacy, recognized as an essential competence for the development of public policies in an increasingly scientific and technological world. Deriving GE biology and related science texts from majors texts designed to meet very different learning objectives may defeat the scientific literacy goals of most schools' GE curricula.

  4. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

    PubMed

    Koehler, Jacob; Rawlings, Chris; Verrier, Paul; Mitchell, Rowan; Skusa, Andre; Ruegg, Alexander; Philippi, Stephan

    2005-01-01

    The structure of a closely integrated data warehouse is described that is designed to link different types and varying numbers of biological networks, sequence analysis methods and experimental results such as those coming from microarrays. The data schema is inspired by a combination of graph based methods and generalised data structures and makes use of ontologies and meta-data. The core idea is to consider and store biological networks as graphs, and to use generalised data structures (GDS) for the storage of further relevant information. This is possible because many biological networks can be stored as graphs: protein interactions, signal transduction networks, metabolic pathways, gene regulatory networks etc. Nodes in biological graphs represent entities such as promoters, proteins, genes and transcripts whereas the edges of such graphs specify how the nodes are related. The semantics of the nodes and edges are defined using ontologies of node and relation types. Besides generic attributes that most biological entities possess (name, attribute description), further information is stored using generalised data structures. By directly linking to underlying sequences (exons, introns, promoters, amino acid sequences) in a systematic way, close interoperability to sequence analysis methods can be achieved. This approach allows us to store, query and update a wide variety of biological information in a way that is semantically compact without requiring changes at the database schema level when new kinds of biological information is added. We describe how this datawarehouse is being implemented by extending the text-mining framework ONDEX to link, support and complement different bioinformatics applications and research activities such as microarray analysis, sequence analysis and modelling/simulation of biological systems. The system is developed under the GPL license and can be downloaded from http://sourceforge.net/projects/ondex/

  5. Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing

    PubMed Central

    Mee, Edward T.; Preston, Mark D.; Minor, Philip D.; Schepelmann, Silke; Huang, Xuening; Nguyen, Jenny; Wall, David; Hargrove, Stacey; Fu, Thomas; Xu, George; Li, Li; Cote, Colette; Delwart, Eric; Li, Linlin; Hewlett, Indira; Simonyan, Vahan; Ragupathy, Viswanath; Alin, Voskanian-Kordi; Mermod, Nicolas; Hill, Christiane; Ottenwälder, Birgit; Richter, Daniel C.; Tehrani, Arman; Jacqueline, Weber-Lehmann; Cassart, Jean-Pol; Letellier, Carine; Vandeputte, Olivier; Ruelle, Jean-Louis; Deyati, Avisek; La Neve, Fabio; Modena, Chiara; Mee, Edward; Schepelmann, Silke; Preston, Mark; Minor, Philip; Eloit, Marc; Muth, Erika; Lamamy, Arnaud; Jagorel, Florence; Cheval, Justine; Anscombe, Catherine; Misra, Raju; Wooldridge, David; Gharbia, Saheer; Rose, Graham; Ng, Siemon H.S.; Charlebois, Robert L.; Gisonni-Lex, Lucy; Mallet, Laurent; Dorange, Fabien; Chiu, Charles; Naccache, Samia; Kellam, Paul; van der Hoek, Lia; Cotten, Matt; Mitchell, Christine; Baier, Brian S.; Sun, Wenping; Malicki, Heather D.

    2016-01-01

    Background Unbiased deep sequencing offers the potential for improved adventitious virus screening in vaccines and biotherapeutics. Successful implementation of such assays will require appropriate control materials to confirm assay performance and sensitivity. Methods A common reference material containing 25 target viruses was produced and 16 laboratories were invited to process it using their preferred adventitious virus detection assay. Results Fifteen laboratories returned results, obtained using a wide range of wet-lab and informatics methods. Six of 25 target viruses were detected by all laboratories, with the remaining viruses detected by 4–14 laboratories. Six non-target viruses were detected by three or more laboratories. Conclusion The study demonstrated that a wide range of methods are currently used for adventitious virus detection screening in biological products by deep sequencing and that they can yield significantly different results. This underscores the need for common reference materials to ensure satisfactory assay performance and enable comparisons between laboratories. PMID:26709640

  6. Genomic Sequence Comparisons, 1987-2003 Final Report

    SciTech Connect

    George M. Church

    2004-07-29

    This project was to develop new DNA sequencing and RNA and protein quantitation methods and related genome annotation tools. The project began in 1987 with the development of multiplex sequencing (published in Science in 1988), and one of the first automated sequencing methods. This lead to the first commercial genome sequence in 1994 and to the establishment of the main commercial participants (GTC then Agencourt) in the public DOE/NIH genome project. In collaboration with GTC we contributed to one of the first complete DOE genome sequences, in 1997, that of Methanobacterium thermoautotropicum, a species of great relevance to energy-rich gas production.

  7. Multidomain Peptides: Sequence-Nanostructure Relationships and Biological Applications

    NASA Astrophysics Data System (ADS)

    Bakota, Erica Laraine

    2011-12-01

    Peptides are materials that, as a result of their polymeric nature, possess enormous versatility and customizability. Multidomain peptides are a class of peptides that self-assemble to form stable, cytocompatible hydrogels. They have an ABA block motif, in which the A block is composed of charged amino acids, such as lysine, and the B block consists of alternating hydrophilic and hydrophobic amino acids, such as glutamine and leucine. The B block forms a facial amphiphile that drives self-assembly. The charged A blocks simultaneously limit self-assembly and improve solubility. Self-assembly is triggered by charge screening of these charged amino acids, enabling the formation of beta-sheet fibers. The development of an extended nanofiber network can result in the formation of a hydrogel. Systematic modifications to both the A and B blocks were investigated, and it was found that sequence modifications have a large impact on peptide nanostructure and hydrogel rheology. The first modification examined is the substitution of amino acids within the hydrophilic positions of the B block. The second set of modifications investigated was the incorporation of aromatic amino acids in the B block. Finally, the charged block was varied to generate different net charges on the peptides, a change which impacted the ability to use these peptides in cell culture. Two applications of multidomain peptide nanofibers are explored, the first of which is the delivery of novel therapies in vivo. One multidomain peptide is able to form hydrogels that undergo shear-thinning and rapid recovery. This gel can be loaded with cytokines and growth factors that have been secreted by embryonic stem cells, and these molecules can be subsequently released in a therapeutic setting. Another application for multidomain peptide is their use as biocompatible surfactants. Single-walled carbon nanotubes have been widely investigated for their unique optical and electrical properties, but their solubility in

  8. Comparative systems biology between human and animal models based on next-generation sequencing methods.

    PubMed

    Zhao, Yu-Qi; Li, Gong-Hua; Huang, Jing-Fei

    2013-04-01

    Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

  9. Direct Chloroplast Sequencing: Comparison of Sequencing Platforms and Analysis Tools for Whole Chloroplast Barcoding

    PubMed Central

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert James

    2014-01-01

    Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis. PMID:25329378

  10. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    PubMed

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert James

    2014-01-01

    Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina) and Ion Torrent (Life Technology) sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare). Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels) between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  11. Graphical visualization of the biologically significant segments in the sequence sets of the relative plant viruses.

    PubMed

    Shcherbatenko, I S

    2012-01-01

    The author's and collaborators' computational investigations of the conserved biologically significant segments within viral nucleotide and amino acid sequences are considered in the article. The results obtained suggest that the interactive graphical visualization of the short identical or similar sites in the sequence sets of relative viruses allows to reveal various specific elements such as right, inverted tandem, opposite and regular repeals; deletion/insertion; GC/AT-rich sites; contexts of translation initiation and termination codons; transcription initiation signals; spontaneous nucleotide substitutions; codon usage bias etc. To reveal and investigate different biologically significant sequences very short and simple computer programs, based on common sequence scanning algorithm, may be employed. Various graphic objects, which appeared during visualization of similar sites, may be computationally converted into corresponding nucleotide or amino acid sequences followed by writing within a text file. The change of some scanning parameters or slight modification of certain program modules allows to enlarge the program potentialities. A set of little and simplified computer programs obtained by successive modifications of the initial program is a suitable tool for quick revealing and investigating various biologically significant sequence sites.

  12. WWW-query: an on-line retrieval system for biological sequence banks.

    PubMed

    Perrière, G; Gouy, M

    1996-01-01

    We have developed a World Wide Web (WWW) version of the sequence retrieval system Query: WWW-Query. This server allows to query nucleotide sequence banks in the EMBL/GenBank/DDBJ formats and protein sequence banks in the NBRF/PIR format. WWW-Query includes all the features of the on-line sequences browsers already available: possibility to build complex queries, integration of cross-references with different data banks, and access to the functional zones of biological interest. It also provides original services not available elsewhere: introduction of the notion of re-usable sequence lists, integration of dedicated helper applications for visualizing alignments and phylogenetic trees and links with multivariate methods for studying codon usage or for complementing phylogenies.

  13. Two Dimensional Yau-Hausdorff Distance with Applications on Comparison of DNA and Protein Sequences

    PubMed Central

    Tian, Kun; Yang, Xiaoqian; Kong, Qin; Yin, Changchuan; He, Rong L.; Yau, Stephen S.-T.

    2015-01-01

    Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences. We propose a new approach, the Yau-Hausdorff method, which considers all translations and rotations when seeking the best match of graphical curves of DNA or protein sequences. The complexity of this method is lower than that of any other two dimensional minimum Hausdorff algorithm. The Yau-Hausdorff method can be used for measuring the similarity of DNA sequences based on two important tools: the Yau-Hausdorff distance and graphical representation of DNA sequences. The graphical representations of DNA sequences conserve all sequence information and the Yau-Hausdorff distance is mathematically proved as a true metric. Therefore, the proposed distance can preciously measure the similarity of DNA sequences. The phylogenetic analyses of DNA sequences by the Yau-Hausdorff distance show the accuracy and stability of our approach in similarity comparison of DNA or protein sequences. This study demonstrates that Yau-Hausdorff distance is a natural metric for DNA and protein sequences with high level of stability. The approach can be also applied to similarity analysis of protein sequences by graphic representations, as well as general two dimensional shape matching. PMID:26384293

  14. The genome sequence of taurine cattle: A window to ruminant biology and evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (ma...

  15. The role of adalimumab in rheumatic and autoimmune disorders: comparison with other biologic agents

    PubMed Central

    Reimold, Andreas M

    2012-01-01

    Adalimumab (ADA) is a biologic medication that dampens inflammatory pathways by binding to the cytokine tumor necrosis factor alpha. The US Food and Drug Administration has approved ADA as a medication for use in rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn’s disease, psoriasis, and juvenile idiopathic arthritis. This year marks 10 years of clinical experience with ADA. Long-term extension studies of some of the initial clinical trials, as well as data from large patient registries, are demonstrating ongoing benefit for responders. Potential side effects such as increased risk of infection, lymphoma, congestive heart failure, and demyelination continue to be examined, as the available data are not unanimous in showing an increase in incidence. In balancing both the advantages and the disadvantages of using ADA, the drug’s overall effectiveness and its availability for use in patients with hepatic or renal comorbidities are weighed against the high cost. ADA is expected to have a leading role in the treatment of rheumatoid arthritis and other inflammatory conditions for years to come. Future studies will need to address the optimal sequence of disease-modifying antirheumatic drugs and biologics to use, combinations of disease-modifying antirheumatic drugs and biologics, and head-to-head comparisons of biologics in clinical trials. For those who go into clinical remission on an anti-tumor necrosis factor medication, unanswered questions remain about identifying the patients who can maintain the remission off all drugs, or at least off injected medication. Given the cost of biologic drugs, even studies that increase the interval between drug doses in well-controlled patients could provide financial benefits.

  16. A data parallel strategy for aligning multiple biological sequences on multi-core computers.

    PubMed

    Zhu, Xiangyuan; Li, Kenli; Salah, Ahmad

    2013-05-01

    In this paper, we address the large-scale biological sequence alignment problem, which has an increasing demand in computational biology. We employ data parallelism paradigm that is suitable for handling large-scale processing on multi-core computers to achieve a high degree of parallelism. Using the data parallelism paradigm, we propose a general strategy which can be used to speed up any multiple sequence alignment method. We applied five different clustering algorithms in our strategy and implemented rigorous tests on an 8-core computer using four traditional benchmarks and artificially generated sequences. The results show that our multi-core-based implementations can achieve up to 151-fold improvements in execution time while losing 2.19% accuracy on average. The source code of the proposed strategy, together with the test sets used in our analysis, is available on request.

  17. Meiofaunal community analysis by high-throughput sequencing: comparison of extraction, quality filtering, and clustering methods.

    PubMed

    Brannock, Pamela M; Halanych, Kenneth M

    2015-10-01

    Using molecular tools to examine community composition of meiofauna, animals 45μm to 1mm in size living between sediment grains in aquatic environments, is relatively new in comparison to bacterial and archaeal microbial studies. Although high-throughput molecular approaches are starting to be applied to these ccommunities, effectiveness of different approaches for nucleic acid extraction from meiofauna is poorly known and bioinformatic pipelines vary between studies. Given this situation, there is a need for protocols to be developed that promote consistency in sample collection and processing, sequence quality filtering, and Operational Taxonomic Unit (OTU) clustering methods. Herein, we assess different approaches used for DNA extraction (DNA extracted directly from sediment versus elutriated material retained on a 45μm sieve) as well as how different quality filtering methods of sequences and OTU clustering algorithms impact genetic assessment of meiofauna community composition. DNA extracted directly from sediment resulted in higher presence of non-metazoan eukaryotic taxa; in contrast, an elutriation (resuspension with decanting) approach increased meiofauna abundance and enriched metazoan OTUs. In regards to bioinformatics analyses, the number of overall OTUs varied by clustering algorithm, primarily due to the applied method of sequence quality filtering. However, alpha and beta diversity analyses showed similar trends regardless of bioinformatics pipeline utilized. Based on our results, we recommend studies of meiofauna communities first elutriate samples prior to DNA extraction and include multiple biological replicates to account for variation in community-level composition. The quality filtering method should be carefully considered as this step accounted for large discrepancy in the number of OTUs inferred.

  18. Comparison of simple sequence repeats in 19 Archaea.

    PubMed

    Trivedi, S

    2006-01-01

    All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome. PMID:17183484

  19. Quantitative comparison between a multiecho sequence and a single-echo sequence for susceptibility-weighted phase imaging.

    PubMed

    Gilbert, Guillaume; Savard, Geneviève; Bard, Céline; Beaudoin, Gilles

    2012-06-01

    The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps.

  20. Phylogenetic relationships of Cryptosporidium determined by ribosomal RNA sequence comparison.

    PubMed

    Johnson, A M; Fielke, R; Lumb, R; Baverstock, P R

    1990-04-01

    Reverse transcription of total cellular RNA was used to obtain a partial sequence of the small subunit ribosomal RNA of Cryptosporidium, a protist currently placed in the phylum Apicomplexa. The semi-conserved regions were aligned with homologous sequences in a range of other eukaryotes, and the evolutionary relationships of Cryptosporidium were determined by two different methods of phylogenetic analysis. The prokaryotes Escherichia coli and Halobacterium cuti were included as outgroups. The results do not show an especially close relationship of Cryptosporidium to other members of the phylum Apicomplexa. PMID:2332273

  1. Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest.

    PubMed

    Wragg, P; Randall, L; Whatmore, A M

    2014-10-01

    Recent advances in phenotypic and chemotaxonomic methods have improved the ability of systems to resolve bacterial identities at the species level. Key to the effective use of these systems is the ability to draw upon databases which can be augmented with new data gleaned from atypical or novel isolates. In this study we compared the performance of the Biolog GEN III identification system (hereafter, GEN III) with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing in the identification of isolates of veterinary interest. The use of strains that had proven more difficult to identify by routine methods was designed to test the systems' abilities at the extremes of their performance range. Over an 18month period, 100 strains were analysed by all three methods. To highlight the importance of identification to species level, a weighted scoring system was devised to differentiate the capacity to identify at genus and species levels. The overall relative weighted scores were 0.869:0.781:0.769, achieved by 16S rRNA gene sequencing, GEN III and MALDI-TOF MS respectively, when compared to the 'gold standard'. Performance to the genus level was significantly better using 16S rRNA gene sequencing; however, performance to the species level was similar for all three systems. PMID:25014253

  2. Searching for a family of orphan sequences with SAMBA, a parallel hardware dedicated to biological applications.

    PubMed

    Guerdoux-Jamet, P; Risler, J L

    1996-01-01

    A significant proportion of coding sequences or open reading frames discovered in the course of sequencing projects do not show any similarity with other sequences deposited with the protein databanks. In such cases the search for similarities must be performed with as many comparison algorithms as possible, so as to increase the chance of finding weak relationships. A specialised parallel hardware (SAMBA) implementing the Smith & Waterman algorithm has been developed at the 'Institut de Recherche en Informatique et Systèmes Aléatoìres' (IRISA). It makes it possible to scan protein databanks at a speed comparable with that of BLAST or FASTA. We report here a study performed with SAMBA on 814 orphan sequences from S cerevisiae and compare the results with those from BLAST and FASTA.

  3. Development and Assessment of a Horizontally Integrated Biological Sciences Course Sequence for Pharmacy Education

    PubMed Central

    Wright, Nicholas J.D.; Alston, Gregory L.

    2015-01-01

    Objective. To design and assess a horizontally integrated biological sciences course sequence and to determine its effectiveness in imparting the foundational science knowledge necessary to successfully progress through the pharmacy school curriculum and produce competent pharmacy school graduates. Design. A 2-semester course sequence integrated principles from several basic science disciplines: biochemistry, molecular biology, cellular biology, anatomy, physiology, and pathophysiology. Each is a 5-credit course taught 5 days per week, with 50-minute class periods. Assessment. Achievement of outcomes was determined with course examinations, student lecture, and an annual skills mastery assessment. The North American Pharmacist Licensure Examination (NAPLEX) results were used as an indicator of competency to practice pharmacy. Conclusion. Students achieved course objectives and program level outcomes. The biological sciences integrated course sequence was successful in providing students with foundational basic science knowledge required to progress through the pharmacy program and to pass the NAPLEX. The percentage of the school’s students who passed the NAPLEX was not statistically different from the national percentage. PMID:26430276

  4. A novel algorithm for detecting multiple covariance and clustering of biological sequences

    PubMed Central

    Shen, Wei; Li, Yan

    2016-01-01

    Single genetic mutations are always followed by a set of compensatory mutations. Thus, multiple changes commonly occur in biological sequences and play crucial roles in maintaining conformational and functional stability. Although many methods are available to detect single mutations or covariant pairs, detecting non-synchronous multiple changes at different sites in sequences remains challenging. Here, we develop a novel algorithm, named Fastcov, to identify multiple correlated changes in biological sequences using an independent pair model followed by a tandem model of site-residue elements based on inter-restriction thinking. Fastcov performed exceptionally well at harvesting co-pairs and detecting multiple covariant patterns. By 10-fold cross-validation using datasets of different scales, the characteristic patterns successfully classified the sequences into target groups with an accuracy of greater than 98%. Moreover, we demonstrated that the multiple covariant patterns represent co-evolutionary modes corresponding to the phylogenetic tree, and provide a new understanding of protein structural stability. In contrast to other methods, Fastcov provides not only a reliable and effective approach to identify covariant pairs but also more powerful functions, including multiple covariance detection and sequence classification, that are most useful for studying the point and compensatory mutations caused by natural selection, drug induction, environmental pressure, etc. PMID:27451921

  5. An Efficient Machine Learning Approach To Low-Complexity Filtering In Biological Sequences

    SciTech Connect

    Barber, Christopher A; Oehmen, Christopher S

    2012-06-09

    Biological sequences contain low-complexity regions (LCRs) which produce superfluous matches in homology searches, and lead to slow execution of database search algorithms such as BLAST. These regions are efficiently identified by low-complexity filtering algorithms such as SDUST and SEG, which are included in the BLAST tool-suite. These algorithms target differing notions of complexity, so an algorithm which combines their sensitivities is pursued. A variety of features are derived from these algorithms, as well as a new filtering algorithm based on Lempel-Ziv complexity. Artificial sequences with known LCRs are used to train and evaluate an SVM classifier, which significantly outperforms the standalone filtering algorithms.

  6. Identifying and Mitigating Bias in Next-Generation Sequencing Methods for Chromatin Biology

    PubMed Central

    Meyer, Clifford A.; Liu, X. Shirley

    2015-01-01

    Next generation sequencing (NGS) technologies have been used in diverse ways to investigate facets of chromatin biology by identifying genomic loci that are bound by transcription factors, occupied by nucleosomes, accessible to nuclease cleavage, or physically interact with remote genomic loci. Reaching sound biological conclusions from such NGS enrichment profiles, however, requires that many potential biases be taken into account. In this Review we discuss common ways in which bias may be introduced into NGS chromatin profiling data, ways in which these biases can be diagnosed, and analytical techniques to mitigate their effect. PMID:25223782

  7. 3D reconstruction software comparison for short sequences

    NASA Astrophysics Data System (ADS)

    Strupczewski, Adam; Czupryński, BłaŻej

    2014-11-01

    Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

  8. [Biological ingredient analysis of traditional Chinese medicines utilizing metagenomic approach based on high-throughput-sequencing and big-data-mining].

    PubMed

    Bai, Hong; Ning, Kang; Wang, Chang-yun

    2015-03-01

    The quality of traditional Chinese medicines (TCMs) has been mainly evaluated based on chemical ingredients, yet recently more attentions have been paid on biological ingredients, especially for pill-based preparations. It is a key approach to establish a fast, accurate and systematic method of biological ingredient analysis for realization of modernization, industrialization and internationalization of TCMs. The biological ingredient analysis of TCM preparations could be abstracted as the identification of multiple species from a biological mixture. The metagenomic approach based on high-throughput-sequencing (HTS) and big-data-mining has been considered as one of the most effective methods for multiple species analysis of a biological mixture, which would also be helpful for the analysis of biological ingredients in TCMs. Simultaneous identification of diverse species, including the prescribed species, adulterants, toxic species, protected species and even the biological impurities introduced through production process, could be achieved by selecting appropriate DNA biomarkers, as well as applying large-scale sequence comparison and data mining. By this approach, it is prospective to offer an evaluation basis for the effectiveness, safety and legality of TCM preparations. PMID:26118104

  9. A special-purpose computer for exploring similar biological sequences: Bioler-2 with multi-pipeline and multi-sequence architecture

    NASA Astrophysics Data System (ADS)

    Sugie, Takashige; Ito, Tomoyoshi; Ebisuzaki, Toshikazu

    2004-09-01

    We developed a special-purpose computer for exploring similar biological sequences by Smith-Waterman method, Bioler-2 (BIOLogical sequence explorER). It can compute a complete similarity score between two biological sequences which have less than 10,000 characters. We integrated the system on two FPGA (Field Programmable Gate Array) chips, XC2V6000 (6M gates) by Xilinx corporation. They are mounted on the 32 bit PCI (Peripheral Component Interconnect) bus card which is connected to the host computer. The performance of Bioler-2 is 142 times faster than a general-purpose computer installed the Linux kernel version 2.4.25 compiled by gcc (Gnu Compiler Collection) version 3.3.3 with Pentium4 enabled hyper threading technology at 3.2 GHz. Bioler-2 is effective in the biological sequence analysis.

  10. Nucleotide sequence of a cloned duck hepatitis B virus genome: comparison with woodchuck and human hepatitis B virus sequences.

    PubMed Central

    Mandart, E; Kay, A; Galibert, F

    1984-01-01

    The nucleotide sequence of an EcoRI duck hepatitis B virus (DHBV) clone was elucidated by using the Maxam and Gilbert method. This sequence, which is 3,021 nucleotides long, was compared with the two previously analyzed hepatitis B-like viruses (human and woodchuck). From this comparison, it was shown that DHBV is derived from an ancestor common to the two others but has a slightly different genomic organization. There was no intergenic region between genes 5 and 8, which were fused into a single open reading frame in DHBV. Genes for the surface and core proteins were assigned to open reading frames 7 and 5/8. Amino acid comparisons showed some structural relationship between gene 6 product and avian reverse transcriptase, suggesting either evolution from a common ancestor or convergence to some particular structure to fulfill a specific function. This should be correlated with the synthesis of an RNA intermediate during DNA replication. This is also taken as an argument in favor of the hypothesis that gene 6 codes for the DNA polymerase that is found within the virion. DNA sequence comparison also showed that the two mammalian hepatitis B viruses are more homologous to each other than they are to DHBV, indicating that DHBV starts to evolve on its own earlier than the two other viruses, as do birds compared with mammals. From this it is proposed that the viruses evolved in a fashion parallel to the species they infect. PMID:6699938

  11. Networking Biology: The Origins of Sequence-Sharing Practices in Genomics.

    PubMed

    Stevens, Hallam

    2015-10-01

    The wide sharing of biological data, especially nucleotide sequences, is now considered to be a key feature of genomics. Historians and sociologists have attempted to account for the rise of this sharing by pointing to precedents in model organism communities and in natural history. This article supplements these approaches by examining the role that electronic networking technologies played in generating the specific forms of sharing that emerged in genomics. The links between early computer users at the Stanford Artificial Intelligence Laboratory in the 1960s, biologists using local computer networks in the 1970s, and GenBank in the 1980s, show how networking technologies carried particular practices of communication, circulation, and data distribution from computing into biology. In particular, networking practices helped to transform sequences themselves into objects that had value as a community resource. PMID:26593711

  12. Dynamic visual data mining: biological sequence analysis and annotation using SeqVISTA.

    PubMed

    Niu, Tianhua; Hu, Zhenjun

    2005-01-01

    In the post-genomic era, the volume of public sequence databases is increasing exponentially and visualisation-centric techniques have become more and more important in biological sequence analysis and annotation. In this paper, we present a methodology called dynamic visual data mining (DVDM), which combines biological object modelling, interactive display, and data analysis tools into one integrative platform. Using Java Development Kit v1.4, an object-oriented software named SeqVISTA has been developed based on DVDM. To illustrate the application of SeqVISTA, the following examples are shown: regular expression pattern matching; comparative analysis of alternative exon splicing patterns; Fourier analyses; exon prediction (MZEF and GENSCAN). Overall, we argue that DVDM is an important technique for biologists to unveil the information hidden behind the large genomic and proteomic databases, and SeqVISTA provides a versatile tool that integrates multiple computational algorithms for meeting biologists' data mining needs. PMID:18048119

  13. Networking Biology: The Origins of Sequence-Sharing Practices in Genomics.

    PubMed

    Stevens, Hallam

    2015-10-01

    The wide sharing of biological data, especially nucleotide sequences, is now considered to be a key feature of genomics. Historians and sociologists have attempted to account for the rise of this sharing by pointing to precedents in model organism communities and in natural history. This article supplements these approaches by examining the role that electronic networking technologies played in generating the specific forms of sharing that emerged in genomics. The links between early computer users at the Stanford Artificial Intelligence Laboratory in the 1960s, biologists using local computer networks in the 1970s, and GenBank in the 1980s, show how networking technologies carried particular practices of communication, circulation, and data distribution from computing into biology. In particular, networking practices helped to transform sequences themselves into objects that had value as a community resource.

  14. A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

    ERIC Educational Resources Information Center

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

  15. Close Sequence Comparisons are Sufficient to Identify Humancis-Regulatory Elements

    SciTech Connect

    Prabhakar, Shyam; Poulin, Francis; Shoukry, Malak; Afzal, Veena; Rubin, Edward M.; Couronne, Olivier; Pennacchio, Len A.

    2005-12-01

    Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of evolutionarily close and distant sequence comparisons, due to the lack of a universal metric for sequence conservation, and also the paucity of empirically defined benchmark sets of cis-regulatory elements. To address this problem, we developed a general-purpose algorithm (Gumby) that detects slowly-evolving regions in primate, mammalian and more distant comparisons without requiring adjustment of parameters, and ranks conserved elements by P-value using Karlin-Altschul statistics. We benchmarked Gumby predictions against previously identified cis-regulatory elements at diverse genomic loci, and also tested numerous extremely conserved human-rodent sequences for transcriptional enhancer activity using reporter-gene assays in transgenic mice. Human regulatory elements were identified with acceptable sensitivity and specificity by comparison with 1-5 other eutherian mammals or 6 other simian primates. More distant comparisons (marsupial, avian, amphibian and fish) failed to identify many of the empirically defined functional noncoding elements. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole genome comparative analysis, which explains some of these findings. Lastly, we determined that, in addition to strength of conservation, genomic location and/or density of surrounding conserved elements must also be considered in selecting candidate enhancers for testing at embryonic time points.

  16. Basal Murphy belt and Chilhowee Group -- Sequence stratigraphic comparison

    SciTech Connect

    Aylor, J.G. Jr. . Dept. of Geology)

    1994-03-01

    The lower Murphy belt in the central western Blue Ridge is interpreted to be correlative to the Early Cambrian Chilhowee Group of the westernmost Blue Ridge and Appalachian fold and thrust belt. Basal Murphy belt depositional sequence stratigraphy represents a second-order, type-2 transgressive systems tract initiated with deposition of lowstand turbidites of the Dean Formation. These transgressive deposits of the Nantahala and Brasstown Formations are interpreted as middle to outer continental shelf deposits. Cyclic and stacked third-order regressive, coarsening upwards sequences of the Nantahala Formation display an overall increase in feldspar content stratigraphically upsection. These transgressive siliciclastic deposits are interpreted to be conformably overlain by a carbonate highstand systems tract of the Murphy Marble. Palinspastic reconstruction indicates that the Nantahala and Brasstown Formations possibly represent a basinward extension of up to 3 km thick siliciclastic wedge. The wedge tapers to the southwest along the strike of the Murphy belt at 10[degree] and thins northwestward to 2 km in the Tennessee depocenter where it is represented by the Chilhowee Group. The Murphy belt basin is believed to represent a transitional rift-to-drift facies deposited on the lower plate of the southern Blue Ridge rift zone.

  17. The Genomic Sequence of Pseudomonas fluorescens Pf-5: Insights Into Biological Control.

    PubMed

    Loper, Joyce E; Kobayashi, Donald Y; Paulsen, Ian T

    2007-02-01

    ABSTRACT The complete sequence of the 7.07 Mb genome of the biological control agent Pseudomonas fluorescens Pf-5 is now available, providing a new opportunity to advance knowledge of biological control through genomics. P. fluorescens Pf-5 is a rhizosphere bacterium that suppresses seedling emergence diseases and produces a spectrum of antibiotics toxic to plant-pathogenic fungi and oomycetes. In addition to six known secondary metabolites produced by Pf-5, three novel secondary metabolite biosynthesis gene clusters identified in the genome could also contribute to biological control. The genomic sequence provides numerous clues as to mechanisms used by the bacterium to survive in the spermosphere and rhizosphere. These features include broad catabolic and transport capabilities for utilizing seed and root exudates, an expanded collection of efflux systems for defense against environmental stress and microbial competition, and the presence of 45 outer membrane receptors that should allow for the uptake of iron from a wide array of siderophores produced by soil microorganisms. As expected for a bacterium with a large genome that lives in a rapidly changing environment, Pf-5 has an extensive collection of regulatory genes, only some of which have been characterized for their roles in regulation of secondary metabolite production or biological control. Consistent with its commensal lifestyle, Pf-5 appears to lack a number of virulence and pathogenicity factors found in plant pathogens. PMID:18944380

  18. Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

    PubMed Central

    2015-01-01

    Background We propose the computational reconstruction of a whole bacterial ancestral genome at the nucleotide scale, and its validation by a sequence of ancient DNA. This rare possibility is offered by an ancient sequence of the late middle ages plague agent. It has been hypothesized to be ancestral to extant Yersinia pestis strains based on the pattern of nucleotide substitutions. But the dynamics of indels, duplications, insertion sequences and rearrangements has impacted all genomes much more than the substitution process, which makes the ancestral reconstruction task challenging. Results We use a set of gene families from 13 Yersinia species, construct reconciled phylogenies for all of them, and determine gene orders in ancestral species. Gene trees integrate information from the sequence, the species tree and gene order. We reconstruct ancestral sequences for ancestral genic and intergenic regions, providing nearly a complete genome sequence for the ancestor, containing a chromosome and three plasmids. Conclusion The comparison of the ancestral and ancient sequences provides a unique opportunity to assess the quality of ancestral genome reconstruction methods. But the quality of the sequencing and assembly of the ancient sequence can also be questioned by this comparison. PMID:26450112

  19. Comparison of agriculture biology and general biology testing outcomes in Utah

    NASA Astrophysics Data System (ADS)

    Despain, Deric Walter

    Agriculture education can take scientific topics to higher levels, emphasize scientific concepts, involve hands-on learning, and develop interrelationships with the other sciences, thus making the living and non-living world around them relevant for students. Prior to 1996, agriculture education was not considered adequate to prepare Utah high school students to meet state biology requirements. The appropriateness of making that equalizing decision in 1996 was not tested until this 2014 study, comparing student test scores on the state biology test for general biology and agriculture biology students. The 2008-2012 data were collected from the Utah Department of Education Data and Statistics, utilizing a descriptive comparative post-test only analysis. As seen in this study, not only did B/AS students tend to score lower than their General Biology counterparts, in multiple cases this difference was significant (p ≤ .05). This contrary finding challenges the theoretical foundation of this study. As a result of this study three implications were made; (a) the Utah CRT-Biology test is not a reliable gauge of academic achievement in agriculture biology, (b) agriculture students in the sample population have not been taught with rigorous biology standards, and (c) biology standards taught in agricultural biology classes are not aligned with content tested by the biology portion of the Utah CRT-Biology test standards. The results of this study indicate to stakeholders that there is a gap occurring within the B/AS education, and the need to reevaluate the biology curriculum delivery to its population may possibly be in need of immediate action.

  20. Secure distributed genome analysis for GWAS and sequence comparison computation

    PubMed Central

    2015-01-01

    Background The rapid increase in the availability and volume of genomic data makes significant advances in biomedical research possible, but sharing of genomic data poses challenges due to the highly sensitive nature of such data. To address the challenges, a competition for secure distributed processing of genomic data was organized by the iDASH research center. Methods In this work we propose techniques for securing computation with real-life genomic data for minor allele frequency and chi-squared statistics computation, as well as distance computation between two genomic sequences, as specified by the iDASH competition tasks. We put forward novel optimizations, including a generalization of a version of mergesort, which might be of independent interest. Results We provide implementation results of our techniques based on secret sharing that demonstrate practicality of the suggested protocols and also report on performance improvements due to our optimization techniques. Conclusions This work describes our techniques, findings, and experimental results developed and obtained as part of iDASH 2015 research competition to secure real-life genomic computations and shows feasibility of securely computing with genomic data in practice. PMID:26733307

  1. MOLECULAR CLONING, SEQUENCING, EXPRESSION AND BIOLOGICAL ACTIVITY OF GIANT PANDA (AILUROPODA MELANOLEUCA) INTERFERON-GAMMA.

    PubMed

    Zhu, Hui; Wang, Wen-Xiu; Wang, Bao-Qin; Zhu, Xiao-Fu; Wu, Xu-Jin; Ma, Qing-Yi; Chen, De-Kun

    2012-06-29

    The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. Interferon-gamma (IFN-γ) is the only member of type □ IFN and is vital for the regulation of host adapted immunity and inflammatory response. Little is known aboutthe FN-γ gene and its roles in giant panda.In this study, IFN-γ gene of Qinling giant panda was amplified from total blood RNA by RT-CPR, cloned, sequenced and analysed. The open reading frame (ORF) of Qinling giant panda IFN-γ encodes 152 amino acidsand is highly similar to Sichuan giant panda with an identity of 99.3% in cDNA sequence. The IFN-γ cDNA sequence was ligated to the pET32a vector and transformed into E. coli BL21 competent cells. Expression of recombinant IFN-γ protein of Qinling giant panda in E. coli was confirmed by SDS-PAGE and Western blot analysis. Biological activity assay indicated that the recombinant IFN-γ protein at the concentration of 4-10 µg/ml activated the giant panda peripheral blood lymphocytes,while at 12 µg/mlinhibited. the activation of the lymphocytes.These findings provide insights into the evolution of giant panda IFN-γ and information regarding amino acid residues essential for their biological activity.

  2. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies.

    PubMed

    Torkamaneh, Davoud; Laroche, Jérôme; Belzile, François

    2016-01-01

    Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method capable of producing thousands to millions of SNPs across a wide range of species. Undoubtedly, the greatest barrier to its broader use is the challenge of data analysis. Herein we describe a comprehensive comparison of seven GBS bioinformatics pipelines developed to process raw GBS sequence data into SNP genotypes. We compared five pipelines requiring a reference genome (TASSEL-GBS v1& v2, Stacks, IGST, and Fast-GBS) and two de novo pipelines that do not require a reference genome (UNEAK and Stacks). Using Illumina sequence data from a set of 24 re-sequenced soybean lines, we performed SNP calling with these pipelines and compared the GBS SNP calls with the re-sequencing data to assess their accuracy. The number of SNPs called without a reference genome was lower (13k to 24k) than with a reference genome (25k to 54k SNPs) while accuracy was high (92.3 to 98.7%) for all but one pipeline (TASSEL-GBSv1, 76.1%). Among pipelines offering a high accuracy (>95%), Fast-GBS called the greatest number of polymorphisms (close to 35,000 SNPs + Indels) and yielded the highest accuracy (98.7%). Using Ion Torrent sequence data for the same 24 lines, we compared the performance of Fast-GBS with that of TASSEL-GBSv2. It again called more polymorphisms (25.8K vs 22.9K) and these proved more accurate (95.2 vs 91.1%). Typically, SNP catalogues called from the same sequencing data using different pipelines resulted in highly overlapping SNP catalogues (79-92% overlap). In contrast, overlap between SNP catalogues obtained using the same pipeline but different sequencing technologies was less extensive (~50-70%). PMID:27547936

  3. Genome-Wide SNP Calling from Genotyping by Sequencing (GBS) Data: A Comparison of Seven Pipelines and Two Sequencing Technologies

    PubMed Central

    Torkamaneh, Davoud; Laroche, Jérôme; Belzile, François

    2016-01-01

    Next-generation sequencing (NGS) has revolutionized plant and animal research in many ways including new methods of high throughput genotyping. Genotyping-by-sequencing (GBS) has been demonstrated to be a robust and cost-effective genotyping method capable of producing thousands to millions of SNPs across a wide range of species. Undoubtedly, the greatest barrier to its broader use is the challenge of data analysis. Herein we describe a comprehensive comparison of seven GBS bioinformatics pipelines developed to process raw GBS sequence data into SNP genotypes. We compared five pipelines requiring a reference genome (TASSEL-GBS v1& v2, Stacks, IGST, and Fast-GBS) and two de novo pipelines that do not require a reference genome (UNEAK and Stacks). Using Illumina sequence data from a set of 24 re-sequenced soybean lines, we performed SNP calling with these pipelines and compared the GBS SNP calls with the re-sequencing data to assess their accuracy. The number of SNPs called without a reference genome was lower (13k to 24k) than with a reference genome (25k to 54k SNPs) while accuracy was high (92.3 to 98.7%) for all but one pipeline (TASSEL-GBSv1, 76.1%). Among pipelines offering a high accuracy (>95%), Fast-GBS called the greatest number of polymorphisms (close to 35,000 SNPs + Indels) and yielded the highest accuracy (98.7%). Using Ion Torrent sequence data for the same 24 lines, we compared the performance of Fast-GBS with that of TASSEL-GBSv2. It again called more polymorphisms (25.8K vs 22.9K) and these proved more accurate (95.2 vs 91.1%). Typically, SNP catalogues called from the same sequencing data using different pipelines resulted in highly overlapping SNP catalogues (79–92% overlap). In contrast, overlap between SNP catalogues obtained using the same pipeline but different sequencing technologies was less extensive (~50–70%). PMID:27547936

  4. Comparison of Biology Student Performance in Quarter and Semester Systems

    ERIC Educational Resources Information Center

    Gibbens, Brian; Williams, Mary A.; Strain, Anna K.; Hoff, Courtney D. M.

    2015-01-01

    Curricula at most colleges and universities in the United States are scheduled according to quarters or semesters. While each schedule has several potential advantages over the other, it is unclear what effect each has on student performance. This study compares biology student performance during the two and a half years before and after the 1999…

  5. Understanding sequence similarity and framework analysis between centromere proteins using computational biology.

    PubMed

    Doss, C George Priya; Chakrabarty, Chiranjib; Debajyoti, C; Debottam, S

    2014-11-01

    Certain mysteries pointing toward their recruitment pathways, cell cycle regulation mechanisms, spindle checkpoint assembly, and chromosome segregation process are considered the centre of attraction in cancer research. In modern times, with the established databases, ranges of computational platforms have provided a platform to examine almost all the physiological and biochemical evidences in disease-associated phenotypes. Using existing computational methods, we have utilized the amino acid residues to understand the similarity within the evolutionary variance of different associated centromere proteins. This study related to sequence similarity, protein-protein networking, co-expression analysis, and evolutionary trajectory of centromere proteins will speed up the understanding about centromere biology and will create a road map for upcoming researchers who are initiating their work of clinical sequencing using centromere proteins.

  6. The genome sequence of taurine cattle: a window to ruminant biology and evolution.

    PubMed

    Elsik, Christine G; Tellam, Ross L; Worley, Kim C; Gibbs, Richard A; Muzny, Donna M; Weinstock, George M; Adelson, David L; Eichler, Evan E; Elnitski, Laura; Guigó, Roderic; Hamernik, Debora L; Kappes, Steve M; Lewin, Harris A; Lynn, David J; Nicholas, Frank W; Reymond, Alexandre; Rijnkels, Monique; Skow, Loren C; Zdobnov, Evgeny M; Schook, Lawrence; Womack, James; Alioto, Tyler; Antonarakis, Stylianos E; Astashyn, Alex; Chapple, Charles E; Chen, Hsiu-Chuan; Chrast, Jacqueline; Câmara, Francisco; Ermolaeva, Olga; Henrichsen, Charlotte N; Hlavina, Wratko; Kapustin, Yuri; Kiryutin, Boris; Kitts, Paul; Kokocinski, Felix; Landrum, Melissa; Maglott, Donna; Pruitt, Kim; Sapojnikov, Victor; Searle, Stephen M; Solovyev, Victor; Souvorov, Alexandre; Ucla, Catherine; Wyss, Carine; Anzola, Juan M; Gerlach, Daniel; Elhaik, Eran; Graur, Dan; Reese, Justin T; Edgar, Robert C; McEwan, John C; Payne, Gemma M; Raison, Joy M; Junier, Thomas; Kriventseva, Evgenia V; Eyras, Eduardo; Plass, Mireya; Donthu, Ravikiran; Larkin, Denis M; Reecy, James; Yang, Mary Q; Chen, Lin; Cheng, Ze; Chitko-McKown, Carol G; Liu, George E; Matukumalli, Lakshmi K; Song, Jiuzhou; Zhu, Bin; Bradley, Daniel G; Brinkman, Fiona S L; Lau, Lilian P L; Whiteside, Matthew D; Walker, Angela; Wheeler, Thomas T; Casey, Theresa; German, J Bruce; Lemay, Danielle G; Maqbool, Nauman J; Molenaar, Adrian J; Seo, Seongwon; Stothard, Paul; Baldwin, Cynthia L; Baxter, Rebecca; Brinkmeyer-Langford, Candice L; Brown, Wendy C; Childers, Christopher P; Connelley, Timothy; Ellis, Shirley A; Fritz, Krista; Glass, Elizabeth J; Herzig, Carolyn T A; Iivanainen, Antti; Lahmers, Kevin K; Bennett, Anna K; Dickens, C Michael; Gilbert, James G R; Hagen, Darren E; Salih, Hanni; Aerts, Jan; Caetano, Alexandre R; Dalrymple, Brian; Garcia, Jose Fernando; Gill, Clare A; Hiendleder, Stefan G; Memili, Erdogan; Spurlock, Diane; Williams, John L; Alexander, Lee; Brownstein, Michael J; Guan, Leluo; Holt, Robert A; Jones, Steven J M; Marra, Marco A; Moore, Richard; Moore, Stephen S; Roberts, Andy; Taniguchi, Masaaki; Waterman, Richard C; Chacko, Joseph; Chandrabose, Mimi M; Cree, Andy; Dao, Marvin Diep; Dinh, Huyen H; Gabisi, Ramatu Ayiesha; Hines, Sandra; Hume, Jennifer; Jhangiani, Shalini N; Joshi, Vandita; Kovar, Christie L; Lewis, Lora R; Liu, Yih-Shin; Lopez, John; Morgan, Margaret B; Nguyen, Ngoc Bich; Okwuonu, Geoffrey O; Ruiz, San Juana; Santibanez, Jireh; Wright, Rita A; Buhay, Christian; Ding, Yan; Dugan-Rocha, Shannon; Herdandez, Judith; Holder, Michael; Sabo, Aniko; Egan, Amy; Goodell, Jason; Wilczek-Boney, Katarzyna; Fowler, Gerald R; Hitchens, Matthew Edward; Lozado, Ryan J; Moen, Charles; Steffen, David; Warren, James T; Zhang, Jingkun; Chiu, Readman; Schein, Jacqueline E; Durbin, K James; Havlak, Paul; Jiang, Huaiyang; Liu, Yue; Qin, Xiang; Ren, Yanru; Shen, Yufeng; Song, Henry; Bell, Stephanie Nicole; Davis, Clay; Johnson, Angela Jolivet; Lee, Sandra; Nazareth, Lynne V; Patel, Bella Mayurkumar; Pu, Ling-Ling; Vattathil, Selina; Williams, Rex Lee; Curry, Stacey; Hamilton, Cerissa; Sodergren, Erica; Wheeler, David A; Barris, Wes; Bennett, Gary L; Eggen, André; Green, Ronnie D; Harhay, Gregory P; Hobbs, Matthew; Jann, Oliver; Keele, John W; Kent, Matthew P; Lien, Sigbjørn; McKay, Stephanie D; McWilliam, Sean; Ratnakumar, Abhirami; Schnabel, Robert D; Smith, Timothy; Snelling, Warren M; Sonstegard, Tad S; Stone, Roger T; Sugimoto, Yoshikazu; Takasuga, Akiko; Taylor, Jeremy F; Van Tassell, Curtis P; Macneil, Michael D; Abatepaulo, Antonio R R; Abbey, Colette A; Ahola, Virpi; Almeida, Iassudara G; Amadio, Ariel F; Anatriello, Elen; Bahadue, Suria M; Biase, Fernando H; Boldt, Clayton R; Carroll, Jeffery A; Carvalho, Wanessa A; Cervelatti, Eliane P; Chacko, Elsa; Chapin, Jennifer E; Cheng, Ye; Choi, Jungwoo; Colley, Adam J; de Campos, Tatiana A; De Donato, Marcos; Santos, Isabel K F de Miranda; de Oliveira, Carlo J F; Deobald, Heather; Devinoy, Eve; Donohue, Kaitlin E; Dovc, Peter; Eberlein, Annett; Fitzsimmons, Carolyn J; Franzin, Alessandra M; Garcia, Gustavo R; Genini, Sem; Gladney, Cody J; Grant, Jason R; Greaser, Marion L; Green, Jonathan A; Hadsell, Darryl L; Hakimov, Hatam A; Halgren, Rob; Harrow, Jennifer L; Hart, Elizabeth A; Hastings, Nicola; Hernandez, Marta; Hu, Zhi-Liang; Ingham, Aaron; Iso-Touru, Terhi; Jamis, Catherine; Jensen, Kirsty; Kapetis, Dimos; Kerr, Tovah; Khalil, Sari S; Khatib, Hasan; Kolbehdari, Davood; Kumar, Charu G; Kumar, Dinesh; Leach, Richard; Lee, Justin C-M; Li, Changxi; Logan, Krystin M; Malinverni, Roberto; Marques, Elisa; Martin, William F; Martins, Natalia F; Maruyama, Sandra R; Mazza, Raffaele; McLean, Kim L; Medrano, Juan F; Moreno, Barbara T; Moré, Daniela D; Muntean, Carl T; Nandakumar, Hari P; Nogueira, Marcelo F G; Olsaker, Ingrid; Pant, Sameer D; Panzitta, Francesca; Pastor, Rosemeire C P; Poli, Mario A; Poslusny, Nathan; Rachagani, Satyanarayana; Ranganathan, Shoba; Razpet, Andrej; Riggs, Penny K; Rincon, Gonzalo; Rodriguez-Osorio, Nelida; Rodriguez-Zas, Sandra L; Romero, Natasha E; Rosenwald, Anne; Sando, Lillian; Schmutz, Sheila M; Shen, Libing; Sherman, Laura; Southey, Bruce R; Lutzow, Ylva Strandberg; Sweedler, Jonathan V; Tammen, Imke; Telugu, Bhanu Prakash V L; Urbanski, Jennifer M; Utsunomiya, Yuri T; Verschoor, Chris P; Waardenberg, Ashley J; Wang, Zhiquan; Ward, Robert; Weikard, Rosemarie; Welsh, Thomas H; White, Stephen N; Wilming, Laurens G; Wunderlich, Kris R; Yang, Jianqi; Zhao, Feng-Qi

    2009-04-24

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

  7. Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

    PubMed

    Harper, B; McClain, S; Ganko, E W

    2012-08-01

    Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence.

  8. Biological characterization and complete genomic sequence of Apium virus Y infecting celery.

    PubMed

    Xu, Donglin; Liu, Hsing-Yeh; Koike, Steven T; Li, Fan; Li, Ruhui

    2011-01-01

    A celery isolate of Apium virus Y (ApVY-Ce) from diseased plants in a commercial field in California was characterized. The experimental host range of the virus included 13 plant species in the families Apiaceae, Chenopodiaceae and Solanaceae. Almost all infected plant species showed foliar chlorosis and distortion or severe stunting and systemic chlorosis. ApVY-Ce was transmitted to all 10 host species in the Apiaceae by green peach aphids. It reacted with the potyvirus group antibody and Celery mosaic virus (CeMV) antiserum. The complete genomic sequence of ApVY-Ce was determined to be 9917 nucleotides, excluding the 3' poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3184 amino acid residues. Its genomic organization is typical of potyviruses, and contains conserved motifs found in the genus Potyvirus. Comparisons with available genomic sequences of other potyviruses indicate that ApVY-Ce shares 26.1-52.9% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Extensive phylogenetic analysis based on the 3'-partial sequences confirms that ApVY-Ce is most closely related to CeMV and is a distinct species of the genus Potyvirus.

  9. Customized care 2020: how medical sequencing and network biology will enable personalized medicine.

    PubMed

    Boguski, Mark S; Arnaout, Ramy; Hill, Colin

    2009-01-01

    Applications of next-generation nucleic acid sequencing technologies will lead to the development of precision diagnostics that will, in turn, be a major technology enabler of precision medicine. Terabyte-scale, multidimensional data sets derived using these technologies will be used to reverse engineer the specific disease networks that underlie individual patients' conditions. Modeling and simulation of these networks in the presence of virtual drugs, and combinations of drugs, will identify the most efficacious therapy for precision medicine and customized care. In coming years the practice of medicine will routinely employ network biology analytics supported by high-performance supercomputing.

  10. MOTION FLOW ESTIMATION FROM IMAGE SEQUENCES WITH APPLICATIONS TO BIOLOGICAL GROWTH AND MOTILITY

    PubMed Central

    Dong, Gang; Baskin, Tobias I.; Palaniappan, Kannappan

    2009-01-01

    In this paper, a new method for motion flow estimation that considers errors in all the derivative measurements is presented. Based on the total least squares (TLS) model, we accurately estimate the motion flow in the general noise case by combining noise model (in form of covariance matrix) with a parametric motion model. The proposed algorithm is tested on two different types of biological motion, a growing plant root and a gastrulating embryo, with sequences obtained microscopically. The local, instantaneous velocity field estimated by the algorithm reveals the behavior of the underlying cellular elements. PMID:19424454

  11. Understanding the granulation process of activated sludge in a biological phosphorus removal sequencing batch reactor.

    PubMed

    Wu, Chang-Yong; Peng, Yong-Zhen; Wang, Ran-Deng; Zhou, Yue-Xi

    2012-02-01

    The granulation of activated sludge was investigated using two parallel sequencing batch reactors (SBRs) operated in biological nitrogen and phosphorus removal conditions though the reactor configuration and operating parameters did not favor the granulation. Granules were not observed when the SBR was operated in biological nitrogen removal period for 30d. However, aerobic granules were formed naturally without the increase of aeration intensity when enhanced biological phosphorus removal (EBPR) was achieved. It can be detected that plenty of positive charged particles were formed with the release of phosphorus during the anaerobic period of EBPR. The size of the particles was about 5-20 μm and their highest positive ζ potential was about 73 mV. These positive charged particles can stimulate the granulation. Based on the experimental results, a hypothesis was proposed to interpret the granulation process of activated sludge in the EBPR process in SBR. Dense and compact subgranules were formed stimulated by the positive charged particles. The subgranules grew gradually by collision, adhesion and attached growth of bacteria. Finally, the extrusion and shear of hydrodynamic shear force would help the maturation of granules. Aerobic granular SBR showed excellent biological phosphorus removal ability. The average phosphorus removal efficiency was over 95% and the phosphorus in the effluent was below 0.50 mg L(-1) during the operation.

  12. Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.

    PubMed

    Kawaji, Hideya; Lizio, Marina; Itoh, Masayoshi; Kanamori-Katayama, Mutsumi; Kaiho, Ai; Nishiyori-Sueki, Hiromi; Shin, Jay W; Kojima-Ishiyama, Miki; Kawano, Mitsuoki; Murata, Mitsuyoshi; Ninomiya-Fukuda, Noriko; Ishikawa-Kato, Sachi; Nagao-Sato, Sayaka; Noma, Shohei; Hayashizaki, Yoshihide; Forrest, Alistair R R; Carninci, Piero

    2014-04-01

    CAGE (cap analysis gene expression) and RNA-seq are two major technologies used to identify transcript abundances as well as structures. They measure expression by sequencing from either the 5' end of capped molecules (CAGE) or tags randomly distributed along the length of a transcript (RNA-seq). Library protocols for clonally amplified (Illumina, SOLiD, 454 Life Sciences [Roche], Ion Torrent), second-generation sequencing platforms typically employ PCR preamplification prior to clonal amplification, while third-generation, single-molecule sequencers can sequence unamplified libraries. Although these transcriptome profiling platforms have been demonstrated to be individually reproducible, no systematic comparison has been carried out between them. Here we compare CAGE, using both second- and third-generation sequencers, and RNA-seq, using a second-generation sequencer based on a panel of RNA mixtures from two human cell lines to examine power in the discrimination of biological states, detection of differentially expressed genes, linearity of measurements, and quantification reproducibility. We found that the quantified levels of gene expression are largely comparable across platforms and conclude that CAGE and RNA-seq are complementary technologies that can be used to improve incomplete gene models. We also found systematic bias in the second- and third-generation platforms, which is likely due to steps such as linker ligation, cleavage by restriction enzymes, and PCR amplification. This study provides a perspective on the performance of these platforms, which will be a baseline in the design of further experiments to tackle complex transcriptomes uncovered in a wide range of cell types.

  13. Comparisons of the Distribution of Nucleotides and Common Sequences in Deoxyribonucleic Acid from Selected Bacteriophages

    PubMed Central

    Skalka, A.; Hanson, P.

    1972-01-01

    Results from comparisons of deoxyribonucleic acid (DNA) from several classes of bacteriophages suggest that most phage chromosomes contain either a homogeneous distribution of nucleotides or are made up of a few, rather large segments of different quanine plus cytosine (G + C) contents which are internally homogeneous. Among those temperate phages tested, most contained segmented DNA. Comparisons of sequence similarities among segments from lambdoid phage DNA species revealed the following order in relatedness to λ: 82 (and 434) > 21 > 424 > φ80. Most common sequences are found in the highest G + C segments, which in λ contain head and tail genes. Hybridization tests with λ and 186 or P2 DNA species verified that the lambdoids and 186 and P2 belong to two distinct groups. There are fewer homologous sequences between the DNA species of coliphages λ and P2 or 186 than there are between the DNA species of coliphage λ and salmonella phage P22. PMID:4553679

  14. Beyond Linear Sequence Comparisons: The use of genome-levelcharacters for phylogenetic reconstruction

    SciTech Connect

    Boore, Jeffrey L.

    2004-11-27

    Although the phylogenetic relationships of many organisms have been convincingly resolved by the comparisons of nucleotide or amino acid sequences, others have remained equivocal despite great effort. Now that large-scale genome sequencing projects are sampling many lineages, it is becoming feasible to compare large data sets of genome-level features and to develop this as a tool for phylogenetic reconstruction that has advantages over conventional sequence comparisons. Although it is unlikely that these will address a large number of evolutionary branch points across the broad tree of life due to the infeasibility of such sampling, they have great potential for convincingly resolving many critical, contested relationships for which no other data seems promising. However, it is important that we recognize potential pitfalls, establish reasonable standards for acceptance, and employ rigorous methodology to guard against a return to earlier days of scenario-driven evolutionary reconstructions.

  15. Assessing the Drosophila melanogaster and Anopheles gambiae Genome Annotations Using Genome-Wide Sequence Comparisons

    PubMed Central

    Jaillon, Olivier; Dossat, Carole; Eckenberg, Ralph; Eiglmeier, Karin; Segurens, Béatrice; Aury, Jean-Marc; Roth, Charles W.; Scarpelli, Claude; Brey, Paul T.; Weissenbach, Jean; Wincker, Patrick

    2003-01-01

    We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily conserved regions (ecores) that can be used for a qualitative and quantitative evaluation of the available annotations of both genomes. They also provide novel candidate features for annotation. The percentage of ecores mapping outside annotations in the A. gambiae genome is about fourfold higher than in D. melanogaster. The A. gambiae genome assembly also contains a high proportion of duplicated ecores, possibly resulting from artefactual sequence duplications in the genome assembly. The occurrence of 4063 ecores in the D. melanogaster genome outside annotations suggests that some genes are not yet or only partially annotated. The present work illustrates the power of comparative genomics approaches towards an exhaustive and accurate establishment of gene models and gene catalogues in insect genomes. PMID:12840038

  16. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

    PubMed Central

    Currin, Andrew; Swainston, Neil; Day, Philip J.

    2015-01-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole

  17. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.

    PubMed

    Currin, Andrew; Swainston, Neil; Day, Philip J; Kell, Douglas B

    2015-03-01

    The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this

  18. The landscape of fusion transcripts in spitzoid melanoma and biologically indeterminate spitzoid tumors by RNA sequencing

    PubMed Central

    Wu, Gang; Barnhill, Raymond L.; Lee, Seungjae; Li, Yongjin; Shao, Ying; Easton, John; Dalton, James; Zhang, Jinghui; Pappo, Alberto; Bahrami, Armita

    2016-01-01

    Kinase activation by chromosomal translocations is a common mechanism that drives tumorigenesis in spitzoid neoplasms. To explore the landscape of fusion transcripts in these tumors, we performed whole-transcriptome sequencing using formalin-fixed paraffin-embedded tissues in malignant or biologically indeterminate spitzoid tumors from 7 patients (age 2–14 years). RNA sequence libraries enriched for coding regions were prepared and the sequencing was analyzed by a novel assembly-based algorithm designed for detecting complex fusions. In addition, tumor samples were screened for hotspot TERT promoter mutations, and telomerase expression was assessed by TERT mRNA in situ hybridization (ISH). Two patients had widespread metastasis and subsequently died of disease, and 5 patients had a benign clinical course on limited follow-up (mean: 30 months). RNA sequencing and TERT mRNA ISH were successful in 6 tumors and unsuccessful in 1 disseminating tumor due to low RNA quality. RNA sequencing identified a kinase fusion in 5 of the 6 sequenced tumors: TPM3–NTRK1 (2 tumors), complex rearrangements involving TPM3, ALK, and IL6R (1 tumor), BAIAP2L1–BRAF (1 tumor), and EML4–BRAF (1 disseminating tumor). All predicted chimeric transcripts were expressed at high levels and contained the intact kinase domain. In addition, 2 tumors each contained a second fusion gene, ARID1B-SNX9 or PTPRZ1-NFAM1. The detected chimeric genes were validated by home-brew break-apart or fusion fluorescence in situ hybridization. The 2 disseminating tumors each harbored the TERT promoter −124C>T (Chr 5:1,295,228 hg19 coordinate) mutation whereas the remaining 5 tumors retained the wild-type gene. The presence of the −124C>T mutation correlated with telomerase expression by TERT mRNA ISH. In summary, we demonstrated complex fusion transcripts and novel partner genes for BRAF by RNA sequencing of FFPE samples. The diversity of gene fusions demonstrated by RNA sequencing defines the molecular

  19. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    SciTech Connect

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  20. Sequence comparison alignment-free approach based on suffix tree and L-words frequency.

    PubMed

    Soares, Inês; Goios, Ana; Amorim, António

    2012-01-01

    The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L-L-words--in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.

  1. The Effects of Meiosis/Genetics Integration and Instructional Sequence on College Biology Student Achievement in Genetics.

    ERIC Educational Resources Information Center

    Browning, Mark

    The purpose of the research was to manipulate two aspects of genetics instruction in order to measure their effects on college, introductory biology students' achievement in genetics. One instructional sequence that was used dealt first with monohybrid autosomal inheritance patterns, then sex-linkage. The alternate sequence was the reverse.…

  2. Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing

    PubMed Central

    2013-01-01

    Background Legionella pneumophila is an opportunistic pathogen of humans where the source of infection is usually from contaminated man-made water systems. When an outbreak of Legionnaires’ disease caused by L. pneumophila occurs, it is necessary to discover the source of infection. A seven allele sequence-based typing scheme (SBT) has been very successful in providing the means to attribute outbreaks of L. pneumophila to a particular source or sources. Particular sequence types described by this scheme are known to exhibit specific phenotypes. For instance some types are seen often in clinical cases but are rarely isolated from the environment and vice versa. Of those causing human disease some types are thought to be more likely to cause more severe disease. It is possible that the genetic basis for these differences are vertically inherited and associated with particular genetic lineages within the population. In order to provide a framework within which to test this hypothesis and others relating to the population biology of L. pneumophila, a set of genomes covering the known diversity of the organism is required. Results Firstly, this study describes a means to group L. pneumophila strains into pragmatic clusters, using a methodology that takes into consideration the genetic forces operating on the population. These clusters can be used as a standardised nomenclature, so those wishing to describe a group of strains can do so. Secondly, the clusters generated from the first part of the study were used to select strains rationally for whole genome sequencing (WGS). The data generated was used to compare phylogenies derived from SBT and WGS. In general the SBT sequence type (ST) accurately reflects the whole genome-based genotype. Where there are exceptions and recombination has resulted in the ST no longer reflecting the genetic lineage described by the whole genome sequence, the clustering technique employed detects these sequence types as being admixed

  3. Proceedings of the workshop on advanced computer technologies and biological sequencing

    SciTech Connect

    Not Available

    1988-11-01

    The participants in the workshop agree that advanced computer technologies will play a significant role in biological sequencing. They suggest a strategy based on the following four recommendations: define a set of model projects, and develop a complete set of data management and analysis tools for these model projects; seek to consolidate appropriate databases, while allowing for the flexible development and design of tools that will permit further consolidation, In the longer term, develop a coordinated effort that will allow networking of all relevant databases; encourage the development, collection, and distribution of analysis tools; and address user interface issues and encourage the development of graphics and visualization tools. Section 3 of this report elaborates on each of these recommendations. Section 2 contains the tutorials presented at the workshop and a summary of the comments made in the discussion period following the tutorials. These tutorials were an integral part of the workshop: they provided a forum for the discussion of the needs of biologists in managing and analyzing biological sequencing data, and the capabilities of advanced computer technologies in meeting those needs. Also included in Section 2 is an informal paper on fifth generation technologies, prepared by two of the participants. Appendix A contains the documents (edited for grammar) prepared by the participants and groups at the workshop. Appendix B contains the workshop program.

  4. Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches.

    PubMed

    Horwege, Sebastian; Lindner, Sebastian; Boden, Marcus; Hatje, Klas; Kollmar, Martin; Leimeister, Chris-André; Morgenstern, Burkhard

    2014-07-01

    In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free methods rely on exact word matches to estimate pairwise similarities or distances between the input sequences. By contrast, our new algorithms are based on inexact word matches. The first of these approaches uses the relative frequencies of so-called spaced words in the input sequences, i.e. words containing 'don't care' or 'wildcard' symbols at certain pre-defined positions. Various distance measures can then be defined on sequences based on their different spaced-word composition. Our second approach defines the distance between two sequences by estimating for each position in the first sequence the length of the longest substring at this position that also occurs in the second sequence with up to k mismatches. Both approaches take a set of deoxyribonucleic acid (DNA) or protein sequences as input and return a matrix of pairwise distance values that can be used as a starting point for clustering algorithms or distance-based phylogeny reconstruction. The two alignment-free programmes are accessible through a web interface at 'Göttingen Bioinformatics Compute Server (GOBICS)': http://spaced.gobics.de http://kmacs.gobics.de and the source codes can be downloaded.

  5. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

    PubMed

    Kanost, Michael R; Arrese, Estela L; Cao, Xiaolong; Chen, Yun-Ru; Chellapilla, Sanjay; Goldsmith, Marian R; Grosse-Wilde, Ewald; Heckel, David G; Herndon, Nicolae; Jiang, Haobo; Papanicolaou, Alexie; Qu, Jiaxin; Soulages, Jose L; Vogel, Heiko; Walters, James; Waterhouse, Robert M; Ahn, Seung-Joon; Almeida, Francisca C; An, Chunju; Aqrawi, Peshtewani; Bretschneider, Anne; Bryant, William B; Bucks, Sascha; Chao, Hsu; Chevignon, Germain; Christen, Jayne M; Clarke, David F; Dittmer, Neal T; Ferguson, Laura C F; Garavelou, Spyridoula; Gordon, Karl H J; Gunaratna, Ramesh T; Han, Yi; Hauser, Frank; He, Yan; Heidel-Fischer, Hanna; Hirsh, Ariana; Hu, Yingxia; Jiang, Hongbo; Kalra, Divya; Klinner, Christian; König, Christopher; Kovar, Christie; Kroll, Ashley R; Kuwar, Suyog S; Lee, Sandy L; Lehman, Rüdiger; Li, Kai; Li, Zhaofei; Liang, Hanquan; Lovelace, Shanna; Lu, Zhiqiang; Mansfield, Jennifer H; McCulloch, Kyle J; Mathew, Tittu; Morton, Brian; Muzny, Donna M; Neunemann, David; Ongeri, Fiona; Pauchet, Yannick; Pu, Ling-Ling; Pyrousis, Ioannis; Rao, Xiang-Jun; Redding, Amanda; Roesel, Charles; Sanchez-Gracia, Alejandro; Schaack, Sarah; Shukla, Aditi; Tetreau, Guillaume; Wang, Yang; Xiong, Guang-Hua; Traut, Walther; Walsh, Tom K; Worley, Kim C; Wu, Di; Wu, Wenbi; Wu, Yuan-Qing; Zhang, Xiufeng; Zou, Zhen; Zucker, Hannah; Briscoe, Adriana D; Burmester, Thorsten; Clem, Rollie J; Feyereisen, René; Grimmelikhuijzen, Cornelis J P; Hamodrakas, Stavros J; Hansson, Bill S; Huguet, Elisabeth; Jermiin, Lars S; Lan, Que; Lehman, Herman K; Lorenzen, Marce; Merzendorfer, Hans; Michalopoulos, Ioannis; Morton, David B; Muthukrishnan, Subbaratnam; Oakeshott, John G; Palmer, Will; Park, Yoonseong; Passarelli, A Lorena; Rozas, Julio; Schwartz, Lawrence M; Smith, Wendy; Southgate, Agnes; Vilcinskas, Andreas; Vogt, Richard; Wang, Ping; Werren, John; Yu, Xiao-Qiang; Zhou, Jing-Jiang; Brown, Susan J; Scherer, Steven E; Richards, Stephen; Blissard, Gary W

    2016-09-01

    Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

  6. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

    PubMed

    Kanost, Michael R; Arrese, Estela L; Cao, Xiaolong; Chen, Yun-Ru; Chellapilla, Sanjay; Goldsmith, Marian R; Grosse-Wilde, Ewald; Heckel, David G; Herndon, Nicolae; Jiang, Haobo; Papanicolaou, Alexie; Qu, Jiaxin; Soulages, Jose L; Vogel, Heiko; Walters, James; Waterhouse, Robert M; Ahn, Seung-Joon; Almeida, Francisca C; An, Chunju; Aqrawi, Peshtewani; Bretschneider, Anne; Bryant, William B; Bucks, Sascha; Chao, Hsu; Chevignon, Germain; Christen, Jayne M; Clarke, David F; Dittmer, Neal T; Ferguson, Laura C F; Garavelou, Spyridoula; Gordon, Karl H J; Gunaratna, Ramesh T; Han, Yi; Hauser, Frank; He, Yan; Heidel-Fischer, Hanna; Hirsh, Ariana; Hu, Yingxia; Jiang, Hongbo; Kalra, Divya; Klinner, Christian; König, Christopher; Kovar, Christie; Kroll, Ashley R; Kuwar, Suyog S; Lee, Sandy L; Lehman, Rüdiger; Li, Kai; Li, Zhaofei; Liang, Hanquan; Lovelace, Shanna; Lu, Zhiqiang; Mansfield, Jennifer H; McCulloch, Kyle J; Mathew, Tittu; Morton, Brian; Muzny, Donna M; Neunemann, David; Ongeri, Fiona; Pauchet, Yannick; Pu, Ling-Ling; Pyrousis, Ioannis; Rao, Xiang-Jun; Redding, Amanda; Roesel, Charles; Sanchez-Gracia, Alejandro; Schaack, Sarah; Shukla, Aditi; Tetreau, Guillaume; Wang, Yang; Xiong, Guang-Hua; Traut, Walther; Walsh, Tom K; Worley, Kim C; Wu, Di; Wu, Wenbi; Wu, Yuan-Qing; Zhang, Xiufeng; Zou, Zhen; Zucker, Hannah; Briscoe, Adriana D; Burmester, Thorsten; Clem, Rollie J; Feyereisen, René; Grimmelikhuijzen, Cornelis J P; Hamodrakas, Stavros J; Hansson, Bill S; Huguet, Elisabeth; Jermiin, Lars S; Lan, Que; Lehman, Herman K; Lorenzen, Marce; Merzendorfer, Hans; Michalopoulos, Ioannis; Morton, David B; Muthukrishnan, Subbaratnam; Oakeshott, John G; Palmer, Will; Park, Yoonseong; Passarelli, A Lorena; Rozas, Julio; Schwartz, Lawrence M; Smith, Wendy; Southgate, Agnes; Vilcinskas, Andreas; Vogt, Richard; Wang, Ping; Werren, John; Yu, Xiao-Qiang; Zhou, Jing-Jiang; Brown, Susan J; Scherer, Steven E; Richards, Stephen; Blissard, Gary W

    2016-09-01

    Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects. PMID:27522922

  7. Comparison of Prostate IMRT and VMAT Biologically Optimised Treatment Plans

    SciTech Connect

    Hardcastle, Nicholas; Tome, Wolfgang A.; Foo, Kerwyn; Miller, Andrew; Carolan, Martin; Metcalfe, Peter

    2011-10-01

    Recently, a new radiotherapy delivery technique has become clinically available-volumetric modulated arc therapy (VMAT). VMAT is the delivery of IMRT while the gantry is in motion using dynamic leaf motion. The perceived benefit of VMAT over IMRT is a reduction in delivery time. In this study, VMAT was compared directly with IMRT for a series of prostate cases. For 10 patients, a biologically optimized seven-field IMRT plan was compared with a biologically optimized VMAT plan using the same planning objectives. The Pinnacle RTPS was used. The resultant target and organ-at-risk dose-volume histograms (DVHs) were compared. The normal tissue complication probability (NTCP) for the IMRT and VMAT plans was calculated for 3 model parameter sets. The delivery efficiency and time for the IMRT and VMAT plans was compared. The VMAT plans resulted in a statistically significant reduction in the rectal V25Gy parameter of 8.2% on average over the IMRT plans. For one of the NTCP parameter sets, the VMAT plans had a statistically significant lower rectal NTCP. These reductions in rectal dose were achieved using 18.6% fewer monitor units and a delivery time reduction of up to 69%. VMAT plans resulted in reductions in rectal doses for all 10 patients in the study. This was achieved with significant reductions in delivery time and monitor units. Given the target coverage was equivalent, the VMAT plans were superior.

  8. Comparison of prostate IMRT and VMAT biologically optimised treatment plans.

    PubMed

    Hardcastle, Nicholas; Tomé, Wolfgang A; Foo, Kerwyn; Miller, Andrew; Carolan, Martin; Metcalfe, Peter

    2011-01-01

    Recently, a new radiotherapy delivery technique has become clinically available--volumetric modulated arc therapy (VMAT). VMAT is the delivery of IMRT while the gantry is in motion using dynamic leaf motion. The perceived benefit of VMAT over IMRT is a reduction in delivery time. In this study, VMAT was compared directly with IMRT for a series of prostate cases. For 10 patients, a biologically optimized seven-field IMRT plan was compared with a biologically optimized VMAT plan using the same planning objectives. The Pinnacle RTPS was used. The resultant target and organ-at-risk dose-volume histograms (DVHs) were compared. The normal tissue complication probability (NTCP) for the IMRT and VMAT plans was calculated for 3 model parameter sets. The delivery efficiency and time for the IMRT and VMAT plans was compared. The VMAT plans resulted in a statistically significant reduction in the rectal V25Gy parameter of 8.2% on average over the IMRT plans. For one of the NTCP parameter sets, the VMAT plans had a statistically significant lower rectal NTCP. These reductions in rectal dose were achieved using 18.6% fewer monitor units and a delivery time reduction of up to 69%. VMAT plans resulted in reductions in rectal doses for all 10 patients in the study. This was achieved with significant reductions in delivery time and monitor units. Given the target coverage was equivalent, the VMAT plans were superior.

  9. A national comparison of biochemistry and molecular biology capstone experiences.

    PubMed

    Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

    2015-01-01

    Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices.

  10. Comparison between donor substrates for biologically enhanced tetrachloroethene DNAPL dissolution.

    PubMed

    Yang, Yanru; McCarty, Perry L

    2002-08-01

    Tetrachloroethene (PCE) dense nonaqueous-phase liquid (DNAPL) can act as a persistent groundwater contamination source for decades. Biologically enhanced dissolution of pure PCE DNAPL has potential for reducing DNAPL longevity as indicated previously (Environ. Sci. Technol. 2000, 34, 2979). Reported here are expanded studies to evaluate donor substrates that offer different remediation strategies for bioenhanced DNAPL dissolution, including pentanol (soluble substrate, fed continuously), calcium oleate (insoluble substrate, placed in column initially by alternate pumping of sodium oleate and calcium chloride), and olive oil (mixed with PCE and placed in column initially). Compared with a no-substrate column control, the DNAPL dissolution rate was enhanced about three times when directly coupled with biological transformation. The major degradation product formed was cDCE, but significant amounts of VC and ethene were also found with some columns. Extensive methanogenesis, which reduced PCE transformation, occurred in both the pentanol-fed and oleate-amended columns, but not in the olive-oil-amended column, suggesting that methanogens managed to colonize column niches where PCE DNAPL was not present. Detrimental methane production in the pentanol-fed column was nearly eliminated by presaturating the feed solution with PCE. These results suggest potential DNAPL remediation strategies to enhance dehalogenation while controlling competitive methanogenic utilization of donor substrates.

  11. Developing JSequitur to Study the Hierarchical Structure of Biological Sequences in a Grammatical Inference Framework of String Compression Algorithms.

    PubMed

    Galbadrakh, Bulgan; Lee, Kyung-Eun; Park, Hyun-Seok

    2012-12-01

    Grammatical inference methods are expected to find grammatical structures hidden in biological sequences. One hopes that studies of grammar serve as an appropriate tool for theory formation. Thus, we have developed JSequitur for automatically generating the grammatical structure of biological sequences in an inference framework of string compression algorithms. Our original motivation was to find any grammatical traits of several cancer genes that can be detected by string compression algorithms. Through this research, we could not find any meaningful unique traits of the cancer genes yet, but we could observe some interesting traits in regards to the relationship among gene length, similarity of sequences, the patterns of the generated grammar, and compression rate.

  12. Genomic 3' terminal sequence comparison of three isolates of rabbit haemorrhagic disease virus.

    PubMed

    Milton, I D; Vlasak, R; Nowotny, N; Rodak, L; Carter, M J

    1992-05-15

    Comparison of sequence data is necessary in older to investigate virus origins, identify features common to virulent strains, and characterize genomic organization within virus families. A virulent caliciviral disease of rabbits recently emerged in China. We have sequenced 1100 bases from the 3' ends of two independent European isolates of this virus, and compared these with previously determined calicivirus sequences. Rabbit caliciviruses were closely related, despite the different countries in which isolation was made. This supports the rapid spread of a new virus across Europe. The capsid protein sequences of these rabbit viruses differ markedly from those determined for feline calicivirus, but a hypothetical 3' open reading frame is relatively well conserved between the caliciviruses of these two different hosts and argues for a functional role.

  13. Comparison of Dixon Sequences for Estimation of Percent Breast Fibroglandular Tissue

    PubMed Central

    Ledger, Araminta E. W.; Scurr, Erica D.; Hughes, Julie; Macdonald, Alison; Wallace, Toni; Thomas, Karen; Wilson, Robin; Leach, Martin O.; Schmidt, Maria A.

    2016-01-01

    Objectives To evaluate sources of error in the Magnetic Resonance Imaging (MRI) measurement of percent fibroglandular tissue (%FGT) using two-point Dixon sequences for fat-water separation. Methods Ten female volunteers (median age: 31 yrs, range: 23–50 yrs) gave informed consent following Research Ethics Committee approval. Each volunteer was scanned twice following repositioning to enable an estimation of measurement repeatability from high-resolution gradient-echo (GRE) proton-density (PD)-weighted Dixon sequences. Differences in measures of %FGT attributable to resolution, T1 weighting and sequence type were assessed by comparison of this Dixon sequence with low-resolution GRE PD-weighted Dixon data, and against gradient-echo (GRE) or spin-echo (SE) based T1-weighted Dixon datasets, respectively. Results %FGT measurement from high-resolution PD-weighted Dixon sequences had a coefficient of repeatability of ±4.3%. There was no significant difference in %FGT between high-resolution and low-resolution PD-weighted data. Values of %FGT from GRE and SE T1-weighted data were strongly correlated with that derived from PD-weighted data (r = 0.995 and 0.96, respectively). However, both sequences exhibited higher mean %FGT by 2.9% (p < 0.0001) and 12.6% (p < 0.0001), respectively, in comparison with PD-weighted data; the increase in %FGT from the SE T1-weighted sequence was significantly larger at lower breast densities. Conclusion Although measurement of %FGT at low resolution is feasible, T1 weighting and sequence type impact on the accuracy of Dixon-based %FGT measurements; Dixon MRI protocols for %FGT measurement should be carefully considered, particularly for longitudinal or multi-centre studies. PMID:27011312

  14. rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

    PubMed Central

    Hahn, Lars; Leimeister, Chris-André; Morgenstern, Burkhard

    2016-01-01

    Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don’t-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de/ PMID:27760124

  15. Genome sequencing and systems biology analysis of a lipase-producing bacterial strain.

    PubMed

    Li, N; Li, D D; Zhang, Y Z; Yuan, Y Z; Geng, H; Xiong, L; Liu, D L

    2016-01-01

    Lipase-producing bacteria are naturally-occurring, industrially-relevant microorganisms that produce lipases, which can be used to synthesize biodiesel from waste oils. The efficiency of lipase expression varies between various microbial strains. Therefore, strains that can produce lipases with high efficiency must be screened, and the conditions of lipase metabolism and optimization of the production process in a given environment must be thoroughly studied. A high efficiency lipase-producing strain was isolated from the sediments of Jinsha River, identified by 16S rRNA sequence analysis as Serratia marcescens, and designated as HS-L5. A schematic diagram of the genome sequence was constructed by high-throughput genome sequencing. A series of genes related to lipid degradation were identified by functional gene annotation through sequence homology analysis. A genome-scale metabolic model of HS-ML5 was constructed using systems biology techniques. The model consisted of 1722 genes and 1567 metabolic reactions. The topological graph of the genome-scale metabolic model was compared to that of conventional metabolic pathways using a visualization software and KEGG database. The basic components and boundaries of the tributyrin degradation subnetwork were determined, and its flux balance analyzed using Matlab and COBRA Toolbox to simulate the effects of different conditions on the catalytic efficiency of lipases produced by HS-ML5. We proved that the catalytic activity of microbial lipases was closely related to the carbon metabolic pathway. As production and catalytic efficiency of lipases varied greatly with the environment, the catalytic efficiency and environmental adaptability of microbial lipases can be improved by proper control of the production conditions. PMID:27050954

  16. mtDNAprofiler: a Web application for the nomenclature and comparison of human mitochondrial DNA sequences.

    PubMed

    Yang, In Seok; Lee, Hwan Young; Yang, Woo Ick; Shin, Kyoung-Jin

    2013-07-01

    Mitochondrial DNA (mtDNA) is a valuable tool in the fields of forensic, population, and medical genetics. However, recording and comparing mtDNA control region or entire genome sequences would be difficult if researchers are not familiar with mtDNA nomenclature conventions. Therefore, mtDNAprofiler, a Web application, was designed for the analysis and comparison of mtDNA sequences in a string format or as a list of mtDNA single-nucleotide polymorphisms (mtSNPs). mtDNAprofiler which comprises four mtDNA sequence-analysis tools (mtDNA nomenclature, mtDNA assembly, mtSNP conversion, and mtSNP concordance-check) supports not only the accurate analysis of mtDNA sequences via an automated nomenclature function, but also consistent management of mtSNP data via direct comparison and validity-check functions. Since mtDNAprofiler consists of four tools that are associated with key steps of mtDNA sequence analysis, mtDNAprofiler will be helpful for researchers working with mtDNA. mtDNAprofiler is freely available at http://mtprofiler.yonsei.ac.kr. PMID:23682804

  17. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  18. Definition and Analysis of a System for the Automated Comparison of Curriculum Sequencing Algorithms in Adaptive Distance Learning

    ERIC Educational Resources Information Center

    Limongelli, Carla; Sciarrone, Filippo; Temperini, Marco; Vaste, Giulia

    2011-01-01

    LS-Lab provides automatic support to comparison/evaluation of the Learning Object Sequences produced by different Curriculum Sequencing Algorithms. Through this framework a teacher can verify the correspondence between the behaviour of different sequencing algorithms and her pedagogical preferences. In fact the teacher can compare algorithms…

  19. Comparison of workplace protection factors for different biological contaminants.

    PubMed

    Cho, Kyungmin Jacob; Reponen, Tiina; McKay, Roy; Dwivedi, Alok; Adhikari, Atin; Singh, Umesh; Shukla, Rakesh; Jones, Susan; Jones, Gordon; Grinshpun, Sergey A

    2011-07-01

    observed between different contaminants may be attributed to differences in the sensitivity of analytical methods to detect low inside concentrations, rather than the nature of particles (biological or non-biological). PMID:21732855

  20. Comparison of biological chromophores: photophysical properties of cyanophenylalanine derivatives.

    PubMed

    Martin, Joshua P; Fetto, Natalie R; Tucker, Matthew J

    2016-07-27

    Within this work, the family of cyanophenylalanine spectroscopic reporters is extended by showing the ortho and meta derivatives have intrinsic photophysical properties that are useful for studies of protein structure and dynamics. The molar absorptivities of 2-cyanophenylalanine and 3-cyanophenylalanine are shown to be comparable to that of 4-cyanophenylalanine with similar spectral features in their absorbance and emission profiles, demonstrating that these probes can be utilized interchangeably. The fluorescence quantum yields are also on the same scale as commonly used fluorophores in peptides and proteins, tyrosine and tryptophan. These new cyano-fluorophores can be paired with either 4-cyanophenylalanine or tryptophan to capture distances in peptide structure through Förster resonance energy transfer. Additionally, the spectroscopic properties of these chromophores can report the local solvent environment via changes in fluorescence emission intensity as a result of hydrogen bonding and/or hydration. A decrease in the quantum yield is also observed in basic environments due to photoinduced electron transfer from a deprotonated amine in the free PheCN species and at the N-terminus of a short peptide, providing an avenue to detect pH in biological systems. Our results show the potential of these probes, 2-cyanophenylalanine and 3-cyanophenylalanine, to be incorporated into a single peptide chain, either individually or in tandem with 4-cyanophenylalanine, tryptophan, or tyrosine, in order to obtain information about peptide structure and dynamics. PMID:27412819

  1. Chaotic motif sampler: detecting motifs from biological sequences by using chaotic neurodynamics

    NASA Astrophysics Data System (ADS)

    Matsuura, Takafumi; Ikeguchi, Tohru

    Identification of a region in biological sequences, motif extraction problem (MEP) is solved in bioinformatics. However, the MEP is an NP-hard problem. Therefore, it is almost impossible to obtain an optimal solution within a reasonable time frame. To find near optimal solutions for NP-hard combinatorial optimization problems such as traveling salesman problems, quadratic assignment problems, and vehicle routing problems, chaotic search, which is one of the deterministic approaches, has been proposed and exhibits better performance than stochastic approaches. In this paper, we propose a new alignment method that employs chaotic dynamics to solve the MEPs. It is called the Chaotic Motif Sampler. We show that the performance of the Chaotic Motif Sampler is considerably better than that of the conventional methods such as the Gibbs Site Sampler and the Neighborhood Optimization for Multiple Alignment Discovery.

  2. Biological removal of carbon, nitrogen, and phosphorus in a sequencing batch reactor.

    PubMed

    Akin, Beril S; Ugurlu, Ayenur

    2003-08-01

    In this research the process performance of enhanced biological phosphorus removal was investigated in a sequencing batch reactor (SBR) having a new operational mode. The SBR system used in this study had simultaneous feeding and decanting conditions. The laboratory scale reactor (10 L) was operated for 392 days. The system was operated under 4 different sets each having 2 cycles per day. In each cycle, fill (4 h), anoxic (0.5 h), aerobic (7 h) and settling phases were present. In the fill phase, wastewater was fed from the bottom and the anoxic/anaerobic conditions were established in the settled sludge. During filling, the water left the system by water displacement. The system provided nitrification, denitrification as well as phosphorus and organic removal. High COD (90-98%), PO4-P (77-100%), and NH4-N (90-95%) removals were achieved by this system.

  3. The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing.

    PubMed

    Boland, Joseph F; Chung, Charles C; Roberson, David; Mitchell, Jason; Zhang, Xijun; Im, Kate M; He, Ji; Chanock, Stephen J; Yeager, Meredith; Dean, Michael

    2013-10-01

    We assessed the performance of the new Life Technologies Proton sequencer by comparing whole-exome sequence data in a Centre d'Etude du Polymorphisme Humain trio (family 1463) to the Illumina HiSeq instrument. To simulate a typical user's results, we utilized the standard capture, alignment and variant calling methods specific to each platform. We restricted data analysis to include the capture region common to both methods. The Proton produced high quality data at a comparable average depth and read length, and the Ion Reporter variant caller identified 96 % of single nucleotide polymorphisms (SNPs) detected by the HiSeq and GATK pipeline. However, only 40 % of small insertion and deletion variants (indels) were identified by both methods. Usage of the trio structure and segregation of platform-specific alleles supported this result. Further comparison of the trio data with Complete Genomics sequence data and Illumina SNP microarray genotypes documented high concordance and accurate SNP genotyping of both Proton and Illumina platforms. However, our study underscored the problem of accurate detection of indels for both the Proton and HiSeq platforms.

  4. 3D representations of amino acids—applications to protein sequence comparison and classification

    PubMed Central

    Li, Jie; Koehl, Patrice

    2014-01-01

    The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acids in ways that the representation of such a protein sequence facilitates the decoding of its information content. We show that a feature-based representation in a three-dimensional (3D) space derived from amino acid substitution matrices provides an adequate representation that can be used for direct comparison of protein sequences based on geometry. We measure the performance of such a representation in the context of the protein structural fold prediction problem. We compare the results of classifying different sets of proteins belonging to distinct structural folds against classifications of the same proteins obtained from sequence alone or directly from structural information. We find that sequence alone performs poorly as a structure classifier. We show in contrast that the use of the three dimensional representation of the sequences significantly improves the classification accuracy. We conclude with a discussion of the current limitations of such a representation and with a description of potential improvements. PMID:25379143

  5. Longitudinal studies on maternal HIV-1 variants by biological phenotyping, sequence analysis and viral load.

    PubMed

    Renta, J Y; Cadilla, C L; Vega, M E; Hillyer, G V; Estrada, C; Jiménez, E; Abreu, E; Méndez, I; Gandía, J; Meléndez-Guerrero, L M

    1997-11-01

    In this study, the HIV-1 variant viruses from ten pregnant women and their infants were isolated and characterized longitudinally in order to determine the role that viral envelope (gp120-V3 loop) gene variation and viral tropism play in vertical transmission. Biological phenotyping of each HIV variant was accomplished by growth in MT-2, and macrophages from healthy and non-HIV-infected donors. Genetic characterization of the variants was accomplished by DNA sequence analysis. All the women enrolled in this study received ZDV therapy. Virus was cultured from eight out of ten env V3-PCR positive mothers. HIV-1 isolates were all non-syncitium inducing variants. None of the mothers were found to transmit HIV, as determined by DNA PCR and quantitative co-cultures on their infants which were seronegative for HIV-1 through one year after birth. Viral cultures from infant blood samples were negative and infants were all healthy. However, nested env V3-PCR detected proviral DNA in five out of ten infants. In contrast, conventional gag-PCR was negative in the same five infants. Sequences of the five maternal-infant pairs were different, suggesting unique infant HIV-1 variants. The three highest maternal viral load values corresponded to infants that were env V3-PCR positive. These results suggest that HIV-1 particles are transmitted from ZDV-treated mothers to infants. Infant follow up is recommended to determine if HIV-1 has been inhibited by the immune system of the infants.

  6. COMPARISON OF ANALYTICAL METHODS FOR THE MEASUREMENT OF NON-VIABLE BIOLOGICAL PM

    EPA Science Inventory

    The paper describes a preliminary research effort to develop a methodology for the measurement of non-viable biologically based particulate matter (PM), analyzing for mold, dust mite, and ragweed antigens and endotoxins. Using a comparison of analytical methods, the research obj...

  7. Visual Literacy in Biology: A Comparison of Visual Representations in Textbooks and Journal Articles

    ERIC Educational Resources Information Center

    Rybarczyk, Brian

    2011-01-01

    Using course materials to promote visual literacy skills is an important aspect of undergraduate science education. A comparison study was undertaken to determine the composition of visual representations, specifically representations of data generated from experimental research, found in general biology and discipline-specific textbooks compared…

  8. Effects of idle time on biological phosphorus removal by sequencing batch reactors.

    PubMed

    Gao, Dawen; Yin, Hang; Liu, Lin; Li, Xing; Liang, Hong

    2013-12-01

    Three identical sequencing batch reactors (SBRs) were operated to investigate the effects of various idle times on the biological phosphorus (P) removal. The idle times were set to 3 hr (R1), 10 hr (R2) and 17 hr (R3). The results showed that the idle time of a SBR had potential impact on biological phosphorus removal, especially when the influent phosphorus concentration increased. The phosphorus removal efficiencies of the R2 and R3 systems declined dramatically compared with the stable R1 system, and the P-release and P-uptake rates of the R3 system in particular decreased dramatically. The PCR-DGGE analysis showed that uncultured Pseudomonas sp. (GQ183242.1) and beta-Proteobacteria (AY823971) were the dominant phosphorus removal bacteria for the R1 and R2 systems, while uncultured gamma-Proteobacteria were the dominant phosphorus removal bacteria for the R3 system. Glycogen-accumulating organisms (GAOs), such as uncultured Sphingomonas sp. (AM889077), were found in the R2 and R3 systems. Overall, the R1 system was the most stable and exhibited the best phosphorus removal efficiency. It was found that although the idle time can be prolonged to allow the formation of intracellular polymers when the phosphorus concentration of the influent is low, systems with a long idle time can become unstable when the influent phosphorus concentration is increased.

  9. Effects of idle time on biological phosphorus removal by sequencing batch reactors.

    PubMed

    Gao, Dawen; Yin, Hang; Liu, Lin; Li, Xing; Liang, Hong

    2013-12-01

    Three identical sequencing batch reactors (SBRs) were operated to investigate the effects of various idle times on the biological phosphorus (P) removal. The idle times were set to 3 hr (R1), 10 hr (R2) and 17 hr (R3). The results showed that the idle time of a SBR had potential impact on biological phosphorus removal, especially when the influent phosphorus concentration increased. The phosphorus removal efficiencies of the R2 and R3 systems declined dramatically compared with the stable R1 system, and the P-release and P-uptake rates of the R3 system in particular decreased dramatically. The PCR-DGGE analysis showed that uncultured Pseudomonas sp. (GQ183242.1) and beta-Proteobacteria (AY823971) were the dominant phosphorus removal bacteria for the R1 and R2 systems, while uncultured gamma-Proteobacteria were the dominant phosphorus removal bacteria for the R3 system. Glycogen-accumulating organisms (GAOs), such as uncultured Sphingomonas sp. (AM889077), were found in the R2 and R3 systems. Overall, the R1 system was the most stable and exhibited the best phosphorus removal efficiency. It was found that although the idle time can be prolonged to allow the formation of intracellular polymers when the phosphorus concentration of the influent is low, systems with a long idle time can become unstable when the influent phosphorus concentration is increased. PMID:24649669

  10. Effect of cycle changes on simultaneous biological nutrient removal in a sequencing batch reactor (SBR).

    PubMed

    Coma, M; Puig, S; Monclús, H; Balaguer, M D; Colprim, J

    2010-03-01

    The destabilization of a microbial population is sometimes hard to solve when different biological reactions are coupled in the same reactor as in sequencing batch reactors (SBRs). This paper will try to guide through practical experiences the recovery of simultaneous nitrogen and phosphorus removal in an SBR after increasing the demand of wastewater treatment by taking advantage of its flexibility. The results demonstrate that the length of phases and the optimization of influent distribution are key factors in stabilizing the system for long-term periods with high nutrient removal (88%, 93% and 99% of carbon, nitrogen and phosphorus, respectively). In order to recover a biological nutrient removal (BNR) system, different interactions such as simultaneous nitrification and denitrification and also phosphorus removal must be taken into account. As a general conclusion, it can be stated there is no such thing as a perfect SBR operation, and that much will depend on the state of the BNR system. Hence, the SBR operating strategy must be based on a dynamic cycle definition in line with process efficiency. PMID:20426270

  11. Biological characterization and next-generation genome sequencing of the unclassified Cotia virus SPAn232 (Poxviridae).

    PubMed

    Afonso, Priscila P; Silva, Patrícia M; Schnellrath, Laila C; Jesus, Desyreé M; Hu, Jianhong; Yang, Yajie; Renne, Rolf; Attias, Marcia; Condit, Richard C; Moussatché, Nissin; Damaso, Clarissa R

    2012-05-01

    Cotia virus (COTV) SPAn232 was isolated in 1961 from sentinel mice at Cotia field station, São Paulo, Brazil. Attempts to classify COTV within a recognized genus of the Poxviridae have generated contradictory findings. Studies by different researchers suggested some similarity to myxoma virus and swinepox virus, whereas another investigation characterized COTV SPAn232 as a vaccinia virus strain. Because of the lack of consensus, we have conducted an independent biological and molecular characterization of COTV. Virus growth curves reached maximum yields at approximately 24 to 48 h and were accompanied by virus DNA replication and a characteristic early/late pattern of viral protein synthesis. Interestingly, COTV did not induce detectable cytopathic effects in BSC-40 cells until 4 days postinfection and generated viral plaques only after 8 days. We determined the complete genomic sequence of COTV by using a combination of the next-generation DNA sequencing technologies 454 and Illumina. A unique contiguous sequence of 185,139 bp containing 185 genes, including the 90 genes conserved in all chordopoxviruses, was obtained. COTV has an interesting panel of open reading frames (ORFs) related to the evasion of host defense, including two novel genes encoding C-C chemokine-like proteins, each present in duplicate copies. Phylogenetic analysis revealed the highest amino acid identity scores with Cervidpoxvirus, Capripoxvirus, Suipoxvirus, Leporipoxvirus, and Yatapoxvirus. However, COTV grouped as an independent branch within this clade, which clearly excluded its classification as an Orthopoxvirus. Therefore, our data suggest that COTV could represent a new poxvirus genus.

  12. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

    SciTech Connect

    Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-20

    Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

  13. Comparison of pulse sequences for R1-based electron paramagnetic resonance oxygen imaging

    NASA Astrophysics Data System (ADS)

    Epel, Boris; Halpern, Howard J.

    2015-05-01

    Electron paramagnetic resonance (EPR) spin-lattice relaxation (SLR) oxygen imaging has proven to be an indispensable tool for assessing oxygen partial pressure in live animals. EPR oxygen images show remarkable oxygen accuracy when combined with high precision and spatial resolution. Developing more effective means for obtaining SLR rates is of great practical, biological and medical importance. In this work we compared different pulse EPR imaging protocols and pulse sequences to establish advantages and areas of applicability for each method. Tests were performed using phantoms containing spin probes with oxygen concentrations relevant to in vivo oxymetry. We have found that for small animal size objects the inversion recovery sequence combined with the filtered backprojection reconstruction method delivers the best accuracy and precision. For large animals, in which large radio frequency energy deposition might be critical, free induction decay and three pulse stimulated echo sequences might find better practical usage.

  14. Disciplinary baptisms: a comparison of the naming stories of genetics, molecular biology, genomics, and systems biology.

    PubMed

    Powell, Alexander; O'Malley, Maureen A; Müller-Wille, Staffan; Calvert, Jane; Dupré, John

    2007-01-01

    Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance--albeit highly variable--of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development. PMID:18411835

  15. Multi-species sequence comparison reveals conservation of ghrelin gene-derived splice variants encoding a truncated ghrelin peptide.

    PubMed

    Seim, Inge; Jeffery, Penny L; Thomas, Patrick B; Walpole, Carina M; Maugham, Michelle; Fung, Jenny N T; Yap, Pei-Yi; O'Keeffe, Angela J; Lai, John; Whiteside, Eliza J; Herington, Adrian C; Chopin, Lisa K

    2016-06-01

    The peptide hormone ghrelin is a potent orexigen produced predominantly in the stomach. It has a number of other biological actions, including roles in appetite stimulation, energy balance, the stimulation of growth hormone release and the regulation of cell proliferation. Recently, several ghrelin gene splice variants have been described. Here, we attempted to identify conserved alternative splicing of the ghrelin gene by cross-species sequence comparisons. We identified a novel human exon 2-deleted variant and provide preliminary evidence that this splice variant and in1-ghrelin encode a C-terminally truncated form of the ghrelin peptide, termed minighrelin. These variants are expressed in humans and mice, demonstrating conservation of alternative splicing spanning 90 million years. Minighrelin appears to have similar actions to full-length ghrelin, as treatment with exogenous minighrelin peptide stimulates appetite and feeding in mice. Forced expression of the exon 2-deleted preproghrelin variant mirrors the effect of the canonical preproghrelin, stimulating cell proliferation and migration in the PC3 prostate cancer cell line. This is the first study to characterise an exon 2-deleted preproghrelin variant and to demonstrate sequence conservation of ghrelin gene-derived splice variants that encode a truncated ghrelin peptide. This adds further impetus for studies into the alternative splicing of the ghrelin gene and the function of novel ghrelin peptides in vertebrates.

  16. Relationships amongst bluetongue viruses revealed by comparisons of capsid and outer coat protein nucleotide sequences.

    PubMed

    Gould, A R; Pritchard, L I

    1990-08-01

    Sequence data from the gene segments coding for the capsid protein. VP3, of all eight Australian bluetongue virus serotypes were compared. The high degree of nucleotide sequence homology for VP3 genes amongst BTV isolates from the same geographic region supported previous studies (Gould, 1987; 1988b, c; Gould et al., 1988b) and was proposed as a basis for "topotyping" a bluetongue virus isolate (Gould et al., 1989). The complete nucleotide sequences which coded for the VP2 outer coat proteins of South African BTV serotypes 1 and 3 (vaccine strains) were determined and compared to cognate gene sequences from North American and Australian BTVs. These VP2 comparisons demonstrated that BTVs of the same serotype, but from different geographical regions, were closely related at the nucleotide and amino acid levels. However, close inter-relationships were also demonstrated amongst other BTVs irrespective of serotype or geographic origin. These data enabled phylogenic relationships of the BTV serotypes to be analysed using VP2 nucleotide sequences as a determinant.

  17. Correlation between MCAT Biology Content Specifications and Topic Scope and Sequence of General Education College Biology Textbooks

    ERIC Educational Resources Information Center

    Rissing, Steven W.

    2013-01-01

    Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing…

  18. Simultaneous removal of nanosilver and fullerene in sequencing batch reactors for biological wastewater treatment.

    PubMed

    Yang, Yu; Wang, Yifei; Hristovski, Kiril; Westerhoff, Paul

    2015-04-01

    Increasing use of engineered nanomaterials (ENMs) inevitably leads to their potential release to the sewer system. The co-removal of nano fullerenes (nC60) and nanosilver as well as their impact on COD removal were studied in biological sequencing batch reactors (SBR) for a year. When dosing nC60 at 0.07-2mgL(-1), the SBR removed greater than 95% of nC60 except for short-term interruptions occurred (i.e., dysfunction of bioreactor by nanosilver addition) when nC60 and nanosilver were dosed simultaneously. During repeated 30-d periods of adding both 2 mg L(-1) nC60 and 2 mg L(-1) nanosilver, short-term interruption of SBRs for 4d was observed and accompanied by (1) reduced total suspended solids in the reactor, (2) poor COD removal rate as low as 22%, and (3) decreased nC60 removal to 0%. After the short-term interruption, COD removal gradually returned to normal within one solids retention time. Except for during these "short-term interruptions", the silver removal rate was above 90%. A series of bottle-point batch experiments was conducted to determine the distribution coefficients of nC60 between liquid and biomass phases. A linear distribution model on nC60 combined with a mass balance equation simulated well its removal rate at a range of 0.07-0.76 mg L(-1) in SBRs. This paper illustrates the effect of "pulse" inputs (i.e., addition for a short period of time) of ENMs into biological reactors, demonstrates long-term capability of SBRs to remove ENMs and COD, and provides an example to predict the removal of ENMs in SBRs upon batch experiments.

  19. Reconstructing ancestral genomic sequences by co-evolution: formal definitions, computational issues, and biological examples.

    PubMed

    Tuller, Tamir; Birin, Hadas; Kupiec, Martin; Ruppin, Eytan

    2010-09-01

    The inference of ancestral genomes is a fundamental problem in molecular evolution. Due to the statistical nature of this problem, the most likely or the most parsimonious ancestral genomes usually include considerable error rates. In general, these errors cannot be abolished by utilizing more exhaustive computational approaches, by using longer genomic sequences, or by analyzing more taxa. In recent studies, we showed that co-evolution is an important force that can be used for significantly improving the inference of ancestral genome content. In this work we formally define a computational problem for the inference of ancestral genome content by co-evolution. We show that this problem is NP-hard and hard to approximate and present both a Fixed Parameter Tractable (FPT) algorithm, and heuristic approximation algorithms for solving it. The running time of these algorithms on simulated inputs with hundreds of protein families and hundreds of co-evolutionary relations was fast (up to four minutes) and it achieved an approximation ratio of <1.3. We use our approach to study the ancestral genome content of the Fungi. To this end, we implement our approach on a dataset of 33, 931 protein families and 20, 317 co-evolutionary relations. Our algorithm added and removed hundreds of proteins from the ancestral genomes inferred by maximum likelihood (ML) or maximum parsimony (MP) while slightly affecting the likelihood/parsimony score of the results. A biological analysis revealed various pieces of evidence that support the biological plausibility of the new solutions. In addition, we showed that our approach reconstructs missing values at the leaves of the Fungi evolutionary tree better than ML or MP.

  20. A comparison of inquiry-based teaching through concept maps and traditional teaching in biology

    NASA Astrophysics Data System (ADS)

    Gulati, Sangeeta

    2005-11-01

    The purpose of this study was to investigate affective outcomes and academic achievement for students enrolled in high school biology when instruction included concept-mapping. The research design was quasi-experimental and allowed for a comparison between an experimental group who constructed concept maps and a control group who received traditional biology instruction. The subjects were 140 ninth-grade students, distributed into six intact biology classes, three honors and three general biology classes. Chapter tests and a textbook generated 9-week comprehensive posttest were used to measure achievement. ANCOVA analysis on the comprehensive posttest indicated no significant overall effect of concept mapping on biology achievement across the whole quarter when controlling for the quarter pretest. Chi-square analyses were performed to measure students' attitude toward biology class and activities. The experimental group indicated higher than expected tendency to be positive about the instructional methods, however, the control group indicated fewer than expected positive responses. T-tests were conducted to determine the differences between the experimental and control groups on chapter tests with or without concept mapping. The group with concept mapping scored significantly better than those with traditional methods. Honors class comparisons indicated a significant difference between groups at p<.05 level on the chapter pretest. There was also a significant difference on the chapter test after intervention, but this time at p<.001 level. Although the general class comparisons indicated no significant difference on the chapter pretest, the experimental group scored significantly better than the control group on the chapter test following intervention. This suggests that average ability students benefit from concept mapping more than traditional instruction. In narrative self-evaluations, only a small percentage of participants overall listed concept mapping as the

  1. Whole-Genome Sequence of Pseudomonas graminis Strain UASWS1507, a Potential Biological Control Agent and Biofertilizer Isolated in Switzerland

    PubMed Central

    Crovadore, Julien; Calmin, Gautier; Chablais, Romain; Cochard, Bastien; Schulz, Torsten

    2016-01-01

    We report here the whole-genome shotgun sequence of the strain UASWS1507 of the species Pseudomonas graminis, isolated in Switzerland from an apple tree. This is the first genome registered for this species, which is considered as a potential and valuable resource of biological control agents and biofertilizers for agriculture. PMID:27795260

  2. Metagenomes obtained by 'deep sequencing' - what do they tell about the enhanced biological phosphorus removal communities?

    PubMed

    Albertsen, Mads; Saunders, Aaron M; Nielsen, Kåre L; Nielsen, Per H

    2013-01-01

    Metagenomics enables studies of the genomic potential of complex microbial communities by sequencing bulk genomic DNA directly from the environment. Knowledge of the genetic potential of a community can be used to formulate and test ecological hypotheses about stability and performance. In this study deep metagenomics and fluorescence in situ hybridization (FISH) were used to study a full-scale wastewater treatment plant with enhanced biological phosphorus removal (EBPR), and the results were compared to an existing EBPR metagenome. EBPR is a widely used process that relies on a complex community of microorganisms to function properly. Insight into community and species level stability and dynamics is valuable for knowledge-driven optimization of the EBPR process. The metagenomes of the EBPR communities were distinct compared to metagenomes of communities from a wide range of other environments, which could be attributed to selection pressures of the EBPR process. The metabolic potential of one of the key microorganisms in the EPBR process, Accumulibacter, was investigated in more detail in the two plants, revealing a potential importance of phage predation on the dynamics of Accumulibacter populations. The results demonstrate that metagenomics can be used as a powerful tool for system wide characterization of the EBPR community as well as for a deeper understanding of the function of specific community members. Furthermore, we discuss and illustrate some of the general pitfalls in metagenomics and stress the need of additional DNA extraction independent information in metagenome studies.

  3. Biological nitrogen removal with enhanced phosphate uptake in a sequencing batch reactor using single sludge system.

    PubMed

    Lee, D S; Jeon, C O; Park, J M

    2001-11-01

    Simultaneous biological phosphorus and nitrogen removal with enhanced anoxic phosphate uptake was investigated in an anaerobic-aerobic-anoxic-aerobic sequencing batch reactor ((AO)2 SBR). Significant amounts of phosphorus-accumulation organisms (PAOs) capable of denitrification could be accumulated in a single sludge system coexisting with nitrifiers. The ratio of the anoxic phosphate uptake to the aerobic phosphate uptake capacity was increased from 11% to 64% by introducing an anoxic phase in an anaerobic aerobic SBR. The (AO)2 SBR system showed stable phosphorus and nitrogen removal performance. Average removal efficiencies of TOC, total nitrogen, and phosphorus were 92%, 88%, and 100%, respectively. It was found that nitrite (up to 10 mg NO2(-)-N/l) was not detrimental to the anoxic phosphate uptake and could serve as an electron acceptor like nitrate. In fact, the phosphate uptake rate was even faster in the presence of nitrite as an electron acceptor compared to the presence of nitrate. It was found that on-line sensor values of pH, ORP, and DO were somehow related with the dynamic behaviours of nutrient concentrations (NH4+, NO3-, and PO4(3-)) in the SBR. These on-line sensor values were used as real-time control parameters to adjust the duration of each operational phase in the (AO)2 SBR. The real-time controlled SBR exhibited better performance in the removal of phosphorus and nitrogen than the SBR with fixed-time operation. PMID:12230180

  4. The sequence of carnation etched ring virus DNA: comparison with cauliflower mosaic virus and retroviruses

    PubMed Central

    Hull, R.; Sadler, J.; Longstaff, M.

    1986-01-01

    Carnation etched ring virus (CERV) DNA comprises 7932 bp. CERV primer binding sites and overall genome organization are similar to those of the related cauliflower mosaic virus (CaMV). The six open reading frames of CERV showed amino acid homology (50-80%) with CaMV ORFs I-VI; no homologues of CaMV ORFs VII or VIII were found. CERV ORFs 1-5 interface each other with the sequence ATGA. The comparison of CERV ORF5 with CaMV ORFV highlighted regions which show homologies to retrovirus gag/pol protease, RNase H and DNA polymerase domains; the possibility that the DNA polymerase domain comprises two subdomains, operating off different templates, is discussed. Both CERV and CaMV ORFs I have sequence homology to tobacco mosaic virus P30 and plastocyanin. PMID:16453731

  5. A statistical physics perspective on alignment-independent protein sequence comparison

    PubMed Central

    Chattopadhyay, Amit K.; Nasiev, Diar; Flower, Darren R.

    2015-01-01

    Motivation: Within bioinformatics, the textual alignment of amino acid sequences has long dominated the determination of similarity between proteins, with all that implies for shared structure, function and evolutionary descent. Despite the relative success of modern-day sequence alignment algorithms, so-called alignment-free approaches offer a complementary means of determining and expressing similarity, with potential benefits in certain key applications, such as regression analysis of protein structure-function studies, where alignment-base similarity has performed poorly. Results: Here, we offer a fresh, statistical physics-based perspective focusing on the question of alignment-free comparison, in the process adapting results from ‘first passage probability distribution’ to summarize statistics of ensemble averaged amino acid propensity values. In this article, we introduce and elaborate this approach. Contact: d.r.flower@aston.ac.uk PMID:25810434

  6. In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

    PubMed Central

    Vásquez, Andrea; López, Camilo

    2014-01-01

    We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava's SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp) and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp). It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava's genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution. PMID:25374887

  7. Comparison of exon 5 sequences from 35 class I genes of the BALB/c mouse

    PubMed Central

    1989-01-01

    DNA sequences of the fifth exon, which encodes the transmembrane domain, were determined for the BALB/c mouse class I MHC genes and used to study the relationships between them. Based on nucleotide sequence similarity, the exon 5 sequences can be divided into seven groups. Although most members within each group are at least 80% similar to each other, comparison between groups reveals that the groups share little similarity. However, in spite of the extensive variation of the fifth exon sequences, analysis of their predicted amino acid translations reveals that only four class I gene fifth exons have frameshifts or stop codons that terminate their translation and prevent them from encoding a domain that is both hydrophobic and long enough to span a lipid bilayer. Exactly 27 of the remaining fifth exons could encode a domain that is similar to those of the transplantation antigens in that it consists of a proline-rich connecting peptide, a transmembrane segment, and a cytoplasmic portion with membrane- anchoring basic residues. The conservation of this motif in the majority of the fifth exon translations in spite of extensive variation suggests that selective pressure exists for these exons to maintain their ability to encode a functional transmembrane domain, raising the possibility that many of the nonclassical class I genes encode functionally important products. PMID:2584927

  8. Long-Range Correlations in the Sequence of Human Heartbeats and Other Biological Signals

    NASA Astrophysics Data System (ADS)

    Teich, Malvin C.

    1998-03-01

    The sequence of heartbeat occurrence times provides information about the state of health of the heart. We used a variety of measures, including multiresolution wavelet analysis, to identify the form of the point process that describes the human heartbeat. These measures, which are based on both interbeat (R-R) intervals and counts (heart rate), have been applied to records for both normal and heart-failure patients drawn from a standard database, and various surrogate versions thereof. Several of these measures reveal scaling behavior (1/f-type fluctuations; long-range power-law correlations).(R. G. Turcott and M. C. Teich, Proc. SPIE) 2036 (Chaos in Biology and Medicine), 22--39 (1993). Essentially all of the R-R and count-based measures we investigated, including those that exhibit scaling, differ in statistically significant ways for the normal and heart-failure patients. The wavelet measures, however, reveal a heretofore unknown scale window, between 16 and 32 heartbeats, over which the magnitudes of the wavelet-coefficient variances fall into disjoint sets for the normal and heart-failure patients.(R. G. Turcott and M. C. Teich, Ann. Biomed. Eng.) 24, 269--293 (1996).^,(S. Thurner, M. C. Feurstein, and M. C. Teich, Phys. Rev. Lett.) (in press). This enables us to correctly classify every patient in the standard data set as either belonging to the heart-failure or normal group with 100% accuracy, thereby providing a clinically significant measure of the presence of heart-failure. Previous approaches have provided only statistically significant measures. The tradeoff between sensitivity and

  9. nWayComp: a genome-wide sequence comparison tool for multiple strains/species of phylogenetically related microorganisms.

    PubMed

    Yao, Jiqiang; Lin, Hong; Doddapaneni, Harshavardhan; Civerolo, Edwin L

    2007-01-01

    The increasing number of whole genomic sequences of microorganisms has led to the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we have developed nWayComp software that compares DNA and protein sequences of phylogenetically-related microorganisms. This package integrates a series of bioinformatics tools such as BLAST, ClustalW, ALIGN, PHYLIP and PRIMER3 for sequence comparison. It searches for homologous sequences among multiple organisms and identifies genes that are unique to a particular organism. The homologous gene sets are then ranked in the descending order of the sequence similarity. For each set of homologous sequences, a table of sequence identity among homologous genes along with sequence variations such as SNPs and INDELS is developed, and a phylogenetic tree is constructed. In addition, a common set of primers that can amplify all the homologous sequences are generated. The nWayComp package provides users with a quick and convenient tool to compare genomic sequences among multiple organisms at the whole-genome level. PMID:17688445

  10. Phallometric comparison of pedophilic interest in nonadmitting sexual offenders against stepdaughters, biological daughters, other biologically related girls, and unrelated girls.

    PubMed

    Blanchard, Ray; Kuban, Michael E; Blak, Thomas; Cantor, James M; Klassen, Philip; Dickey, Robert

    2006-01-01

    This study compared the mean levels of sexual response to children produced by four groups of men with sexual offences against prepubescent girls and two comparison groups with other offences or no offences. All groups (N = 291) consisted of patients referred for clinical assessment of their sexual behavior or interests. Group assignment was determined by the victim's age and her relation to the patient: biological daughter; stepdaughter; other biologically related girl (e.g., sister, niece, granddaughter); unrelated girl; adult woman; and no known victim. The men with sexual offences had precisely one known victim each. The patients with offences may or may not have denied the act of which they were accused, but all patients denied an erotic preference for children. Sexual response to children was assessed by means of phallometric testing, a psychophysiological technique in which the individual's penile blood volume is monitored while he is presented with a standardized set of laboratory stimuli depicting male and female children and adults. The results indicated that the mean level of pedophilic response in men with offences against daughters or stepdaughters is intermediate between that in men with offences against otherwise-related or unrelated girls and that in men with no offences against girls at all. PMID:16598663

  11. Implicit Sequence Learning in Dyslexia: A Within-Sequence Comparison of First- and Higher-Order Information

    ERIC Educational Resources Information Center

    Du, Wenchong; Kelly, Steve W.

    2013-01-01

    The present study examines implicit sequence learning in adult dyslexics with a focus on comparing sequence transitions with different statistical complexities. Learning of a 12-item deterministic sequence was assessed in 12 dyslexic and 12 non-dyslexic university students. Both groups showed equivalent standard reaction time increments when the…

  12. Biological nutrient removal from pre-treated landfill leachate in a sequencing batch reactor.

    PubMed

    Uygur, Ahmet; Kargi, Fikret

    2004-05-01

    Biological treatment of landfill leachate usually results in low nutrient removals because of high chemical oxygen demand (COD), high ammonium-N content and the presence of toxic compounds such as heavy metals. Landfill leachate with high COD content was pre-treated by coagulation-flocculation with lime followed by air stripping of ammonia at pH=12. Nutrient removal from pre-treated leachate was carried out using a lab-scale sequencing batch reactor (SBR). Three different operations consisting of different numbers of steps were tested and their performances were compared. These operations were the three-step anaerobic (An)/anoxic (Ax)/oxic (Ox); the four-step (An/Ox/Ax/Ox), and the five-step (An/Ax/Ox/Ax/Ox) operations with total residence time of seven hours each. Experiments were carried out using three consecutive operations with a total cycle time of 21 h at a constant sludge age of 10 days. The lowest effluent nutrient levels were realized by using the five-step operation which resulted in effluent COD, NH4-N and PO4-P contents of 1,400, 107 and 65 mg l(-1), respectively, at the end of 21 h. Addition of domestic wastewater (1/1, v/v) and powdered activated carbon (PAC, 1 g l(-1)) to the pre-treated leachate improved nutrient removals in the five-step SBR operation, resulting in 75% COD, 44% NH4-N and 44% PO4-P removals after 21 hours of operation.

  13. Comparison of ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica.

    PubMed

    Register, Karen B; Nicholson, Tracy L; Brunelle, Brian W

    2016-10-01

    PvuII ribotyping and MLST are each highly discriminatory methods for genotyping Bordetella bronchiseptica, but a direct comparison between these approaches has not been undertaken. The goal of this study was to directly compare the discriminatory power of PvuII ribotyping and MLST, using a single set of geographically and genetically diverse strains, and to determine whether subtyping based on repeat region sequences of the pertactin gene (prn) provides additional resolution. One hundred twenty-two isolates were analyzed, representing 11 mammalian or avian hosts, sourced from the United States, Europe, Israel and Australia. Thirty-two ribotype patterns were identified; one isolate could not be typed. In comparison, all isolates were typeable by MLST and a total of 30 sequence types was identified. An analysis based on Simpson's Index of Diversity (SID) revealed that ribotyping and MLST are nearly equally discriminatory, with SIDs of 0.920 for ribotyping and 0.919 for MLST. Nonetheless, for ten ribotypes and eight MLST sequence types, the alternative method discriminates among isolates that otherwise type identically. Pairing prn repeat region typing with ribotyping yielded 54 genotypes and increased the SID to 0.954. Repeat region typing combined with MLST resulted in 47 genotypes and an SID of 0.944. Given the technical and practical advantages of MLST over ribotyping, and the nominal difference in their SIDs, we conclude MLST is the preferred primary typing tool. We recommend the combination of MLST and prn repeat region typing as a high-resolution, objective and standardized approach valuable for investigating the population structure and epidemiology of B. bronchiseptica. PMID:27542997

  14. Substrate-Driven Mapping of the Degradome by Comparison of Sequence Logos

    PubMed Central

    Fuchs, Julian E.; von Grafenstein, Susanne; Huber, Roland G.; Kramer, Christian; Liedl, Klaus R.

    2013-01-01

    Sequence logos are frequently used to illustrate substrate preferences and specificity of proteases. Here, we employed the compiled substrates of the MEROPS database to introduce a novel metric for comparison of protease substrate preferences. The constructed similarity matrix of 62 proteases can be used to intuitively visualize similarities in protease substrate readout via principal component analysis and construction of protease specificity trees. Since our new metric is solely based on substrate data, we can engraft the protease tree including proteolytic enzymes of different evolutionary origin. Thereby, our analyses confirm pronounced overlaps in substrate recognition not only between proteases closely related on sequence basis but also between proteolytic enzymes of different evolutionary origin and catalytic type. To illustrate the applicability of our approach we analyze the distribution of targets of small molecules from the ChEMBL database in our substrate-based protease specificity trees. We observe a striking clustering of annotated targets in tree branches even though these grouped targets do not necessarily share similarity on protein sequence level. This highlights the value and applicability of knowledge acquired from peptide substrates in drug design of small molecules, e.g., for the prediction of off-target effects or drug repurposing. Consequently, our similarity metric allows to map the degradome and its associated drug target network via comparison of known substrate peptides. The substrate-driven view of protein-protein interfaces is not limited to the field of proteases but can be applied to any target class where a sufficient amount of known substrate data is available. PMID:24244149

  15. Comparison of ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica.

    PubMed

    Register, Karen B; Nicholson, Tracy L; Brunelle, Brian W

    2016-10-01

    PvuII ribotyping and MLST are each highly discriminatory methods for genotyping Bordetella bronchiseptica, but a direct comparison between these approaches has not been undertaken. The goal of this study was to directly compare the discriminatory power of PvuII ribotyping and MLST, using a single set of geographically and genetically diverse strains, and to determine whether subtyping based on repeat region sequences of the pertactin gene (prn) provides additional resolution. One hundred twenty-two isolates were analyzed, representing 11 mammalian or avian hosts, sourced from the United States, Europe, Israel and Australia. Thirty-two ribotype patterns were identified; one isolate could not be typed. In comparison, all isolates were typeable by MLST and a total of 30 sequence types was identified. An analysis based on Simpson's Index of Diversity (SID) revealed that ribotyping and MLST are nearly equally discriminatory, with SIDs of 0.920 for ribotyping and 0.919 for MLST. Nonetheless, for ten ribotypes and eight MLST sequence types, the alternative method discriminates among isolates that otherwise type identically. Pairing prn repeat region typing with ribotyping yielded 54 genotypes and increased the SID to 0.954. Repeat region typing combined with MLST resulted in 47 genotypes and an SID of 0.944. Given the technical and practical advantages of MLST over ribotyping, and the nominal difference in their SIDs, we conclude MLST is the preferred primary typing tool. We recommend the combination of MLST and prn repeat region typing as a high-resolution, objective and standardized approach valuable for investigating the population structure and epidemiology of B. bronchiseptica.

  16. Dickeya species relatedness and clade structure determined by comparison of recA sequences.

    PubMed

    Parkinson, Neil; Stead, David; Bew, Janice; Heeney, John; Tsror Lahkim, Leah; Elphinstone, John

    2009-10-01

    Using sequences from the recA locus, we have produced a phylogeny of 188 Dickeya strains from culture collections and identified species relatedness and subspecies clade structure within the genus. Of the six recognized species, Dickeya paradisiaca, D. chrysanthemi and D. zeae were discriminated with long branch lengths. The clade containing the D. paradisiaca type strain included just one additional strain, isolated from banana in Colombia. Strains isolated from Chrysanthemum and Parthenium species made up most of the clade containing the D. chrysanthemi type strain, and the host range of this species was extended to include potato. The D. zeae clade had the largest number of sequevars and branched into two major sister clades that contained all of the Zea mays isolates, and were identified as phylotypes PI and PII. The host range was increased from six to 13 species, including potato. The recA sequence of an Australian sugar-cane strain was sufficiently distinct to rank as a new species-level branch. In contrast to these species, Dickeya dadantii, D. dianthicola and D. dieffenbachiae were distinguished with shorter branch lengths, indicating relatively closer relatedness. The recA sequence for the type strain of D. dadantii clustered separately from other strains of the species. However, sequence comparison of three additional loci revealed that the D. dadantii type strain grouped together with the six other D. dadantii strains that were sequenced. Analysis of all four loci indicated that the D. dadantii strains were most closely related to D. dieffenbachiae. Three further branches (DUC-1, -2 and -3) were associated with these three species, which all diverged from a common origin and can be considered as a species complex. The large clade containing the D. dianthicola type strain comprised 58 strains and had little sequence diversity. One sequevar accounted for the majority of these strains, which were isolated nearly exclusively from eight hosts from Europe

  17. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    PubMed

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.

  18. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

    PubMed Central

    Greenbury, S. F.; Ahnert, S. E.

    2015-01-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained' and ‘unconstrained' sequences, in the broadest possible sense. As ‘constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding' and ‘non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  19. The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.

    PubMed

    Greenbury, S F; Ahnert, S E

    2015-12-01

    Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps. PMID:26609063

  20. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species

    NASA Technical Reports Server (NTRS)

    Haney, P. J.; Badger, J. H.; Buldak, G. L.; Reich, C. I.; Woese, C. R.; Olsen, G. J.

    1999-01-01

    The genome sequence of the extremely thermophilic archaeon Methanococcus jannaschii provides a wealth of data on proteins from a thermophile. In this paper, sequences of 115 proteins from M. jannaschii are compared with their homologs from mesophilic Methanococcus species. Although the growth temperatures of the mesophiles are about 50 degrees C below that of M. jannaschii, their genomic G+C contents are nearly identical. The properties most correlated with the proteins of the thermophile include higher residue volume, higher residue hydrophobicity, more charged amino acids (especially Glu, Arg, and Lys), and fewer uncharged polar residues (Ser, Thr, Asn, and Gln). These are recurring themes, with all trends applying to 83-92% of the proteins for which complete sequences were available. Nearly all of the amino acid replacements most significantly correlated with the temperature change are the same relatively conservative changes observed in all proteins, but in the case of the mesophile/thermophile comparison there is a directional bias. We identify 26 specific pairs of amino acids with a statistically significant (P < 0.01) preferred direction of replacement.

  1. Sequence comparisons in the aminoacyl-tRNA synthetases with emphasis on regions of likely homology with sequences in the Rossmann fold in the methionyl and tyrosyl enzymes.

    PubMed

    Walker, E J; Jeffrey, P D

    1988-02-01

    Amino acid sequences of aminoacyl-tRNA synthetases specific for 12 different amino acids have now been published. Differences in origin at the species and organelle level result in 20 distinct sequences being available for comparison. Some of these were compared in small groups as they were determined and, although some homologies were detected, it was generally concluded that there was surprisingly little sequence homology in this functionally related group of enzymes. We have made comparisons of all of the available sequences by using a combination of computer and manual alignment methods and knowledge of the sequences in the Rossmann fold region of methionyl-tRNA synthetase from E. coli and tyrosyl-tRNA synthetase from B. stearothermophilus, enzymes whose three-dimensional structures have been described. It emerges that all of the aminoacyl-tRNA synthetase sequences thus examined show considerable homology with each other over at least parts of this region, some over virtually all of it. We conclude that a great deal more similarity than had previously been suspected exists in these proteins. In particular, the alignments we have made strongly imply the existence of a mononucleotide binding site of the Rossmann fold configuration in all of the synthetases compared. PMID:3283733

  2. Next-Generation Sequencing in the Understanding of Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) Biology

    PubMed Central

    Strahan, Roxanne; Uppal, Timsy; Verma, Subhash C.

    2016-01-01

    Non-Sanger-based novel nucleic acid sequencing techniques, referred to as Next-Generation Sequencing (NGS), provide a rapid, reliable, high-throughput, and massively parallel sequencing methodology that has improved our understanding of human cancers and cancer-related viruses. NGS has become a quintessential research tool for more effective characterization of complex viral and host genomes through its ever-expanding repertoire, which consists of whole-genome sequencing, whole-transcriptome sequencing, and whole-epigenome sequencing. These new NGS platforms provide a comprehensive and systematic genome-wide analysis of genomic sequences and a full transcriptional profile at a single nucleotide resolution. When combined, these techniques help unlock the function of novel genes and the related pathways that contribute to the overall viral pathogenesis. Ongoing research in the field of virology endeavors to identify the role of various underlying mechanisms that control the regulation of the herpesvirus biphasic lifecycle in order to discover potential therapeutic targets and treatment strategies. In this review, we have complied the most recent findings about the application of NGS in Kaposi’s sarcoma-associated herpesvirus (KSHV) biology, including identification of novel genomic features and whole-genome KSHV diversities, global gene regulatory network profiling for intricate transcriptome analyses, and surveying of epigenetic marks (DNA methylation, modified histones, and chromatin remodelers) during de novo, latent, and productive KSHV infections. PMID:27043613

  3. Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

    PubMed Central

    2014-01-01

    Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the

  4. Structural biology of disease-associated repetitive DNA sequences and protein-DNA complexes involved in DNA damage and repair

    SciTech Connect

    Gupta, G.; Santhana Mariappan, S.V.; Chen, X.; Catasti, P.; Silks, L.A. III; Moyzis, R.K.; Bradbury, E.M.; Garcia, A.E.

    1997-07-01

    This project is aimed at formulating the sequence-structure-function correlations of various microsatellites in the human (and other eukaryotic) genomes. Here the authors have been able to develop and apply structure biology tools to understand the following: the molecular mechanism of length polymorphism microsatellites; the molecular mechanism by which the microsatellites in the noncoding regions alter the regulation of the associated gene; and finally, the molecular mechanism by which the expansion of these microsatellites impairs gene expression and causes the disease. Their multidisciplinary structural biology approach is quantitative and can be applied to all coding and noncoding DNA sequences associated with any gene. Both NIH and DOE are interested in developing quantitative tools for understanding the function of various human genes for prevention against diseases caused by genetic and environmental effects.

  5. Further Examples of Evolution by Gene Duplication Revealed through DNA Sequence Comparisons

    PubMed Central

    Ohta, T.

    1994-01-01

    To test the theory that evolution by gene duplication occurs as a result of positive Darwinian selection that accompanies the acceleration of mutant substitutions, DNA sequences of recent duplication were analyzed by estimating the numbers of synonymous and nonsynonymous substitutions. For the troponin C family, at the period of differentiation of the fast and slow isoforms, amino acid substitutions were shown to have been accelerated relative to synonymous substitutions. Comparison of the first exon of α-actin genes revealed that amino acid substitutions were accelerated when the smooth muscle, skeletal and cardiac isoforms differentiated. Analysis of members of the heat shock protein 70 gene family of mammals indicates that heat shock responsive genes including duplicated copies are evolving rapidly, contrary to the cognitive genes which have been evolutionarily conservative. For the α(1)-antitrypsin reactive center, the acceleration of amino acid substitution has been found for gene pairs of recent duplication. PMID:7896112

  6. Efficient Query-by-Content Audio Retrieval by Locality Sensitive Hashing and Partial Sequence Comparison

    NASA Astrophysics Data System (ADS)

    Yu, Yi; Joe, Kazuki; Downie, J. Stephen

    This paper investigates suitable indexing techniques to enable efficient content-based audio retrieval in large acoustic databases. To make an index-based retrieval mechanism applicable to audio content, we investigate the design of Locality Sensitive Hashing (LSH) and the partial sequence comparison. We propose a fast and efficient audio retrieval framework of query-by-content and develop an audio retrieval system. Based on this framework, four different audio retrieval schemes, LSH-Dynamic Programming (DP), LSH-Sparse DP (SDP), Exact Euclidian LSH (E2LSH)-DP, E2LSH-SDP, are introduced and evaluated in order to better understand the performance of audio retrieval algorithms. The experimental results indicate that compared with the traditional DP and the other three compititive schemes, E2LSH-SDP exhibits the best tradeoff in terms of the response time, retrieval accuracy and computation cost.

  7. Development of amplified consensus genetic markers (ACGM) in Brassica napus from Arabidopsis thaliana sequences of known biological function.

    PubMed

    Brunel, D; Froger, N; Pelletier, G

    1999-06-01

    A method for the development of consensus genetic markers between species of the same taxonomic family is described in this paper. It is based on the conservation of the peptide sequences and on the potential polymorphism within non-coding sequences. Six loci sequenced from Arabidopsis thaliana, AG, LFY3, AP3, FAD7, FAD3, and ADH, were analysed for one ecotype of A. thaliana, four lines of Brassica napus, and one line for each parental species, Brassica oleracea and Brassica rapa. Positive amplifications with the degenerate primers showed one band for A. thaliana, two to four bands in rapeseed, and one to two bands in the parental species. Direct sequencing of the PCR products confirms their peptide similarity with the "mother" sequence. By comparison of intron sequences, the correspondence between each rapeseed gene and its homologue in one of the parental species can be determined without ambiguity. Another important result is the presence of a polymorphism inside these fragments between the rapeseed lines. This variability could generally be detected by differences of electrophoretic migration on long non-denaturing polyacrylamide gels. This method enables a quick and easy shuttle between A. thaliana and Brassica species without cloning.

  8. Molecular, biological, and morphometric comparisons between different geographical populations of Rhipicephalus sanguineus sensu lato (Acari: Ixodidae).

    PubMed

    Sanches, Gustavo S; Évora, Patrícia M; Mangold, Atílio J; Jittapalapong, Sattaporn; Rodriguez-Mallon, Alina; Guzmán, Pedro E E; Bechara, Gervásio H; Camargo-Mathias, Maria I

    2016-01-15

    In this study, different geographical populations of Rhipicephalus sanguineus sensu lato were compared by molecular, biological, and morphometric methods. Phylogenetic trees were constructed using 12S and 16S rDNA sequences and showed two distinct clades: one composed of ticks from Brazil (Jaboticabal, SP), Cuba (Havana) Thailand (Bangkok) and the so-called "tropical strain" ticks. The second clade was composed of ticks from Spain (Zaragoza), Argentina (Rafaela, Santa Fe) and the so-called "temperate strain" ticks. Morphometric analysis showed good separation between females of the two clades and within the temperate clade. Males also exhibited separation between the two clades, but with some overlap. Multiple biological parameters revealed differences between the two clades, especially the weight of the engorged female. These results confirm the existence of at least two species under the name "R. sanguineus". PMID:26790741

  9. Molecular, biological, and morphometric comparisons between different geographical populations of Rhipicephalus sanguineus sensu lato (Acari: Ixodidae).

    PubMed

    Sanches, Gustavo S; Évora, Patrícia M; Mangold, Atílio J; Jittapalapong, Sattaporn; Rodriguez-Mallon, Alina; Guzmán, Pedro E E; Bechara, Gervásio H; Camargo-Mathias, Maria I

    2016-01-15

    In this study, different geographical populations of Rhipicephalus sanguineus sensu lato were compared by molecular, biological, and morphometric methods. Phylogenetic trees were constructed using 12S and 16S rDNA sequences and showed two distinct clades: one composed of ticks from Brazil (Jaboticabal, SP), Cuba (Havana) Thailand (Bangkok) and the so-called "tropical strain" ticks. The second clade was composed of ticks from Spain (Zaragoza), Argentina (Rafaela, Santa Fe) and the so-called "temperate strain" ticks. Morphometric analysis showed good separation between females of the two clades and within the temperate clade. Males also exhibited separation between the two clades, but with some overlap. Multiple biological parameters revealed differences between the two clades, especially the weight of the engorged female. These results confirm the existence of at least two species under the name "R. sanguineus".

  10. Sequence-dependent collective properties of DNAs and their role in biological systems

    NASA Astrophysics Data System (ADS)

    De Santis, Pasquale; Scipioni, Anita

    2013-03-01

    DNA actively interacts with proteins involved in replication, transcription, repair, and regulation processes inside the cell. The base sequence encodes the dynamics of these transformations from the atomic to the nanometre scale length, and over higher spatial scales. In fact, although an important part of the DNA informational content acts locally, it exerts its functions as collective properties of relatively long sequences and manifests as static and dynamic curvature. Physical models that explore different aspects of DNA collective properties associated to such superstructural properties encoded in the sequence will be reviewed. The B-DNA periodicity operates as band-pass-filter; only the local physical-chemical variance associated to the sequence, in phase with the helical periodicity, sums up and reveals at higher scale. In this light, the gel electrophoresis behaviour of DNAs, the nucleosome thermodynamic stability and positioning along genomes were interpreted and discussed. Finally, a part of this review is reserved to describe the ability of some inorganic crystal surfaces to recognize and stabilize certain DNA tracts with peculiar sequences. The collective superstructural properties of DNAs could be involved in the selective interaction between DNA sequence and particular crystal surfaces. It may be conceived that sequences strongly adsorbed on surface could nucleate and expand bits of information in primeval DNA (and/or RNA) chains, early characterized by random sequences, since more protected against the physical-chemical injuries by the environment, and therefore involved in the evolution of their informational content.

  11. Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood

    PubMed Central

    2014-01-01

    Background The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Concurrently, metagenomic sequencing (MGS) is rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. In addition, next-generation sequencers are increasingly being used in clinical or related settings, for instance to track outbreaks. However, information regarding the analytical sensitivity or limit of detection (LoD) of benchtop sequencers is currently lacking. Furthermore, the specificity of sequence information at or near the LoD is unknown. Results In the present study, we assess the ability of three next-generation sequencing platforms to identify a pathogen (viral or bacterial) present in low titers in a clinically relevant sample (blood). Our results indicate that the Roche-454 Titanium platform is capable of detecting Dengue virus at titers as low as 1X102.5 pfu/mL, corresponding to an estimated 5.4X104 genome copies/ml maximum. The increased throughput of the benchtop sequencers, the Ion Torrent PGM and Illumina MiSeq platforms, enabled detection of viral genomes at concentrations as low as 1X104 genome copies/mL. Platform-specific biases were evident in sequence read distributions as well as viral genome coverage. For bacterial samples, only the MiSeq platform was able to provide sequencing reads that could be unambiguously classified as originating from Bacillus anthracis. Conclusion The analytical sensitivity of all three platforms approaches that of standard qPCR assays. Although all platforms were able to detect pathogens at the levels tested, there were several noteworthy differences. The Roche-454 Titanium platform produced consistently longer reads, even when compared with the latest chemistry updates for the PGM platform. The MiSeq platform produced consistently greater depth and breadth of coverage, while the Ion Torrent was unequaled for speed of

  12. Genetic mapping of expressed sequences in onion and in silico comparisons with rice show scant colinearity.

    PubMed

    Martin, William J; McCallum, John; Shigyo, Masayoshi; Jakse, Jernej; Kuhl, Joseph C; Yamane, Naoko; Pither-Joyce, Meeghan; Gokce, Ali Fuat; Sink, Kenneth C; Town, Christopher D; Havey, Michael J

    2005-10-01

    The Poales (which include the grasses) and Asparagales [which include onion (Allium cepa L.) and other Allium species] are the two most economically important monocot orders. Enormous genomic resources have been developed for the grasses; however, their applicability to other major monocot groups, such as the Asparagales, is unclear. Expressed sequence tags (ESTs) from onion that showed significant similarities (80% similarity over at least 70% of the sequence) to single positions in the rice genome were selected. One hundred new genetic markers developed from these ESTs were added to the intraspecific map derived from the BYG15-23xAC43 segregating family, producing 14 linkage groups encompassing 1,907 cM at LOD 4. Onion linkage groups were assigned to chromosomes using alien addition lines of Allium fistulosum L. carrying single onion chromosomes. Visual comparisons of genetic linkage in onion with physical linkage in rice revealed scant colinearity; however, short regions of colinearity could be identified. Our results demonstrate that the grasses may not be appropriate genomic models for other major monocot groups such as the Asparagales; this will make it necessary to develop genomic resources for these important plants. PMID:16025250

  13. Whole-genome sequence comparison as a method for improving bacterial species definition.

    PubMed

    Zhang, Wen; Du, Pengcheng; Zheng, Han; Yu, Weiwen; Wan, Li; Chen, Chen

    2014-01-01

    We compared pairs of 1,226 bacterial strains with whole genome sequences and calculated their average nucleotide identity (ANI) between genomes to determine whether whole genome comparison can be directly used for bacterial species definition. We found that genome comparisons of two bacterial strains from the same species (SGC) have a significantly higher ANI than those of two strains from different species (DGC), and that the ANI between the query and the reference genomes can be used to determine whether two genomes come from the same species. Bacterial species definition based on ANI with a cut-off value of 0.92 matched well (81.5%) with the current bacterial species definition. The ANI value was shown to be consistent with the standard for traditional bacterial species definition, and it could be used in bacterial taxonomy for species definition. A new bioinformatics program (ANItools) was also provided in this study for users to obtain the ANI value of any two bacterial genome pairs (http://genome.bioinfo-icdc.org/). This program can match a query strain to all bacterial genomes, and identify the highest ANI value of the strain at the species, genus and family levels respectively, providing valuable insights for species definition.

  14. Complete genome sequences of two biologically distinct isolates of Asparagus virus 1.

    PubMed

    Blockus, S; Lesker, T; Maiss, E

    2015-02-01

    The complete genome sequences of two asparagus virus 1 (AV-1) isolates differing in their ability to cause systemic infection in Nicotiana benthamiana were determined. Their genomes had 9,741 nucleotides excluding the 3'-terminal poly(A) tail, encoded a polyprotein of 3,112 amino acids, and shared 99.6 % nucleotide sequence identity. They differed at 37 nucleotide and 15 amino acid sequence positions (99.5 % identity) scattered over the polyprotein. The closest relatives of AV-1 in amino acid sequence identity were plum pox virus (54 %) and turnip mosaic virus (53 %), corroborating the classification of AV-1 as a member of a distinct species in the genus Potyvirus.

  15. Complete genome sequences of two biologically distinct isolates of Asparagus virus 1.

    PubMed

    Blockus, S; Lesker, T; Maiss, E

    2015-02-01

    The complete genome sequences of two asparagus virus 1 (AV-1) isolates differing in their ability to cause systemic infection in Nicotiana benthamiana were determined. Their genomes had 9,741 nucleotides excluding the 3'-terminal poly(A) tail, encoded a polyprotein of 3,112 amino acids, and shared 99.6 % nucleotide sequence identity. They differed at 37 nucleotide and 15 amino acid sequence positions (99.5 % identity) scattered over the polyprotein. The closest relatives of AV-1 in amino acid sequence identity were plum pox virus (54 %) and turnip mosaic virus (53 %), corroborating the classification of AV-1 as a member of a distinct species in the genus Potyvirus. PMID:25216774

  16. What Next? The Next Transit from Biology to Diagnostics: Next Generation Sequencing for Immunogenetics

    PubMed Central

    Gabriel, Christian; Stabentheiner, Stephanie; Danzer, Martin; Pröll, Johannes

    2011-01-01

    The human genome project triggered the introduction of next generation sequencing (NGS) systems. Although originally developed for total genome sequencing, metagenomics and plant genetics, the ultra-deep sequencing feature of NGS was utilized for diagnostic purposes in HIV resistance and tropism as well in detecting new mutations and tumor clones in oncology. Recent publications exploited the feature of clonal sequencing for immunogenetics to dissolve the growing number of ambiguities. This concept is quite reliable if all exons of interest are tested and the amplification region includes flanking introns. Challenging questions on quality control, cost effectiveness, workflow, and management of enormous loads of data remain if NGS is considered as routine method in the immunogenetics laboratory. If solved, NGS has big potential to have a major impact on immunogenetics by way of providing ambiguity-free HLA-typing results faster, but will also have a great influence on how immunogenetics testing and workflows are organized. PMID:22670120

  17. Bayesian Model Comparison and Parameter Inference in Systems Biology Using Nested Sampling

    PubMed Central

    Pullen, Nick; Morris, Richard J.

    2014-01-01

    Inferring parameters for models of biological processes is a current challenge in systems biology, as is the related problem of comparing competing models that explain the data. In this work we apply Skilling's nested sampling to address both of these problems. Nested sampling is a Bayesian method for exploring parameter space that transforms a multi-dimensional integral to a 1D integration over likelihood space. This approach focusses on the computation of the marginal likelihood or evidence. The ratio of evidences of different models leads to the Bayes factor, which can be used for model comparison. We demonstrate how nested sampling can be used to reverse-engineer a system's behaviour whilst accounting for the uncertainty in the results. The effect of missing initial conditions of the variables as well as unknown parameters is investigated. We show how the evidence and the model ranking can change as a function of the available data. Furthermore, the addition of data from extra variables of the system can deliver more information for model comparison than increasing the data from one variable, thus providing a basis for experimental design. PMID:24523891

  18. Bayesian model comparison and parameter inference in systems biology using nested sampling.

    PubMed

    Pullen, Nick; Morris, Richard J

    2014-01-01

    Inferring parameters for models of biological processes is a current challenge in systems biology, as is the related problem of comparing competing models that explain the data. In this work we apply Skilling's nested sampling to address both of these problems. Nested sampling is a Bayesian method for exploring parameter space that transforms a multi-dimensional integral to a 1D integration over likelihood space. This approach focuses on the computation of the marginal likelihood or evidence. The ratio of evidences of different models leads to the Bayes factor, which can be used for model comparison. We demonstrate how nested sampling can be used to reverse-engineer a system's behaviour whilst accounting for the uncertainty in the results. The effect of missing initial conditions of the variables as well as unknown parameters is investigated. We show how the evidence and the model ranking can change as a function of the available data. Furthermore, the addition of data from extra variables of the system can deliver more information for model comparison than increasing the data from one variable, thus providing a basis for experimental design. PMID:24523891

  19. The future role of next-generation DNA sequencing and metagenetics in aquatic biology monitoring programs

    EPA Science Inventory

    The development of current biological monitoring and bioassessment programs was a drastic improvement over previous programs created for monitoring a limited number of specific chemical pollutants. Although these assessment programs are better designed to address the transient an...

  20. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

    PubMed

    Bertelli, Claire; Aeby, Sébastien; Chassot, Bérénice; Clulow, James; Hilfiker, Olivier; Rappo, Samuel; Ritzmann, Sébastien; Schumacher, Paolo; Terrettaz, Céline; Benaglio, Paola; Falquet, Laurent; Farinelli, Laurent; Gharib, Walid H; Goesmann, Alexander; Harshman, Keith; Linke, Burkhard; Miyazaki, Ryo; Rivolta, Carlo; Robinson-Rechavi, Marc; van der Meer, Jan Roelof; Greub, Gilbert

    2015-01-01

    With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

  1. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

    PubMed Central

    Bertelli, Claire; Aeby, Sébastien; Chassot, Bérénice; Clulow, James; Hilfiker, Olivier; Rappo, Samuel; Ritzmann, Sébastien; Schumacher, Paolo; Terrettaz, Céline; Benaglio, Paola; Falquet, Laurent; Farinelli, Laurent; Gharib, Walid H.; Goesmann, Alexander; Harshman, Keith; Linke, Burkhard; Miyazaki, Ryo; Rivolta, Carlo; Robinson-Rechavi, Marc; van der Meer, Jan Roelof; Greub, Gilbert

    2015-01-01

    With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by “embedded bioinformaticians,” i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the “Sequence a genome” class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses. PMID:25745418

  2. A Comparison of Biological and Adoptive Mothers and Fathers: The Relevance of Biological Kinship and Gendered Constructs of Parenthood.

    ERIC Educational Resources Information Center

    Miall, Charlene E.; March, Karen

    2003-01-01

    Used qualitative interviews to examine beliefs and values about biological and adoptive parents. Considered how biological kinship, gender, and actual parenting behavior affect the assessments respondents made of the emotional bonding between parents and children. Found that biological and adoptive parents viewed motherhood as instinctive and…

  3. Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology1

    PubMed Central

    Robarts, Daniel W. H.; Wolfe, Andrea D.

    2014-01-01

    In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance. PMID:25202637

  4. Unique nucleotide sequence-guided assembly of repetitive DNA parts for synthetic biology applications

    SciTech Connect

    Torella, JP; Lienert, F; Boehm, CR; Chen, JH; Way, JC; Silver, PA

    2014-08-07

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts, and they hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies-for example, repeated terminator and insulator sequences-that complicate recombination-based assembly. We and others have recently developed DNA assembly methods, which we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly assembled constructs, or into high-quality combinatorial libraries in only 2-3 d. If the DNA parts must be generated from scratch, an additional 2-5 d are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques.

  5. Unique nucleotide sequence (UNS)-guided assembly of repetitive DNA parts for synthetic biology applications

    PubMed Central

    Torella, Joseph P.; Lienert, Florian; Boehm, Christian R.; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

    2016-01-01

    Recombination-based DNA construction methods, such as Gibson assembly, have made it possible to easily and simultaneously assemble multiple DNA parts and hold promise for the development and optimization of metabolic pathways and functional genetic circuits. Over time, however, these pathways and circuits have become more complex, and the increasing need for standardization and insulation of genetic parts has resulted in sequence redundancies — for example repeated terminator and insulator sequences — that complicate recombination-based assembly. We and others have recently developed DNA assembly methods that we refer to collectively as unique nucleotide sequence (UNS)-guided assembly, in which individual DNA parts are flanked with UNSs to facilitate the ordered, recombination-based assembly of repetitive sequences. Here we present a detailed protocol for UNS-guided assembly that enables researchers to convert multiple DNA parts into sequenced, correctly-assembled constructs, or into high-quality combinatorial libraries in only 2–3 days. If the DNA parts must be generated from scratch, an additional 2–5 days are necessary. This protocol requires no specialized equipment and can easily be implemented by a student with experience in basic cloning techniques. PMID:25101822

  6. Nucleotide sequence of dengue 2 RNA and comparison of the encoded proteins with those of other flaviviruses.

    PubMed

    Hahn, Y S; Galler, R; Hunkapiller, T; Dalrymple, J M; Strauss, J H; Strauss, E G

    1988-01-01

    We have determined the complete sequence of the RNA of dengue 2 virus (S1 candidate vaccine strain derived from the PR-159 isolate) with the exception of about 15 nucleotides at the 5' end. The genome organization is the same as that deduced earlier for other flaviviruses and the amino acid sequences of the encoded dengue 2 proteins show striking homology to those of other flaviviruses. The overall amino acid sequence similarity between dengue 2 and yellow fever virus is 44.7%, whereas that between dengue 2 and West Nile virus is 50.7%. These viruses represent three different serological subgroups of mosquito-borne flaviviruses. Comparison of the amino acid sequences shows that amino acid sequence homology is not uniformly distributed among the proteins; highest homology is found in some domains of nonstructural protein NS5 and lowest homology in the hydrophobic polypeptides ns2a and 2b. In general the structural proteins are less well conserved than the nonstructural proteins. Hydrophobicity profiles, however, are remarkably similar throughout the translated region. Comparison of the dengue 2 PR-159 sequence to partial sequence data from dengue 4 and another strain of dengue 2 virus reveals amino acid sequence homologies of about 64 and 96%, respectively, in the structural protein region. Thus as a general rule for flaviviruses examined to date, members of different serological subgroups demonstrate 50% or less amino acid sequence homology, members of the same subgroup average 65-75% homology, and strains of the same virus demonstrate greater than 95% amino acid sequence similarity.

  7. Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 microbead sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heterodera glycines, the soybean cyst nematode (SCN), is the most important pathogen of soybean in the Midwestern United States. Genomic DNA sequence information for this nematode is limited and thus progress in devising genomic approaches to control this pathogen has been slow. To remedy this pro...

  8. Microbial Analysis of Bite Marks by Sequence Comparison of Streptococcal DNA

    PubMed Central

    Kennedy, Darnell M.; Stanton, Jo-Ann L.; García, José A.; Mason, Chris; Rand, Christy J.; Kieser, Jules A.; Tompkins, Geoffrey R.

    2012-01-01

    Bite mark injuries often feature in violent crimes. Conventional morphometric methods for the forensic analysis of bite marks involve elements of subjective interpretation that threaten the credibility of this field. Human DNA recovered from bite marks has the highest evidentiary value, however recovery can be compromised by salivary components. This study assessed the feasibility of matching bacterial DNA sequences amplified from experimental bite marks to those obtained from the teeth responsible, with the aim of evaluating the capability of three genomic regions of streptococcal DNA to discriminate between participant samples. Bite mark and teeth swabs were collected from 16 participants. Bacterial DNA was extracted to provide the template for PCR primers specific for streptococcal 16S ribosomal RNA (16S rRNA) gene, 16S–23S intergenic spacer (ITS) and RNA polymerase beta subunit (rpoB). High throughput sequencing (GS FLX 454), followed by stringent quality filtering, generated reads from bite marks for comparison to those generated from teeth samples. For all three regions, the greatest overlaps of identical reads were between bite mark samples and the corresponding teeth samples. The average proportions of reads identical between bite mark and corresponding teeth samples were 0.31, 0.41 and 0.31, and for non-corresponding samples were 0.11, 0.20 and 0.016, for 16S rRNA, ITS and rpoB, respectively. The probabilities of correctly distinguishing matching and non-matching teeth samples were 0.92 for ITS, 0.99 for 16S rRNA and 1.0 for rpoB. These findings strongly support the tenet that bacterial DNA amplified from bite marks and teeth can provide corroborating information in the identification of assailants. PMID:23284761

  9. The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse▿ †

    PubMed Central

    Durfee, Tim; Nelson, Richard; Baldwin, Schuyler; Plunkett, Guy; Burland, Valerie; Mau, Bob; Petrosino, Joseph F.; Qin, Xiang; Muzny, Donna M.; Ayele, Mulu; Gibbs, Richard A.; Csörgő, Bálint; Pósfai, György; Weinstock, George M.; Blattner, Frederick R.

    2008-01-01

    Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B. PMID:18245285

  10. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.

    PubMed

    Zheng, Wenjun; Brooks, Bernard R; Thirumalai, D

    2006-05-16

    By representing the high-resolution crystal structures of a number of enzymes using the elastic network model, it has been shown that only a few low-frequency normal modes are needed to describe the large-scale domain movements that are triggered by ligand binding. Here we explore a link between the nearly invariant nature of the modes that describe functional dynamics at the mesoscopic level and the large evolutionary sequence variations at the residue level. By using a structural perturbation method (SPM), which probes the residue-specific response to perturbations (or mutations), we identify a sparse network of strongly conserved residues that transmit allosteric signals in three structurally unrelated biological nanomachines, namely, DNA polymerase, myosin motor, and the Escherichia coli chaperonin. Based on the response of every mode to perturbations, which are generated by interchanging specific sequence pairs in a multiple sequence alignment, we show that the functionally relevant low-frequency modes are most robust to sequence variations. Our work shows that robustness of dynamical modes at the mesoscopic level is encoded in the structure through a sparse network of residues that transmit allosteric signals.

  11. Complete genome sequence and biological characterization of Moroccan pepper virus (MPV) and reclassification of Lettuce necrotic stunt virus as MPV.

    PubMed

    Wintermantel, William M; Hladky, Laura L

    2013-05-01

    Moroccan pepper virus (MPV) and Lettuce necrotic stunt virus (LNSV) have been steadily increasing in prevalence in central Asia and western North America, respectively, over the past decade. Recent sequence analysis of LNSV demonstrated a close relationship between the coat proteins of LNSV and MPV. To determine the full extent of the relationship between LNSV and MPV, the genomes of three MPV isolates were sequenced and compared with that of LNSV. Sequence analysis demonstrated that genomic nucleotide sequences as well as virus-encoded proteins of the three MPV isolates and LNSV shared 97% or greater identity. A full-length clone of a California LNSV isolate was developed and virus derived from infectious transcripts was used to evaluate host plant reactions under controlled conditions. Symptoms of LNSV matched those described previously for MPV on most of a select series of host plants, although some differences were observed. Collectively, these molecular and biological results demonstrate that LNSV should be classified as MPV within the family Tombusviridae, genus Tombusvirus, and confirm the presence of MPV in North America. PMID:23360531

  12. Application Sequence and soil biology influence anaerobic soil disinfestation induced disease suppression

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Anaerobic soil disinfestation (ASD) and mustard seed meal (MSM) soil amendments can yield significant control of a diversity of soil-borne pests and pathogens. The mechanisms functional in disease suppression are diverse and with regard to MSM amendment, soil biology has been shown to have a signif...

  13. Accelerated Integrated Science Sequence (AISS): An Introductory Biology, Chemistry, and Physics Course

    ERIC Educational Resources Information Center

    Purvis-Roberts, Kathleen L.; Edwalds-Gilbert, Gretchen; Landsberg, Adam S.; Copp, Newton; Ulsh, Lisa; Drew, David E.

    2009-01-01

    A new interdisciplinary, introductory science course was offered for the first time during the 2007-2008 school year. The purpose of the course is to introduce students to the idea of working at the intersections of biology, chemistry, and physics and to recognize interconnections between the disciplines. Interdisciplinary laboratories are a key…

  14. Research and Teaching: Instructor Use of Group Active Learning in an Introductory Biology Sequence

    ERIC Educational Resources Information Center

    Auerbach, Anna Jo; Schussler, Elisabeth E.

    2016-01-01

    Active learning (or learner-centered) pedagogies have been shown to enhance student learning in introductory biology courses. Student collaboration has also been shown to enhance student learning and may be a critical part of effective active learning practices. This study focused on documenting the use of individual active learning and group…

  15. Biology-Chemistry-Physics, Teachers' Guide, a Three-Year Sequence, Parts I and II.

    ERIC Educational Resources Information Center

    Scott, Arthur; And Others

    This is one of two teacher's guides for a three-year integrated biology, chemistry, and physics course being prepared by the Portland Project Committee. This committee reviewed and selected material developed by the national course improvement groups--Physical Science Study Committee, Chemical Bond Approach, Chemical Education Materials Study,…

  16. Designing and Evaluating a Context-Based Lesson Sequence Promoting Conceptual Coherence in Biology

    ERIC Educational Resources Information Center

    Ummels, M. H. J.; Kamp, M. J. A.; de Kroon, H.; Boersma, K. Th.

    2015-01-01

    Context-based education, in which students deal with biological concepts in a meaningful way, is showing promise in promoting the development of students' conceptual coherence. However, literature gives little guidance about how this kind of education should be designed. Therefore, our study aims at designing and evaluating the practicability…

  17. Sequencing Genetics Information: Integrating Data into Information Literacy for Undergraduate Biology Students

    ERIC Educational Resources Information Center

    MacMillan, Don

    2010-01-01

    This case study describes an information literacy lab for an undergraduate biology course that leads students through a range of resources to discover aspects of genetic information. The lab provides over 560 students per semester with the opportunity for hands-on exploration of resources in steps that simulate the pathways of higher-level…

  18. Biological nutrient removal in a sequencing batch reactor operated as oxic/anoxic/extended-idle regime.

    PubMed

    Li, Xiao-ming; Chen, Hong-bo; Yang, Qi; Wang, Dong-bo; Luo, Kun; Zeng, Guang-ming

    2014-06-01

    Previous researches have demonstrated that biological phosphorus removal from wastewater could be induced by oxic/extended-idle (O/EI) regime. In this study, an anoxic period was introduced after the aeration to realize biological nutrient removal. High nitrite accumulation ratio and polyhydroxyalkanoates biosynthesis were obtained in the aeration and biological nutrient removal could be well achieved in oxic/anoxic/extended-idle (O/A/EI) regime for the wastewater used. In addition, nitrogen and phosphorus removal performance in O/A/EI regime was compared with that in conventional anaerobic/anoxic/aerobic (A(2)/O) and O/EI processes. The results showed that O/A/EI regime exhibited higher nitrogen and phosphorus removal than A(2)/O and O/EI processes. More ammonium oxidizing bacteria and polyphosphate accumulating organisms and less glycogen accumulating organisms containing in the biomass might be the principal reason for the better nitrogen and phosphorus removal in O/A/EI regime. Furthermore, biological nutrient removal with O/A/EI regime was demonstrated with municipal wastewater. The average TN, SOP and COD removal efficiencies were 93%, 95% and 87%, respectively.

  19. Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes

    PubMed Central

    Fukui, Toshiaki; Atomi, Haruyuki; Kanai, Tamotsu; Matsumi, Rie; Fujiwara, Shinsuke; Imanaka, Tadayuki

    2005-01-01

    The genus Thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order Thermococcales in Euryarchaeota along with the closely related genus Pyrococcus. The members of Thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. To obtain insight into this important genus, we have determined and annotated the complete 2,088,737-base genome of Thermococcus kodakaraensis strain KOD1, followed by a comparison with the three complete genomes of Pyrococcus spp. A total of 2306 coding DNA sequences (CDSs) have been identified, among which half (1165 CDSs) are annotatable, whereas the functions of 41% (936 CDSs) cannot be predicted from the primary structures. The genome contains seven genes for probable transposases and four virus-related regions. Several proteins within these genetic elements show high similarities to those in Pyrococcus spp., implying the natural occurrence of horizontal gene transfer of such mobile elements among the order Thermococcales. Comparative genomics clarified that 1204 proteins, including those for information processing and basic metabolisms, are shared among T. kodakaraensis and the three Pyrococcus spp. On the other hand, among the set of 689 proteins unique to T. kodakaraensis, there are several intriguing proteins that might be responsible for the specific trait of the genus Thermococcus, such as proteins involved in additional pyruvate oxidation, nucleotide metabolisms, unique or additional metal ion transporters, improved stress response system, and a distinct restriction system. PMID:15710748

  20. A comparison between equations describing in vivo MT: The effects of noise and sequence parameters

    NASA Astrophysics Data System (ADS)

    Cercignani, Mara; Barker, Gareth J.

    2008-04-01

    Quantitative models of magnetization transfer (MT) allow the estimation of physical properties of tissue which are thought to reflect myelination, and are therefore likely to be useful for clinical application. Although a model describing a two-pool system under continuous wave-saturation has been available for two decades, generalizing such a model to pulsed MT, and therefore to in vivo applications, is not straightforward, and only recently have a range of equations predicting the outcome of pulsed MT experiments been proposed. These solutions of the 2-pool model are based on differing assumptions and involve differing degrees of complexity, so their individual advantages and limitations are not always obvious. This paper is concerned with the comparison of three differing signal equations. After reviewing the theory behind each of them, their accuracy and precision is investigated using numerical simulations under variable experimental conditions such as degree of T1-weighting of the acquisition sequence and SNR, and the consistency of numerical results is tested using in vivo data. We show that while in conditions of minimal T1-weighting, high SNR, and large duty cycle the solutions of the three equations are consistent, they have a different tolerance to deviations from the basic assumptions behind their development, which should be taken into account when designing a quantitative MT protocol.

  1. Comparison of the Biological Characteristics of Mesenchymal Stem Cells Derived from Bone Marrow and Skin.

    PubMed

    Liu, Ruifeng; Chang, Wenjuan; Wei, Hong; Zhang, Kaiming

    2016-01-01

    Mesenchymal stem cells (MSCs) exhibit high proliferation and self-renewal capabilities and are critical for tissue repair and regeneration during ontogenesis. They also play a role in immunomodulation. MSCs can be isolated from a variety of tissues and have many potential applications in the clinical setting. However, MSCs of different origins may possess different biological characteristics. In this study, we performed a comprehensive comparison of MSCs isolated from bone marrow and skin (BMMSCs and SMSCs, resp.), including analysis of the skin sampling area, separation method, culture conditions, primary and passage culture times, cell surface markers, multipotency, cytokine secretion, gene expression, and fibroblast-like features. The results showed that the MSCs from both sources had similar cell morphologies, surface markers, and differentiation capacities. However, the two cell types exhibited major differences in growth characteristics; the primary culture time of BMMSCs was significantly shorter than that of SMSCs, whereas the growth rate of BMMSCs was lower than that of SMSCs after passaging. Moreover, differences in gene expression and cytokine secretion profiles were observed. For example, secretion of proliferative cytokines was significantly higher for SMSCs than for BMMSCs. Our findings provide insights into the different biological functions of both cell types.

  2. Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods

    PubMed Central

    Chis, Oana-Teodora; Banga, Julio R.; Balsa-Canto, Eva

    2011-01-01

    Analysing the properties of a biological system through in silico experimentation requires a satisfactory mathematical representation of the system including accurate values of the model parameters. Fortunately, modern experimental techniques allow obtaining time-series data of appropriate quality which may then be used to estimate unknown parameters. However, in many cases, a subset of those parameters may not be uniquely estimated, independently of the experimental data available or the numerical techniques used for estimation. This lack of identifiability is related to the structure of the model, i.e. the system dynamics plus the observation function. Despite the interest in knowing a priori whether there is any chance of uniquely estimating all model unknown parameters, the structural identifiability analysis for general non-linear dynamic models is still an open question. There is no method amenable to every model, thus at some point we have to face the selection of one of the possibilities. This work presents a critical comparison of the currently available techniques. To this end, we perform the structural identifiability analysis of a collection of biological models. The results reveal that the generating series approach, in combination with identifiability tableaus, offers the most advantageous compromise among range of applicability, computational complexity and information provided. PMID:22132135

  3. Comparison of the Biological Characteristics of Mesenchymal Stem Cells Derived from Bone Marrow and Skin

    PubMed Central

    Liu, Ruifeng; Chang, Wenjuan; Wei, Hong; Zhang, Kaiming

    2016-01-01

    Mesenchymal stem cells (MSCs) exhibit high proliferation and self-renewal capabilities and are critical for tissue repair and regeneration during ontogenesis. They also play a role in immunomodulation. MSCs can be isolated from a variety of tissues and have many potential applications in the clinical setting. However, MSCs of different origins may possess different biological characteristics. In this study, we performed a comprehensive comparison of MSCs isolated from bone marrow and skin (BMMSCs and SMSCs, resp.), including analysis of the skin sampling area, separation method, culture conditions, primary and passage culture times, cell surface markers, multipotency, cytokine secretion, gene expression, and fibroblast-like features. The results showed that the MSCs from both sources had similar cell morphologies, surface markers, and differentiation capacities. However, the two cell types exhibited major differences in growth characteristics; the primary culture time of BMMSCs was significantly shorter than that of SMSCs, whereas the growth rate of BMMSCs was lower than that of SMSCs after passaging. Moreover, differences in gene expression and cytokine secretion profiles were observed. For example, secretion of proliferative cytokines was significantly higher for SMSCs than for BMMSCs. Our findings provide insights into the different biological functions of both cell types. PMID:27239202

  4. Thermal biology, torpor and behaviour in sugar gliders: a laboratory-field comparison.

    PubMed

    Geiser, Fritz; Holloway, Joanne C; Körtner, Gerhard

    2007-07-01

    Most studies on animal physiology and behaviour are conducted in captivity without verification that data are representative of free-ranging animals. We provide the first quantitative comparison of daily torpor, thermal biology and activity patterns, conducted on two groups of sugar gliders (Petaurus breviceps, Marsupialia) exposed to similar thermal conditions, one in captivity and the other in the field. Our study shows that activity in captive gliders in an outdoor aviary is restricted to the night and largely unaffected by weather, whereas free-ranging gliders omit foraging on cold/wet nights and may also forage in the afternoon. Torpor occurrence in gliders was significantly lower in captivity (8.4% after food deprivation; 1.1% for all observations) than in the field (25.9%), mean torpor bout duration was shorter in captivity (6.9 h) than in the field (13.1 h), and mean body temperatures during torpor were higher in captivity (25.3 degrees C) than in the field (19.6 degrees C). Moreover, normothermic body temperature as a function of air temperature differed between captive and free-ranging gliders, with a >3 degrees C difference at low air temperatures. Our comparison shows that activity patterns, thermal physiology, use of torpor and patterns of torpor may differ substantially between the laboratory and field, and provides further evidence that functional and behavioural data on captive individuals may not necessarily be representative of those living in the wild.

  5. Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology.

    PubMed Central

    Gao, F; Yue, L; Robertson, D L; Hill, S C; Hui, H; Biggar, R J; Neequaye, A E; Whelan, T M; Ho, D D; Shaw, G M

    1994-01-01

    The virulence properties of human immunodeficiency virus type 2 (HIV-2) are known to vary significantly and to range from relative attenuation in certain individuals to high-level pathogenicity in others. These differences in clinical manifestations may, at least in part, be determined by genetic differences among infecting virus strains. Evaluation of the full spectrum of HIV-2 genetic diversity is thus a necessary first step towards understanding its molecular epidemiology, natural history of infection, and biological diversity. In this study, we have used nested PCR techniques to amplify viral sequences from the DNA of uncultured peripheral blood mononuclear cells from 12 patients with HIV-2 seroreactivity. Sequence analysis of four nonoverlapping genomic regions allowed a comprehensive analysis of HIV-2 phylogeny. The results revealed (i) the existence of five distinct and roughly equidistant evolutionary lineages of HIV-2 which, by analogy with HIV-1, have been termed sequence subtypes A to E; (ii) evidence for a mosaic HIV-2 genome, indicating that coinfection with genetically divergent strains and recombination can occur in HIV-2-infected individuals; and (iii) evidence supporting the conclusion that some of the HIV-2 subtypes may have arisen from independent introductions of genetically diverse sooty mangabey viruses into the human population. Importantly, only a subset of HIV-2 strains replicated in culture: all subtype A viruses grew to high titers, but attempts to isolate representatives of subtypes C, D, and E, as well as the majority of subtype B viruses, remained unsuccessful. Infection with all five viral subtypes was detectable by commercially available serological (Western immunoblot) assays, despite intersubtype sequence differences of up to 25% in the gag, pol, and env regions. These results indicate that the genetic and biological diversity of HIV-2 is far greater than previously appreciated and suggest that there may be subtype

  6. Multiple Comparison Analysis of Two New Genomic Sequences of ILTV Strains from China with Other Strains from Different Geographic Regions.

    PubMed

    Zhao, Yan; Kong, Congcong; Wang, Yunfeng

    2015-01-01

    To date, twenty complete genome sequences of ILTV strains have been published in GenBank, including one strain from China, and nineteen strains from Australian and the United States. To investigate the genomic information on ILTVs from different geographic regions, two additional individual complete genome sequences of WG and K317 strains from China were determined. The genomes of WG and K317 strains were 153,505 and 153,639 bp in length, respectively. Alignments performed on the amino acid sequences of the twelve glycoproteins showed that 13 out of 116 mutational sites were present only among the Chinese strain WG and the Australian strains SA2 and A20. The phylogenetic tree analysis suggested that the WG strain established close relationships with the Australian strain SA2. The recombination events were detected and confirmed in different subregions of the WG strain with the sequences of SA2 and K317 strains as parental. In this study, two new complete genome sequences of Chinese ILTV strains were used in comparative analysis with other complete genome sequences of ILTV strains from China, the United States, and Australia. The analysis of genome comparison, phylogenetic trees, and recombination events showed close relationships among the Chinese strain WG and the Australian strains SA2. The information of the two new complete genome sequences from China will help to facilitate the analysis of phylogenetic relationships and the molecular differences among ILTV strains from different geographic regions.

  7. Multiple Comparison Analysis of Two New Genomic Sequences of ILTV Strains from China with Other Strains from Different Geographic Regions

    PubMed Central

    Zhao, Yan; Kong, Congcong; Wang, Yunfeng

    2015-01-01

    To date, twenty complete genome sequences of ILTV strains have been published in GenBank, including one strain from China, and nineteen strains from Australian and the United States. To investigate the genomic information on ILTVs from different geographic regions, two additional individual complete genome sequences of WG and K317 strains from China were determined. The genomes of WG and K317 strains were 153,505 and 153,639 bp in length, respectively. Alignments performed on the amino acid sequences of the twelve glycoproteins showed that 13 out of 116 mutational sites were present only among the Chinese strain WG and the Australian strains SA2 and A20. The phylogenetic tree analysis suggested that the WG strain established close relationships with the Australian strain SA2. The recombination events were detected and confirmed in different subregions of the WG strain with the sequences of SA2 and K317 strains as parental. In this study, two new complete genome sequences of Chinese ILTV strains were used in comparative analysis with other complete genome sequences of ILTV strains from China, the United States, and Australia. The analysis of genome comparison, phylogenetic trees, and recombination events showed close relationships among the Chinese strain WG and the Australian strains SA2. The information of the two new complete genome sequences from China will help to facilitate the analysis of phylogenetic relationships and the molecular differences among ILTV strains from different geographic regions. PMID:26186451

  8. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences.

    PubMed

    Faure, Denis; Joly, Dominique

    2015-04-01

    Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.

  9. Biological phosphorus and nitrogen removal in sequencing batch reactors: effects of cycle length, dissolved oxygen concentration and influent particulate matter.

    PubMed

    Ginige, Maneesha P; Kayaalp, Ahmet S; Cheng, Ka Yu; Wylie, Jason; Kaksonen, Anna H

    2013-01-01

    Removal of phosphorus (P) and nitrogen (N) from municipal wastewaters is required to mitigate eutrophication of receiving water bodies. While most treatment plants achieve good N removal using influent carbon (C), the use of influent C to facilitate enhanced biological phosphorus removal (EBPR) is poorly explored. A number of operational parameters can facilitate optimum use of influent C and this study investigated the effects of cycle length, dissolved oxygen (DO) concentration during aerobic period and influent solids on biological P and N removal in sequencing batch reactors (SRBs) using municipal wastewaters. Increasing cycle length from 3 to 6 h increased P removal efficiency, which was attributed to larger portion of N being removed via nitrite pathway and more biodegradable organic C becoming available for EBPR. Further increasing cycle length from 6 to 8 h decreased P removal efficiencies as the demand for biodegradable organic C for denitrification increased as a result of complete nitrification. Decreasing DO concentration in the aerobic period from 2 to 0.8 mg L(-1) increased P removal efficiency but decreased nitrification rates possibly due to oxygen limitation. Further, sedimented wastewater was proved to be a better influent stream than non-sedimented wastewater possibility due to the detrimental effect of particulate matter on biological nutrient removal.

  10. Uveitis, the Comparison of Age-Related Macular Degeneration Treatments Trials (CATT), and Intravitreal Biologics for Ocular Inflammation Short title: Uveitis, CATT, and intravitreal biologics

    PubMed Central

    Yeh, Steven; Albini, Thomas A.; Moshfeghi, Andrew A.; Nussenblatt, Robert B.

    2012-01-01

    Purpose To provide perspective on the implications of the Comparison of Age-Related Macular Degeneration Treatments Trials (CATT) on intravitreal biologic agents in uveitis and retinal diseases in which ocular inflammatory pathways are central to their pathogenesis Design Interpretative essay Methods Literature review and interpretation Results Besides the clear importance of CATT from a patient treatment perspective in age-related macular degeneration (AMD), these data highlight the critical relevance of highly specific protein immunotherapies offered with biologic agents. The CATT trial also provides a reminder regarding the importance of rigorous efficacy and safety monitoring required when administering intravitreal biologic therapy. Within the field of uveitis, systemic and local biologics have been utilized to effectively treat uveitis, targeting pathways implicated in both angiogenesis and inflammation (e.g. tumor necrosis factor-α [TNF-α] and interleukin-2 pathways), and research on intravitreal biologic therapy for uveitis and AMD will continue to expand. With over 25 ongoing clinical trials on intravitreal biologic therapy for AMD, enthusiasm for vanguard biologic therapies should be tempered by judicious monitoring for adverse events. Conclusion The importance of the CATT trial encompasses day-to-day treatment decisions for AMD, as well as lessons on how biologics for ocular disease should be implemented into clinical practice. Specifically, the introduction of intravitreal biologic therapies into clinical practice for uveitis, AMD, and other ocular diseases in which inflammation is involved, should be guided by a clear understanding of the immunotherapeutic agent and its molecular target and with rigorous monitoring for both patient benefit and patient safety. PMID:22898344

  11. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

  12. Sequence of a New World primate insulin having low biological potency and immunoreactivity

    SciTech Connect

    Seino, S.; Steiner, D.F.; Bell, G.I.

    1987-11-01

    The organization of the insulin gene of the owl or night monkey (Aotus trivirgatus), a New World primate, is similar to that of the human gene. The sequences of these two genes and flanking regions possess 84.3% homology. An unusual feature of the owl monkey gene is the partial duplication and insertion of a portion of the A-chain coding sequence into the 3' untranslated region. The insulin gene of this primate also lacks a region of tandem repeats that is present in the 5' flanking region of the human and chimpanzee genes. Owl monkey preproinsulin has 85.5% identity with the human insulin precursor and is the most divergent of the primate insulins/preproinsulins yet described. The differences between owl monkey and human preproinsulin include three substitutions in the signal peptide, two in the B chain, seven in the C peptide, and three in the A chain. One of these replacements is the conservative substitution of valine for isoleucine a position A2, an invariant site in all other vertebrate insulins and insulin-like growth factors. The substitutions in owl monkey insulin at B9, B27, A2, A4, and A17 alter its structure so that it has only 20% of the receptor-binding activity and 1% of the affinity with guinea pig anti-porcine insulin antibodies as compared to human insulin.

  13. Sequencing treatment of landfill leachate using ammonia stripping, Fenton oxidation and biological treatment.

    PubMed

    Nurisepehr, Mohammad; Jorfi, Sahand; Rezaei Kalantary, Roshanak; Akbari, Hamideh; Soltani, Reza Darvishi Cheshmeh; Samaei, Mohamad

    2012-09-01

    Landfill leachates contain a wide variety of pollutants such as organic matter, refractory compounds, ammonia, particulate and dissolved solids and hazardous metals requiring application of advanced and well designed treatment processes before release to the environment. The main purpose of this research was to evaluate the efficiency of combined air stripping, Fenton oxidation and biological treatment in treating landfill leachate, especially the elimination of ammonia and refractory organics. The laboratory scale set-up consisted of three sequential but separate steps. The optimum conditions for air stripping and the Fenton oxidation were determined for landfill leachate from Karaj city, Iran. The final step was a moving bed bioreactor with HRTs of 18, 12 and 6 h. The highest NH(3)-N removal was 79% in the air stripping process at pH 10.5. At the optimum conditions for the Fenton reaction at a reaction time of 90 min, pH 3 and a H(2)O(2)/Fe(2+) mass ratio of 20, the COD removal was 61% and improved the BOD/COD ratio from 0.42 to 0.78. The overall COD removal including the final biological reactor with a HRT of 6 h resulted in an effluent COD concentration of less than 100 mg L(-1).

  14. From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

    PubMed Central

    Benos, Panayiotis V.; Gatt, Melanie K.; Murphy, Lee; Harris, David; Barrell, Bart; Ferraz, Concepcion; Vidal, Sophie; Brun, Christine; Demaille, Jacques; Cadieu, Edouard; Dreano, Stephane; Gloux, Stéphanie; Lelaure, Valerie; Mottier, Stephanie; Galibert, Francis; Borkova, Dana; Miñana, Belen; Kafatos, Fotis C.; Bolshakov, Slava; Sidén-Kiamos, Inga; Papagiannakis, George; Spanos, Lefteris; Louis, Christos; Madueño, Encarnación; de Pablos, Beatriz; Modolell, Juan; Peter, Annette; Schöttler, Petra; Werner, Meike; Mourkioti, Fotini; Beinert, Nicole; Dowe, Gordon; Schäfer, Ulrich; Jäckle, Herbert; Bucheton, Alain; Callister, Debbie; Campbell, Lorna; Henderson, Nadine S.; McMillan, Paul J.; Salles, Cathy; Tait, Evelyn; Valenti, Phillipe; Saunders, Robert D.C.; Billaud, Alain; Pachter, Lior; Glover, David M.; Ashburner, Michael

    2001-01-01

    We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through “shotgun” sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation. [All of the sequences analyzed in this paper have been deposited in the EMBL-Bank database under the following accession nos.: AL009146, AL009147, AL009171, AL009188–AL009196, AL021067, AL021086, AL021106–AL021108, AL021726, AL

  15. Comparing Effects of Biologic Agents in Treating Patients with Rheumatoid Arthritis: A Multiple Treatment Comparison Regression Analysis

    PubMed Central

    Tvete, Ingunn Fride; Natvig, Bent; Gåsemyr, Jørund; Meland, Nils; Røine, Marianne; Klemp, Marianne

    2015-01-01

    Rheumatoid arthritis patients have been treated with disease modifying anti-rheumatic drugs (DMARDs) and the newer biologic drugs. We sought to compare and rank the biologics with respect to efficacy. We performed a literature search identifying 54 publications encompassing 9 biologics. We conducted a multiple treatment comparison regression analysis letting the number experiencing a 50% improvement on the ACR score be dependent upon dose level and disease duration for assessing the comparable relative effect between biologics and placebo or DMARD. The analysis embraced all treatment and comparator arms over all publications. Hence, all measured effects of any biologic agent contributed to the comparison of all biologic agents relative to each other either given alone or combined with DMARD. We found the drug effect to be dependent on dose level, but not on disease duration, and the impact of a high versus low dose level was the same for all drugs (higher doses indicated a higher frequency of ACR50 scores). The ranking of the drugs when given without DMARD was certolizumab (ranked highest), etanercept, tocilizumab/ abatacept and adalimumab. The ranking of the drugs when given with DMARD was certolizumab (ranked highest), tocilizumab, anakinra, rituximab, golimumab/ infliximab/ abatacept, adalimumab/ etanercept. Still, all drugs were effective. All biologic agents were effective compared to placebo, with certolizumab the most effective and adalimumab (without DMARD treatment) and adalimumab/ etanercept (combined with DMARD treatment) the least effective. The drugs were in general more effective, except for etanercept, when given together with DMARDs. PMID:26356639

  16. The complete genome sequences of poxviruses isolated from a penguin and a pigeon in South Africa and comparison to other sequenced avipoxviruses

    PubMed Central

    2014-01-01

    Background Two novel avipoxviruses from South Africa have been sequenced, one from a Feral Pigeon (Columba livia) (FeP2) and the other from an African penguin (Spheniscus demersus) (PEPV). We present a purpose-designed bioinformatics pipeline for analysis of next generation sequence data of avian poxviruses and compare the different avipoxviruses sequenced to date with specific emphasis on their evolution and gene content. Results The FeP2 (282 kbp) and PEPV (306 kbp) genomes encode 271 and 284 open reading frames respectively and are more closely related to one another (94.4%) than to either fowlpox virus (FWPV) (85.3% and 84.0% respectively) or Canarypox virus (CNPV) (62.0% and 63.4% respectively). Overall, FeP2, PEPV and FWPV have syntenic gene arrangements; however, major differences exist throughout their genomes. The most striking difference between FeP2 and the FWPV-like avipoxviruses is a large deletion of ~16 kbp from the central region of the genome of FeP2 deleting a cc-chemokine-like gene, two Variola virus B22R orthologues, an N1R/p28-like gene and a V-type Ig domain family gene. FeP2 and PEPV both encode orthologues of vaccinia virus C7L and Interleukin 10. PEPV contains a 77 amino acid long orthologue of Ubiquitin sharing 97% amino acid identity to human ubiquitin. Conclusions The genome sequences of FeP2 and PEPV have greatly added to the limited repository of genomic information available for the Avipoxvirus genus. In the comparison of FeP2 and PEPV to existing sequences, FWPV and CNPV, we have established insights into African avipoxvirus evolution. Our data supports the independent evolution of these South African avipoxviruses from a common ancestral virus to FWPV and CNPV. PMID:24919868

  17. Sequence analysis of frog alpha B-crystallin cDNA: sequence homology and evolutionary comparison of alpha A, alpha B and heat shock proteins.

    PubMed

    Lu, S F; Pan, F M; Chiou, S H

    1995-11-22

    alpha-Crystallin is a major lens protein present in the lenses of all vertebrate species. Recent studies have revealed that bovine alpha-crystallins possess genuine chaperone activity similar to small heat-shock proteins. In order to facilitate the determination of the primary sequence of amphibian alpha B-crystallin, cDNA encoding alpha B subunit chain was amplified using a new "Rapid Amplification of cDNA Ends" (RACE) protocol of Polymerase Chain Reaction (PCR). PCR-amplified product corresponding to alpha B subunit was then subcloned into pUC18 vector and transformed into E. coli strain JM109. Plasmids purified from the positive clones were prepared for nucleotide sequencing by the automatic fluorescence-based dideoxynucleotide chain-termination method. Sequencing more than five clones containing DNA inserts coding for alpha B-crystallin subunit constructed only one complete full-length reading frame of 522 base pairs similar to that of alpha A subunit, covering a deduced protein sequence of 173 amino acids including the universal translation-initiating methionine. The frog alpha B crystallin shows 69, 66 and 56% whereas alpha A crystallin shows 83, 81 and 69% sequence similarity to the homologous chains of bovine, chicken and dogfish, respectively, revealing a more divergent structural relationship among these alpha B subunits as compared to alpha A subunits. Structural analysis and comparison of alpha A- and alpha B-crystallin subunits from eye lenses of different classes of vertebrates also shed some light on the evolutionary relatedness between alpha B/alpha A crystallins and the small heat-shock proteins.

  18. Evolutionary connections of biological kingdoms based on protein and nucleic acid sequence evidence

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.

    1983-01-01

    Prokaryotic and eukaryotic evolutionary trees are developed from protein and nucleic-acid sequences by the methods of numerical taxonomy. Trees are presented for bacterial ferredoxins, 5S ribosomal RNA, c-type cytochromes , cytochromes c2 and c', and 5.8S ribosomal RNA; the implications for early evolution are discussed; and a composite tree showing the branching of the anaerobes, aerobes, archaebacteria, and eukaryotes is shown. Single lines are found for all oxygen-evolving photosynthetic forms and for the salt-loving and high-temperature forms of archaebacteria. It is argued that the eukaryote mitochondria, chloroplasts, and cytoplasmic host material are descended from free-living prokaryotes that formed symbiotic associations, with more than one symbiotic event involved in the evolution of each organelle.

  19. An experimental study for biological nitrogen removal and control strategies in a sequencing batch reactor (SBR).

    PubMed

    Manga, J; Venegas, C; Palma-Acosta, M J; Abad, D

    2007-07-01

    The aim of this work is to present an overview about an experimental study for biological nitrogen removal implemented in a pilot-scale plant, located in the Universidad Del Norte in Barranquilla, Colombia. This plant was studied in two different periods. The first period, which was carried out in 90 days, was dedicated to study the influence of the daily variations on the influent and effluent wastewater, and prove some control routines for nitrogen removal. In the second period, which was carried out in 120 days, the removal process was optimized with the addition of acetic acid as an external carbon source, and the implementation of the final control strategy was performed based on the results of the previous period.

  20. An experimental study for biological nitrogen removal and control strategies in a sequencing batch reactor (SBR).

    PubMed

    Manga, J; Venegas, C; Palma-Acosta, M J; Abad, D

    2007-07-01

    The aim of this work is to present an overview about an experimental study for biological nitrogen removal implemented in a pilot-scale plant, located in the Universidad Del Norte in Barranquilla, Colombia. This plant was studied in two different periods. The first period, which was carried out in 90 days, was dedicated to study the influence of the daily variations on the influent and effluent wastewater, and prove some control routines for nitrogen removal. In the second period, which was carried out in 120 days, the removal process was optimized with the addition of acetic acid as an external carbon source, and the implementation of the final control strategy was performed based on the results of the previous period. PMID:17674653

  1. Protein sequence comparisons show that the 'pseudoproteases' encoded by poxviruses and certain retroviruses belong to the deoxyuridine triphosphatase family.

    PubMed Central

    McGeoch, D J

    1990-01-01

    Amino acid sequence comparisons show extensive similarities among the deoxyuridine triphosphatases (dUTPases) of Escherichia coli and of herpesviruses, and the 'protease-like' or 'pseudoprotease' sequences encoded by certain retroviruses in the oncovirus and lentivirus families and by poxviruses. These relationships suggest strongly that the 'pseudoproteases' actually are dUTPases, and have not arisen by duplication of an oncovirus protease gene as had been suggested. The herpesvirus dUTPase sequences differ from the others in that they are longer (about 370 residues, against around 140) and one conserved element ('Motif 3') is displaced relative to its position in the other sequences; a model involving internal duplication of the herpesvirus gene can account effectively for these observations. Sequences closely similar to Motif 3 are also found in phosphofructokinases, where they form part of the active site and fructose phosphate binding structure; thus these sequences may represent a class of structural element generally involved in phosphate transfer to and from glycosides. PMID:2165588

  2. Quantification of layered patterns with structural anisotropy: a comparison of biological and geological systems.

    PubMed

    Smolyar, I; Bromage, T; Wikelski, M

    2016-03-01

    Large-scale patterns evident from satellite images of aeolian landforms on Earth and other planets; those of intermediate scale in marine and terrestrial sand ripples and sediment profiles; and small-scale patterns such as lamellae in the bones of vertebrates and annuli in fish scales are each represented by layers of different thicknesses and lengths. Layered patterns are important because they form a record of the state of internal and external factors that regulate pattern formation in these geological and biological systems. It is therefore potentially possible to recognize trends, periodicities, and events in the history of the formation of these systems among the incremental sequences. Though the structures and sizes of these 2-D patterns are typically scale-free, they are also characteristically anisotropic; that is, the number of layers and their absolute thicknesses vary significantly during formation. The aim of the present work is to quantify the structure of layered patterns and to reveal similarities and differences in the processing and interpretation of layered landforms and biological systems. To reach this goal we used N-partite graph and Boolean functions to quantify the structure of layers and plot charts for "layer thickness vs. layer number" and "layer area vs. layer number". These charts serve as a source of information about events in the history of formation of layered systems. The concept of synchronization of layer formation across a 2-D plane is introduced to develop the procedure for plotting "layer thickness vs. layer number" and "layer area vs. layer number", which takes into account the structural anisotropy of layered patterns and increase signal-to-noise ratio in charts. Examples include landforms on Mars and Earth and incremental layers in human and iguana bones.

  3. Quantification of layered patterns with structural anisotropy: a comparison of biological and geological systems.

    PubMed

    Smolyar, I; Bromage, T; Wikelski, M

    2016-03-01

    Large-scale patterns evident from satellite images of aeolian landforms on Earth and other planets; those of intermediate scale in marine and terrestrial sand ripples and sediment profiles; and small-scale patterns such as lamellae in the bones of vertebrates and annuli in fish scales are each represented by layers of different thicknesses and lengths. Layered patterns are important because they form a record of the state of internal and external factors that regulate pattern formation in these geological and biological systems. It is therefore potentially possible to recognize trends, periodicities, and events in the history of the formation of these systems among the incremental sequences. Though the structures and sizes of these 2-D patterns are typically scale-free, they are also characteristically anisotropic; that is, the number of layers and their absolute thicknesses vary significantly during formation. The aim of the present work is to quantify the structure of layered patterns and to reveal similarities and differences in the processing and interpretation of layered landforms and biological systems. To reach this goal we used N-partite graph and Boolean functions to quantify the structure of layers and plot charts for "layer thickness vs. layer number" and "layer area vs. layer number". These charts serve as a source of information about events in the history of formation of layered systems. The concept of synchronization of layer formation across a 2-D plane is introduced to develop the procedure for plotting "layer thickness vs. layer number" and "layer area vs. layer number", which takes into account the structural anisotropy of layered patterns and increase signal-to-noise ratio in charts. Examples include landforms on Mars and Earth and incremental layers in human and iguana bones. PMID:27441261

  4. Comparison of base composition analysis and Sanger sequencing of mitochondrial DNA for four U.S. population groups.

    PubMed

    Kiesler, Kevin M; Coble, Michael D; Hall, Thomas A; Vallone, Peter M

    2014-01-01

    A set of 711 samples from four U.S. population groups was analyzed using a novel mass spectrometry based method for mitochondrial DNA (mtDNA) base composition profiling. Comparison of the mass spectrometry results with Sanger sequencing derived data yielded a concordance rate of 99.97%. Length heteroplasmy was identified in 46% of samples and point heteroplasmy was observed in 6.6% of samples in the combined mass spectral and Sanger data set. Using discrimination capacity as a metric, Sanger sequencing of the full control region had the highest discriminatory power, followed by the mass spectrometry base composition method, which was more discriminating than Sanger sequencing of just the hypervariable regions. This trend is in agreement with the number of nucleotides covered by each of the three assays.

  5. Attenuation of very virulent infectious bursal disease virus and comparison of full sequences of virulent and attenuated strains.

    PubMed

    Lazarus, D; Pasmanik-Chor, M; Gutter, B; Gallili, G; Barbakov, M; Krispel, S; Pitcovski, J

    2008-04-01

    A very virulent strain of infectious bursal disease virus (IBDVks) was isolated from the bursae of Fabricius of IBDV-affected broiler chickens. Following 43 serial passages in specific pathogen-free embryonated eggs, an attenuated strain was established (IBDVmb). Dosages of IBDVmb in the range 10(2) to 10(4) embryo infective dose of 50% were found to be safe and protective for commercial chicks. Chickens vaccinated with live vaccine containing IBDVmb responded with precipitating and type-specific neutralizing antibodies, and were immune to subsequent challenge with a very virulent IBDV. IBDVmb has been used as an attenuated vaccine throughout the world since 1993. A comparison of the full sequences of the virulent and attenuated strains (IBDVks and IBDVmb, respectively) revealed seven nucleotides that were different, four of them leading to changes in the amino-acid sequence. Comparison of the protein sequence of these strains and published sequences of very virulent and attenuated phenotypes lead us to suggest that the novel difference responsible for virulence of the Israeli strains are: residue 272 (VP2, very conserved site) and residue 527 (VP4), both in segment A, and in segment B (VP1) residues 96 and 161 (both conserved). Our study strengthens the possibility that more than one protein is involved in IBDV attenuation. In all reports, including ours, virulence was reduced without affecting antigenicity of the neutralizing epitopes in VP2. This could have practical implications for attenuated-vaccine development.

  6. Effect of redox conditions on pharmaceutical loss during biological wastewater treatment using sequencing batch reactors.

    PubMed

    Stadler, Lauren B; Su, Lijuan; Moline, Christopher J; Ernstoff, Alexi S; Aga, Diana S; Love, Nancy G

    2015-01-23

    We lack a clear understanding of how wastewater treatment plant (WWTP) process parameters, such as redox environment, impact pharmaceutical fate. WWTPs increasingly install more advanced aeration control systems to save energy and achieve better nutrient removal performance. The impact of redox condition, and specifically the use of microaerobic (low dissolved oxygen) treatment, is poorly understood. In this study, the fate of a mixture of pharmaceuticals and several of their transformation products present in the primary effluent of a local WWTP was assessed in sequencing batch reactors operated under different redox conditions: fully aerobic, anoxic/aerobic, and microaerobic (DO concentration ≈0.3mg/L). Among the pharmaceuticals that were tracked during this study (atenolol, trimethoprim, sulfamethoxazole, desvenlafaxine, venlafaxine, and phenytoin), overall loss varied between them and between redox environments. Losses of atenolol and trimethoprim were highest in the aerobic reactor; sulfamethoxazole loss was highest in the microaerobic reactors; and phenytoin was recalcitrant in all reactors. Transformation products of sulfamethoxazole and desvenlafaxine resulted in the reformation of their parent compounds during treatment. The results suggest that transformation products must be accounted for when assessing removal efficiencies and that redox environment influences the degree of pharmaceutical loss.

  7. Molecular biological identification of Babesia, Theileria, and Anaplasma species in cattle in Egypt using PCR assays, gene sequence analysis and a novel DNA microarray.

    PubMed

    El-Ashker, Maged; Hotzel, Helmut; Gwida, Mayada; El-Beskawy, Mohamed; Silaghi, Cornelia; Tomaso, Herbert

    2015-01-30

    In this preliminary study, a novel DNA microarray system was tested for the diagnosis of bovine piroplasmosis and anaplasmosis in comparison with microscopy and PCR assay results. In the Dakahlia Governorate, Egypt, 164 cattle were investigated for the presence of piroplasms and Anaplasma species. All investigated cattle were clinically examined. Blood samples were screened for the presence of blood parasites using microscopy and PCR assays. Seventy-one animals were acutely ill, whereas 93 were apparently healthy. In acutely ill cattle, Babesia/Theileria species (n=11) and Anaplasma marginale (n=10) were detected. Mixed infections with Babesia/Theileria spp. and A. marginale were present in two further cases. A. marginale infections were also detected in apparently healthy subjects (n=23). The results of PCR assays were confirmed by DNA sequencing. All samples that were positive by PCR for Babesia/Theileria spp. gave also positive results in the microarray analysis. The microarray chips identified Babesia bovis (n=12) and Babesia bigemina (n=2). Cattle with babesiosis were likely to have hemoglobinuria and nervous signs when compared to those with anaplasmosis that frequently had bloody feces. We conclude that clinical examination in combination with microscopy are still very useful in diagnosing acute cases of babesiosis and anaplasmosis, but a combination of molecular biological diagnostic assays will detect even asymptomatic carriers. In perspective, parallel detection of Babesia/Theileria spp. and A. marginale infections using a single microarray system will be a valuable improvement.

  8. Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing

    PubMed Central

    Piñero, Janet; Berenstein, Ariel; Gonzalez-Perez, Abel; Chernomoretz, Ariel; Furlong, Laura I.

    2016-01-01

    Characterizing the behavior of disease genes in the context of biological networks has the potential to shed light on disease mechanisms, and to reveal both new candidate disease genes and therapeutic targets. Previous studies addressing the network properties of disease genes have produced contradictory results. Here we have explored the causes of these discrepancies and assessed the relationship between the network roles of disease genes and their tolerance to deleterious germline variants in human populations leveraging on: the abundance of interactome resources, a comprehensive catalog of disease genes and exome variation data. We found that the most salient network features of disease genes are driven by cancer genes and that genes related to different types of diseases play network roles whose centrality is inversely correlated to their tolerance to likely deleterious germline mutations. This proved to be a multiscale signature, including global, mesoscopic and local network centrality features. Cancer driver genes, the most sensitive to deleterious variants, occupy the most central positions, followed by dominant disease genes and then by recessive disease genes, which are tolerant to variants and isolated within their network modules. PMID:27080396

  9. Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing.

    PubMed

    Harris, J Kirk; Sahl, Jason W; Castoe, Todd A; Wagner, Brandie D; Pollock, David D; Spear, John R

    2010-06-01

    Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel. PMID:20418443

  10. A comparison of magnetic resonance imaging sequences in evaluating pathological changes in the canine spinal cord.

    PubMed

    Adamiak, Z; Pomianowski, A; Zhalniarovich, Y; Kwiatkowska, M; Jaskólska, M; Bocheńska, A

    2011-01-01

    This paper discusses 28 canine patients subjected to low-field magnetic resonance imaging (MRI) of the spinal cord for neurological indications. The authors describe and compare the used MRI sequences with an indication of the most effective sequences in MRI examinations that require short scanning time. The most effective sequences supporting a quick diagnosis of spinal diseases in dogs were SE (spin echo), FSE (fast spin echo) and 3D HYCE (hybrid contrast enhancement). PMID:21957746

  11. Complete Genome Sequence of the Pokeweed Mosaic Virus (PkMV)-New Jersey Isolate and Its Comparison to PkMV-MD and PkMV-PA.

    PubMed

    Di, Rong

    2016-09-08

    Pokeweed mosaic virus (PkMV) causes systemically mosaic symptoms on pokeweed (Phytolacca americana L.) plants. The genome of the PkMV-NJ (New Jersey) isolate was cloned by PCR and sequenced by the Sanger sequencing method. The sequence comparison indicates that PkMV-NJ is more divergent from the other two sequenced isolates, PkMV-MD and PkMV-PA.

  12. Complete Genome Sequence of the Pokeweed Mosaic Virus (PkMV)-New Jersey Isolate and Its Comparison to PkMV-MD and PkMV-PA

    PubMed Central

    2016-01-01

    Pokeweed mosaic virus (PkMV) causes systemically mosaic symptoms on pokeweed (Phytolacca americana L.) plants. The genome of the PkMV-NJ (New Jersey) isolate was cloned by PCR and sequenced by the Sanger sequencing method. The sequence comparison indicates that PkMV-NJ is more divergent from the other two sequenced isolates, PkMV-MD and PkMV-PA. PMID:27609914

  13. Complete Genome Sequence of the Pokeweed Mosaic Virus (PkMV)-New Jersey Isolate and Its Comparison to PkMV-MD and PkMV-PA.

    PubMed

    Di, Rong

    2016-01-01

    Pokeweed mosaic virus (PkMV) causes systemically mosaic symptoms on pokeweed (Phytolacca americana L.) plants. The genome of the PkMV-NJ (New Jersey) isolate was cloned by PCR and sequenced by the Sanger sequencing method. The sequence comparison indicates that PkMV-NJ is more divergent from the other two sequenced isolates, PkMV-MD and PkMV-PA. PMID:27609914

  14. Application of MLST and pilus gene sequence comparisons to investigate the population structures of Actinomyces naeslundii and Actinomyces oris.

    PubMed

    Henssge, Uta; Do, Thuy; Gilbert, Steven C; Cox, Steven; Clark, Douglas; Wickström, Claes; Ligtenberg, A J M; Radford, David R; Beighton, David

    2011-01-01

    Actinomyces naeslundii and Actinomyces oris are members of the oral biofilm. Their identification using 16S rRNA sequencing is problematic and better achieved by comparison of metG partial sequences. A. oris is more abundant and more frequently isolated than A. naeslundii. We used a multi-locus sequence typing approach to investigate the genotypic diversity of these species and assigned A. naeslundii (n = 37) and A. oris (n = 68) isolates to 32 and 68 sequence types (ST), respectively. Neighbor-joining and ClonalFrame dendrograms derived from the concatenated partial sequences of 7 house-keeping genes identified at least 4 significant subclusters within A. oris and 3 within A. naeslundii. The strain collection we had investigated was an under-representation of the total population since at least 3 STs composed of single strains may represent discrete clusters of strains not well represented in the collection. The integrity of these sub-clusters was supported by the sequence analysis of fimP and fimA, genes coding for the type 1 and 2 fimbriae, respectively. An A. naeslundii subcluster was identified with both fimA and fimP genes and these strains were able to bind to MUC7 and statherin while all other A. naeslundii strains possessed only fimA and did not bind to statherin. An A. oris subcluster harboured a fimA gene similar to that of Actinomyces odontolyticus but no detectable fimP failed to bind significantly to either MUC7 or statherin. These data are evidence of extensive genotypic and phenotypic diversity within the species A. oris and A. naeslundii but the status of the subclusters identified here will require genome comparisons before their phylogenic position can be unequivocally established.

  15. Comparison of Sequencing Platforms for Single Nucleotide Variant Calls in a Human Sample

    PubMed Central

    Miller, Webb; Guillory, Joseph; Stinson, Jeremy; Seshagiri, Somasekar

    2013-01-01

    Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required. PMID:23405114

  16. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

    PubMed Central

    Lelieveld, Stefan H.; Spielmann, Malte; Mundlos, Stefan; Veltman, Joris A.

    2015-01-01

    ABSTRACT For next‐generation sequencing technologies, sufficient base‐pair coverage is the foremost requirement for the reliable detection of genomic variants. We investigated whether whole‐genome sequencing (WGS) platforms offer improved coverage of coding regions compared with whole‐exome sequencing (WES) platforms, and compared single‐base coverage for a large set of exome and genome samples. We find that WES platforms have improved considerably in the last years, but at comparable sequencing depth, WGS outperforms WES in terms of covered coding regions. At higher sequencing depth (95x–160x), WES successfully captures 95% of the coding regions with a minimal coverage of 20x, compared with 98% for WGS at 87‐fold coverage. Three different assessments of sequence coverage bias showed consistent biases for WES but not for WGS. We found no clear differences for the technologies concerning their ability to achieve complete coverage of 2,759 clinically relevant genes. We show that WES performs comparable to WGS in terms of covered bases if sequenced at two to three times higher coverage. This does, however, go at the cost of substantially more sequencing biases in WES approaches. Our findings will guide laboratories to make an informed decision on which sequencing platform and coverage to choose. PMID:25973577

  17. Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

    PubMed

    Ratan, Aakrosh; Miller, Webb; Guillory, Joseph; Stinson, Jeremy; Seshagiri, Somasekar; Schuster, Stephan C

    2013-01-01

    Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required.

  18. Comparison of Biological Effectiveness of Carbon-Ion Beams in Japan and Germany

    SciTech Connect

    Uzawa, Akiko; Ando, Koichi Koike, Sachiko; Furusawa, Yoshiya; Matsumoto, Yoshitaka; Takai, Nobuhiko; Hirayama, Ryoichi; Watanabe, Masahiko; Scholz, Michael; Elsaesser, Thilo; Peschke, Peter

    2009-04-01

    Purpose: To compare the biological effectiveness of 290 MeV/amu carbon-ion beams in Chiba, Japan and in Darmstadt, Germany, given that different methods for beam delivery are used for each. Methods and Materials: Murine small intestine and human salivary gland tumor (HSG) cells exponentially growing in vitro were irradiated with 6-cm width of spread-out Bragg peaks (SOBPs) adjusted to achieve nearly identical beam depth-dose profiles at the Heavy-Ion Medical Accelerator in Chiba, and the SchwerIonen Synchrotron in Darmstadt. Cell kill efficiencies of carbon ions were measured by colony formation for HSG cells and jejunum crypts survival in mice. Cobalt-60 {gamma} rays were used as the reference radiation. Isoeffective doses at given survivals were used for relative biological effectiveness (RBE) calculations and interinstitutional comparisons. Results: Isoeffective D{sub 10} doses (mean {+-} standard deviation) of HSG cells ranged from 2.37 {+-} 0.14 Gy to 3.47 {+-} 0.19 Gy for Chiba and from 2.31 {+-} 0.11 Gy to 3.66 {+-} 0.17 Gy for Darmstadt. Isoeffective D{sub 10} doses of gut crypts after single doses ranged from 8.25 {+-} 0.17 Gy to 10.32 {+-} 0.14 Gy for Chiba and from 8.27 {+-} 0.10 Gy to 10.27 {+-} 0.27 Gy for Darmstadt, whereas isoeffective D{sub 30} doses after three fractionated doses were 9.89 {+-} 0.17 Gy through 13.70 {+-} 0.54 Gy and 10.14 {+-} 0.20 Gy through 13.30 {+-} 0.41 Gy for Chiba and Darmstadt, respectively. Overall difference of RBE between the two facilities was 0-5% or 3-7% for gut crypt survival or HSG cell kill, respectively. Conclusion: The carbon-ion beams at the National Institute of Radiological Sciences in Chiba, Japan and the Gesellschaft fuer Schwerionenforschung in Darmstadt, Germany are biologically identical after single and daily fractionated irradiation.

  19. Comparison Between a Rapid Biological Screening Method (EPA 4425) for TCDDs/TCDFs and Chemical Analytical Methods

    SciTech Connect

    Anderson, Jack W.; Jones, Jennifer M.; McCoy, Daniel L.; Fujita, Akira; Yamamoto, Taichi; Iijima, Satoshi

    2003-08-01

    Seven polychlorinated dibenzo-p-dioxins (PCDDs), ten polychlorinated dibenzofurans (PCDFs) as well as twelve polychlorinated biphenyls (PCBs) are collectively referred to as dioxin-like compounds. The World Health Organization toxic equivalency factors (TEFs) for these persistent chlorinated organic compounds and their measured concentrations are used to produce the toxic equivalency quotient (TEQ) of a sample. TEF values are partially based on a common mechanism involving binding of the chemical to the aryl hydrocarbon receptor (AhR). Biological methods for the determination of TEQs are based on the assumption that all dioxin-related compounds act through the Ah receptor signal transduction pathway. Based on the biochemical response of CYP1A activation via the AhR, in vitro systems that utilize a reporter gene under transcriptional control of CYP1A have been developed. Several investigations have reported on the success of utilizing biological test systems to detect PCDDs, PCDFs, PCBs in environmental samples. The P450 Human Reporter Gene System assay (EPA Method 4425) utilizes a human hepatoma cell line (HepG2) in which a plasmid containing the human CYP1A1 promoter and 5'-flanking sequences with three xenobiotic responsive elements (XREs) fused to the luciferase reporter gene. The enzyme luciferase is produced in the presence of compounds that bind the XREs, and can be detected by a simple assay that measures relative light units with a luminometer. Method 4425, used by Columbia Analytical Services (CAS), has gained acceptance as a rapid and inexpensive approach for screening solvent extracts of environmental samples of soil, sediment, tissue, and water to detect compounds that activate the AhR. Investigations in the U. S. and Japan comparing the results of 4425 and standard high-resolution GC/MS (HRGC/HRMS) will be reported here. The purpose of making these comparisons is to determine if risk assessments for large dioxin sites both before and after remediation

  20. Pleistocene glaciation of volcano Ajusco, central Mexico, and comparison with the standard Mexican glacial sequence

    NASA Astrophysics Data System (ADS)

    White, Sidney E.; Valastro, Salvatore

    1984-01-01

    Three Pleistocene glaciations and two Holocene Neoglacial advances occurred on volcano Ajusco in central Mexico. Lateral moraines of the oldest glaciation, the Marqués, above 3250 m are made of light-gray indurated till and are extensively modified by erosion. Below 3200 m the till is dark red, decomposed, and buried beneath volcanic colluvium and tephra. Very strongly to strongly developed soil profiles (Inceptisols) have formed in the Marqués till and in overlying colluvia and tephra. Large sharp-crested moraines of the second glaciation, the Santo Tomás, above 3300 m are composed of pale-brown firm till and are somewhat eroded by gullies. Below 3250 m the till is light reddish brown, cemented, and weathered. Less-strongly developed soil profiles (Inceptisols) have formed in the Santo Tomás till and in overlying colluvia and tephra. Narrow-crested moraines of yellowish-brown loose till of the third glaciation, the Albergue, are uneroded. Weakly developed soil profiles (Inceptisols) in the Albergue till have black ash in the upper horizon. Two small Neoglacial moraines of yellowish-brown bouldery till on the cirque floor of the largest valley support weakly developed soil profiles with only A and Cox horizons and no ash in the upper soil horizons. Radiocarbon dating of organic matter of the B horizons developed in tills, volcanic ash, and colluvial volcanic sand includes ages for both the soil-organic residue and the humic-acid fraction, with differences from 140 to 660 yr. The dating provides minimum ages of about 27,000 yr for the Marqués glaciation and about 25,000 yr for the Santo Tomás glaciation. Dates for the overlying tephra indicate a complex volcanic history for at least another 15,000 yr. Comparison of the Ajusco glacial sequence with that on Iztaccíhuatl to the east suggests that the Marqués and Santo Tomás glaciations may be equivalent to the Diamantes glaciation First and Second advances, the Albergue to the Alcalican glaciations, and the

  1. Technologically important extremophile 16S rRNA sequence Shannon entropy and fractal property comparison with long term dormant microbes

    NASA Astrophysics Data System (ADS)

    Holden, Todd; Gadura, N.; Dehipawala, S.; Cheung, E.; Tuffour, M.; Schneider, P.; Tremberger, G., Jr.; Lieberman, D.; Cheung, T.

    2011-10-01

    Technologically important extremophiles including oil eating microbes, uranium and rocket fuel perchlorate reduction microbes, electron producing microbes and electrode electrons feeding microbes were compared in terms of their 16S rRNA sequences, a standard targeted sequence in comparative phylogeny studies. Microbes that were reported to have survived a prolonged dormant duration were also studied. Examples included the recently discovered microbe that survives after 34,000 years in a salty environment while feeding off organic compounds from other trapped dead microbes. Shannon entropy of the 16S rRNA nucleotide composition and fractal dimension of the nucleotide sequence in terms of its atomic number fluctuation analyses suggest a selected range for these extremophiles as compared to other microbes; consistent with the experience of relatively mild evolutionary pressure. However, most of the microbes that have been reported to survive in prolonged dormant duration carry sequences with fractal dimension between 1.995 and 2.005 (N = 10 out of 13). Similar results are observed for halophiles, red-shifted chlorophyll and radiation resistant microbes. The results suggest that prolonged dormant duration, in analogous to high salty or radiation environment, would select high fractal 16S rRNA sequences. Path analysis in structural equation modeling supports a causal relation between entropy and fractal dimension for the studied 16S rRNA sequences (N = 7). Candidate choices for high fractal 16S rRNA microbes could offer protection for prolonged spaceflights. BioBrick gene network manipulation could include extremophile 16S rRNA sequences in synthetic biology and shed more light on exobiology and future colonization in shielded spaceflights. Whether the high fractal 16S rRNA sequences contain an asteroidlike extra-terrestrial source could be speculative but interesting.

  2. Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses.

    PubMed

    Siering, P L; Ghiorse, W C

    1996-01-01

    Phase-contrast light microscopy revealed that only one of eight cultivated strains belonging to the Sphaerotilus-Leptothrix group of sheathed bacteria actually produced a sheath in standard growth media. Two Sphaerotilus natans strains produced branched cells, but other morphological characteristics that were used to identify these bacteria were consistent with previously published descriptions. Genomic fingerprints, which were obtained by performing PCR amplification with primers corresponding to enterobacterial repetitive intergenic consensus sequences, were useful for distinguishing between the genera Sphaerotilus and Leptothrix, as well as among individual strains. The complete 16S ribosomal DNA (rDNA) sequences of two strains of "Leptothrix discophora" (strains SP-6 and SS-1) were determined. In addition, partial sequences (approximately 300 nucleotides) of one strain of Leptothrix cholodnii (strain LMG 7171), an unidentified Leptothrix strain (strain NC-1), and four strains of Sphaerotilus natans (strains ATCC 13338T [T = type strain], ATCC 15291, ATCC 29329, and ATCC 29330) were determined. We found that two of the S. natans strains (ATCC 15291 and ATCC 13338T), which differed in morphology and in their genomic fingerprints, had identical sequences in the 300-nucleotide region sequenced. Both parsimony and distance matrix methods were used to infer the evolutionary relationships of the eight strains in a comparison of the 16S rDNA sequences of these organisms with 16S rDNA sequences obtained from ribosomal sequence databases. All of the strains clustered in the Rubrivivax subdivision of the beta subclass of the Proteobacteria, which confirmed previously published conclusions concerning selected individual strains. Additional analyses revealed that all of the S. natans strains clustered in one closely related group, while the Leptothrix strains clustered in two separate lineages that were approximately equidistant from the S. natans cluster. This finding

  3. Phylogeny of the Sphaerotilus-Leptothrix group inferred from morphological comparisons, genomic fingerprinting, and 16S ribosomal DNA sequence analyses.

    PubMed

    Siering, P L; Ghiorse, W C

    1996-01-01

    Phase-contrast light microscopy revealed that only one of eight cultivated strains belonging to the Sphaerotilus-Leptothrix group of sheathed bacteria actually produced a sheath in standard growth media. Two Sphaerotilus natans strains produced branched cells, but other morphological characteristics that were used to identify these bacteria were consistent with previously published descriptions. Genomic fingerprints, which were obtained by performing PCR amplification with primers corresponding to enterobacterial repetitive intergenic consensus sequences, were useful for distinguishing between the genera Sphaerotilus and Leptothrix, as well as among individual strains. The complete 16S ribosomal DNA (rDNA) sequences of two strains of "Leptothrix discophora" (strains SP-6 and SS-1) were determined. In addition, partial sequences (approximately 300 nucleotides) of one strain of Leptothrix cholodnii (strain LMG 7171), an unidentified Leptothrix strain (strain NC-1), and four strains of Sphaerotilus natans (strains ATCC 13338T [T = type strain], ATCC 15291, ATCC 29329, and ATCC 29330) were determined. We found that two of the S. natans strains (ATCC 15291 and ATCC 13338T), which differed in morphology and in their genomic fingerprints, had identical sequences in the 300-nucleotide region sequenced. Both parsimony and distance matrix methods were used to infer the evolutionary relationships of the eight strains in a comparison of the 16S rDNA sequences of these organisms with 16S rDNA sequences obtained from ribosomal sequence databases. All of the strains clustered in the Rubrivivax subdivision of the beta subclass of the Proteobacteria, which confirmed previously published conclusions concerning selected individual strains. Additional analyses revealed that all of the S. natans strains clustered in one closely related group, while the Leptothrix strains clustered in two separate lineages that were approximately equidistant from the S. natans cluster. This finding

  4. Biological degradation of catechol in wastewater using the sequencing continuous-inflow reactor (SCR).

    PubMed

    Aghapour, Ali Ahmad; Moussavi, Gholamreza; Yaghmaeian, Kamyar

    2013-05-24

    Catechol is used in many industries. It can be removed from wastewater by various methods but biological processes are the most superior and commonly used technology. The SCR is a modified form of SBR used to degrade catechol. The objective of this study was to investigate the performance of SCR for biodegradation and mineralization of catechol under various inlet concentrations (630-1500 mg/L) and hydraulic retention times (HRT) (18-9 h). This study used a bench scale SCR setup to test catechol degradation. The acclimation time of biomass for catechol at degradation at 630 mg/L was 41 d. The SCR operating cycle time was 6 h and the consecutive times taken for aerating, settling and decanting were 4, 1.5 and 0.5 h, respectively. This study investigated the effects of inlet catechol concentration (630-1560 mg/L) and HRT (18-9 h). The average catechol removal efficiencies in steady-state conditions of 630, 930, 12954 and 1559 mg/L of catechol were 98.5%, 98.5%, 98.2% and 96.9% in terms catechol and 97.8%, 97.7%, 96.4% and 94.3% for COD, respectively. SCR with acclimated biomasses could effectively remove the catechol and the corresponding COD from wastewater with concentrations of up to 1560, at the loading rate of 5.38 kg COD/m3.d and at a HRT of up to 13 h. The HRT was determined as an important variable affecting catechol removal from wastewater. Reducing the HRT to below 13 h led to reduced removal of catechol and COD.

  5. Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.

    PubMed

    Tyler, Andrea D; Christianson, Sara; Knox, Natalie C; Mabon, Philip; Wolfe, Joyce; Van Domselaar, Gary; Graham, Morag R; Sharma, Meenu K

    2016-01-01

    The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis. Our results confirm that MTB NGS data quality is highly dependent on the purity of the DNA sample submitted for sequencing and its guanine-cytosine content (or GC-content). Our data additionally demonstrate that the choice of library preparation method plays an important role in mitigating downstream sequencing quality issues. Importantly for MTB, the Illumina TruSeq library preparation kit produces more uniform data quality than the Nextera XT method, regardless of the quality of the input DNA. Furthermore, specific genomic sequence motifs are commonly missed by the Nextera XT method, as are regions of especially high GC-content relative to the rest of the MTB genome. As coverage bias is highly undesirable, this study illustrates the importance of appropriate protocol selection when performing NGS studies in order to ensure that sound inferences can be made regarding mycobacterial genomes. PMID:26849565

  6. Solid-State and Biological Nanopore for Real-Time Sensing of Single Chemical and Sequencing of DNA

    PubMed Central

    Haque, Farzin; Li, Jinghong; Wu, Hai-Chen; Liang, Xing-Jie; Guo, Peixuan

    2013-01-01

    Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed. PMID:23504223

  7. Sequence analysis and comparison of ribosomal DNA from bovine Neospora to similar coccidial parasites.

    PubMed

    Marsh, A E; Barr, B C; Sverlow, K; Ho, M; Dubey, J P; Conrad, P A

    1995-08-01

    The nuclear small subunit ribosomal RNA (nss-rRNA) gene sequence of Neospora spp. isolated from cattle was analyzed and compared to the sequences from several closely related cyst-forming coccidial parasites. Double-stranded DNA sequencing of 5 bovine Neospora spp. isolates (BPA1-4), 2 Neospora caninum isolates (NC-1 and NC-3), and 3 Toxoplasma gondii isolates (RH, GT-1, CT-1) were performed and compared to each other, as well as to other sequences available in GenBank for the NC-1 isolate, Sarcocystis muris, and Cryptosporidium parvum. There were no nucleotide differences detected between the Neospora spp. isolates from cattle and dogs. Four nucleotide differences were consistently detected when sequences of Neospora spp. isolates were compared to those of the T. gondii isolates. These results indicate that Neospora spp. and T. gondii are closely related, but distinct, species.

  8. Comparison of winding-number sequences for symmetric and asymmetric oscillatory systems.

    PubMed

    Englisch, Volker; Parlitz, Ulrich; Lauterborn, Werner

    2015-08-01

    The bifurcation sets of symmetric and asymmetric periodically driven oscillators are investigated and classified by means of winding numbers. It is shown that periodic windows within chaotic regions are forming winding-number sequences on different levels. These sequences can be described by a simple formula that makes it possible to predict winding numbers at bifurcation points. Symmetric and asymmetric systems follow similar rules for the development of winding numbers within different sequences and these sequences can be combined into a single general rule. The role of the two distinct period-doubling cascades is investigated in the light of the winding-number sequences discovered. Examples are taken from the double-well Duffing oscillator, a special two-parameter Duffing oscillator, and a bubble oscillator. PMID:26382476

  9. How is the serial order of a verbal sequence coded? Some comparisons between models.

    PubMed

    Hitch, Graham J; Fastame, Maria Chiara; Flude, Brenda

    2005-01-01

    Current models of verbal short-term memory (STM) propose various mechanisms for serial order. These include a gradient of activation over items, associations between items, and associations between items and their positions relative to the start or end of a sequence. We compared models using a variant of Hebb's procedure in which immediate serial recall of a sequence improves if the sequence is presented more than once. However, instead of repeating a complete sequence, we repeated different aspects of serial order information common to training lists and a subsequent test list. In Experiment 1, training lists repeated all the item-item pairings in the test list, with or without the position-item pairings in the test list. Substantial learning relative to a control condition was observed only when training lists repeated item-item pairs with position-item pairs, and position was defined relative to the start rather than end of a sequence. Experiment 2 attempted to analyse the basis of this learning effect further by repeating fragments of the test list during training, where fragments consisted of either isolated position-item pairings or clusters of both position-item and item-item pairings. Repetition of sequence fragments led to only weak learning effects. However, where learning was observed it was for specific position-item pairings. We conclude that positional cues play an important role in the coding of serial order in memory but that the information required to learn a sequence goes beyond position-item associations. We suggest that whereas STM for a novel sequence is based on positional cues, learning a sequence involves the development of some additional representation of the sequence as a whole.

  10. A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units.

    PubMed

    Jackson, Matthew A; Bell, Jordana T; Spector, Tim D; Steves, Claire J

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods' ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts' properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. PMID:27635321

  11. A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

    PubMed Central

    Bell, Jordana T.; Spector, Tim D.; Steves, Claire J.

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions. PMID:27635321

  12. A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units

    PubMed Central

    Bell, Jordana T.; Spector, Tim D.; Steves, Claire J.

    2016-01-01

    A variety of methods are available to collapse 16S rRNA gene sequencing reads to the operational taxonomic units (OTUs) used in microbiome analyses. A number of studies have aimed to compare the quality of the resulting OTUs. However, in the absence of a standard method to define and enumerate the different taxa within a microbial community, existing comparisons have been unable to compare the ability of clustering methods to generate units that accurately represent functional taxonomic segregation. We have previously demonstrated heritability of the microbiome and we propose this as a measure of each methods’ ability to generate OTUs representing biologically relevant units. Our approach assumes that OTUs that best represent the functional units interacting with the hosts’ properties will produce the highest heritability estimates. Using 1,750 unselected individuals from the TwinsUK cohort, we compared 11 approaches to OTU clustering in heritability analyses. We find that de novo clustering methods produce more heritable OTUs than reference based approaches, with VSEARCH and SUMACLUST performing well. We also show that differences resulting from each clustering method are minimal once reads are collapsed by taxonomic assignment, although sample diversity estimates are clearly influenced by OTU clustering approach. These results should help the selection of sequence clustering methods in future microbiome studies, particularly for studies of human host-microbiome interactions.

  13. Balbiani ring DNA: sequence comparisons and evolutionary history of a family of hierarchically repetitive protein-coding genes.

    PubMed

    Pustell, J; Kafatos, F C; Wobus, U; Bäumlein, H

    1984-01-01

    All known types of Balbiani ring (BR) genes consist of multiple, tandemly arranged, ca. 180 to 300-bp repeat units that can be divided into a constant region and a subrepeat region. The latter region includes short tandem subrepeats (SRs). Comparison of all available BR sequences using computer methods has enabled us (a) to define more precisely the constant and subrepeat regions, (b) to infer the evolutionary relationships among the various types of BR repeats, (c) to derive a consensus approximation of an ancestral sequence from a small segment of which the highly diverse present-day SRs may have originated, and (d) to detect an underlying substructure in the constant region, evident in the consensus but not in the present-day sequences and possibly corresponding to an original 39-bp DNA segment from which the extant, giant BR sequences may have evolved. We discuss the processes of reduplication, diversification, and homogenization within the hierarchically repetitive BR sequences as examples of how a simple DNA element may evolve into a diverse family of large, protein-coding genes.

  14. Application of Two-Part Statistics for Comparison of Sequence Variant Counts

    PubMed Central

    Wagner, Brandie D.; Robertson, Charles E.; Harris, J. Kirk

    2011-01-01

    Investigation of microbial communities, particularly human associated communities, is significantly enhanced by the vast amounts of sequence data produced by high throughput sequencing technologies. However, these data create high-dimensional complex data sets that consist of a large proportion of zeros, non-negative skewed counts, and frequently, limited number of samples. These features distinguish sequence data from other forms of high-dimensional data, and are not adequately addressed by statistical approaches in common use. Ultimately, medical studies may identify targeted interventions or treatments, but lack of analytic tools for feature selection and identification of taxa responsible for differences between groups, is hindering advancement. The objective of this paper is to examine the application of a two-part statistic to identify taxa that differ between two groups. The advantages of the two-part statistic over common statistical tests applied to sequence count datasets are discussed. Results from the t-test, the Wilcoxon test, and the two-part test are compared using sequence counts from microbial ecology studies in cystic fibrosis and from cenote samples. We show superior performance of the two-part statistic for analysis of sequence data. The improved performance in microbial ecology studies was independent of study type and sequence technology used. PMID:21629788

  15. A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples

    PubMed Central

    2010-01-01

    Background We have compared mutation analysis by DNA sequencing and Amplification Refractory Mutation System™ (ARMS™) for their ability to detect mutations in clinical biopsy specimens. Methods We have evaluated five real-time ARMS assays: BRAF 1799T>A, [this includes V600E and V600K] and NRAS 182A>G [Q61R] and 181C>A [Q61K] in melanoma, EGFR 2573T>G [L858R], 2235-2249del15 [E746-A750del] in non-small-cell lung cancer, and compared the results to DNA sequencing of the mutation 'hot-spots' in these genes in formalin-fixed paraffin-embedded tumour (FF-PET) DNA. Results The ARMS assays maximised the number of samples that could be analysed when both the quality and quantity of DNA was low, and improved both the sensitivity and speed of analysis compared with sequencing. ARMS was more robust with fewer reaction failures compared with sequencing and was more sensitive as it was able to detect functional mutations that were not detected by DNA sequencing. DNA sequencing was able to detect a small number of lower frequency recurrent mutations across the exons screened that were not interrogated using the specific ARMS assays in these studies. Conclusions ARMS was more sensitive and robust at detecting defined somatic mutations than DNA sequencing on clinical samples where the predominant sample type was FF-PET. PMID:20925915

  16. Comparison with Magnetic Resonance Three-Dimensional Sequence for Lumbar Nerve Root with Intervertebral Foramen

    PubMed Central

    Takashima, Hiroyuki; Shishido, Hiroki; Yoshimoto, Mitsunori; Imamura, Rui; Akatsuka, Yoshihiro; Terashima, Yoshinori; Fujiwara, Hiroyoshi; Nagae, Masateru; Kubo, Toshikazu; Yamashita, Toshihiko

    2016-01-01

    Study Design Prospective study based on magnetic resonance (MR) imaging of the lumbar spinal root of the intervertebral foramen. Purpose This study was to compare MR three-dimensional (3D) sequences for the evaluation of the lumbar spinal root of the intervertebral foramen. Overview of Literature The diagnosis of spinal disorders by MR imaging is commonly performed using two-dimensional T1- and T2-weighted images, whereas 3D MR images can be used for acquiring further detailed data using thin slices with multi-planar reconstruction. Methods On twenty healthy volunteers, we investigated the contrast-to-noise ratio (CNR) of the lumbar spinal root of the intervertebral foramen with a 3D balanced sequence. The sequences used were the fast imaging employing steady state acquisition and the coherent oscillatory state acquisition for the manipulation of image contrast (COSMIC). COSMIC can be used with or without fat suppression (FS). We compared these sequence to determine the optimized visualization sequence for the lumbar spinal root of the intervertebral foramen. Results For the CNR between the nerve root and the peripheral tissue, these were no significant differences between the sequences at the entry of foramen. There was a significant difference and the highest CNR was seen with COSMIC-FS for the intra- and extra-foramen. Conclusions In this study, the findings suggest that the COSMIC-FS sequences should be used for the internal or external foramen for spinal root disorders. PMID:26949459

  17. The nucleotide sequence of the mitochondrial DNA molecule of the grey seal, Halichoerus grypus, and a comparison with mitochondrial sequences of other true seals.

    PubMed

    Arnason, U; Gullberg, A; Johnsson, E; Ledje, C

    1993-10-01

    The sequence of the mtDNA of the grey seal, Halichoerus grypus, was determined. The length of the molecule was 16,797 base pairs. The organization of the molecule conformed with that of other eutherian mammals but the control region was unusually long due to the presence of two types of repeated motifs. The grey seal and the previously reported harbor seal, Phoca vitulina, belong to different but closely related genera of family Phocidae, true (or earless) seals. In order to determine the degree of differences that may occur between mtDNAs of closely related mammalian genera, the 2 rRNA genes, the 13 peptide coding genes, and the 22 tRNA genes of the 2 species were compared. Total nucleotide difference in the peptide coding genes was 2.0-6.1%. The range of conservative difference was 0.0-1.5%. In the inferred peptide sequences the amino acid difference was 0.0-4.5%, and the difference with respect to chemical properties of amino acids was 0.0-3.0%. A gene that showed a limited degree of difference in one mode of comparison did not necessarily show a corresponding limited difference in another mode. The ratio for differences in codon positions 1, 2, and 3 was approximately 2.7:1:16. The corresponding ratio for conservative differences was approximately 1.8:1.1:1. The evolutionary separation of the two species was calculated to have taken place 2-2.5 million years ago. This dating gives the figure approximately 8 x 10(-9) as the mean rate of substitution per site and year in the entire mtDNA molecule. Comparison with the cytochrome b gene of the Hawaiian monk seal and the Weddell seal suggested that the lineage of these two species and that of the grey and harbor seals separated approximately 8 million years ago. PMID:8308902

  18. Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes

    SciTech Connect

    Gihring, Thomas; Green, Stefan; Schadt, Christopher Warren

    2011-01-01

    Technologies for massively parallel sequencing are revolutionizing microbial ecology and are vastly increasing the scale of ribosomal RNA (rRNA) gene studies. Although pyrosequencing has increased the breadth and depth of possible rRNA gene sampling, one drawback is that the number of reads obtained per sample is difficult to control. Pyrosequencing libraries typically vary widely in the number of sequences per sample, even within individual studies, and there is a need to revisit the behaviour of richness estimators and diversity indices with variable gene sequence library sizes. Multiple reports and review papers have demonstrated the bias in non-parametric richness estimators (e.g. Chao1 and ACE) and diversity indices when using clone libraries. However, we found that biased community comparisons are accumulating in the literature. Here we demonstrate the effects of sample size on Chao1, ACE, CatchAll, Shannon, Chao-Shen and Simpson's estimations specifically using pyrosequencing libraries. The need to equalize the number of reads being compared across libraries is reiterated, and investigators are directed towards available tools for making unbiased diversity comparisons.

  19. Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

    PubMed Central

    Devailly, Guillaume; Mantsoki, Anna; Joshi, Anagha

    2016-01-01

    Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats. Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/. Source code: https://github.com/gdevailly. Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27378302

  20. Statistical physics inspired methods to assign statistical significance in bioinformatics and proteomics: From sequence comparison to mass spectrometry based peptide sequencing

    NASA Astrophysics Data System (ADS)

    Alves, Gelio

    After the sequencing of many complete genomes, we are in a post-genomic era in which the most important task has changed from gathering genetic information to organizing the mass of data as well as under standing how components interact with each other. The former is usually undertaking using bioinformatics methods, while the latter task is generally termed proteomics. Success in both parts demands correct statistical significance assignments for results found. In my dissertation. I study two concrete examples: global sequence alignment statistics and peptide sequencing/identification using mass spectrometry. High-performance liquid chromatography coupled to a mass spectrometer (HPLC/MS/MS), enabling peptide identifications and thus protein identifications, has become the tool of choice in large-scale proteomics experiments. Peptide identification is usually done by database searches methods. The lack of robust statistical significance assignment among current methods motivated the development of a novel de novo algorithm, RAId, whose score statistics then provide statistical significance for high scoring peptides found in our custom, enzyme-digested peptide library. The ease of incorporating post-translation modifications is another important feature of RAId. To organize the massive protein/DNA data accumulated, biologists often cluster proteins according to their similarity via tools such as sequence alignment. Homologous proteins share similar domains. To assess the similarity of two domains usually requires alignment from head to toe, ie. a global alignment. A good alignment score statistics with an appropriate null model enable us to distinguish the biologically meaningful similarity from chance similarity. There has been much progress in local alignment statistics, which characterize score statistics when alignments tend to appear as a short segment of the whole sequence. For global alignment, which is useful in domain alignment, there is still much room for

  1. A test of mink microsatellite markers in the ferret: amplification and sequence comparisons.

    PubMed

    Anistoroaei, R; Christensen, K

    2006-12-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variation at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite markers from American mink were tested in the ferret, under the same conditions as for the mink. Of the 59, 43 of them (73.5%) amplified a ferret sequence; 5 amplification products differed in size from the respective mink sequences. Ten amplified fragments from ferret were sequenced. The sequences that were identical in size to those from mink displayed a high degree of conservation, with some differences at the repeat motif sites. These results could aid cross-utilization of markers between these two species. PMID:17362355

  2. Evaluating the genomic and sequence integrity of human ES cell lines; comparison to normal genomes.

    PubMed

    Funk, Walter D; Labat, Ivan; Sampathkumar, Janani; Gourraud, Pierre-Antoine; Oksenberg, Jorge R; Rosler, Elen; Steiger, Daniel; Sheibani, Nadia; Caillier, Stacy; Stache-Crain, Birgit; Johnson, Julie A; Meisner, Lorraine; Lacher, Markus D; Chapman, Karen B; Park, Myung Jin; Shin, Kyoung-Jin; Drmanac, Rade; West, Michael D

    2012-03-01

    Copy number variation (CNV) is a common chromosomal alteration that can occur during in vitro cultivation of human cells and can be accompanied by the accumulation of mutations in coding region sequences. We describe here a systematic application of current molecular technologies to provide a detailed understanding of genomic and sequence profiles of human embryonic stem cell (hESC) lines that were derived under GMP-compliant conditions. We first examined the overall chromosomal integrity using cytogenetic techniques to determine chromosome count, and to detect the presence of cytogenetically aberrant cells in the culture (mosaicism). Assays of copy number variation, using both microarray and sequence-based analyses, provide a detailed view genomic variation in these lines and shows that in early passage cultures of these lines, the size range and distribution of CNVs are entirely consistent with those seen in the genomes of normal individuals. Similarly, genome sequencing shows variation within these lines that is completely within the range seen in normal genomes. Important gene classes, such as tumor suppressors and genetic disease genes, do not display overtly disruptive mutations that could affect the overall safety of cell-based therapeutics. Complete sequence also allows the analysis of important transplantation antigens, such as ABO and HLA types. The combined application of cytogenetic and molecular technologies provides a detailed understanding of genomic and sequence profiles of GMP produced ES lines for potential use as therapeutic agents. PMID:22265736

  3. Sequence analysis and comparison of cDNAs of the zein multigene family .

    PubMed Central

    Geraghty, D E; Messing, J; Rubenstein, I

    1982-01-01

    The nucleotide sequence of two zein cDNAs in hybrid plasmids A20 and B49 have been determined. The insert in A20 is 921 bp long including a 5' non-coding region of 60 nucleotides, preceded by what is believed to be an artifactual sequence of 41 nucleotides, and a 3' non-coding region of 87 nucleotides. The B49 insert is 467 bp long and includes approximately one-half the protein coding sequence as well as a 3' non-coding region of 97 nucleotides. These sequences have been compared with the previously published sequence of another zein clone, A30 . A20 and A30 , both encoding 19 000 mol. wt. zeins , have approximately 85% homology at the nucleotide level. The B49 sequence, corresponding to a 22 000 mol. wt. zein, has approximately 65% homology to either A20 or A30 . All three zeins share common features including nearly identical amino acid compositions. In addition, the tandem repeats of 20 amino acids first seen in A30 are also present in A20 and B49 . PMID:6897917

  4. AGenDA: gene prediction by cross-species sequence comparison.

    PubMed

    Taher, Leila; Rinner, Oliver; Garg, Saurabh; Sczyrba, Alexander; Morgenstern, Burkhard

    2004-07-01

    Automatic gene prediction is one of the major challenges in computational sequence analysis. Traditional approaches to gene finding rely on statistical models derived from previously known genes. By contrast, a new class of comparative methods relies on comparing genomic sequences from evolutionary related organisms to each other. These methods are based on the concept of phylogenetic footprinting: they exploit the fact that functionally important regions in genomic sequences are usually more conserved than non-functional regions. We created a WWW-based software program for homology-based gene prediction at BiBiServ (Bielefeld Bioinformatics Server). Our tool takes pairs of evolutionary related genomic sequences as input data, e.g. from human and mouse. The server runs CHAOS and DIALIGN to create an alignment of the input sequences and subsequently searches for conserved splicing signals and start/stop codons near regions of local sequence conservation. Genes are predicted based on local homology information and splice signals. The server returns predicted genes together with a graphical representation of the underlying alignment. The program is available at http://bibiserv.TechFak.Uni-Bielefeld.DE/agenda/.

  5. Biological diversity of created forested wetlands in comparison to reference forested wetlands in the Bay watershed

    USGS Publications Warehouse

    Perry, M.C.; Osenton, P.C.; Stoll, C.S.; Therres, Glenn D.

    2001-01-01

    Amphibians, reptiles, birds, and mammals were surveyed at six created forested wetlands in central Maryland and at six adjacent reference forested wetlands during 1993-1996 to determine comparative biological diversity of these habitats. Amphibians and reptiles were caught in pitfall and funnel traps associated with 15.4m (50 ft) drift fences. Birds were surveyed with a complete count while walking through each area. Mammals were surveyed by capture in live traps. More species and total individuals of amphibians were caught on the reference wetlands than on the created wetlands. The red-backed salamander (Plethodon cinereus), the four-toed salamander (Hemidactylium scutatum), the eastern spadefoot (Scaphiopus holbrooki), and the wood frog (Rana sylvatica) were captured on the reference wetlands, but not on the created sites. The wood frog was captured at all reference sites and may represent the best amphibian species to characterize a forested wetland. Reptiles were not caught in sufficient numbers to warrant comparisons. Ninety-two bird species were recorded on created sites and 55 bird species on the reference sites. Bird species on the created sites represented those typically found in nonforested habitats. Mammal species were similar on both sites, but overall the reference sites had three times the number caught on created sites. The meadow vole (Microtus pennsylvanicus) was the dominant species captured on created sites, and the white-footed mouse (Peromyscus leucopus) was the dominant species on reference sites, with little habitat overlap for these two species. Although species richness and total number of animals were high for created forested wetlands, these survey results show major differences from species expected for a forested wetland. The created forested wetlands appear to provide good habitat for wildlife, but are probably not providing the full functions and values of the forested wetlands that they were constructed to replace.

  6. Comparison of Biological and Immunological Characterization of Lipopolysaccharides From Brucella abortus RB51 and S19

    PubMed Central

    Kianmehr, Zahra; Kaboudanian Ardestani, Sussan; Soleimanjahi, Hoorieh; Fotouhi, Fatemeh; Alamian, Saeed; Ahmadian, Shahin

    2015-01-01

    Background: Brucella abortus RB51 is a rough stable mutant strain, which has been widely used as a live vaccine for prevention of brucellosis in cattle instead of B. abortus strain S19. B. abortus lipopolysaccharide (LPS) has unique properties in comparison to other bacterial LPS. Objectives: In the current study, two types of LPS, smooth (S-LPS) and rough (R-LPS) were purified from B. abortus S19 and RB51, respectively. The aim of this study was to evaluate biological and immunological properties of purified LPS as an immunogenical determinant. Materials and Methods: Primarily, S19 and RB51 LPS were extracted and purified by two different modifications of the phenol water method. The final purity of LPS was determined by chemical analysis (2-keto-3-deoxyoctonate (KDO), glycan, phosphate and protein content) and different staining methods, following sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). C57BL/6 mice were immunized subcutaneously three times at biweekly intervals with the same amount of purified LPSs. The humoral immunity was evaluated by measuring specific IgG levels and also different cytokine levels, such as IFN-γ, TNF-α, IL-4 and IL-10, were determined for assessing T-cell immune response. Results: Biochemical analysis data and SDS-PAGE profile showed that the chemical nature of S19 LPS is different from RB51 LPS. Both S and R-LPS induce an immune response. T-cell immune response induced by both S and R-LPS had almost the same pattern whereas S19 LPS elicited humoral immunity, which was higher than RB51 LPS. Conclusions: Purified LPS can be considered as a safe adjuvant and can be used as a component in prophylactic and therapeutic vaccines targeting infectious disease, cancer and allergies. PMID:26862376

  7. Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample

    PubMed Central

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T.

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ∼90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R2>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ∼1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ∼3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies. PMID:22347999

  8. HBOC multi-gene panel testing: comparison of two sequencing centers.

    PubMed

    Schroeder, Christopher; Faust, Ulrike; Sturm, Marc; Hackmann, Karl; Grundmann, Kathrin; Harmuth, Florian; Bosse, Kristin; Kehrer, Martin; Benkert, Tanja; Klink, Barbara; Mackenroth, Luisa; Betcheva-Krajcir, Elitza; Wimberger, Pauline; Kast, Karin; Heilig, Mechthilde; Nguyen, Huu Phuc; Riess, Olaf; Schröck, Evelin; Bauer, Peter; Rump, Andreas

    2015-07-01

    Multi-gene panels are used to identify genetic causes of hereditary breast and ovarian cancer (HBOC) in large patient cohorts. This study compares the diagnostic workflow in two centers and gives valuable insights into different next-generation sequencing (NGS) strategies. Moreover, we present data from 620 patients sequenced at both centers. Both sequencing centers are part of the German consortium for hereditary breast and ovarian cancer (GC-HBOC). All 620 patients included in this study were selected following standard BRCA1/2 testing guidelines. A set of 10 sequenced genes was analyzed per patient. Twelve samples were exchanged and sequenced at both centers. NGS results were highly concordant in 12 exchanged samples (205/206 variants = 99.51 %). One non-pathogenic variant was missed at center B due to a sequencing gap (no technical coverage). The custom enrichment at center B was optimized during this study; for example, the average number of missing bases was reduced by a factor of four (vers. 1: 1939.41, vers. 4: 506.01 bp). There were no sequencing gaps at center A, but four CCDS exons were not included in the enrichment. Pathogenic mutations were found in 12.10 % (75/620) of all patients: 4.84 % (30/620) in BRCA1, 4.35 % in BRCA2 (27/620), 0.97 % in CHEK2 (6/620), 0.65 % in ATM (4/620), 0.48 % in CDH1 (3/620), 0.32 % in PALB2 (2/620), 0.32 % in NBN (2/620), and 0.16 % in TP53 (1/620). NGS diagnostics for HBOC-related genes is robust, cost effective, and the method of choice for genetic testing in large cohorts. Adding 8 genes to standard BRCA1- and BRCA2-testing increased the mutation detection rate by one-third. PMID:26022348

  9. Cloning, sequencing, and expression of the Zymomonas mobilis fructokinase gene and structural comparison of the enzyme with other hexose kinases.

    PubMed Central

    Zembrzuski, B; Chilco, P; Liu, X L; Liu, J; Conway, T; Scopes, R

    1992-01-01

    The frk gene encoding the enzyme fructokinase (fructose 6-phosphotransferase [EC 2.7.1.4]) from Zymomonas mobilis has been isolated on a partial TaqI digest fragment of the genome and sequenced. An open reading frame of 906 bp corresponding to 302 amino acids was identified on a 3-kbp TaqI fragment. The deduced amino acid sequence corresponds to the first 20 amino acids (including an N-terminal methionine) determined by amino acid sequencing of the purified protein. The 118 bp preceding the methionine codon on this fragment does not appear to contain a promoter sequence. There was weak expression of the active enzyme in the recombinant Escherichia coli clone under control of the lac promoter on the pUC plasmid. Comparison of the amino acid sequence with that of the glucokinase enzyme (EC 2.7.1.2) from Z. mobilis reveals relatively little homology, despite the fact that fructokinase also binds glucose and has kinetic and structural properties similar to those of glucokinase. Also, there is little homology with hexose kinases that have been sequenced from other organisms. Northern (RNA) blot analysis showed that the frk transcript is 1.2 kb long. Fructokinase activity is elevated up to twofold when Z. mobilis was grown on fructose instead of glucose, and there was a parallel increase in frk mRNA levels. Differential mRNA stability was not a factor, since the half-lives of the frk transcript were 6.2 min for glucose-grown cells and 6.6 min for fructose-grown cells. Images PMID:1317376

  10. Comparison of hepatocellular carcinoma miRNA expression profiling as evaluated by next generation sequencing and microarray.

    PubMed

    Murakami, Yoshiki; Tanahashi, Toshihito; Okada, Rina; Toyoda, Hidenori; Kumada, Takashi; Enomoto, Masaru; Tamori, Akihiro; Kawada, Norifumi; Taguchi, Y-h; Azuma, Takeshi

    2014-01-01

    MicroRNA (miRNA) expression profiling has proven useful in diagnosing and understanding the development and progression of several diseases. Microarray is the standard method for analyzing miRNA expression profiles; however, it has several disadvantages, including its limited detection of miRNAs. In recent years, advances in genome sequencing have led to the development of next-generation sequencing (NGS) technologies, which significantly advance genome sequencing speed and discovery. In this study, we compared the expression profiles obtained by next generation sequencing (NGS) with the profiles created using microarray to assess if NGS could produce a more accurate and complete miRNA profile. Total RNA from 14 hepatocellular carcinoma tumors (HCC) and 6 matched non-tumor control tissues were sequenced with Illumina MiSeq 50-bp single-end reads. Micro RNA expression profiles were estimated using miRDeep2 software. As a comparison, miRNA expression profiles for 11 out of 14 HCCs were also established by microarray (Agilent human microRNA microarray). The average total sequencing exceeded 2.2 million reads per sample and of those reads, approximately 57% mapped to the human genome. The average correlation for miRNA expression between microarray and NGS and subtraction were 0.613 and 0.587, respectively, while miRNA expression between technical replicates was 0.976. The diagnostic accuracy of HCC, p-value, and AUC were 90.0%, 7.22×10(-4), and 0.92, respectively. In summary, NGS created an miRNA expression profile that was reproducible and comparable to that produced by microarray. Moreover, NGS discovered novel miRNAs that were otherwise undetectable by microarray. We believe that miRNA expression profiling by NGS can be a useful diagnostic tool applicable to multiple fields of medicine.

  11. Comparison and analysis of the nucleotide sequences of pilin genes from Haemophilus influenzae type b strains Eagan and M43.

    PubMed Central

    Forney, L J; Marrs, C F; Bektesh, S L; Gilsdorf, J R

    1991-01-01

    Previous studies have demonstrated antigenic differences among the pili expressed by various strains of Haemophilus influenzae type b (Hib). In order to understand the molecular basis for these differences, the structural gene for pilin was cloned from Hib strain Eagan (p+) and the nucleotide sequence was compared to those of strains M43 (p+) and 770235 b0f+, which had been previously determined. The pilin gene of Hib strain Eagan (p+) had a 648-bp open reading frame that encoded a 20-amino-acid leader sequence followed by the 196 amino acids found in mature pilin. The translated sequence was three amino acids larger than pilins of strains M43 (p+) and 770235 b0f+ and was 78% identical and 95% homologous when conservative amino acid substitutions were considered. Differences between the amino acid sequences were not localized to any one region but rather were distributed throughout the proteins. Comparison of protein hydrophilicity profiles showed several hydrophilic regions with sequences that were conserved between strain Eagan (p+) and pilins of other Hib strains, and these regions represent potentially conserved antigenic domains. Southern blot analyses using an intragenic probe from the pilin gene of strain Eagan (p+) showed that the pilin gene was conserved among all type b and nontypeable strains of H. influenzae examined, and only a single copy was present in these strains. Homologous genes were not present in the phylogenetically related species Pasteurella multocida, Pasteurella haemolytica, and Actinobacillus pleuropneumoniae. These data indicate that the pilin gene was highly conserved among different strains of H. influenzae and that small differences in the pilin amino acid sequences account for the observed antigenic differences of assembled pili from these strains. Images PMID:2037360

  12. Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?

    PubMed Central

    Fetrow, Jacquelyn S.; Siew, Naomi; Di Gennaro, Jeannine A.; Martinez-Yamout, Maria; Dyson, H. Jane; Skolnick, Jeffrey

    2001-01-01

    A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false-positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone. PMID:11316881

  13. Drosophila melanogaster mitochondrial DNA: completion of the nucleotide sequence and evolutionary comparisons.

    PubMed

    Lewis, D L; Farr, C L; Kaguni, L S

    1995-11-01

    The nucleotide sequence of the regions flanking the A+T region of Drosophila melanogaster mitochondrial DNA (mtDNA) has been determined. Included are the genes encoding the transfer RNAs for valine, isoleucine, glutamine and methionine, the small ribosomal RNA and the 5'-coding sequences of the large ribosomal RNA and NADH dehydrogenase subunit II. This completes the nucleotide sequence of the D. melanogaster mitochondrial genome. The circular mtDNA of D. melanogaster varies in size among different populations largely due to length differences in the control region (Fauron & Wolstenholme, 1976; Fauron & Wolstenholme, 1980a, b); the mtDNA region we have sequenced, combined with those sequenced by others, yields a composite genome that is 19,517 bp in length as compared to 16,019 bp for the mtDNA of D. yakuba. D. melanogaster mtDNA exhibits an extreme bias in base composition; it comprises 82.2% deoxyadenylate and thymidylate residues as compared to 78.6% in D. yakuba mtDNA. All genes encoded in the mtDNA of both species are in identical locations and orientations. Nucleotide substitution analysis reveals that tRNA and rRNA genes evolve at less than half the rate of protein coding genes.

  14. Ossification sequence of the avian order anseriformes, with comparison to other precocial birds.

    PubMed

    Maxwell, Erin E

    2008-09-01

    Ossification sequences are poorly known for most amniotes, and yet they represent an important source of morphogenetic, phylogenetic, and life history information. Here, the author describes the ossification sequences of three ducks, the Common Eider Somateria mollissima dresseri, the Pekin Duck Anas platyrhynchos, and the Muscovy Duck Cairina moschata. Sequence differences exist both within and among these species, but are generally minor. The Common Eider has the most ossified skeleton prior to hatching, contrary to what is expected in a subarctic migrant species. This may be attributed to a tradeoff between growth rate and locomotory performance. Growth rate is higher in hatchlings with more cartilaginous skeletons, but this may compromise locomotion. No major ossification sequence differences were observed in the craniofacial skeleton when compared with Galliformes, which suggests that the influence of adult morphology on ossification sequence might be relatively minor in many taxa. Galliformes and Anseriformes, while both highly ossified at hatching, differ in the location of their late-stage ossification centers. In Anseriformes, these are most often located in the appendicular skeleton, whereas in Galliformes they are in the thoracic region and form the ventilatory apparatus.

  15. Comparison of sequences formed in Marine sabkha (subaerial) and salina (Subaqueous) settings-modern and ancient

    SciTech Connect

    Warren, J.K.; St. Kendall, C.G.

    1985-06-01

    Marine evaporites occurring in modern subaqueous (salina) settings and subaerial (sabkha) settings are different. Subaqueous Holocene evaporites occur as shoalingupward lacustrine sequences up to 10 m thick. They are evaporite dominated and are composed primarily of bottom-nucleated crystals that may be deposited as massive, laminated, or rippled units. Each coastal lake is dominated by laminated evaporites with subordinate carbonate sediments. In plan view, they show a well-developed bull's-eye pattern with a sulfate center and a carbonate rim. In contrast, subaerial (sabkha) evaporites occur as part of a laterally prograding, shoaling-upward, peritidal sequence in which the supratidal unit is usually no more than 1 m thick. Sabkha sequences are matrix dominated, not evaporite dominated, with the bulk of the sulfate phase occurring as diagenetic nodules, enteroliths, or diapirlike structures. These sulfates were formed during syndepositional diagenesis by replacement and displacement processes. The various facies of the sequence tend to accumulate in belts parallel with the shoreline. Relative to the sea level or the brine level, sabkhas tend to form over paleotopographic highs whereas salinas tend to occur in paleotopographic lows. Some of the characteristics that distinguish Holocene subaerial and subaqueous evaporite sequences can be used to do the same for similar ancient facies, even when gypsum has been converted to nodular anhydrite. The distinction is important for it can be used by explorationists in the oil industry to define the paleotopography of the associated underlying porous and nonporous carbonates.

  16. A comparison of virus genome sequences with their host silkworm, Bombyx mori.

    PubMed

    Tang, Xu-Dong; Yue, Ya-Jie; Wang, Wei; Li, Nan; Shen, Zhong-Yuan

    2016-01-15

    With the recent availability of the genomes of many viruses and the silkworm, Bombyx mori, as well as a variety of Basic Local Alignment Search Tool (BLAST) programs, a new opportunity to gain insight into the interaction of viruses with the silkworm is possible. This study aims to determine the possible existence of sequence identities between the genomes of viruses and the silkworm and attempts to explain this phenomenon. BLAST searches of the genomes of viruses against the silkworm genome were performed using the resources of the National Center for Biotechnology Information. All studied viruses contained variable numbers of short regions with sequence identity to the genome of the silkworm. The short regions of sequence identity in the genome of the silkworm may be derived from the genomes of viruses in the long history of silkworm-virus interaction. This study is the first to compare these genomes, and may contribute to research on the interaction between viruses and the silkworm.

  17. Genotypic comparison of five isolates of Rickettsia prowazekii by multilocus sequence typing.

    PubMed

    Ge, Hong; Tong, Min; Jiang, Ju; Dasch, Gregory A; Richards, Allen L

    2007-06-01

    Genetic traits of five Rickettsia prowazekii isolates, including the first from Africa and North America, and representatives from human and flying squirrels were compared using multilocus sequence typing. Four rickettsial genes encoding 17 kDa genus-common antigen (17 kDa gene), citrate synthase (gltA), OmpB immunodominant antigen (ompB) and 120 kDa cytoplasmic antigen (sca4) were examined. Sequence identities of 17 kDa gene and gltA were 100% among the isolates. Limited sequence diversity of ompB (0.02-0.11%) and sca4 (0.03-0.20%) was enough to distinguish the isolates, and evaluation of the combined four genes provided a method to easily differentiate R. prowazekii from other rickettsiae. PMID:17419766

  18. A phylogenetic analysis of the brassicales clade based on an alignment-free sequence comparison method.

    PubMed

    Hatje, Klas; Kollmar, Martin

    2012-01-01

    Phylogenetic analyses reveal the evolutionary derivation of species. A phylogenetic tree can be inferred from multiple sequence alignments of proteins or genes. The alignment of whole genome sequences of higher eukaryotes is a computational intensive and ambitious task as is the computation of phylogenetic trees based on these alignments. To overcome these limitations, we here used an alignment-free method to compare genomes of the Brassicales clade. For each nucleotide sequence a Chaos Game Representation (CGR) can be computed, which represents each nucleotide of the sequence as a point in a square defined by the four nucleotides as vertices. Each CGR is therefore a unique fingerprint of the underlying sequence. If the CGRs are divided by grid lines each grid square denotes the occurrence of oligonucleotides of a specific length in the sequence (Frequency Chaos Game Representation, FCGR). Here, we used distance measures between FCGRs to infer phylogenetic trees of Brassicales species. Three types of data were analyzed because of their different characteristics: (A) Whole genome assemblies as far as available for species belonging to the Malvidae taxon. (B) EST data of species of the Brassicales clade. (C) Mitochondrial genomes of the Rosids branch, a supergroup of the Malvidae. The trees reconstructed based on the Euclidean distance method are in general agreement with single gene trees. The Fitch-Margoliash and Neighbor joining algorithms resulted in similar to identical trees. Here, for the first time we have applied the bootstrap re-sampling concept to trees based on FCGRs to determine the support of the branchings. FCGRs have the advantage that they are fast to calculate, and can be used as additional information to alignment based data and morphological characteristics to improve the phylogenetic classification of species in ambiguous cases.

  19. Comparison of Commercially Available Target Enrichment Methods for Next-Generation Sequencing

    PubMed Central

    Bodi, K.; Perera, A. G.; Adams, P. S.; Bintzler, D.; Dewar, K.; Grove, D. S.; Kieleczawa, J.; Lyons, R. H.; Neubert, T. A.; Noll, A. C.; Singh, S.; Steen, R.; Zianni, M.

    2013-01-01

    Isolating high-priority segments of genomes greatly enhances the efficiency of next-generation sequencing (NGS) by allowing researchers to focus on their regions of interest. For the 2010–11 DNA Sequencing Research Group (DSRG) study, we compared outcomes from two leading companies, Agilent Technologies (Santa Clara, CA, USA) and Roche NimbleGen (Madison, WI, USA), which offer custom-targeted genomic enrichment methods. Both companies were provided with the same genomic sample and challenged to capture identical genomic locations for DNA NGS. The target region totaled 3.5 Mb and included 31 individual genes and a 2-Mb contiguous interval. Each company was asked to design its best assay, perform the capture in replicates, and return the captured material to the DSRG-participating laboratories. Sequencing was performed in two different laboratories on Genome Analyzer IIx systems (Illumina, San Diego, CA, USA). Sequencing data were analyzed for sensitivity, specificity, and coverage of the desired regions. The success of the enrichment was highly dependent on the design of the capture probes. Overall, coverage variability was higher for the Agilent samples. As variant discovery is the ultimate goal for a typical targeted sequencing project, we compared samples for their ability to sequence single-nucleotide polymorphisms (SNPs) as a test of the ability to capture both chromosomes from the sample. In the targeted regions, we detected 2546 SNPs with the NimbleGen samples and 2071 with Agilent's. When limited to the regions that both companies included as baits, the number of SNPs was ∼1000 for each, with Agilent and NimbleGen finding a small number of unique SNPs not found by the other. PMID:23814499

  20. rRNA sequence comparison of Beauveria bassiana, Tolypocladium cylindrosporum, and Tolypocladium extinguens.

    PubMed

    Rakotonirainy, M S; Dutertre, M; Brygoo, Y; Riba, G

    1991-01-01

    Five strains of Tolypocladium cylindrosporum, one strain of Tolypocladium extinguens, and nine strains of Beauveria bassiana were analyzed using a rapid rRNA sequencing technique. The sequences of two highly variable domains (D1 and D2) located at the 5' end of the 28S-like rRNA molecule were determined. The phylogenetic tree computed from the absolute number of nucleotide differences shows the separation between the genus Beauveria and the genus Tolypocladium and points out that T. cylindrosporum and T. extinguens probably do not belong to the same genus.

  1. Genome sequence of "Candidatus Microthrix parvicella" Bio17-1, a long-chain-fatty-acid-accumulating filamentous actinobacterium from a biological wastewater treatment plant.

    PubMed

    Muller, Emilie E L; Pinel, Nicolás; Gillece, John D; Schupp, James M; Price, Lance B; Engelthaler, David M; Levantesi, Caterina; Tandoi, Valter; Luong, Khai; Baliga, Nitin S; Korlach, Jonas; Keim, Paul S; Wilmes, Paul

    2012-12-01

    "Candidatus Microthrix" bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: "Candidatus Microthrix parvicella" strain Bio17-1. PMID:23144412

  2. Genome Sequence of “Candidatus Microthrix parvicella” Bio17-1, a Long-Chain-Fatty-Acid-Accumulating Filamentous Actinobacterium from a Biological Wastewater Treatment Plant

    PubMed Central

    Muller, Emilie E. L.; Pinel, Nicolás; Gillece, John D.; Schupp, James M.; Price, Lance B.; Engelthaler, David M.; Levantesi, Caterina; Tandoi, Valter; Luong, Khai; Baliga, Nitin S.; Korlach, Jonas; Keim, Paul S.

    2012-01-01

    “Candidatus Microthrix” bacteria are deeply branching filamentous actinobacteria which occur at the water-air interface of biological wastewater treatment plants, where they are often responsible for foaming and bulking. Here, we report the first draft genome sequence of a strain from this genus: “Candidatus Microthrix parvicella” strain Bio17-1. PMID:23144412

  3. Assessing the effects of silver nanoparticles on biological nutrient removal in bench-scale activated sludge sequencing batch reactors.

    PubMed

    Alito, Christina L; Gunsch, Claudia K

    2014-01-21

    Consumer products such as clothing and medical products are increasingly integrating silver and silver nanoparticles (AgNPs) into base materials to serve as an antimicrobial agent. Thus, it is critical to assess the effects of AgNPs on wastewater microorganisms essential to biological nutrient removal. In the present study, pulse and continuous additions of 0.2 and 2 ppm gum arabic and citrate coated AgNPs as well as Ag as AgNO3 were fed into sequencing batch reactors (SBRs) inoculated with nitrifying sludge. Treatment efficiency (chemical oxygen demand (COD) and ammonia removal), Ag dissolution measurements, and 16S rRNA bacterial community analyses (terminal restriction fragment length polymorphism, T-RFLP) were performed to evaluate the response of the SBRs to Ag addition. Results suggest that the AgNPs may have been precipitating in the SBRs. While COD and ammonia removal decreased by as much as 30% or greater directly after spikes, SBRs were able to recover within 24 h (3 hydraulic retention times (HRTs)) and resume removal near 95%. T-RFLP results indicate Ag spiked SBRs were similar in a 16s rRNA bacterial community. The results shown in this study indicate that wastewater treatment could be impacted by Ag and AgNPs in the short term but the amount of treatment disruption will depend on the magnitude of influent Ag. PMID:24364625

  4. Temporal sequence learning, prediction, and control: a review of different models and their relation to biological mechanisms.

    PubMed

    Wörgötter, Florentin; Porr, Bernd

    2005-02-01

    In this review, we compare methods for temporal sequence learning (TSL) across the disciplines machine-control, classical conditioning, neuronal models for TSL as well as spike-timing-dependent plasticity (STDP). This review introduces the most influential models and focuses on two questions: To what degree are reward-based (e.g., TD learning) and correlation-based (Hebbian) learning related? and How do the different models correspond to possibly underlying biological mechanisms of synaptic plasticity? We first compare the different models in an open-loop condition, where behavioral feedback does not alter the learning. Here we observe that reward-based and correlation-based learning are indeed very similar. Machine control is then used to introduce the problem of closed-loop control (e.g., actor-critic architectures). Here the problem of evaluative (rewards) versus nonevaluative (correlations) feedback from the environment will be discussed, showing that both learning approaches are fundamentally different in the closed-loop condition. In trying to answer the second question, we compare neuronal versions of the different learning architectures to the anatomy of the involved brain structures (basal-ganglia, thalamus, and cortex) and the molecular biophysics of glutamatergic and dopaminergic synapses. Finally, we discuss the different algorithms used to model STDP and compare them to reward-based learning rules. Certain similarities are found in spite of the strongly different timescales. Here we focus on the biophysics of the different calcium-release mechanisms known to be involved in STDP. PMID:15720770

  5. A review of the prevalence, utility, and caveats of using chloroplast simple sequence repeats for studies of plant biology1

    PubMed Central

    Wheeler, Gregory L.; Dorman, Hanna E.; Buchanan, Alenda; Challagundla, Lavanya; Wallace, Lisa E.

    2014-01-01

    Microsatellites occur in all plant genomes and provide useful markers for studies of genetic diversity and structure. Chloroplast microsatellites (cpSSRs) are frequently targeted because they are more easily isolated than nuclear microsatellites. Here, we quantified the frequency and uses of cpSSRs based on a literature review of over 400 studies published 1995–2013. These markers are an important and economical tool for plant biologists and continue to be used alongside modern genomics approaches to study genetic diversity and structure, evolutionary history, and hybridization in native and agricultural species. Studies using species-specific primers reported a greater number of polymorphic loci than those employing universal primers. A major disadvantage to cpSSRs is fragment size homoplasy; therefore, we documented its occurrence at several cpSSR loci within and between species of Acmispon (Fabaceae). Based on our empirical data set, we recommend targeted sequencing of a subset of samples combined with fragment genotyping as a cost-efficient, data-rich approach to the use of cpSSRs and as a test of homoplasy. The availability of genomic resources for plants aids in the development of primers for new study systems, thereby enhancing the utility of cpSSRs across plant biology. PMID:25506520

  6. Operation and model description of a sequencing batch reactor treating reject water for biological nitrogen removal via nitrite.

    PubMed

    Dosta, J; Galí, A; Benabdallah El-Hadj, T; Macé, S; Mata-Alvarez, J

    2007-08-01

    The aim of this study was the operation and model description of a sequencing batch reactor (SBR) for biological nitrogen removal (BNR) from a reject water (800-900 mg NH(4)(+)-NL(-1)) from a municipal wastewater treatment plant (WWTP). The SBR was operated with three cycles per day, temperature 30 degrees C, SRT 11 days and HRT 1 day. During the operational cycle, three alternating oxic/anoxic periods were performed to avoid alkalinity restrictions. Oxygen supply and working pH range were controlled to achieve the BNR via nitrite, which makes the process more economical. Under steady state conditions, a total nitrogen removal of 0.87 kg N (m(3)day)(-1) was reached. A four-step nitrogen removal model was developed to describe the process. This model enlarges the IWA activated sludge models for a more detailed description of the nitrogen elimination processes and their inhibitions. A closed intermittent-flow respirometer was set up for the estimation of the most relevant model parameters. Once calibrated, model predictions reproduced experimental data accurately. PMID:17292605

  7. Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities

    PubMed Central

    Vivien, Régis; Lejzerowicz, Franck; Pawlowski, Jan

    2016-01-01

    Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities. PMID:26866802

  8. Comparison of Ribotyping and sequence-based typing for discriminating among isolates of Bordetella bronchiseptica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aims: Our goal was to compare the discriminatory power of PvuII ribotyping and MLST using a single set of diverse Bordetella bronchiseptica isolates and to determine whether subtyping based on repeat region sequences of the pertactin gene (prn) provides additional resolution. Methods and Results: ...

  9. Comparison of Computer Vision and Photogrammetric Approaches for Epipolar Resampling of Image Sequence

    PubMed Central

    Kim, Jae-In; Kim, Taejung

    2016-01-01

    Epipolar resampling is the procedure of eliminating vertical disparity between stereo images. Due to its importance, many methods have been developed in the computer vision and photogrammetry field. However, we argue that epipolar resampling of image sequences, instead of a single pair, has not been studied thoroughly. In this paper, we compare epipolar resampling methods developed in both fields for handling image sequences. Firstly we briefly review the uncalibrated and calibrated epipolar resampling methods developed in computer vision and photogrammetric epipolar resampling methods. While it is well known that epipolar resampling methods developed in computer vision and in photogrammetry are mathematically identical, we also point out differences in parameter estimation between them. Secondly, we tested representative resampling methods in both fields and performed an analysis. We showed that for epipolar resampling of a single image pair all uncalibrated and photogrammetric methods tested could be used. More importantly, we also showed that, for image sequences, all methods tested, except the photogrammetric Bayesian method, showed significant variations in epipolar resampling performance. Our results indicate that the Bayesian method is favorable for epipolar resampling of image sequences. PMID:27011186

  10. The 5'-flanking regions of three pea legumin genes: comparison of the DNA sequences.

    PubMed Central

    Lycett, G W; Croy, R R; Shirsat, A H; Richards, D M; Boulter, D

    1985-01-01

    Approximately 1200 nucleotides of sequence data from the promoter and 5'-flanking regions of each of three pea (Pisum sativum L.) legumin genes (legA, legB and legC) are presented. The promoter regions of all three genes were found to be identical including the "TATA box", and "CAAT box', and sequences showing homology to the SV40 enhancers. The legA sequence begins to diverge from the others about 300bp from the start codon, whereas the other two genes remain identical for another 550bp. The regions of partial homology exhibit deletions or insertions and some short, comparatively well conserved sequences. The significance of these features is discussed in terms of evolutionary mechanisms and their possible functional roles. The legC gene contains a region that may potentially form either of two mutually exclusive stem-loop structures, one of which has a stem 42bp long, which suggests that it could be fairly stable. We suggest that a mechanism of switching between such alternative structures may play some role in gene control or may represent the insertion of a transposable element. PMID:2997721

  11. Bovine herpesvirus-1: comparison and differentiation of vaccine and field strains based on genomic sequence variation.

    PubMed

    Fulton, R W; d'Offay, J M; Eberle, R

    2013-03-01

    Bovine herpesvirus-1 (BoHV-1) causes significant disease in cattle including respiratory, fetal diseases, and reproductive tract infections. Control programs usually include vaccination with a modified live viral (MLV) vaccine. On occasion BoHV-1 strains are isolated from diseased animals or fetuses postvaccination. Currently there are no markers for differentiating MLV strains from field strains of BoHV-1. In this study several BoHV-1 strains were sequenced using whole-genome sequencing technologies and the data analyzed to identify single nucleotide polymorphisms (SNPs). Strains sequenced included the reference BoHV-1 Cooper strain (GenBank Accession JX898220), eight commercial MLV vaccine strains, and 14 field strains from cases presented for diagnosis. Based on SNP analyses, the viruses could be classified into groups having similar SNP patterns. The eight MLV strains could be differentiated from one another although some were closely related to each other. A number of field strains isolated from animals with a history of prior vaccination had SNP patterns similar to specific MLV viruses, while other field isolates were very distinct from all vaccine strains. The results indicate that some BoHV-1 isolates from clinically ill cattle/fetuses can be associated with a prior MLV vaccination history, but more information is needed on the rate of BoHV-1 genome sequence change before irrefutable associations can be drawn. PMID:23333211

  12. Comparison of two approaches for the classification of 16S rRNA gene sequences.

    PubMed

    Chatellier, Sonia; Mugnier, Nathalie; Allard, Françoise; Bonnaud, Bertrand; Collin, Valérie; van Belkum, Alex; Veyrieras, Jean-Baptiste; Emler, Stefan

    2014-10-01

    The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods.

  13. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

    PubMed

    Thoendel, Matthew; Jeraldo, Patricio R; Greenwood-Quaintance, Kerryl E; Yao, Janet Z; Chia, Nicholas; Hanssen, Arlen D; Abdel, Matthew P; Patel, Robin

    2016-08-01

    Metagenomic whole genome sequencing for detection of pathogens in clinical samples is an exciting new area for discovery and clinical testing. A major barrier to this approach is the overwhelming ratio of human to pathogen DNA in samples with low pathogen abundance, which is typical of most clinical specimens. Microbial DNA enrichment methods offer the potential to relieve this limitation by improving this ratio. Two commercially available enrichment kits, the NEBNext Microbiome DNA Enrichment Kit and the Molzym MolYsis Basic kit, were tested for their ability to enrich for microbial DNA from resected arthroplasty component sonicate fluids from prosthetic joint infections or uninfected sonicate fluids spiked with Staphylococcus aureus. Using spiked uninfected sonicate fluid there was a 6-fold enrichment of bacterial DNA with the NEBNext kit and 76-fold enrichment with the MolYsis kit. Metagenomic whole genome sequencing of sonicate fluid revealed 13- to 85-fold enrichment of bacterial DNA using the NEBNext enrichment kit. The MolYsis approach achieved 481- to 9580-fold enrichment, resulting in 7 to 59% of sequencing reads being from the pathogens known to be present in the samples. These results demonstrate the usefulness of these tools when testing clinical samples with low microbial burden using next generation sequencing. PMID:27237775

  14. Next-Generation Sequencing of Aquatic Oligochaetes: Comparison of Experimental Communities.

    PubMed

    Vivien, Régis; Lejzerowicz, Franck; Pawlowski, Jan

    2016-01-01

    Aquatic oligochaetes are a common group of freshwater benthic invertebrates known to be very sensitive to environmental changes and currently used as bioindicators in some countries. However, more extensive application of oligochaetes for assessing the ecological quality of sediments in watercourses and lakes would require overcoming the difficulties related to morphology-based identification of oligochaetes species. This study tested the Next-Generation Sequencing (NGS) of a standard cytochrome c oxydase I (COI) barcode as a tool for the rapid assessment of oligochaete diversity in environmental samples, based on mixed specimen samples. To know the composition of each sample we Sanger sequenced every specimen present in these samples. Our study showed that a large majority of OTUs (Operational Taxonomic Unit) could be detected by NGS analyses. We also observed congruence between the NGS and specimen abundance data for several but not all OTUs. Because the differences in sequence abundance data were consistent across samples, we exploited these variations to empirically design correction factors. We showed that such factors increased the congruence between the values of oligochaetes-based indices inferred from the NGS and the Sanger-sequenced specimen data. The validation of these correction factors by further experimental studies will be needed for the adaptation and use of NGS technology in biomonitoring studies based on oligochaete communities. PMID:26866802

  15. Comparison of Computer Vision and Photogrammetric Approaches for Epipolar Resampling of Image Sequence.

    PubMed

    Kim, Jae-In; Kim, Taejung

    2016-03-22

    Epipolar resampling is the procedure of eliminating vertical disparity between stereo images. Due to its importance, many methods have been developed in the computer vision and photogrammetry field. However, we argue that epipolar resampling of image sequences, instead of a single pair, has not been studied thoroughly. In this paper, we compare epipolar resampling methods developed in both fields for handling image sequences. Firstly we briefly review the uncalibrated and calibrated epipolar resampling methods developed in computer vision and photogrammetric epipolar resampling methods. While it is well known that epipolar resampling methods developed in computer vision and in photogrammetry are mathematically identical, we also point out differences in parameter estimation between them. Secondly, we tested representative resampling methods in both fields and performed an analysis. We showed that for epipolar resampling of a single image pair all uncalibrated and photogrammetric methods tested could be used. More importantly, we also showed that, for image sequences, all methods tested, except the photogrammetric Bayesian method, showed significant variations in epipolar resampling performance. Our results indicate that the Bayesian method is favorable for epipolar resampling of image sequences.

  16. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species

    PubMed Central

    Wu, Fengnian; Cen, Yijing; Wallis, Christopher M.; Trumble, John T.; Prager, Sean; Yokomi, Ray; Zheng, Zheng; Deng, Xiaoling; Chen, Jianchi; Liang, Guangwen

    2016-01-01

    Potato psyllid (Bactericera cockerelli) is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit “Candidatus Liberibacter solanacearum”, the putative bacterial pathogen of potato zebra chip (ZC) disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome) sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq). The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli. PMID:27227976

  17. Comparison of the main sequence of reflexive saccades and the quick phases of optokinetic nystagmus

    PubMed Central

    Garbutt, S.; Harwood, M.; Harris, C.

    2001-01-01

    BACKGROUND/AIMS—Abnormalities in the saccadic main sequence are an important finding and may indicate pathology of the ocular motor periphery or central neurological disorders. In young or uncooperative patients it can be difficult eliciting a sufficient number of saccades to measure the main sequence. It is often assumed that the quick phases of optokinetic nystagmus (OKN) are identical to saccades. If this were the case, it would be feasible to use OKN, an involuntary response that is easily evoked, as a simple way of eliciting many saccades. The aim of this study was to determine whether reflexive saccades and the quick phases of OKN are indeed identical, and whether OKN quick phases could have a clinical role in identifying patients with slow saccades.
METHODS—OKN and reflexive saccades were recorded from 10 healthy adults using an infrared limbus eye tracker and bitemporal DC electro-oculography simultaneously. OKN was stimulated by rotating a full field patterned curtain around the subject at 10-50°/s. Reflexive saccades were elicited to red LED targets at 5-20° eccentricity.
RESULTS—OKN quick phases tended to have a longer duration compared to saccades, but these differences were not significant. OKN quick phases had a slightly lower peak velocity compared to saccades, which was statistically significant (p<0.05).
CONCLUSION—The main sequence for duration is the same for reflexive saccades and OKN quick phases. The main sequence for peak velocity is slightly faster for reflexive saccades than OKN quick phases, but the difference is unlikely to be of clinical significance. As an illustration of the potential of this technique, the authors demonstrate that OKN quick phases show similar slowness to saccades in a child with brainstem pathology caused by Gaucher disease type III. It is concluded that recording OKN may be a simple clinical means for approximating the main sequence.

 PMID:11734524

  18. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species.

    PubMed

    Wu, Fengnian; Cen, Yijing; Wallis, Christopher M; Trumble, John T; Prager, Sean; Yokomi, Ray; Zheng, Zheng; Deng, Xiaoling; Chen, Jianchi; Liang, Guangwen

    2016-01-01

    Potato psyllid (Bactericera cockerelli) is an important pest of potato, tomato and pepper. Not only could a toxin secreted by nymphs results in serious phytotoxemia in some host plants, but also over the past few years B. cockerelli was shown to transmit "Candidatus Liberibacter solanacearum", the putative bacterial pathogen of potato zebra chip (ZC) disease, to potato and tomato. ZC has caused devastating losses to potato production in the western U.S., Mexico, and elsewhere. New knowledge of the genetic diversity of the B. cockerelli is needed to develop improved strategies to manage pest populations. Mitochondrial genome (mitogenome) sequencing provides important knowledge about insect evolution and diversity in and among populations. This report provides the first complete B. cockerelli mitogenome sequence as determined by next generation sequencing technology (Illumina MiSeq). The circular B. cockerelli mitogenome had a size of 15,220 bp with 13 protein-coding gene (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a non-coding region of 975 bp. The overall gene order of the B. cockerelli mitogenome is identical to three other published Psylloidea mitogenomes: one species from the Triozidae, Paratrioza sinica; and two species from the Psyllidae, Cacopsylla coccinea and Pachypsylla venusta. This suggests all of these species share a common ancestral mitogenome. However, sequence analyses revealed differences between and among the insect families, in particular a unique region that can be folded into three stem-loop secondary structures present only within the B. cockerelli mitogenome. A phylogenetic tree based on the 13 PCGs matched an existing taxonomy scheme that was based on morphological characteristics. The available complete mitogenome sequence makes it accessible to all genes for future population diversity evaluation of B. cockerelli. PMID:27227976

  19. Interspecific sequence comparison of the muscle-myosin heavy-chain genes from Drosophila hydei and Drosophila melanogaster.

    PubMed

    Miedema, K; Harhangi, H; Mentzel, S; Wilbrink, M; Akhmanova, A; Hooiveld, M; Bindels, P; Hennig, W

    1994-10-01

    The muscle-myosin heavy-chain (mMHC) gene of Drosophila hydei has been sequenced completely (size 23.3 kb). The sequence comparison with the D. melanogaster mMHC gene revealed that the exon-intron pattern is identical. The protein coding regions show a high degree of conservation (97%). The alternatively spliced exons (3a-b, 7a-d, 9a-c, 11a-e, and 15a-b) display more variations in the number of nonsynonymous and synonymous substitutions than the common exons (2, 4, 5, 6, 8, 10, 12, 13, 14, 16, 17, and 19). The base composition at synonymous sites of fourfold degenerate codons (third position) is not biased in the alternative exons. In the common exons there exists a bias for C and against A. These findings imply that the alternative exons of the Drosophila mMHC gene evolve at a different, in several cases higher, rate than the common ones. The 5' splice junctions and 5' and 3' untranslated regions show a high level of similarity, indicating a functional constraint on these sequences. The intron regions vary considerably in length within one species, but the corresponding introns are very similar in length between the two species and all contain stretches of sequence similarity. A particular example is the first intron, which contains multiple regions of similarity. In the conserved regions of intron 12 (head-tail border) sequences were found which have the potential to direct another smaller mMHC transcript.

  20. The mitochondrial DNA sequence specificity of the anti-tumour drug bleomycin using end-labeled DNA and capillary electrophoresis and a comparison with genome-wide DNA sequencing.

    PubMed

    Chung, Long H; Murray, Vincent

    2016-01-01

    The DNA sequence specificity of the cancer chemotherapeutic agent, bleomycin, was investigated in two human mitochondrial DNA sequences. Bleomycin was found to cleave preferentially at 5'-TGT*A-3' DNA sequences (where * is the cleavage site). The bleomycin analysis using capillary electrophoresis with laser-induced fluorescence was determined on both DNA strands and each strand was independently fluorescently labelled at the 3'- and 5'-ends. There was a high level of correlation between the intensity of bleomycin cleavage sites analysed by 3'- and 5'-end labelling. This is the first occasion that a comprehensive comparison has been made between these two end-labelling procedures to quantify cleavage by a DNA damaging agent and to investigate end-label bias. A comparison was also made between the bleomycin DNA sequence specificity obtained from genome-wide next-generation sequencing with that obtained from purified plasmid DNA sequences. This was accomplished by cloning sections of human mitochondrial DNA and comparing these identical mitochondrial DNA in the human mitochondrial genome. At individual sites, there was a very low level of correlation between bleomycin cleavage in plasmid sequencing and genome-wide sequencing. However, the overall bleomycin DNA sequence specificity was very similar in the two environments, namely 5'-TGT*A-3'.

  1. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

    PubMed Central

    Rebolledo-Mendez, Jovan; Hestand, Matthew S.; Coleman, Stephen J.; Zeng, Zheng; Orlando, Ludovic; MacLeod, James N.; Kalbfleisch, Ted

    2015-01-01

    The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new

  2. The Main Sequence of Explosive Solar Active Regions: Comparison of Emerging and Mature Active Regions

    NASA Technical Reports Server (NTRS)

    Falconer, David; Moore, Ron

    2011-01-01

    For mature active regions, an active region s magnetic flux content determines the maximum free energy the active region can have. Most Large flares and CMEs occur in active regions that are near their free-energy limit. Active-region flare power radiated in the GOES 1-8 band increases steeply as the free-energy limit is approached. We infer that the free-energy limit is set by the rate of release of an active region s free magnetic energy by flares, CMEs and coronal heating balancing the maximum rate the Sun can put free energy into the active region s magnetic field. This balance of maximum power results in explosive active regions residing in a "mainsequence" in active-region (flux content, free energy content) phase space, which sequence is analogous to the main sequence of hydrogen-burning stars in (mass, luminosity) phase space.

  3. Comparison of Two Multilocus Sequence Based Genotyping Schemes for Leptospira Species

    PubMed Central

    Boonsilp, Siriphan; Wuthiekanun, Vanaporn; Nalam, Kishore; Spratt, Brian G.; Aanensen, David M.; Smythe, Lee D.; Ahmed, Niyaz; Feil, Edward J.; Hartskeerl, Rudy A.; Peacock, Sharon J.

    2011-01-01

    Background Several sequence based genotyping schemes have been developed for Leptospira spp. The objective of this study was to genotype a collection of clinical and reference isolates using the two most commonly used schemes and compare and contrast the results. Methods and Findings A total of 48 isolates consisting of L. interrogans (n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme described by Thaipadungpanit et al., and the 6 locus genotyping scheme described by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates were not typed using 6L because of a deletion of three nucleotides in lipL32. The remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30 genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence) was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5–96.5) vs. 93.5 (95% CI 88.6–98.4). The dN/dS ratios calculated for each locus indicated that none were under positive selection. Neighbor joining trees were reconstructed based on the concatenated sequences for each scheme. Both trees showed two distinct groups corresponding to L. interrogans and L. kirschneri, and both identified two clones containing 10 and 7 clinical isolates, respectively. There were six instances in which 6L split single STs as defined by 7L into closely related clusters. We noted two discrepancies between the trees in which the genetic relatedness between two pairs of strains were more closely related by 7L than by 6L. Conclusions This genetic analysis indicates that the two schemes are comparable. We discuss their practical advantages and disadvantages. PMID:22087342

  4. Steam sterilization: a comparison of Steam-Clox and some european biological indicators.

    PubMed

    Hoborn, J

    1975-07-01

    Results of a study of the reaction of a chemical indicator (Steam-Clox) and of two biological indicators exposed to steam sterilization with varying amounts of air introduced with the steam, indicate that the chemical indicator is capable of detecting significantly smaller amounts of air than either of the biological indicators tested. PMID:1236614

  5. A Comparison of a Programed Course and a Traditional Lecture Course in General Biology.

    ERIC Educational Resources Information Center

    Strickland, Winfred Randolph

    The major purpose of this study was to compare the achievement of junior college biology students taught by two different methods (programed vs. lecture). It was also noted how the two methods of instruction compared in terms of ACT levels with regard to biological achievement scores and, to compare the methods in terms of reading levels, critical…

  6. Intraspecific comparison of complete mitogenome sequences from two Asian raccoon dogs (Canidae: Nyctereutes procyonoides).

    PubMed

    Kim, Hye Ri; Cho, Jae Youl; Park, Yung Chul

    2015-01-01

    We determined the complete mitochondrial genome (GenBank accession number: KF709435) of the Korean raccoon dog Nyctereutes procyonoides koreensis and compared it with a previously published mitogenome (GenBank accession number: GU256221) of a Chinese raccoon dog. The total length of N. p. koreensis mitogenome is 16,802 bp, with a base composition of 32.1% A, 26.9% T, 26.8% C and 14.2% G. High similarity of 98.7% was found between the complete mitogenome sequences of Korean and Chinese raccoon dogs. Sequence similarity of the two mitogenomes was 99.3% in the other gene regions except for D-loop. The sequence similarity of 99.1% was found in the 13 protein-coding gene regions, whereas 99.6% was identical in mtDNA regions covering all the 22 tRNA genes. There was no variation between 12S rRNAs, whereas 0.5% difference was found between 16S rRNAs.

  7. Comparison of Ribosomal RNA Removal Methods for Transcriptome Sequencing Workflows in Teleost Fish.

    PubMed

    Abernathy, Jason; Overturf, Ken

    2016-01-01

    RNA sequencing (RNA-Seq) is becoming the standard for transcriptome analysis. Removal of contaminating ribosomal RNA (rRNA) is a priority in the preparation of libraries suitable for sequencing. These methods have been well documented in mammals but typically require some optimization for lower vertebrates. Three commercial kits, including Dynabeads mRNA Purification Kit, RiboMinus Eukaryote System v2, and Ribo-Zero Gold rRNA Removal Kit were examined for the ability to remove rRNAs from rainbow trout (Oncorhynchus mykiss) RNA isolations. Total RNA was isolated from liver and muscle tissue samples (n = 24) and rRNAs removed using one of the three kits. Samples were analyzed visually on the Agilent Bioanalyzer and by Illumina RNA-seq, screening for Oncorhynchus rRNAs. There were significant differences between the kits in regards to their ability to remove rRNA, ranging from 2.74% - 10.94% rRNA sequences left behind per kit on average. Using the Bioanalyzer to evaluate ribosomal contamination in rRNA-depleted samples for RNA-Seq was good for detecting samples with higher concentrations of rRNA (>5%), but not very accurate at lower levels. Although all three kits were able to remove a substantial portion of the rRNA from different fish tissues, the Ribo-Zero Gold rRNA Removal Kit eliminated significantly more contaminating ribosomal RNAs than the others.

  8. Comparison of the Triassic Gondwana sequences in the Transantarctic Mountains and Tasmania

    NASA Astrophysics Data System (ADS)

    Collinson, James W.; Kemp, Noel R.; Eggert, J. Thomas

    Triassic sedimentary sequences in the Transantarctic Mountains and Tasmania are both dominated by fluvial sandstones. Triassic exposures in Antarctica occur in three separate areas along the Ross Sea sector, one in the central Transantarctic Mountains and the other two in Victoria Land. In detail the Antarctic sequences and the Tasmanian sequence are different and cannot be correlated lithologically, but paleocurrent vectors and the distribution of the fluvial facies and detrital constituents suggest that they could have been deposited in a single foreland basin. This foreland basin, the Nilsen Mackay Basin, was a trough shaped depression between the East Antarctic craton and the Gondwanian orogen. A major river system may have flowed along the axis of this basin toward Tasmania. Three major types of fluvial facies are represented: braided, meandering, and transitional. The braided stream facies is dominated by sandstone with relatively little siltstone and mudstone. In the meandering stream facies, both fine-grained sediments and sandstones are common, but sandstone bodies fine upward and contain large-scale lateral accretion beds. In the transitional facies, channel form sandstones of the braided type occur with fine-grained floodplain sediments. Detrital constituents indicate source terranes of sedimentary, crystalline, and volcanic rocks. Tributaries from the East Antarctic craton were dominated by quartz sand. A large influx of volcanic detritus was supplied by tributaries from a calc-alkaline arc complex along the Pacific margin. The axis of the basin migrated toward the craton as the influx of volcanics increased during the Triassic.

  9. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    SciTech Connect

    Dahlen, Oda Erp, Titus S. van

    2015-06-21

    Using rare event simulation techniques, we calculated DNA denaturation rate constants for a range of sequences and temperatures for the Peyrard-Bishop-Dauxois (PBD) model with two different parameter sets. We studied a larger variety of sequences compared to previous studies that only consider DNA homopolymers and DNA sequences containing an equal amount of weak AT- and strong GC-base pairs. Our results show that, contrary to previous findings, an even distribution of the strong GC-base pairs does not always result in the fastest possible denaturation. In addition, we applied an adaptation of the PBD model to study hairpin denaturation for which experimental data are available. This is the first quantitative study in which dynamical results from the mesoscopic PBD model have been compared with experiments. Our results show that present parameterized models, although giving good results regarding thermodynamic properties, overestimate denaturation rates by orders of magnitude. We believe that our dynamical approach is, therefore, an important tool for verifying DNA models and for developing next generation models that have higher predictive power than present ones.

  10. Sequence comparison and phylogenetic analysis by the Maximum Likelihood method of ribosome-inactivating proteins from angiosperms.

    PubMed

    Di Maro, Antimo; Citores, Lucía; Russo, Rosita; Iglesias, Rosario; Ferreras, José Miguel

    2014-08-01

    Ribosome-inactivating proteins (RIPs) from angiosperms are rRNA N-glycosidases that have been proposed as defence proteins against virus and fungi. They have been classified as type 1 RIPs, consisting of single-chain proteins, and type 2 RIPs, consisting of an A chain with RIP properties covalently linked to a B chain with lectin properties. In this work we have carried out a broad search of RIP sequence data banks from angiosperms in order to study their main structural characteristics and phylogenetic evolution. The comparison of the sequences revealed the presence, outside of the active site, of a novel structure that might be involved in the internal protein dynamics linked to enzyme catalysis. Also the B-chains presented another conserved structure that might function either supporting the beta-trefoil structure or in the communication between both sugar-binding sites. A systematic phylogenetic analysis of RIP sequences revealed that the most primitive type 1 RIPs were similar to that of the actual monocots (Poaceae and Asparagaceae). The primitive RIPs evolved to the dicot type 1 related RIPs (like those from Caryophyllales, Lamiales and Euphorbiales). The gene of a type 1 RIP related with the actual Euphorbiaceae type 1 RIPs fused with a double beta trefoil lectin gene similar to the actual Cucurbitaceae lectins to generate the type 2 RIPs and finally this gene underwent deletions rendering either type 1 RIPs (like those from Cucurbitaceae, Rosaceae and Iridaceae) or lectins without A chain (like those from Adoxaceae).

  11. Shotgun sequencing analysis of Trypanosoma cruzi I Sylvio X10/1 and comparison with T. cruzi VI CL Brener.

    PubMed

    Franzén, Oscar; Ochaya, Stephen; Sherwood, Ellen; Lewis, Michael D; Llewellyn, Martin S; Miles, Michael A; Andersson, Björn

    2011-03-08

    Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite.

  12. Nucleotide sequence of the DNA polymerase gene of herpes simplex virus type 2 and comparison with the type 1 counterpart.

    PubMed

    Tsurumi, T; Maeno, K; Nishiyama, Y

    1987-01-01

    The complete nucleotide sequence of the DNA polymerase gene of herpes simplex virus (HSV) type 2 strain 186 has been determined. The gene included a 3720-bp major open reading frame capable of encoding 1240 amino acids. The predicted primary translation product had an Mr of 137,354, which was slightly larger than its HSV-1 counterpart. A comparison of the predicted functional amino acid sequences of the HSV-1 and HSV-2 DNA polymerases revealed 95.5% overall amino acid homology, the value of which was the highest among those of the other known polypeptides encoded by HSV-1 and HSV-2. The functional amino acid changes were spread in the N-terminal one-third of the protein, whereas the C-terminal two-third was almost identical between the two types except a particular hydrophilic region. A highly conserved sequence of 6 aa, YGDTDS, which has been observed in DNA polymerases of HSV-1, Epstein-Barr virus, adenovirus, and vaccinia virus, was also present at positions 889 to 894 in the C-terminal region of HSV-2 DNA polymerase.

  13. Complete mitochondrial DNA sequence of the yellowfin seabream Acanthopagrus latus and a genomic comparison among closely related sparid species.

    PubMed

    Xia, Junhong; Xia, Kuaifei; Jiang, Shigui

    2008-08-01

    The complete mitochondrial genome of the yellowfin seabream Acanthopagrus latus was determined in the present study. The genome was 16,609 bp in length and contained 37 genes (2 ribosomal RNA, 22 transfer RNA and 13 protein-coding genes) and the control region (CR), with the content and order of genes being similar to those in typical teleosts. Comparisons of the 37 genes and CR among species indicate the CR was the highest divergent (0.3341), but tRNA(Gly) possesses the lowest genetic variation (0.0542). Much greater p-genetic distances [mean = 0.1559, standard deviation (SD) = 0.0235; n = 1653] for the interspecies level with high frequency (99.4%) than those of the intraspecies level (mean = 0.0098, SD = 0.0090; n = 20) were inferred from 212 Cyt b sequence data, suggesting the Cyt b gene is conserved within Sparidae species and supporting the barcoding validity of Cyt b sequence data for Sparidae species identification. Phylogenetic analysis using amino acid sequences of 13 protein-coding genes supported that the genus Pagrus was not monophyletic, showing the need to re-evaluate the morphological characteristics of Pagrus fishes.

  14. Comparison Study between North Texas Earthquake Sequences from 2008-2015

    NASA Astrophysics Data System (ADS)

    DeShon, H. R.; Hayward, C.; Scales, M. M.; Magnani, M. B.; Hornbach, M. J.; Stump, B. W.

    2015-12-01

    High-resolution earthquake locations and fault plane solutions are combined with information on subsurface geology, fault structure, well data, and 3D pore pressure modeling to provide further insight into the relationship between fluid migration at depth and modern seismicity in North Texas. Since 2008, the USGS has reported over 165 felt earthquakes in the Fort Worth (Barnett Shale) Basin located in northern Texas. Five earthquake sequences warranted deployment of local seismic networks, and there are currently 30+ temporary seismic stations operating in the basin. Event size has increased over time. The 2008/2012 DFW Airport and 2009 Cleburne sequences had maximum event magnitudes of 3.3 and 2.8, respectively. The 2013/2014 Azle-Reno and 2014/2015 Irving-Dallas swarms contain multiple M3.5 earthquakes, and the M4.0 May 2015 Venus earthquake is the largest event recorded to date. Causative faults strike NNE-SSW to NE-SW and are associated with normal faulting, consistent with fault reactivation in the current stress regime. The active faults range from 2-5 km in length, are steeply dipping (45-70º) and can dip to the SE (DFW Airport; Irving-Dallas) or NW (Azle-Reno; Venus). Events occur between 2-6 km depth in the DFW, Cleburne, and Venus sequences but extend to 8 km in the Irving-Dallas and Azle-Reno earthquake swarms. These depths are consistent with reactivation of ancient faults located in the basement granites and/or overlying sedimentary units. The top of the Ordovician Ellenburger group, which serves as a wastewater injection unit in the basin, ranges from 1.4-2.7 km depth across the seismogenic area, is ~1 km thick on average, and generally overlies the Precambrian basement. The DFW Airport, Cleburne, and Azle-Reno sequences have been linked to nearby wastewater injection and/or production activity associated with shale gas extraction. Causal studies of the 2014/2015 Irving-Dallas and 2015 Venus sequences are ongoing and will be updated here.

  15. Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis.

    PubMed

    Li, Yi; Hsiang, Tom; Yang, Rui-Heng; Hu, Xiao-Di; Wang, Ke; Wang, Wen-Jing; Wang, Xiao-Liang; Jiao, Lei; Yao, Yi-Jian

    2016-09-01

    Ophiocordyceps sinensis is one of the most expensive medicinal fungi world-wide, and has been used as a traditional Chinese medicine for centuries. In a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of Roche 454 (223Mb) and Illumina HiSeq (10.6Gb) sequencing data, producing a genome of 87.7Mb with an N50 scaffold length of 12kb and 6972 predicted genes. To test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic DNA extractions of a single ascospore isolate (strain 1229) on an Illumina HiSeq platform (25Gb total data). Assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (ABySS, SOAP and Velvet). In nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher N50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher N50 values. Depending on the assembly program and data type, the maximal N50 was reached with between 50% to 90% of the total read data, equivalent to 100× to 200× coverage. The draft genome assembly was improved over the previously published version resulting in a 114Mb assembly, scaffold N50 of 70kb and 9610 predicted genes. Among the predicted genes, 9213 were validated by RNA-Seq analysis in this study, of which 8896 were found to be singletons. Evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100× and 200×. PMID:27343682

  16. Comparison of different sequencing and assembly strategies for a repeat-rich fungal genome, Ophiocordyceps sinensis.

    PubMed

    Li, Yi; Hsiang, Tom; Yang, Rui-Heng; Hu, Xiao-Di; Wang, Ke; Wang, Wen-Jing; Wang, Xiao-Liang; Jiao, Lei; Yao, Yi-Jian

    2016-09-01

    Ophiocordyceps sinensis is one of the most expensive medicinal fungi world-wide, and has been used as a traditional Chinese medicine for centuries. In a recent report, the genome of this fungus was found to be expanded by extensive repetitive elements after assembly of Roche 454 (223Mb) and Illumina HiSeq (10.6Gb) sequencing data, producing a genome of 87.7Mb with an N50 scaffold length of 12kb and 6972 predicted genes. To test whether the assembly could be improved by deeper sequencing and to assess the amount of data needed for optimal assembly, genomic sequencing was run several times on genomic DNA extractions of a single ascospore isolate (strain 1229) on an Illumina HiSeq platform (25Gb total data). Assemblies were produced using different data types (raw vs. trimmed) and data amounts, and using three freely available assembly programs (ABySS, SOAP and Velvet). In nearly all cases, trimming the data for low quality base calls did not provide assemblies with higher N50 values compared to the non-trimmed data, and increasing the amount of input data (i.e. sequence reads) did not always lead to higher N50 values. Depending on the assembly program and data type, the maximal N50 was reached with between 50% to 90% of the total read data, equivalent to 100× to 200× coverage. The draft genome assembly was improved over the previously published version resulting in a 114Mb assembly, scaffold N50 of 70kb and 9610 predicted genes. Among the predicted genes, 9213 were validated by RNA-Seq analysis in this study, of which 8896 were found to be singletons. Evidence from genome and transcriptome analyses indicated that species assemblies could be improved with defined input material (e.g. haploid mono-ascospore isolate) without the requirement of multiple sequencing technologies, multiple library sizes or data trimming for low quality base calls, and with genome coverages between 100× and 200×.

  17. Application of genotyping-by-sequencing on semiconductor sequencing platforms: A comparison of genetic and reference-based marker ordering in barley

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The rapid development of next generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach fo...

  18. Functional characterisation of novel enantioselective lipase TALipA from Trichosporon asahii MSR54: sequence comparison revealed new signature sequence AXSXG among yeast lipases.

    PubMed

    Kumari, Arti; Gupta, Rani

    2015-01-01

    A gene encoding lipase TALipA from Trichosporon asahii MSR54 was successfully isolated, cloned and expressed in Pichia pastoris X-33. It was purified to homogeneity by affinity chromatography with 1.7 purification fold. SDS-PAGE revealed it as a monomeric 27-kDa protein. Sequence comparison showed that it has close affinity with bacterial and actinobacterial lipases. It has unique oxyanion hole "GL" and conserved pentapeptide AHSMG where alanine is present instead of glycine, which is unique to yeast lipase database. The temperature and pH optima for activity were 60 °C and pH 8.0, respectively. It is thermostable with t1/2 of 68 min at 70 °C. It hydrolyzed p-np esters with better specificity on p-np palmitate, which was again confirmed during hydrolysis of triacylglyceride mixture. The enzyme was found to be regioselective during hydrolysis of triolein. It exhibited enantio preference during esterification of phenylethanol depending upon solvent used. It was S-enantioselective in 1,4-dioxane and R-selective in isopropanol and hexane. It is a magnesium-activated metalloenzyme inhibited by 10-mM EDTA. It was stable towards most of the polar and non-polar solvents.

  19. Functional characterisation of novel enantioselective lipase TALipA from Trichosporon asahii MSR54: sequence comparison revealed new signature sequence AXSXG among yeast lipases.

    PubMed

    Kumari, Arti; Gupta, Rani

    2015-01-01

    A gene encoding lipase TALipA from Trichosporon asahii MSR54 was successfully isolated, cloned and expressed in Pichia pastoris X-33. It was purified to homogeneity by affinity chromatography with 1.7 purification fold. SDS-PAGE revealed it as a monomeric 27-kDa protein. Sequence comparison showed that it has close affinity with bacterial and actinobacterial lipases. It has unique oxyanion hole "GL" and conserved pentapeptide AHSMG where alanine is present instead of glycine, which is unique to yeast lipase database. The temperature and pH optima for activity were 60 °C and pH 8.0, respectively. It is thermostable with t1/2 of 68 min at 70 °C. It hydrolyzed p-np esters with better specificity on p-np palmitate, which was again confirmed during hydrolysis of triacylglyceride mixture. The enzyme was found to be regioselective during hydrolysis of triolein. It exhibited enantio preference during esterification of phenylethanol depending upon solvent used. It was S-enantioselective in 1,4-dioxane and R-selective in isopropanol and hexane. It is a magnesium-activated metalloenzyme inhibited by 10-mM EDTA. It was stable towards most of the polar and non-polar solvents. PMID:25280633

  20. Efficacy of biological agents administered as monotherapy in rheumatoid arthritis: a Bayesian mixed-treatment comparison analysis

    PubMed Central

    Migliore, Alberto; Bizzi, Emanuele; Egan, Colin Gerard; Bernardi, Mauro; Petrella, Lea

    2015-01-01

    Background Biological agents provide an important therapeutic alternative for rheumatoid arthritis patients refractory to conventional disease-modifying antirheumatic drugs. Few head-to-head comparative trials are available. Purpose The aim of this meta-analysis was to compare the relative efficacy of different biologic agents indicated for use as monotherapy in rheumatoid arthritis. Methods A systemic literature search was performed on electronic databases to identify articles reporting double-blind randomized controlled trials investigating the efficacy of biologic agents indicated for monotherapy. Efficacy was assessed using American College of Rheumatology (ACR) 20, 50, and 70 criteria at 16–24 weeks. Relative efficacy was estimated using Bayesian mixed-treatment comparison models. Outcome measures were expressed as odds ratio and 95% credible intervals. Results Ten randomized controlled trials were selected for data extraction and analysis. Mixed-treatment comparison analysis revealed that tocilizumab offered 100% probability of being the best treatment for inducing an ACR20 response versus placebo, methotrexate, adalimumab, or etanercept. Likewise, for ACR50 and ACR70 outcome responses, tocilizumab had a 99.8% or 98.7% probability of being the best treatment, respectively, compared to other treatments or placebo. Tocilizumab increased the relative probability of being the best treatment (vs methotrexate) by 3.2-fold (odds ratio: 2.1–3.89) for all ACR outcomes. Conclusion Tocilizumab offered the greatest possibility of obtaining an ACR20, ACR50, and ACR70 outcome vs other monotherapies or placebo. PMID:26366085

  1. A highly conserved N-terminal sequence for teleost vitellogenin with potential value to the biochemistry, molecular biology and pathology of vitellogenesis

    USGS Publications Warehouse

    Folmar, L.D.; Denslow, N.D.; Wallace, R.A.; LaFleur, G.; Gross, T.S.; Bonomelli, S.; Sullivan, C.V.

    1995-01-01

    N-terminal amino acid sequences for vitellogenin (Vtg) from six species of teleost fish (striped bass, mummichog, pinfish, brown bullhead, medaka, yellow perch and the sturgeon) are compared with published N-terminal Vtg sequences for the lamprey, clawed frog and domestic chicken. Striped bass and mummichog had 100% identical amino acids between positions 7 and 21, while pinfish, brown bullhead, sturgeon, lamprey, Xenopus and chicken had 87%, 93%, 60%, 47%, 47-60%) for four transcripts and had 40% identical, respectively, with striped bass for the same positions. Partial sequences obtained for medaka and yellow perch were 100% identical between positions 5 to 10. The potential utility of this conserved sequence for studies on the biochemistry, molecular biology and pathology of vitellogenesis is discussed.

  2. Comparison and Analysis of Biological Agent Category Lists Based On Biosafety and Biodefense

    PubMed Central

    Tian, Deqiao; Zheng, Tao

    2014-01-01

    Biological agents pose a serious threat to human health, economic development, social stability and even national security. The classification of biological agents is a basic requirement for both biosafety and biodefense. We compared and analyzed the Biological Agent Laboratory Biosafety Category list and the defining criteria according to the World Health Organization (WHO), the National Institutes of Health (NIH), the European Union (EU) and China. We also compared and analyzed the Biological Agent Biodefense Category list and the defining criteria according to the Centers for Disease Control and Prevention (CDC) of the United States, the EU and Russia. The results show some inconsistencies among or between the two types of category lists and criteria. We suggest that the classification of biological agents based on laboratory biosafety should reduce the number of inconsistencies and contradictions. Developing countries should also produce lists of biological agents to direct their development of biodefense capabilities.To develop a suitable biological agent list should also strengthen international collaboration and cooperation. PMID:24979754

  3. Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I.

    PubMed

    Zhu, Dan-Tong; Xia, Wen-Qiang; Rao, Qiong; Liu, Shu-Sheng; Ghanim, Murad; Wang, Xiao-Wei

    2016-08-01

    The whitefly, Bemisia tabaci, harbors the primary symbiont 'Candidatus Portiera aleyrodidarum' and a variety of secondary symbionts. Among these secondary symbionts, Rickettsia is the only one that can be detected both inside and outside the bacteriomes. Infection with Rickettsia has been reported to influence several aspects of the whitefly biology, such as fitness, sex ratio, virus transmission and resistance to pesticides. However, mechanisms underlying these differences remain unclear, largely due to the lack of genomic information of Rickettsia. In this study, we sequenced the genome of two Rickettsia strains isolated from the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex in China and Israel. Both Rickettsia genomes were of high coding density and AT-rich, containing more than 1000 coding sequences, much larger than that of the coexisted primary symbiont, Portiera. Moreover, the two Rickettsia strains isolated from China and Israel shared most of the genes with 100% identity and only nine genes showed sequence differences. The phylogenetic analysis using orthologs shared in the genus, inferred the proximity of Rickettsia in MEAM1 and Rickettsia bellii. Functional analysis revealed that Rickettsia was unable to synthesize amino acids required for complementing the whitefly nutrition. Besides, a type IV secretion system and a number of virulence-related genes were detected in the Rickettsia genome. The presence of virulence-related genes might benefit the symbiotic life of the bacteria, and hint on potential effects of Rickettsia on whiteflies. The genome sequences of Rickettsia provided a basis for further understanding the function of Rickettsia in whiteflies. PMID:27273750

  4. Human Immunodeficiency Virus Type 1 Drug Resistance Testing: a Comparison of Three Sequence-Based Methods

    PubMed Central

    Erali, Maria; Page, Sam; Reimer, Larry G.; Hillyard, David R.

    2001-01-01

    The use of genotypic assays for determining drug resistance in human immunodeficiency virus (HIV) type 1 (HIV-1)-infected patients is increasing. These tests lack standardization and validation. The aim of this study was to evaluate several tests used for the determination of HIV-1 drug resistance. Two genotypic tests, the Visible Genetics TruGene HIV-1 Genotyping Kit and the Applied Biosystems HIV Genotyping System, were compared using 22 clinical samples. Genotyping results were also obtained from an independent reference laboratory. The Visible Genetics and Applied Biosystems genotyping tests identified similar mutations when differences in the drug databases and reference strains were taken into account, and 19 of 21 samples were equivalent. The concordance between the two assays was 99% (249 of 252 mutation sites). Mutations identified by the reference laboratory varied the most among those identified by the three genotypic tests, possibly because of differences in the databases. The concordance of the reference laboratory results with the results of the other two assays was 80% (201 of 252). Samples with 500 to 750 HIV RNA copies/ml could be sequenced by the Visible Genetics and Applied Biosystems assays using 1 ml of input. The Visible Genetics and Applied Biosystems assays both generated an accurate sequence. However, the throughput of the Visible Genetics assay is more limited and may require additional instruments. The two assays differ technically but are similar in overall complexity. Data analysis in the two assays is straightforward, but only the reports provided by Visible Genetics contain information relating mutations to drug resistance. HIV drug resistance genotyping by sequencing is a complex technology which presents a challenge for analysis, interpretation, and reporting. PMID:11376051

  5. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies

    PubMed Central

    Schueler, Markus; Halbritter, Jan; Phelps, Ian G.; Braun, Daniela A.; Otto, Edgar A.; Porath, Jonathan D.; Gee, Heon Yung; Shendure, Jay; O’Roak, Brian J.; Lawson, Jennifer A.; Soliman, Neveen A.; Nabhan, Marwa M.; Doherty, Dan; Hildebrandt, Friedhelm

    2016-01-01

    The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterized by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes. Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe (MIPs) strategy in an international cohort of 384 patients diagnosed with NPHP-RC. As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared to the previous approach, MIPs re-detected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants. In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity. PMID:26673778

  6. Comparison of the aflR gene sequences of strains in Aspergillus section Flavi.

    PubMed

    Lee, Chao-Zong; Liou, Guey-Yuh; Yuan, Gwo-Fang

    2006-01-01

    Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus parasiticus, Aspergillus flavus, Aspergillus nomius and a few other species. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. Although Aspergillus oryzae and Aspergillus sojae, which are used in fermented foods and in ingredient manufacture, have no record of producing aflatoxin, they have been shown to possess an aflR gene. This study examined 34 strains of Aspergillus section Flavi. The aflR gene of 23 of these strains was successfully amplified and sequenced. No aflR PCR products were found in five A. sojae strains or six strains of A. oryzae. These PCR results suggested that the aflR gene is absent or significantly different in some A. sojae and A. oryzae strains. The sequenced aflR genes from the 23 positive strains had greater than 96.6 % similarity, which was particularly conserved in the zinc-finger DNA-binding domain. The aflR gene of A. sojae has two obvious characteristics: an extra CTCATG sequence fragment and a C to T transition that causes premature termination of AFLR protein synthesis. Differences between A. parasiticus/A. sojae and A. flavus/A. oryzae aflR genes were also identified. Some strains of A. flavus as well as A. flavus var. viridis, A. oryzae var. viridis and A. oryzae var. effuses have an A. oryzae-type aflR gene. For all strains with the A. oryzae-type aflR gene, there was no evidence of aflatoxin production. It is suggested that for safety reasons, the aflR gene could be examined to assess possible aflatoxin production by Aspergillus section Flavi strains.

  7. A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife

    PubMed Central

    Razzauti, Maria; Galan, Maxime; Bernard, Maria; Maman, Sarah; Klopp, Christophe; Charbonnel, Nathalie; Vayssier-Taussat, Muriel; Eloit, Marc; Cosson, Jean-François

    2015-01-01

    Background Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq) and 16S-metagenomics, assessing their ability to survey neglected zoonotic bacteria in rodent populations. Methodology/Principal Findings We first extracted nucleic acids from the spleens of 190 voles collected in France. RNA extracts were pooled, randomly retro-transcribed, then RNA-Seq was performed using HiSeq. Assembled bacterial sequences were assigned to the closest taxon registered in GenBank. DNA extracts were analyzed via a 16S-metagenomics approach using two sequencers: the 454 GS-FLX and the MiSeq. The V4 region of the gene coding for 16S rRNA was amplified for each sample using barcoded universal primers. Amplicons were multiplexed and processed on the distinct sequencers. The resulting datasets were de-multiplexed, and each read was processed through a pipeline to be taxonomically classified using the Ribosomal Database Project. Altogether, 45 pathogenic bacterial genera were detected. The bacteria identified by RNA-Seq were comparable to those detected by 16S-metagenomics approach processed with MiSeq (16S-MiSeq). In contrast, 21 of these pathogens went unnoticed when the 16S-metagenomics approach was processed via 454-pyrosequencing (16S-454). In addition, the 16S-metagenomics approaches revealed a high level of coinfection in bank voles. Conclusions/Significance We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each

  8. The tobacco genome sequence and its comparison with those of tomato and potato

    PubMed Central

    Sierro, Nicolas; Battey, James N.D.; Ouadi, Sonia; Bakaher, Nicolas; Bovet, Lucien; Willig, Adrian; Goepfert, Simon; Peitsch, Manuel C.; Ivanov, Nikolai V.

    2014-01-01

    The allotetraploid plant Nicotiana tabacum (common tobacco) is a major crop species and a model organism, for which only very fragmented genomic sequences are currently available. Here we report high-quality draft genomes for three main tobacco varieties. These genomes show both the low divergence of tobacco from its ancestors and microsynteny with other Solanaceae species. We identify over 90,000 gene models and determine the ancestral origin of tobacco mosaic virus and potyvirus disease resistance in tobacco. We anticipate that the draft genomes will strengthen the use of N. tabacum as a versatile model organism for functional genomics and biotechnology applications. PMID:24807620

  9. Strain-stress simulation and comparison of different welding sequences during manufacturing of packing vacuum cover

    NASA Astrophysics Data System (ADS)

    Wang, Yanhu; Chen, Xizhang; Konovalov, Sergey

    2016-09-01

    Double ellipsoid heat source model was used to simulate the welding strain-stress evolution during the welding of a vacuum cover for packing machine. Results showed that each welding process has influence about the deformation and residual stress distribution over product. Stress concentration area was found in an area of the cover and the improved structure, manufacturing technologies were proposed to minimize residual stress after simulation and comparison of different manufacturing process, it is an available method to improve the product quality and reduce residual stresses.

  10. Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

    PubMed

    Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

    2015-03-01

    The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

  11. Sequence comparisons among dispersed members of the Brassica S multigene family in an S9 genome.

    PubMed

    Kai, N; Suzuki, G; Watanabe, M; Isogai, A; Hinata, K

    2001-05-01

    Self-incompatibility (SI) systems prevent self-pollination and promote outbreeding. In Brassica, the SI genes SLG (for S-locus glycoprotein) and SRK (for S-receptor kinase) are members of the S multigene family, which share the SLG-like domain (S domain), which encodes a putative receptor. We have cloned members of the S multigene family from the S9 haplotype of B. campestris (syn. rapa). In addition, eight distinct genomic regions harboring 10 SLG/SRK-like genes were characterized in the present study. Sequence analysis revealed two novel SRK-like genes, BcRK3 and BcRK6 (for B. campestris receptor kinases 3 and 6, respectively). Other genes that were characterized included SFR2 (for S gene family receptor 2), SLR2 (for S locus related gene 2), and a pseudogene. Based on phylogenetic analysis of the nucleotide sequences of the S domain regions, SLG and SRK appear to be distinct from other members of the S multigene family. Linkage analysis showed that most members of the S multigene family are dispersed in the Brassica genome, and that SLR1 (S locus related gene 1) is not linked to the SLR2 in B. campestris.

  12. Comparison of dengue-1 virus envelope glycoprotein gene sequences from French Polynesia.

    PubMed

    Laille, Manola; Roche, Claudine

    2004-10-01

    Dengue (DEN) is the leading arboviral infection of humans, with 100 million cases annually in the tropical areas of the world. The recent severe DEN-1 epidemic in French Polynesia in 2001, with an incidence rate of 16% and more than 45% of the cases with dengue hemorrhagic fever/dengue shock syndrome among 1,400 hospitalized children and eight fatalities, led us to study this new circulating strain. The entire envelope (E) gene of two French Polynesian DEN-1 virus isolates from the two epidemics of 1988-1989 (FP89) and 2001 (FP01) were sequenced and compared with 29 published DEN-1 virus E gene sequences. Phylogenetic relationships showed that the FP89 strain belonged to genotype V and the FP01 strain to genotype IV based on studies on the same region of DEN-1 virus genome (1,485 nucleotides). The recent dengue epidemic in French Polynesia in 2001 was probably due to the introduction of a new DEN-1 virus from Southeast Asia, since the minimum nucleotide divergence was 3.3% with A88, the Indonesian strain isolated in 1988 in Jakarta.

  13. A comparison of Massachusetts and Texas high school biology teachers' attitudes towards the teaching of evolution

    NASA Astrophysics Data System (ADS)

    Howarth, Richard T.

    Darwin's theory of evolution by natural selection is considered to be the unifying theory for all life sciences (American Association for the Advancement of Science, AAAS, 1990; National Academy of Sciences, 1998; National Research Council, NRC, 1996; National Science Teachers Association, NSTA, 2010a) and as such, the biology topic has been established as a central learning standard by the National Science Education Science Standards (NSES, 2005). The purpose of this study was to compare how Massachusetts and Texas high school biology teachers' attitudes toward the teaching of evolution differ as compared to other biology topics. Texas and Massachusetts are two states that exemplify standards based education yet differ dramatically in their histories surrounding the topic of evolution. A survey was conducted among 217 Massachusetts and 139 Texas in-service high school biology teachers to help provide a sense of the phenomena surrounding biology teachers in respect to how their attitudes towards the teaching of evolution are shaped. Additionally, an open-ended question was asked to help contextualize the results of the survey between teachers of these two states. The findings in this study suggest that community appears to be a powerful persuasive message and socialization experience that shapes the development of attitudes towards evolution for some educators, especially when it is highly intertwined with religion. For biology teachers in the state of Texas, the synergistic result of this relationship has resulted in statistically significant differences in regards to attitudes towards evolution as compared to teachers in Massachusetts. These findings yield implications regarding scientific literacy, student learning, assessment, the quality of science instruction, curriculum, undergraduate biology programs, and the needs of biology teachers in terms of professional development.

  14. SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis

    NASA Astrophysics Data System (ADS)

    Charif, Delphine; Lobry, Jean R.

    The seqinR package for the R environment is a library of utilities to retrieve and analyze biological sequences. It provides an interface between: (i) the R language and environment for statistical computing and graphics, and (ii) the ACNUC sequence retrieval system for nucleotide and protein sequence databases such as GenBank, EMBL, SWISS-PROT. ACNUC is very efficient in providing direct access to subsequences of biological interest (e.g., protein coding regions, tRNA, or rRNA coding regions) present in GenBank and in EMBL. Thanks to a simple query language, it is then easy under R to select sequences of interest and then use all the power of the R environment to analyze them. The ACNUC databases can be locally installed but they are more conveniently accessed through a web server to take advantage of centralized daily updates. The aim of this chapter is to provide a handout on basic sequence analyses under seqinR with a special focus on multivariate methods.

  15. Comparison of the complete genome sequence of two closely related isolates of ‘Candidatus Phytoplasma australiense’ reveals genome plasticity

    PubMed Central

    2013-01-01

    Background ‘Candidatus Phytoplasma australiense’ is associated with at least nine diseases in Australia and New Zealand. The impact of this phytoplasma is considerable, both economically and environmentally. The genome of a NZ isolate was sequenced in an effort to understand its pathogenicity and ecology. Comparison with a closely related Australian isolate enabled us to examine mechanisms of genomic rearrangement. Results The complete genome sequence of a strawberry lethal yellows (SLY) isolate of ‘Candidatus Phytoplasma australiense’ was determined. It is a circular genome of 959,779 base pairs with 1126 predicted open reading frames. Despite being 80 kbp larger than another ‘Ca. Phytoplasma australiense’ isolate PAa, the variation between housekeeping genes was generally less than 1% at a nucleotide level. The difference in size between the two isolates was largely due to the number and size of potential mobile units (PMUs), which contributed to some changes in gene order. Comparison of the genomes of the two isolates revealed that the highly conserved 5′ UTR of a putative DNA-directed RNA polymerase seems to be associated with insertion and rearrangement events. Two types of PMUs have been identified on the basis of the order of three to four conserved genes, with both PMUs appearing to have been present in the last common ancestor of ‘Ca. Phytoplasma asteris’ and ‘Ca. Phytoplasma australiense’. Comparison with other phytoplasma genomes showed that modification methylases were, in general, species-specific. A putative methylase (xorIIM) found in ‘Ca. Phytoplasma australiense’ appeared to have no analogue in any other firmicute, and we believe has been introduced by way of lateral gene transfer. A putative retrostransposon (ltrA) analogous to that found in OY-M was present in both isolates, although all examples in PAa appear to be fragments. Comparative analysis identified highly conserved 5′ and 3′ UTR regions of ltrA, which may

  16. Antigenic characterisation of influenza B virus with a new microneutralisation assay: comparison to haemagglutination and sequence analysis.

    PubMed

    Ansaldi, Filippo; Bacilieri, Sabrina; Amicizia, Daniela; Valle, Laura; Banfi, Federica; Durando, Paolo; Sticchi, Laura; Gasparini, Roberto; Icardi, Giancarlo; Crovari, Pietro

    2004-09-01

    Although the haemagglutination inhibition assay is considered the "gold standard" for antigenic characterisation of influenza viruses, some limitations of this technique are well known. A new microneutralisation assay, as a tool for antigenic characterisation of influenza B viruses, has been standardised and its performance evaluated in comparison with the haemagglutination inhibition test in the light of molecular characterisation of the haemagglutinin. Twelve B viruses belonging to the two lineages and the four sub-lineages discriminated by phylogenetic analysis of HA were tested. The microneutralisation assay clearly distinguishes viruses belonging to different lineages and, in addition, discriminates strains belonging to different sub-lineages that are poorly or not discriminated using the haemagglutination inhibition test. This new microneutralisation assay could provide a useful tool for antigenic characterisation of circulating influenza viruses and contribute, together with the haemagglutination inhibition test and sequence analysis of the haemagglutinin and neuraminidase, in the choice of the strain for use in vaccine composition.

  17. Pairwise Comparisons of Mitochondrial DNA Sequences in Subdivided Populations and Implications for Early Human Evolution

    PubMed Central

    Marjoram, P.; Donnelly, P.

    1994-01-01

    We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious. PMID:8150290

  18. A structural and functional comparison of nematode and crustacean PDH-like sequences.

    PubMed

    Meelkop, E; Marco, H G; Janssen, T; Temmerman, L; Vanhove, M P M; Schoofs, L

    2012-03-01

    The elucidation of the whole genome of the nematode Caenorhabditis elegans allowed for the identification of ortholog genes belonging to the pigment dispersing hormone/factor (PDH/PDF) peptide family. Members of this peptide family are known from crustaceans, insects and nematodes and seem to exist exclusively in ecdysozoans where they play a role in different processes, ranging from the dispersion of integumental and eye (retinal) pigments in decapod crustaceans to circadian rhythms in insects and locomotion in C. elegans. Two pdf genes (pdf-1 and pdf-2) encoding three different peptides: PDF-1a, PDF-1b and PDF-2 have been identified in C. elegans. These three C. elegans PDH-like peptides are similar but not identical in primary structure to PDHs from decapod crustaceans. We investigate whether this divergence has an influence on the pigment dispersing function of the peptides in a decapod crustacean, namely the shrimp Palaemon pacificus. We show that C. elegans PDF-1a and b peptides display cross-functional activity by dispersing pigments in the epithelium of P. pacificus at physiological doses. Moreover, by means of a comparative amino acid sequence analysis of nematode and crustacean PDH-like peptides, we can pinpoint several potentially important residues for eliciting pigment dispersing activity in decapod crustaceans. Although there is no sequence information on a receptor for PDH in decapod crustaceans, we postulate that there is general conservation of the PDH/PDF signaling system based on structural similarities of precursor proteins and receptors (including those from a branchiopod crustacean and from C. elegans).

  19. Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains.

    PubMed

    Norman, Keri N; Clawson, Michael L; Strockbine, Nancy A; Mandrell, Robert E; Johnson, Roger; Ziebell, Kim; Zhao, Shaohua; Fratamico, Pina M; Stones, Robert; Allard, Marc W; Bono, James L

    2015-01-01

    Shiga toxin-producing Escherichia coli (STEC) O26 is the second leading E. coli serogroup responsible for human illness outbreaks behind E. coli O157:H7. Recent outbreaks have been linked to emerging pathogenic O26:H11 strains harboring stx 2 only. Cattle have been recognized as an important reservoir of O26 strains harboring stx 1; however the reservoir of these emerging stx 2 strains is unknown. The objective of this study was to identify nucleotide polymorphisms in human and cattle-derived strains in order to compare differences in polymorphism derived genotypes and virulence gene profiles between the two host species. Whole genome sequencing was performed on 182 epidemiologically unrelated O26 strains, including 109 human-derived strains and 73 non-human-derived strains. A panel of 289 O26 strains (241 STEC and 48 non-STEC) was subsequently genotyped using a set of 283 polymorphisms identified by whole genome sequencing, resulting in 64 unique genotypes. Phylogenetic analyses identified seven clusters within the O26 strains. The seven clusters did not distinguish between isolates originating from humans or cattle; however, clusters did correspond with particular virulence gene profiles. Human and non-human-derived strains harboring stx 1 clustered separately from strains harboring stx 2, strains harboring eae, and non-STEC strains. Strains harboring stx 2 were more closely related to non-STEC strains and strains harboring eae than to strains harboring stx 1. The finding of human and cattle-derived strains with the same polymorphism derived genotypes and similar virulence gene profiles, provides evidence that similar strains are found in cattle and humans and transmission between the two species may occur.

  20. Comparison of whole genome sequences from human and non-human Escherichia coli O26 strains

    PubMed Central

    Norman, Keri N.; Clawson, Michael L.; Strockbine, Nancy A.; Mandrell, Robert E.; Johnson, Roger; Ziebell, Kim; Zhao, Shaohua; Fratamico, Pina M.; Stones, Robert; Allard, Marc W.; Bono, James L.

    2015-01-01

    Shiga toxin-producing Escherichia coli (STEC) O26 is the second leading E. coli serogroup responsible for human illness outbreaks behind E. coli O157:H7. Recent outbreaks have been linked to emerging pathogenic O26:H11 strains harboring stx2 only. Cattle have been recognized as an important reservoir of O26 strains harboring stx1; however the reservoir of these emerging stx2 strains is unknown. The objective of this study was to identify nucleotide polymorphisms in human and cattle-derived strains in order to compare differences in polymorphism derived genotypes and virulence gene profiles between the two host species. Whole genome sequencing was performed on 182 epidemiologically unrelated O26 strains, including 109 human-derived strains and 73 non-human-derived strains. A panel of 289 O26 strains (241 STEC and 48 non-STEC) was subsequently genotyped using a set of 283 polymorphisms identified by whole genome sequencing, resulting in 64 unique genotypes. Phylogenetic analyses identified seven clusters within the O26 strains. The seven clusters did not distinguish between isolates originating from humans or cattle; however, clusters did correspond with particular virulence gene profiles. Human and non-human-derived strains harboring stx1 clustered separately from strains harboring stx2, strains harboring eae, and non-STEC strains. Strains harboring stx2 were more closely related to non-STEC strains and strains harboring eae than to strains harboring stx1. The finding of human and cattle-derived strains with the same polymorphism derived genotypes and similar virulence gene profiles, provides evidence that similar strains are found in cattle and humans and transmission between the two species may occur. PMID:25815275

  1. Forensic soil DNA analysis using high-throughput sequencing: a comparison of four molecular markers.

    PubMed

    Young, Jennifer M; Weyrich, Laura S; Cooper, Alan

    2014-11-01

    Soil analysis, such as mineralogy, geophysics, texture and colour, are commonly used in forensic casework to link a suspect to a crime scene. However, DNA analysis can also be applied to characterise the vast diversity of organisms present in soils. DNA metabarcoding and high-throughput sequencing (HTS) now offer a means to improve discrimination between forensic soil samples by identifying individual taxa and exploring non-culturable microbial species. Here, we compare the small-scale reproducibility and resolution of four molecular markers targeting different taxa (bacterial 16S rRNA, eukaryotic18S rRNA, plant trnL intron and fungal internal transcribed spacer I (ITS1) rDNA) to distinguish two sample sites. We also assess the background DNA level associated with each marker and examine the effects of filtering Operational Taxonomic Units (OTUs) detected in extraction blank controls. From this study, we show that non-bacterial taxa in soil, particularly fungi, can provide the greatest resolution between the sites, whereas plant markers may be problematic for forensic discrimination. ITS and 18S markers exhibit reliable amplification, and both show high discriminatory power with low background DNA levels. The 16S rRNA marker showed comparable discriminatory power post filtering; however, presented the highest level of background DNA. The discriminatory power of all markers was increased by applying OTU filtering steps, with the greatest improvement observed by the removal of any sequences detected in extraction blanks. This study demonstrates the potential use of multiple DNA markers for forensic soil analysis using HTS, and identifies some of the standardisation and evaluation steps necessary before this technique can be applied in casework.

  2. Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing.

    PubMed

    McClenahan, Shasta D; Uhlenhaut, Christine; Krause, Philip R

    2014-12-12

    We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types

  3. Evaluation of cells and biological reagents for adventitious agents using degenerate primer PCR and massively parallel sequencing.

    PubMed

    McClenahan, Shasta D; Uhlenhaut, Christine; Krause, Philip R

    2014-12-12

    We employed a massively parallel sequencing (MPS)-based approach to test reagents and model cell substrates including Chinese hamster ovary (CHO), Madin-Darby canine kidney (MDCK), African green monkey kidney (Vero), and High Five insect cell lines for adventitious agents. RNA and DNA were extracted either directly from the samples or from viral capsid-enriched preparations, and then subjected to MPS-based non-specific virus detection with degenerate oligonucleotide primer (DOP) PCR. MPS by 454, Illumina MiSeq, and Illumina HiSeq was compared on independent samples. Virus detection using these methods was reproducibly achieved. Unclassified sequences from CHO cells represented cellular sequences not yet submitted to the databases typically used for sequence identification. The sensitivity of MPS-based virus detection was consistent with theoretically expected limits based on dilution of virus in cellular nucleic acids. Capsid preparation increased the number of viral sequences detected. Potential viral sequences were detected in several samples; in each case, these sequences were either artifactual or (based on additional studies) shown not to be associated with replication-competent viruses. Virus-like sequences were more likely to be identified in BLAST searches using virus-specific databases that did not contain cellular sequences. Detected viral sequences included previously described retrovirus and retrovirus-like sequences in CHO, Vero, MDCK and High Five cells, and nodavirus and endogenous bracovirus sequences in High Five insect cells. Bovine viral diarrhea virus, bovine hokovirus, and porcine circovirus sequences were detected in some reagents. A recently described parvo-like virus present in some nucleic acid extraction resins was also identified in cells and extraction controls from some samples. The present study helps to illustrate the potential for MPS-based strategies in evaluating the presence of viral nucleic acids in various sample types

  4. Scorpion toxins from Centruroides noxius and Tityus serrulatus. Primary structures and sequence comparison by metric analysis.

    PubMed Central

    Possani, L D; Martin, B M; Svendsen, I; Rode, G S; Erickson, B W

    1985-01-01

    The complete primary structures of toxin II-14 from the Mexican scorpion Centruroides noxius Hoffmann and toxin gamma from the Brazilian scorpion Tityus serrulatus Lutz and Mello have been determined. Cleavage of toxin gamma after Met-6 with CNBr produced the 55-residue peptide 7-61, which maintained the four disulphide bonds but was not toxic to mice at a dose 3 times the lethal dose of native toxin gamma. Pairwise comparison by metric analysis of segment 1-50 of toxin gamma and the corresponding segments from two other South American scorpion toxins, five North American scorpion toxins, nine North African scorpion toxins and one Central Asian scorpion toxin showed that the three Brazilian toxins are intermediate between the North American and North African toxins. This result is consistent with the hypothesis that the South American and African continents were joined by a land connection in the distant past. Images Fig. 1. PMID:4052021

  5. Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations

    NASA Astrophysics Data System (ADS)

    Dannemiller, Karen C.; Lang-Yona, Naama; Yamamoto, Naomichi; Rudich, Yinon; Peccia, Jordan

    2014-02-01

    We examined fungal communities associated with the PM10 mass of Rehovot, Israel outdoor air samples collected in the spring and fall seasons. Fungal communities were described by 454 pyrosequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal RNA encoding gene. To allow for a more quantitative comparison of fungal exposure in humans, the relative abundance values of specific taxa were transformed to absolute concentrations through multiplying these values by the sample's total fungal spore concentration (derived from universal fungal qPCR). Next, the sequencing-based absolute concentrations for Alternaria alternata, Cladosporium cladosporioides, Epicoccum nigrum, and Penicillium/Aspergillus spp. were compared to taxon-specific qPCR concentrations for A. alternata, C. cladosporioides, E. nigrum, and Penicillium/Aspergillus spp. derived from the same spring and fall aerosol samples. Results of these comparisons showed that the absolute concentration values generated from pyrosequencing were strongly associated with the concentration values derived from taxon-specific qPCR (for all four species, p < 0.005, all R > 0.70). The correlation coefficients were greater for species present in higher concentrations. Our microbial aerosol population analyses demonstrated that fungal diversity (number of fungal operational taxonomic units) was higher in the spring compared to the fall (p = 0.02), and principal coordinate analysis showed distinct seasonal differences in taxa distribution (ANOSIM p = 0.004). Among genera containing allergenic and/or pathogenic species, the absolute concentrations of Alternaria, Aspergillus, Fusarium, and Cladosporium were greater in the fall, while Cryptococcus, Penicillium, and Ulocladium concentrations were greater in the spring. The transformation of pyrosequencing fungal population relative abundance data to absolute concentrations can improve next-generation DNA sequencing-based quantitative aerosol exposure

  6. Identification of Lactobacillus Isolates from the Gastrointestinal Tract, Silage, and Yoghurt by 16S-23S rRNA Gene Intergenic Spacer Region Sequence Comparisons

    PubMed Central

    Tannock, G. W.; Tilsala-Timisjarvi, A.; Rodtong, S.; Ng, J.; Munro, K.; Alatossava, T.

    1999-01-01

    Lactobacillus isolates were identified by PCR amplification and sequencing of the region between the 16S and 23S rRNA genes (spacer region). The sequences obtained from the isolates were compared to those of reference strains held in GenBank. A similarity of 97.5% or greater was considered to provide identification. To check the reliability of the method, the V2-V3 region of the 16S rRNA gene was amplified and sequenced in the case of isolates whose spacer region sequences were less than 99% similar to that of a reference strain. Confirmation of identity was obtained in all instances. Spacer region sequencing provided rapid and accurate identification of Lactobacillus isolates obtained from gastrointestinal, yoghurt, and silage samples. It had an advantage over 16S V2-V3 sequence comparisons because it distinguished between isolates of Lactobacillus casei and Lactobacillus rhamnosus. PMID:10473450

  7. Sequence analysis of four acidic beta-crystallin subunits of amphibian lenses: phylogenetic comparison between beta- and gamma-crystallins.

    PubMed

    Lu, S F; Pan, F M; Chiou, S H

    1996-04-16

    beta-Crystallins composed of the most heterogeneous group of subunit chains among the three major crystallin families of vertebrates, i.e. alpha-, beta- and gamma-crystallins, are less well understood at the structural and functional levels than the other two. They comprise a multigene family with at least three basic (betaB1-3) and four acidic (betaA1-4) subunit polypeptides. In order to facilitate the determination of the primary sequences of all these ubiquitous crystallin subunits present in all vertebrate species, cDNA mixture was synthesized from the poly(A)+ mRNA isolated from bullfrog eye lenses. We report here a protocol of Rapid Amplification of cDNA Ends (RACE) was used to amplify cDNAs encoding beta-crystallin acidic subunit polypeptides by polymerase chain reaction (PCR). Four complete full-length reading frames with two each of 597 and 648 base pairs, which cover four deduced protein sequences of 198 (betaA1-1 and betaA1-2) and 215 (betaA3-1 and betaA3-2) amino acids including the universal initiating methionine, were revealed by nucleotide sequencing. They show about 96-98% sequence similarity among themselves and 76-80%, 80-83% to the homologous betaA1/A3 crystallins of bovine and human species respectively, revealing the close structural relationship among acidic subunits of all beta-crystallins even from remotely related species. In this study a phylogenetic comparison based on amino-acid sequences of various betaA1/A3 crystallins plus the major basic beta-crystallin (betaBp) and gamma-crystallin from different vertebrate species is made using a combination of distance matrix and approximate parsimony methods, which correctly groups these betaA crystallin chains together as one family distinct from basic beta-crystallins and gamma-crystallin and further corroborates the supposition that beta- and gamma-crystallins form a superfamily with a common ancestry.

  8. Genome Sequencing of the Pyruvate-producing Strain Candida glabrata CCTCC M202019 and Genomic Comparison with Strain CBS138

    PubMed Central

    Xu, Nan; Ye, Chao; Chen, Xiulai; Liu, Jia; Liu, Liming; Chen, Jian

    2016-01-01

    Candida glabrata CCTCC M202019 as an industrial yeast strain that is widely used to produce α-oxocarboxylic acid. Strain M202019 has been proven to have a higher pyruvate-producing capacity than the reference strain CBS138. To characterize the genotype of the M202019 strain, we generated a draft sequence of its genome, which has a size of 12.1 Mbp and a GC content of 38.47%. Evidence accumulated during genome annotation suggests that strain M202019 has strong capacities for glucose transport and pyruvate biosynthesis, defects in pyruvate catabolism, as well as variations in genes involved in nutrient and dicarboxylic acid transport, oxidative phosphorylation, and other relevant aspects of carbon metabolism, which might promote pyruvate accumulation. In addition to differences in its central carbon metabolism, a genomic analysis revealed genetic differences in adhesion metabolism. Forty-nine adhesin-like proteins of strain M202019 were identified classified into seven subfamilies. Decreased amounts of adhesive proteins, and deletions or changes of low-complexity repeats and functional domains might lead to lower adhesion and reduced pathogenicity. Further virulence experiments validated the biological safety of strain M202019. Analysis of the C. glabrata CCTCC M202019 genome sequence provides useful insights into its genetic context, physical characteristics, and potential metabolic capacity. PMID:27713500

  9. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

    PubMed Central

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  10. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.

    PubMed

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie; Pitta, Dipti

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M (2) = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  11. Naked but not Hairless: the pitfalls of analyses of molecular adaptation based on few genome sequence comparisons.

    PubMed

    Delsuc, Frédéric; Tilak, Marie-Ka

    2015-02-20

    The naked mole-rat (Heterocephalus glaber) is the only rodent species that naturally lacks fur. Genome sequencing of this atypical rodent species recently shed light on a number of its morphological and physiological adaptations. More specifically, its hairless phenotype has been traced back to a single amino acid change (C397W) in the hair growth associated (HR) protein (or Hairless). By considering the available species diversity, we show that this specific position is in fact variable across mammals, including in the horse that was misleadingly reported to have the ancestral Cysteine. Moreover, by sequencing the corresponding HR exon in additional rodent species, we demonstrate that the C397W substitution is actually not a peculiarity of the naked mole-rat. Instead, this specific amino acid substitution is present in all hystricognath rodents investigated, which are all fully furred, including the naked mole-rat closest relative, the Damaraland mole-rat (Fukomys damarensis). Overall, we found no statistical correlation between amino acid changes at position 397 of the HR protein and reduced pilosity across the mammalian phylogeny. This demonstrates that this single amino acid change does not explain the naked mole-rat hairless phenotype. Our case study calls for caution before making strong claims regarding the molecular basis of phenotypic adaptation based on the screening of specific amino acid substitutions using only few model species in genome sequence comparisons. It also exposes the more general problem of the dilution of essential information in the supplementary material of genome papers thereby increasing the probability that misleading results will escape the scrutiny of editors, reviewers, and ultimately readers.

  12. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000

    SciTech Connect

    Feil, H; Feil, W S; Chain, P; Larimer, F; DiBartolo, G; Copeland, A; Lykidis, A; Trong, S; Nolan, M; Goltsman, E; Thiel, J; Malfatti, S; Loper, J E; Lapidus, A; Detter, J C; Land, M; Richardson, P M; Kyrpides, N C; Ivanova, N; Lindow, S E

    2005-07-14

    The complete genomic sequence of Pseudomonas syringae pathovar syringae B728a (Pss B728a), has been determined and is compared with that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 megabases) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. While a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared to Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences (REPs) unique to Pss B728a when compared to Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands vary, with one containing a prophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin (SP), syringomycin (SR), indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to epiphytic fitness and stress tolerance of this organism.

  13. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000

    SciTech Connect

    Feil, Helene; Feil, William; Chain, Patrick S. G.; Larimer, Frank W; DiBartolo, Genevieve; Copeland, A; Lykidis, A; Trong, Stephen; Nolan, Matt; Goltsman, Eugene; Thiel, James; Malfatti, Stephanie; Loper, Joyce E.; Detter, J C; Lapidus, Alla L.; Land, Miriam L; Richardson, P M; Kyrpides, Nikos C; Ivanova, N; Lindow, Steven E.

    2005-01-01

    The complete genomic sequence of Pseudomonas syringae pv. syringae B728a (Pss B728a) has been determined and is compared with that of A syringae pv. tomato DC3000 (Pst DC3000). The two pathovars of this economically important species of plant pathogenic bacteria differ in host range and other interactions with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 Mb) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. Although a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared with Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences unique to Pss B728a when compared with Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands varies, with one containing a prophage and another the plasmid pKLC102 of Pseudomonas aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin, syringomycin, indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to the epiphytic fitness and stress tolerance of this organism.

  14. Characterization and comparison of gene-based simple sequence repeats across Brassica species.

    PubMed

    Gao, Caihua; Tang, Zhanglin; Yin, Jiaming; An, Zeshan; Fu, Donghui; Li, Jiana

    2011-08-01

    Simple sequence repeats (SSRs) are important components of eukaryotic genomes and may play an important role in regulating gene expression. However, the characteristics of genic SSRs and the effect of interspecific hybridization and polyploidization on genic SSRs seem not to have received desired attention in terms of scientific investigations. To determine the features of genic SSRs and elucidate their role in polyploidization process of the Brassica family, we identified SSRs in Plant Genome Database-assembled unique transcripts (PUTs) of Brassica species. A higher density of SSRs and a greater number of compound motif SSRs and mononucleotide motif types with large average number of repeats were detected in allotetraploid Brassica napus than in the diploid parental species (Brassica rapa and Brassica oleracea). In addition, a greater proportion of SSR-PUTs were found to be associated with the stress response and developmental processes in B. napus than in the parents. A negative correlation between the repeat number and the motif type and the total length, and a positive correlation between the repeat number and the total length of SSRs were observed. PUT-SSR might be generated from A/T-rich regions. The successful development of 123 pairs of SSR primers for Brassica PUTs showed that SSR-PUTs could be exploited as gene-based SSR functional markers for application in Brassica breeding. These results indicate that interspecific hybridization and polyploidization could trigger the amplification of SSRs, and long SSRs might become shorter to enable the plant to adapt to environmental and artificial selection.

  15. [Comparison between Astragalus membranaceus var. mongholicus and Hedysarum polybotrys based on ITS sequences and metabolomics].

    PubMed

    Jiao, Mei-li; Li, Zhen-yu; Zhang, Fu-sheng; Qin, Xue-mei

    2015-12-01

    Astragalus membranaceus var. mongholicus and Hedysarum polybotrys belong to different genera, but have similar drug efficacy in traditional Chinese medicine theory, and H. polybotrys was used as the legal A. membranaceus var. mongholicus previously. In this study, similarities and differences between them were analyzed via their ITS/ITS2 fragments information. The ITS (internal transcribed spacer) regions were amplified using polymerase chain reaction and then sequenced in two-way. The alignment lengths of ITS regions were 616 bp, in which 508 loci were consistent, and 103 loci were different, accounting for 82.47% and 16.72% of the total ITS nucleotides in length, respectively. As genotype determines phenotype, 1HNMR-based metabolomic approach was further used to reveal the chemical similarities and differences between them. Thirty-four metabolites were identified in the 1H NMR spectra, and twenty-seven metabolites were the common components. Amino acids, carbohydrates and other primary metabolites were similar, while a large difference existed in the flavonoids and astragalosides. This study suggests that A. membranaceus var. mongholicus and H. polybotrys show similarities and differences from molecular and chemical perspectives, which has laid a foundation for elucidating the effective material basis of drug with similar efficacy and resources utilization. PMID:27169287

  16. Exon-intron organization and sequence comparison of human and murine T11 (CD2) genes

    SciTech Connect

    Diamond, D.J.; Clayton, L.K.; Sayre, P.H.; Reinherz, E.L.

    1988-03-01

    Genomic DNA clones containing the human and murine genes coding for the 50-kDa T11 (CD2) T-cell surface glycoprotein were characterized. The human T11 gene is approx. = 12 kilobases long and comprised of five exons. A leader exon (L) contains the 5'-untranslated region and most of the nucleotides defining the signal peptide (amino acids (aa) -24 to -5). Two exons encode the extracellular segment; exon Ex1 is 321 base pairs (bp) long and codes for four residues of the leader peptide and aa 1-103 of the mature protein, and exon Ex2 is 231 bp long and encodes aa 104-180. Exon TM is 123 bp long and codes for the single transmembrane region of the molecule (aa 181-221). Exon C is a large 765-bp exon encoding virtually the entire cytoplasmic domain (aa 222-327) and the 3'-untranslated region. The murine region T11 gene has a similar organization with exon-intron boundaries essentially identical to the human gene. Substantial conservation of nucleotide sequences between species in both 5'- and 3'-gene flanking regions equivalent to that among homologous exons suggests that murine and human genes may be regulated in a similar fashion. The probable relationship of the individual T11 exons to functional and structural protein domains is discussed.

  17. Comparison of inherently essential genes of Porphyromonas gingivalis identified in two transposon-sequencing libraries.

    PubMed

    Hutcherson, J A; Gogeneni, H; Yoder-Himes, D; Hendrickson, E L; Hackett, M; Whiteley, M; Lamont, R J; Scott, D A

    2016-08-01

    Porphyromonas gingivalis is a Gram-negative anaerobe and keystone periodontal pathogen. A mariner transposon insertion mutant library has recently been used to define 463 genes as putatively essential for the in vitro growth of P. gingivalis ATCC 33277 in planktonic culture (Library 1). We have independently generated a transposon insertion mutant library (Library 2) for the same P. gingivalis strain and herein compare genes that are putatively essential for in vitro growth in complex media, as defined by both libraries. In all, 281 genes (61%) identified by Library 1 were common to Library 2. Many of these common genes are involved in fundamentally important metabolic pathways, notably pyrimidine cycling as well as lipopolysaccharide, peptidoglycan, pantothenate and coenzyme A biosynthesis, and nicotinate and nicotinamide metabolism. Also in common are genes encoding heat-shock protein homologues, sigma factors, enzymes with proteolytic activity, and the majority of sec-related protein export genes. In addition to facilitating a better understanding of critical physiological processes, transposon-sequencing technology has the potential to identify novel strategies for the control of P. gingivalis infections. Those genes defined as essential by two independently generated TnSeq mutant libraries are likely to represent particularly attractive therapeutic targets.

  18. Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools

    PubMed Central

    Patel, Jaymin M.; Knopf, Joshua; Reiner, Eric; Bossuyt, Veerle; Epstein, Lianne; DiGiovanna, Michael; Chung, Gina; Silber, Andrea; Sanft, Tara; Hofstatter, Erin; Mougalian, Sarah; Abu-Khalaf, Maysa; Platt, James; Shi, Weiwei; Gershkovich, Peter; Hatzis, Christos; Pusztai, Lajos

    2016-01-01

    Interpretation of complex cancer genome data, generated by tumor target profiling platforms, is key for the success of personalized cancer therapy. How to draw therapeutic conclusions from tumor profiling results is not standardized and may vary among commercial and academically-affiliated recommendation tools. We performed targeted sequencing of 315 genes from 75 metastatic breast cancer biopsies using the FoundationOne assay. Results were run through 4 different web tools including the Drug-Gene Interaction Database (DGidb), My Cancer Genome (MCG), Personalized Cancer Therapy (PCT), and cBioPortal, for drug and clinical trial recommendations. These recommendations were compared amongst each other and to those provided by FoundationOne. The identification of a gene as targetable varied across the different recommendation sources. Only 33% of cases had 4 or more sources recommend the same drug for at least one of the usually several altered genes found in tumor biopsies. These results indicate further development and standardization of broadly applicable software tools that assist in our therapeutic interpretation of genomic data is needed. Existing algorithms for data acquisition, integration and interpretation will likely need to incorporate artificial intelligence tools to improve both content and real-time status. PMID:26980737

  19. HLA genotyping in the clinical laboratory: comparison of next-generation sequencing methods.

    PubMed

    Profaizer, T; Lázár-Molnár, E; Close, D W; Delgado, J C; Kumánovics, A

    2016-07-01

    Implementation of human leukocyte antigen (HLA) genotyping by next-generation sequencing (NGS) in the clinical lab brings new challenges to the laboratories performing this testing. With the advent of commercially available HLA-NGS typing kits, labs must make numerous decisions concerning capital equipment and address labor considerations. Therefore, careful and unbiased evaluation of available methods is imperative. In this report, we compared our in-house developed HLA NGS typing with two commercially available kits from Illumina and Omixon using 10 International Histocompatibility Working Group (IHWG) and 36 clinical samples. Although all three methods employ long range polymerase chain reaction (PCR) and have been developed on the Illumina MiSeq platform, the methodologies for library preparation show significant variations. There was 100% typing concordance between all three methods at the first field when a HLA type could be assigned. Overall, HLA typing by NGS using in-house or commercially available methods is now feasible in clinical laboratories. However, technical variables such as hands-on time and indexing strategies are sufficiently different among these approaches to impact the workflow of the clinical laboratory. PMID:27524804

  20. De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China.

    PubMed

    Nguyen Thanh, Hai; Zhao, Liangjie; Liu, Qigen

    2014-01-01

    Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog-ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we

  1. De Novo Transcriptome Sequencing Analysis and Comparison of Differentially Expressed Genes (DEGs) in Macrobrachium rosenbergii in China

    PubMed Central

    Liu, Qigen

    2014-01-01

    Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples of hepatopancreas organ in individuals from 4 GFP groups (A1, A2, B1 and B2). De novo transcriptome sequencing generated 66,953 isogenes. Using BLASTX to search the Non-redundant (NR), Search Tool for the Retrieval of Interacting Genes (STRING), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases; 21,224 unigenes were annotated, 9,552 matched unigenes with the Gene Ontology (GO) classification; 5,782 matched unigenes in 25 categories of Clusters of Orthologous Groups of proteins (COG) and 20,859 unigenes were consequently assigned to 312 KEGG pathways. Between the A and B groups 147 differentially expressed genes (DEGs) were identified; between the A1 and A2 groups 6,860 DEGs were identified and between the B1 and B2 groups 5,229 DEGs were identified. After enrichment, the A and B groups identified 38 DEGs, but none of them were significantly enriched. The A1 and A2 groups identified 21,856 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function and the KEGG pathway defined 2,459 genes had a KEGG Ortholog - ID (KO-ID) and could be categorized into 251 pathways, of those, 9 pathways were significantly enriched. The B1 and B2 groups identified 5,940 DEGs in three main categories based on functional groups: biological process, cellular_component and molecular function, and the KEGG pathway defined 1,543 genes had a KO-ID and could be categorized into 240 pathways, of those, 2 pathways were significantly enriched. We investigated 99 queries (GO) which related to growth of GFP in 4 groups. After enrichment we

  2. Comparison of Technology Use between Biology and Physics Teachers in a 1:1 Laptop Environment

    ERIC Educational Resources Information Center

    Crook, Simon J.; Sharma, Manjula D.; Wilson, Rachel

    2015-01-01

    Using a mixed-methods approach the authors compared the associated practices of senior physics teachers (n = 7) and students (n = 53) in a 1:1 laptop environment with those of senior biology teachers (n = 10) and students (n = 125) also in a 1:1 laptop environment, in seven high schools in Sydney, NSW, Australia. They found that the physics…

  3. Comparison of SWAT Predictions with Stream Biological Integrity Observations in an Agricultural Watershed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The SWAT model is calibrated with USGS data for an agricultural watershed located on the Eastern Shore of Maryland. Model predictions of runoff, sediment, nitrogen and phosphorus amounts, at the outlet of sub-watersheds, are compared to measurements of stream biological integrity conducted throughou...

  4. Biology Instruction by Interactive Videodisc or Conventional Laboratory: A Qualitative Comparison.

    ERIC Educational Resources Information Center

    Leonard, William H.

    This study was designed to learn if students perceived an interactive computer/videodisc learning system to represent a viable alternative to (or extension of) the conventional laboratory for learning biology skills and concepts normally taught under classroom laboratory conditions. Data were collected by questionnaire in introductory biology…

  5. Parental Divorce, Marital Conflict and Children's Behavior Problems: A Comparison of Adopted and Biological Children

    ERIC Educational Resources Information Center

    Amato, Paul R.; Cheadle, Jacob E.

    2008-01-01

    We used adopted and biological children from Waves 1 and 2 of the National Survey of Families and Households to study the links between parents' marital conflict, divorce and children's behavior problems. The standard family environment model assumes that marital conflict and divorce increase the risk of children's behavior problems. The passive…

  6. Scalable Kernel Methods and Algorithms for General Sequence Analysis

    ERIC Educational Resources Information Center

    Kuksa, Pavel

    2011-01-01

    Analysis of large-scale sequential data has become an important task in machine learning and pattern recognition, inspired in part by numerous scientific and technological applications such as the document and text classification or the analysis of biological sequences. However, current computational methods for sequence comparison still lack…

  7. Comparison of Model Calculations of Biological Damage from Exposure to Heavy Ions with Measurements

    NASA Technical Reports Server (NTRS)

    Kim, Myung-Hee Y.; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2014-01-01

    The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LET gamma or X rays, the presence of shielding does not always reduce the radiation risks for energetic charged-particle exposure. Dose delivered by the charged particle increases sharply at the Bragg peak. However, the Bragg curve does not necessarily represent the biological damage along the particle path since biological effects are influenced by the track structures of both primary and secondary particles. Therefore, the ''biological Bragg curve'' is dependent on the energy and the type of the primary particle and may vary for different biological end points. Measurements of the induction of micronuclei (MN) have made across the Bragg curve in human fibroblasts exposed to energetic silicon and iron ions in vitro at two different energies, 300 MeV/nucleon and 1 GeV/nucleon. Although the data did not reveal an increased yield of MN at the location of the Bragg peak, the increased inhibition of cell progression, which is related to cell death, was found at the Bragg peak location. These results are compared to the calculations of biological damage using a stochastic Monte-Carlo track structure model, Galactic Cosmic Ray Event-based Risk Model (GERM) code (Cucinotta, et al., 2011). The GERM code estimates the basic physical properties along the passage of heavy ions in tissue and shielding materials, by which the experimental set-up can be interpreted. The code can also be used to describe the biophysical events of interest in radiobiology, cancer therapy, and space exploration. The calculation has shown that the severely damaged cells at the Bragg peak are more likely to go through reproductive death, the so called "overkill".

  8. A comparison of form processing involved in the perception of biological and nonbiological movements

    PubMed Central

    Thurman, Steven M.; Lu, Hongjing

    2016-01-01

    Although there is evidence for specialization in the human brain for processing biological motion per se, few studies have directly examined the specialization of form processing in biological motion perception. The current study was designed to systematically compare form processing in perception of biological (human walkers) to nonbiological (rotating squares) stimuli. Dynamic form-based stimuli were constructed with conflicting form cues (position and orientation), such that the objects were perceived to be moving ambiguously in two directions at once. In Experiment 1, we used the classification image technique to examine how local form cues are integrated across space and time in a bottom-up manner. By comparing with a Bayesian observer model that embodies generic principles of form analysis (e.g., template matching) and integrates form information according to cue reliability, we found that human observers employ domain-general processes to recognize both human actions and nonbiological object movements. Experiments 2 and 3 found differential top-down effects of spatial context on perception of biological and nonbiological forms. When a background does not involve social information, observers are biased to perceive foreground object movements in the direction opposite to surrounding motion. However, when a background involves social cues, such as a crowd of similar objects, perception is biased toward the same direction as the crowd for biological walking stimuli, but not for rotating nonbiological stimuli. The model provided an accurate account of top-down modulations by adjusting the prior probabilities associated with the internal templates, demonstrating the power and flexibility of the Bayesian approach for visual form perception. PMID:26746875

  9. A comparison of form processing involved in the perception of biological and nonbiological movements.

    PubMed

    Thurman, Steven M; Lu, Hongjing

    2016-01-01

    Although there is evidence for specialization in the human brain for processing biological motion per se, few studies have directly examined the specialization of form processing in biological motion perception. The current study was designed to systematically compare form processing in perception of biological (human walkers) to nonbiological (rotating squares) stimuli. Dynamic form-based stimuli were constructed with conflicting form cues (position and orientation), such that the objects were perceived to be moving ambiguously in two directions at once. In Experiment 1, we used the classification image technique to examine how local form cues are integrated across space and time in a bottom-up manner. By comparing with a Bayesian observer model that embodies generic principles of form analysis (e.g., template matching) and integrates form information according to cue reliability, we found that human observers employ domain-general processes to recognize both human actions and nonbiological object movements. Experiments 2 and 3 found differential top-down effects of spatial context on perception of biological and nonbiological forms. When a background does not involve social information, observers are biased to perceive foreground object movements in the direction opposite to surrounding motion. However, when a background involves social cues, such as a crowd of similar objects, perception is biased toward the same direction as the crowd for biological walking stimuli, but not for rotating nonbiological stimuli. The model provided an accurate account of top-down modulations by adjusting the prior probabilities associated with the internal templates, demonstrating the power and flexibility of the Bayesian approach for visual form perception. PMID:26746875

  10. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies

    PubMed Central

    Dong, Chengliang; Wei, Peng; Jian, Xueqiu; Gibbs, Richard; Boerwinkle, Eric; Wang, Kai; Liu, Xiaoming

    2015-01-01

    Accurate deleteriousness prediction for nonsynonymous variants is crucial for distinguishing pathogenic mutations from background polymorphisms in whole exome sequencing (WES) studies. Although many deleteriousness prediction methods have been developed, their prediction results are sometimes inconsistent with each other and their relative merits are still unclear in practical applications. To address these issues, we comprehensively evaluated the predictive performance of 18 current deleteriousness-scoring methods, including 11 function prediction scores (PolyPhen-2, SIFT, MutationTaster, Mutation Assessor, FATHMM, LRT, PANTHER, PhD-SNP, SNAP, SNPs&GO and MutPred), 3 conservation scores (GERP++, SiPhy and PhyloP) and 4 ensemble scores (CADD, PON-P, KGGSeq and CONDEL). We found that FATHMM and KGGSeq had the highest discriminative power among independent scores and ensemble scores, respectively. Moreover, to ensure unbiased performance evaluation of these prediction scores, we manually collected three distinct testing datasets, on which no current prediction scores were tuned. In addition, we developed two new ensemble scores that integrate nine independent scores and allele frequency. Our scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Finally, to facilitate variant prioritization in WES studies, we have pre-computed our ensemble scores for 87 347 044 possible variants in the whole-exome and made them publicly available through the ANNOVAR software and the dbNSFP database. PMID:25552646

  11. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies.

    PubMed

    Dong, Chengliang; Wei, Peng; Jian, Xueqiu; Gibbs, Richard; Boerwinkle, Eric; Wang, Kai; Liu, Xiaoming

    2015-04-15

    Accurate deleteriousness prediction for nonsynonymous variants is crucial for distinguishing pathogenic mutations from background polymorphisms in whole exome sequencing (WES) studies. Although many deleteriousness prediction methods have been developed, their prediction results are sometimes inconsistent with each other and their relative merits are still unclear in practical applications. To address these issues, we comprehensively evaluated the predictive performance of 18 current deleteriousness-scoring methods, including 11 function prediction scores (PolyPhen-2, SIFT, MutationTaster, Mutation Assessor, FATHMM, LRT, PANTHER, PhD-SNP, SNAP, SNPs&GO and MutPred), 3 conservation scores (GERP++, SiPhy and PhyloP) and 4 ensemble scores (CADD, PON-P, KGGSeq and CONDEL). We found that FATHMM and KGGSeq had the highest discriminative power among independent scores and ensemble scores, respectively. Moreover, to ensure unbiased performance evaluation of these prediction scores, we manually collected three distinct testing datasets, on which no current prediction scores were tuned. In addition, we developed two new ensemble scores that integrate nine independent scores and allele frequency. Our scores achieved the highest discriminative power compared with all the deleteriousness prediction scores tested and showed low false-positive prediction rate for benign yet rare nonsynonymous variants, which demonstrated the value of combining information from multiple orthologous approaches. Finally, to facilitate variant prioritization in WES studies, we have pre-computed our ensemble scores for 87 347 044 possible variants in the whole-exome and made them publicly available through the ANNOVAR software and the dbNSFP database. PMID:25552646

  12. The complete genomic sequence of the modified vaccinia Ankara strain: comparison with other orthopoxviruses.

    PubMed

    Antoine, G; Scheiflinger, F; Dorner, F; Falkner, F G

    1998-05-10

    The complete genomic DNA sequence of the highly attenuated vaccinia strain modified vaccinia Ankara (MVA) was determined. The genome of MVA is 178 kb in length, significantly smaller than that of the vaccinia Copenhagen genome, which is 192 kb. The 193 open reading frames (ORFs) mapped in the MVA genome probably correspond to 177 genes, 25 of which are split and/or have suffered mutations resulting in truncated proteins. The left terminal genomic region of MVA contains four large deletions and one large insertion relative to the Copenhagen strain. In addition, many ORFs in this region are fragmented, leaving only eight genes structurally intact and therefore presumably functional. The inserted DNA codes for a cluster of genes that is also found in the vaccinia WR strain and in cowpox virus and includes a highly fragmented gene homologous to the cowpox virus host range gene, providing further evidence that a cowpox-like virus was the ancestor of vaccinia. Surprisingly, the central conserved region of the genome also contains some fragmented genes, including ORF F5L, encoding a major membrane protein, and ORFs F11L and O1L, encoding proteins of 39.7 and 77.6 kDa, respectively. The right terminal genomic region carries three large deletions all classical poxviral immune evasion genes and all ankyrin-like genes located in this region are fragmented except for those encoding the interleukin-1 beta receptor and the 68-kDa ankyrin-like protein B18R. Thus, the attenuated phenotype of MVA is the result of numerous mutations, particularly affecting the host interactive proteins, including the ankyrin-like genes, but also involving some structural proteins.

  13. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    PubMed

    Mascher, Martin; Wu, Shuangye; Amand, Paul St; Stein, Nils; Poland, Jesse

    2013-01-01

    The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing

  14. Comparison of the biological H2S removal characteristics among four inorganic packing materials.

    PubMed

    Hirai, M; Kamamoto, M; Yani, M; Shoda, M

    2001-01-01

    Four inorganic packing materials were evaluated in terms of their availability as packing materials of a packed tower deodorization apparatus (biofilter) from the viewpoints of biological H2S removal characteristics and some physical properties. Among porous ceramics (A), calcinated cristobalite (B), calcinated and formed obsidian (C), granulated and calcinated soil (D), the superiority of these packing materials determined based on the values of non-biological removal per unit weight or unit volume of packing material, complete removal capacity of H2S per unit weight of packing material per day or unit volume of packing material per day and pressure drop of the packed bed was in the order of A approximately equal to C > D approximately equal to B, which is correlated with the maximum water content, porosity, and mean pore diameter. PMID:16233011

  15. Comparison of the biological NH3 removal characteristics among four inorganic packing materials.

    PubMed

    Hirai, M; Kamamoto, M; Yani, M; Shoda, M

    2001-01-01

    Four inorganic packing materials were evaluated in terms of their availability as a packing material of a packed tower deodorization apparatus (biofilter) from the viewpoints of biological NH3 removal characteristics and some physical properties. Porous ceramics (A), calcinated cristobalite (B), calcinated and formed obsidian (C), granulated and calculated soil (D) were used. The superiority of these packing materials determined based on the values of non-biological removal per unit weight or unit volume of packing material, complete removal capacity of NH3 per unit weight of packing material per day or unit volume of packing material per day and pressure drop of the packed bed was in the order of A approximately = C > B > or = D. Packing materials A and C with high porosity, maximum water content, and suitable mean pore diameter showed excellent removal capacity. PMID:16233018

  16. Comparison of the biological NH3 removal characteristics among four inorganic packing materials.

    PubMed

    Hirai, M; Kamamoto, M; Yani, M; Shoda, M

    2001-01-01

    Four inorganic packing materials were evaluated in terms of their availability as a packing material of a packed tower deodorization apparatus (biofilter) from the viewpoints of biological NH3 removal characteristics and some physical properties. Porous ceramics (A), calcinated cristobalite (B), calcinated and formed obsidian (C), granulated and calculated soil (D) were used. The superiority of these packing materials determined based on the values of non-biological removal per unit weight or unit volume of packing material, complete removal capacity of NH3 per unit weight of packing material per day or unit volume of packing material per day and pressure drop of the packed bed was in the order of A approximately = C > B > or = D. Packing materials A and C with high porosity, maximum water content, and suitable mean pore diameter showed excellent removal capacity.

  17. Comparison of the biological H2S removal characteristics among four inorganic packing materials.

    PubMed

    Hirai, M; Kamamoto, M; Yani, M; Shoda, M

    2001-01-01

    Four inorganic packing materials were evaluated in terms of their availability as packing materials of a packed tower deodorization apparatus (biofilter) from the viewpoints of biological H2S removal characteristics and some physical properties. Among porous ceramics (A), calcinated cristobalite (B), calcinated and formed obsidian (C), granulated and calcinated soil (D), the superiority of these packing materials determined based on the values of non-biological removal per unit weight or unit volume of packing material, complete removal capacity of H2S per unit weight of packing material per day or unit volume of packing material per day and pressure drop of the packed bed was in the order of A approximately equal to C > D approximately equal to B, which is correlated with the maximum water content, porosity, and mean pore diameter.

  18. Candidate gene analyses by scanning or brute force fluorescent sequencing: a comparison of DOVAM-S with gel-based and capillary-based sequencing.

    PubMed

    Feng, Jinong; Yan, Jin; Li, Wenyan; Chen, Jiesheng; Sommer, Steve S

    2007-01-01

    For epidemiological and diagnostic applications, detection of virtually all mutations is desired. Herein, blinded analyses of DOVAM-S (Detection Of Virtually All Mutations-SSCP), a robotically enhanced multiplex SSCP method, demonstrate that all of 525 mutations (391 unique) are detected by the method. In addition, the costs of DOVAM-S, gel-based fluorescent sequencing and capillary-based fluorescent sequencing are compared. The relative cost effectiveness of gel-based and capillary-based sequence analysis depends on throughput and whether depreciation and service are considered. DOVAM-S reduces the cost of candidate gene analyses relative to brute force sequencing by about threefold. PMID:17949284

  19. Monitoring PAH contamination in water: comparison of biological and physico-chemical tools.

    PubMed

    Bourgeault, A; Gourlay-Francé, C

    2013-06-01

    The suitability of biological methods and chemical-based passive samplers to determine exposure to PAHs was tested by deploying zebra mussels and SPMDs along the Seine River over 11 months. The concentration of 13 PAHs was analyzed every month in both water and mussels. The sum of the PAH concentrations in mussels, initially at 299 ng gdry wt(-1), reached 2654, 3972 and 3727 ng g(-1) at the end of exposure in the three sampling points taken through the river. The respective SPMD-available concentrations of TPAHs reached 9, 52 and 34 ng L(-1). Results showed seasonal variations of total PAH concentrations in the mussels, characterized by a decrease during spawning. The non-achievement of steady state concentration that was observed in mussels may be accounted for by the temporal variation of environmental concentrations. Thus, a bioaccumulation model based on kinetic rather than simple equilibrium partitioning was found to be more appropriate to describe PAH content in mussels. Moreover, biodynamic kinetic modeling proved useful to better understand the uptake and loss processes of pyrene. It clearly shows that these processes are markedly influenced by the biological state of the zebra mussels. The most realistic hypothesis is that the temporal variation of the biodynamic parameters may originate from a decrease of the mussels' metabolization of PAHs during spawning. Since SPMD passive samplers cannot integrate such biological factors, they are poor predictors of PAH bioavailability in mussels. PMID:23562685

  20. Comparison of Three Bed Packings for the Biological Removal of Nitric Oxide from Gas Streams

    SciTech Connect

    Lee, Brady Douglas; Flanagan, W. P.; Barnes, Charles Marshall; Barrett, Karen B.; Zaccardi, Larry Bryan; Apel, William Arnold

    2000-10-01

    Environmental and health issues coupled with increasingly stringent nitrogen oxide (NOx) emission standards indicates a need for the development of alternative low-cost technologies for the removal of NOx from gas streams. Biological NOx conversion offers promise as a novel treatment method. Thermophilic denitrifying bacteria indigenous to composts and soils are capable of converting NOx to environmentally benign nitrogen via a dissimilatory reductive pathway. The present study compares the performance of three bioreactor packing materials (compost, perlite, and biofoam) for the removal of nitric oxide (NO) from a simulated wet-scrubbed combustion gas. Although all three materials performed well (>85% NO removal) at residence times of 70-80 seconds, the compost performed better than the other materials at shorter residence times (13-44 seconds). The perlite and biofoam materials, however, both offer long-term thermal stability and lower pressure drop compared with compost. The feasibility of biological NOx conversion processes will depend on the combined factors of NOx removal ability and pressure drop. The results presented here suggest that the compost, perlite and biofoam systems, subject to further optimization, offer potential for the biological removal of NOx from gas streams.

  1. Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.

    PubMed

    Lie, Alle A Y; Liu, Zhenfeng; Hu, Sarah K; Jones, Adriane C; Kim, Diane Y; Countway, Peter D; Amaral-Zettler, Linda A; Cary, S Craig; Sherr, Evelyn B; Sherr, Barry F; Gast, Rebecca J; Caron, David A

    2014-07-01

    Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

  2. Comparison of Model Calculations of Biological Damage from Exposure to Heavy Ions with Measurements

    NASA Astrophysics Data System (ADS)

    Kim, Myung-Hee Y.; Wu, Honglu; Hada, Megumi; Cucinotta, Francis

    The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LET g or X rays, the presence of shielding does not always reduce the radiation risks for energetic charged-particle exposure. Dose delivered by the charged particle increases sharply at the Bragg peak. However, the Bragg curve does not necessarily represent the biological damage along the particle path since biological effects are influenced by the track structures of both primary and secondary particles. Therefore, the ‘‘biological Bragg curve’’ is dependent on the energy and the type of the primary particle and may vary for different biological end points. Measurements of the induction of micronuclei (MN) have made across the Bragg curve in human fibroblasts exposed to energetic silicon and iron ions in vitro at two different energies, 300 MeV/nucleon and 1 GeV/nucleon. Although the data did not reveal an increased yield of MN at the location of the Bragg peak, the increased inhibition of cell progression, which is related to cell death, was found at the Bragg peak location. These results are compared to the calculations of biological damage using a stochastic Monte-Carlo track structure model, Galactic Cosmic Ray Event-based Risk Model (GERM) code (Cucinotta et al., 2011). The GERM code estimates the basic physical properties along the passage of heavy ions in tissue and shielding materials, by which the experimental set-up can be interpreted. The code can also be used to describe the biophysical events of interest in radiobiology, cancer therapy, and space exploration. The calculation has shown that the severely damaged cells at the Bragg peak are more likely to go through reproductive death, the so called “overkill”. F. A. Cucinotta, I. Plante, A. L. Ponomarev, and M. Y. Kim, Nuclear Interactions in Heavy Ion Transport and Event

  3. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach.

    PubMed

    Adamala, Katarzyna; Anella, Fabrizio; Wieczorek, Rafal; Stano, Pasquale; Chiarabelli, Cristiano; Luisi, Pier Luigi

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge "sequence space", leading to the question "why these macromolecules, and not the others?" We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called "never born biopolymer" project) with respect to the production of folded structures. Being still far from solved, the main aspects of these "open questions" are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection.

  4. Elemental distribution and sample integrity comparison of freeze-dried and frozen-hydrated biological tissue samples with nuclear microprobe

    NASA Astrophysics Data System (ADS)

    Vavpetič, P.; Vogel-Mikuš, K.; Jeromel, L.; Ogrinc Potočnik, N.; Pongrac, P.; Drobne, D.; Pipan Tkalec, Ž.; Novak, S.; Kos, M.; Koren, Š.; Regvar, M.; Pelicon, P.

    2015-04-01

    The analysis of biological samples in frozen-hydrated state with micro-PIXE technique at Jožef Stefan Institute (JSI) nuclear microprobe has matured to a point that enables us to measure and examine frozen tissue samples routinely as a standard research method. Cryotome-cut slice of frozen-hydrated biological sample is mounted between two thin foils and positioned on the sample holder. The temperature of the cold stage in the measuring chamber is kept below 130 K throughout the insertion of the samples and the proton beam exposure. Matrix composition of frozen-hydrated tissue is consisted mostly of ice. Sample deterioration during proton beam exposure is monitored during the experiment, as both Elastic Backscattering Spectrometry (EBS) and Scanning Transmission Ion Microscopy (STIM) in on-off axis geometry are recorded together with the events in two PIXE detectors and backscattered ions from the chopper in a single list-mode file. The aim of this experiment was to determine differences and similarities between two kinds of biological sample preparation techniques for micro-PIXE analysis, namely freeze-drying and frozen-hydrated sample preparation in order to evaluate the improvements in the elemental localisation of the latter technique if any. In the presented work, a standard micro-PIXE configuration for tissue mapping at JSI was used with five detection systems operating in parallel, with proton beam cross section of 1.0 × 1.0 μm2 and a beam current of 100 pA. The comparison of the resulting elemental distributions measured at the biological tissue prepared in the frozen-hydrated and in the freeze-dried state revealed differences in elemental distribution of particular elements at the cellular level due to the morphology alteration in particular tissue compartments induced either by water removal in the lyophilisation process or by unsatisfactory preparation of samples for cutting and mounting during the shock-freezing phase of sample preparation.

  5. Genome Sequence of the Endosymbiont Rickettsia peacockii and Comparison with Virulent Rickettsia rickettsii: Identification of Virulence Factors

    PubMed Central

    Felsheim, Roderick F.; Kurtti, Timothy J.; Munderloh, Ulrike G.

    2009-01-01

    Rickettsia peacockii, also known as the East Side Agent, is a non-pathogenic obligate intracellular bacterium found as an endosymbiont in Dermacentor andersoni ticks in the western USA and Canada. Its presence in ticks is correlated with reduced prevalence of Rickettsia rickettsii, the agent of Rocky Mountain Spotted Fever. It has been proposed that a virulent SFG rickettsia underwent changes to become the East Side Agent. We determined the genome sequence of R. peacockii and provide a comparison to a closely related virulent R. rickettsii. The presence of 42 chromosomal copies of the ISRpe1 transposon in the genome of R. peacockii is associated with a lack of synteny with the genome of R. rickettsii and numerous deletions via recombination between transposon copies. The plasmid contains a number of genes from distantly related organisms, such as part of the glycosylation island of Pseudomonas aeruginosa. Genes deleted or mutated in R. peacockii which may relate to loss of virulence include those coding for an ankyrin repeat containing protein, DsbA, RickA, protease II, OmpA, ScaI, and a putative phosphoethanolamine transferase. The gene coding for the ankyrin repeat containing protein is especially implicated as it is mutated in R. rickettsii strain Iowa, which has attenuated virulence. Presence of numerous copies of the ISRpe1 transposon, likely acquired by lateral transfer from a Cardinium species, are associated with extensive genomic reorganization and deletions. The deletion and mutation of genes possibly involved in loss of virulence have been identified by this genomic comparison. It also illustrates that the introduction of a transposon into the genome can have varied effects; either correlating with an increase in pathogenicity as in Francisella tularensis or a loss of pathogenicity as in R. peacockii and the recombination enabled by multiple transposon copies can cause significant deletions in some genomes while not in others. PMID:20027221

  6. Comparison of various dissolution techniques for determination of Po-210 in biological samples.

    PubMed

    Planinšek, P; Benedik, L; Smodiš, B

    2013-11-01

    The aim of the present study was to compare three wet digestion procedures for dissolution of biological samples in the determination of Po-210. Classical wet ashing over a gas flame with acids in a long-necked Kjeldahl flask, digestion with acids in an Erlenmeyer flask and microwave digestion in a Teflon vessel at temperatures at up to 200°C were investigated. The results obtained showed that the activity concentrations of Po-210 found in the samples analysed were comparable for all the procedures used.

  7. Comparison of Single Channel Potassium Current in Biological and Synthetic Systems --- Dependence on Voltage

    NASA Astrophysics Data System (ADS)

    Siwy, Zuzanna; Mercik, Szymon; Weron, Karina; Spohr, Reimar; Wolf, Alexander; Grzywna, Zbigniew

    2000-05-01

    The influence of an external field on an ion current pattern in biological and synthetic systems was investigated. The patch clamp recordings of potassium current through a big conductance locust potassium channel (BK-channel) and a track-etched polyethylene terephthalate membrane were examined by the power spectrum, fractal analysis and relative dispersion analysis. A similar dependence of potassium current behaviour on the external voltage in both systems was found. The generalized dimension formalism is redefined to make it applicable to the analysis of time series.

  8. A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

    NASA Astrophysics Data System (ADS)

    Beasley, D. G.; Alves, L. C.; Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C.; Le Trequesser, Q.; Marques, A. C.; Seznec, H.; da Silva, R. C.

    2014-07-01

    The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans - a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

  9. A comparison of student reactions to biology instruction by interactive videodisc or conventional laboratory

    NASA Astrophysics Data System (ADS)

    Leonard, William H.

    This study was designed to learn if students perceived an interactive computer/videodisc learning system to represent a viable alternative to (or extension of) the conventional laboratory for learning biology skills and concepts normally taught under classroom laboratory conditions. Data were collected by questionnaire for introductory biology classes at a large midwestern university where students were randomly assigned to two interactive videodisc/computer lessons titled Respiration and Climate and Life or traditional laboratory investigation with the same titles and concepts. The interactive videodisc system consisted of a TRS-80 Model III microcomputer interfaced to a Pioneer laser-disc player and a color TV monitor. Students indicated an overall level satisfaction with this strategy very similar to that of conventional laboratory instruction. Students frequently remarked that videodisc instruction gave them more experimental and procedural options and more efficient use of instructional time than did the conventional laboratory mode. These two results are consistent with past CAI research. Students also had a strong perception that the images on the videodisc were not real and this factor was perceived as having both advantages and disadvantages. Students found the two approaches to be equivalent to conventional laboratory instruction in the areas of general interest, understanding of basic principles, help on examinations, and attitude toward science. The student-opinion data in this study do not suggest that interactive videodisc technology serve as a substitute to the wet laboratory experience, but that this medium may enrich the spectrum of educational experiences usually not possible in typical classroom settings.

  10. Comparison of the biological effects of {sup 18}F at different intracellular levels

    SciTech Connect

    Kashino, Genro; Hayashi, Kazutaka; Douhara, Kazumasa; Kobashigawa, Shinko; Mori, Hiromu

    2014-11-07

    Highlights: • We estimated the inductions of DNA DSB in cell treated with {sup 18}F-FDG. • We found that inductions of DNA DSB are dependent on accumulation of {sup 18}F in cell. • Accumulation of {sup 18}F in cell may be indispensable for risk estimation of PET. - Abstract: We herein examined the biological effects of cells treated with {sup 18}F labeled drugs for positron emission tomography (PET). The relationship between the intracellular distribution of {sup 18}F and levels of damaged DNA has yet to be clarified in detail. We used culture cells (Chinese Hamster Ovary cells) treated with two types of {sup 18}F labeled drugs, fluorodeoxyglucose (FDG) and fluorine ion (HF). FDG efficiently accumulated in cells, whereas HF did not. To examine the induction of DNA double strand breaks (DSB), we measured the number of foci for 53BP1 that formed at the site of DNA DSB. The results revealed that although radioactivity levels were the same, the induction of 53BP1 foci was stronger in cells treated with {sup 18}F-FDG than in those treated with {sup 18}F-HF. The clonogenic survival of cells was significantly lower with {sup 18}F-FDG than with {sup 18}F-HF. We concluded that the efficient accumulation of {sup 18}F in cells led to stronger biological effects due to more severe cellular lethality via the induction of DNA DSB.

  11. Chemical and biological assessment of Angelica herbal decoction: comparison of different preparations during historical applications.

    PubMed

    Zhang, Wendy Li; Zheng, Ken Yu-Zhong; Zhu, Kevin Yue; Zhan, Janis Ya-Xian; Bi, Cathy Wen-Chuan; Chen, Jian-Ping; Du, Crystal Ying-Qing; Zhao, Kui-Jun; Lau, David Tai-Wai; Dong, Tina Ting-Xia; Tsim, Karl Wah-Keung

    2012-08-15

    The commonly used Angelica herbal decoction today is Danggui Buxue Tang (DBT), which is a dietary supplement in treating menopausal irregularity in women, i.e. to nourish "Qi" and to enrich "Blood". According to historical record, many herbal decoctions were also named DBT, but the most popular formulation of DBT was written in Jin dynasty (1247 AD) of China, which contained Astragali Radix (AR) and Angelicae Sinensis Radix (ASR) with a weight ratio of 5:1. However, at least two other Angelica herbal decoctions recorded as DBT were prescribed in Song (1155 AD) and Qing dynasties (1687 AD). Although AR and ASR are still the major components in the DBT herbal decoctions, they are slightly varied in the herb composition. In order to reveal the efficiency of different Angelica herbal decoctions, the chemical and biological properties of three DBT herbal extracts were compared. Significantly, the highest amounts of AR-derived astragaloside III, astragaloside IV, calycosin and formononetin and ASR-derived ferulic acid were found in DBT described in 1247 AD: this preparation showed stronger activities in osteogenic, estrogenic and erythropoetic effects than the other two DBT. The current results supported the difference of three DBT in chemical and biological properties, which could be a result of different herbal combinations. For the first time, this study supports the popularity of DBT described in 1247 AD.

  12. Comparison of five different RNA sources to examine the lactating bovine mammary gland transcriptome using RNA-Sequencing.

    PubMed

    Cánovas, Angela; Rincón, Gonzalo; Bevilacqua, Claudia; Islas-Trejo, Alma; Brenaut, Pauline; Hovey, Russell C; Boutinaud, Marion; Morgenthaler, Caroline; VanKlompenberg, Monica K; Martin, Patrice; Medrano, Juan F

    2014-07-08

    The objective of this study was to examine five different sources of RNA, namely mammary gland tissue (MGT), milk somatic cells (SC), laser microdissected mammary epithelial cells (LCMEC), milk fat globules (MFG) and antibody-captured milk mammary epithelial cells (mMEC) to analyze the bovine mammary gland transcriptome using RNA-Sequencing. Our results provide a comparison between different sampling methods (invasive and non-invasive) to define the transcriptome of mammary gland tissue and milk cells. This information will be of value to investigators in choosing the most appropriate sampling method for different research applications to study specific physiological states during lactation. One of the simplest procedures to study the transcriptome associated with milk appears to be the isolation of total RNA directly from SC or MFG released into milk during lactation. Our results indicate that the SC and MFG transcriptome are representative of MGT and LCMEC and can be used as effective and alternative samples to study mammary gland expression without the need to perform a tissue biopsy.

  13. Comparison of the rates of ozonation of biological antioxidants and oleate and linoleate esters

    SciTech Connect

    Giamalva, D.; Church, D.F.; Pryor, W.A.

    1985-12-17

    The rates of reaction with ozone of some biological antioxidants and simple polyunsaturated fatty acids (PUFA) have been measured in water or in aqueous micellar solutions. At pH 7.0 the rate constants are ca. 10(6) M-1 sec-1 for urate, alpha-tocopherol, and PUFA, and 6 X 10(7) M-1 sec-1 for ascorbate. When ozone-containing air is breathed, ascorbate in the lung may undergo direct ozonation. However, alpha-tocopherol is probably spared direct reaction with ozone because it doesn't effectively compete with PUFA in pulmonary membranes; rather, tocopherol is used to scavenge radicals produced from the ozone-PUFA reaction.

  14. Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination

    USGS Publications Warehouse

    Thomson, E.A.; Luoma, S.N.; Johansson, C.E.; Cain, D.J.

    1984-01-01

    Sediments and an indicator organism (Macoma balthica, a deposit-feeding bivalve) were used to assess the relative importance of secondary sewage, urban runoff, a landfill containing metal-enriched ash wastes and a yacht harbor in contributing to Ag, Cu and Zn enrichment in South San Francisco Bay. Spatial gradients in sediments and organisms showed Cu and Ag enrichment originated from sewage discharge, whereas Zn enrichment originated from both sewage and urban runoff. Elevated concentrations of Cu in the sediments of the yacht harbor resulted from a high abundance of fine particles. The biological availability of Cu, Ag and Zn did not coincide with metal enrichment in sediments. The availability of Cu and Ag was greatest nearest the sewage outfall and greater in winter and spring than in summer. The availability of Zn in urban runoff appeared to be lower than the availability of Zn associated with sewage.

  15. Chemical and biological comparison of the fruit extracts of Citrus wilsonii Tanaka and Citrus medica L.

    PubMed

    Zhao, Pan; Duan, Li; Guo, Long; Dou, Li-Li; Dong, Xin; Zhou, Ping; Li, Ping; Liu, E-Hu

    2015-04-15

    Citri Fructus (CF), the mature fruit of Citrus wilsonii Tanaka (CWT) or Citrus medica L. (CML), is an important citrus by-product with health promoting and nutritive properties. The present study compares the chemical and biological differences of CWT and CML. Thin layer chromatography and high performance liquid chromatography, coupled with quadrupole time-of-flight tandem mass spectrometry techniques, were employed to compare the chemical profiles of CWT and CML. A total of 25 compounds were identified and the results indicated that there were significant differences in chemical composition between the two CF species. The quantitative results obtained by HPLC coupled with diode array detector method demonstrated that naringin was present in the highest amounts in CWT, whilst nomilin was the most dominant constituent in CML. It was also found that CWT had significantly higher free radical-scavenging activity than CML.

  16. Comparison of Selective Culturing and Biochemical Techniques for Measuring Biological Activity in Geothermal Process Fluids

    SciTech Connect

    Pryfogle, Peter Albert

    2000-09-01

    For the past three years, scientists at the Idaho National Engineering and Environmental Laboratory have been conducting studies aimed at determining the presence and influence of bacteria found in geothermal plant cooling water systems. In particular, the efforts have been directed at understanding the conditions that lead to the growth and accumulation of biomass within these systems, reducing the operational and thermal efficiency. Initially, the methods selected were based upon the current practices used by the industry and included the collection of water quality parameters, the measurement of soluble carbon, and the use of selective medial for the determination of the number density of various types of organisms. This data has been collected on a seasonal basis at six different facilities located at the Geysers’ in Northern California. While this data is valuable in establishing biological growth trends in the facilities and providing an initial determination of upset or off-normal conditions, more detailed information about the biological activity is needed to determine what is triggering or sustaining the growth in these facilities in order to develop improved monitoring and treatment techniques. In recent years, new biochemical approaches, based upon the analyses of phospholipid fatty acids and DNA recovered from environmental samples, have been developed and commercialized. These techniques, in addition to allowing the determination of the quantity of biomass, also provide information on the community composition and the nutritional status of the organisms. During the past year, samples collected from the condenser effluents of four of the plants from The Geysers’ were analyzed using these methods and compared with the results obtained from selective culturing techniques. The purpose of this effort was to evaluate the cost-benefit of implementing these techniques for tracking microbial activity in the plant study, in place of the selective culturing

  17. Comparison of Career Concerns among College Women and Men Enrolled in Biological and Physical Sciences

    NASA Astrophysics Data System (ADS)

    Dodson, Maria

    The underrepresentation of women enrolled in the physical sciences continues to challenge academic leaders despite over 40 years of programming to promote gender equity within these curricula. This study employed a quantitative, causal comparative method to explore if and to what extent career concerns differed among female and male undergraduate physical and biological science students. The theory of planned behavior and life-span, life-space theory served as the theoretical framework for the study. Quantitative survey data were collected from 43 students at four institutions across the United States. The findings indicated that undergraduate women in physical science programs of study had a significantly different level of concern about the Innovating sub-category of the third stage of career development, Maintenance, as compared to undergraduate women in biological science curricula [F(1,33) = 6.244, p = 0.018]. Additionally, there was a statistically significant difference between female undergraduate physical science students and undergraduate male science students in the sub-categories of Implementation [F(1,19) = 7.228, p = 0.015], Advancing [F(1,19) = 11.877, p = 0.003], and Innovating [F(1,19) = 11.782, p = 0.003] within the first three stages of career development (Exploration, Establishment, and Maintenance). The comparative differences among the study groups offers new information about undergraduate career concerns that may contribute to the underrepresentation of women enrolled in the physical sciences. Suggestions for future research and programs within higher education targeted at reducing the career concerns of current and prospective female students in physical science curricula are discussed.

  18. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.

    PubMed

    Dabney, Jesse; Meyer, Matthias

    2012-02-01

    High-throughput sequencing technologies frequently necessitate the use of PCR for sequencing library amplification. PCR is a sometimes enigmatic process and is known to introduce biases. Here we perform a simple amplification-sequencing assay using 10 commercially available polymerase-buffer systems to amplify libraries prepared from both modern and ancient DNA. We compare the performance of the polymerases with respect to a previously uncharacterized template length bias, as well as GC-content bias, and find that simply avoiding certain polymerase can dramatically decrease the occurrence of both. For amplification of ancient DNA, we found that some commonly used polymerases strongly bias against amplification of endogenous DNA in favor of GC-rich microbial contamination, in our case reducing the fraction of endogenous sequences to almost half.

  19. Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity.

    PubMed

    Nováková, S; Svoboda, J; Glasa, M

    2014-01-01

    The complete genome sequences of two Slovak Zucchini yellow mosaic virus isolates (ZYMV-H and ZYMV-SE04T) were determined. These isolates differ significantly in their pathogenicity, producing either severe or very mild symptoms on susceptible cucurbit hosts. The viral genome of both isolates consisted of 9593 nucleotides in size, and contained an open reading frame encoding a single polyprotein of 3080 amino acids. Despite their different biological properties, an extremely high nucleotide identity could be noted (99.8%), resulting in differences of only 5 aa, located in the HC-Pro, P3, and NIb, respectively. In silico analysis including 5 additional fully-sequenced and phylogenetically closely-related isolates known to induce different symptoms in cucurbits was performed. This suggested that the key single mutation responsible for virus pathogenicity is likely located in the N-terminal part of P3, adjacent to the PIPO. PMID:25518719

  20. Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity.

    PubMed

    Nováková, S; Svoboda, J; Glasa, M

    2014-01-01

    The complete genome sequences of two Slovak Zucchini yellow mosaic virus isolates (ZYMV-H and ZYMV-SE04T) were determined. These isolates differ significantly in their pathogenicity, producing either severe or very mild symptoms on susceptible cucurbit hosts. The viral genome of both isolates consisted of 9593 nucleotides in size, and contained an open reading frame encoding a single polyprotein of 3080 amino acids. Despite their different biological properties, an extremely high nucleotide identity could be noted (99.8%), resulting in differences of only 5 aa, located in the HC-Pro, P3, and NIb, respectively. In silico analysis including 5 additional fully-sequenced and phylogenetically closely-related isolates known to induce different symptoms in cucurbits was performed. This suggested that the key single mutation responsible for virus pathogenicity is likely located in the N-terminal part of P3, adjacent to the PIPO.

  1. A comparison of hands-on inquiry instruction to lectureinstruction with special needs high school biology students

    NASA Astrophysics Data System (ADS)

    Jensen-Ruopp, Helga Spitko

    A comparison of hands-on inquiry instruction with lecture instruction was presented to 134 Patterns and Process Biology students. Students participated in seven biology lessons that were selected from Biology Survey of Living Things (1992). A pre and post paper and pencil assessment was used as the data collecting instrument. The treatment group was taught using hands-on inquiry strategies while the non-treatment group was taught in the lecture method of instruction. The team teaching model was used as the mode of presentation to the treatment group and the non-treatment group. Achievement levels using specific criterion; novice (0% to 50%), developing proficiency (51% to 69%), accomplished (70% to 84) and exceptional or mastery level (85% to 100%) were used as a guideline to tabulate the results of the pre and post assessment. Rubric tabulation was done to interpret the testing results. The raw data was plotted using percentage change in test score totals versus reading level score by gender as well as percentage change in test score totals versus auditory vocabulary score by gender. Box Whisker plot comparative descriptive of individual pre and post test scores for the treatment and non-treatment group was performed. Analysis of covariance (ANCOVA) using MINITAB Statistical Software version 14.11 was run on data of the seven lessons, as well as on gender (male results individual and combined, and female results individual and combined) results. Normal Probability Plots for total scores as well as individual test scores were performed. The results suggest that hands-on inquiry based instruction when presented to special needs students including; at-risk; English as a second language limited, English proficiency and special education inclusive students' learning may enhance individual student achievement.

  2. Whole-Genome Sequence of Pseudomonas xanthomarina Strain UASWS0955, a Potential Biological Agent for Agricultural and Environmental Uses

    PubMed Central

    Crovadore, Julien; Cochard, Bastien; Calmin, Gautier; Chablais, Romain; Schulz, Torsten

    2016-01-01

    We report here the whole-genome shotgun sequence of the strain UASWS0955 of the species Pseudomonas xanthomarina, isolated from sewage sludge. This genome was obtained with an Illumina MiniSeq and is the second genome registered for this species, which is considered as a promising resource for agriculture and bioremediation of contaminated soils. PMID:27738044

  3. Draft Genome Sequence of Microvirga sp. Strain BSC39, Isolated from Biological Soil Crust of Moab, Utah.

    PubMed

    Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

    2014-01-01

    Microvirga sp. BSC39 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC39 genome contains iron siderophore uptake and hydrolysis enzymes; however, it lacks siderophore synthesis pathways, suggesting the uptake of siderophores produced by neighboring microbes. PMID:25395650

  4. Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah.

    PubMed

    Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

    2014-01-01

    Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

  5. Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah.

    PubMed

    Bailey, Alexis C; Kellom, Matthew; Poret-Peterson, Amisha T; Noonan, Kathryn; Hartnett, Hilairy E; Raymond, Jason

    2014-01-01

    Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate reduction pathway as well as a TCA cycle, making it a facultative anaerobe. PMID:25395652

  6. Draft Genome Sequence of Bacillus sp. Strain BSC154, Isolated from Biological Soil Crust of Moab, Utah

    PubMed Central

    Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

    2014-01-01

    Bacillus sp. BSC154 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and biofilm production. The BSC154 genome contains iron siderophore production, nitrate reduction, mixed acid-butanediol fermentation, and assimilatory and dissimilatory sulfate metabolism pathways. PMID:25395651

  7. Draft Genome Sequence of Massilia sp. Strain BSC265, Isolated from Biological Soil Crust of Moab, Utah

    PubMed Central

    Bailey, Alexis C.; Kellom, Matthew; Poret-Peterson, Amisha T.; Noonan, Kathryn; Hartnett, Hilairy E.

    2014-01-01

    Massilia sp. BSC265 was isolated from a biological soil crust near Moab, Utah. The strain appears to be capable of chemotaxis and exopolysaccharide synthesis for biofilm adhesion. The BSC265 genome contains a complete dissimilatory nitrate reduction pathway as well as a TCA cycle, making it a facultative anaerobe. PMID:25395652

  8. Comparison of amino acid sequence of bovine coagulation Factor IX (Christmas Factor) with that of other vitamin K-dependent plasma proteins.

    PubMed

    Katayama, K; Ericsson, L H; Enfield, D L; Walsh, K A; Neurath, H; Davie, E W; Titani, K

    1979-10-01

    The amino acid sequence of bovine blood coagulation Factor IX (Christmas Factor) is presented and compared with the sequences of other vitamin K-dependent plasma proteins and pancreatic trypsinogen. The 416-residue sequence of Factor IX was determined largely by automated Edman degradation of two large segments, containing 181 and 235 residues, isolated after activating Factor IX with a protease from Russell's viper venom. Subfragments of the two segments were produced by enzymatic digestion and by chemical cleavage of methionyl, tryptophyl, and asparaginyl-glycyl bonds. Comparison of the amino acid sequences of Factor IX, Factor X, and Protein C demonstrates that they are homologous throughout. Their homology with prothrombin, however, is restricted to the amino-terminal region, which is rich in gamma-carboxyglutamic acid, and the carboxyl-terminal region, which represents the catalytic domain of these proteins and corresponds to that of pancreatic serine proteases.

  9. Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.

    SciTech Connect

    Feil, Helene; Feil, William S.; Chain, Patrick; Larimer, Frank; DiBartolo, Genevieve; Copeland, Alex; Lykidis, Athanasios; Trong,Stephen; Nolan, Matt; Goltsman, Eugene; Thiel, James; Malfatti,Stephanie; Loper, Joyce E.; Lapidus, Alla; Detter, John C.; Land, Miriam; Richardson, Paul M.; Kyrpides, Nikos C.; Ivanova, Natalia; Lindow, StevenE.

    2005-04-01

    The complete genomic sequence of Pseudomonas syringaepathovar syringae B728a (Pss B728a), has been determined and is comparedwith that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Thesetwo pathovars of this economically important species of plant pathogenicbacteria differ in host range and apparent patterns of interaction withplants, with Pss having a more pronounced epiphytic stage of growth andhigher abiotic stress tolerance and Pst DC3000 having a more pronouncedapoplastic growth habitat. The Pss B728a genome (6.1 megabases) containsa circular chromosome and no plasmid, whereas the Pst DC3000 genome is6.5 mbp in size, composed of a circular chromosome and two plasmids.While a high degree of similarity exists between the two sequencedPseudomonads, 976 protein-encoding genes are unique to Pss B728a whencompared to Pst DC3000, including large genomic islands likely tocontribute to virulence and host specificity. Over 375 repetitiveextragenic palindromic sequences (REPs) unique to Pss B728a when comparedto Pst DC3000 are widely distributed throughout the chromosome except in14 genomic islands, which generally had lower GC content than the genomeas a whole. Content of the genomic islands vary, with one containing aprophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the976 genes of Pss B728a with no counterpart in Pst DC3000 are thoseencoding for syringopeptin (SP), syringomycin (SR), indole acetic acidbiosynthesis, arginine degradation, and production of ice nuclei. Thegenomic comparison suggests that several unique genes for Pss B728a suchas ectoine synthase, DNA repair, and antibiotic production may contributeto epiphytic fitness and stress tolerance of this organism. Pseudomonassyringae, a member of the gamma subgroup of the Proteobacteria, is awidespread bacterial pathogen of many plant species. The species P.syringae is subdivided into approximately 50 pathovars based onpathogenicity and host range. P. syringae is capable of

  10. Comparison of MALDI-TOF MS, Housekeeping Gene Sequencing, and 16S rRNA Gene Sequencing for Identification of Aeromonas Clinical Isolates

    PubMed Central

    Shin, Hee Bong; Yoon, Jihoon; Lee, Yangsoon; Kim, Myung Sook

    2015-01-01

    Purpose The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB). Materials and Methods We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS. Results The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level. Conclusion The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate. PMID:25684008

  11. Hydrothane(R) interactions with biological components: a comparison with Chronoflex(R).

    PubMed

    Santin, M; Wassall, M A; Ambrosio, L; Nicolais, L; Petillo, O; Peluso, G; Denyer, S P

    2003-01-01

    The interaction of a glycol-containing polyurethane, Hydrothane(R), was assessed with respect to protein adsorption and cell and bacterial adhesion. The results obtained were compared with those from a second polyurethane, Chronoflex(R). Dynamic contact angle (DCA) and protein adsorption studies indicated that the overall hydrophilic nature of Hydrothane in physiological environment was affected by the possible presence of hydrophobic domains still exposed at the surface after wetting. Indeed, despite the high degree of hydrophilicity in an aqueous environment, a stronger protein binding was evidenced on Hydrothane when the two serum- and urine-conditioned polyurethane surfaces were selectively washed by isopropanol/water mixtures of increasing concentrations. Furthermore, immunoblotting of the serum proteins adsorbed on Hydrothane demonstrated the presence on its surface of proteins able to establish hydrophobic interactions such as human serum albumin (HSA) and á 1-microglobulin ( á 1-m). The C3 fragment of complement showed an immunoblotting profile different from the control serum suggesting an activation of this fragment. The adhesion of fibroblasts and Pseudomonas aeruginosa on the surface of the two materials was evaluated and the data were related to protein adsorption. In both cases Hydrothane showed levels of adhesion of eukaryotic and prokaryotic cells significantly lower than Chronoflex. These data were related to the absence of a significant binding of proteins such as fibronectin bringing amino acid receptor sequences in their structure. (Journal of Applied Biomaterials & Biomechanics 2003; 1: 67-75). PMID:20803474

  12. Light-assisted drying (LAD) of small volume biologics: a comparison of two IR light sources

    NASA Astrophysics Data System (ADS)

    Young, Madison A.; Van Vorst, Matthew; Elliott, Gloria D.; Trammell, Susan R.

    2016-03-01

    Protein therapeutics have been developed to treat diseases ranging from arthritis and psoriasis to cancer. A challenge in the development of protein-based drugs is maintaining the protein in the folded state during processing and storage. We are developing a novel processing method, light-assisted drying (LAD), to dehydrate proteins suspended in a sugar (trehalose) solution for storage at supra-zero temperatures. Our technique selectively heats the water in small volume samples using near-IR light to speed dehydration which prevents sugar crystallization that can damage embedded proteins. In this study, we compare the end moisture content (EMC) as a function of processing time of samples dried with two different light sources, Nd:YAG (1064 nm) and Thulium fiber (1850 nm) lasers. EMC is the ratio of water to dry weight in a sample and the lower the EMC the higher the possible storage temperature. LAD with the 1064 and 1850 nm lasers yielded 78% and 65% lower EMC, respectively, than standard air-drying. After 40 minutes of LAD with 1064 and 1850 nm sources, EMCs of 0.27+/-.27 and 0.15+/-.05 gH2O/gDryWeight were reached, which are near the desired value of 0.10 gH2O/gDryWeight that enables storage in a glassy state without refrigeration. LAD is a promising new technique for the preparation of biologics for anhydrous preservation.

  13. Histological and biological comparisons between complete and incomplete discoid lateral meniscus.

    PubMed

    Inoue, Hiroto; Furumatsu, Takayuki; Maehara, Ami; Tanaka, Takaaki; Ozaki, Toshifumi

    2016-09-01

    The discoid lateral meniscus (DLM) is an anatomically abnormal meniscus that covers a greater area of the tibial plateau than the normal meniscus. The DLM is classified into two types: complete (CDLM) and incomplete (ICDLM) types. In this study, we investigated the histological and cell biological characteristics of CDLM and ICDLM. The number of blood vessels, proteoglycan deposition, and collagen distribution were assessed using meniscal tissues. Collagen production was also investigated in CDLM and ICDLM cells. The intercondylar region of the CDLM had a higher number of blood vessels than the inner region of the ICDLM. Safranin O staining density and type II collagen deposition in ICDLM were higher than those in CDLM. Type II collagen-positive cells were higher in ICLDM than in CDLM. CDLM cells showed slender fibroblastic morphology, while ICDLM cells were triangular chondrocytic in shape. This study demonstrated that the intercondylar region of the CDLM showed similar properties to the outer region of the meniscus. The inner region of the ICDLM, on the other hand, differed from the intercondylar region of the CDLM. Our results suggest that the intercondylar region of the CDLM may have a high healing potential like the outer meniscus.

  14. Comparison of Biological Responses in Rats Under Various Cigarette Smoke Exposure Conditions

    PubMed Central

    Tsuji, Hiroyuki; Fujimoto, Hitoshi; Matsuura, Daiki; Nishino, Tomoki; Lee, K Monica; Yoshimura, Hiroyuki

    2013-01-01

    A variety of exposure regimens of cigarette smoke have been used in animal models of lung diseases. In this study, we compared biological responses of smoke exposure in rats, using different smoke concentrations (wet total particulate matter [WTPM]), daily exposure durations, and total days of exposure. As a range-finding acute study, we first compared pulmonary responses between SD and F344 strains after a single nose-only exposure to mainstream cigarette smoke or LPS. Secondly, F344 rats were exposed to cigarette smoke for 2 or 13 weeks under the comparable daily exposure dose (WTPM concentration x daily exposure duration; according to Haber’s rule) but at a different WTPM concentration or daily exposure duration. Blood carboxylhemoglobin was increased linearly to the WTPM concentration, while urinary nicotine plus cotinine value was higher for the longer daily exposure than the corresponding shorter exposure groups. Gamma glutamyl transferase activity in bronchoalveolar lavage fluid (BALF) was increased dose dependently after 2 and 13 weeks of cigarette smoke exposure, while the neutrophil content in BALF was not increased notably. Smoke-exposed groups showed reduced body weight gain and increased relative lung and heart weights. While BALF parameters and the relative lung weights suggest pulmonary responses, histopathological examination showed epithelial lesions mainly in the upper respiratory organs (nose and larynx). Collectively, the results indicate that, under the employed study design, the equivalent daily exposure dose (exposure concentration x duration) induces equivalent pulmonary responses in rats. PMID:23914058

  15. Fermentation of biologically pretreated wheat straw for ethanol production: comparison of fermentative microorganisms and process configurations.

    PubMed

    López-Abelairas, María; Lu-Chau, Thelmo Alejandro; Lema, Juan Manuel

    2013-08-01

    The pretreatment of lignocellulosic biomass with white-rot fungi to produce bioethanol is an environmentally friendly alternative to the commonly used physico-chemical processes. After biological pretreatment, a solid substrate composed of cellulose, hemicellulose and lignin, the two latter with a composition lower than that of the initial substrate, is obtained. In this study, six microorganisms and four process configurations were utilised to ferment a hydrolysate obtained from wheat straw pretreated with the white-rot fungus Irpex lacteus. To enhance total sugars utilisation, five of these microorganisms are able to metabolise, in addition to glucose, most of the pentoses obtained after the hydrolysis of wheat straw by the application of a mixture of hemicellulolytic and cellulolytic enzymes. The highest overall ethanol yield was obtained with the yeast Pachysolen tannophilus. Its application in combination with the best process configuration yielded 163 mg ethanol per gram of raw wheat straw, which was between 23 and 35 % greater than the yields typically obtained with a conventional bioethanol process, in which wheat straw is pretreated using steam explosion and fermented with the yeast Saccharomyces cerevisiae.

  16. Quantitative comparison of alternative methods for coarse-graining biological networks.

    PubMed

    Bowman, Gregory R; Meng, Luming; Huang, Xuhui

    2013-09-28

    Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results. PMID:24089717

  17. Quantitative comparison of alternative methods for coarse-graining biological networks

    NASA Astrophysics Data System (ADS)

    Bowman, Gregory R.; Meng, Luming; Huang, Xuhui

    2013-09-01

    Markov models and master equations are a powerful means of modeling dynamic processes like protein conformational changes. However, these models are often difficult to understand because of the enormous number of components and connections between them. Therefore, a variety of methods have been developed to facilitate understanding by coarse-graining these complex models. Here, we employ Bayesian model comparison to determine which of these coarse-graining methods provides the models that are most faithful to the original set of states. We find that the Bayesian agglomerative clustering engine and the hierarchical Nyström expansion graph (HNEG) typically provide the best performance. Surprisingly, the original Perron cluster cluster analysis (PCCA) method often provides the next best results, outperforming the newer PCCA+ method and the most probable paths algorithm. We also show that the differences between the models are qualitatively significant, rather than being minor shifts in the boundaries between states. The performance of the methods correlates well with the entropy of the resulting coarse-grainings, suggesting that finding states with more similar populations (i.e., avoiding low population states that may just be noise) gives better results.

  18. RNAome sequencing delineates the complete RNA landscape.

    PubMed

    Derks, Kasper W J; Pothof, Joris

    2015-09-01

    Standard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specific method to determine the expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. RNAome sequencing quantitatively preserves all RNA classes. This characteristic allows comparisons between RNA classes, thereby facilitating relationships between different RNA classes. Here, we describe in detail the experimental procedure associated with RNAome sequencing published by Derks and colleagues in RNA Biology (2015) [1]. We also provide the R code for the developed Total Rna Analysis Pipeline (TRAP), an algorithm to analyze RNAome sequencing datasets (deposited at the Gene Expression Omnibus data repository, accession number GSE48084). PMID:26484291

  19. alpha. -Amylase of Clostridium thermosulfurogenes EM1: Nucleotide sequence of the gene, processing of the enzyme, and comparison to other. alpha. -amylases

    SciTech Connect

    Bahl, H.; Burchhardt, G.; Spreinat, A.; Haeckel, K.; Wienecke, A.; Antranikian, G.; Schmidt, B. )

    1991-05-01

    The nucleotide sequence of the {alpha}-amylase gene (amyA) from Clostridium thermosulfurogenes EM1 cloned in Escherichia coli was determined. The reading frame of the gene consisted of 2,121 bp. Comparison of the DNA sequence data with the amino acid sequence of the N terminus of the purified secreted protein of C. thermosulfurogenes Em1 suggested that the {alpha}-amylase is translated form mRNA as a secretory precursor with a signal peptide of 27 amino acid residues. The deduced amino acid sequence of the mature {alpha}-amylase contained 679 residues, resulting in a protein with a molecular mass of 75,112 Da. In E. coli the enzyme was transported to the periplasmic space and the signal peptide was cleaved at exactly the same site between two alanine residues. Comparison of the amino acid sequence of the C. thermosulfurogenes EM1 {alpha}-amylase with those from other bacterial and eukaryotic {alpha}-amylases showed several homologous regions, probably in the enzymatically functioning regions. The tentative Ca{sup 2+}-binding site (consensus region I) of this Ca{sub 2+}-independent enzyme showed only limited homology. The deduced amino acid sequence of a second obviously truncated open reading frame showed significant homology to the malG gene product of E. coli. Comparison of the {alpha}-amylase gene region of C. thermosulfurogenes EM1 (DSM3896) with the {beta}-amylase gene region of C. thermosulfurogenes (ATCC 33743) indicated that both genes have been exchanged with each other at identical sites in the chromosomes of these strains.

  20. Ecological significance of Synergistetes in the biological treatment of tuna cooking wastewater by an anaerobic sequencing batch reactor.

    PubMed

    Militon, Cécile; Hamdi, Olfa; Michotey, Valerie; Fardeau, Marie-Laure; Ollivier, Bernard; Bouallagui, Hassib; Hamdi, Moktar; Bonin, Patricia

    2015-11-01

    Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes. At the steady state, a very efficient removal of protein (92%) was observed. Our results demonstrate a decrease of archaeal and bacterial abundance over time. Members of the phylum Synergistetes, with a peculiar emphasis for those pertaining to families Dethiosulfovibrionaceae and Aminiphilaceae, are of major ecological significance regarding the treatment of this industrial wastewater. The prominent role to be played by members of the phylum Synergistetes regarding protein and/or amino acid degradation is discussed.

  1. Ecological significance of Synergistetes in the biological treatment of tuna cooking wastewater by an anaerobic sequencing batch reactor.

    PubMed

    Militon, Cécile; Hamdi, Olfa; Michotey, Valerie; Fardeau, Marie-Laure; Ollivier, Bernard; Bouallagui, Hassib; Hamdi, Moktar; Bonin, Patricia

    2015-11-01

    Lab-scale 2L-anaerobic sequencing batch reactor was operated under mesothermic conditions. The degradation of protein-rich organic matter was determined by chemical oxygen demand, biogas production, and protein-removal activity over the operation. The structure of the microbial community was determined by qPCR and next-generation sequencing on 16S rRNA genes. At the steady state, a very efficient removal of protein (92%) was observed. Our results demonstrate a decrease of archaeal and bacterial abundance over time. Members of the phylum Synergistetes, with a peculiar emphasis for those pertaining to families Dethiosulfovibrionaceae and Aminiphilaceae, are of major ecological significance regarding the treatment of this industrial wastewater. The prominent role to be played by members of the phylum Synergistetes regarding protein and/or amino acid degradation is discussed. PMID:26194235

  2. Comparisons of the interaction of propranolol and timolol with model and biological membrane systems

    SciTech Connect

    Herbette, L.; Katz, A.M.; Sturtevant, J.M.

    1983-09-01

    The nonspecific interaction of the beta-adrenergic blocking drugs, propranolol and timolol, with model and biological membranes has been investigated. Radioisotope measurements of the association of these drugs with dimyristoyl lecithin (DMPC) bilayers showed that both propranolol and timolol had a significantly greater molar association (mole of drug per mole of lipid) with DMPC above its phase transition temperature than below. Timolol had a much lower molar association with DMPC as compared with propranolol both above and below the phase transition temperature. For the DMPC model membrane system, the molar association of propranolol as measured by radioisotope and inferred from calorimetric studies was similar. Neutron diffraction utilizing propranolol deuterated in the naphthalene moiety showed that the naphthalene moiety of propranolol partitions into the hydrocarbon core of the DMPC lipid bilayer, and that the charged amine side chain is most likely positioned in the aqueous phospholipid head group region. For timolol, the association as measured by radioisotope methods was apparently greater than the partitioning inferred from calorimetric studies using freezing point depression analysis, suggesting a more complex interaction of timolol as compared with propranolol with the DMPC lipid bilayer. The association of propranolol with the SR membrane (mole of propranolol per mole of SR phospholipid) correlated with its ability to inhibit calcium uptake, whereas only a fraction of the total association of timolol with the SR membrane appeared to lead to inhibition of calcium uptake. Both propranolol and timolol appear to perturb the functional properties of the calcium pump protein in the SR membrane (inhibition of ATP-induced calcium uptake) indirectly by partitioning into the bulk lipid matrix of the SR lipid bilayer, although other sites of interaction cannot be excluded.

  3. Comparison of the Biological Impacts of the Fluoride Compounds by Graphical Risk Visualization Map Technique.

    PubMed

    Usuda, Kan; Kono, Rei; Ueno, Takaaki; Ito, Yuichi; Dote, Tomotaro; Yokoyama, Hirotaka; Kono, Koichi; Tamaki, Junko

    2015-09-01

    Various fluoride compounds are widely used in industry. The present risk assessment study was conducted using a series of inorganic binary fluorides of the type XFn, where X(n) = Na(+), K(+), Li(+), Mg(2+), Ca(2+), Sr(2+), Ba(2+), Al(3+), Nd(3+), La(3+), Ce(3+), Sm(3+), Gd(3+), Y(3+), Yb(2+), and Zn(2+). The aqueous solutions of these salts were orally administrated to 16 experimental groups (one for each of the salts tested). The levels of fluoride, N-acetyl-β-D-glucosaminidase in cumulative 24-h urine samples and creatinine clearance were measured to assess possible acute renal damages. The levels of fluoride, alanine aminotransferase, and aspartate aminotransferase were also determined in serum samples to assess possible acute hepatic damages. The results reveal that sodium fluoride (NaF), potassium fluoride (KF), and zinc fluoride tetrahydrate (ZnF2 (.)4H2O) can carry the fluoride ion into the bloodstream and that it is excreted via urine more readily than the other compounds tested. These fluorides were assigned the highest risk impact factor. Most of the rare earth fluorides are insoluble in water while those groups 2 and 13 of the periodic table are slightly soluble, so that they do not have a significant negative risk. These findings suggest that the biological impact of fluoride depends on the accompanying counter ion and its solubility. The risk map obtained in the present study shows that the graphical visualization map technique employed is a valuable new tool to assess the toxicological risk of chemical compounds.

  4. A comparison of methods for the determination of sound velocity in biological materials: a case study.

    PubMed

    Nowak, Konrad W; Markowski, Marek

    2013-07-01

    Non-destructive ultrasonic methods for testing biological materials are applied in medicine as well as in food engineering to determine the physical parameters and the quality of agricultural products and raw materials such as meat. The purpose of this work was to identify the simplest and the most accurate of five methods for sound velocity determination across the fibers of the porcine longissimus dorsi muscle. The through-transmission technique (TT) was used for ultrasound signal acquisition with 2MHz transducers. The first two methods (M1, M2) are based on the acquisition of a single ultrasound signal in the analyzed material, another two methods (M3, M4) rely on the acquisition of two ultrasound signals in samples with different thicknesses (two-distance method) and the last method (M5) involves the acquisition of a single ultrasound signal in the analyzed material and the acquisition of a single ultrasound signal in distilled water at the same distance between ultrasonic transducers (relative method). The results were processed by the nonparametric Kruskal-Wallis test and compared with published data. The mean values of sound velocity obtained with the use of the above methods in pork samples at post-storage, room and vital temperatures were as follows: method M1-1549.2/1581.7/1597.4m/s, method M2-1477.7/1509.8/1597.4m/s, method M3-1552.0/1599.0/1623.3m/s, method M4-1557.4/1598.3/1623.6m/s, method M5-1554.3/1583.7/1598m/s. The experiment indicates that the choice of method for determining sound velocity significantly influences the results. Two of the five analyzed methods (namely M3 and M4), which involved measurements of the time of sound wave propagation through samples of the same material with varied thickness, produced velocity values most consistent with published data.

  5. Arsenic Relative Bioavailability in Contaminated Soils: Comparison of Animal Models, Dosing Schemes, and Biological End Points.

    PubMed

    Li, Jie; Li, Chao; Sun, Hong-Jie; Juhasz, Albert L; Luo, Jun; Li, Hong-Bo; Ma, Lena Q

    2016-01-01

    Different animals and biomarkers have been used to measure the relative bioavailability of arsenic (As-RBA) in contaminated soils. However, there is a lack of As-RBA comparison based on different animals (i.e., swine and mouse) and biomarkers [area under blood As concentration curve (AUC) after a single gavaged dose vs steady-state As urinary excretion (SSUE) and As accumulation in liver or kidney after multiple doses via diet]. In this study, As-RBA in 12 As-contaminated soils with known As-RBA via swine blood AUC model were measured by mouse blood AUC, SSUE, and liver and kidney analyses. As-RBA ranges for the four mouse assays were 2.8-61%, 3.6-64%, 3.9-74%, and 3.4-61%. Compared to swine blood AUC assay (7.0-81%), though well correlated (R(2) = 0.83), the mouse blood AUC assay yielded lower values (2.8-61%). Similarly, strong correlations of As-RBA were observed between mouse blood AUC and mouse SSUE (R(2) = 0.86) and between urine, liver, and kidney (R(2) = 0.75-0.89), suggesting As-RBA was congruent among different animals and end points. Different animals and biomarkers had little impact on the outcome of in vivo assays to validate in vitro assays. On the basis of its simplicity, mouse liver or kidney assay following repeated doses of soil-amended diet is recommended for future As-RBA studies. PMID:26595746

  6. Ambient measurements of biological aerosol particles near Killarney, Ireland: a comparison between real-time fluorescence and microscopy techniques

    NASA Astrophysics Data System (ADS)

    Healy, D. A.; Huffman, J. A.; O'Connor, D. J.; Pöhlker, C.; Pöschl, U.; Sodeau, J. R.

    2014-02-01

    Primary biological aerosol particles (PBAP) can contribute significantly to the coarse particle burden in many environments, may thus influence climate and precipitation systems as cloud nuclei, and can spread disease to humans, animals, and plants. Measurements of PBAP in natural environments taken at high time- and size- resolution are, however, sparse and so large uncertainties remain in the role that biological particles play in the Earth system. In this study two commercial real-time fluorescence particle sensors and a Sporewatch single-stage particle impactor were operated continuously from 2 August to 2 September 2010 at a rural sampling location in Killarney National Park in south western Ireland. A cascade impactor was operated periodically to collect size-resolved particles during exemplary periods. Here we report the first ambient comparison of the waveband integrated bioaerosol sensor (WIBS-4) with the ultraviolet aerodynamic particle sizer (UV-APS) and also compare these real-time fluorescence techniques with results of fluorescence and optical microscopy of impacted samples. Both real-time instruments showed qualitatively similar behaviour, with increased fluorescent bioparticle concentrations at night when relative humidity was highest and temperature was lowest. The fluorescent particle number from the FL3 channel of the WIBS-4 and from the UV-APS were strongly correlated and dominated by a 3 μm mode in the particle size distribution. The WIBS FL2 channel exhibited particle modes at approx. 1 and 3 μm, and each were correlated with the concentration of fungal spores commonly observed in air samples collected at the site (ascospores, basidiospores, Ganoderma spp.). The WIBS FL1 channel exhibited variable multi-modal distributions turning into a broad featureless single mode after averaging and exhibited poor correlation with fungal spore concentrations, which may be due to the detection of bacterial and non-biological fluorescent particles

  7. Ambient measurements of biological aerosol particles near Killarney, Ireland: a comparison between real-time fluorescence and microscopy techniques

    NASA Astrophysics Data System (ADS)

    Healy, D. A.; Huffman, J. A.; O'Connor, D. J.; Pöhlker, C.; Pöschl, U.; Sodeau, J. R.

    2014-08-01

    Primary biological aerosol particles (PBAPs) can contribute significantly to the coarse particle burden in many environments. PBAPs can thus influence climate and precipitation systems as cloud nuclei and can spread disease to humans, animals, and plants. Measurement data and techniques for PBAPs in natural environments at high time- and size resolution are, however, sparse, and so large uncertainties remain in the role that biological particles play in the Earth system. In this study two commercial real-time fluorescence particle sensors and a Sporewatch single-stage particle impactor were operated continuously from 2 August to 2 September 2010 at a rural sampling location in Killarney National Park in southwestern Ireland. A cascade impactor was operated periodically to collect size-resolved particles during exemplary periods. Here we report the first ambient comparison of a waveband integrated bioaerosol sensor (WIBS-4) with a ultraviolet aerodynamic particle sizer (UV-APS) and also compare these real-time fluorescence techniques with results of fluorescence and optical microscopy of impacted samples. Both real-time instruments showed qualitatively similar behavior, with increased fluorescent bioparticle concentrations at night, when relative humidity was highest and temperature was lowest. The fluorescent particle number from the FL3 channel of the WIBS-4 and from the UV-APS were strongly correlated and dominated by a 3 μm mode in the particle size distribution. The WIBS FL2 channel exhibited particle modes at approx. 1 and 3 μm, and each was correlated with the concentration of fungal spores commonly observed in air samples collected at the site (ascospores, basidiospores, Ganoderma spp.). The WIBS FL1 channel exhibited variable multimodal distributions turning into a broad featureless single mode after averaging, and exhibited poor correlation with fungal spore concentrations, which may be due to the detection of bacterial and non-biological fluorescent

  8. Comparison of the amino acid sequence of the major immunogen from three serotypes of foot and mouth disease virus.

    PubMed Central

    Makoff, A J; Paynter, C A; Rowlands, D J; Boothroyd, J C

    1982-01-01

    Cloned cDNA molecules from three serotypes of FMDV have been sequenced around the VP1-coding region. The predicted amino acid sequences for VP1 were compared with the published sequences and variable regions identified. The amino acid sequences were also analysed for hydrophilic regions. Two of the variable regions, numbered 129-160 and 193-204 overlapped hydrophilic regions, and were therefore identified as potentially immunogenic. These regions overlap regions shown by others to be immunogenic. PMID:6298715

  9. A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer.

    PubMed

    Jiang, Runze; Lu, Yi-Tsung; Ho, Hao; Li, Bo; Chen, Jie-Fu; Lin, Millicent; Li, Fuqiang; Wu, Kui; Wu, Hanjie; Lichterman, Jake; Wan, Haolei; Lu, Chia-Lun; OuYang, William; Ni, Ming; Wang, Linlin; Li, Guibo; Lee, Tom; Zhang, Xiuqing; Yang, Jonathan; Rettig, Matthew; Chung, Leland W K; Yang, Huanming; Li, Ker-Chau; Hou, Yong; Tseng, Hsian-Rong; Hou, Shuang; Xu, Xun; Wang, Jun; Posadas, Edwin M

    2015-12-29

    Previous studies have demonstrated focal but limited molecular similarities between circulating tumor cells (CTCs) and biopsies using isolated genetic assays. We hypothesized that molecular similarity between CTCs and tissue exists at the single cell level when characterized by whole genome sequencing (WGS). By combining the NanoVelcro CTC Chip with laser capture microdissection (LCM), we developed a platform for single-CTC WGS. We performed this procedure on CTCs and tissue samples from a patient with advanced prostate cancer who had serial biopsies over the course of his clinical history. We achieved 30X depth and ≥ 95% coverage. Twenty-nine percent of the somatic single nucleotide variations (SSNVs) identified were founder mutations that were also identified in CTCs. In addition, 86% of the clonal mutations identified in CTCs could be traced back to either the primary or metastatic tumors. In this patient, we identified structural variations (SVs) including an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements were shared between tumor tissues and CTCs. At the same time, highly heterogeneous short structural variants were discovered in PTEN, RB1, and BRCA2 in all tumor and CTC samples. Using high-quality WGS on single-CTCs, we identified the shared genomic alterations between CTCs and tumor tissues. This approach yielded insight into the heterogeneity of the mutational landscape of SSNVs and SVs. It may be possible to use this approach to study heterogeneity and characterize the biological evolution of a cancer during the course of its natural history. PMID:26575023

  10. A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer.

    PubMed

    Jiang, Runze; Lu, Yi-Tsung; Ho, Hao; Li, Bo; Chen, Jie-Fu; Lin, Millicent; Li, Fuqiang; Wu, Kui; Wu, Hanjie; Lichterman, Jake; Wan, Haolei; Lu, Chia-Lun; OuYang, William; Ni, Ming; Wang, Linlin; Li, Guibo; Lee, Tom; Zhang, Xiuqing; Yang, Jonathan; Rettig, Matthew; Chung, Leland W K; Yang, Huanming; Li, Ker-Chau; Hou, Yong; Tseng, Hsian-Rong; Hou, Shuang; Xu, Xun; Wang, Jun; Posadas, Edwin M

    2015-12-29

    Previous studies have demonstrated focal but limited molecular similarities between circulating tumor cells (CTCs) and biopsies using isolated genetic assays. We hypothesized that molecular similarity between CTCs and tissue exists at the single cell level when characterized by whole genome sequencing (WGS). By combining the NanoVelcro CTC Chip with laser capture microdissection (LCM), we developed a platform for single-CTC WGS. We performed this procedure on CTCs and tissue samples from a patient with advanced prostate cancer who had serial biopsies over the course of his clinical history. We achieved 30X depth and ≥ 95% coverage. Twenty-nine percent of the somatic single nucleotide variations (SSNVs) identified were founder mutations that were also identified in CTCs. In addition, 86% of the clonal mutations identified in CTCs could be traced back to either the primary or metastatic tumors. In this patient, we identified structural variations (SVs) including an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements were shared between tumor tissues and CTCs. At the same time, highly heterogeneous short structural variants were discovered in PTEN, RB1, and BRCA2 in all tumor and CTC samples. Using high-quality WGS on single-CTCs, we identified the shared genomic alterations between CTCs and tumor tissues. This approach yielded insight into the heterogeneity of the mutational landscape of SSNVs and SVs. It may be possible to use this approach to study heterogeneity and characterize the biological evolution of a cancer during the course of its natural history.

  11. Open questions in origin of life: experimental studies on the origin of nucleic acids and proteins with specific and functional sequences by a chemical synthetic biology approach

    PubMed Central

    Adamala, Katarzyna; Anella, Fabrizio; Wieczorek, Rafal; Stano, Pasquale; Chiarabelli, Cristiano; Luisi, Pier Luigi

    2014-01-01

    In this mini-review we present some experimental approaches to the important issue in the origin of life, namely the origin of nucleic acids and proteins with specific and functional sequences. The formation of macromolecules on prebiotic Earth faces practical and conceptual difficulties. From the chemical viewpoint, macromolecules are formed by chemical pathways leading to the condensation of building blocks (amino acids, or nucleotides) in long-chain copolymers (proteins and nucleic acids, respectively). The second difficulty deals with a conceptual problem, namely with the emergence of specific sequences among a vast array of possible ones, the huge “sequence space”, leading to the question “why these macromolecules, and not the others?” We have recently addressed these questions by using a chemical synthetic biology approach. In particular, we have tested the catalytic activity of small peptides, like Ser-His, with respect to peptide- and nucleotides-condensation, as a realistic model of primitive organocatalysis. We have also set up a strategy for exploring the sequence space of random proteins and RNAs (the so-called “never born biopolymer” project) with respect to the production of folded structures. Being still far from solved, the main aspects of these “open questions” are discussed here, by commenting on recent results obtained in our groups and by providing a unifying view on the problem and possible solutions. In particular, we propose a general scenario for macromolecule formation via fragment-condensation, as a scheme for the emergence of specific sequences based on molecular growth and selection. PMID:24757502

  12. A Comparison of the Effects of an Advanced Organizer and/or Behavioral Objectives on the Achievement of Disadvantaged Biology Students.

    ERIC Educational Resources Information Center

    Kahle, Jane Butler

    The use of an advanced organizer (a generalizable, encompassing concept) prior to an individualized instructional sequence in a self-paced, audiotutorial learning format was accompanied by gains in individual unit achievement and in retention by disadvantaged biology students. Although behavioral objectives generally were shown to make no…

  13. Genomes, Phylogeny, and Evolutionary Systems Biology

    SciTech Connect

    Medina, Monica

    2005-03-25

    With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

  14. Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer.

    PubMed

    Jia, Haiying; Guo, Yunfei; Zhao, Weiwei; Wang, Kai

    2014-01-01

    Long-range PCR remains a flexible, fast, efficient and cost-effective choice for sequencing candidate genomic regions in a small number of samples, especially when combined with next-generation sequencing (NGS) platforms. Several long-range DNA polymerases are advertised as being able to amplify up to 15 kb or longer genomic DNA. However, their real-world performance characteristics and their suitability for NGS remain unclear. We evaluated six long-range DNA polymerases (Invitrogen SequalPrep, Invitrogen AccuPrime, TaKaRa PrimeSTAR GXL, TaKaRa LA Taq Hot Start, KAPA Long Range HotStart and QIAGEN LongRange PCR Polymerase) to amplify three amplicons, with sizes of 12.9 kb, 9.7 kb, and 5.8 kb, respectively. Subsequently, we used the PrimeSTAR enzyme to amplify entire BRCA1 (83.2 kb) and BRCA2 (84.2 kb) genes from nine subjects and sequenced them on an Illumina MiSeq sequencer. We found that the TaKaRa PrimeSTAR GXL DNA polymerase can amplify almost all amplicons with different sizes and Tm values under identical PCR conditions. Other enzymes require alteration of PCR conditions to obtain optimal performance. From the MiSeq run, we identified multiple intronic and exonic single-nucleotide variations (SNVs), including one mutation (c.5946delT in BRCA2) in a positive control. Our study provided useful results for sequencing research focused on large genomic regions. PMID:25034901

  15. Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus.

    PubMed

    Liu, Tong-Jian; Zhang, Cai-Yun; Yan, Hai-Fei; Zhang, Lu; Ge, Xue-Jun; Hao, Gang

    2016-01-01

    Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36-rps8, rps16-trnQ, trnH-psbA and ndhC-trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

  16. Complete plastid genome sequence of Primula sinensis (Primulaceae): structure comparison, sequence variation and evidence for accD transfer to nucleus

    PubMed Central

    Liu, Tong-Jian; Zhang, Cai-Yun; Yan, Hai-Fei; Zhang, Lu

    2016-01-01

    Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis. PMID:27375965

  17. Comparison of amino acid sequences of the trypsin inhibitors from taro (Colocasia esculenta), giant taro (Alocasia macrorrhiza) and giant swamp taro (Cyrtosperma chamissonis).

    PubMed

    Peng, L; Bradbury, J H; Hammer, B C; Shaw, D C

    1993-09-01

    The amino acid sequences of the trypsin inhibitors from taro Colocasia esculenta var. esculenta and giant swamp taro Cyrtosperma chamissonis have been determined and are compared with the protein sequence of the trypsin/chymotrypsin inhibitor from giant taro Alocasia macrorrhiza. Both inhibitors display polymorphism and there is evidence of two components in the giant swamp taro. The positional identity between the proteins is highest at 73-75% for the comparison of the giant taro (GT) with the polymorphic forms of the taro (T) inhibitors and lowest at 56-58% for the pairs of taro and giant swamp taro (GST) proteins. The comparisons show that the inhibitors from T and GT are more related to each other than to GST, which supports their taxonomic classification into different tribes. Location of the P1 site for the trypsin inhibitors of aroids is different from that of other Kunitz-type inhibitors and could be at Leu56.

  18. Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis

    PubMed Central

    Diogo, Dorothée; Kurreeman, Fina; Stahl, Eli A.; Liao, Katherine P.; Gupta, Namrata; Greenberg, Jeffrey D.; Rivas, Manuel A.; Hickey, Brendan; Flannick, Jason; Thomson, Brian; Guiducci, Candace; Ripke, Stephan; Adzhubey, Ivan; Barton, Anne; Kremer, Joel M.; Alfredsson, Lars; Sunyaev, Shamil; Martin, Javier; Zhernakova, Alexandra; Bowes, John; Eyre, Steve; Siminovitch, Katherine A.; Gregersen, Peter K.; Worthington, Jane; Klareskog, Lars; Padyukov, Leonid; Raychaudhuri, Soumya; Plenge, Robert M.

    2013-01-01

    The extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry. We observed an accumulation of rare nonsynonymous variants exclusive to RA cases in IL2RA and IL2RB (burden test: p = 0.007 and p = 0.018, respectively). Next, we assessed the aggregate contribution of low-frequency and common coding variants to the risk of RA by dense genotyping of the 25 gene loci in 10,609 RA cases and 35,605 controls. We observed a strong enrichment of coding variants with a nominal signal of association with RA (p < 0.05) after adjusting for the best signal of association at the loci (penrichment = 6.4 × 10−4). For one locus containing CD2, we found that a missense variant, rs699738 (c.798C>A [p.His266Gln]), and a noncoding variant, rs624988, reside on distinct haplotypes and independently contribute to the risk of RA (p = 4.6 × 10−6). Overall, our results indicate that variants (distributed across the allele-frequency spectrum) within the protein-coding portion of a subset of biological candidate genes identified by GWASs contribute to the risk of RA. Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA. PMID:23261300

  19. Comparison of biological activities of two low molecular weight heparins in 10 healthy volunteers.

    PubMed Central

    Azizi, M; Veyssier-Belot, C; Alhenc-Gelas, M; Chatellier, G; Billaud-Mesguish, E; Fiessinger, J N; Aiach, M

    1995-01-01

    1. Low molecular weight heparins (LMWHs) are produced by different depolymerization processes and may therefore differ with respect to their pharmacokinetic properties. 2. We designed a single dose, randomized cross-over study in 10 healthy volunteers to compare the 24 h pharmacokinetics of two LMWHs, reviparin and enoxaparin, which have been previously shown to be clinically equivalent in terms of post-operative deep vein thrombosis prevention, despite significant differences in their in vivo biological activity. The two LMWHs were subcutaneously administered at the same dosages that are used in clinical studies: 4250 anti-Xa iu for reviparin and 40 mg for enoxaparin which have similar in vitro anti-Xa activities. 3. The overall 24 h profiles of the plasma anti-Xa and anti-thrombin activities were similar for reviparin and enoxaparin. The Amax and the AUC(0, 24h) of plasma anti-Xa activity after reviparin administration were both slightly but significantly lower than those observed after enoxaparin administration (difference between treatments of 0.03 95% CI[0.01-0.05] iu ml-1 h and 0.56 95% CI[0.22-0.90] iu ml-1 for Amax and AUC(0, 24h) respectively). After adjustment for in vitro anti-Xa activity, the statistical differe