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Sample records for biological sequence comparison

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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…

  8. 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....

  9. 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

  10. Biological sequence classification with multivariate string kernels.

    PubMed

    Kuksa, Pavel P

    2013-01-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on the analysis of discrete 1D string data (e.g., DNA or amino acid sequences). In this paper, we address the multiclass biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physicochemical descriptors) and a class of multivariate string kernels that exploit these representations. On three protein sequence classification tasks, the proposed multivariate representations and kernels show significant 15-20 percent improvements compared to existing state-of-the-art sequence classification methods. PMID:24384708

  11. Biological Sequence Analysis with Multivariate String Kernels.

    PubMed

    Kuksa, Pavel P

    2013-03-01

    String kernel-based machine learning methods have yielded great success in practical tasks of structured/sequential data analysis. They often exhibit state-of-the-art performance on many practical tasks of sequence analysis such as biological sequence classification, remote homology detection, or protein superfamily and fold prediction. However, typical string kernel methods rely on analysis of discrete one-dimensional (1D) string data (e.g., DNA or amino acid sequences). In this work we address the multi-class biological sequence classification problems using multivariate representations in the form of sequences of features vectors (as in biological sequence profiles, or sequences of individual amino acid physico-chemical descriptors) and a class of multivariate string kernels that exploit these representations. On a number of protein sequence classification tasks proposed multivariate representations and kernels show significant 15-20\\% improvements compared to existing state-of-the-art sequence classification methods. PMID:23509193

  12. Adaptive seeds tame genomic sequence comparison.

    PubMed

    Kiełbasa, Szymon M; Wan, Raymond; Sato, Kengo; Horton, Paul; Frith, Martin C

    2011-03-01

    The main way of analyzing biological sequences is by comparing and aligning them to each other. It remains difficult, however, to compare modern multi-billionbase DNA data sets. The difficulty is caused by the nonuniform (oligo)nucleotide composition of these sequences, rather than their size per se. To solve this problem, we modified the standard seed-and-extend approach (e.g., BLAST) to use adaptive seeds. Adaptive seeds are matches that are chosen based on their rareness, instead of using fixed-length matches. This method guarantees that the number of matches, and thus the running time, increases linearly, instead of quadratically, with sequence length. LAST, our open source implementation of adaptive seeds, enables fast and sensitive comparison of large sequences with arbitrarily nonuniform composition. PMID:21209072

  13. Meeting Highlights: Genome Sequencing and Biology 2001

    PubMed Central

    2001-01-01

    We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics. PMID:18628920

  14. Sequence comparison via polar coordinates representation and curve tree.

    PubMed

    Dai, Qi; Guo, Xiaodong; Li, Lihua

    2012-01-01

    Sequence comparison has become one of the essential bioinformatics tools in bioinformatics research, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations among the sequences. Existing graphical representation methods have achieved promising results in sequence comparison, but there are some design challenges with the graphical representations and feature-based measures. We reported here a new method for sequence comparison. It considers whole distribution of dual bases and employs polar coordinates method to map a biological sequence into a closed curve. The curve tree was then constructed to numerically characterize the closed curve of biological sequences, and further compared biological sequences by evaluating the distance of the curve tree of the query sequence matching against a corresponding curve tree of the template sequence. The proposed method was tested by phylogenetic analysis, and its performance was further compared with alignment-based methods. The results demonstrate that using polar coordinates representation and curve tree to compare sequences is more efficient. PMID:22001081

  15. 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…

  16. Learning Interpretable SVMs for Biological Sequence Classification

    PubMed Central

    Rätsch, Gunnar; Sonnenburg, Sören; Schäfer, Christin

    2006-01-01

    Background Support Vector Machines (SVMs) – using a variety of string kernels – have been successfully applied to biological sequence classification problems. While SVMs achieve high classification accuracy they lack interpretability. In many applications, it does not suffice that an algorithm just detects a biological signal in the sequence, but it should also provide means to interpret its solution in order to gain biological insight. Results We propose novel and efficient algorithms for solving the so-called Support Vector Multiple Kernel Learning problem. The developed techniques can be used to understand the obtained support vector decision function in order to extract biologically relevant knowledge about the sequence analysis problem at hand. We apply the proposed methods to the task of acceptor splice site prediction and to the problem of recognizing alternatively spliced exons. Our algorithms compute sparse weightings of substring locations, highlighting which parts of the sequence are important for discrimination. Conclusion The proposed method is able to deal with thousands of examples while combining hundreds of kernels within reasonable time, and reliably identifies a few statistically significant positions. PMID:16723012

  17. 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.

  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. PMID:25721271

  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 simple method for global sequence comparison.

    PubMed Central

    Pizzi, E; Attimonelli, M; Liuni, S; Frontali, C; Saccone, C

    1992-01-01

    A simple method of sequence comparison, based on a correlation analysis of oligonucleotide frequency distributions, is here shown to be a reliable test of overall sequence similarity. The method does not involve sequence alignment procedures and permits the rapid screening of large amounts of sequence data. It identifies those sequences which deserve more careful analysis of sequence similarity at the level of resolution of the single nucleotide. It uses observed quantities only and does not involve the adoption of any theoretical model. PMID:1738591

  2. 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

  3. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Nucleic acid sequencing of viruses collected from Florida tomatoes contained a reassortment of two distinct species with the S and L segments belonging to Groundnut ringspot virus (GRSV), whereas the M segment belonged to tomato chlorotic spot virus (TCSV). Inoculations on resistance gene containin...

  5. Classification and identification of geminiviruses using sequence comparisons.

    PubMed

    Padidam, M; Beachy, R N; Fauquet, C M

    1995-02-01

    The genomes and ORFs of 36 geminiviruses were compared to obtain phylogenetic trees and frequency distributions of all possible pairwise comparisons with an objective to classify geminiviruses. Such comparisons show that geminiviruses form two distinct clusters of leafhopper-transmitted viruses that infect monocots (subgroup I) and whitefly-transmitted viruses that infect dicots (subgroup III), irrespective of the part of the genome considered. Of the two leafhopper-transmitted viruses that infect dicots, tobacco yellow dwarf virus has a sequence most similar to subgroup I viruses, and that of beet curly top virus differed depending upon the ORF considered. The distributions of identities within subgroups are significantly different suggesting that the taxonomic status of a particular isolate within a subgroup can be quantified. All the recognized strains of any one virus have greater than 90% sequence identity. It was observed that the 200 nucleotide intercistronic regions of geminiviruses are more variable than the remainder of the genome. The amino acid sequences of the coat protein (CP) of subgroup III viruses are more conserved than the remainder of the genome. However, a short N-terminal region (60-70 amino acids) of the CP is more variable than the rest of the CP sequence and is a close representation of the genome. PCR primers based on conserved sequences can be used to clone and sequence the N-terminal sequences of the CP of the geminiviruses; this sequence is sufficient to classify a virus isolate. A possible taxonomic structure for geminiviruses is proposed after considering the sequence comparisons and biological properties. PMID:7844548

  6. A Parallel Non-Alignment Based Approach to Efficient Sequence Comparison using Longest Common Subsequences

    NASA Astrophysics Data System (ADS)

    Bhowmick, S.; Shafiullah, M.; Rai, H.; Bastola, D.

    2010-11-01

    Biological sequence comparison programs have revolutionized the practice of biochemistry, and molecular and evolutionary biology. Pairwise comparison of genomic sequences is a popular method of choice for analyzing genetic sequence data. However the quality of results from most sequence comparison methods are significantly affected by small perturbations in the data and furthermore, there is a dearth of computational tools to compare sequences beyond a certain length. In this paper, we describe a parallel algorithm for comparing genetic sequences using an alignment free-method based on computing the Longest Common Subsequence (LCS) between genetic sequences. We validate the quality of our results by comparing the phylogenetic tress obtained from ClustalW and LCS. We also show through complexity analysis of the isoefficiency and by empirical measurement of the running time that our algorithm is very scalable.

  7. Mining frequent biological sequences based on bitmap without candidate sequence generation.

    PubMed

    Wang, Qian; Davis, Darryl N; Ren, Jiadong

    2016-02-01

    Biological sequences carry a lot of important genetic information of organisms. Furthermore, there is an inheritance law related to protein function and structure which is useful for applications such as disease prediction. Frequent sequence mining is a core technique for association rule discovery, but existing algorithms suffer from low efficiency or poor error rate because biological sequences differ from general sequences with more characteristics. In this paper, an algorithm for mining Frequent Biological Sequence based on Bitmap, FBSB, is proposed. FBSB uses bitmaps as the simple data structure and transforms each row into a quicksort list QS-list for sequence growth. For the continuity and accuracy requirement of biological sequence mining, tested sequences used during the mining process of FBSB are real ones instead of generated candidates, and all the frequent sequences can be mined without any errors. Comparing with other algorithms, the experimental results show that FBSB can achieve a better performance on both run time and scalability. PMID:26773937

  8. A prime number approach to biological sequencing.

    PubMed

    Greer, W; Barrett, A N; Sowden, J M

    1985-03-01

    Computational sequencing of nucleic acid and amino acid sequences is placing increasing demands on computer resources. The use of prime numbers is explored as a convenient means of improving program speed and reducing storage requirements. It is concluded that the application of the prime number approach leads to significant increases in speed and some reduction in storage requirements. PMID:3840126

  9. 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. PMID:16710414

  10. RCARE: RNA Sequence Comparison and Annotation for RNA Editing

    PubMed Central

    2015-01-01

    The post-transcriptional sequence modification of transcripts through RNA editing is an important mechanism for regulating protein function and is associated with human disease phenotypes. The identification of RNA editing or RNA-DNA difference (RDD) sites is a fundamental step in the study of RNA editing. However, a substantial number of false-positive RDD sites have been identified recently. A major challenge in identifying RDD sites is to distinguish between the true RNA editing sites and the false positives. Furthermore, determining the location of condition-specific RDD sites and elucidating their functional roles will help toward understanding various biological phenomena that are mediated by RNA editing. The present study developed RNA-sequence comparison and annotation for RNA editing (RCARE) for searching, annotating, and visualizing RDD sites using thousands of previously known editing sites, which can be used for comparative analyses between multiple samples. RCARE also provides evidence for improving the reliability of identified RDD sites. RCARE is a web-based comparison, annotation, and visualization tool, which provides rich biological annotations and useful summary plots. The developers of previous tools that identify or annotate RNA-editing sites seldom mention the reliability of their respective tools. In order to address the issue, RCARE utilizes a number of scientific publications and databases to find specific documentations respective to a particular RNA-editing site, which generates evidence levels to convey the reliability of RCARE. Sequence-based alignment files can be converted into VCF files using a Python script and uploaded to the RCARE server for further analysis. RCARE is available for free at http://www.snubi.org/software/rcare/. PMID:26043858

  11. 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.

  12. Biological Processes Discovered by High-Throughput Sequencing.

    PubMed

    Reon, Brian J; Dutta, Anindya

    2016-04-01

    Advances in DNA and RNA sequencing technologies have completely transformed the field of genomics. High-throughput sequencing (HTS) is now a widely used and accessible technology that allows scientists to sequence an entire transcriptome or genome in a timely and cost-effective manner. Application of HTS techniques has led to many key discoveries, including the identification of long noncoding RNAs, microDNAs, a family of small extrachromosomal circular DNA species, and tRNA-derived fragments, which are a group of small non-miRNAs that are derived from tRNAs. Furthermore, public sequencing repositories provide unique opportunities for laboratories to parse large sequencing databases to identify proteins and noncoding RNAs at a scale that was not possible a decade ago. Herein, we review how HTS has led to the discovery of novel nucleic acid species and uncovered new biological processes during the course. PMID:26828742

  13. Local predictability in biological sequences, algorithm and applications.

    PubMed

    Lebbe, J; Vignes, R

    1993-01-01

    The goal of this paper is to propose an algorithm based on the k nearest neighbours to compute a local predictability measure in biological sequences. Some ideas about the usefulness of this measure are discussed on the basis of preliminary experimentations. PMID:8347724

  14. Reads meet rotamers: structural biology in the age of deep sequencing.

    PubMed

    Sethi, Anurag; Clarke, Declan; Chen, Jieming; Kumar, Sushant; Galeev, Timur R; Regan, Lynne; Gerstein, Mark

    2015-12-01

    Structure has traditionally been interrelated with sequence, usually in the framework of comparing sequences across species sharing a common fold. However, the nature of information within the sequence and structure databases is evolving, changing the type of comparisons possible. In particular, we now have a vast amount of personal genome sequences from human populations and a greater fraction of new structures contain interacting proteins within large complexes. Consequently, we have to recast our conception of sequence conservation and its relation to structure-for example, focusing more on selection within the human population. Moreover, within structural biology there is less emphasis on the discovery of novel folds and more on relating structures to networks of protein interactions. We cover this changing mindset here. PMID:26658741

  15. Computing distribution of scale independent motifs in biological sequences

    PubMed Central

    Almeida, Jonas S; Vinga, Susana

    2006-01-01

    The use of Chaos Game Representation (CGR) or its generalization, Universal Sequence Maps (USM), to describe the distribution of biological sequences has been found objectionable because of the fractal structure of that coordinate system. Consequently, the investigation of distribution of symbolic motifs at multiple scales is hampered by an inexact association between distance and sequence dissimilarity. A solution to this problem could unleash the use of iterative maps as phase-state representation of sequences where its statistical properties can be conveniently investigated. In this study a family of kernel density functions is described that accommodates the fractal nature of iterative function representations of symbolic sequences and, consequently, enables the exact investigation of sequence motifs of arbitrary lengths in that scale-independent representation. Furthermore, the proposed kernel density includes both Markovian succession and currently used alignment-free sequence dissimilarity metrics as special solutions. Therefore, the fractal kernel described is in fact a generalization that provides a common framework for a diverse suite of sequence analysis techniques. PMID:17049089

  16. Comparison of Next-Generation Sequencing Systems

    PubMed Central

    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. PMID:22829749

  17. 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.

  18. CloneQC: lightweight sequence verification for synthetic biology

    PubMed Central

    Lee, Pablo A.; Dymond, Jessica S.; Scheifele, Lisa Z.; Richardson, Sarah M.; Foelber, Katrina J.; Boeke, Jef D.; Bader, Joel S.

    2010-01-01

    Synthetic biology projects aim to produce physical DNA that matches a designed target sequence. Chemically synthesized oligomers are generally used as the starting point for building larger and larger sequences. Due to the error rate of chemical synthesis, these oligomers can have many differences from the target sequence. As oligomers are joined together to make larger and larger synthetic intermediates, it becomes essential to perform quality control to eliminate intermediates with errors and retain only those DNA molecules that are error free with respect to the target. This step is often performed by transforming bacteria with synthetic DNA and sequencing colonies until a clone with a perfect sequence is identified. Here we present CloneQC, a lightweight software pipeline available as a free web server and as source code that performs quality control on sequenced clones. Input to the server is a list of desired sequences and forward and reverse reads for each clone. The server generates summary statistics (error rates and success rates target-by-target) and a detailed report of perfect clones. This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source. PMID:20211841

  19. 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

  20. Recognition of Yeast Species from Gene Sequence Comparisons

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This review discusses recognition of yeast species from gene sequence comparisons, which have been responsible for doubling the number of known yeasts over the past decade. The resolution provided by various single gene sequences is examined for both ascomycetous and basidiomycetous species, and th...

  1. Pegasys: software for executing and integrating analyses of biological sequences

    PubMed Central

    Shah, Sohrab P; He, David YM; Sawkins, Jessica N; Druce, Jeffrey C; Quon, Gerald; Lett, Drew; Zheng, Grace XY; Xu, Tao; Ouellette, BF Francis

    2004-01-01

    Background We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools. Results The Pegasys system includes numerous tools for pair-wise and multiple sequence alignment, ab initio gene prediction, RNA gene detection, masking repetitive sequences in genomic DNA as well as filters for database formatting and processing raw output from various analysis tools. We introduce a novel data structure for creating workflows of sequence analyses and a unified data model to store its results. The software allows users to dynamically create analysis workflows at run-time by manipulating a graphical user interface. All non-serial dependent analyses are executed in parallel on a compute cluster for efficiency of data generation. The uniform data model and backend relational database management system of Pegasys allow for results of heterogeneous programs included in the workflow to be integrated and exported into General Feature Format for further analyses in GFF-dependent tools, or GAME XML for import into the Apollo genome editor. The modularity of the design allows for new tools to be added to the system with little programmer overhead. The database application programming interface allows programmatic access to the data stored in the backend through SQL queries. Conclusions The Pegasys system enables biologists and bioinformaticians to create and manage sequence analysis workflows. The software is released under the Open Source GNU General Public License. All source code and documentation is available for download at . PMID:15096276

  2. Effective Automated Feature Construction and Selection for Classification of Biological Sequences

    PubMed Central

    Kamath, Uday; De Jong, Kenneth; Shehu, Amarda

    2014-01-01

    Background Many open problems in bioinformatics involve elucidating underlying functional signals in biological sequences. DNA sequences, in particular, are characterized by rich architectures in which functional signals are increasingly found to combine local and distal interactions at the nucleotide level. Problems of interest include detection of regulatory regions, splice sites, exons, hypersensitive sites, and more. These problems naturally lend themselves to formulation as classification problems in machine learning. When classification is based on features extracted from the sequences under investigation, success is critically dependent on the chosen set of features. Methodology We present an algorithmic framework (EFFECT) for automated detection of functional signals in biological sequences. We focus here on classification problems involving DNA sequences which state-of-the-art work in machine learning shows to be challenging and involve complex combinations of local and distal features. EFFECT uses a two-stage process to first construct a set of candidate sequence-based features and then select a most effective subset for the classification task at hand. Both stages make heavy use of evolutionary algorithms to efficiently guide the search towards informative features capable of discriminating between sequences that contain a particular functional signal and those that do not. Results To demonstrate its generality, EFFECT is applied to three separate problems of importance in DNA research: the recognition of hypersensitive sites, splice sites, and ALU sites. Comparisons with state-of-the-art algorithms show that the framework is both general and powerful. In addition, a detailed analysis of the constructed features shows that they contain valuable biological information about DNA architecture, allowing biologists and other researchers to directly inspect the features and potentially use the insights obtained to assist wet-laboratory studies on retainment or

  3. High-resolution network biology: connecting sequence with function

    PubMed Central

    Ryan, Colm J.; Cimermančič, Peter; Szpiech, Zachary A.; Sali, Andrej; Hernandez, Ryan D.; Krogan, Nevan J.

    2014-01-01

    Proteins are not monolithic entities; rather, they can contain multiple domains that mediate distinct interactions, and their functionality can be regulated through post-translational modifications at multiple distinct sites. Traditionally, network biology has ignored such properties of proteins and has instead examined either the physical interactions of whole proteins or the consequences of removing entire genes. In this Review, we discuss experimental and computational methods to increase the resolution of protein– protein, genetic and drug–gene interaction studies to the domain and residue levels. Such work will be crucial for using interaction networks to connect sequence and structural information, and to understand the biological consequences of disease-associated mutations, which will hopefully lead to more effective therapeutic strategies. PMID:24197012

  4. 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

  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. PMID:18621748

  6. Membrane platforms for biological nanopore sensing and sequencing.

    PubMed

    Schmidt, Jacob

    2016-06-01

    In the past two decades, biological nanopores have been developed and explored for use in sensing applications as a result of their exquisite sensitivity and easily engineered, reproducible, and economically manufactured structures. Nanopore sensing has been shown to differentiate between highly similar analytes, measure polymer size, detect the presence of specific genes, and rapidly sequence nucleic acids translocating through the pore. Devices featuring protein nanopores have been limited in part by the membrane support containing the nanopore, the shortcomings of which have been addressed in recent work developing new materials, approaches, and apparatus resulting in membrane platforms featuring automatability and increased robustness, lifetime, and measurement throughput. PMID:26773300

  7. 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...

  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 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.

  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. PMID:25746396

  11. Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.

    PubMed

    Lienhard, Matthias; Chavez, Lukas

    2016-01-01

    DNA enrichment followed by sequencing (DNA-IP seq) is a versatile tool in molecular biology with a wide variety of applications. Computational analysis of differential DNA enrichment between conditions is important for identifying epigenetic alterations in disease compared to healthy controls and for revealing dynamic epigenetic modifications throughout normal and distorted cell differentiation and development. We present a protocol for genome-wide comparative analysis of DNA-IP sequencing data to identify statistically significant differential sequencing coverage between two conditions by considering variation across replicates. The protocol provides a detailed description for the comparative analysis of DNA-IP sequencing data including basic data processing, quality controls, and identification of differential enrichment using the Bioconductor package "MEDIPS". PMID:27008016

  12. Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads

    PubMed Central

    Song, Kai; Ren, Jie; Zhai, Zhiyuan; Liu, Xuemei

    2013-01-01

    Abstract Next-generation sequencing (NGS) technologies have generated enormous amounts of shotgun read data, and assembly of the reads can be challenging, especially for organisms without template sequences. We study the power of genome comparison based on shotgun read data without assembly using three alignment-free sequence comparison statistics, D2, \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document}, and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^S$$ \\end{document}, both theoretically and by simulations. Theoretical formulas for the power of detecting the relationship between two sequences related through a common motif model are derived. It is shown that both \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin{document} $$\\textbf{\\textit{D}}_{\\bf 2}^{\\bf *}$$ \\end{document} and \\documentclass{aastex}\\usepackage{amsbsy}\\usepackage{amsfonts}\\usepackage{amssymb}\\usepackage{bm}\\usepackage{mathrsfs}\\usepackage{pifont}\\usepackage{stmaryrd}\\usepackage{textcomp}\\usepackage{portland, xspace}\\usepackage{amsmath, amsxtra}\\pagestyle{empty}\\DeclareMathSizes{10}{9}{7}{6}\\begin

  13. 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

  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. Detecting frame shifts by amino acid sequence comparison.

    PubMed

    Claverie, J M

    1993-12-20

    Various amino acid substitution scoring matrices are used in conjunction with local alignments programs to detect regions of similarity and infer potential common ancestry between proteins. The usual scoring schemes derive from the implicit hypothesis that related proteins evolve from a common ancestor by the accumulation of point mutations and that amino acids tend to be progressively substituted by others with similar properties. However, other frequent single mutation events, like nucleotide insertion or deletion and gene inversion, change the translation reading frame and cause previously encoded amino acid sequences to become unrecognizable at once. Here, I derive five new types of scoring matrix, each capable of detecting a specific frame shift (deletion, insertion and inversion in 3 frames) and use them with a regular local alignments program to detect amino acid sequences that may have derived from alternative reading frames of the same nucleotide sequence. Frame shifts are inferred from the sole comparison of the protein sequences. The five scoring matrices were used with the BLASTP program to compare all the protein sequences in the Swissprot database. Surprisingly, the searches revealed hundreds of highly significant frame shift matches, of which many are likely to represent sequencing errors. Others provide some evidence that frame shift mutations might be used in protein evolution as a way to create new amino acid sequences from pre-existing coding regions. PMID:7903399

  16. 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

  17. 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...

  18. 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.

  19. 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.

  20. Extraction of high quality k-words for alignment-free sequence comparison.

    PubMed

    Gunasinghe, Upuli; Alahakoon, Damminda; Bedingfield, Susan

    2014-10-01

    The weighted Euclidean distance (D(2)) is one of the earliest dissimilarity measures used for alignment free comparison of biological sequences. This distance measure and its variants have been used in numerous applications due to its fast computation, and many variants of it have been subsequently introduced. The D(2) distance measure is based on the count of k-words in the two sequences that are compared. Traditionally, all k-words are compared when computing the distance. In this paper we show that similar accuracy in sequence comparison can be achieved by using a selected subset of k-words. We introduce a term variance based quality measure for identifying the important k-words. We demonstrate the application of the proposed technique in phylogeny reconstruction and show that up to 99% of the k-words can be filtered out for certain datasets, resulting in faster sequence comparison. The paper also presents an exploratory analysis based evaluation of optimal k-word values and discusses the impact of using subsets of k-words in such optimal instances. PMID:24846728

  1. 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.

  2. The nucleotide sequence of the mouse immunoglobulin epsilon gene: comparison with the human epsilon gene sequence.

    PubMed Central

    Ishida, N; Ueda, S; Hayashida, H; Miyata, T; Honjo, T

    1982-01-01

    We have determined the nucleotide sequence of the immunoglobulin epsilon gene cloned from newborn mouse DNA. The epsilon gene sequence allows prediction of the amino acid sequence of the constant region of the epsilon chain and comparison of it with sequences of the human epsilon and other mouse immunoglobulin genes. The epsilon gene was shown to be under the weakest selection pressure at the protein level among the immunoglobulin genes although the divergence at the synonymous position is similar. Our results suggest that the epsilon gene may be dispensable, which is in accord with the fact that IgE has only obscure roles in the immune defense system but has an undesirable role as a mediator of hypersensitivity. The sequence data suggest that the human and murine epsilon genes were derived from different ancestors duplicated a long time ago. The amino acid sequence of the epsilon chain is more homologous to those of the gamma chains than the other mouse heavy chains. Two membrane exons, separated by an 80-base intron, were identified 1.7 kb 3' to the CH4 domain of the epsilon gene and shown to conserve a hydrophobic portion similar to those of other heavy chain genes. RNA blot hybridization showed that the epsilon membrane exons are transcribed into two species of mRNA in an IgE hybridoma. Images Fig. 4. PMID:6329728

  3. 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

  4. Comparison of DNA Quantification Methods for Next Generation Sequencing.

    PubMed

    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

  5. High-throughput sequencing in veterinary infection biology and diagnostics.

    PubMed

    Belák, S; Karlsson, O E; Leijon, M; Granberg, F

    2013-12-01

    Sequencing methods have improved rapidly since the first versions of the Sanger techniques, facilitating the development of very powerful tools for detecting and identifying various pathogens, such as viruses, bacteria and other microbes. The ongoing development of high-throughput sequencing (HTS; also known as next-generation sequencing) technologies has resulted in a dramatic reduction in DNA sequencing costs, making the technology more accessible to the average laboratory. In this White Paper of the World Organisation for Animal Health (OIE) Collaborating Centre for the Biotechnology-based Diagnosis of Infectious Diseases in Veterinary Medicine (Uppsala, Sweden), several approaches and examples of HTS are summarised, and their diagnostic applicability is briefly discussed. Selected future aspects of HTS are outlined, including the need for bioinformatic resources, with a focus on improving the diagnosis and control of infectious diseases in veterinary medicine. PMID:24761741

  6. Bacterial epidemiology and biology - lessons from genome sequencing

    PubMed Central

    2011-01-01

    Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution. PMID:22027015

  7. A singular value decomposition approach for improved taxonomic classification of biological sequences

    PubMed Central

    2011-01-01

    Background Singular value decomposition (SVD) is a powerful technique for information retrieval; it helps uncover relationships between elements that are not prima facie related. SVD was initially developed to reduce the time needed for information retrieval and analysis of very large data sets in the complex internet environment. Since information retrieval from large-scale genome and proteome data sets has a similar level of complexity, SVD-based methods could also facilitate data analysis in this research area. Results We found that SVD applied to amino acid sequences demonstrates relationships and provides a basis for producing clusters and cladograms, demonstrating evolutionary relatedness of species that correlates well with Linnaean taxonomy. The choice of a reasonable number of singular values is crucial for SVD-based studies. We found that fewer singular values are needed to produce biologically significant clusters when SVD is employed. Subsequently, we developed a method to determine the lowest number of singular values and fewest clusters needed to guarantee biological significance; this system was developed and validated by comparison with Linnaean taxonomic classification. Conclusions By using SVD, we can reduce uncertainty concerning the appropriate rank value necessary to perform accurate information retrieval analyses. In tests, clusters that we developed with SVD perfectly matched what was expected based on Linnaean taxonomy. PMID:22369633

  8. Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

    PubMed Central

    Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

    2015-01-01

    Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

  9. 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

  10. 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

  11. Test on the structure of biological sequences via Chaos Game Representation.

    PubMed

    Cénac, Peggy

    2005-01-01

    In this paper biological sequences are modelled by stationary ergodic sequences. A new family of statistical tests to characterize the randomness of the inputs is proposed and analyzed. Tests for independence and for the determination of the appropriate order of a Markov chain are constructed with the Chaos Game Representation (CGR), and applied to several genomes. PMID:16646845

  12. TRANSFAC database as a bridge between sequence data libraries and biological function

    SciTech Connect

    Wingender, E.; Karas, H.; Knueppel, R.

    1996-12-31

    The TRANSFAC database contains information about regulatory DNA sequences and the proteins (transcription factors) binding to and acting through them. It may thus serve as a dictionary for the biological meaning of these sequence elements. Moreover, the TRANSFAC data can be used to describe these elements, to define consensi and matrices for elements of certain function, and thus to provide means of identifying regulatory signals in newly unravelled genomic sequences. 12 refs., 1 fig.

  13. A fast algorithm for exact sequence search in biological sequences using polyphase decomposition

    PubMed Central

    Srikantha, Abhilash; Bopardikar, Ajit S.; Kaipa, Kalyan Kumar; Venkataraman, Parthasarathy; Lee, Kyusang; Ahn, TaeJin; Narayanan, Rangavittal

    2010-01-01

    Motivation: Exact sequence search allows a user to search for a specific DNA subsequence in a larger DNA sequence or database. It serves as a vital block in many areas such as Pharmacogenetics, Phylogenetics and Personal Genomics. As sequencing of genomic data becomes increasingly affordable, the amount of sequence data that must be processed will also increase exponentially. In this context, fast sequence search algorithms will play an important role in exploiting the information contained in the newly sequenced data. Many existing algorithms do not scale up well for large sequences or databases because of their high-computational costs. This article describes an efficient algorithm for performing fast searches on large DNA sequences. It makes use of hash tables of Q-grams that are constructed after downsampling the database, to enable efficient search and memory use. Time complexity for pattern search is reduced using beam pruning techniques. Theoretical complexity calculations and performance figures are presented to indicate the potential of the proposed algorithm. Contact: s.abhilash@samsung.com; ajit.b@samsung.com PMID:20823301

  14. Whole Chloroplast Genome Sequencing in Fragaria Using Deep Sequencing: A Comparison of Three Methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chloroplast sequences previously investigated in Fragaria revealed low amounts of variation. Deep sequencing technologies enable economical sequencing of complete chloroplast genomes. These sequences can potentially provide robust phylogenetic resolution, even at low taxonomic levels within plant gr...

  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. 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. PMID:27217169

  18. Alignment-free comparison of genome sequences by a new numerical characterization.

    PubMed

    Huang, Guohua; Zhou, Houqing; Li, Yongfan; Xu, Lixin

    2011-07-21

    In order to compare different genome sequences, an alignment-free method has proposed. First, we presented a new graphical representation of DNA sequences without degeneracy, which is conducive to intuitive comparison of sequences. Then, a new numerical characterization based on the representation was introduced to quantitatively depict the intrinsic nature of genome sequences, and considered as a 10-dimensional vector in the mathematical space. Alignment-free comparison of sequences was performed by computing the distances between vectors of the corresponding numerical characterizations, which define the evolutionary relationship. Two data sets of DNA sequences were constructed to assess the performance on sequence comparison. The results illustrate well validity of the method. The new numerical characterization provides a powerful tool for genome comparison. PMID:21536050

  19. 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. PMID:26188431

  20. Comparison on extreme pathways reveals nature of different biological processes

    PubMed Central

    2014-01-01

    Background Constraint-based reconstruction and analysis (COBRA) is used for modeling genome-scale metabolic networks (MNs). In a COBRA model, extreme pathways (ExPas) are the edges of its conical solution space, which is formed by all viable steady-state flux distributions. ExPa analysis has been successfully applied to MNs to reveal their phenotypic capabilities and properties. Recently, the COBRA framework has been extended to transcriptional regulatory networks (TRNs) and transcriptional and translational networks (TTNs), so efforts are needed to determine whether ExPa analysis is also effective on these two types of networks. Results In this paper, the ExPas resulting from the COBRA models of E.coli's MN, TRN and TTN were horizontally compared from 5 aspects: (1) Total number and the ratio of their amount to reaction amount; (2) Length distribution; (3) Reaction participation; (4) Correlated reaction sets (CoSets); (5) interconnectivity degree. Significant discrepancies in above properties were observed during the comparison, which reveals the biological natures of different biological processes. Besides, by demonstrating the application of ExPa analysis on E.coli, we provide a practical guidance of an improved approach to compute ExPas on COBRA models of TRNs. Conclusions ExPas of E.coli's MN, TRN and TTN have different properties, which are strongly connected with various biological natures of biochemical networks, such as topological structure, specificity and redundancy. Our study shows that ExPas are biologically meaningful on the newborn models and suggests the effectiveness of ExPa analysis on them. PMID:24565046

  1. FastAlert--an automatic search system to alert about new entries in biological sequence databanks.

    PubMed

    Eggenberger, F; Redaschi, N; Doelz, R

    1996-04-01

    This paper describes a new tool enabling awareness of new sequence databank entries of interest. The FastAlert system relieves the researcher from the burden of repeating FASTA searches in order to keep up with the rapidly growing amount of information found in biological sequence databanks. The query sequence can be submitted from any computer connected to the Internet. Upon registration, the databank, including the updates, is scanned at periodic intervals with the sequence provided. The results, so-called FastAlert reports, are delivered via electronic mail. The reports contain the FASTA best-scores list and the similarity statistics for each entry listed. PMID:8744775

  2. 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. PMID:24006392

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

    PubMed Central

    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. PMID:24006392

  4. 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.

  5. Alignment-free genetic sequence comparisons: a review of recent approaches by word analysis.

    PubMed

    Bonham-Carter, Oliver; Steele, Joe; Bastola, Dhundy

    2014-11-01

    Modern sequencing and genome assembly technologies have provided a wealth of data, which will soon require an analysis by comparison for discovery. Sequence alignment, a fundamental task in bioinformatics research, may be used but with some caveats. Seminal techniques and methods from dynamic programming are proving ineffective for this work owing to their inherent computational expense when processing large amounts of sequence data. These methods are prone to giving misleading information because of genetic recombination, genetic shuffling and other inherent biological events. New approaches from information theory, frequency analysis and data compression are available and provide powerful alternatives to dynamic programming. These new methods are often preferred, as their algorithms are simpler and are not affected by synteny-related problems. In this review, we provide a detailed discussion of computational tools, which stem from alignment-free methods based on statistical analysis from word frequencies. We provide several clear examples to demonstrate applications and the interpretations over several different areas of alignment-free analysis such as base-base correlations, feature frequency profiles, compositional vectors, an improved string composition and the D2 statistic metric. Additionally, we provide detailed discussion and an example of analysis by Lempel-Ziv techniques from data compression. PMID:23904502

  6. 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

  7. Water Mediates Recognition of DNA Sequence via Ionic Current Blockade in a Biological Nanopore.

    PubMed

    Bhattacharya, Swati; Yoo, Jejoong; Aksimentiev, Aleksei

    2016-04-26

    Electric field-driven translocation of DNA strands through biological nanopores has been shown to produce blockades of the nanopore ionic current that depend on the nucleotide composition of the strands. Coupling a biological nanopore MspA to a DNA processing enzyme has made DNA sequencing via measurement of ionic current blockades possible. Nevertheless, the physical mechanism enabling the DNA sequence readout has remained undetermined. Here, we report the results of all-atom molecular dynamics simulations that elucidated the physical mechanism of ionic current blockades in the biological nanopore MspA. We find that the amount of water displaced from the nanopore by the DNA strand determines the nanopore ionic current, whereas the steric and base-stacking properties of the DNA nucleotides determine the amount of water displaced. Unexpectedly, we find the effective force on DNA in MspA to undergo large fluctuations, which may produce insertion errors in the DNA sequence readout. PMID:27054820

  8. 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

  9. Elucidation of the sequence of canine (pro)-calcitonin. A molecular biological and protein chemical approach.

    PubMed

    Mol, J A; Kwant, M M; Arnold, I C; Hazewinkel, H A

    1991-09-01

    From the canine thyroid gland a calcitonin (CT) immunoreactive peptide was purified by successive aqueous acid acetone extraction, gel filtration and HPLC. Gas-phase sequencing of the purified peptide showed that the first 25 amino acids had 65% sequence homology with the amino-terminus of the human CT prohormone. A canine cDNA library was then made from the thyroid gland. A plasmid was isolated containing a sequence that is homologous to part of exon 3, and the complete sequence of exon 4 of the human mRNA encoding preproCT. From this cDNA the amino acid sequence of canine CT is predicted. In comparison with well-known CT sequences of other species, the strongest homology exists with bovine, porcine and ovine CT. PMID:1758974

  10. nWayComp: A Tool for Universal Comparison of DNA and Protein Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The increasing number of whole genomic sequences of microorganisms has increased the complexity of genome-wide annotation and gene sequence comparison among multiple microorganisms. To address this problem, we developed nWayComp software that compares DNA and protein sequences of phylogenetically-r...

  11. Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei

    PubMed Central

    Hsueh, Pei-Tan; Chen, Yao-Shen; Lin, Hsi-Hsu; Liu, Pei-Ju; Ni, Wen-Fan; Liu, Mei-Chun

    2015-01-01

    The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants. PMID:26472836

  12. 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.

  13. 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

  14. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As a major step toward understanding the biology and evolution of ruminants, the cattle genome was sequenced to ~7x coverage using a combined whole genome shotgun and BAC skim approach. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs found in seven mammalian...

  15. 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...

  16. Evolutionary sequence comparisons using high-density oligonucleotide arrays.

    PubMed

    Hacia, J G; Makalowski, W; Edgemon, K; Erdos, M R; Robbins, C M; Fodor, S P; Brody, L C; Collins, F S

    1998-02-01

    We explored the utility of high-density oligonucleotide arrays (DNA chips) for obtaining sequence information from homologous genes in closely related species. Orthologues of the human BRCA1 exon 11, all approximately 3.4 kb in length and ranging from 98.2% to 83.5% nucleotide identity, were subjected to hybridization-based and conventional dideoxysequencing analysis. Retrospective guidelines for identifying high-fidelity hybridization-based sequence calls were formulated based upon dideoxysequencing results. Prospective application of these rules yielded base-calling with at least 98.8% accuracy over orthologous sequence tracts shown to have approximately 99% identity. For higher primate sequences with greater than 97% nucleotide identity, base-calling was made with at least 99.91% accuracy covering a minimum of 97% of the sequence. Using a second-tier confirmatory hybridization chip strategy, shown in several cases to confirm the identity of predicted sequence changes, the complete sequence of the chimpanzee, gorilla and orangutan orthologues should be deducible solely through hybridization-based methodologies. Analysis of less highly conserved orthologues can still identify conserved nucleotide tracts of at least 15 nucleotides and can provide useful information for designing primers. DNA-chip based assays can be a valuable new technology for obtaining high-throughput cost-effective sequence information from related genomes. PMID:9462745

  17. KeBABS: an R package for kernel-based analysis of biological sequences.

    PubMed

    Palme, Johannes; Hochreiter, Sepp; Bodenhofer, Ulrich

    2015-08-01

    KeBABS provides a powerful, flexible and easy to use framework for KE: rnel- B: ased A: nalysis of B: iological S: equences in R. It includes efficient implementations of the most important sequence kernels, also including variants that allow for taking sequence annotations and positional information into account. KeBABS seamlessly integrates three common support vector machine (SVM) implementations with a unified interface. It allows for hyperparameter selection by cross validation, nested cross validation and also features grouped cross validation. The biological interpretation of SVM models is supported by (1) the computation of weights of sequence patterns and (2) prediction profiles that highlight the contributions of individual sequence positions or sections. PMID:25812745

  18. 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

  19. Close sequence comparisons are sufficient to identify human cis-regulatory elements.

    PubMed

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

    2006-07-01

    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. To address this problem, we identified evolutionarily conserved noncoding regions in primate, mammalian, and more distant comparisons using a uniform approach (Gumby) that facilitates unbiased assessment of the impact of evolutionary distance on predictive power. We benchmarked computational 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 an in vivo enhancer assay in transgenic mice. Human regulatory elements were identified with acceptable sensitivity (53%-80%) and true-positive rate (27%-67%) by comparison with one to five other eutherian mammals or six other simian primates. More distant comparisons (marsupial, avian, amphibian, and fish) failed to identify many of the empirically defined functional noncoding elements. Our results highlight the practical utility of close sequence comparisons, and the loss of sensitivity entailed by more distant comparisons. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole-genome comparative analysis that explains most of the observations from empirical benchmarking. 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 in vivo testing at embryonic time points. PMID:16769978

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

    PubMed

    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

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

    PubMed

    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

  2. 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

  3. 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

  4. Use of gene sequence analyses and genome comparisons for yeast systematics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Detection, identification, and classification of yeasts has undergone a major transformation in the past decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined gene sequences from domains 1 and 2 of large sub...

  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. 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

  8. 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.

  9. Sequence-based genotyping clarifies conflicting historical morphometric and biological data for 5 Eimeria species infecting turkeys.

    PubMed

    El-Sherry, S; Ogedengbe, M E; Hafeez, M A; Sayf-Al-Din, M; Gad, N; Barta, J R

    2015-02-01

    Unlike with Eimeria species infecting chickens, specific identification and nomenclature of Eimeria species infecting turkeys is complicated, and in the absence of molecular data, imprecise. In an attempt to reconcile contradictory data reported on oocyst morphometrics and biological descriptions of various Eimeria species infecting turkey, we established single oocyst derived lines of 5 important Eimeria species infecting turkeys, Eimeria meleagrimitis (USMN08-01 strain), Eimeria adenoeides (Guelph strain), Eimeria gallopavonis (Weybridge strain), Eimeria meleagridis (USAR97-01 strain), and Eimeria dispersa (Briston strain). Short portions (514 bp) of mitochondrial cytochrome c oxidase subunit I gene (mt COI) from each were amplified and sequenced. Comparison of these sequences showed sufficient species-specific sequence variation to recommend these short mt COI sequences as species-specific markers. Uniformity of oocyst features (dimensions and oocyst structure) of each pure line was observed. Additional morphological features of the oocysts of these species are described as useful for the microscopic differentiation of these Eimeria species. Combined molecular and morphometric data on these single species lines compared with the original species descriptions and more recent data have helped to clarify some confusing, and sometimes conflicting, features associated with these Eimeria spp. For example, these new data suggest that the KCH and KR strains of E. adenoeides reported previously represent 2 distinct species, E. adenoeides and E. meleagridis, respectively. Likewise, analysis of the Weybridge strain of E. adenoeides, which has long been used as a reference strain in various studies conducted on the pathogenicity of E. adenoeides, indicates that this coccidium is actually a strain of E. gallopavonis. We highly recommend mt COI sequence-based genotyping be incorporated into all studies using Eimeria spp. of turkeys to confirm species identifications and so

  10. 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

  11. A COMPARISON OF FIXED SEQUENCE AND OPTIONAL BRANCHING AUTIOINSTRUCTIONAL METHODS.

    ERIC Educational Resources Information Center

    MELARAGNO, RALPH J.; AND OTHERS

    HYPOTHESES RELATED TO PROCEDURES PERMITTING STUDENTS TO BRANCH AT THEIR OWN OPTION WERE TESTED. THE FIRST HYPOTHESIS WAS THAT A FIXED-SEQUENCE PROGRAM WOULD BE LESS EFFECTIVE THAN THE SAME ITEMS CAST AS STATEMENTS IN TEXTBOOK FORMAT THROUGH WHICH THE STUDENT COULD SKIP AT HIS OWN OPTION. THE SECOND HYPOTHESIS WAS THAT PERFORMANCE ON A PROGRAM…

  12. Model annotation for synthetic biology: automating model to nucleotide sequence conversion

    PubMed Central

    Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

    2011-01-01

    Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

  13. Marine organism cell biology and regulatory sequence discoveryin comparative functional genomics.

    PubMed

    Barnes, David W; Mattingly, Carolyn J; Parton, Angela; Dowell, Lori M; Bayne, Christopher J; Forrest, John N

    2004-10-01

    The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure-function relationships between coding sequences and protein activities, comparative studies also promote understanding of molecular evolution and the relationship between genomic sequence and morphological and physiological specialization. Recently recognized is the potential of comparative studies to identify functionally significant regulatory regions and to generate experimentally testable hypotheses that contribute to understanding mechanisms that regulate gene expression, including transcriptional activity, alternative splicing and transcript stability. Functional tests of hypotheses generated by computational approaches require experimentally tractable in vitro systems, including cell cultures. Comparative sequence analysis strategies that use genomic sequences from a variety of evolutionarily diverse organisms are critical for identifying conserved regulatory motifs in the 5'-upstream, 3'-downstream and introns of genes. Genomic sequences and gene orthologues in the first aquatic vertebrate and protovertebrate organisms to be fully sequenced (Fugu rubripes, Ciona intestinalis, Tetraodon nigroviridis, Danio rerio) as well as in the elasmobranchs, spiny dogfish shark (Squalus acanthias) and little skate (Raja erinacea), and marine invertebrate models such as the sea urchin (Strongylocentrotus purpuratus) are valuable in the prediction of putative genomic regulatory regions. Cell cultures have been derived for these and other model species. Data and tools resulting from these kinds of studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention. PMID:19003267

  14. Structuring temporal sequences: comparison of models and factors of complexity.

    PubMed

    Essens, P

    1995-05-01

    Two stages for structuring tone sequences have been distinguished by Povel and Essens (1985). In the first, a mental clock segments a sequence into equal time units (clock model); in the second, intervals are specified in terms of subdivisions of these units. The present findings support the clock model in that it predicts human performance better than three other algorithmic models. Two further experiments in which clock and subdivision characteristics were varied did not support the hypothesized effect of the nature of the subdivisions on complexity. A model focusing on the variations in the beat-anchored envelopes of the tone clusters was proposed. Errors in reproduction suggest a dual-code representation comprising temporal and figural characteristics. The temporal part of the representation is based on the clock model but specifies, in addition, the metric of the level below the clock. The beat-tone-cluster envelope concept was proposed to specify the figural part. PMID:7596749

  15. 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,…

  16. 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.

  17. High school biology students' participation in a year-long sequence of analogical activities: The relationship of development of analogical thought to student learning and classroom interactions

    NASA Astrophysics Data System (ADS)

    Hackney, Marcella Wichser

    1999-10-01

    This research explored development of analogical thought through high school biology students' participation in a year-long sequence of analogical activities. Analogizing involves: selecting a familiar analog; mapping similarities and differences between the analog and less familiar target; making inferences from the analogy; evaluating validity of the inferences; and ultimately, understanding the biological target (Holyoak & Thagard, 1995). This investigation considered: student development of independence in learning through analogical thought, student learning of biology, the relationship between development of students' analogical thinking and students' learning of biology, and the quality of student interactions in the classroom This researcher, as teacher participant, used three approaches for teaching by analogy: traditional didactic, teacher-guided, and analogy-generated-by-the-student (Zeitoun, 1983). Within cooperative groups, students in one honors biology class actively engaged in research-based analogical activities that targeted specific biological topics. Two honors biology classes participated in similar, but nonanalogical activities that targeted the same biological topics. This two-class comparison group permitted analytical separation of effects of the analogical emphasis from the effects of biology content and activity-based learning. Data collected included: fieldnotes of researcher observations, student responses to guidesheets, tapes of group interactions, student products, student perceptions survey evaluations, ratings of students' expressed analogical development, pre- and posttest scores on a biology achievement test, essay responses, and selected student interviews. These data formed the basis for researcher qualitative analysis, augmented by quantitative techniques. Through participation in the sequence of analogical activities, students developed their abilities to engage in the processes of analogical thinking, but attained different

  18. Comparison of inoculation strategies to assess biological interactions between sorghum lines and fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Comparison of inoculation strategies to assess biological interactions between sorghum lines and fungi Bioassays were assessed for utility to characterize fungal species associated with sorghum or to screen germplasm for advancement in breeding programs. Isolates of Alternaria alternata, Fusarium e...

  19. 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.

  20. 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

  1. Correlation between Protein Sequence Similarity and Crystallization Reagents in the Biological Macromolecule Crystallization Database

    PubMed Central

    Lu, Hui-Meng; Yin, Da-Chuan; Liu, Yong-Ming; Guo, Wei-Hong; Zhou, Ren-Bin

    2012-01-01

    The protein structural entries grew far slower than the sequence entries. This is partly due to the bottleneck in obtaining diffraction quality protein crystals for structural determination using X-ray crystallography. The first step to achieve protein crystallization is to find out suitable chemical reagents. However, it is not an easy task. Exhausting trial and error tests of numerous combinations of different reagents mixed with the protein solution are usually necessary to screen out the pursuing crystallization conditions. Therefore, any attempts to help find suitable reagents for protein crystallization are helpful. In this paper, an analysis of the relationship between the protein sequence similarity and the crystallization reagents according to the information from the existing databases is presented. We extracted information of reagents and sequences from the Biological Macromolecule Crystallization Database (BMCD) and the Protein Data Bank (PDB) database, classified the proteins into different clusters according to the sequence similarity, and statistically analyzed the relationship between the sequence similarity and the crystallization reagents. The results showed that there is a pronounced positive correlation between them. Therefore, according to the correlation, prediction of feasible chemical reagents that are suitable to be used in crystallization screens for a specific protein is possible. PMID:22949812

  2. 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.

  3. Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons.

    PubMed

    Milkman, R; Bridges, M M

    1993-03-01

    DNA sequences have been compared in a 4,400-bp region for Escherichia coli K12 and 36 ECOR strains. Discontinuities in degree of similarity, previously inferred, are confirmed in detail. Three clonal frames are described on the basis of the present local high-resolution data, as well as previous analyses of restriction fragment length polymorphism (RFLP) and of multilocus enzyme electrophoresis (MLEE) covering small regions more widely dispersed on the chromosome. These three approaches show important consistency. The data illustrate the fact that, in the limited context of intraspecific genomic sequence variation, clonality and homology are synonymous. Two estimable quantitative properties are defined: recency of common ancestry (the reciprocal of the log10 of the number of generations since the most recent common ancestor), and the number of nucleotide pairs over which a given recency of common ancestry applies. In principle, these parameters are measures of the degree and physical extent of homology. The small size of apparent recombinational replacements, together with the observation that they occasionally occur in discontinuous series, raises the question of whether they result from the superimposition of replacements of much larger size (as expected from an elementary interpretation of conjugation and transduction in experimental E. coli systems) or via an alternative mechanism. Length polymorphisms of several sorts are described. PMID:8095913

  4. Comparison of Sequencing (Barcode Region) and Sequence-Tagged-Site PCR for Blastocystis Subtyping

    PubMed Central

    2013-01-01

    Blastocystis is the most common nonfungal microeukaryote of the human intestinal tract and comprises numerous subtypes (STs), nine of which have been found in humans (ST1 to ST9). While efforts continue to explore the relationship between human health status and subtypes, no consensus regarding subtyping methodology exists. It has been speculated that differences detected in subtype distribution in various cohorts may to some extent reflect different approaches. Blastocystis subtypes have been determined primarily in one of two ways: (i) sequencing of small subunit rRNA gene (SSU-rDNA) PCR products and (ii) PCR with subtype-specific sequence-tagged-site (STS) diagnostic primers. Here, STS primers were evaluated against a panel of samples (n = 58) already subtyped by SSU-rDNA sequencing (barcode region), including subtypes for which STS primers are not available, and a small panel of DNAs from four other eukaryotes often present in feces (n = 18). Although the STS primers appeared to be highly specific, their sensitivity was only moderate, and the results indicated that some infections may go undetected when this method is used. False-negative STS results were not linked exclusively to certain subtypes or alleles, and evidence of substantial genetic variation in STS loci was obtained. Since the majority of DNAs included here were extracted from feces, it is possible that STS primers may generally work better with DNAs extracted from Blastocystis cultures. In conclusion, due to its higher applicability and sensitivity, and since sequence information is useful for other forms of research, SSU-rDNA barcoding is recommended as the method of choice for Blastocystis subtyping. PMID:23115257

  5. Nucleotide sequence of a cloned woodchuck hepatitis virus genome: comparison with the hepatitis B virus sequence.

    PubMed Central

    Galibert, F; Chen, T N; Mandart, E

    1982-01-01

    The complete nucleotide sequence of a woodchuck hepatitis virus genome cloned in Escherichia coli was determined by the method of Maxam and Gilbert. This sequence was found to be 3,308 nucleotides long. Potential ATG initiator triplets and nonsense codons were identified and used to locate regions with a substantial coding capacity. A striking similarity was observed between the organization of human hepatitis B virus and woodchuck hepatitis virus. Nucleotide sequences of these open regions in the woodchuck virus were compared with corresponding regions present in hepatitis B virus. This allowed the location of four viral genes on the L strand and indicated the absence of protein coded by the S strand. Evolution rates of the various parts of the genome as well as of the four different proteins coded by hepatitis B virus and woodchuck hepatitis virus were compared. These results indicated that: (i) the core protein has evolved slightly less rapidly than the other proteins; and (ii) when a region of DNA codes for two different proteins, there is less freedom for the DNA to evolve and, moreover, one of the proteins can evolve more rapidly than the other. A hairpin structure, very well conserved in the two genomes, was located in the only region devoid of coding function, suggesting the location of the origin of replication of the viral DNA. Images PMID:7086958

  6. 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

  7. Biologically inspired multilevel approach for multiple moving targets detection from airborne forward-looking infrared sequences.

    PubMed

    Li, Yansheng; Tan, Yihua; Li, Hang; Li, Tao; Tian, Jinwen

    2014-04-01

    In this paper, a biologically inspired multilevel approach for simultaneously detecting multiple independently moving targets from airborne forward-looking infrared (FLIR) sequences is proposed. Due to the moving platform, low contrast infrared images, and nonrepeatability of the target signature, moving targets detection from FLIR sequences is still an open problem. Avoiding six parameter affine or eight parameter planar projective transformation matrix estimation of two adjacent frames, which are utilized by existing moving targets detection approaches to cope with the moving infrared camera and have become the bottleneck for the further elevation of the moving targets detection performance, the proposed moving targets detection approach comprises three sequential modules: motion perception for efficiently extracting motion cues, attended motion views extraction for coarsely localizing moving targets, and appearance perception in the local attended motion views for accurately detecting moving targets. Experimental results demonstrate that the proposed approach is efficient and outperforms the compared state-of-the-art approaches. PMID:24695135

  8. 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. PMID:19390049

  9. The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution

    PubMed Central

    Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.

    2010-01-01

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to ∼7× 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 1,217 are absent or undetected in non-eutherian (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 an enabling resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. PMID:19390049

  10. Biology of Treponema pallidum: correlation of functional activities with genome sequence data.

    PubMed

    Norris, S J; Cox, D L; Weinstock, G M

    2001-01-01

    Aspects of the biology of T. pallidum subsp. pallidum, the agent of syphilis, are examined in the context of a century of experimental studies and the recently determined genome sequence. T. pallidum and a group of closely related pathogenic spirochetes have evolved to become highly invasive, persistent pathogens with little toxigenic activity and an inability to survive outside the mammalian host. Analysis of the genome sequence confirms morphologic studies indicating the lack of lipopolysaccharide and lipid biosynthesis mechanisms, as well as a paucity of outer membrane protein candidates. The metabolic capabilities and adaptability of T. pallidum are minimal, and this relative deficiency is reflected by the absence of many pathways, including the tricarboxylic acid cycle, components of oxidative phosphorylation, and most biosynthetic pathways. Although multiplication of T. pallidum has been obtained in a tissue culture system, continuous in vitro culture has not been achieved. The balance of oxygen utilization and toxicity is key to the survival and growth of T. pallidum, and the genome sequence reveals a similarity to lactic acid bacteria that may be useful in understanding this relationship. The identification of relatively few genes potentially involved in pathogenesis reflects our lack of understanding of invasive pathogens relative to toxigenic organisms. The genome sequence will provide useful raw data for additional functional studies on the structure, metabolism, and pathogenesis of this enigmatic organism. PMID:11200228

  11. Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences

    PubMed Central

    Ekisheva, Svetlana

    2010-01-01

    Probabilistic models for biological sequences (DNA and proteins) have many useful applications in bioinformatics. Normally, the values of parameters of these models have to be estimated from empirical data. However, even for the most common estimates, the maximum likelihood (ML) estimates, properties have not been completely explored. Here we assess the uniform accuracy of the ML estimates for models of several types: the independence model, the Markov chain and the hidden Markov model (HMM). Particularly, we derive rates of decay of the maximum estimation error by employing the measure concentration as well as the Gaussian approximation, and compare these rates. PMID:21318122

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

    PubMed Central

    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. PMID:20948615

  13. 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…

  14. 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

  15. 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

  16. Identification of the bacteriophage T5 dUTPase by protein sequence comparisons.

    PubMed

    Kaliman, A V

    1996-01-01

    It is shown by protein sequence comparisons that a 148 amino acid open reading frame (ORF 148) located at 67% of the bacteriophage T5 genome encodes a protein with strong similarity to known dUTPases. This protein contains five characteristic amino acid sequence motifs that are common to the dUTPase gene family. A similarity in size and high degree of sequence identity strongly suggest that the protein encoded by the ORF 148 of bacteriophage T5 is dUTPase. PMID:8988373

  17. 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

  18. Ribosomal DNA ITS-1 and ITS-2 sequence comparisons as a tool for predicting genetic relatedness.

    PubMed

    Coleman, A W; Mai, J C

    1997-08-01

    The determination of the secondary structure of the internal transcribed spacer (ITS) regions separating nuclear ribosomal RNA genes of Chlorophytes has improved the fidelity of alignment of nuclear ribosomal ITS sequences from related organisms. Application of this information to sequences from green algae and plants suggested that a subset of the ITS-2 positions is relatively conserved. Organisms that can mate are identical at all of these 116 positions, or differ by at most, one nucleotide change. Here we sequenced and compared the ITS-1 and ITS-2 of 40 green flagellates in search of the nearest relative to Chlamydomonas reinhardtii. The analysis clearly revealed one unique candidate, C. incerta. Several ancillary benefits of the analysis included the identification of mislabelled cultures, the resolution of confusion concerning C. smithii, the discovery of misidentified sequences in GenBank derived from a green algal contaminant, and an overview of evolutionary relationships among the Volvocales, which is congruent with that derived from rDNA gene sequence comparisons but improves upon its resolution. The study further delineates the taxonomic level at which ITS sequences, in comparison to ribosomal gene sequences, are most useful in systematic and other studies. PMID:9236277

  19. Comparison of alignment software for genome-wide bisulphite sequence data

    PubMed Central

    Chatterjee, Aniruddha; Stockwell, Peter A.; Rodger, Euan J.; Morison, Ian M.

    2012-01-01

    Recent advances in next generation sequencing (NGS) technology now provide the opportunity to rapidly interrogate the methylation status of the genome. However, there are challenges in handling and interpretation of the methylation sequence data because of its large volume and the consequences of bisulphite modification. We sequenced reduced representation human genomes on the Illumina platform and efficiently mapped and visualized the data with different pipelines and software packages. We examined three pipelines for aligning bisulphite converted sequencing reads and compared their performance. We also comment on pre-processing and quality control of Illumina data. This comparison highlights differences in methods for NGS data processing and provides guidance to advance sequence-based methylation data analysis for molecular biologists. PMID:22344695

  20. 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

  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 solution-based exome capture methods for next generation sequencing

    PubMed Central

    2011-01-01

    Background Techniques enabling targeted re-sequencing of the protein coding sequences of the human genome on next generation sequencing instruments are of great interest. We conducted a systematic comparison of the solution-based exome capture kits provided by Agilent and Roche NimbleGen. A control DNA sample was captured with all four capture methods and prepared for Illumina GAII sequencing. Sequence data from additional samples prepared with the same protocols were also used in the comparison. Results We developed a bioinformatics pipeline for quality control, short read alignment, variant identification and annotation of the sequence data. In our analysis, a larger percentage of the high quality reads from the NimbleGen captures than from the Agilent captures aligned to the capture target regions. High GC content of the target sequence was associated with poor capture success in all exome enrichment methods. Comparison of mean allele balances for heterozygous variants indicated a tendency to have more reference bases than variant bases in the heterozygous variant positions within the target regions in all methods. There was virtually no difference in the genotype concordance compared to genotypes derived from SNP arrays. A minimum of 11× coverage was required to make a heterozygote genotype call with 99% accuracy when compared to common SNPs on genome-wide association arrays. Conclusions Libraries captured with NimbleGen kits aligned more accurately to the target regions. The updated NimbleGen kit most efficiently covered the exome with a minimum coverage of 20×, yet none of the kits captured all the Consensus Coding Sequence annotated exons. PMID:21955854

  3. Mining and comparison of haplotype-based expressed sequence tag single nucleotide polymorphisms among citrus cultivars

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this paper, haplotype-based SNPs were mined out of publicly available citrus expressed sequence tags (ESTs) from different citrus cultivars (genotypes) individually and collectively for comparison. There were a total of 567,297 ESTs belonging to 27 cultivars in varying numbers and consequentially...

  4. Genomic sequence comparison of eif(iso)4E between Arabidopsis and melon

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Eukaryotic initiation factors (eifs) bind to mRNA and initiate translation in plants. Mutations in eifs condition recessively inherited virus resistances. While coding regions among eifs have been compared both within and among species, comparisons among flanking genomic sequences are lacking. We ...

  5. Comparison and quantitative verification of mapping algorithms for whole genome bisulfite sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitat...

  6. Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.

    PubMed

    Joseph, Agnel Praveen; Srinivasan, Narayanaswamy; de Brevern, Alexandre G

    2012-09-01

    Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a 1D sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. PMID:22676903

  7. 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

  8. 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.

  9. Biological treatment of shrimp aquaculture wastewater using a sequencing batch reactor.

    PubMed

    Lyles, C; Boopathy, R; Fontenot, Q; Kilgen, M

    2008-12-01

    To improve the water quality in the shrimp aquaculture, a sequencing batch reactor (SBR) has been tested for the treatment of shrimp wastewater. A SBR is a variation of the activated sludge biological treatment process. This process uses multiple steps in the same tank to take the place of multiple tanks in a conventional treatment system. The SBR accomplishes equalization, aeration, and clarification in a timed sequence in a single reactor basin. This is achieved in a simple tank, through sequencing stages, which include fill, react, settle, decant, and idle. A laboratory scale SBR and a pilot scale SBR was successfully operated using shrimp aquaculture wastewater. The wastewater contained high concentration of carbon and nitrogen. By operating the reactor sequentially, viz, aerobic and anoxic modes, nitrification and denitrification were achieved as well as removal of carbon in a laboratory scale SBR. To be specific, the initial chemical oxygen demand (COD) concentration of 1,593 mg/l was reduced to 44 mg/l within 10 days of reactor operation. Ammonia in the sludge was nitrified within 3 days. The denitrification of nitrate was achieved by the anaerobic process and 99% removal of nitrate was observed. Based on the laboratory study, a pilot scale SBR was designed and operated to remove excess nitrogen in the shrimp wastewater. The results mimicked the laboratory scale SBR. PMID:18561032

  10. Clinical next-generation sequencing reveals aggressive cancer biology in adolescent and young adult patients

    PubMed Central

    Subbiah, Vivek; Bupathi, Manojkumar; Kato, Shumei; Livingston, Andrew; Slopis, John; Anderson, Pete M.; Hong, David S.

    2015-01-01

    Background The aggressive biology of cancers arising in adolescent and young adult (AYA; ages 15–39 years) patients is thought to contribute to poor survival outcomes. Methods We used clinical next-generation sequencing (NGS) results to examine the molecular alterations and diverse biology of cancer in AYA patients referred to the Phase 1 program at UT MD Anderson Cancer Center. Results Among the 28 patients analyzed (14 female and 14 male), 12 had pediatric-type cancers, six had adult-type cancers, and ten had orphan cancers. Unique, hitherto unreported aberrations were identified in all types of cancers. Aberrations in TP53, NKX2-1, KRAS, CDKN2A, MDM4, MCL1, MYC, BCL2L2, and RB1 were demonstrated across all tumor types. Five patients harbored TP53 aberrations; three patients harbored MYC, MCL1, and CDKN2A aberrations; and two patients harbored NKX2-1, KRAS, MDM4, BCL2L2, and RB1 alterations. Several patients had multiple aberrations; a patient with wild-type gastrointestinal stromal tumor harbored five alterations (MDM4, MCL1, KIT, AKT3, and PDGRFA). Conclusions This preliminary report of NGS of cancer in AYA patients reveals diverse and unique aberrations. Further molecular profiling and a deeper understanding of the biology of these unique aberrations are warranted and may lead to targeted therapeutic interventions. PMID:26328274

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. A Multiple-Sequence Variant of the Multiple-Baseline Design: A Strategy for Analysis of Sequence Effects and Treatment Comparison.

    ERIC Educational Resources Information Center

    Noell, George H.; Gresham, Frank M.

    2001-01-01

    Describes design logic and potential uses of a variant of the multiple-baseline design. The multiple-baseline multiple-sequence (MBL-MS) consists of multiple-baseline designs that are interlaced with one another and include all possible sequences of treatments. The MBL-MS design appears to be primarily useful for comparison of treatments taking…

  17. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.

    PubMed

    Cole, S T; Brosch, R; Parkhill, J; Garnier, T; Churcher, C; Harris, D; Gordon, S V; Eiglmeier, K; Gas, S; Barry, C E; Tekaia, F; Badcock, K; Basham, D; Brown, D; Chillingworth, T; Connor, R; Davies, R; Devlin, K; Feltwell, T; Gentles, S; Hamlin, N; Holroyd, S; Hornsby, T; Jagels, K; Krogh, A; McLean, J; Moule, S; Murphy, L; Oliver, K; Osborne, J; Quail, M A; Rajandream, M A; Rogers, J; Rutter, S; Seeger, K; Skelton, J; Squares, R; Squares, S; Sulston, J E; Taylor, K; Whitehead, S; Barrell, B G

    1998-06-11

    Countless millions of people have died from tuberculosis, a chronic infectious disease caused by the tubercle bacillus. The complete genome sequence of the best-characterized strain of Mycobacterium tuberculosis, H37Rv, has been determined and analysed in order to improve our understanding of the biology of this slow-growing pathogen and to help the conception of new prophylactic and therapeutic interventions. The genome comprises 4,411,529 base pairs, contains around 4,000 genes, and has a very high guanine + cytosine content that is reflected in the biased amino-acid content of the proteins. M. tuberculosis differs radically from other bacteria in that a very large portion of its coding capacity is devoted to the production of enzymes involved in lipogenesis and lipolysis, and to two new families of glycine-rich proteins with a repetitive structure that may represent a source of antigenic variation. PMID:9634230

  18. PepTool and GeneTool: platform-independent tools for biological sequence analysis.

    PubMed

    Wishart, D S; Stothard, P; Van Domselaar, G H

    2000-01-01

    Although we are unable to discuss all of the functionality available in PepTool and GeneTool, it should be evident from this brief review that both packages offer a great deal in terms of functionality and ease-of-use. Furthermore, a number of useful innovations including platform-independent GUI design, networked parallelism, direct internet connectivity, database compression, and a variety of enhanced or improved algorithms should make these two programs particularly useful in the rapidly changing world of biological sequence analysis. More complete descriptions of the programs, algorithms and operation of PepTool and GeneTool are available on the BioTools web site (www.biotools.com), in the associated program user manuals and in the on-line Help pages. PMID:10547833

  19. 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

  20. 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…

  1. 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.

  2. 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

  3. 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

  4. Biological Characterization and Next-Generation Genome Sequencing of the Unclassified Cotia Virus SPAn232 (Poxviridae)

    PubMed Central

    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

    2012-01-01

    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. PMID:22345477

  5. 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...

  6. 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…

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

    PubMed

    Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; Johnson, Brett E; Fouse, Shaun D; Delaney, Allen; Zhao, Yongjun; Olshen, Adam; Ballinger, Tracy; Zhou, Xin; Forsberg, Kevin J; Gu, Junchen; Echipare, Lorigail; O'Geen, Henriette; Lister, Ryan; Pelizzola, Mattia; Xi, Yuanxin; Epstein, Charles B; Bernstein, Bradley E; Hawkins, R David; Ren, Bing; Chung, Wen-Yu; Gu, Hongcang; Bock, Christoph; Gnirke, Andreas; Zhang, Michael Q; Haussler, David; Ecker, Joseph R; Li, Wei; Farnham, Peggy J; Waterland, Robert A; Meissner, Alexander; Marra, Marco A; Hirst, Martin; Milosavljevic, Aleksandar; Costello, Joseph F

    2010-10-01

    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 methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA binding domain sequencing (MBD-seq). We applied all four methods to biological replicates of human embryonic stem cells to assess their genome-wide CpG coverage, resolution, cost, concordance and the influence of CpG density and genomic context. The methylation levels assessed by the two bisulfite methods were concordant (their difference did not exceed a given threshold) for 82% for CpGs and 99% of the non-CpG cytosines. Using binary methylation calls, the two enrichment methods were 99% concordant and regions assessed by all four methods were 97% concordant. We combined MeDIP-seq with methylation-sensitive restriction enzyme (MRE-seq) sequencing for comprehensive methylome coverage at lower cost. This, along with RNA-seq and ChIP-seq of the ES cells enabled us to detect regions with allele-specific epigenetic states, identifying most known imprinted regions and new loci with monoallelic epigenetic marks and monoallelic expression. PMID:20852635

  8. 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

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

    PubMed

    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. PMID:25828242

  10. 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.

  11. Comparison of Pulse Sequences for R1–based Electron Paramagnetic Resonance Oxygen Imaging

    PubMed Central

    Epel, Boris; Halpern, Howard J.

    2015-01-01

    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. PMID:25828242

  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. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements

    PubMed Central

    Mecham, Brigham H.; Klus, Gregory T.; Strovel, Jeffrey; Augustus, Meena; Byrne, David; Bozso, Peter; Wetmore, Daniel Z.; Mariani, Thomas J.; Kohane, Isaac S.; Szallasi, Zoltan

    2004-01-01

    Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms. PMID:15161944

  14. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.

    PubMed

    Mecham, Brigham H; Klus, Gregory T; Strovel, Jeffrey; Augustus, Meena; Byrne, David; Bozso, Peter; Wetmore, Daniel Z; Mariani, Thomas J; Kohane, Isaac S; Szallasi, Zoltan

    2004-01-01

    Cancer derived microarray data sets are routinely produced by various platforms that are either commercially available or manufactured by academic groups. The fundamental difference in their probe selection strategies holds the promise that identical observations produced by more than one platform prove to be more robust when validated by biology. However, cross-platform comparison requires matching corresponding probe sets. We are introducing here sequence-based matching of probes instead of gene identifier-based matching. We analyzed breast cancer cell line derived RNA aliquots using Agilent cDNA and Affymetrix oligonucleotide microarray platforms to assess the advantage of this method. We show, that at different levels of the analysis, including gene expression ratios and difference calls, cross-platform consistency is significantly improved by sequence- based matching. We also present evidence that sequence-based probe matching produces more consistent results when comparing similar biological data sets obtained by different microarray platforms. This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms. PMID:15161944

  15. 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…

  16. 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. PMID:25532763

  17. 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. PMID:26792793

  18. 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

  19. Genome sequence comparison of two United States live attenuated vaccines of infectious laryngotracheitis virus (ILTV).

    PubMed

    Chandra, Yohanna Gita; Lee, Jeongyoon; Kong, Byung-Whi

    2012-06-01

    This study was conducted to identify unique nucleotide differences in two U.S. chicken embryo origin (CEO) vaccines [LT Blen (GenBank accession: JQ083493) designated as vaccine 1; Laryngo-Vac(®) (GenBank accession: JQ083494) designated as vaccine 2] of infectious laryngotracheitis virus (ILTV) genomes compared to an Australian Serva vaccine reference ILTV genome sequence [Gallid herpesvirus 1 (GaHV-1); GenBank accession number: HQ630064]. Genomes of the two vaccine ILTV strains were sequenced using Illumina Genome Analyzer 2X of 36 cycles of single-end reads. Results revealed that few nucleotide differences (23 in vaccine 1; 31 in vaccine 2) were found and indicate that the US CEO strains are practically identical to the Australian Serva CEO strain, which is a European-origin vaccine. The sequence differences demonstrated the spectrum of variability among vaccine strains. Only eight amino acid differences were found in ILTV proteins including UL54, UL27, UL28, UL20, UL1, ICP4, and US8 in vaccine 1. Similarly, in vaccine 2, eight amino acid differences were found in UL54, UL27, UL28, UL36, UL1, ICP4, US10, and US8. Further comparison of US CEO vaccines to several ILTV genome sequences revealed that US CEO vaccines are genetically close to both the Serva vaccine and 63140/C/08/BR (GenBank accession: HM188407) and are distinct from the two Australian-origin CEO vaccines, SA2 (GenBank accession: JN596962) and A20 (GenBank accession: JN596963), which showed close similarity to each other. These data demonstrate the potential of high-throughput sequencing technology to yield insight into the sequence variation of different ILTV strains. This information can be used to discriminate between vaccine ILTV strains and further, to identify newly emerging mutant strains of field isolates. PMID:22382591

  20. A comparison of tools for the simulation of genomic next-generation sequencing data.

    PubMed

    Escalona, Merly; Rocha, Sara; Posada, David

    2016-08-01

    Computer simulation of genomic data has become increasingly popular for assessing and validating biological models or for gaining an understanding of specific data sets. Several computational tools for the simulation of next-generation sequencing (NGS) data have been developed in recent years, which could be used to compare existing and new NGS analytical pipelines. Here we review 23 of these tools, highlighting their distinct functionality, requirements and potential applications. We also provide a decision tree for the informed selection of an appropriate NGS simulation tool for the specific question at hand. PMID:27320129

  1. 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

  2. Comparison of Complete Genome Sequences of Usutu Virus Strains Detected in Spain, Central Europe, and Africa

    PubMed Central

    Busquets, Núria; Nowotny, Norbert

    2014-01-01

    Abstract The complete genomic sequence of Usutu virus (USUV, genus Flavivirus, family Flaviviridae) strain MB119/06, detected in a pool of Culex pipiens mosquitoes in northeastern Spain (Viladecans, Catalonia) in 2006, was determined and analyzed. The phylogenetic relationship with all other available complete USUV genome sequences was established. The Spanish sequence investigated showed the closest relationship to the USUV prototype strain SA AR 1776 isolated in South Africa in 1959 (96.9% nucleotide and 98.8% amino acid identities). Conserved structural elements and enzyme motifs of the putative polyprotein precursor were identified. Unique amino acid substitutions were recognized; however, their potential roles as virulence markers could not be verified. Comparisons of the polyprotein precursor sequences of USUV strains detected in mosquitoes, birds, and humans could not confirm the predicted role of unique amino acid substitutions in relation to virulence in humans. Phylogenetic analysis of a partial coding section of the NS5 protein gene region indicated that USUV strains circulating in Europe form three different genetic clusters. Broad and targeted surveys for USUV in mosquitoes could reveal further details of the geographic distribution and genetic diversity of the virus in Europe and in Africa. PMID:24746182

  3. PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

    PubMed

    Elnitski, Laura; Riemer, Cathy; Petrykowska, Hanna; Florea, Liliana; Schwartz, Scott; Miller, Webb; Hardison, Ross

    2002-12-01

    Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells. PMID:12504859

  4. 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

  5. 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

  6. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan.

    PubMed

    Cheng, Xinwei; Su, Xiaoquan; Chen, Xiaohua; Zhao, Huanxin; Bo, Cunpei; Xu, Jian; Bai, Hong; Ning, Kang

    2014-01-01

    Although Traditional Chinese Medicine (TCM) preparations have long history with successful applications, the scientific and systematic quality assessment of TCM preparations mainly focuses on chemical constituents and is far from comprehensive. There are currently only few primitive studies on assessment of biological ingredients in TCM preparations. Here, we have proposed a method, M-TCM, for biological assessment of the quality of TCM preparations based on high-throughput sequencing and metagenomic analysis. We have tested this method on Liuwei Dihuang Wan (LDW), a TCM whose ingredients have been well-defined. Our results have shown that firstly, this method could determine the biological ingredients of LDW preparations. Secondly, the quality and stability of LDW varies significantly among different manufacturers. Thirdly, the overall quality of LDW samples is significantly affected by their biological contaminations. This novel strategy has the potential to achieve comprehensive ingredient profiling of TCM preparations. PMID:24888649

  7. Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan

    PubMed Central

    Cheng, Xinwei; Su, Xiaoquan; Chen, Xiaohua; Zhao, Huanxin; Bo, Cunpei; Xu, Jian; Bai, Hong; Ning, Kang

    2014-01-01

    Although Traditional Chinese Medicine (TCM) preparations have long history with successful applications, the scientific and systematic quality assessment of TCM preparations mainly focuses on chemical constituents and is far from comprehensive. There are currently only few primitive studies on assessment of biological ingredients in TCM preparations. Here, we have proposed a method, M-TCM, for biological assessment of the quality of TCM preparations based on high-throughput sequencing and metagenomic analysis. We have tested this method on Liuwei Dihuang Wan (LDW), a TCM whose ingredients have been well-defined. Our results have shown that firstly, this method could determine the biological ingredients of LDW preparations. Secondly, the quality and stability of LDW varies significantly among different manufacturers. Thirdly, the overall quality of LDW samples is significantly affected by their biological contaminations. This novel strategy has the potential to achieve comprehensive ingredient profiling of TCM preparations. PMID:24888649

  8. Phylogenetic comparison of the pre-mRNA adenosine deaminase ADAR2 genes and transcripts: conservation and diversity in editing site sequence and alternative splicing patterns.

    PubMed

    Slavov, D; Gardiner, K

    2002-10-16

    Adenosine deaminase that acts on RNA -2 (ADAR2) is a member of a family of vertebrate genes that encode adenosine (A)-to-inosine (I) RNA deaminases, enzymes that deaminate specific A residues in specific pre-mRNAs to produce I. Known substrates of ADAR2 include sites within the coding regions of pre-mRNAs of the ionotropic glutamate receptors, GluR2-6, and the serotonin receptor, 5HT2C. Mammalian ADAR2 expression is itself regulated by A-to-I editing and by several alternative splicing events. Because the biological consequences of ADAR2 function are significant, we have undertaken a phylogenetic comparison of these features. Here we report a comparison of cDNA sequences, genomic organization, editing site sequences and patterns of alternative splicing of ADAR2 genes from human, mouse, chicken, pufferfish and zebrafish. Coding sequences and intron/exon organization are highly conserved. All ADAR2 genes show evidence of transcript editing with required sequences and predicted secondary structures very highly conserved. Patterns and levels of editing and alternative splicing vary among organisms, and include novel N-terminal exons and splicing events. PMID:12459255

  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. 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

  11. 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

  12. 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…

  13. 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

  14. Computational and biological analysis of 680 kb of DNA sequence from the human 5q31 cytokine gene cluster region.

    PubMed

    Frazer, K A; Ueda, Y; Zhu, Y; Gifford, V R; Garofalo, M R; Mohandas, N; Martin, C H; Palazzolo, M J; Cheng, J F; Rubin, E M

    1997-05-01

    With the human genome project advancing into what will be a 7- to 10-year DNA sequencing phase, we are presented with the challenge of developing strategies to convert genomic sequence data, as they become available, into biologically meaningful information. We have analyzed 680 kb of noncontiguous DNA sequence from a 1-Mb region of human chromosome 5q31, coupling computational analysis with gene expression studies of tissues isolated from humans as well as from mice containing human YAC transgenes. This genomic interval has been noted previously for containing the cytokine gene cluster and a quantitative trait locus associated with inflammatory diseases. Our analysis identified and verified expression of 16 new genes, as well as 7 previously known genes. Of the total of 23 genes in this region, 78% had similarity matches to sequences in protein databases and 83% had exact expressed sequence tag (EST) database matches. Comparative mapping studies of eight of the new human genes discovered in the 5q31 region revealed that all are located in the syntenic region of mouse chromosome 11q. Our analysis demonstrates an approach for examining human sequence as it is made available from large sequencing programs and has resulted in the discovery of several biomedically important genes, including a cyclin, a transcription factor that is homologous to an oncogene, a protein involved in DNA repair, and several new members of a family of transporter proteins. PMID:9149945

  15. Biological activities of a synthetic peptide composed of two unlinked domains from a retroviral transmembrane protein sequence.

    PubMed Central

    Wegemer, D E; Kabat, K G; Kloetzer, W S

    1990-01-01

    We report several biological activities of a synthetic peptide whose sequence contains the highly conserved region of feline leukemia virus transmembrane protein (TM) synthetically linked to another short TM-derived sequence particularly rich in polar positive residues. This 29-amino-acid peptide blocked [3H]thymidine uptake 30 to 50% by concanavalin A-stimulated CD4(+)--but not CD8(+)-enriched murine splenocytes. Maximal suppression was detected at 12.5 micrograms (3 microM) to 75 micrograms (19 microM) per ml of growth medium; stimulation of [3H]thymidine uptake was observed at higher peptide concentrations. The synthetic peptide inhibited but did not stimulate [3H]thymidine uptake by mitogen-activated thymocytes and antibody production by splenocytes as determined in a liquid hemolytic plaque assay. Similarities are reported between a consensus sequence of diverse retroviral TMs and a region of alpha interferons shown by others to be important for antiviral and cytostatic properties. The TM sequence-derived synthetic peptide blocked in a nontoxic and sequence-specific manner the release of murine leukemia virus from two chronically infected cell lines. We suggest that some of the biological effects of retroviral TM are mediated through a common pathway shared with alpha interferons. Images PMID:1969500

  16. uShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts

    PubMed Central

    Jiang, Minghui; Anderson, James; Gillespie, Joel; Mayne, Martin

    2008-01-01

    Background Randomly shuffled sequences are routinely used in sequence analysis to evaluate the statistical significance of a biological sequence. In many cases, biologists need sophisticated shuffling tools that preserve not only the counts of distinct letters but also higher-order statistics such as doublet counts, triplet counts, and, in general, k-let counts. Results We present a sequence analysis tool (named uShuffle) for generating uniform random permutations of biological sequences (such as DNAs, RNAs, and proteins) that preserve the exact k-let counts. The uShuffle tool implements the latest variant of the Euler algorithm and uses Wilson's algorithm in the crucial step of arborescence generation. It is carefully engineered and extremely efficient. The uShuffle tool achieves maximum flexibility by allowing arbitrary alphabet size and let size. It can be used as a command-line program, a web application, or a utility library. Source code in C, Java, and C#, and integration instructions for Perl and Python are provided. Conclusion The uShuffle tool surpasses existing implementation of the Euler algorithm in both performance and flexibility. It is a useful tool for the bioinformatics community. PMID:18405375

  17. BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

    PubMed

    Worley, K C; Wiese, B A; Smith, R F

    1995-09-01

    BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search

  18. Sequence of subunit c of the Na(+)-translocating F1F0 ATPase of Acetobacterium woodii: proposal for determinants of Na+ specificity as revealed by sequence comparisons.

    PubMed

    Rahlfs, S; Müller, V

    1997-03-10

    A 3.2 kb EcoRI fragment carrying genes for Na(+)-F1F0 ATPase was cloned from chromosomal DNA of Acetobacterium woodii. DNA sequence analysis revealed the presence of an open reading frame which was identified by data base searches and comparison with the experimentally derived N-terminal amino acid sequence to code for subunit c of Na(+)-F1F0 ATPase. A comparison of the primary sequences of the two well established Na(+)-translocating F1F0 ATPases from Acetobacterium woodii and Propionigenium modestum with H(+)-translocating enzymes indicates the length of the C-terminus as well as specific residues located in the cytoplasmic membrane to be important for Na+ transport. PMID:9119076

  19. 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

  20. 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

  1. 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.

  2. A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

    PubMed Central

    Zhang, Wenyu; Chen, Jiajia; Yang, Yang; Tang, Yifei; Shang, Jing; Shen, Bairong

    2011-01-01

    The advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform. Considering the computational time, maximum random access memory (RAM) occupancy, assembly accuracy and integrity, our study indicate that string-based assemblers, overlap-layout-consensus (OLC) assemblers are well-suited for very short reads and longer reads of small genomes respectively. For large datasets of more than hundred millions of short reads, De Bruijn graph-based assemblers would be more appropriate. In terms of software implementation, string-based assemblers are superior to graph-based ones, of which SOAPdenovo is complex for the creation of configuration file. Our comparison study will assist researchers in selecting a well-suited assembler and offer essential information for the improvement of existing assemblers or the developing of novel assemblers. PMID:21423806

  3. 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.

  4. 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

  5. Statistical physics approach to categorize biologic signals: From heart rate dynamics to DNA sequences

    NASA Astrophysics Data System (ADS)

    Peng, C.-K.; Yang, Albert C.-C.; Goldberger, Ary L.

    2007-03-01

    We recently proposed a novel approach to categorize information carried by symbolic sequences based on their usage of repetitive patterns. A simple quantitative index to measure the dissimilarity between two symbolic sequences can be defined. This information dissimilarity index, defined by our formula, is closely related to the Shannon entropy and rank order of the repetitive patterns in the symbolic sequences. Here we discuss the underlying statistical physics assumptions of this dissimilarity index. We use human cardiac interbeat interval time series and DNA sequences as examples to illustrate the applicability of this generic approach to real-world problems.

  6. Eimeria maxima phosphatidylinositol 4-phosphate 5-kinase: locus sequencing, characterization, and cross-phylum comparison.

    PubMed

    Goh, Mei-Yen; Pan, Mei-Zhen; Blake, Damer P; Wan, Kiew-Lian; Song, Beng-Kah

    2011-03-01

    Phosphatidylinositol 4-phosphate 5-kinase (PIP5K) may play an important role in host-cell invasion by the Eimeria species, protozoan parasites which can cause severe intestinal disease in livestock. Here, we report the structural organization of the PIP5K gene in Eimeria maxima (Weybridge strain). Two E. maxima BAC clones carrying the E. maxima PIP5K (EmPIP5K) coding sequences were selected for shotgun sequencing, yielding a 9.1-kb genomic segment. The EmPIP5K coding region was initially identified using in silico gene-prediction approaches and subsequently confirmed by mapping rapid amplification of cDNA ends and RT-PCR-generated cDNA sequence to its genomic segment. The putative EmPIP5K gene was located at position 710-8036 nt on the complimentary strand and comprised of 23 exons. Alignment of the 1147 amino acid sequence with previously annotated PIP5K proteins from other Apicomplexa species detected three conserved motifs encompassing the kinase core domain, which has been shown by previous protein deletion studies to be necessary for PIP5K protein function. Phylogenetic analysis provided further evidence that the putative EmPIP5K protein is orthologous to that of other Apicomplexa. Subsequent comparative gene structure characterization revealed events of intron loss/gain throughout the evolution of the apicomplexan PIP5K gene. Further scrutiny of the genomic structure revealed a possible trend towards "intron gain" between two of the motif regions. Our findings offer preliminary insights into the structural variations that have occurred during the evolution of the PIP5K locus and may aid in understanding the functional role of this gene in the cellular biology of apicomplexan parasites. PMID:20938684

  7. 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

  8. Protein identities from 'Graphocephala atropunctata' expressed sequence tags: Expanding leafhopper vector biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heat shock proteins and 44 protein sequences from the blue-green sharpshooter, BGSS, were produced and identified. The sequences were submitted and published under accession numbers: DQ445499-DQ445542, in the National Center for Biotechnology Information, NCBI, Public Database. The blue-green sharps...

  9. Biological characterization and complete genomic sequence of Carrot thin leaf virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The host range of a cilantro isolate of Carrot thin leaf virus (CTLV-Cs) was determined to include 15 plant species. The virus was also transmitted to 9 of 11 tested apiaceous species by aphids. Complete genomic sequences of CTLV-Cs and a carrot isolate of CTLV were determined. Their genomic sequenc...

  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. Analysis of expressed sequence tags from Uromyces appendiculatus hyphae and haustoria and their comparison to sequences from other rust fungi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two separate cDNA libraries were prepared for RNA extracted from bean rust (Uromyces appendiculatus) hyphae and haustoria isolated from infected leaves bean leaves (Phaseolus vulgaris cv Pint 111) between 2 and 8 dpi. Approximately 13,000 clones were sequenced from both ends and the sequences assem...

  12. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants.

    PubMed

    Ho, Cynthia K Y; Welkers, Matthijs R A; Thomas, Xiomara V; Sullivan, James C; Kieffer, Tara L; Reesink, Henk W; Rebers, Sjoerd P H; de Jong, Menno D; Schinkel, Janke; Molenkamp, Richard

    2015-07-01

    We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were used to compare the consensus sequence, average pairwise distance, normalized Shannon entropy, phylogenetic tree topology and the number and frequency of variants derived from both sequencing techniques. In general, a good concordance was observed between both techniques for the majority of datasets. Discordant results were observed for 5 out of 39 clonal and 454 datasets, which could be attributed to primer-related selective amplification used for clonal sequencing. Both 454 and clonal datasets consisted of a few major variants and a large number of low-frequency variants. Telaprevir resistance-associated variants were observed in low frequencies and were detected more often by 454. We conclude that performance of 454 and clonal sequencing is comparable for the characterization of intra-host virus populations. Not surprisingly, 454 is superior for the detection of low frequency resistance-associated variants. However, despite the greater coverage, 454 failed to detect some low frequency variants detected by clonal sequencing. PMID:25818622

  13. H3 and H4 histone cDNA sequences from Xenopus: a sequence comparison of H4 genes.

    PubMed Central

    Turner, P C; Woodland, H R

    1982-01-01

    Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are presented. These new sequences are compared with other H3 and H4 DNA sequences both in the coding and 3' noncoding regions. We find that there is considerable non-random codon usage in ten H4 genes. In addition there are some sequence similarities in the 3' noncoding regions of H3 and H4 genes. PMID:6896750

  14. Comparison of the nucleotide sequences of wheat dwarf virus (WDV) isolates from Hungary and Ukraine.

    PubMed

    Tóbiás, Istvan; Shevchenko, Oleksiy; Kiss, Balázs; Bysov, Andriy; Snihur, Halina; Polischuk, Valery; Salánki, Katalin; Palkovics, László

    2011-01-01

    Wheat dwarf virus (WDV) is the most ubiquitous virus in cereals causing huge losses in both Hungary and Ukraine. The presence of barley-and wheat-adapted strains has been confirmed, suggesting that the barley strain is restricted to barley, while the wheat strain is present in both wheat and barley plants. Five WDV isolates from wheat plants sampled in Hungary and Ukraine were sequenced and compared with known WDV isolates from GenBank. Four WDV isolates belonged to the wheat strain. Our results indicate that WDV-Odessa is an isolate of special interest since it has originated from wheat, but belongs to the barley-adapted strain, providing novel data on WDV biology and raising issues of pathogen epidemiology. PMID:21905629

  15. Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology.

    PubMed

    Rounsley, Steven D; Last, Robert L

    2010-03-01

    In 1998 Cereon Genomics LLC, a subsidiary of Monsanto Co., performed a shotgun sequencing of the Arabidopsis thaliana Landsberg erecta genome to a depth of twofold coverage using 'classic' Sanger sequencing. This sequence was assembled and aligned to the Columbia ecotype sequence produced by the Arabidopsis Genome Initiative. The analysis provided tens of thousands of high-confidence predictions of polymorphisms between these two varieties of A. thaliana, and the predicted polymorphisms and Landsberg erecta sequence were subsequently made available to the not-for-profit research community by Monsanto. These data have been used for a wide variety of published studies, including map-based gene identification from forward genetic screens, studies of recombination and organelle genetics, and gene expression studies. The combination of resequencing approaches with next-generation sequencing technology has led to an increasing number of similar studies of genome-wide genetic diversity in A. thaliana, including the 1001 genomes project (http://1001genomes.org). Similar approaches are becoming possible in any number of crop species as DNA sequencing costs plummet and throughput rapidly increases, promising to lay the groundwork for revolutionizing our understanding of the relationship between genotype and phenotype in plants. PMID:20409267

  16. 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

  17. 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

  18. Comparison of fungi within the Gaeumannomyces-Phialophora complex by analysis of ribosomal DNA sequences.

    PubMed Central

    Bryan, G T; Daniels, M J; Osbourn, A E

    1995-01-01

    Four ascomycete species of the genus Gaeumannomyces infect roots of monocotyledons. Gaeumannomyces graminis contains four varieties, var. tritici, var. avenae, var. graminis, and var. maydis. G. graminis varieties tritici, avenae, and graminis have Phialophora-like anamorphs and, together with the other Gaeumannomyces and Phialophora species found on cereal roots, constitute the Gaeumannomyces-Phialophora complex. Relatedness of a number of Gaeumannomyces and Phialophora isolates was assessed by comparison of DNA sequences of the 18S rRNA gene, the 5.8S rRNA gene, and the internal transcribed spacers (ITS). G. graminis var. tritici, G. graminis var. avenae, and G. graminis var. graminis isolates can be distinguished from each other by nucleotide sequence differences in the ITS regions. The G. graminis var. tritici isolates can be further subdivided into R and N isolates (correlating with ability [R] or inability [N] to infect rye). Phylogenetic analysis of the ITS regions of several oat-infecting G. graminis var. tritici isolates suggests that these isolates are actually more closely related to G. graminis var. avenae. The isolates of Magnaporthe grisea included in the analysis showed a surprising degree of relatedness to members of the Gaeumannomyces-Phialophora complex. G. graminis variety-specific oligonucleotide primers were used in PCRs to amplify DNA from cereal seedlings infected with G. graminis var. tritici or G. graminis var. avenae, and these should be valuable for sensitive detection of pathogenic isolates and for diagnosis of take-all. PMID:7574606

  19. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing.

    PubMed

    Kunde-Ramamoorthy, Govindarajan; Coarfa, Cristian; Laritsky, Eleonora; Kessler, Noah J; Harris, R Alan; Xu, Mingchu; Chen, Rui; Shen, Lanlan; Milosavljevic, Aleksandar; Waterland, Robert A

    2014-04-01

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r(2) ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8-12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. PMID:24391148

  20. Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing

    PubMed Central

    Kunde-Ramamoorthy, Govindarajan; Coarfa, Cristian; Laritsky, Eleonora; Kessler, Noah J.; Harris, R. Alan; Xu, Mingchu; Chen, Rui; Shen, Lanlan; Milosavljevic, Aleksandar; Waterland, Robert A.

    2014-01-01

    Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitative accuracy has been reported. We sequenced bisulfite-converted DNA from two tissues from each of two healthy human adults and systematically compared five widely used Bisulfite-seq mapping algorithms: Bismark, BSMAP, Pash, BatMeth and BS Seeker. We evaluated their computational speed and genomic coverage and verified their percentage methylation estimates. With the exception of BatMeth, all mappers covered >70% of CpG sites genome-wide and yielded highly concordant estimates of percentage methylation (r2 ≥ 0.95). Fourfold variation in mapping time was found between BSMAP (fastest) and Pash (slowest). In each library, 8–12% of genomic regions covered by Bismark and Pash were not covered by BSMAP. An experiment using simulated reads confirmed that Pash has an exceptional ability to uniquely map reads in genomic regions of structural variation. Independent verification by bisulfite pyrosequencing generally confirmed the percentage methylation estimates by the mappers. Of these algorithms, Bismark provides an attractive combination of processing speed, genomic coverage and quantitative accuracy, whereas Pash offers considerably higher genomic coverage. PMID:24391148

  1. 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...

  2. 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. PMID:25745418

  3. 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

  4. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

    PubMed Central

    2012-01-01

    Background Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent’s PGM, Pacific Biosciences’ RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Results Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. Conclusions All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support. PMID:22827831

  5. 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

  6. 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

  7. 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

  8. 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…

  9. 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

  10. Mean-Field Analysis of Recursive Entropic Segmentation of Biological Sequences

    NASA Astrophysics Data System (ADS)

    Cheong, Siew-Ann; Stodghill, Paul; Schneider, David; Myers, Christopher

    2007-03-01

    Horizontal gene transfer in bacteria results in genomic sequences which are mosaic in nature. An important first step in the analysis of a bacterial genome would thus be to model the statistically nonstationary nucleotide or protein sequence with a collection of P stationary Markov chains, and partition the sequence of length N into M statistically stationary segments/domains. This can be done for Markov chains of order K = 0 using a recursive segmentation scheme based on the Jensen-Shannon divergence, where the unknown parameters P and M are estimated from a hypothesis testing/model selection process. In this talk, we describe how the Jensen-Shannon divergence can be generalized to Markov chains of order K > 0, as well as an algorithm optimizing the positions of a fixed number of domain walls. We then describe a mean field analysis of the generalized recursive Jensen-Shannon segmentation scheme, and show how most domain walls appear as local maxima in the divergence spectrum of the sequence, before highlighting the main problem associated with the recursive segmentation scheme, i.e. the strengths of the domain walls selected recursively do not decrease monotonically. This problem is especially severe in repetitive sequences, whose statistical signatures we will also discuss.

  11. 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.

  12. Nucleotide sequence of the phosphoglycerate kinase gene from the extreme thermophile Thermus thermophilus. Comparison of the deduced amino acid sequence with that of the mesophilic yeast phosphoglycerate kinase.

    PubMed Central

    Bowen, D; Littlechild, J A; Fothergill, J E; Watson, H C; Hall, L

    1988-01-01

    Using oligonucleotide probes derived from amino acid sequencing information, the structural gene for phosphoglycerate kinase from the extreme thermophile, Thermus thermophilus, was cloned in Escherichia coli and its complete nucleotide sequence determined. The gene consists of an open reading frame corresponding to a protein of 390 amino acid residues (calculated Mr 41,791) with an extreme bias for G or C (93.1%) in the codon third base position. Comparison of the deduced amino acid sequence with that of the corresponding mesophilic yeast enzyme indicated a number of significant differences. These are discussed in terms of the unusual codon bias and their possible role in enhanced protein thermal stability. Images Fig. 1. PMID:3052437

  13. 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

  14. Protein identities - Graphocephala atropunctata expressed sequenced tags: expanding leafhopper vector biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A small heat shock protein was isolated and sequenced from the Blue-green sharpshooter, BGSS, Graphocephala atropunctata (Signoret) (Hemiptera: Cicadellidae). The BGSS has been the native vector of Pierce’s disease in vineyards in California for nearly a century. The importance of this vector spec...

  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. PMID:24393562

  19. 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…

  20. The Short ITS2 Sequence Serves as an Efficient Taxonomic Sequence Tag in Comparison with the Full-Length ITS

    PubMed Central

    Han, Jianping; Zhu, Yingjie; Chen, Xiaochen; Liao, Baoshen; Yao, Hui; Song, Jingyuan; Chen, Shilin; Meng, Fanyun

    2013-01-01

    An ideal DNA barcoding region should be short enough to be amplified from degraded DNA. In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. The results showed that ITS2 could recover 91% while ITS could recover only 23% efficiency of PCR and sequencing by using one pair of primer. Second, 12861 ITS and ITS2 plant sequences were used to compare the identification efficiency of the two regions. Four identification criteria (BLAST, inter- and intradivergence Wilcoxon signed rank tests, and TaxonDNA) were evaluated. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials. PMID:23484151

  1. 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

  2. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological Examples

    NASA Astrophysics Data System (ADS)

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

    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.

  3. 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

  4. Removal of typical endocrine disrupting chemicals by membrane bioreactor: in comparison with sequencing batch reactor.

    PubMed

    Zhou, Yingjun; Huang, Xia; Zhou, Haidong; Chen, Jianhua; Xue, Wenchao

    2011-01-01

    The removal of endocrine disrupting chemicals (EDCs) by a laboratory-scale membrane bioreactor (MBR) fed with synthetic sewage was evaluated and moreover, compared with that by a sequencing batch reactor (SBR) operated under same conditions in parallel. Eight kinds of typical EDCs, including 17β-estradiol (E2), estrone (E1), estriol (E3), 17α-ethynilestradiol (EE2), 4-octylphenol (4-OP), 4-nonylphenol (4-NP), bisphenol A (BPA) and nonylphenol ethoxylates (NPnEO), were spiked into the feed. Their concentrations in influent, effluent and supernatant were determined by gas chromatography-mass spectrometry method. The overall estrogenecity was evaluated as 17β-estradiol equivalent quantity (EEQ), determined via yeast estrogen screen (YES) assay. E2, E3, BPA and 4-OP were well removed by both MBR and SBR, with removal rates more than 95% and no significant differences between the two reactors. However, with regard to the other four EDCs, of which the removal rates were lower, MBR performed better. Comparison between supernatant and effluent of the two reactors indicated that membrane separation of sludge and effluent, compared with sedimentation, can relatively improve elimination of target EDCs and total estrogenecity. By applying different solids retention times (SRTs) (5, 10, 20 and 40 d) to the MBR, 10 and 5 d were found to be the lower critical SRTs for efficient target EDCs and EEQ removal, respectively. PMID:22105134

  5. 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.

  6. Identification of Simple Sequence Repeat Biomarkers through Cross-Species Comparison in a Tag Cloud Representation

    PubMed Central

    2014-01-01

    Simple sequence repeats (SSRs) are not only applied as genetic markers in evolutionary studies but they also play an important role in gene regulatory activities. Efficient identification of conserved and exclusive SSRs through cross-species comparison is helpful for understanding the evolutionary mechanisms and associations between specific gene groups and SSR motifs. In this paper, we developed an online cross-species comparative system and integrated it with a tag cloud visualization technique for identifying potential SSR biomarkers within fourteen frequently used model species. Ultraconserved or exclusive SSRs among cross-species orthologous genes could be effectively retrieved and displayed through a friendly interface design. Four different types of testing cases were applied to demonstrate and verify the retrieved SSR biomarker candidates. Through statistical analysis and enhanced tag cloud representation on defined functional related genes and cross-species clusters, the proposed system can correctly represent the patterns, loci, colors, and sizes of identified SSRs in accordance with gene functions, pattern qualities, and conserved characteristics among species. PMID:24800246

  7. 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

  8. 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

  9. 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

  10. 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. PMID:27239202

  11. Whole-genome sequencing of Bacillus subtilis XF-1 reveals mechanisms for biological control and multiple beneficial properties in plants.

    PubMed

    Guo, Shengye; Li, Xingyu; He, Pengfei; Ho, Honhing; Wu, Yixin; He, Yueqiu

    2015-06-01

    Bacillus subtilis XF-1 is a gram-positive, plant-associated bacterium that stimulates plant growth and produces secondary metabolites that suppress soil-borne plant pathogens. In particular, it is especially highly efficient at controlling the clubroot disease of cruciferous crops. Its 4,061,186-bp genome contains an estimated 3853 protein-coding sequences and the 1155 genes of XF-1 are present in most genome-sequenced Bacillus strains: 3757 genes in B. subtilis 168, and 1164 in B. amyloliquefaciens FZB42. Analysis using the Cluster of Orthologous Groups database of proteins shows that 60 genes control bacterial mobility, 221 genes are related to cell wall and membrane biosynthesis, and more than 112 are genes associated with secondary metabolites. In addition, the genes contributed to the strain's plant colonization, bio-control and stimulation of plant growth. Sequencing of the genome is a fundamental step for developing a desired strain to serve as an efficient biological control agent and plant growth stimulator. Similar to other members of the taxon, XF-1 has a genome that contains giant gene clusters for the non-ribosomal synthesis of antifungal lipopeptides (surfactin and fengycin), the polyketides (macrolactin and bacillaene), the siderophore bacillibactin, and the dipeptide bacilysin. There are two synthesis pathways for volatile growth-promoting compounds. The expression of biosynthesized antibiotic peptides in XF-1 was revealed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry. PMID:25860123

  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. Complete genome sequence of Saccharothrix espanaensis DSM 44229T and comparison to the other completely sequenced Pseudonocardiaceae

    PubMed Central

    2012-01-01

    Background The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast. Results To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified. Conclusion S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain’s potential for natural product synthesis. PMID:22958348

  14. 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

  15. 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. PMID:26186451

  16. Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing.

    PubMed

    Yamamoto, F; Höglund, B; Fernandez-Vina, M; Tyan, D; Rastrou, M; Williams, T; Moonsamy, P; Goodridge, D; Anderson, M; Erlich, H A; Holcomb, C L

    2015-12-01

    Compared to Sanger sequencing, next-generation sequencing offers advantages for high resolution HLA genotyping including increased throughput, lower cost, and reduced genotype ambiguity. Here we describe an enhancement of the Roche 454 GS GType HLA genotyping assay to provide very high resolution (VHR) typing, by the addition of 8 primer pairs to the original 14, to genotype 11 HLA loci. These additional amplicons help resolve common and well-documented alleles and exclude commonly found null alleles in genotype ambiguity strings. Simplification of workflow to reduce the initial preparation effort using early pooling of amplicons or the Fluidigm Access Array™ is also described. Performance of the VHR assay was evaluated on 28 well characterized cell lines using Conexio Assign MPS software which uses genomic, rather than cDNA, reference sequence. Concordance was 98.4%; 1.6% had no genotype assignment. Of concordant calls, 53% were unambiguous. To further assess the assay, 59 clinical samples were genotyped and results compared to unambiguous allele assignments obtained by prior sequence-based typing supplemented with SSO and/or SSP. Concordance was 98.7% with 58.2% as unambiguous calls; 1.3% could not be assigned. Our results show that the amplicon-based VHR assay is robust and can replace current Sanger methodology. Together with software enhancements, it has the potential to provide even higher resolution HLA typing. PMID:26037172

  17. 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

  18. Complete amino acid sequence of globin chains and biological activity of fragmented crocodile hemoglobin (Crocodylus siamensis).

    PubMed

    Srihongthong, Saowaluck; Pakdeesuwan, Anawat; Daduang, Sakda; Araki, Tomohiro; Dhiravisit, Apisak; Thammasirirak, Sompong

    2012-08-01

    Hemoglobin, α-chain, β-chain and fragmented hemoglobin of Crocodylus siamensis demonstrated both antibacterial and antioxidant activities. Antibacterial and antioxidant properties of the hemoglobin did not depend on the heme structure but could result from the compositions of amino acid residues and structures present in their primary structure. Furthermore, thirteen purified active peptides were obtained by RP-HPLC analyses, corresponding to fragments in the α-globin chain and the β-globin chain which are mostly located at the N-terminal and C-terminal parts. These active peptides operate on the bacterial cell membrane. The globin chains of Crocodylus siamensis showed similar amino acids to the sequences of Crocodylus niloticus. The novel amino acid substitutions of α-chain and β-chain are not associated with the heme binding site or the bicarbonate ion binding site, but could be important through their interactions with membranes of bacteria. PMID:22648692

  19. 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.

  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. Nucleotide and derived amino acid sequences of the major porin of Comamonas acidovorans and comparison of porin primary structures.

    PubMed Central

    Gerbl-Rieger, S; Peters, J; Kellermann, J; Lottspeich, F; Baumeister, W

    1991-01-01

    The DNA sequence of the gene which codes for the major outer membrane porin (Omp32) of Comamonas acidovorans has been determined. The structural gene encodes a precursor consisting of 351 amino acid residues with a signal peptide of 19 amino acid residues. Comparisons with amino acid sequences of outer membrane proteins and porins from several other members of the class Proteobacteria and of the Chlamydia trachomatis porin and the Neurospora crassa mitochondrial porin revealed a motif of eight regions of local homology. The results of this analysis are discussed with regard to common structural features of porins. PMID:1848840

  2. 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

  3. 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...

  4. 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

  5. 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

  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. PMID:25200120

  7. Biological treatment of produced water in a sequencing batch reactor by a consortium of isolated halophilic microorganisms.

    PubMed

    Pendashteh, A R; Fakhru'l-Razi, A; Chuah, T G; Radiah, A B Dayang; Madaeni, S S; Zurina, Z A

    2010-10-01

    Produced water or oilfield wastewater is the largest volume ofa waste stream associated with oil and gas production. The aim of this study was to investigate the biological pretreatment of synthetic and real produced water in a sequencing batch reactor (SBR) to remove hydrocarbon compounds. The SBR was inoculated with isolated tropical halophilic microorganisms capable of degrading crude oil. A total sequence of 24 h (60 min filling phase; 21 h aeration; 60 min settling and 60 min decant phase) was employed and studied. Synthetic produced water was treated with various organic loading rates (OLR) (0.9 kg COD m(-3) d(-1), 1.8 kg COD m(-3) d(-1) and 3.6 kg COD m(-3) d(-1)) and different total dissolved solids (TDS) concentration (35,000 mg L(-1), 100,000 mg L(-1), 150,000 mg L(-1), 200,000 mg L(-1) and 250,000 mg L(-1)). It was found that with an OLR of 0.9 kg COD m(-3) d(-1) and 1.8 kg COD m(-3) d(-1), average oil and grease (O&G) concentrations in the effluent were 7 mg L(-1) and 12 mg L(-1), respectively. At TDS concentration of 35,000 mg L(-1) and at an OLR of 1.8 kg COD m(-3)d(-1), COD and O&G removal efficiencies were more than 90%. However, with increase in salt content to 250,000 mg L(-1), COD and O&G removal efficiencies decreased to 74% and 63%, respectively. The results of biological treatment of real produced water showed that the removal rates of the main pollutants of wastewater, such as COD, TOC and O&G, were above 81%, 83%, and 85%, respectively. PMID:21046953

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

    PubMed

    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

  10. 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

  11. 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

  12. Gene Sequence Homology of Chemokines Across Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The abundance of expressed gene and protein sequences available in the biological information databases facilitates comparison of protein homologies. A high degree of sequence similarity typically implies homology regarding structure and function and may provide clues to antibody cross-reactivities...

  13. GENE SEQUENCE HOMOLOGY OF CHEMOKINES ACROSS SPECIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The abundance of expressed gene and protein sequences available in the biological information databases facilitates comparison of protein homologies. A high degree of sequence similarity typically implies homology regarding structure and function and may provide clues to antibody cross-react...

  14. 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.

  15. 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

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

    PubMed

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

    2013-02-01

    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

  17. 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

  18. 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.

  19. Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques for Clostridium difficile Strain Typing.

    PubMed

    Dominguez, Samuel R; Anderson, Lydia J; Kotter, Cassandra V; Littlehorn, Cynthia A; Arms, Lesley E; Dowell, Elaine; Todd, James K; Frank, Daniel N

    2016-09-01

    We analyzed in parallel 27 pediatric Clostridium difficile isolates by repetitive sequence-based polymerase chain reaction (RepPCR), pulsed-field gel electrophoresis (PFGE), and whole-genome next-generation sequencing. Next-generation sequencing distinguished 3 groups of isolates that were indistinguishable by RepPCR and 1 isolate that clustered in the same PFGE group as other isolates. PMID:26407257

  20. 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. PMID:21738661

  1. 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

  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. Validation of targeted next-generation sequencing for RAS mutation detection in FFPE colorectal cancer tissues: comparison with Sanger sequencing and ARMS-Scorpion real-time PCR

    PubMed Central

    Gao, Jie; Wu, Huanwen; Wang, Li; Zhang, Hui; Duan, Huanli; Lu, Junliang; Liang, Zhiyong

    2016-01-01

    Objective To validate the targeted next-generation sequencing (NGS) platform-Ion Torrent PGM for KRAS exon 2 and expanded RAS mutations detection in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) specimens, with comparison of Sanger sequencing and ARMS-Scorpion real-time PCR. Setting Beijing, China. Participants 51 archived FFPE CRC samples (36 men, 15 women) were retrospectively randomly selected and then checked by an experienced pathologist for sequencing based on histological confirmation of CRC and availability of sufficient tissue. Methods RAS mutations were detected in the 51 FFPE CRC samples by PGM analysis, Sanger sequencing and the Therascreen KRAS assay, respectively. Agreement among the 3 methods was assessed. Assay sensitivity was further determined by sequencing serially diluted DNA from FFPE cell lines with known mutation statuses. Results 13 of 51 (25.5%) cases had a mutation in KRAS exon 2, as determined by PGM analysis. PGM analysis showed 100% (51/51) concordance with Sanger sequencing (κ=1.000, 95% CI 1 to 1) and 98.04% (50/51) agreement with the Therascreen assay (κ=0.947, 95% CI 0.844 to 1) for detecting KRAS exon 2 mutations, respectively. The only discrepant case harboured a KRAS exon 2 mutation (c.37G>T) that was not covered by the Therascreen kit. The dilution series experiment results showed that PGM was able to detect KRAS mutations at a frequency of as low as 1%. Importantly, RAS mutations other than KRAS exon 2 mutations were also detected in 10 samples by PGM. Furthermore, mutations in other CRC-related genes could be simultaneously detected in a single test by PGM. Conclusions The targeted NGS platform is specific and sensitive for KRAS exon 2 mutation detection and is appropriate for use in routine clinical testing. Moreover, it is sample saving and cost-efficient and time-efficient, and has great potential for clinical application to expand testing to include mutations in RAS and other CRC-related genes. PMID

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

    PubMed Central

    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

  5. Comparison of ribosomal RNA removal methods for transcriptome sequencing workflows in teleost fish

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. rRNAs are commonly removed from total RNA via either mRNA selection or rRNA depletion. These methods have...

  6. Genomic sequence and virulence comparison of four type 2 porcine reproductive and respiratory syndrome virus strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a ubiquitous and costly virus that exhibits substantial sequence and virulence disparity among diverse isolates. In this study, we compared the whole genomic sequence and virulence of 4 North American Type 2 PRRSV isolates. Among the 4 i...

  7. 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

  8. 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.

  9. 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

  10. Innovation sequence application to aircraft sensor fault detection: comparison of checking covariance matrix algorithms

    PubMed

    Caliskan; Hajiyev

    2000-01-01

    In this paper, the algorithms verifying the covariance matrix of the Kalman filter innovation sequence are compared with respect to detected minimum fault rate and detection time. Four algorithms are dealt with; the algorithm verifying the trace of the covariance matrix of the innovation sequence, the algorithm verifying the sum of all elements of the inverse covariance matrix of the innovation sequence, the optimal algorithm verifying the ratio of two quadratic forms of which matrices are theoretic and selected covariance matrices of Kalman filter innovation sequence, and the algorithm verifying the generalized variance of the covariance matrix of the innovation sequence. The algorithms are implemented for longitudinal dynamics of an aircraft to detect sensor faults, and some suggestions are given on the use of the algorithms in flight control systems. PMID:10826285

  11. Computational approach towards promoter sequence comparison via TF mapping using a new distance measure.

    PubMed

    Meera, A; Rangarajan, Lalitha; Bhat, Savithri

    2011-03-01

    We propose a method for identifying transcription factor binding sites (TFBS) in the given promoter sequence and mapping the transcription factors (TFs). The proposed algorithm searches the +1 transcription start site (TSS) for eukaryotic and prokaryotic sequences individually. The algorithm was tested with sequences from both eukaryotes and prokaryotes for at least 9 experimentally verified and validated functional TFs in promoter sequences. The order and type of TF binding to the promoter of genes encoding central metabolic pathway (CMP) enzyme was tabulated. A new similarity measure was devised for scoring the similarity between a pair of promoter sequences based on the number and order of motifs. Further, these were grouped in clusters considering the scores between them. The distance between each of the clusters in individual pathway was calculated and a phylogenetic tree was developed. This method is further applied to other pathways such as lipid and amino acid biosynthesis to retrieve and compare experimentally verified and conserved TFBS. PMID:21369887

  12. Comparison of the rotavirus nonstructural protein NSP1 (NS53) from different species by sequence analysis and northern blot hybridization.

    PubMed

    Dunn, S J; Cross, T L; Greenberg, H B

    1994-08-15

    The nucleotide sequence of gene 5 encoding the rotavirus nonstructural protein NSP1 (NS53) of 6 strains (EW, EHP, RRV, I321, OSU, and Gottfried) was determined and compared to 6 previously reported strains (SA11, UK, RF, Hu803, DS-1, and Wa). The 12 rotavirus strains were derived from a total of five separate species (murine, bovine, simian, porcine, and human). Gene sizes ranged from 1564 to 1611 nucleotides in length and the deduced protein sequences were found to be 486 to 495 amino acids in length. Comparisons of NSP1 amino acid sequences showed identities ranging from 36 to 92%. This diversity was most evident between strains from different species. Phylogenetic analysis revealed a clustering of NSP1 sequences according to species origin with the exception that the human and porcine strains were included in a single grouping. Northern blot hybridizations using additional rotavirus strains from the five species confirmed the grouping found by sequence analysis. The species specificity of NSP1 is consistent with the hypothesis that NSP1 plays a role in host range restriction. PMID:8030275

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

    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.

  18. Solving a sequencing problem in the vertebrate mitochondrial control region using phylogenetic comparisons.

    PubMed

    Feinstein, Julie; Cracraft, Joel

    2004-01-01

    The mitochondrial control region (mtCR) of the bird-of-paradise, Phonygammus keraudrenii, the Trumpet Manucode, contains a unique arrangement of homopolymers and short tandem repeats. Homopolymers occur within a few hundred bases of each other, trapping sequence information between unsequenceable barriers. A comparative strategy, involving other manucode species, allowed the prediction of primer sites in the inaccessible region. The method is suggested for similar sequencing problems. PMID:15621664

  19. Pierre Robin Sequence and Treacher Collins Hypoplastic Mandible Comparison Using Three-Dimensional Morphometric Analysis

    PubMed Central

    Chung, Michael T.; Levi, Benjamin; Hyun, Jeong S.; Lo, David D.; Montoro, Daniel T.; Lisiecki, Jeffrey; Bradley, James P.; Buchman, Steven R.; Longaker, Michael T.; Wan, Derrick C.

    2012-01-01

    Pierre Robin sequence and Treacher Collins syndrome are both associated with mandibular hypoplasia. It has been hypothesized, however, that the mandible may be differentially affected. The purpose of this study was to therefore compare mandibular morphology in children with Pierre Robin sequence to children with Treacher Collins syndrome using three-dimensional analysis of computed tomography (CT) scans. A retrospective analysis was performed identifying children with Pierre Robin sequence and Treacher Collins syndrome receiving CT scans. Three-dimensional reconstruction was performed and ramus height, mandibular body length, and gonial angle were measured. These were then compared to control children with normal mandibles and to clinical norms corrected for age and sex based on previously published measurements. Mandibular body length was found to be significantly shorter for children with Pierre Robin sequence while ramus height was significantly shorter for children with Treacher Collins syndrome. This resulted in distinctly different ramus height/mandibular body length ratios. In addition, the gonial angle was more obtuse in both the Pierre Robin sequence and Treacher Collins syndrome groups compared with the controls. Three-dimensional mandibular morphometric analysis in patients with Pierre Robin sequence and Treacher Collins syndrome thus revealed distinctly different patterns of mandibular hypoplasia relative to normal controls. These findings underscore distinct considerations which must be made in surgical planning for reconstruction. PMID:23154353

  20. 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

  1. 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

  2. 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. PMID:25215888

  3. 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

  4. 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

  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. Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study.

    PubMed

    Jesmok, Ellen M; Hopkins, James M; Foran, David R

    2016-05-01

    Soil has the potential to be valuable forensic evidence linking a person or item to a crime scene; however, there is no established soil individualization technique. In this study, the utility of soil bacterial profiling via next-generation sequencing of the 16S rRNA gene was examined for associating soils with their place of origin. Soil samples were collected from ten diverse and nine similar habitats over time, and within three habitats at various horizontal and vertical distances. Bacterial profiles were analyzed using four methods: abundance charts and nonmetric multidimensional scaling provided simplification and visualization of the massive datasets, potentially aiding in expert testimony, while analysis of similarities and k-nearest neighbor offered objective statistical comparisons. The vast majority of soil bacterial profiles (95.4%) were classified to their location of origin, highlighting the potential of bacterial profiling via next-generation sequencing for the forensic analysis of soil samples. PMID:27122396

  7. A direct comparison of MELCOR 1.8.3 and MAAP4 results for several PWR & BWR accident sequences

    SciTech Connect

    Leonard, M.T.; Ashbaugh, S.G.; Cole, R.K.; Bergeron, K.D.; Nagashima, K.

    1996-08-01

    This paper presents a comparison of calculations of severe accident progression for several postulated accident sequences for representative Pressurized Water Reactors (PWR) and Boiling Water Reactors (BWR) nuclear power plants performed with the MELCOR 1.8.3 and the MAAP4 computer codes. The PWR system examined in this study is a 1100 MWe system similar in design to a Westinghouse 3-loop plant with a large dry containment; the BWR is a 1100 MWe system similar in design to General Electric BWR/4 with a Mark I containment. A total of nine accident sequences were studied with both codes. Results of these calculations are compared to identify major differences in the timing of key events in the calculated accident progression or other important aspects of severe accident behavior, and to identify specific sources of the observed differences.

  8. 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

  9. Quantitative phase-flow MR imaging in dogs by using standard sequences: comparison with in vivo flow-meter measurements.

    PubMed

    Pettigrew, R I; Dannels, W; Galloway, J R; Pearson, T; Millikan, W; Henderson, J M; Peterson, J; Bernardino, M E

    1987-02-01

    For evaluation of the feasibility and clinical potential of using the phase data from standard MR imaging sequences to measure blood flow, 11 vessels with diameters of 4 to 7 mm were imaged in seven dogs. The flow in either the superior mesenteric vein or the inferior vena cava was measured first at laparotomy (in ml/min) with electromagnetic flow meters. Immediately thereafter, these vessels were imaged by MR in 25-mm thick sections by using a standard spin echo (SE) 750/30 sequence with a Philips 0.5-T imager. Previous phase-flow calibration of the imager and sequence allowed calculation of the blood flow rates from the phase images that were used to measure the vessels' cross-sectional areas and blood phase values. Comparison of the measurements obtained with each technique showed a significant correlation (r = .977, p less than .05) between MR-imaging values and flow-meter measurements when the blood velocity was less than approximately 40 cm/sec, the known upper limit of the flow dynamic range for the MR hardware and sequence used. There was no correlation for blood velocities greater than 40 cm/sec. However, the range of blood flow velocities in dogs and man extends to more than 100 cm/sec. Thus, these results suggest that this technique might yield valuable adjunctive flow data in routine clinical imaging provided that improvements in hardware and software permit a larger dynamic range. PMID:2948376

  10. Comparison of Custom Capture for Targeted Next-Generation DNA Sequencing

    PubMed Central

    Samorodnitsky, Eric; Datta, Jharna; Jewell, Benjamin M.; Hagopian, Raffi; Miya, Jharna; Wing, Michele R.; Damodaran, Senthilkumar; Lippus, Juliana M.; Reeser, Julie W.; Bhatt, Darshna; Timmers, Cynthia D.; Roychowdhury, Sameek

    2016-01-01

    Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We evaluated four commercially available custom-targeted DNA technologies for next-generation sequencing with respect to on-target sequencing, uniformity, and ability to detect single-nucleotide variations (SNVs) and copy number variations. The technologies that used sonication for DNA fragmentation displayed impressive uniformity of capture, whereas the others had shorter preparation times, but sacrificed uniformity. One of those technologies, which uses transposase for DNA fragmentation, has a drawback requiring sample pooling, and the last one, which uses restriction enzymes, has a limitation depending on restriction enzyme digest sites. Although all technologies displayed some level of concordance for calling SNVs, the technologies that require restriction enzymes or transposase missed several SNVs largely because of the lack of coverage. All technologies performed well for copy number variation calling when compared to single-nucleotide polymorphism arrays. These results enable laboratories to compare these methods to make informed decisions for their intended applications. PMID:25528188

  11. Comparison of custom capture for targeted next-generation DNA sequencing.

    PubMed

    Samorodnitsky, Eric; Datta, Jharna; Jewell, Benjamin M; Hagopian, Raffi; Miya, Jharna; Wing, Michele R; Damodaran, Senthilkumar; Lippus, Juliana M; Reeser, Julie W; Bhatt, Darshna; Timmers, Cynthia D; Roychowdhury, Sameek

    2015-01-01

    Targeted, capture-based DNA sequencing is a cost-effective method to focus sequencing on a coding region or other customized region of the genome. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. We evaluated four commercially available custom-targeted DNA technologies for next-generation sequencing with respect to on-target sequencing, uniformity, and ability to detect single-nucleotide variations (SNVs) and copy number variations. The technologies that used sonication for DNA fragmentation displayed impressive uniformity of capture, whereas the others had shorter preparation times, but sacrificed uniformity. One of those technologies, which uses transposase for DNA fragmentation, has a drawback requiring sample pooling, and the last one, which uses restriction enzymes, has a limitation depending on restriction enzyme digest sites. Although all technologies displayed some level of concordance for calling SNVs, the technologies that require restriction enzymes or transposase missed several SNVs largely because of the lack of coverage. All technologies performed well for copy number variation calling when compared to single-nucleotide polymorphism arrays. These results enable laboratories to compare these methods to make informed decisions for their intended applications. PMID:25528188

  12. 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. PMID:26432002

  13. 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

  14. A Phylogenetic Analysis of the Brassicales Clade Based on an Alignment-Free Sequence Comparison Method

    PubMed Central

    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. PMID:22952468

  15. Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.

    PubMed

    Teer, Jamie K; Bonnycastle, Lori L; Chines, Peter S; Hansen, Nancy F; Aoyama, Natsuyo; Swift, Amy J; Abaan, Hatice Ozel; Albert, Thomas J; Margulies, Elliott H; Green, Eric D; Collins, Francis S; Mullikin, James C; Biesecker, Leslie G

    2010-10-01

    Massively parallel DNA sequencing technologies have greatly increased our ability to generate large amounts of sequencing data at a rapid pace. Several methods have been developed to enrich for genomic regions of interest for targeted sequencing. We have compared three of these methods: Molecular Inversion Probes (MIP), Solution Hybrid Selection (SHS), and Microarray-based Genomic Selection (MGS). Using HapMap DNA samples, we compared each of these methods with respect to their ability to capture an identical set of exons and evolutionarily conserved regions associated with 528 genes (2.61 Mb). For sequence analysis, we developed and used a novel Bayesian genotype-assigning algorithm, Most Probable Genotype (MPG). All three capture methods were effective, but sensitivities (percentage of targeted bases associated with high-quality genotypes) varied for an equivalent amount of pass-filtered sequence: for example, 70% (MIP), 84% (SHS), and 91% (MGS) for 400 Mb. In contrast, all methods yielded similar accuracies of >99.84% when compared to Infinium 1M SNP BeadChip-derived genotypes and >99.998% when compared to 30-fold coverage whole-genome shotgun sequencing data. We also observed a low false-positive rate with all three methods; of the heterozygous positions identified by each of the capture methods, >99.57% agreed with 1M SNP BeadChip, and >98.840% agreed with the whole-genome shotgun data. In addition, we successfully piloted the genomic enrichment of a set of 12 pooled samples via the MGS method using molecular bar codes. We find that these three genomic enrichment methods are highly accurate and practical, with sensitivities comparable to that of 30-fold coverage whole-genome shotgun data. PMID:20810667

  16. Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

    PubMed Central

    Shi, Jiaqin; Huang, Shunmou; Fu, Donghui; Yu, Jinyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

    2013-01-01

    Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with

  17. Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Shiga toxin-producing Escherichia coli (STEC) O104 strains have been associated with sporadic cases of illness and have caused outbreaks associated with milk and sprouts. E. coli O104:H21 caused an outbreak associated with milk in the U.S. in 1994. In this study, next generation sequencing techno...

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. Comparison of Computer Vision and Photogrammetric Approaches for Epipolar Resampling of Image Sequence.

    PubMed

    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

  4. 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: ...

  5. Comparison of Synthetic and Biologic Mesh in Ventral Hernia Repair Using Components Separation Technique.

    PubMed

    Sandvall, Brinkley K; Suver, Daniel W; Said, Hakim K; Mathes, David W; Neligan, Peter C; Dellinger, E Patchen; Louie, Otway

    2016-06-01

    Ventral hernia repair (VHR) for large abdominal wall defects is challenging. Prior research established that the use of mesh is superior to suture closure alone and that component separation is an effective technique to combat loss of abdominal domain. Studies comparing component separation technique (CST) outcomes utilizing synthetic versus biologic mesh are limited. A retrospective review was conducted of 72 consecutive patients who underwent VHR with CST between 2006 and 2010 at our institution. Surgeon preference and the presence of contamination guided whether synthetic mesh (27 patients) or biologic mesh (45 patients) was used. Mean follow-up interval for all comers was 13.9 months and similar in both groups (P > 0.05). Degree of contamination and severity of premorbid medical conditions were significantly higher in the biologic mesh group, as reflected in the higher Ventral Hernia Working Group (VHWG) score (2.04 versus 2.86). Clinical outcomes, as measured by both minor and major complication rates and recurrence rates, were not significantly different. Minor complication rates were 26% in the synthetic group and 37% in the biologic group and major complication rates 15% in the synthetic group and 22% in the biologic group. There was 1 recurrence (4%) in the synthetic mesh group versus 5 (11%) in the biologic mesh group. Multivariable analysis for major complications revealed no significant difference for either synthetic or biologic mesh while controlling for other variables. Subset analysis of uncontaminated cases revealed recurrence rates of 4% in the synthetic mesh group and 6% in the biologic mesh group. VHR using CST and either synthetic mesh or biologic mesh resulted in low recurrence rates with similar overall complication profiles, despite the higher average VHWG grading score in the biologic mesh group. Our results support the VHWG recommendation for biologic mesh utilization in higher VHWG grade patients. In VHWG grade 2 patients, our clinical

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. Sequence comparisons of the variable VP2 region of eight infectious bursal disease virus isolates.

    PubMed

    Dormitorio, T V; Giambrone, J J; Duck, L W

    1997-01-01

    The VP2 gene is part of the genomic segment A of infectious bursal disease virus (IBDV). It has been identified as the major host-protective antigen of IBDV and is known to contain conformationally dependent protective epitopes. A 643-base pair segment covering the hypervariable region of this gene from three recent serologic variant IBDV isolates from the southeastern United States, two variants from the Delmarva Peninsula, and three serologic standard viruses were amplified and sequenced using the reverse transcription polymerase chain reaction and cycle sequencing techniques. This was done to determine the molecular similarity among isolates that differ antigenically and pathologically. Sequence analysis suggested that the Arkansas (Ark) and Mississippi (Miss) isolates evolved closely and separately from the Delmarva variants (GLS and DELE), in contrast to the other southeastern variant Georgia (Ga), which is more closely related (98.32%) to Delaware E (DELE). All variants, except for Miss, underwent a shift in amino acid number 222 from proline to threonine. The sequence of Univax BD virus, a commercially available intermediate vaccine, was markedly different, evolving from a separate lineage than the others. Restriction enzyme sites could differentiate most isolates. Except for Miss, variants do not have EcoRII site at the larger hydrophilic domain. All variants lost their HaeIII, StuI, and StyI cutting sites with a change in base number 856. The TaqI site is in DELE, whereas the SpeI site is absent in the standard vaccine viruses. The SWASASGS heptapeptide is conserved in all virulent viruses, including APHIS, but not in the attenuated (Univax BD and Bursa Vac 3) and published (D78 and PBG98) vaccines. PMID:9087318

  14. Proteus mirabilis urease: nucleotide sequence determination and comparison with jack bean urease.

    PubMed

    Jones, B D; Mobley, H L

    1989-12-01

    Proteus mirabilis, a common cause of urinary tract infection, produces a potent urease that hydrolyzes urea to NH3 and CO2, initiating kidney stone formation. Urease genes, which were localized to a 7.6-kilobase-pair region of DNA, were sequenced by using the dideoxy method. Six open reading frames were found within a region of 4,952 base pairs which were predicted to encode polypeptides of 31.0 (ureD), 11.0 (ureA), 12.2 (ureB), 61.0 (ureC), 17.9 (ureE), and 23.0 (ureF) kilodaltons (kDa). Each open reading frame was preceded by a ribosome-binding site, with the exception of ureE. Putative promoterlike sequences were identified upstream of ureD, ureA, and ureF. Possible termination sites were found downstream of ureD, ureC, and ureF. Structural subunits of the enzyme were encoded by ureA, ureB, and ureC and were translated from a single transcript in the order of 11.0, 12.2, and 61.0 kDa. When the deduced amino acid sequences of the P. mirabilis urease subunits were compared with the amino acid sequence of the jack bean urease, significant amino acid similarity was observed (58% exact matches; 73% exact plus conservative replacements). The 11.0-kDa polypeptide aligned with the N-terminal residues of the plant enzyme, the 12.2-kDa polypeptide lined up with internal residues, and the 61.0-kDa polypeptide matched with the C-terminal residues, suggesting an evolutionary relationship of the urease genes of jack bean and P. mirabilis. PMID:2687233

  15. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.

    PubMed

    DeKosky, Brandon J; Lungu, Oana I; Park, Daechan; Johnson, Erik L; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D; Ippolito, Gregory C; Gray, Jeffrey J; Georgiou, George

    2016-05-10

    Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19(+)CD20(+)CD27(-) IgM-naive B cells, >120,000 antibody clusters from CD19(+)CD20(+)CD27(+) antigen-experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ-Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease. PMID:27114511

  16. WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme

    PubMed Central

    Straver, Roy; Sistermans, Erik A.; Holstege, Henne; Visser, Allerdien; Oudejans, Cees B. M.; Reinders, Marcel J. T.

    2014-01-01

    Genetic disorders can be detected by prenatal diagnosis using Chorionic Villus Sampling, but the 1:100 chance to result in miscarriage restricts the use to fetuses that are suspected to have an aberration. Detection of trisomy 21 cases noninvasively is now possible owing to the upswing of next-generation sequencing (NGS) because a small percentage of fetal DNA is present in maternal plasma. However, detecting other trisomies and smaller aberrations can only be realized using high-coverage NGS, making it too expensive for routine practice. We present a method, WISECONDOR (WIthin-SamplE COpy Number aberration DetectOR), which detects small aberrations using low-coverage NGS. The increased detection resolution was achieved by comparing read counts within the tested sample of each genomic region with regions on other chromosomes that behave similarly in control samples. This within-sample comparison avoids the need to re-sequence control samples. WISECONDOR correctly identified all T13, T18 and T21 cases while coverages were as low as 0.15–1.66. No false positives were identified. Moreover, WISECONDOR also identified smaller aberrations, down to 20 Mb, such as del(13)(q12.3q14.3), +i(12)(p10) and i(18)(q10). This shows that prevalent fetal copy number aberrations can be detected accurately and affordably by shallow sequencing maternal plasma. WISECONDOR is available at bioinformatics.tudelft.nl/wisecondor. PMID:24170809

  17. Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener

    PubMed Central

    Franzén, Oscar; Ochaya, Stephen; Sherwood, Ellen; Lewis, Michael D.; Llewellyn, Martin S.; Miles, Michael A.; Andersson, Björn

    2011-01-01

    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. PMID:21408126

  18. A comparison of teacher and principal perception of an outstanding biology teacher

    NASA Astrophysics Data System (ADS)

    Searles, William E.; Ng, Raymond W. M.

    The purpose of this study was to ascertain the level of agreement or disagreement between principals and teachers when using established criteria to measure the effectiveness of a biology teacher. To obtain information regarding their perceptions of an outstanding biology teacher, twenty-two principals and forty-one biology teachers were chosen randomly from English-speaking high schools within a 50 km radius of metropolitan Montreal, Quebec, Canada. The measuring instrument was a modified version of Dieter's questionnaire that evolved from his doctoral study of the National Association of Biology Teachers-Outstanding Biology Teacher Award Program. The data collected from the two populations were tested using one-way ANOVA (analysis of variance) or by applying normal approximation. Results indicated that both the principals and teachers agree on the relative importance of most criteria, particularly those related to the teacher's classroom behavior and academic background in biology. From such results, it was possible to construct one stereotype of the outstanding biology teacher. A number of recommendations were made from the results of the study, which were directed to the (a) teachers and their professional organization, (b) principals and the school boards, (c) teacher training institutions, and (d) researchers in teacher evaluation.

  19. 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

  20. Comparison and analysis of biological agent category lists based on biosafety and biodefense.

    PubMed

    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

  1. 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...

  2. 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.

  3. Using complete genome comparisons to identify sequences whose presence accurately predicts clinically important phenotypes.

    PubMed

    Hall, Barry G; Cardenas, Heliodoro; Barlow, Miriam

    2013-01-01

    In clinical settings it is often important to know not just the identity of a microorganism, but also the danger posed by that particular strain. For instance, Escherichia coli can range from being a harmless commensal to being a very dangerous enterohemorrhagic (EHEC) strain. Determining pathogenic phenotypes can be both time consuming and expensive. Here we propose a simple, rapid, and inexpensive method of predicting pathogenic phenotypes on the basis of the presence or absence of short homologous DNA segments in an isolate. Our method compares completely sequenced genomes without the necessity of genome alignments in order to identify the presence or absence of the segments to produce an automatic alignment of the binary string that describes each genome. Analysis of the segment alignment allows identification of those segments whose presence strongly predicts a phenotype. Clinical application of the method requires nothing more that PCR amplification of each of the set of predictive segments. Here we apply the method to identifying EHEC strains of E. coli and to distinguishing E. coli from Shigella. We show in silico that with as few as 8 predictive sequences, if even three of those predictive sequences are amplified the probability of being EHEC or Shigella is >0.99. The method is thus very robust to the occasional amplification failure for spurious reasons. Experimentally, we apply the method to screening a set of 98 isolates to distinguishing E. coli from Shigella, and EHEC from non-EHEC E. coli strains and show that all isolates are correctly identified. PMID:23935901

  4. 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

  5. Demonstration of biological activity and nucleotide sequence of an in vitro synthesized clone of the Moloney murine sarcoma virus mos gene.

    PubMed Central

    Donoghue, D J

    1982-01-01

    A clone of the Moloney murine sarcoma virus mos gene derived by in vitro reverse transcription was characterized. When assayed for focus formation by DNA transfection on NIH/3T3 cells, this clone was biologically inactive, presumably due to the absence of a long terminal repeat sequence. Therefore, a long terminal repeat was inserted into the clone by in vitro recombination, after which the most gene was able to transform NIH/3T3 cells efficiently. The nucleotide sequence encompassing the transforming region of this clone was determined. A single long open reading frame was observed, which potentially encodes a polypeptide of 41,000 daltons. This open reading frame initiates with the first five amino acids of the murine leukemia virus env gene, after which it enters the mos sequence, where it terminates. The nucleotide sequence described in this paper was compared with other sequences of mos in an effort to resolve discrepancies in the position of the long open reading frame. Although Moloney murine sarcoma virus retains the 3' splicing site of the murine leukemia virus env gene, a mos-specific mRNA which corresponds structurally to the murine leukemia virus env mRNA was not identified. The sequence described here revealed a single nucleotide change in the proposed env gene 3' splicing site which was retained in Moloney murine sarcoma virus. This deviation from the consensus 3' splicing sequence may underlie the observed absence of mos expression via the env gene splicing pathway. Images PMID:7045395

  6. 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

  7. 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

  8. 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

  9. 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.

  10. An economic comparison of biological and conventional control strategies for whiteflies (Homoptera: Aleyrodidae) in greenhouse poinsettias.

    PubMed

    Stevens, T J; Kilmer, R L; Glenn, S J

    2000-06-01

    The objective of this study was to evaluate the costs of biologically controlling infestations of silverleaf whitefly, Bemisia argentifolii Bellows & Perring, in New England greenhouse operations on poinsettia, Euphorbia pulcherrima Wild, ex Koltz, using the parasitic wasp Encarsia formosa Gahan (Nile Delta strain). Partial budget analysis was used to compare costs for conventional verses biological control regimens. Four alternative whitefly control budgets are developed; two conventional chemical-based control budgets formulated with and without the use of imidacloprid, and two biological control budgets which demonstrate the impact of possibly greater pest monitoring efforts necessary to implement this type strategy successfully. The analysis shows that biological whitefly control costs were > 300% greater than conventional chemical-based control strategy costs. Most of this increase is caused by the higher costs of Encarsia formosa as the material control input. If monitoring costs are held constant across different strategies, labor costs actually decline for biological control. This is because of a significant reduction in the number of control applications made and the relatively lower cost of applying E. formosa. If more extensive monitoring efforts are required to implement biological control successfully, labor costs increase by 56% over the conventional pre-imidacloprid regimen. Based on these results, the authors conclude that cheaper and more reliable means of producing E. formosa must be developed before this strategy will become economically viable for commercial poinsettia greenhouse production. PMID:10902307

  11. Comparison of Multi-Sample Variant Calling Methods for Whole Genome Sequencing

    PubMed Central

    Nho, Kwangsik; West, John D.; Li, Huian; Henschel, Robert; Bharthur, Apoorva; Tavares, Michel C.; Saykin, Andrew J.

    2015-01-01

    Rapid advancement of next-generation sequencing (NGS) technologies has facilitated the search for genetic susceptibility factors that influence disease risk in the field of human genetics. In particular whole genome sequencing (WGS) has been used to obtain the most comprehensive genetic variation of an individual and perform detailed evaluation of all genetic variation. To this end, sophisticated methods to accurately call high-quality variants and genotypes simultaneously on a cohort of individuals from raw sequence data are required. On chromosome 22 of 818 WGS data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), which is the largest WGS related to a single disease, we compared two multi-sample variant calling methods for the detection of single nucleotide variants (SNVs) and short insertions and deletions (indels) in WGS: (1) reduce the analysis-ready reads (BAM) file to a manageable size by keeping only essential information for variant calling (“REDUCE”) and (2) call variants individually on each sample and then perform a joint genotyping analysis of the variant files produced for all samples in a cohort (“JOINT”). JOINT identified 515,210 SNVs and 60,042 indels, while REDUCE identified 358,303 SNVs and 52,855 indels. JOINT identified many more SNVs and indels compared to REDUCE. Both methods had concordance rate of 99.60% for SNVs and 99.06% for indels. For SNVs, evaluation with HumanOmni 2.5M genotyping arrays revealed a concordance rate of 99.68% for JOINT and 99.50% for REDUCE. REDUCE needed more computational time and memory compared to JOINT. Our findings indicate that the multi-sample variant calling method using the JOINT process is a promising strategy for the variant detection, which should facilitate our understanding of the underlying pathogenesis of human diseases. PMID:26167514

  12. 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

  13. NOTE: Comparison of biologically damaging spectral solar ultraviolet radiation at a southern hemisphere sub-tropical site

    NASA Astrophysics Data System (ADS)

    Parisi, A. V.; Sabburg, J.; Kimlin, M. G.

    2003-04-01

    The first dataset of a complete year of biologically damaging spectral UV at a sub-tropical latitude in the southern hemisphere has been presented. The new data provides a baseline dataset against which comparisons can be made in the future to establish if there have been any long term trends in the biologically damaging UV. The general shape of the variation of the daily biologically damaging exposures through the year depends on the relative response of the various action spectra at the different wavelengths. The ratio of the daily erythemal to actinic exposures drops by approximately 20 to 25% from winter to summer. The ratio of the erythemal to DNA exposures drops by approximately 50% over the same period. In contrast, the ratio of the erythemal to plant damage exposures is higher in summer compared to winter. This is due to the changes in the relative proportion of UVA to UVB wavebands and relative responses of the different action spectra. The relative changes for the different action spectra show that the erythemal action spectrum cannot be used as a proxy for other biologically damaging responses.

  14. Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences.

    PubMed

    Sercundes, Michelle Klein; Valadas, Samantha Yuri Oshiro Branco; Keid, Lara Borges; Oliveira, Tricia Maria Ferreira Souza; Ferreira, Helena Lage; Vitor, Ricardo Wagner de Almeida; Gregori, Fábio; Soares, Rodrigo Martins

    2016-01-01

    Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genus Hammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well. PMID:27007245

  15. Comparison of DNA extraction methodologies used for assessing fungal diversity via ITS sequencing

    PubMed Central

    Rittenour, William R.; Park, Ju-Hyeong; Cox-Ganser, Jean M.; Beezhold, Donald H.; Green, Brett J.

    2015-01-01

    Traditional methods of assessing fungal exposure have been confounded by a number of limiting variables. The recent utilization of molecular methods such as internal transcribed spacer (ITS) sequencing of ribosomal RNA genes has provided improved insight into the diversity of fungal bioaerosols in indoor, outdoor and occupational environments. However, ITS analyses may also be confounded by a number of methodological limitations. In this study, we have optimized this technology for use in occupational or environmental studies. Three commonly used DNA extraction methodologies (UltraClean Soil kit, High Pure PCR Template kit, and EluQuik/DNeasy kit) were compared in terms of sensitivity and susceptibility to PCR inhibitors in dust for three common fungal bioaerosols, Aspergillus versicolor, Rhizopus microsporus and Wallemia sebi. Environmental dust samples were then studied using each extraction methodology and results were compared to viable culture data. The extraction methods differed in terms of their ability to efficiently extract DNA from particular species of fungi (e.g. Aspergillus versicolor). In addition, the ability to remove PCR inhibitors from dust samples was most effective using the soil DNA extraction kit. The species composition varied greatly between ITS clone libraries generated with the different DNA extraction kits. However, compared to viable culture data, ITS clone libraries included additional fungal species that are incapable of growth on solid culture medium. Collectively, our data indicated that DNA extraction methodologies used in ITS sequencing studies of occupational or environmental dust samples can greatly influence the fungal species that are detected. PMID:22230933

  16. Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

    PubMed

    Meganathan, P R; Dubey, Bhawna; Batzer, Mark A; Ray, David A; Haque, Ikramul

    2011-06-01

    Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution. PMID:21310220

  17. 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

  18. Whole-genome sequence comparisons reveal the evolution of Vibrio cholerae O1.

    PubMed

    Kim, Eun Jin; Lee, Chan Hee; Nair, G Balakrish; Kim, Dong Wook

    2015-08-01

    The analysis of the whole-genome sequences of Vibrio cholerae strains from previous and current cholera pandemics has demonstrated that genomic changes and alterations in phage CTX (particularly in the gene encoding the B subunit of cholera toxin) were major features in the evolution of V. cholerae. Recent studies have revealed the genetic mechanisms in these bacteria by which new variants of V. cholerae are generated from type-specific strains; these mechanisms suggest that certain strains are selected by environmental or human factors over time. By understanding the mechanisms and driving forces of historical and current changes in the V. cholerae population, it would be possible to predict the direction of such changes and the evolution of new variants; this has implications for the battle against cholera. PMID:25913612

  19. Sequencing instructional tasks. A comparison of contingent and noncontingent interspersal of preferred academic tasks.

    PubMed

    Noell, George H; Whitmarsh, Ernest L; VanDerHeyden, Amanda M; Gatti, Susan L; Slider, Natalie J

    2003-04-01

    This study compared two strategies for increasing accurate responding on a low-preference academic task by interspersing presentations of a preferred academic task. Five children attending a preschool program for children with delayed language development participated in this study. Preferred and nonpreferred tasks were identified through a multiple-stimulus, free-operant preference assessment. Contingent access to a preferred academic task was associated with improved response accuracy when compared to noncontingent access to that activity for 3 students. For 1 student, noncontingent access to the preferred activity led to improved response accuracy, and 1 student's analysis suggested the importance of procedural variety. The implications of these findings for use of preference assessments to devise instructional sequences that improve student responding are discussed. PMID:12705105

  20. 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

  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. PMID:25151602

  2. Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum.

    PubMed

    Smith, Kirsty F; Abbott, Cathryn L; Saito, Yasunori; Fidler, Andrew E

    2015-02-01

    The mitochondria are the main source of cellular energy production and have an important role in development, fertility, and thermal limitations. Adaptive mitochondrial DNA mutations have the potential to be of great importance in determining aspects of the life history of an organism. Phylogenetic analyses of the globally invasive marine ascidian Didemnum vexillum using the mitochondrial cytochrome c oxidase 1 (COX1) coding region, revealed two distinct clades. Representatives of one clade (denoted by 'B') are geographically restricted to D. vexillum's native region (north-west Pacific Ocean, including Japan), whereas members of the other clade (denoted by 'A') have been introduced and become invasive in temperate coastal areas around the world. Persistence of clade B's restricted distribution may reflect it being inherently less invasive than clade A. To investigate this we sought to determine if the two clades differ significantly in other mitochondrial genes of functional significance, specifically, alterations in amino acids encoded in mitochondrial enzyme subunits. Differences in functional mitochondrial genes could indicate an increased ability for clade A colonies to tolerate a wider range of environmental temperature. Full mitochondrial genomic sequences from D. vexillum clades A and B were obtained and they predict significant sequence differences in genes encoding for enzymes involved in oxidative phosphorylation. Diversity levels were relatively high and showed divergence across almost all genes, with p-distance values between the two clades indicating recent divergence. Both clades showed an excess of rare variants, which is consistent with balancing selection or a recent population expansion. Results presented here will inform future research focusing on examining the functional properties of the corresponding mitochondrial respiration enzymes, of A and B clade enzymes. By comparing closely related taxa that have differing distributions it is possible

  3. Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity▿

    PubMed Central

    White, A. P.; Sibley, K. A.; Sibley, C. D.; Wasmuth, J. D.; Schaefer, R.; Surette, M. G.; Edge, T. A.; Neumann, N. F.

    2011-01-01

    Establishing the risk of human infection is one of the goals of public health. For bacterial pathogens, the virulence and zoonotic potential can often be related to their host source. Escherichia coli bacteria are common contaminants of water associated with human recreation and consumption, and many strains are pathogenic. In this study, we analyzed three promoter-containing intergenic regions from 284 diverse E. coli isolates in an attempt to identify molecular signatures associated with specific host types. Promoter sequences controlling production of curli fimbriae, flagella, and nutrient import yielded a phylogenetic tree with isolates clustered by established phylogenetic grouping (A, B1, B2, and D) but not by host source. Virulence genes were more prevalent in groups B2 and D isolates and in human isolates. Group B1 isolates, primarily from nonhuman sources, were the most genetically similar, indicating that they lacked molecular adaptations to specific host environments and were likely host generalists. Conversely, B2 isolates, primarily from human sources, displayed greater genetic distances and were more likely to be host adapted. In agreement with these hypotheses, prevalence of σS activity and the rdar morphotype, phenotypes associated with environmental survival, were significantly higher in B1 isolates than in B2 isolates. Based on our findings, we speculate that E. coli host specificity is not defined by genome-wide sequence changes but, rather, by the presence or absence of specific genes and associated promoter elements. Furthermore, the requirements for colonization of the human gastrointestinal tract may lead to E. coli lifestyle changes along with selection for increased virulence. PMID:21908635

  4. DNA sequence and comparison of virulence plasmids from Rhodococcus equi ATCC 33701 and 103.

    PubMed

    Takai, S; Hines, S A; Sekizaki, T; Nicholson, V M; Alperin, D A; Osaki, M; Takamatsu, D; Nakamura, M; Suzuki, K; Ogino, N; Kakuda, T; Dan, H; Prescott, J F

    2000-12-01

    The virulence plasmids of the equine virulent strains Rhodococcus equi ATCC 33701 and 103 were sequenced, and their genetic structure was analyzed. p33701 was 80,610 bp in length, and p103 was 1 bp shorter; their sequences were virtually identical. The plasmids contained 64 open reading frames (ORFs), 22 of which were homologous with genes of known function and 3 of which were homologous with putative genes of unknown function in other species. Putative functions were assigned to five ORFs based on protein family characteristics. The most striking feature of the virulence plasmids was the presence of a 27,536-bp pathogenicity island containing seven virulence-associated protein (vap) genes, including vapA. These vap genes have extensive homology to vapA, which encodes a thermoregulated and surface-expressed protein. The pathogenicity island contained a LysR family transcriptional regulator and a two-component response regulator upstream of six of the vap genes. The vap genes were present as a cluster of three (vapA, vapC, and vapD), as a pair (vapE and vapF), or individually (vapG; vapH). A region of extensive direct repeats of unknown function, possibly associated with thermoregulation, was present immediately upstream of the clustered and the paired genes but not the individual vap genes. There was extensive homology among the C-terminal halves of all vap genes but not generally among the N-terminal halves. The remainder of the plasmid consisted of a large region which appears to be associated with conjugation functions and a large region which appears to be associated with replication and partitioning functions. PMID:11083803

  5. 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

  6. 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). PMID:22115566

  7. 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

  8. 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

  9. 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…

  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. 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

  12. 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...

  13. A COMPARISON OF TWO RAPID BIOLOGICAL ASSESSMENT SAMPLING METHODS FOR MACROINVERTEBRATES

    EPA Science Inventory

    In 2003, the Office of Research and Developments (ORD's) National Exposure Research Laboratory initiated a collaborative research effort with U.S. EPA Region 3 to conduct a study comparing two rapid biological assessment methods for collecting stream macroinvertebrates. One metho...

  14. 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…

  15. Case study: Comparison of biological active compounds in milk from organic and conventional dairy herds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Conflicting reports of the quantities of biologically active compounds present in milk from organic grass-fed and conventional herds show that more research is required, especially as these compounds are linked to human health benefits and can improve the health value consumers place on dairy produc...

  16. Comparison of ground and aerial application, fungicide deposition and biological activity in large pecan tree canopies.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The study was conducted to determine vertical spray deposition in pecan canopies of large trees and to estimate the biological activity of the deposited fungicides. Tracer elements were used at molar concentrations equivalent to the molar amount of active ingredient found in the recommended rates o...

  17. 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…

  18. 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…

  19. 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.

  20. 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.

  1. Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences.

    PubMed

    Laakmann, S; Gerdts, G; Erler, R; Knebelsberger, T; Martínez Arbizu, P; Raupach, M J

    2013-09-01

    Calanoid copepods play an important role in the pelagic ecosystem making them subject to various taxonomic and ecological studies, as well as indicators for detecting changes in the marine habitat. For all these investigations, valid identification, mainly of sibling and cryptic species as well as early life history stages, represents a central issue. In this study, we compare species identification methods for pelagic calanoid copepod species from the North Sea and adjacent regions in a total of 333 specimens. Morphologically identified specimens were analysed on the basis of nucleotide sequences (i.e. partial mitochondrial cytochrome c oxidase subunit I (COI) and complete 18S rDNA) and on proteome fingerprints using the technology of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). On all three molecular approaches, all specimens were classified to species level indicated by low intraspecific and high interspecific variability. Sequence divergences in both markers revealed a second Pseudocalanus species for the southern North Sea identified as Pseudocalanus moultoni by COI sequence comparisons to GenBank. Proteome fingerprints were valid for species clusters irrespective of high intraspecific variability, including significant differences between early developmental stages and adults. There was no effect of sampling region or time; thus, trophic effect, when analysing the whole organisms, was observed in species-specific protein mass spectra, underlining the power of this tool in the application on metazoan species identification. Because of less sample preparation steps, we recommend proteomic fingerprinting using the MALDI-TOF MS as an alternative or supplementary approach for rapid, cost-effective species identification. PMID:23848968

  2. 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

  3. 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".

  4. 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

  5. Comparison of Bond Scission Sequence of Methanol on Tungsten Monocarbide and Pt-Modified Tungsten Monocarbide

    SciTech Connect

    Liu, P.; Stottlemyer, A.L.; Chen, J.G.

    2010-09-14

    The ability to control the bond scission sequence of O-H, C-H, and C-O bonds is of critical importance in the effective utilization of oxygenate molecules, such as in reforming reactions and in alcohol fuel cells. In the current study, we use methanol as a probe molecule to demonstrate the possibility to control the decomposition pathways by supporting monolayer coverage of Pt on a tungsten monocarbide (WC) surface. Density functional theory (DFT) results reveal that on the WC and Pt/WC surfaces CH{sub 3}OH decomposes via O-H bond scission to form the methoxy (*CH{sub 3} O) intermediate. The subsequent decomposition of methoxy on the WC surface occurs through the C-O bond scission to form *CH{sub 3}, which reacts with surface *H to produce CH{sub 4}. In contrast, the decomposition of methoxy on the Pt/WC surface favors the C-H bond scission to produce *CH{sub 2} O, which prevents the formation of the *CH{sub 3} species and leads to the formation of a *CO intermediate through subsequent deprotonation steps. The DFT predictions are validated using temperature programmed desorption to quantify the gas-phase product yields and high resolution electron energy loss spectroscopy to determine the surface intermediates from methanol decomposition on Pt, WC, and Pt/WC surfaces.

  6. Performance comparison of dynamical decoupling sequences for a qubit in a rapidly fluctuating spin bath

    NASA Astrophysics Data System (ADS)

    Álvarez, Gonzalo A.; Ajoy, Ashok; Peng, Xinhua; Suter, Dieter

    2010-10-01

    Avoiding the loss of coherence of quantum mechanical states is an important prerequisite for quantum information processing. Dynamical decoupling (DD) is one of the most effective experimental methods for maintaining coherence, especially when one can access only the qubit system and not its environment (bath). It involves the application of pulses to the system whose net effect is a reversal of the system-environment interaction. In any real system, however, the environment is not static, and therefore the reversal of the system-environment interaction becomes imperfect if the spacing between refocusing pulses becomes comparable to or longer than the correlation time of the environment. The efficiency of the refocusing improves therefore if the spacing between the pulses is reduced. Here, we quantify the efficiency of different DD sequences in preserving different quantum states. We use C13 nuclear spins as qubits and an environment of H1 nuclear spins as the environment, which couples to the qubit via magnetic dipole-dipole couplings. Strong dipole-dipole couplings between the proton spins result in a rapidly fluctuating environment with a correlation time of the order of 100 μs. Our experimental results show that short delays between the pulses yield better performance if they are compared with the bath correlation time. However, as the pulse spacing becomes shorter than the bath correlation time, an optimum is reached. For even shorter delays, the pulse imperfections dominate over the decoherence losses and cause the quantum state to decay.

  7. 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.

  8. 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. PMID:26358096

  9. Comparison of bond scission sequence of methanol on tungsten monocarbide and Pt-modified tungsten monocarbide

    NASA Astrophysics Data System (ADS)

    Stottlemyer, Alan Lee; Liu, Ping; Chen, Jingguang G.

    2010-09-01

    The ability to control the bond scission sequence of OH, CH, and CO bonds is of critical importance in the effective utilization of oxygenate molecules, such as in reforming reactions and in alcohol fuel cells. In the current study, we use methanol as a probe molecule to demonstrate the possibility to control the decomposition pathways by supporting monolayer coverage of Pt on a tungsten monocarbide (WC) surface. Density functional theory (DFT) results reveal that on the WC and Pt/WC surfaces CH3OH decomposes via OH bond scission to form the methoxy (C∗H3 O) intermediate. The subsequent decomposition of methoxy on the WC surface occurs through the CO bond scission to form C∗H3, which reacts with surface H∗ to produce CH4. In contrast, the decomposition of methoxy on the Pt/WC surface favors the CH bond scission to produce C∗H2 O, which prevents the formation of the C∗H3 species and leads to the formation of a C∗O intermediate through subsequent deprotonation steps. The DFT predictions are validated using temperature programmed desorption to quantify the gas-phase product yields and high resolution electron energy loss spectroscopy to determine the surface intermediates from methanol decomposition on Pt, WC, and Pt/WC surfaces.

  10. 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

  11. Comparison of Helicobacter spp. genetic sequences in wild and captive seals, and gulls.

    PubMed

    Oxley, Andrew P A; McKay, David B

    2005-06-01

    Helicobacter species are widely distributed in the gastrointestinal system of humans and many animal taxa. Investigations of natural infections are essential to elucidating their role within the host. The feces of fur seals Arctocephalus pusillus doriferus and sea lions Neophoca cinerea from 3 separate captive populations, as well as a wild colony from Kangaroo Island, Australia, were examined for the occurrence of Helicobacter spp. The feces from several wild silver gulls Larus novahollandiae were also investigated. As detected by PCR, 18 of 21 samples from captive and 12 of 16 samples from wild seals were positive for Helicobacter spp. Three species were identified in these animals. Whilst one possibly novel type was identified from wild fur seals, the majority of wild and captive individuals had the same species. This species also occurred in more than 1 seal type and in silver gulls, and shared a 98.1 to 100% identity to other Helicobacter spp. from harp seals and sea otters. A similar sequence type to species identified from cetaceans was also detected in several captive seals. This study reports for the first time the presence of Helicobacter spp. in wild and captive seals and demonstrates the diversity and broad-host range of these organisms in the marine host. PMID:16060262

  12. 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

  13. Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools.

    PubMed

    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

    2016-04-19

    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

  14. Molecular Characterization of Buffalo Haptoglobin: Sequence Based Structural Comparison Indicates Convergent Evolution Between Ruminants and Human.

    PubMed

    Niranjan, S K; Goyal, S; Dubey, P K; Vohra, V; Singh, S; Kathiravan, P; Kataria, R S

    2016-01-01

    Haptoglobin (Hp) protein has high affinity for hemoglobin (Hb) binding during intravascular hemolysis and scavenges the hemoglobin induced free radicals. Earlier reports indicate about uniqueness of Hp molecule in human and cattle, but in other animals, it is not much studied. In this paper, we characterized buffalo Hp molecule and determined its molecular structure, evolutionary importance, and tissue expression. Comparative analysis and predicted domain structure indicated that the buffalo Hp has an internal duplicated region in α-chain only similar to an alternate Hp2 allele in human. This duplicated part encoded for an extra complement control protein CCP domain. Phylogenetic analysis revealed that buffalo and other ruminants were found to group together separated from all other non-ruminants, including human. The key amino acid residues involved in Hp and Hb as well as Hp and macrophage scavenger receptor, CD163 interactions in buffalo, depicted a significant variation in comparison to other non-ruminant species. Constitutive expression of Hp was also confirmed across all the vital tissues of buffalo, for the first time. Results revealed that buffalo Hp is both structurally and functionally conserved, having internal duplication in α-chain similar to human Hp2 and other ruminant species, which might have evolved separately as a convergent evolutionary process. Furthermore, the presence of extra Hp CCP domain possibly in all ruminants may have an effect during dimerization of molecule in these species. PMID:26646629

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. Trading accuracy for speed: A quantitative comparison of search algorithms in protein sequence design.

    PubMed

    Voigt, C A; Gordon, D B; Mayo, S L

    2000-06-01

    Finding the minimum energy amino acid side-chain conformation is a fundamental problem in both homology modeling and protein design. To address this issue, numerous computational algorithms have been proposed. However, there have been few quantitative comparisons between methods and there is very little general understanding of the types of problems that are appropriate for each algorithm. Here, we study four common search techniques: Monte Carlo (MC) and Monte Carlo plus quench (MCQ); genetic algorithms (GA); self-consistent mean field (SCMF); and dead-end elimination (DEE). Both SCMF and DEE are deterministic, and if DEE converges, it is guaranteed that its solution is the global minimum energy conformation (GMEC). This provides a means to compare the accuracy of SCMF and the stochastic methods. For the side-chain placement calculations, we find that DEE rapidly converges to the GMEC in all the test cases. The other algorithms converge on significantly incorrect solutions; the average fraction of incorrect rotamers for SCMF is 0.12, GA 0.09, and MCQ 0.05. For the protein design calculations, design positions are progressively added to the side-chain placement calculation until the time required for DEE diverges sharply. As the complexity of the problem increases, the accuracy of each method is determined so that the results can be extrapolated into the region where DEE is no longer tractable. We find that both SCMF and MCQ perform reasonably well on core calculations (fraction amino acids incorrect is SCMF 0.07, MCQ 0.04), but fail considerably on the boundary (SCMF 0.28, MCQ 0.32) and surface calculations (SCMF 0.37, MCQ 0.44). PMID:10835284

  1. A phylogenetic comparison of the 16S rRNA sequence of the fish pathogen, Renibacterium salmoninarum, to gram-positive bacteria.

    PubMed

    Gutenberger, S K; Giovannoni, S J; Field, K G; Fryer, J L; Rohovec, J S

    1991-01-15

    The 16S rRNA of Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonids, was sequenced by reverse transcriptase to produce a nearly complete sequence (97%) of 1475 nucleotides. Phylogenetic comparisons to seventeen genera and signature sequence analysis indicated that R. salmoninarum was a member of the high G + C Gram-positive eubacterial subdivision although the reported G + C value is only 53%. A phylogenetic tree details the relationship of R. salmoninarum to ten actinomycetes from diverse environments. PMID:1709893

  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. Comparison of liver microRNA transcriptomes of Tibetan and Yorkshire pigs by deep sequencing.

    PubMed

    Li, Yanyue; Li, Xiaocheng; Sun, Wen-Kui; Cheng, Chi; Chen, Yi-Hui; Zeng, Kai; Chen, Xiaohui; Gu, Yiren; Gao, Rong; Liu, Rui; Lv, Xuebin

    2016-02-15

    MicroRNAs (miRNAs) play an important role in the modulation of various metabolic processes in the liver, yet little is known about the liver microRNAome (miRNAome) of the Tibetan pig. Here we used the Yorkshire pig as a control to analyze the Tibetan pig-specific liver miRNAome, and for preliminary investigation of differentially expressed miRNAs participating in metabolism. A comprehensive analysis of Tibetan and Yorkshire pig liver miRNAomes by small RNA sequencing identified 362 unique miRNAs. Among these, 304 were co-expressed in both libraries, and 10 and 48 miRNAs were specifically expressed. Differential expression analysis of miRNAs, miRNA target prediction and KEGG analysis revealed that differentially expressed miRNAs were associated mainly with the metabolism of glucose, lipid and protein. Six differentially expressed miRNAs (miR-34a, miR-326, miR-1, miR-335, miR-185 and miR-378) participating in the metabolism of glucose and lipid were identified. Additionally, qPCR results revealed that a lower expression of miR-34a in Tibetan pig liver may promote gluconeogenesis by increasing the expression of Sirtuin type 1 (Sirt1); a lower expression of miR-1 in Tibetan pig liver may promote the synthesis and accumulation of lipid by increasing the expression of Liver X receptor α (LXRα); and a lower expression of miR-185 in Tibetan pig liver may promote the uptake of cholesterol from blood and secretion of bile by increasing the expression of the scavenger receptor class B type I (SR-BI). Our results provide new information and understanding of porcine miRNA profiles, which may help explain the regulatory mechanisms of miRNAs in the metabolic functions of Tibetan pig liver, and provide new biomarkers to assist in the development of Tibetan pig breeding characteristics. PMID:26656174

  4. Discrimination of Burkholderia mallei/pseudomallei from Burkholderia thailandensis by sequence comparison of a fragment of the ribosomal protein S21 (rpsU) gene

    PubMed Central

    Frickmann, H.; Chantratita, N.; Gauthier, Y. P.; Neubauer, H.; Hagen, R. M.

    2012-01-01

    Discrimination of Burkholderia (B.) pseudomallei and B. mallei from environmental B. thailandensis is challenging. We describe a discrimination method based on sequence comparison of the ribosomal protein S21 (rpsU) gene. The rpsU gene was sequenced in ten B. pseudomallei, six B. mallei, one B. thailandensis reference strains, six isolates of B. pseudomallei, and 37 of B. thailandensis. Further rpsU sequences of six B. pseudomallei, three B. mallei, and one B. thailandensis were identified via NCBI GenBank. Three to four variable base-positions were identified within a 120-base-pair fragment, allowing discrimination of the B. pseudomallei/mallei-cluster from B. thailandensis, whose sequences clustered identically. All B. mallei and three B. pseudomallei sequences were identical, while 17/22 B. pseudomallei strains differed in one nucleotide (78A>C). Sequences of the rpsU fragment of ‘out-stander’ reference strains of B. cepacia, B. gladioli, B. plantarii, and B. vietnamensis clustered differently. Sequence comparison of the described rpsU gene fragment can be used as a supplementary diagnostic procedure for the discrimination of B. mallei/pseudomallei from B. thailandensis as well as from other species of the genus Burkholderia, keeping in mind that it does not allow for a differentiation between B. mallei and B. pseudomallei. PMID:23227305

  5. 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.

  6. 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. PMID:24814788

  7. 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. PMID:23562435

  8. Comparison of different stationary phases for bioanalytical studies of biologically active compounds.

    PubMed

    Zerzanová, Anna; Císar, Premek; Klimes, Jirí

    2006-09-01

    In this study, the chromatographic behaviour of four mixtures of compounds was tested on columns possessing various surface properties. Cocaine, dimefluron, nabumetone, and tramadol were chosen as the test compounds. Cocaine is a tropane alkaloid, which is relatively often abused as a drug. This is why many papers have already been written about its determination in human biological samples. Dimefluron, a derivative of benzo[c]fluorene, is a new perspective drug being investigated for its potential antineoplastic effects. Nabumetone is a non-steroidal anti-inflammatory prodrug used for treatment of inflammatory and degenerative rheumatic diseases. Tramadol, derived from an opioid structure is used as an anodyne for treatment of severe pain. As a medicament it is usually determined either in biological samples or in pharmaceuticals. The above-mentioned model drugs were separated using chromatographic columns with C18, C8, palmitamidopropyl, and pentafluorophenylpropyl chains. The best conditions for separation of the individual compounds and their metabolites were chosen on the basis of resolution, retention times, and peak symmetry. PMID:17069241

  9. Microdosimetry spectra of the Loma Linda proton beam and relative biological effectiveness comparisons.

    PubMed

    Coutrakon, G; Cortese, J; Ghebremedhin, A; Hubbard, J; Johanning, J; Koss, P; Maudsley, G; Slater, C R; Zuccarelli, C

    1997-09-01

    Protons have long been recognized as low LET radiation in radiotherapy. However, a detailed account of LET (linear energy transfer) and RBE (relative biological effectiveness) changes with incident beam energy and depth in tissue is still unresolved. This issue is particularly important for treatment planning, where the physical dose prescription is calculated from a RBE using cobalt as the reference radiation. Any significant RBE changes with energy or depth will be important to incorporate in treatment planning. In this paper we present microdosimetry spectra for the proton beam at various energies and depths and compare the results to cell survival studies performed at Loma Linda. An empirically determined biological weighting function that depends on lineal energy is used to correlate the microdosimetry spectra with cell survival data. We conclude that the variations in measured RBE with beam energy and depth are small until the distal edge of the beam is reached. On the distal edge, protons achieve stopping powers as high as 100 keV/micron, which is reflected in the lineal energy spectra taken there. Lineal energy spectra 5 cm beyond the distal edge of the Bragg peak also show a high LET component but at a dose rate 600 times smaller than observed inside the proton field. PMID:9304579

  10. Comparison of biological characteristics of H9N2 avian influenza viruses isolated from different hosts.

    PubMed

    Zhu, Yinbiao; Yang, Yang; Liu, Wei; Liu, Xin; Yang, Da; Sun, Zhihao; Ju, Yong; Chen, Sujuan; Peng, Daxin; Liu, Xiufan

    2015-04-01

    The pathogenicity and transmissibility of H9N2 influenza viruses has been widely investigated; however, few studies comparing the biological characteristics of H9N2 viruses isolated from different hosts have been performed. In this study, eight H9N2 viruses, isolated from chickens (Ck/F98, Ck/AH and Ck/TX), pigeons (Pg/XZ), quail/(Ql/A39), ducks (Dk/Y33) and swine (Sw/YZ and Sw/TZ) were selected, and their biological characteristics were determined. The results showed that all H9N2 viruses maintained a preference for both the avian- and human-type receptors, except for Sw/TZ, which had exclusive preference for the human-type receptor. The viruses replicated well in DF-1 and MDCK cells, whereas only three isolates, Ck/F98, Ck/TX and Sw/TZ, could replicate in A549 cells and also replicated in mouse lungs, resulting in body weight loss in mice. All H9N2 viruses were nonpathogenic to chickens and were detected in the trachea and lung tissues. The viruses were shed primarily by the oropharynx and were transmitted efficiently to naïve contact chickens. Our findings suggest that all H9N2 viruses from different hosts exhibit efficient replication and contact-transmission among chickens, and chickens serve as a good reservoir for the persistence and interspecies transmission of H9N2 influenza viruses. PMID:25616845

  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. PMID:22902230

  12. 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.

  13. 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.

  14. 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.

  15. A systematic comparison of two new releases of exome sequencing products: the aim of use determines the choice of product.

    PubMed

    Altmüller, Janine; Motameny, Susanne; Becker, Christian; Thiele, Holger; Chatterjee, Sreyoshi; Wollnik, Bernd; Nürnberg, Peter

    2016-08-01

    We received early access to the newest releases of exome sequencing products, namely Agilent SureSelect v6 (Agilent, Santa Clara, CA, USA) and NimbleGen MedExome (Roche NimbleGen, Basel, Switzerland), and we conducted whole exome sequencing (WES) of several DNA samples with each of these products in order to assess their performance. Here, we provide a detailed evaluation of the original, normalized (with respect to the different target sizes), and trimmed data sets and compare them in terms of the amount of duplicates, the reads on target, and the enrichment evenness. In addition to these general statistics, we performed a detailed analysis of the frequently mutated and newly described genes found in 'The Deciphering Developmental Disorders Study' published very recently (Fitzgerald, T.W., Gerety, S.S., Jones, W.D., van Kogelenberg, M., King, D.A., McRae, J., Morley, K.I., Parthiban, V., Al-Turki, S., Ambridge, K., et al. (2015). Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223-228.). In our comparison, the Agilent v6 exome performs better than the NimbleGen's MedExome both in terms of efficiency and evenness of coverage distribution. With its larger target size, it is also more comprehensive, and therefore the better choice in research projects that aim to identify novel disease-associated genes. In contrast, if the exomes are mainly used in a diagnostic setting, we see advantages for the new NimbleGen MedExome. We find a superior coverage here in those genes of high clinical relevance that likely allows for a better detection of relevant, disease-causing mutations. PMID:27021259

  16. Sequence Comparisons of Odorant Receptors among Tortricid Moths Reveal Different Rates of Molecular Evolution among Family Members

    PubMed Central

    Carraher, Colm; Authier, Astrid; Steinwender, Bernd; Newcomb, Richard D.

    2012-01-01

    In insects, odorant receptors detect volatile cues involved in behaviours such as mate recognition, food location and oviposition. We have investigated the evolution of three odorant receptors from five species within the moth genera Ctenopseustis and Planotrotrix, family Tortricidae, which fall into distinct clades within the odorant receptor multigene family. One receptor is the orthologue of the co-receptor Or83b, now known as Orco (OR2), and encodes the obligate ion channel subunit of the receptor complex. In comparison, the other two receptors, OR1 and OR3, are ligand-binding receptor subunits, activated by volatile compounds produced by plants - methyl salicylate and citral, respectively. Rates of sequence evolution at non-synonymous sites were significantly higher in OR1 compared with OR2 and OR3. Within the dataset OR1 contains 109 variable amino acid positions that are distributed evenly across the entire protein including transmembrane helices, loop regions and termini, while OR2 and OR3 contain 18 and 16 variable sites, respectively. OR2 shows a high level of amino acid conservation as expected due to its essential role in odour detection; however we found unexpected differences in the rate of evolution between two ligand-binding odorant receptors, OR1 and OR3. OR3 shows high sequence conservation suggestive of a conserved role in odour reception, whereas the higher rate of evolution observed in OR1, particularly at non-synonymous sites, may be suggestive of relaxed constraint, perhaps associated with the loss of an ancestral role in sex pheromone reception. PMID:22701634

  17. Youth problems among adoptees living in one-parent homes: a comparison with others from one-parent biological families.

    PubMed

    Feigelman, William; Finley, Gordon E

    2004-07-01

    Exploring how rising family dissolutions affect adopted children, the authors investigated 2 competing viewpoints: (a) a double jeopardy hypothesis, positing adoptees are susceptible to heightened risks of adjustment problems because of a compounding of parental losses, versus (b) a buffering hypothesis, suggesting early birth parent losses buffer an adoptee's ability to accept parental loss from divorce. With data from the 1994 National Longitudinal Study of Adolescent Health (Add Health, 2003), the authors compared adaptations of adolescent adoptees living with 1 adoptive parent (n=143) with those of children living in step- or single-parent biological families (n=7,457) in a nationally representative sample. Results were mixed, showing some support for both hypotheses and mostly nonsignificant differences on the largest number of behavioral comparisons made. PMID:15291707

  18. 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

  19. Comparison of different sample and target preparation procedures for PIXE analysis of biological materials

    NASA Astrophysics Data System (ADS)

    Maenhaut, W.; De Reu, L.; Vandenhaute, J.

    1984-04-01

    Four different methods for preparing PIXE targets from biological samples were compared. All methods involved doping with an internal standard and preparing target deposits of 1-4 mg/cm 2 on a thin substrate. In method A targets were prepared using powdered freeze-dried material. Methods B and C both included a low temperature ashing preconcentration step and method D involved an acid digestion in a teflon bomb. The procedures were applied to reference materials (e.g. NBS standards) and to "real" samples such as human kidneys and a liver, which had been analyzed by neutron activation analysis (NAA). For most elements good agreement was observed between the results of the four target preparation methods and the reference values or the NAA results. Exceptions, however, were Br, Se and Cd, which were lost in some methods. The detection limits in the different methods are compared.

  20. 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.

  1. 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.

  2. NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

    PubMed Central

    2009-01-01

    Background Genome sequences, now available for most pathogens, hold promise for the rational design of new therapies. However, biological resources for genome-scale identification of gene function (notably genes involved in pathogenesis) and/or genes essential for cell viability, which are necessary to achieve this goal, are often sorely lacking. This holds true for Neisseria meningitidis, one of the most feared human bacterial pathogens that causes meningitis and septicemia. Results By determining and manually annotating the complete genome sequence of a serogroup C clinical isolate of N. meningitidis (strain 8013) and assembling a library of defined mutants in up to 60% of its non-essential genes, we have created NeMeSys, a biological resource for Neisseria meningitidis systematic functional analysis. To further enhance the versatility of this toolbox, we have manually (re)annotated eight publicly available Neisseria genome sequences and stored all these data in a publicly accessible online database. The potential of NeMeSys for narrowing the gap between sequence and function is illustrated in several ways, notably by performing a functional genomics analysis of the biogenesis of type IV pili, one of the most widespread virulence factors in bacteria, and by identifying through comparative genomics a complete biochemical pathway (for sulfur metabolism) that may potentially be important for nasopharyngeal colonization. Conclusions By improving our capacity to understand gene function in an important human pathogen, NeMeSys is expected to contribute to the ongoing efforts aimed at understanding a prokaryotic cell comprehensively and eventually to the design of new therapies. PMID:19818133

  3. 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.

  4. Comparison of methods for integrating biological and physical data for marine habitat mapping and classification

    NASA Astrophysics Data System (ADS)

    Shumchenia, E. J.; King, J. W.

    2010-09-01

    An important first step in marine spatial planning and ecosystem-based management efforts is the creation of benthic habitat maps that allow scientists and managers to understand the distribution of living and non-living resources on the seafloor. However, the location of boundaries between and composition of habitats is highly dependent on the approach taken to integrate abiotic and biotic information. The purpose of this study was to test "top-down" and "bottom-up" approaches for integrating physical and biological data derived from commonly used sub-tidal benthic mapping tools to create a habitat map compatible with the US Coastal and Marine Ecological Classification Standard (CMECS). We found that a top-down framework, where we tested for differences in macrofauna assemblages among side scan sonar facies, defined two broad-scale and general habitats. Using the bottom-up approach, where patterns in abiotic and biotic variables were examined with multivariate statistics (BEST, LINKTREE, ANOSIM, SIMPER), we generated seven biotopes based on the macrofauna abundance, percent sand, water depth, and backscatter standard deviation that corresponded well to, but provided more fine-scale detail than the top-down habitats. We were able to use the statistical relationship between abiotic variables and macrofauna assemblages in the LINKTREE to predict the spatial distribution of assemblages over ˜50% of the study area. We created a local catalogue of biotopes specific to our study area that contributes to the CMECS library. In addition, we were able to fully map CMECS Geoform, Surface Geology, and Biotic Cover Components. This mapping effort represented real progress toward reconciling the "data density mismatch" between physical and biological mapping methods, and it provided further evidence that using a bottom-up methodology preserves species-environment relationships.

  5. Comparison of reactor designs for biological ex-situ soil treatment

    SciTech Connect

    Potter, C.; Haught, R.

    1995-10-01

    The goal of this project is to evaluate the potential of biological ex-situ soil treatment systems to remediate soils contaminated with hazardous chemicals. A laminar-type flow pilot-scale reactor with volume of 3 cu. yd has been constructed at EPA`s Test & Evaluation J&D Facility in Cincinnati. Laminar-type flow from one side of the reactor to the other may provide even aeration to all areas of the reactor while avoiding the use of pipes inside the reactor. This design greatly facilitates loading and unloading the reactor and is readily scalable to larger systems. Passing smoke through the reactor for visual observation of flow indicated uniform flow in the empty reactor. Further testing involves filling the reactor with vermiculite, flushing with Argon, and then passing air through the reactor at about 1 volume change per day to evaluate air flow through this uniform solid matrix. Oxygen probes, located at 27 positions within the reactor, provide information on air progression through the system. Analysis of gas flow through an empty reactor and through a uniform matrix (vermiculite) allows separation of reactor flaws from soil inhomogeneities as causes of any nonuniform aeration of the reactor space. Soil contaminated with polynuclear aromatic hydrocarbons (PAHs) from The Reilly Tar Pit Superfund Site in St. Louis Park, MN has been shipped under the small quantity treatability exemption to the T&E Facility for research on soil aeration and effectiveness of this ex-situ reactor design for biological treatment of contaminated soils.

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. Draft Genome Sequence of Microvirga sp. Strain BSC39, 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

    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

  13. Aniridia-associated translocations, DNase hypersensitivity, sequence comparison and transgenic analysis redefine the functional domain of PAX6.

    PubMed

    Kleinjan, D A; Seawright, A; Schedl, A; Quinlan, R A; Danes, S; van Heyningen, V

    2001-09-15

    The transcription factor PAX6 plays a critical, evolutionarily conserved role in eye, brain and olfactory development. Homozygous loss of PAX6 function affects all expressing tissues and is neonatally lethal; heterozygous null mutations cause aniridia in humans and the Small eye (Sey) phenotype in mice. Several upstream and intragenic PAX6 control elements have been defined, generally through transgenesis. However, aniridia cases with chromosomal rearrangements far downstream of an intact PAX6 gene suggested a requirement for additional cis-acting control for correct gene expression. The likely location of such elements is pinpointed through YAC transgenic studies. A 420 kb yeast artificial chromosome (YAC) clone, extending well beyond the most distant patient breakpoint, was previously shown to rescue homozygous Small eye lethality and correct the heterozygous eye phenotype. We now show that a 310 kb YAC clone, terminating just 5' of the breakpoint, fails to influence the Sey phenotypes. Using evolutionary sequence comparison, DNaseI hypersensitivity analysis and transgenic reporter studies, we have identified a region, >150 kb distal to the major PAX6 promoter P1, containing regulatory elements. Components of this downstream regulatory region drive reporter expression in distinct partial PAX6 patterns, indicating that the functional PAX6 gene domain extends far beyond the transcription unit. PMID:11590122

  14. 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.

  15. 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

  16. 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.

  17. Cisplatin and its dibromido analogue: a comparison of chemical and biological profiles.

    PubMed

    Marzo, Tiziano; Bartoli, Gianluca; Gabbiani, Chiara; Pescitelli, Gennaro; Severi, Mirko; Pillozzi, Serena; Michelucci, Elena; Fiorini, Benedetta; Arcangeli, Annarosa; Quiroga, Adóracion G; Messori, Luigi

    2016-06-01

    The dibromido analogue of cisplatin, cis-PtBr2(NH3)2 (cisPtBr2 hereafter), has been prepared and characterised. Its solution behaviour in standard phosphate buffer, at pH 7.4, was investigated spectrophotometrically and found to reproduce quite closely that of cisplatin; indeed, progressive sequential release of the two halide ligands typically occurs as in the case of cisplatin, with a roughly similar kinetics. Afterward, patterns of reactivity toward model proteins and standard ctDNA were explored and the nature of the resulting interactions elucidated. The antiproliferative properties were then evaluated in four representative cancer cell lines, namely A549 (human lung cancer), HCT116 (human colon cancer), IGROV-1 (human ovarian cancer) and FLG 29.1 (human acute myeloid leukaemia). Cytotoxic properties in line with those of cisplatin were highlighted. From these studies an overall chemical and biological profile emerges for cisPtBr2 closely matching that of cisplatin; the few slight, but meaningful differences that were underscored might be advantageously exploited for clinical application. PMID:27086032

  18. Comparison of Binding Properties and Early Biological Effects of Elicitins in Tobacco Cells1

    PubMed Central

    Bourque, Stéphane; Ponchet, Michel; Binet, Marie-Noëlle; Ricci, Pierre; Pugin, Alain; Lebrun-Garcia, Angela

    1998-01-01

    Elicitins are a family of small proteins secreted by Phytophthora species that have a high degree of homology and elicit defense reactions in tobacco (Nicotiana tabacum). They display acidic or basic characteristics, the acidic elicitins being less efficient in inducing plant necrosis. In this study we compared the binding properties of four elicitins (two basic and two acidic) and early-induced signal transduction events (Ca2+ influx, extracellular medium alkalinization, and active oxygen species production). The affinity for tobacco plasma membrane-binding sites and the number of binding sites were similar for all four elicitins. Furthermore, elicitins compete with one another for binding sites, suggesting that they interact with the same receptor. The four elicitins induced Ca2+ influx, extracellular medium alkalinization, and the production of active oxygen species in tobacco cell suspensions, but the intensity and kinetics of these effects were different from one elicitin to another. As a general observation the concentrations that induce similar levels of biological activities were lower for basic elicitins (with the exception of cinnamomin-induced Ca2+ uptake). The qualitative similarity of early events induced by elicitins indicates a common transduction scheme, whereas fine signal transduction tuning is different in each elicitin. PMID:9847105

  19. 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

  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. PMID:26194235

  1. Quantitative comparison of alternative methods for coarse-graining biological networks

    PubMed Central

    Bowman, Gregory R.; Meng, Luming; Huang, Xuhui

    2013-01-01

    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. PMID:24089717

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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…

  8. 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

  9. 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

  10. 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. PMID:25749926

  11. Complete nucleotide sequence, genome organization, and biological properties of human immunodeficiency virus type 1 in vivo: evidence for limited defectiveness and complementation.

    PubMed Central

    Li, Y; Hui, H; Burgess, C J; Price, R W; Sharp, P M; Hahn, B H; Shaw, G M

    1992-01-01

    Previous studies of the genetic and biologic characteristics of human immunodeficiency virus type 1 (HIV-1) have by necessity used tissue culture-derived virus. We recently reported the molecular cloning of four full-length HIV-1 genomes directly from uncultured human brain tissue (Y. Li, J. C. Kappes, J. A. Conway, R. W. Price, G. M. Shaw, and B. H. Hahn, J. Virol. 65:3973-3985, 1991). In this report, we describe the biologic properties of these four clones and the complete nucleotide sequences and genome organization of two of them. Clones HIV-1YU-2 and HIV-1YU-10 were 9,174 and 9,176 nucleotides in length, differed by 0.26% in nucleotide sequence, and except for a frameshift mutation in the pol gene in HIV-1YU-10, contained open reading frames corresponding to 5'-gag-pol-vif-vpr-tat-rev-vpu-env-nef-3' flanked by long terminal repeats. HIV-1YU-2 was fully replication competent, while HIV-1YU-10 and two other clones, HIV-1YU-21 and HIV-1YU-32, were defective. All three defective clones, however, when transfected into Cos-1 cells in any pairwise combination, yielded virions that were replication competent and transmissible by cell-free passage. The cellular host range of HIV-1YU-2 was strictly limited to primary T lymphocytes and monocyte-macrophages, a property conferred by its external envelope glycoprotein. Phylogenetic analyses of HIV-1YU-2 gene sequences revealed this virus to be a member of the North American/European HIV-1 subgroup, with specific similarity to other monocyte-tropic viruses in its V3 envelope amino acid sequence. These results indicate that HIV-1 infection of brain is characterized by the persistence of mixtures of fully competent, minimally defective, and more substantially altered viral forms and that complementation among them is readily attainable. In addition, the limited degree of genotypic heterogeneity observed among HIV-1YU and other brain-derived viruses and their preferential tropism for monocyte-macrophages suggest that viral

  12. 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

  13. Sequence comparison of JSRV with endogenous proviruses: envelope genotypes and a novel ORF with similarity to a G-protein-coupled receptor.

    PubMed

    Bai, J; Bishop, J V; Carlson, J O; DeMartini, J C

    1999-06-01

    Ovine pulmonary carcinoma, a contagious lung cancer of sheep, is caused by the oncogenic jaagsiekte sheep retrovirus (JSRV) that is closely related to a family of endogenous sheep retroviral sequences (ESRVs). By using exogenous virus-specific U3 oligonucleotide primers, the entire JSRV proviral genome or its 3' part was amplified from tumor DNA. Analysis of these proviral sequences revealed a novel open reading frame (ORF) within the pol coding region, designated ORF X, which was well conserved in ESRV and JSRV sequences. Deduced amino acids of ORF X showed similarity to a portion of the mammalian adenosine receptor subtype 3, a member of the G-protein-coupled receptor family. Comparison of deduced env amino acids of six JSRV strains from three continents identified 15 residues that defined two distinct genotypes of JSRVs. Sequence analysis identified two highly variable regions between JSRV and ESRV in the transmembrane domain of env (TM) and the 3' unique sequence (U3) of the long terminal repeat, from which JSRV-specific DNA probes were derived. By using these DNA probes in Southern hybridization, for the first time we successfully identified JSRV proviral sequences in tumor genomic DNA in the presence of multiple ESRV loci, validating the use of exogenous virus-specific DNA probes in the analysis of oncogenic proviral integration sites and identification of integrated exogenous proviral sequences. PMID:10366570

  14. 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.

  15. Sequence comparison of new prokaryotic and mitochondrial members of the polypeptide chain release factor family predicts a five-domain model for release factor structure.

    PubMed Central

    Pel, H J; Rep, M; Grivell, L A

    1992-01-01

    We have recently reported the cloning and sequencing of the gene for the mitochondrial release factor mRF-1. mRF-1 displays high sequence similarity to the bacterial release factors RF-1 and RF-2. A database search for proteins resembling these three factors revealed high similarities to two amino acid sequences deduced from unassigned genomic reading frames in Escherichia coli and Bacillus subtilis. The amino acid sequence derived from the Bacillus reading frame is 47% identical to E.coli and Salmonella typhimurium RF-2, strongly suggesting that it represents B.subtilis RF-2. Our comparison suggests that the expression of the B.subtilis gene is, like that of the E.coli and S. typhimurium RF-2 genes, autoregulated by a stop codon dependent +1 frameshift. A comparison of prokaryotic and mitochondrial release factor sequences, including the putative B.subtilis RF-2, leads us to propose a five-domain model for release factor structure. Possible functions of the various domains are discussed. PMID:1408743

  16. Broadband homonuclear correlation spectroscopy driven by combined R2(n)(v) sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids.

    PubMed

    Hou, Guangjin; Yan, Si; Trébosc, Julien; Amoureux, Jean-Paul; Polenova, Tatyana

    2013-07-01

    We recently described a family of experiments for R2n(v) Driven Spin Diffusion (RDSD) spectroscopy suitable for homonuclear correlation experiments under fast MAS conditions [G. Hou, S. Yan, S.J. Sun, Y. Han, I.J. Byeon, J. Ahn, J. Concel, A. Samoson, A.M. Gronenborn, T. Polenova, Spin diffusion drive by R-symmetry sequencs: applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids, J. Am. Chem. Soc. 133 (2011) 3943-3953]. In these RDSD experiments, since the broadened second-order rotational resonance conditions are dominated by the radio frequency field strength and the phase shifts, as well as the size of reintroduced dipolar couplings, the different R2n(v) sequences display unique polarization transfer behaviors and different recoupling frequency bandwidths. Herein, we present a series of modified R2n(v) sequences, dubbed COmbined R2n(v)-Driven (CORD), that yield broadband homonuclear dipolar recoupling and give rise to uniform distribution of cross peak intensities across the entire correlation spectrum. We report NMR experiments and numerical simulations demonstrating that these CORD spin diffusion sequences are suitable for broadband recoupling at a wide range of magnetic fields and MAS frequencies, including fast-MAS conditions (νr=40 kHz and above). Since these CORD sequences are largely insensitive to dipolar truncation, they are well suited for the determination of long-range distance constraints, which are indispensable for the structural characterization of a broad range of systems. Using U-(13)C,(15)N-alanine and U-(13)C,(15)N-histidine, we show that under fast-MAS conditions, the CORD sequences display polarization transfer efficiencies within broadband frequency regions that are generally higher than those offered by other existing spin diffusion pulse schemes. A 89-residue U-(13)C,(15)N-dynein light chain (LC8) protein has also been used to demonstrate that the CORD sequences exhibit uniformly high cross peak

  17. Genomic sequencing and biological characteristics of a novel Escherichia coli bacteriophage 9g, a putative representative of a new Siphoviridae genus.

    PubMed

    Kulikov, Eugene E; Golomidova, Alla K; Letarova, Maria A; Kostryukova, Elena S; Zelenin, Alexandr S; Prokhorov, Nikolai S; Letarov, Andrey V

    2014-12-01

    Bacteriophage 9 g was isolated from horse feces using Escherichia coli C600 as a host strain. Phage 9 g has a slightly elongated capsid 62 × 76 nm in diameter and a non-contractile tail about 185 nm long. The complete genome sequence of this bacteriophage consists of 56,703 bp encoding 70 predicted open reading frames. The closest relative of phage 9 g is phage PhiJL001 infecting marine alpha-proteobacterium associated with Ircinia strobilina sponge, sharing with phage 9 g 51% of amino acid identity in the main capsid protein sequence. The DNA of 9 g is resistant to most restriction endonucleases tested, indicating the presence of hypermodified bases. The gene cluster encoding a biosynthesis pathway similar to biosynthesis of the unusual nucleoside queuosine was detected in the phage 9 g genome. The genomic map organization is somewhat similar to the typical temperate phage gene layout but no integrase gene was detected. Phage 9 g efficiently forms stable associations with its host that continues to produce the phage over multiple passages, but the phage can be easily eliminated via viricide treatment indicating that no true lysogens are formed. Since the sequence, genomic organization and biological properties of bacteriophage 9 g are clearly distinct from other known Enterobacteriaceae phages, we propose to consider it as the representative of a novel genus of the Siphoviridae family. PMID:25533657

  18. Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche.

    PubMed

    Guimaraes, Ana M S; Santos, Andrea P; SanMiguel, Phillip; Walter, Thomas; Timenetsky, Jorge; Messick, Joanne B

    2011-01-01

    Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454) and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS). The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+) kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems. PMID:21573007

  19. A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer

    PubMed Central

    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.

    2015-01-01

    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

  20. 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

  1. Novel proline-hydroxyproline glycopeptides from the dandelion (Taraxacum officinale Wigg.) flowers: de novo sequencing and biological activity.

    PubMed

    Astafieva, Alexandra A; Enyenihi, Atim A; Rogozhin, Eugene A; Kozlov, Sergey A; Grishin, Eugene V; Odintsova, Tatyana I; Zubarev, Roman A; Egorov, Tsezi A

    2015-09-01

    Two novel homologous peptides named ToHyp1 and ToHyp2 that show no similarity to any known proteins were isolated from Taraxacum officinale Wigg. flowers by multidimensional liquid chromatography. Amino acid and mass spectrometry analyses demonstrated that the peptides have unusual structure: they are cysteine-free, proline-hydroxyproline-rich and post-translationally glycosylated by pentoses, with 5 carbohydrates in ToHyp2 and 10 in ToHyp1. The ToHyp2 peptide with a monoisotopic molecular mass of 4350.3Da was completely sequenced by a combination of Edman degradation and de novo sequencing via top down multistage collision induced dissociation (CID) and higher energy dissociation (HCD) tandem mass spectrometry (MS(n)). ToHyp2 consists of 35 amino acids, contains eighteen proline residues, of which 8 prolines are hydroxylated. The peptide displays antifungal activity and inhibits growth of Gram-positive and Gram-negative bacteria. We further showed that carbohydrate moieties have no significant impact on the peptide structure, but are important for antifungal activity although not absolutely necessary. The deglycosylated ToHyp2 peptide was less active against the susceptible fungus Bipolaris sorokiniana than the native peptide. Unique structural features of the ToHyp2 peptide place it into a new family of plant defense peptides. The discovery of ToHyp peptides in T. officinale flowers expands the repertoire of molecules of plant origin with practical applications. PMID:26259198

  2. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution

    PubMed Central

    Chen, Xiao-Guang; Jiang, Xuanting; Gu, Jinbao; Xu, Meng; Wu, Yang; Deng, Yuhua; Zhang, Chi; Bonizzoni, Mariangela; Vontas, John; Armbruster, Peter; Huang, Xin; Yang, Yulan; Zhang, Hao; He, Weiming; Peng, Hongjuan; Liu, Yongfeng; Wu, Kun; Chen, Jiahua; Lirakis, Manolis; Topalis, Pantelis; Van Leeuwen, Thomas; Hall, Andrew Brantley; Jiang, Xiaofang; Thorpe, Chevon; Mueller, Rachel Lockridge; Sun, Cheng; Waterhouse, Robert Michael; Yan, Guiyun; Tu, Zhijian Jake; Fang, Xiaodong; James, Anthony A.

    2015-01-01

    The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species. PMID:26483478

  3. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution.

    PubMed

    Chen, Xiao-Guang; Jiang, Xuanting; Gu, Jinbao; Xu, Meng; Wu, Yang; Deng, Yuhua; Zhang, Chi; Bonizzoni, Mariangela; Dermauw, Wannes; Vontas, John; Armbruster, Peter; Huang, Xin; Yang, Yulan; Zhang, Hao; He, Weiming; Peng, Hongjuan; Liu, Yongfeng; Wu, Kun; Chen, Jiahua; Lirakis, Manolis; Topalis, Pantelis; Van Leeuwen, Thomas; Hall, Andrew Brantley; Jiang, Xiaofang; Thorpe, Chevon; Mueller, Rachel Lockridge; Sun, Cheng; Waterhouse, Robert Michael; Yan, Guiyun; Tu, Zhijian Jake; Fang, Xiaodong; James, Anthony A

    2015-11-01

    The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species. PMID:26483478

  4. Comparison between polyethylene glycol and zwitterionic polymers as antifouling coatings on wearable devices for selective antigen capture from biological tissue.

    PubMed

    Robinson, Kye J; Coffey, Jacob W; Muller, David A; Young, Paul R; Kendall, Mark A F; Thurecht, Kristofer J; Grøndahl, Lisbeth; Corrie, Simon R

    2015-01-01

    Selective capture of disease-related proteins in complex biological fluids and tissues is an important aim in developing sensitive protein biosensors for in vivo applications. Microprojection arrays are biomedical devices whose mechanical and chemical properties can be tuned to allow efficient penetration of skin, coupled with highly selective biomarker capture from the complex biological environment of skin tissue. Herein, the authors describe an improved surface modification strategy to produce amine-modified polycarbonate arrays, followed by the attachment of an antifouling poly(sulfobetaine-methacrylate) (pSBMA) polymer or a linear polyethylene glycol (PEG) polymer of comparative molecular weight and hydrodynamic radius. Using a "grafting to" approach, pSBMA and linear PEG coatings yielded comparative antifouling behavior in single protein solutions, diluted plasma, or when applied to mouse flank skin penetrating into the vascularized dermal tissue. Interestingly, the density of immobilized immunoglobulin G (IgG) or bovine serum albumin protein on pSBMA surfaces was significantly higher than that on the PEG surfaces, while the nonspecific adsorption was comparable for each protein. When incubated in buffer or plasma solutions containing dengue non-structural protein 1 (NS1), anti-NS1-IgG-coated pSBMA surfaces captured significantly more NS1 in comparison to PEG-coated devices. Similarly, when wearable microprojection arrays were applied to the skin of dengue-infected mice using the same coatings, the pSBMA-coated devices showed significantly higher capture efficiency (>2-fold increase in signal) than the PEG-coated substrates, which showed comparative signal when applied to naïve mice. In conclusion, zwitterionic pSBMA polymers (of equivalent hydrodynamic radii to PEG) allowed detection of dengue NS1 disease biomarker in a preclinical model of dengue infection, showing significantly higher signal-to-noise ratio in comparison to the PEG controls. The results of

  5. Comparison of ochratoxin A levels in edible pig tissues and in biological fluids after exposure to a contaminated diet.

    PubMed

    Pleadin, Jelka; Kudumija, Nina; Kovačević, Dragan; Scortichini, Giampiero; Milone, Salvatore; Kmetič, Ivana

    2016-08-01

    The aim of this study was to compare ochratoxin A (OTA) levels in pig tissues and biological fluids after animal exposure to contaminated diet (250 μg OTA/kg of feed) during 4 weeks of fattening. OTA concentrations were quantified using a validated immunoassay method (ELISA) and high-performance liquid chromatography with fluorescence detector (HPLC-FD). The highest mean OTA concentration in pig tissues was determined in kidneys of exposed animals (13.87 ± 1.41 μg/kg), followed by lungs (10.47 ± 1.97 μg/kg), liver (7.28 ± 1.75 μg/kg), spleen (4.81 ± 0.99 μg/kg), muscle tissue (4.72 ± 0.86 μg/kg), fat tissue (4.11 ± 0.88 μg/kg), heart (3.71 ± 1.09 μg/kg), and brain (3.01 ± 0.25 μg/kg). Furthermore, on the last day of exposure (day 28), significantly higher mean OTA levels were determined in urine (16.06 ± 3.09 μg/L) in comparison to serum (4.77 ± 1.57 μg/L) showing that OTA urine analysis could be a good marker to identify elevated levels of this contaminant in porcine tissues used for human consumption. This study gave guidelines for the most efficient OTA control in pig-derived biological materials that can be exercised at slaughterhouses. PMID:27056395

  6. 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

  7. 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

  8. Indirect comparisons of the efficacy of subsequent biological agents in patients with psoriatic arthritis with an inadequate response to tumor necrosis factor inhibitors: a meta-analysis.

    PubMed

    Ungprasert, Patompong; Thongprayoon, Charat; Davis, John M

    2016-07-01

    Significant portion of patients with psoriatic arthritis (PsA) could not tolerate or do not have a satisfactory response to either non-steroidal anti-inflammatory drugs (NSAIDs), non-biologic disease-modifying anti-rheumatic drugs (DMARDs), or even TNF inhibitors. Non-TNF inhibitor biologic agents have emerged as second-line therapy in such situation. However, the comparative efficacy of these agents remains unknown as head-to-head randomized controlled trials (RCTs) are not available. RCTs examining the efficacy of non-TNF inhibitor biologic agents in patients with PsA who experienced inadequate response or intolerance of TNF inhibitors were identified. If more than one RCT was available for a given biologic agent, the pooled odds ratio (OR) and 95 % confidence interval (CI) of achieving 20 % improvement according to American College of Rheumatology criteria (ACR20) response across trials were calculated. The pooled OR for each biologic agent was then compared using the indirect comparison technique. Five RCTs of four non-TNF inhibitor biologic agents, including abatacept, secukinumab, ustekinumab, and apremilast, with 675 participants were identified and included in the data analyses. We found no significant difference in any comparisons, with the p values ranging from 0.14 to 0.98. Our study demonstrates that the likelihood of achieving the ACR20 response in patients with TNF inhibitor experience is not significantly different between the four non-TNF biologic agents. However, the interpretation of this analysis is limited by the small sample sizes. Head-to-head comparisons are still required to confirm the comparative efficacy. PMID:26852316

  9. Molecular biology of K+ transport across the plant cell membrane: what do we learn from comparison between plant species?

    PubMed

    Véry, Anne-Aliénor; Nieves-Cordones, Manuel; Daly, Meriem; Khan, Imran; Fizames, Cécile; Sentenac, Hervé

    2014-05-15

    Cloning and characterizations of plant K(+) transport systems aside from Arabidopsis have been increasing over the past decade, favored by the availability of more and more plant genome sequences. Information now available enables the comparison of some of these systems between species. In this review, we focus on three families of plant K(+) transport systems that are active at the plasma membrane: the Shaker K(+) channel family, comprised of voltage-gated channels that dominate the plasma membrane conductance to K(+) in most environmental conditions, and two families of transporters, the HAK/KUP/KT K(+) transporter family, which includes some high-affinity transporters, and the HKT K(+) and/or Na(+) transporter family, in which K(+)-permeable members seem to be present in monocots only. The three families are briefly described, giving insights into the structure of their members and on functional properties and their roles in Arabidopsis or rice. The structure of the three families is then compared between plant species through phylogenic analyses. Within clusters of ortologues/paralogues, similarities and differences in terms of expression pattern, functional properties and, when known, regulatory interacting partners, are highlighted. The question of the physiological significance of highlighted differences is also addressed. PMID:24666983

  10. Comparison of a Multimetric Index and a Multivariate Predictive Model for Assessing the Biological Condition of Kentucky Streams

    NASA Astrophysics Data System (ADS)

    Pond, G. J.

    2005-05-01

    There is still debate on the strength of various data analysis tools for assessing biological condition in streams. This study compared two popular assessment approaches (multimetric index and RIVPACS-type O/E model) using macroinvertebrates from Kentucky streams. Data from 557 targeted and randomly selected sites (212 reference, 345 non-reference) sampled between 2000 and 2004 were used in this analysis. The Kentucky Macroinvertebrate Bioassessment Index (MBI) combines seven metrics (total generic richness, EPT generic richness, modified HBI, %Ephemeroptera, %EPT minus Cheumatopsyche, %midges+worms, and %clingers) that are scored by standardizing to the 95th or 5th percentile of the reference distribution and averaged. For comparison, three separate genus-level RIVPACS-type models were constructed (high-, low-, and mixed gradient streams) using four predictive variables (area, latitude, longitude, and week number) and taxa from reference sites. All 3 models preformed well but the low gradient model had the lowest precision. Assessments of non-reference sites based on MBI and O/E scores yielded similar results in terms of discrimination efficiency but the model based on mixed-gradient streams was the least sensitive. Using a subset of data from 84 headwater streams in the Appalachian region, MBI and O/E scores responded almost identically to stressors such as conductivity and habitat degradation.

  11. Sequence of cDNA for rat cystathionine gamma-lyase and comparison of deduced amino acid sequence with related Escherichia coli enzymes.

    PubMed Central

    Erickson, P F; Maxwell, I H; Su, L J; Baumann, M; Glode, L M

    1990-01-01

    A cDNA clone for cystathionine gamma-lyase was isolated from a rat cDNA library in lambda gt11 by screening with a monospecific antiserum. The identity of this clone, containing 600 bp proximal to the 3'-end of the gene, was confirmed by positive hybridization selection. Northern-blot hybridization showed the expected higher abundance of the corresponding mRNA in liver than in brain. Two further cDNA clones from a plasmid pcD library were isolated by colony hybridization with the first clone and were found to contain inserts of 1600 and 1850 bp. One of these was confirmed as encoding cystathionine gamma-lyase by hybridization with two independent pools of oligodeoxynucleotides corresponding to partial amino acid sequence information for cystathionine gamma-lyase. The other clone (estimated to represent all but 8% of the 5'-end of the mRNA) was sequenced and its deduced amino acid sequence showed similarity to those of the Escherichia coli enzymes cystathionine beta-lyase and cystathionine gamma-synthase throughout its length, especially to that of the latter. Images Fig. 1. Fig. 2. Fig. 3. Fig. 5. PMID:2201285

  12. Characterization of spirochetes isolated from ticks (Ixodes tanuki, Ixodes turdus, and Ixodes columnae) and comparison of the sequences with those of Borrelia burgdorferi sensu lato strains.

    PubMed Central

    Fukunaga, M; Hamase, A; Okada, K; Inoue, H; Tsuruta, Y; Miyamoto, K; Nakao, M

    1996-01-01

    Ixodes persulcatus serves as a tick vector for Borrelia garinii and Borrelia afzelii in Japan; however, unidentified spirochetes have been isolated from other species of ticks. In this study, 13 isolates from ticks (6 from Ixodes tanuki, 6 from Ixodes turdus, and 1 from Ixodes columnae) and 3 isolates from voles (Clethrionomys rufocanus) were characterized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, rRNA gene restriction fragment length polymorphism, partial sequencing of the outer surface protein C (OspC) gene, whole DNA-DNA hybridization, and 16S rRNA gene sequence comparison. All of the results revealed that these Borrelia strains clearly represent at least two new species. A third is also likely, although additional strains have to be isolated and characterized before a separate species is designated. We designated all isolates of I. tanuki and C. rufocanus as group Hk501 and all isolates of I. turdus as group Ya501. Phylogenetic analysis based on 16S rRNA gene sequences distinguished these Borrelia strains from those belonging to hitherto known Borrelia species. Furthermore, the genomic groups, each with its own tick vectors with enzootic cycles, were quite different from each other and also from those of Lyme disease Borrelia species known to occur in Japan. The results of 16S rRNA gene sequence comparison suggest that the strain Am501 from I. columnae is related to group Hk501, although its level of DNA relatedness is less than 70%. PMID:8779571

  13. Identification of Clinical Coryneform Bacterial Isolates: Comparison of Biochemical Methods and Sequence Analysis of 16S rRNA and rpoB Genes▿

    PubMed Central

    Adderson, Elisabeth E.; Boudreaux, Jan W.; Cummings, Jessica R.; Pounds, Stanley; Wilson, Deborah A.; Procop, Gary W.; Hayden, Randall T.

    2008-01-01

    We compared the relative levels of effectiveness of three commercial identification kits and three nucleic acid amplification tests for the identification of coryneform bacteria by testing 50 diverse isolates, including 12 well-characterized control strains and 38 organisms obtained from pediatric oncology patients at our institution. Between 33.3 and 75.0% of control strains were correctly identified to the species level by phenotypic systems or nucleic acid amplification assays. The most sensitive tests were the API Coryne system and amplification and sequencing of the 16S rRNA gene using primers optimized for coryneform bacteria, which correctly identified 9 of 12 control isolates to the species level, and all strains with a high-confidence call were correctly identified. Organisms not correctly identified were species not included in the test kit databases or not producing a pattern of reactions included in kit databases or which could not be differentiated among several genospecies based on reaction patterns. Nucleic acid amplification assays had limited abilities to identify some bacteria to the species level, and comparison of sequence homologies was complicated by the inclusion of allele sequences obtained from uncultivated and uncharacterized strains in databases. The utility of rpoB genotyping was limited by the small number of representative gene sequences that are currently available for comparison. The correlation between identifications produced by different classification systems was poor, particularly for clinical isolates. PMID:18160450

  14. Using intron sequence comparisons in the triose-phosphate isomerase gene to study the divergence of the fall armyworm host strains.

    PubMed

    Nagoshi, R N; Meagher, R L

    2016-06-01

    The noctuid moth Spodoptera frugiperda (the fall armyworm) is endemic to the Western Hemisphere and appears to be undergoing sympatric speciation to produce two subpopulations that differ in their choice of host plants. The 'rice strain' and 'corn strain' are morphologically indistinguishable, requiring the use of genetic markers for identification. Because fall armyworm is a major pest of corn and several other agricultural crops, characterizing the strains has important economic consequences. In this study, comparisons were made of the intron sequences from the triose-phosphate isomerase (Tpi) gene isolated from 85 fall armyworm specimens collected from two host plants. Sixteen new strain-specific haplotypes based on intron polymorphisms are described that can facilitate the characterization of fall armyworm populations associated with different host plants. Comparisons of genetic diversity within and between the strains provides evidence that the corn strain is undergoing active selection and supports the proposal of directional interstrain mating occurring in the wild. Comparisons of the polymorphisms indicate that each intron undergoes different patterns of mutation that in some cases corresponds to host plant preferences. The results confirm that intron sequence comparisons are an effective approach to study fall armyworm population genetics. PMID:26991678

  15. Comparison of Predicted Scaffold-Compatible Sequence Variation in the Triple-Hairpin Structure of Human Immunodeficiency Virus Type 1 gp41 with Patient Data

    PubMed Central

    Boutonnet, Nathalie; Janssens, Wouter; Boutton, Carlo; Verschelde, Jean-Luc; Heyndrickx, Leo; Beirnaert, Els; van der Groen, Guido; Lasters, Ignace

    2002-01-01

    It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well. PMID:12097573

  16. Molecular cloning, genomic analysis, and biological properties of rat leukemia virus and the onc sequences of Rasheed rat sarcoma virus.

    PubMed Central

    Gonda, M A; Young, H A; Elser, J E; Rasheed, S; Talmadge, C B; Nagashima, K; Li, C C; Gilden, R V

    1982-01-01

    Rasheed rat sarcoma virus (RaSV) has been shown to code for a protein of 29,000 Mr not present in replication-competent rat type C helper virus (RaLV)-infected cells. This protein is a fused gene product consisting of a portion of the RaLV p15 gag protein and the transformation-specific 21,000 Mr (p21) ras protein, which is also found in Harvey murine sarcoma virus. We now report the molecular cloning of both the SD-1 (Sprague-Dawley) strain of RaLV and the transforming ras sequences of RaSV. Heteroduplex analysis of these cloned DNAs demonstrated that the RaSV ras gene (v-Ra-ras) was inserted into the rat type C viral genome with a small deletion of RaLV genetic information in the 5' region of the gag gene and that the v-Ra-ras gene (0.72 kilobase pair) is homologous to and colinear with the p21 ras gene of Harvey murine sarcoma virus (v-Ha-ras). Restriction enzyme mapping confirmed the homology demonstrated by heteroduplex mapping, showing strong site conservation of restriction endonucleases known to cleave v-Ha-ras. Cloned v-Ra-ras DNA transformed NIH 3T3 cells, inducing the synthesis of the p29 RaSVgag-ras protein. Images PMID:6292516

  17. Comparison of Major and Minor Viral SNPs Identified through Single Template Sequencing and Pyrosequencing in Acute HIV-1 Infection

    PubMed Central

    Bouzek, Heather; Kim, Moon; Deng, Wenjie; Larsen, Brendan B.; Zhao, Hong; Bumgarner, Roger E.; Rolland, Morgane; Mullins, James I.

    2015-01-01

    Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects infected with single founders and 33% of subjects infected with multiple founder variants: among the subjects with disagreements, mismatches were found in less than 1% of the sites evaluated (of a total of nearly 117,000 sites across all subjects). The majority of the SNPs observed only in pyrosequences were present at less than 2% of the subject’s viral sequence population. These results demonstrate the utility of the Sanger approach for study of early HIV infection and provide guidance regarding the design, utility and limitations of population sequencing from variable template sources, and emphasize parameters for improving the interpretation of massively parallel sequencing data to address important questions regarding target sequence evolution. PMID:26317928

  18. Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing.

    PubMed

    da Fonseca, Allex Jardim; Galvão, Renata Silva; Miranda, Angelica Espinosa; Ferreira, Luiz Carlos de Lima; Chen, Zigui

    2016-05-01

    To compare the diagnostic performance for HPV infection using three laboratorial techniques. Ninty-five cervicovaginal samples were randomly selected; each was tested for HPV DNA and genotypes using 3 methods in parallel: Multiplex-PCR, the Nested PCR followed by Sanger sequencing, and the Next_Gen Sequencing (NGS) with two assays (NGS-A1, NGS-A2). The study was approved by the Brazilian National IRB (CONEP protocol 16,800). The prevalence of HPV by the NGS assays was higher than that using the Multiplex-PCR (64.2% vs. 45.2%, respectively; P = 0.001) and the Nested-PCR (64.2% vs. 49.5 %, respectively; P = 0.003). NGS also showed better performance in detecting high-risk HPV (HR-HPV) and HPV16. There was a weak interobservers agreement between the results of Multiplex-PCR and Nested-PCR in relation to NGS for the diagnosis of HPV infection, and a moderate correlation for HR-HPV detection. Both NGS assays showed a strong correlation for detection of HPVs (k = 0.86), HR-HPVs (k = 0.91), HPV16 (k = 0.92) and HPV18 (k = 0.91). NGS is more sensitive than the traditional Sanger sequencing and the Multiplex PCR to genotype HPVs, with promising ability to detect multiple infections, and may have the potential to establish an alternative method for the diagnosis and genotyping of HPV. J. Med. Virol. 88:888-894, 2016. © 2015 Wiley Periodicals, Inc. PMID:26496186

  19. Biological treatment of anaerobically digested palm oil mill effluent (POME) using a Lab-Scale Sequencing Batch Reactor (SBR).

    PubMed

    Chan, Yi Jing; Chong, Mei Fong; Law, Chung Lim

    2010-08-01

    The production of highly polluting palm oil mill effluent (POME) has resulted in serious environmental hazards. While anaerobic digestion is widely accepted as an effective method for the treatment of POME, anaerobic treatment of POME alone has difficulty meeting discharge limits due to the high organic strength of POME. Hence, subsequent post-treatment following aerobic treatment is vital to meet the discharge limits. The objective of the present study is to investigate the aerobic treatment of anaerobically digested POME by using a sequencing batch reactor (SBR). The SBR performance was assessed by measuring Chemical Oxygen Demand (COD), Biochemical Oxygen Demand (BOD) and Total Suspended Solids (TSS) removal as well as Sludge Volume Index (SVI). The operating pH and dissolved oxygen concentrations were found to be 8.25-9.14 and 1.5-6.4 mg/L, respectively, throughout the experiment. The experimental results demonstrate that MLVSS, OLR and sludge loading rate (SLR) play a significant role in the organic removal efficiency of SBR systems and therefore, further investigation on these parameters was conducted to attain optimum SBR performance. Maximum COD (95-96%), BOD (97-98%) and TSS (98-99%) removal efficiencies were achieved at optimum OLR, SLR and MLVSS concentration ranges of 1.8-4.2 kg COD/m(3)day, 2.5-4.6 kg TSS/m(3)day and 22,000-25,000 mg/L, respectively. The effluent quality remained stable and complied with the discharge limit. At the same time, the sludge showed good settling properties with average SVI of 65. It is envisaged that the SBR process could complement the anaerobic treatment to produce final treated effluent which meets the discharge limit. PMID:20430515

  20. Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has show...

  1. Improved efficiency in amplification of Escherichia coli o-antigen gene clusters using genome-wide sequence comparison

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: In many bacteria including E. coli, genes encoding O-antigens are clustered in the chromosome, with a 39-bp JUMPstart sequence and gnd gene located upstream and downstream of the cluster, respectively. For determining the DNA sequence of the E. coli O-antigen gene cluster, one set of P...

  2. Comparison between in-phase and opposed-phase T1-weighted breath-hold FLASH sequences for hepatic imaging

    SciTech Connect

    Rofsky, N.M.; Weinreb, J.C.; Ambrosino, M.M.; Safir, J.; Krinsky, G.

    1996-03-01

    Our goal was to compare in-phase (IP) and opposed-phase (OP) sequences for GRE breath-hold hepatic imaging. Non-contrast-enhanced IP and OP GRE breath-hold images were obtained in 104 consecutive patients referred for abdominal MRI at 1.0 T. For both sequences, the TR, FA, matrix, FOV, slice thickness, interslice gap, and measurements were kept constant. Images were compared quantitatively [liver/spleen and liver/lesion signal difference/noise ratio, (SD/N)] and qualitatively (artifacts, lesion detection and conspicuity, and intrahepatic anatomy). There was no statistically significant difference when comparing IP and OP sequences for liver/spleen and liver/lesion SD/N or for the qualitative parameters. In patients with fatty infiltration, the OP sequences yielded substantially lower values for liver/spleen and liver/lesion SD/N (0.9 and - 1.2, respectively) than the IP sequences (20 and 17, respectively). Furthermore, in several cases with fatty infiltration, many more lesions were identified using IP images. The use of IP and OP GRE sequences provides complementary diagnostic information. Focal liver lesions may be obscured in the setting of fatty infiltration if only OP sequences are employed. A complete assessment of the liver with MR should include both IP and OP imaging. 11 refs., 3 figs., 1 tab.

  3. An optimization approach and its application to compare DNA sequences

    NASA Astrophysics Data System (ADS)

    Liu, Liwei; Li, Chao; Bai, Fenglan; Zhao, Qi; Wang, Ying

    2015-02-01

    Studying the evolutionary relationship between biological sequences has become one of the main tasks in bioinformatics research by means of comparing and analyzing the gene sequence. Many valid methods have been applied to the DNA sequence alignment. In this paper, we propose a novel comparing method based on the Lempel-Ziv (LZ) complexity to compare biological sequences. Moreover, we introduce a new distance measure and make use of the corresponding similarity matrix to construct phylogenic tree without multiple sequence alignment. Further, we construct phylogenic tree for 24 species of Eutherian mammals and 48 countries of Hepatitis E virus (HEV) by an optimization approach. The results indicate that this new method improves the efficiency of sequence comparison and successfully construct phylogenies.

  4. Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India.

    PubMed

    Majumder, S; Baranwal, V K

    2011-06-01

    Shallot virus X (ShVX), a type species in the genus Allexivirus of the family Alfaflexiviridae has been associated with shallot plants in India and other shallot growing countries like Russia, Germany, Netherland, and New Zealand. Coat protein (CP) and nucleic acid binding protein (NB) region of the virus was obtained by reverse transcriptase polymerase chain reaction from scales leaves of shallot bulbs. The partial cDNA contained two open reading frames encoding proteins of molecular weights of 28.66 and 14.18 kDa belonging to Flexi_CP super-family and viral NB super-family, respectively. The percent identity and phylogenetic analysis of amino acid sequences of CP and NB region of the virus associated with shallot indicated that it was a distinct isolate of ShVX. PMID:23637504

  5. Nucleotide sequence and genomic organization of Aleutian mink disease parvovirus (ADV): sequence comparisons between a nonpathogenic and a pathogenic strain of ADV.

    PubMed Central

    Bloom, M E; Alexandersen, S; Perryman, S; Lechner, D; Wolfinbarger, J B

    1988-01-01

    A DNA sequence of 4,592 nucleotides (nt) was derived for the nonpathogenic ADV-G strain of Aleutian mink disease parvovirus (ADV). The 3'(left) end of the virion strand contained a 117-nt palindrome that could assume a Y-shaped configuration similar to, but less stable than, that of other parvoviruses. The sequence obtained for the 5' end was incomplete and did not contain the 5' (right) hairpin structure but ended just after a 25-nt A + T-rich direct repeat. Features of ADV genomic organization are (i) major left (622 amino acids) and right (702 amino acids) open reading frames (ORFs) in different translational frames of the plus-sense strand, (ii) two short mid-ORFs, (iii) eight potential promoter motifs (TATA boxes), including ones at 3 and 36 map units, and (iv) six potential polyadenylation sites, including three clustered near the termination of the right ORF. Although the overall homology to other parvoviruses is less than 50%, there are short conserved amino acid regions in both major ORFs. However, two regions in the right ORF allegedly conserved among the parvoviruses were not present in ADV. At the DNA level, ADV-G is 97.5% related to the pathogenic ADV-Utah 1. A total of 22 amino acid changes were found in the right ORF; changes were found in both hydrophilic and hydrophobic regions and generally did not affect the theoretical hydropathy. However, there is a short heterogeneous region at 64 to 65 map units in which 8 out of 11 residues have diverged; this hypervariable segment may be analogous to short amino acid regions in other parvoviruses that determine host range and pathogenicity. These findings suggested that this region may harbor some of the determinants responsible for the differences in pathogenicity of ADV-G and ADV-Utah 1. PMID:2839709

  6. Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing.

    PubMed

    Becker, Laura; Steglich, Matthias; Fuchs, Stephan; Werner, Guido; Nübel, Ulrich

    2016-01-01

    We compared commercial kits for extraction of genomic DNA from the Gram-negative bacterium Klebsiella pneumoniae for subsequent Miseq sequencing. Purification of DNA was based on matrix binding (silica or anion exchange resin) or differential precipitation (salting out), respectively. The choice of extraction kit had little effect on sequencing quality and coverage across drastically different replicons, except for an apparent depletion of small plasmids (<5 kb) during precipitation-based extractions. Sequencing coverage provided copy-number estimates for small plasmids that were consistently higher than those from quantitative real-time PCR. PMID:27312200

  7. Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing

    PubMed Central

    Becker, Laura; Steglich, Matthias; Fuchs, Stephan; Werner, Guido; Nübel, Ulrich

    2016-01-01

    We compared commercial kits for extraction of genomic DNA from the Gram-negative bacterium Klebsiella pneumoniae for subsequent Miseq sequencing. Purification of DNA was based on matrix binding (silica or anion exchange resin) or differential precipitation (salting out), respectively. The choice of extraction kit had little effect on sequencing quality and coverage across drastically different replicons, except for an apparent depletion of small plasmids (<5 kb) during precipitation-based extractions. Sequencing coverage provided copy-number estimates for small plasmids that were consistently higher than those from quantitative real-time PCR. PMID:27312200

  8. Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples

    PubMed Central

    Kwon, Mi Jeong; Kim, Ryong Nam; Kim, Yu Jin; Song, Ji-Young; Jung, Kyung Soo; Shin, Young Kee

    2015-01-01

    Formalin fixing with paraffin embedding (FFPE) has been a standard sample preparation method for decades, and archival FFPE samples are still very useful resources. Nonetheless, the use of FFPE samples in cancer genome analysis using next-generation sequencing, which is a powerful technique for the identification of genomic alterations at the nucleotide level, has been challenging due to poor DNA quality and artificial sequence alterations. In this study, we performed whole-exome sequencing of matched frozen samples and FFPE samples of tissues from 4 cancer patients and compared the next-generation sequencing data obtained from these samples. The major differences between data obtained from the 2 types of sample were the shorter insert size and artificial base alterations in the FFPE samples. A high proportion of short inserts in the FFPE samples resulted in overlapping paired reads, which could lead to overestimation of certain variants; >20% of the inserts in the FFPE samples were double sequenced. A large number of soft clipped reads was found in the sequencing data of the FFPE samples, and about 30% of total bases were soft clipped. The artificial base alterations, C>T and G>A, were observed in FFPE samples only, and the alteration rate ranged from 200 to 1,200 per 1M bases when sequencing errors were removed. Although high-confidence mutation calls in the FFPE samples were compatible to that in the frozen samples, caution should be exercised in terms of the artifacts, especially for low-confidence calls. Despite the clearly observed artifacts, archival FFPE samples can be a good resource for discovery or validation of biomarkers in cancer research based on whole-exome sequencing. PMID:26641479

  9. Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.

    PubMed

    Oh, Ensel; Choi, Yoon-La; Kwon, Mi Jeong; Kim, Ryong Nam; Kim, Yu Jin; Song, Ji-Young; Jung, Kyung Soo; Shin, Young Kee

    2015-01-01

    Formalin fixing with paraffin embedding (FFPE) has been a standard sample preparation method for decades, and archival FFPE samples are still very useful resources. Nonetheless, the use of FFPE samples in cancer genome analysis using next-generation sequencing, which is a powerful technique for the identification of genomic alterations at the nucleotide level, has been challenging due to poor DNA quality and artificial sequence alterations. In this study, we performed whole-exome sequencing of matched frozen samples and FFPE samples of tissues from 4 cancer patients and compared the next-generation sequencing data obtained from these samples. The major differences between data obtained from the 2 types of sample were the shorter insert size and artificial base alterations in the FFPE samples. A high proportion of short inserts in the FFPE samples resulted in overlapping paired reads, which could lead to overestimation of certain variants; >20% of the inserts in the FFPE samples were double sequenced. A large number of soft clipped reads was found in the sequencing data of the FFPE samples, and about 30% of total bases were soft clipped. The artificial base alterations, C>T and G>A, were observed in FFPE samples only, and the alteration rate ranged from 200 to 1,200 per 1M bases when sequencing errors were removed. Although high-confidence mutation calls in the FFPE samples were compatible to that in the frozen samples, caution should be exercised in terms of the artifacts, especially for low-confidence calls. Despite the clearly observed artifacts, archival FFPE samples can be a good resource for discovery or validation of biomarkers in cancer research based on whole-exome sequencing. PMID:26641479

  10. Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting

    PubMed Central

    2013-01-01

    Background Targeted capture, combined with massively-parallel sequencing, is a powerful technique that allows investigation of specific portions of the genome for less cost than whole genome sequencing. Several methods have been developed, and improvements have resulted in commercial products targeting the human or mouse exonic regions (the exome). In some cases it is desirable to custom-target other regions of the genome, either to reduce the amount of sequence that is targeted or to capture regions that are not targeted by commercial kits. It is important to understand the advantages, limitations, and complexity of a given capture method before embarking on a targeted sequencing experiment. Results We compared two custom targeted capture methods suitable for single chromosome analysis: Solution Hybrid Selection (SHS) and Flow Sorting (FS) of single chromosomes. Both methods can capture targeted material and result in high percentages of genotype identifications across these regions: 59-92% for SHS and 70-79% for FS. FS is amenable to current structural variation detection methods, and variants were detected. Structural variation was also assessed for SHS samples with paired end sequencing, resulting in variant identification. Conclusions While both methods can effectively target genomic regions for genotype determination, several considerations make each method appropriate in different circumstances. SHS is well suited for experiments targeting smaller regions in a larger number of samples. FS is well suited when regions of interest cover large regions of a single chromosome. Although whole genome sequencing is becoming less expensive, the sequencing, data storage, and analysis costs make targeted sequencing using SHS or FS a compelling option. PMID:23586822

  11. Towards a Next-Generation Sequencing Diagnostic Service for Tumour Genotyping: A Comparison of Panels and Platforms.

    PubMed

    Burghel, George J; Hurst, Carolyn D; Watson, Christopher M; Chambers, Phillip A; Dickinson, Helen; Roberts, Paul; Knowles, Margaret A

    2015-01-01

    Detection of clinically actionable mutations in diagnostic tumour specimens aids in the selection of targeted therapeutics. With an ever increasing number of clinically significant mutations identified, tumour genetic diagnostics is moving from single to multigene analysis. As it is still not feasible for routine diagnostic laboratories to perform sequencing of the entire cancer genome, our approach was to undertake targeted mutation detection. To optimise our diagnostic workflow, we evaluated three target enrichment strategies using two next-generation sequencing (NGS) platforms (Illumina MiSeq and Ion PGM). The target enrichment strategies were Fluidigm Access Array custom amplicon panel including 13 genes (MiSeq sequencing), the Oxford Gene Technologies (OGT) SureSeq Solid Tumour hybridisation panel including 60 genes (MiSeq sequencing), and an Ion AmpliSeq Cancer Hotspot Panel including 50 genes (Ion PGM sequencing). DNA extracted from formalin-fixed paraffin-embedded (FFPE) blocks of eight previously characterised cancer cell lines was tested using the three panels. Matching genomic DNA from fresh cultures of these cell lines was also tested using the custom Fluidigm panel and the OGT SureSeq Solid Tumour panel. Each panel allowed mutation detection of core cancer genes including KRAS, BRAF, and EGFR. Our results indicate that the panels enable accurate variant detection despite sequencing from FFPE DNA. PMID:26351634