WorldWideScience

Sample records for close sequence comparisons

  1. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species

    Science.gov (United States)

    Rey, Michael W; Ramaiya, Preethi; Nelson, Beth A; Brody-Karpin, Shari D; Zaretsky, Elizabeth J; Tang, Maria; de Leon, Alfredo Lopez; Xiang, Henry; Gusti, Veronica; Clausen, Ib Groth; Olsen, Peter B; Rasmussen, Michael D; Andersen, Jens T; Jørgensen, Per L; Larsen, Thomas S; Sorokin, Alexei; Bolotin, Alexander; Lapidus, Alla; Galleron, Nathalie; Ehrlich, S Dusko; Berka, Randy M

    2004-01-01

    Background Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. Results We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs. Conclusions Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae. PMID:15461803

  4. eShadow: A tool for comparing closely related sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ovcharenko, Ivan; Boffelli, Dario; Loots, Gabriela G.

    2004-01-15

    Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing, has been pioneered for predicting functional elements in the human genome through the analysis of multiple primate sequence alignments. We have expanded this theoretical approach to create a computational tool, eShadow, for the identification of elements under selective pressure in multiple sequence alignments of closely related genomes, such as in comparisons of human to primate or mouse to rat DNA. This tool integrates two different statistical methods and allows for the dynamic visualization of the resulting conservation profile. eShadow also includes a versatile optimization module capable of training the underlying Hidden Markov Model to differentially predict functional sequences. This module grants the tool high flexibility in the analysis of multiple sequence alignments and in comparing sequences with different divergence rates. Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements. The eShadow tool is publicly available at http://eshadow.dcode.org/

  5. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  6. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  7. Close sequence identity between ribosomal DNA episomes of the ...

    Indian Academy of Sciences (India)

    Unknown

    The restriction map of the E. dispar rDNA circle showed close simi- larity to EhR1 .... for 30 cycles in a DNA Thermal cycler (MJ Research,. USA). 3. .... by asterisk. The gaps show the variation between E. dispar and E. histolytica sequences.

  8. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    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.

  9. Dynamic programming algorithms for biological sequence comparison.

    Science.gov (United States)

    Pearson, W R; Miller, W

    1992-01-01

    Efficient dynamic programming algorithms are available for a broad class of protein and DNA sequence comparison problems. These algorithms require computer time proportional to the product of the lengths of the two sequences being compared [O(N2)] but require memory space proportional only to the sum of these lengths [O(N)]. Although the requirement for O(N2) time limits use of the algorithms to the largest computers when searching protein and DNA sequence databases, many other applications of these algorithms, such as calculation of distances for evolutionary trees and comparison of a new sequence to a library of sequence profiles, are well within the capabilities of desktop computers. In particular, the results of library searches with rapid searching programs, such as FASTA or BLAST, should be confirmed by performing a rigorous optimal alignment. Whereas rapid methods do not overlook significant sequence similarities, FASTA limits the number of gaps that can be inserted into an alignment, so that a rigorous alignment may extend the alignment substantially in some cases. BLAST does not allow gaps in the local regions that it reports; a calculation that allows gaps is very likely to extend the alignment substantially. Although a Monte Carlo evaluation of the statistical significance of a similarity score with a rigorous algorithm is much slower than the heuristic approach used by the RDF2 program, the dynamic programming approach should take less than 1 hr on a 386-based PC or desktop Unix workstation. For descriptive purposes, we have limited our discussion to methods for calculating similarity scores and distances that use gap penalties of the form g = rk. Nevertheless, programs for the more general case (g = q+rk) are readily available. Versions of these programs that run either on Unix workstations, IBM-PC class computers, or the Macintosh can be obtained from either of the authors.

  10. Comparison of energy expenditure and closed-loop performance of thermal and reactive distillation sequences coupled for biodiesel production; Comparacion de gasto energetico y desempeno a lazo cerrado de secuencias de destilacion reactiva y termicamente acopladas para produccion de biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Cornejo-Jacob, J.L [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico); Vazquez-Ojeda, M; Segovia-Hernandez, J.G; Hernandez, S [Universidad de Guanajuato, Guanajuato, Guanajuato (Mexico); Maya-Yescas, R. [Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacan (Mexico)]. E-mail: rmayay@umich.mx

    2013-03-15

    Biodiesel is the common name for fatty acid methyl esters, obtained by esterification (basic catalysis) or trans-esterification (acid catalysis) of vegetable or animal oils with alcohols, and used as liquid fuel. Production involves the reaction, under mild conditions, between the oil and, typically, excess of methanol. Traditional production of biodiesel exhibits some handicaps, such as the shift of equilibrium to fatty acids by using excess of alcohol that must be separated and recycled. As alternative, it is possible to integrate reaction/separation operations into a single intensified unit, a reactive distillation column, followed by a second separation unit. These configurations exhibit several advantages such as shifting equilibrium in the reactive region and, because of the thermal integration with the second unit, energy savings during products separation. In order to design these production sequences taking advantage of steady state knowledge (energy savings) and considering dynamic performance, this work performs a controllability analysis for six possible configurations; open-loop control properties, evaluated by single value decomposition, are probed by implementing PI controllers to the system. The reactive distillation column coupled to a stripper, without reboilers, shows to be the best option in terms of closed-loop performance and energy savings. [Spanish] Biodiesel es el nombre comun dado a metil esteres de acidos grasos obtenidos por esterificacion (catalisis basica) o trans-esterificacion (catalisis acida) de aceites animales o vegetales con alcoholes, y usados como combustibles liquidos. Su produccion involucra la reaccion entre el aceite y, tipicamente, exceso de metanol a condiciones moderadas. La produccion tradicional de biodiesel exhibe algunas desventajas como el desplazamiento del equilibrio hacia acidos grasos debido al exceso de alcohol, que debe ser separado y reciclado. Alternativamente, es posible integrar las operaciones reaccion

  11. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

  12. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    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.

  13. Closed Genome Sequence of Phytopathogen Biocontrol Agent Bacillus velezensis Strain AGVL-005, Isolated from Soybean.

    Science.gov (United States)

    Pylro, Victor Satler; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini; Morais, Daniel Kumazawa; Varani, Alessandro de Mello; Andreote, Cristiane Cipolla Fasanella; Bernardo, Eduardo Roberto de Almeida; Zucchi, Tiago

    2018-02-15

    We report here the closed and near-complete genome sequence and annotation of Bacillus velezensis strain AGVL-005, a bacterium isolated from soybean seeds in Brazil and used for phytopathogen biocontrol. Copyright © 2018 Pylro et al.

  14. Comparison of 61 Sequenced Escherichia coli Genomes

    DEFF Research Database (Denmark)

    Lukjancenko, Oksana; Wassenaar, T. M.; Ussery, David

    2010-01-01

    Escherichia coli is an important component of the biosphere and is an ideal model for studies of processes involved in bacterial genome evolution. Sixty-one publically available E. coli and Shigella spp. sequenced genomes are compared, using basic methods to produce phylogenetic and proteomics...

  15. Extensive sequence divergence among bovine respiratory syncytial viruses isolated during recurrent outbreaks in closed herds

    DEFF Research Database (Denmark)

    Larsen, Lars Erik; Tjørnehøj, Kirsten; Viuff, B.

    2000-01-01

    and veal calf production units) in different years and from all confirmed outbreaks in Denmark within a short period. The results showed that identical viruses were isolated within a herd during outbreaks and that viruses from recurrent infections varied by up to 11% in sequence even in closed herds......The nucleotides coding for the extracellular part of the G glycoprotein and the full SH protein of bovine respiratory syncytial virus (BRSV) were sequenced from viruses isolated from numerous outbreaks of BRSV infection. The isolates included viruses isolated from the same herd (closed dairy farms....... It is possible that a quasispecies variant swarm of BRSV persisted in some of the calves in each herd and that a new and different highly fit virus type (master and consensus sequence) became dominant and spread from a single animal in connection with each new outbreak. Based on the high level of diversity...

  16. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

    Directory of Open Access Journals (Sweden)

    Messeguer Xavier

    2006-10-01

    Full Text Available Abstract Background Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

  17. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

    International Nuclear Information System (INIS)

    Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

    2002-01-01

    The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

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

    Science.gov (United States)

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

    1992-05-15

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

  20. Efficiency comparison of 3 kinds of arterial puncture closing devices

    International Nuclear Information System (INIS)

    Feng Xiaodi; Jin Xian; Chen Yueguang; Xiao Hongbing; Yu Qiang; Chen Chengjun; Zhang Dadong

    2007-01-01

    Objective: To evaluate the efficiencies of arterial puncture closing devices (APCDs) including Angioseal, Perclose and Boomerang in patients undergone coronary angiography or percutaneous vascular interventions. Methods: 1497 patients underwent cardiac catheterization procedures were divided into manual compression group(639 cases) and APCDs closure group (576 cases with Angioseal, 151 cases Perclose and 11.3 cases of Boomerang). The times of maneuver, hemorrhage complication and other rare complications were assessed, recorded and compared. Results: The times for maneuver of standard manual compression group, Angioseal group, Perclose group and Boomerang group were (21.4±2.7) h, (3.5±2.3) h, (3.7± 2.6) h and (3.9±2.8) h respectively. The APCDs could obviously reduce bed rest time in comparing to that of manual compression. The rates of failure of the operations were 2.7%, 1.4%, 8.6% and 3.5% (P =0.006, P<0.001); and the rates of hemorrhage were 9.2%, 5.8%, 12.6% and 8.0% respectively for each of the four mentioned groups (P=0.005). Except the failure operations, the incidence of hemorrhage complications among the groups showed no significant differences. Conclusion: Application of APCDs to close the puncture site can significantly reduce the bed rest time, but not the incidence of hemorrhage complications. (authors)

  1. The phylogeny of Mediterranean tortoises and their close relativesbased on complete mitochondrial genome sequences from museumspecimens

    Energy Technology Data Exchange (ETDEWEB)

    Parham, James F.; Macey, J. Robert; Papenfuss, Theodore J.; Feldman, Chris R.; Turkozan, Oguz; Polymeni, Rosa; Boore, Jeffrey

    2005-04-29

    As part of an ongoing project to generate a mitochondrial database for terrestrial tortoises based on museum specimens, the complete mitochondrial genome sequences of 10 species and a {approx}14 kb sequence from an eleventh species are reported. The sampling of the present study emphasizes Mediterranean tortoises (genus Testudo and their close relatives). Our new sequences are aligned, along with those of two testudinoid turtles from GenBank, Chrysemys picta and Mauremys reevesii, yielding an alignment of 14,858 positions, of which 3,238 are parsimony informative. We develop a phylogenetic taxonomy for Testudo and related species based on well-supported, diagnosable clades. Several well-supported nodes are recovered, including the monophyly of a restricted Testudo, T. kleinmanni + T. marginata (the Chersus clade), and the placement of the enigmatic African pancake tortoise (Malacochersustornieri) within the predominantly Palearctic greater Testudo group (Testudona tax. nov.). Despite the large amount of sequence reported, there is low statistical support for some nodes within Testudona and Sowe do not propose names for those groups. A preliminary and conservative estimation of divergence times implies a late Miocene diversification for the testudonan clade (6-12 million years ago), matching their first appearance in the fossil record. The multi-continental distribution of testudonan turtles can be explained by the establishment of permanent connections between Europe, Africa, and Asia at this time. The arrival of testudonan turtles to Africa occurred after one or more initial tortoise invasions gave rise to the diverse (>25 species) 'Geochelone complex.'Two unusual genomic features are reported for the mtDNA of one tortoise, M. tornieri: (1) nad4 has a shift of reading frame that we suggest is resolved by translational frameshifting of the mRNA on the ribosome during protein synthesis and (2) there are two copies of the control region and trnF, with the

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

    Science.gov (United States)

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

    2016-04-06

    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.

  3. Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi.

    Directory of Open Access Journals (Sweden)

    Judith R Glynn

    Full Text Available The proportion of tuberculosis attributable to transmission from close contacts is not well known. Comparison of the genome of strains from index patients and prior contacts allows transmission to be confirmed or excluded.In Karonga District, Malawi, all tuberculosis patients are asked about prior contact with others with tuberculosis. All available strains from culture-positive patients were sequenced. Up to 10 single nucleotide polymorphisms between index patients and their prior contacts were allowed for confirmation, and ≥ 100 for exclusion. The population attributable fraction was estimated from the proportion of confirmed transmissions and the proportion of patients with contacts.From 1997-2010 there were 1907 new culture-confirmed tuberculosis patients, of whom 32% reported at least one family contact and an additional 11% had at least one other contact; 60% of contacts had smear-positive disease. Among case-contact pairs with sequences available, transmission was confirmed from 38% (62/163 smear-positive prior contacts and 0/17 smear-negative prior contacts. Confirmed transmission was more common in those related to the prior contact (42.4%, 56/132 than in non-relatives (19.4%, 6/31, p = 0.02, and in those with more intense contact, to younger index cases, and in more recent years. The proportion of tuberculosis attributable to known contacts was estimated to be 9.4% overall.In this population known contacts only explained a small proportion of tuberculosis cases. Even those with a prior family contact with smear positive tuberculosis were more likely to have acquired their infection elsewhere.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

  5. Does the sequence of data collection influence participants' responses to closed and open-ended questions? A methodological study.

    Science.gov (United States)

    Covell, Christine L; Sidani, Souraya; Ritchie, Judith A

    2012-06-01

    The sequence used for collecting quantitative and qualitative data in concurrent mixed-methods research may influence participants' responses. Empirical evidence is needed to determine if the order of data collection in concurrent mixed methods research biases participants' responses to closed and open-ended questions. To examine the influence of the quantitative-qualitative sequence on responses to closed and open-ended questions when assessing the same variables or aspects of a phenomenon simultaneously within the same study phase. A descriptive cross-sectional, concurrent mixed-methods design was used to collect quantitative (survey) and qualitative (interview) data. The setting was a large multi-site health care centre in Canada. A convenience sample of 50 registered nurses was selected and participated in the study. Participants were randomly assigned to one of two sequences for data collection, quantitative-qualitative or qualitative-quantitative. Independent t-tests were performed to compare the two groups' responses to the survey items. Directed content analysis was used to compare the participants' responses to the interview questions. The sequence of data collection did not greatly affect the participants' responses to the closed-ended questions (survey items) or the open-ended questions (interview questions). The sequencing of data collection, when using both survey and semi-structured interviews, may not bias participants' responses to closed or open-ended questions. Additional research is required to confirm these findings. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... and antisense primers, a single band of 573 base pairs .... Amino acid sequence alignment of Cluster I and Cluster II of phylogenetic tree. First ten sequences ... sequence weighting, postion-spiecific gap penalties and weight.

  7. The Pathogenomic Sequence Analysis of B. cereus and B.thuringiensis Isolates Closely Related to Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Han, Cliff S.; Xie, Gary; Challacombe, Jean F.; Altherr, MichaelR.; Smriti, B.; Bruce, David; Campbell, Connie S.; Campbell, Mary L.; Chen, Jin; Chertkov, Olga; Cleland, Cathy; Dimitrijevic-Bussod, M.; Doggett, Norman A.; Fawcett, John J.; Glavina, Tijana; Goodwin, Lynne A.; Hill, Karen K.; Hitchcock, Penny; Jackson, Paul J.; Keim, Paul; Kewalramani, Avinash Ramesh; Longmire, Jon; Lucas, Susan; Malfatti,Stephanie; McMurry, Kim; Meincke, Linda J.; Misra, Monica; Moseman,Bernice L.; Mundt, Mark; Munk, A. Christine; Okinaka, Richard T.; Parson-Quintana, B.; Reilly, Lee P.; Richardson, Paul; Robinson, DonnaL.; Rubin, Eddy; Saunders, Elizabeth; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Ticknor, Lawrence O.; Wills, Patti L.; Gilna, Payl; Brettin, Thomas S.

    2005-08-18

    The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B.cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including Banthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.

  8. Improving pairwise comparison of protein sequences with domain co-occurrence

    Science.gov (United States)

    Gascuel, Olivier

    2018-01-01

    Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence PMID:29293498

  9. Comparison of next generation sequencing technologies for transcriptome characterization

    Directory of Open Access Journals (Sweden)

    Soltis Douglas E

    2009-08-01

    Full Text Available Abstract Background We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19. We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica and the magnoliid avocado (Persea americana using a variety of methods for cDNA synthesis. Results The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB, 119,518 (88.7% mapped exactly to known exons, while 1,117 (0.8% mapped to introns, 11,524 (8.6% spanned annotated intron/exon boundaries, and 3,066 (2.3% extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl, an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. Conclusion NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance

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

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

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

  11. Substrate-driven mapping of the degradome by comparison of sequence logos.

    Directory of Open Access Journals (Sweden)

    Julian E Fuchs

    Full Text Available 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.

  12. Small-target leak detection for a closed vessel via infrared image sequences

    Science.gov (United States)

    Zhao, Ling; Yang, Hongjiu

    2017-03-01

    This paper focus on a leak diagnosis and localization method based on infrared image sequences. Some problems on high probability of false warning and negative affect for marginal information are solved by leak detection. An experimental model is established for leak diagnosis and localization on infrared image sequences. The differential background prediction is presented to eliminate the negative affect of marginal information on test vessel based on a kernel regression method. A pipeline filter based on layering voting is designed to reduce probability of leak point false warning. A synthesize leak diagnosis and localization algorithm is proposed based on infrared image sequences. The effectiveness and potential are shown for developed techniques through experimental results.

  13. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  14. The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox.

    Science.gov (United States)

    Gubser, Caroline; Smith, Geoffrey L

    2002-04-01

    Camelpox virus (CMPV) and variola virus (VAR) are orthopoxviruses (OPVs) that share several biological features and cause high mortality and morbidity in their single host species. The sequence of a virulent CMPV strain was determined; it is 202182 bp long, with inverted terminal repeats (ITRs) of 6045 bp and has 206 predicted open reading frames (ORFs). As for other poxviruses, the genes are tightly packed with little non-coding sequence. Most genes within 25 kb of each terminus are transcribed outwards towards the terminus, whereas genes within the centre of the genome are transcribed from either DNA strand. The central region of the genome contains genes that are highly conserved in other OPVs and 87 of these are conserved in all sequenced chordopoxviruses. In contrast, genes towards either terminus are more variable and encode proteins involved in host range, virulence or immunomodulation. In some cases, these are broken versions of genes found in other OPVs. The relationship of CMPV to other OPVs was analysed by comparisons of DNA and predicted protein sequences, repeats within the ITRs and arrangement of ORFs within the terminal regions. Each comparison gave the same conclusion: CMPV is the closest known virus to variola virus, the cause of smallpox.

  15. Comparison of methods for genomic localization of gene trap sequences

    Directory of Open Access Journals (Sweden)

    Ferrin Thomas E

    2006-09-01

    Full Text Available Abstract Background Gene knockouts in a model organism such as mouse provide a valuable resource for the study of basic biology and human disease. Determining which gene has been inactivated by an untargeted gene trapping event poses a challenging annotation problem because gene trap sequence tags, which represent sequence near the vector insertion site of a trapped gene, are typically short and often contain unresolved residues. To understand better the localization of these sequences on the mouse genome, we compared stand-alone versions of the alignment programs BLAT, SSAHA, and MegaBLAST. A set of 3,369 sequence tags was aligned to build 34 of the mouse genome using default parameters for each algorithm. Known genome coordinates for the cognate set of full-length genes (1,659 sequences were used to evaluate localization results. Results In general, all three programs performed well in terms of localizing sequences to a general region of the genome, with only relatively subtle errors identified for a small proportion of the sequence tags. However, large differences in performance were noted with regard to correctly identifying exon boundaries. BLAT correctly identified the vast majority of exon boundaries, while SSAHA and MegaBLAST missed the majority of exon boundaries. SSAHA consistently reported the fewest false positives and is the fastest algorithm. MegaBLAST was comparable to BLAT in speed, but was the most susceptible to localizing sequence tags incorrectly to pseudogenes. Conclusion The differences in performance for sequence tags and full-length reference sequences were surprisingly small. Characteristic variations in localization results for each program were noted that affect the localization of sequence at exon boundaries, in particular.

  16. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution

    OpenAIRE

    Filée, Jonathan

    2015-01-01

    Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no tr...

  17. Complete cDNA sequence of human complement C1s and close physical linkage of the homologous genes C1s and C1r

    International Nuclear Information System (INIS)

    Tosi, M.; Duponchel, C.; Meo, T.; Julier, C.

    1987-01-01

    Overlapping molecular clones encoding the complement subcomponent C1s were isolated from a human liver cDNA library. The nucleotide sequence reconstructed from these clones spans about 85% of the length of the liver C1s messenger RNAs, which occur in three distinct size classes around 3 kilobases in length. Comparisons with the sequence of C1r, the other enzymatic subcomponent of C1, reveal 40% amino acid identity and conservation of all the cysteine residues. Beside the serine protease domain, the following sequence motifs, previously described in C1r, were also found in C1s: (a) two repeats of the type found in the Ba fragment of complement factor B and in several other complement but also noncomplement proteins, (b) a cysteine-rich segment homologous to the repeats of epidermal growth factor precursor, and (c) a duplicated segment found only in C1r and C1s. Differences in each of these structural motifs provide significant clues for the interpretation of the functional divergence of these interacting serine protease zymogens. Hybridizations of C1r and C1s probes to restriction endonuclease fragments of genomic DNA demonstrate close physical linkage of the corresponding genes. The implications of this finding are discussed with respect to the evolution of C1r and C1s after their origin by tandem gene duplication and to the previously observed combined hereditary deficiencies of Clr and Cls

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

    Science.gov (United States)

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

    2012-06-01

    The aim of this study was to investigate the benefits arising from the use of a multiecho sequence for susceptibility-weighted phase imaging using a quantitative comparison with a standard single-echo acquisition. Four healthy adult volunteers were imaged on a clinical 3-T system using a protocol comprising two different three-dimensional susceptibility-weighted gradient-echo sequences: a standard single-echo sequence and a multiecho sequence. Both sequences were repeated twice in order to evaluate the local noise contribution by a subtraction of the two acquisitions. For the multiecho sequence, the phase information from each echo was independently unwrapped, and the background field contribution was removed using either homodyne filtering or the projection onto dipole fields method. The phase information from all echoes was then combined using a weighted linear regression. R2 maps were also calculated from the multiecho acquisitions. The noise standard deviation in the reconstructed phase images was evaluated for six manually segmented regions of interest (frontal white matter, posterior white matter, globus pallidus, putamen, caudate nucleus and lateral ventricle). The use of the multiecho sequence for susceptibility-weighted phase imaging led to a reduction of the noise standard deviation for all subjects and all regions of interest investigated in comparison to the reference single-echo acquisition. On average, the noise reduction ranged from 18.4% for the globus pallidus to 47.9% for the lateral ventricle. In addition, the amount of noise reduction was found to be strongly inversely correlated to the estimated R2 value (R=-0.92). In conclusion, the use of a multiecho sequence is an effective way to decrease the noise contribution in susceptibility-weighted phase images, while preserving both contrast and acquisition time. The proposed approach additionally permits the calculation of R2 maps. Copyright © 2012 Elsevier Inc. All rights reserved.

  19. Triangular fibrocartilage lesions: comparison STIR sequence versus arthroscopy findings

    International Nuclear Information System (INIS)

    Wang Zhi; Meng; Xianghong; Wang Linsen; Suo Yongmei

    2013-01-01

    Objective: To explore the diagnostic value of short TI inversion recovery (STIR) sequence in evaluating triangular fibrocartilage (TFC) lesions, and to compare the findings with the arthroscopy findings. Materials and Methods: Wrist joint MR examination using STIR sequence and arthroscopy were performed in 56 patients with TFC lesions. The parameters of STIR sequence were: TR: 1164 ms, TE: 16 ms, and TI: 90 ms. The sensibility, specificity, positive predictive value, negative predictive value, and accuracy in the diagnosis of TFC lesions with STIR sequence were calculated, using arthroscopy as the standard. Results: (1) STIR manifested 10 patients with normal TFC; 6 with small edema or mucous degeneration in the body portion but not involving joint surface edge; 6 with horizontal avulsion in the body portion, but not involving joint surface edge; 6 with avulsion involving joint surface edge; 11 with perforation in central portion; 6 with avulsion in radial attached end; 5 with avulsion in ulnar attached end; 3 with avulsion in both radial and ulnar attached ends; 3 with irregular shape and thin on the whole TFC. (2) Arthroscopy manifested 21 patients with normal TFC; 8 with avulsion involving joint surface edge; 10 with perforation in central portion; 7 with avulsion in radial attached end; 5 with avulsion in ulnar attached end; 2 with avulsion in both radial and ulnar attached ends; 3 with irregular shape on the whole TFC. Using STIR sequence, the sensibility, specificity, positive predictive value, negative predictive value. and accuracy were 85.7%, 23.8%, 65.2%, 50%, and 62.5%, respectively, in detection of TFC lesions, with arthroscopy as the standard. Conclusion: STIR sequence has high diagnostic value in detection of TFC lesions. (authors)

  20. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.

    2015-04-18

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  1. Revision of Begomovirus taxonomy based on pairwise sequence comparisons

    KAUST Repository

    Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesú s; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé , Elvira; Briddon, Rob W.; Herná ndez-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind

    2015-01-01

    Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.

  2. Comparison of ompP5 sequence-based typing and pulsed-filed gel ...

    African Journals Online (AJOL)

    In this study, comparison of the outer membrane protein P5 gene (ompP5) sequence-based typing with pulsed-field gel electrophoresis (PFGE) for the genotyping of Haemophilus parasuis, the 15 serovar reference strains and 43 isolates were investigated. When comparing the two methods, 31 ompP5 sequence types ...

  3. Guided tooth eruption: Comparison of open and closed eruption techniques in labially impacted maxillary canines

    Directory of Open Access Journals (Sweden)

    S M londhe

    2014-01-01

    Full Text Available Background: After third molars, the maxillary canines are the most commonly impacted permanent teeth and one-third of these are labial impactions. Impacted canines often require orthodontic guidance in the eruption. This study was conducted to assess the posttreatment results of surgically exposed and orthodontically aligned labially impacted maxillary canines comparing two different surgical techniques. Materials and Methods: The study was conducted in two phases, a surgical phase and an orthodontic phase. In surgical phase, events during surgical exposure and recovery of 31 patients with labially impacted maxillary canine were recorded. Patients were managed with open and closed eruption technique. The assessment included comparison of two techniques of surgical exposure, postoperative pain, mobility, vitality, periodontal health, level of impaction, and duration of orthodontic treatment. Results: The postoperative recovery was longer after open eruption than close eruption technique (P = 0.000. Postoperative pain experienced by patients was similar, but regression of pain was faster in closed eruption technique. The mean surgical time for open eruption technique was lesser when compared with closed eruption technique (P = 0.000. The total duration of orthodontic treatment was directly dependent upon the level of impaction, with deeper level of impaction having longer duration of orthodontic treatment. The mobility and vitality of guided canine was similar in both techniques. Conclusion: The closed eruption technique was a longer surgical procedure, but the postoperative pain regression was faster. The duration of orthodontic treatment was longer with deeper level of impaction. The closed eruption surgical techniques provide better periodontal tissues around the guided erupted teeth.

  4. RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

    Science.gov (United States)

    Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

    2011-01-01

    Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

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

    Science.gov (United States)

    Offerman, Kristy; Carulei, Olivia; van der Walt, Anelda Philine; Douglass, Nicola; Williamson, Anna-Lise

    2014-06-12

    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. 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. 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.

  6. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  7. 3D reconstruction software comparison for short sequences

    Science.gov (United States)

    Strupczewski, Adam; Czupryński, BłaŻej

    2014-11-01

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

  8. Evaluation and comparison of closed-loop wash-water system

    International Nuclear Information System (INIS)

    Whitney, P.M.; Greer, C.R.

    1991-01-01

    Effluent from vehicle and equipment cleaning is known to contain a variety of potential pollutants, the most common being hydrocarbons and suspended solids. Proper treatment and discharge of this effluent is a growing concern as environmental awareness increases. In the United States, discharge of this effluent to municipal sewage treatment systems requires a permit from local authorities, discharge to surface waters requires a federal permit and, in most cases, discharge to the ground in prohibited. Furthermore, discharge to ground and surface waters can cause soil or groundwater contamination resulting in property devaluation, adverse impact on human health, fines from regulatory agencies, expensive cleanup and negative publicity. Effluent from vehicle washing typically does not meet the minimum pollutant levels allowed by regulatory agencies for discharge to surface waters or sewage treatment plants. Because of the liability associated with discharge to ground and surface waters and the difficulty in meeting municipal sewer discharge permit requirements, closed-loop wastewater treatment is an attractive alternative to discharge. Evaluation and comparison of systems from each category constitute the basis of this paper. Factors involved in selecting a system and available water-treatment technologies are discussed. The conclusion summarizes the results of the system comparison and makes recommendations for selecting and installing closed-loop water treatment systems for vehicle and equipment cleaning

  9. Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains.

    Science.gov (United States)

    Liao, Weinan; Ren, Jie; Wang, Kun; Wang, Shun; Zeng, Feng; Wang, Ying; Sun, Fengzhu

    2016-11-23

    The comparison between microbial sequencing data is critical to understand the dynamics of microbial communities. The alignment-based tools analyzing metagenomic datasets require reference sequences and read alignments. The available alignment-free dissimilarity approaches model the background sequences with Fixed Order Markov Chain (FOMC) yielding promising results for the comparison of microbial communities. However, in FOMC, the number of parameters grows exponentially with the increase of the order of Markov Chain (MC). Under a fixed high order of MC, the parameters might not be accurately estimated owing to the limitation of sequencing depth. In our study, we investigate an alternative to FOMC to model background sequences with the data-driven Variable Length Markov Chain (VLMC) in metatranscriptomic data. The VLMC originally designed for long sequences was extended to apply to high-throughput sequencing reads and the strategies to estimate the corresponding parameters were developed. The flexible number of parameters in VLMC avoids estimating the vast number of parameters of high-order MC under limited sequencing depth. Different from the manual selection in FOMC, VLMC determines the MC order adaptively. Several beta diversity measures based on VLMC were applied to compare the bacterial RNA-Seq and metatranscriptomic datasets. Experiments show that VLMC outperforms FOMC to model the background sequences in transcriptomic and metatranscriptomic samples. A software pipeline is available at https://d2vlmc.codeplex.com.

  10. The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).

    Science.gov (United States)

    Buti, Matteo; Moretto, Marco; Barghini, Elena; Mascagni, Flavia; Natali, Lucia; Brilli, Matteo; Lomsadze, Alexandre; Sonego, Paolo; Giongo, Lara; Alonge, Michael; Velasco, Riccardo; Varotto, Claudio; Šurbanovski, Nada; Borodovsky, Mark; Ward, Judson A; Engelen, Kristof; Cavallini, Andrea; Cestaro, Alessandro; Sargent, Daniel James

    2018-04-01

    The genus Potentilla is closely related to that of Fragaria, the economically important strawberry genus. Potentilla micrantha is a species that does not develop berries but shares numerous morphological and ecological characteristics with Fragaria vesca. These similarities make P. micrantha an attractive choice for comparative genomics studies with F. vesca. In this study, the P. micrantha genome was sequenced and annotated, and RNA-Seq data from the different developmental stages of flowering and fruiting were used to develop a set of gene predictions. A 327 Mbp sequence and annotation of the genome of P. micrantha, spanning 2674 sequence contigs, with an N50 size of 335,712, estimated to cover 80% of the total genome size of the species was developed. The genus Potentilla has a characteristically larger genome size than Fragaria, but the recovered sequence scaffolds were remarkably collinear at the micro-syntenic level with the genome of F. vesca, its closest sequenced relative. A total of 33,602 genes were predicted, and 95.1% of bench-marking universal single-copy orthologous genes were complete within the presented sequence. Thus, we argue that the majority of the gene-rich regions of the genome have been sequenced. Comparisons of RNA-Seq data from the stages of floral and fruit development revealed genes differentially expressed between P. micrantha and F. vesca.The data presented are a valuable resource for future studies of berry development in Fragaria and the Rosaceae and they also shed light on the evolution of genome size and organization in this family.

  11. Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods

    DEFF Research Database (Denmark)

    Bohlin, Jon; Snipen, Lars; Cloeckaert, Axel

    2010-01-01

    BACKGROUND: Classification of bacteria within the genus Brucella has been difficult due in part to considerable genomic homogeneity between the different species and biovars, in spite of clear differences in phenotypes. Therefore, many different methods have been used to assess Brucella taxonomy....... In the current work, we examine 32 sequenced genomes from genus Brucella representing the six classical species, as well as more recently described species, using bioinformatical methods. Comparisons were made at the level of genomic DNA using oligonucleotide based methods (Markov chain based genomic signatures...... between the oligonucleotide based methods used. Whilst the Markov chain based genomic signatures grouped the different species in genus Brucella according to host preference, the codon and amino acid frequencies based methods reflected small differences between the Brucella species. Only minor differences...

  12. An efficient binomial model-based measure for sequence comparison and its application.

    Science.gov (United States)

    Liu, Xiaoqing; Dai, Qi; Li, Lihua; He, Zerong

    2011-04-01

    Sequence comparison is one of the major tasks in bioinformatics, which could serve as evidence of structural and functional conservation, as well as of evolutionary relations. There are several similarity/dissimilarity measures for sequence comparison, but challenges remains. This paper presented a binomial model-based measure to analyze biological sequences. With help of a random indicator, the occurrence of a word at any position of sequence can be regarded as a random Bernoulli variable, and the distribution of a sum of the word occurrence is well known to be a binomial one. By using a recursive formula, we computed the binomial probability of the word count and proposed a binomial model-based measure based on the relative entropy. The proposed measure was tested by extensive experiments including classification of HEV genotypes and phylogenetic analysis, and further compared with alignment-based and alignment-free measures. The results demonstrate that the proposed measure based on binomial model is more efficient.

  13. Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices

    OpenAIRE

    Munteanu, Cristian Robert

    2014-01-01

    Comparison of Enzymes / Non-Enzymes Proteins Classification Models Based on 3D, Composition, Sequences and Topological Indices, German Conference on Bioinformatics (GCB), Potsdam, Germany (September, 2007)

  14. Image ranking in video sequences using pairwise image comparisons and temporal smoothing

    CSIR Research Space (South Africa)

    Burke, Michael

    2016-12-01

    Full Text Available The ability to predict the importance of an image is highly desirable in computer vision. This work introduces an image ranking scheme suitable for use in video or image sequences. Pairwise image comparisons are used to determine image ‘interest...

  15. Complete nucleotide sequence of a novel Hibiscus-infecting Cilevirus from Florida and its relationship with closely associated Cileviruses

    Science.gov (United States)

    The complete nucleotide sequence of a recently discovered Florida (FL) isolate of Hibiscus infecting Cilevirus (HiCV) was determined by Sanger sequencing. The movement- and coat- protein gene sequences of the HiCV-FL isolate are more divergent than other genes of the previously sequenced HiCV-HA (Ha...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

    Soares, Inês; Goios, Ana; Amorim, António

    2012-01-01

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

  18. Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

    Directory of Open Access Journals (Sweden)

    Inês Soares

    2012-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-06-01

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

  20. AK SCO, FIRST DETECTION OF A HIGHLY DISTURBED ATMOSPHERE IN A PRE-MAIN-SEQUENCE CLOSE BINARY

    International Nuclear Information System (INIS)

    Gomez de Castro, Ana I.

    2009-01-01

    AK Sco is a unique source: a ∼10 Myr old pre-main-sequence (PMS) spectroscopic binary composed of two nearly equal F5 stars that at periastron are separated by barely 11 stellar radii, so the stellar magnetospheres fill the Roche lobe at periastron. The orbit is not yet circularized (e = 0.47) and very strong tides are expected. This makes AK Sco the ideal laboratory to study the effect of gravitational tides in the stellar magnetic field building up during PMS evolution. In this Letter, the detection of a highly disturbed (σ ≅ 100 km s -1 ) and very dense atmosphere (n e = 1.6 x 10 10 cm -3 ) is reported. Significant line broadening blurs any signs of ion belts or bow shocks in the spectrum of the atmospheric plasma. The radiative losses cannot be accounted for solely by the dissipation of energy from the tidal wave propagating in the stellar atmosphere or by the accreting material. The release of internal energy from the star seems to be the most likely source of the plasma heating. This is the first clear indication of a highly disturbed atmosphere surrounding a PMS close binary.

  1. AK Sco, First Detection of a Highly Disturbed Atmosphere in a Pre-Main-Sequence Close Binary

    Science.gov (United States)

    Gómez de Castro, Ana I.

    2009-06-01

    AK Sco is a unique source: a ~10 Myr old pre-main-sequence (PMS) spectroscopic binary composed of two nearly equal F5 stars that at periastron are separated by barely 11 stellar radii, so the stellar magnetospheres fill the Roche lobe at periastron. The orbit is not yet circularized (e = 0.47) and very strong tides are expected. This makes AK Sco the ideal laboratory to study the effect of gravitational tides in the stellar magnetic field building up during PMS evolution. In this Letter, the detection of a highly disturbed (σ sime 100 km s-1) and very dense atmosphere (n e = 1.6 × 1010 cm-3) is reported. Significant line broadening blurs any signs of ion belts or bow shocks in the spectrum of the atmospheric plasma. The radiative losses cannot be accounted for solely by the dissipation of energy from the tidal wave propagating in the stellar atmosphere or by the accreting material. The release of internal energy from the star seems to be the most likely source of the plasma heating. This is the first clear indication of a highly disturbed atmosphere surrounding a PMS close binary.

  2. Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau

    Science.gov (United States)

    Qiao, Qin; Wang, Qia; Han, Xi; Guan, Yanlong; Sun, Hang; Zhong, Yang; Huang, Jinling; Zhang, Ticao

    2016-02-01

    The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.

  3. Assessment of the environmental footprint of nuclear energy systems. Comparison between closed and open fuel cycles

    International Nuclear Information System (INIS)

    Poinssot, Ch.; Bourg, S.; Ouvrier, N.; Combernoux, N.; Rostaing, C.; Vargas-Gonzalez, M.; Bruno, J.

    2014-01-01

    Energy perspectives for the current century are dominated by the anticipated significant increase of energy needs. Particularly, electricity consumption is anticipated to increase by a factor higher than two before 2050. Energy choices are considered as structuring political choices that implies a long-standing and stable policy based on objective criteria. LCA (life cycle analysis) is a structured basis for deriving relevant indicators which can allow the comparison of a wide range of impacts of different energy sources. Among the energy-mix, nuclear power is anticipated to have very low GHG-emissions. However, its viability is severely addressed by the public opinion after the Fukushima accident. Therefore, a global LCA of the French nuclear fuel cycle was performed as a reference model. Results were compared in terms of impact with other energy sources. It emphasized that the French nuclear energy is one of the less impacting energy, comparable with renewable energy. In a second, part, the French scenario was compared with an equivalent open fuel cycle scenario. It demonstrates that an open fuel cycle would require about 16% more natural uranium, would have a bigger environmental footprint on the “non radioactive indicators” and would produce a higher volume of high level radioactive waste. - Highlights: • A life cycle analysis of the French close nuclear fuel cycle is performed. • The French nuclear energy is one of the less environmental impacting energy. • The French close fuel cycle is compared to an equivalent open fuel cycle. • An open fuel cycle would have a bigger environmental impact than the French fuel cycle. • Spent nuclear fuel recycling has a positive impact on the environmental footprint

  4. Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm.

    Directory of Open Access Journals (Sweden)

    Cheng-Hong Yang

    Full Text Available BACKGROUND: Complete mitochondrial (mt genome sequencing is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. For long template sequencing, i.e., like the entire mtDNA, it is essential to design primers for Polymerase Chain Reaction (PCR amplicons which are partly overlapping each other. The presented chromosome walking strategy provides the overlapping design to solve the problem for unreliable sequencing data at the 5' end and provides the effective sequencing. However, current algorithms and tools are mostly focused on the primer design for a local region in the genomic sequence. Accordingly, it is still challenging to provide the primer sets for the entire mtDNA. METHODOLOGY/PRINCIPAL FINDINGS: The purpose of this study is to develop an integrated primer design algorithm for entire mt genome in general, and for the common primer sets for closely-related species in particular. We introduce ClustalW to generate the multiple sequence alignment needed to find the conserved sequences in closely-related species. These conserved sequences are suitable for designing the common primers for the entire mtDNA. Using a heuristic algorithm particle swarm optimization (PSO, all the designed primers were computationally validated to fit the common primer design constraints, such as the melting temperature, primer length and GC content, PCR product length, secondary structure, specificity, and terminal limitation. The overlap requirement for PCR amplicons in the entire mtDNA is satisfied by defining the overlapping region with the sliding window technology. Finally, primer sets were designed within the overlapping region. The primer sets for the entire mtDNA sequences were successfully demonstrated in the example of two closely-related fish species. The pseudo code for the primer design algorithm is provided. CONCLUSIONS/SIGNIFICANCE: In conclusion, it can be said that our proposed sliding window-based PSO

  5. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

    Directory of Open Access Journals (Sweden)

    Jonathan eFilée

    2015-06-01

    Full Text Available Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales. Origin and evolution of these Giant Viruses (GVs remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for 5 groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements, whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

  6. Genomic comparison of closely related Giant Viruses supports an accordion-like model of evolution.

    Science.gov (United States)

    Filée, Jonathan

    2015-01-01

    Genome gigantism occurs so far in Phycodnaviridae and Mimiviridae (order Megavirales). Origin and evolution of these Giant Viruses (GVs) remain open questions. Interestingly, availability of a collection of closely related GV genomes enabling genomic comparisons offer the opportunity to better understand the different evolutionary forces acting on these genomes. Whole genome alignment for five groups of viruses belonging to the Mimiviridae and Phycodnaviridae families show that there is no trend of genome expansion or general tendency of genome contraction. Instead, GV genomes accumulated genomic mutations over the time with gene gains compensating the different losses. In addition, each lineage displays specific patterns of genome evolution. Mimiviridae (megaviruses and mimiviruses) and Chlorella Phycodnaviruses evolved mainly by duplications and losses of genes belonging to large paralogous families (including movements of diverse mobiles genetic elements), whereas Micromonas and Ostreococcus Phycodnaviruses derive most of their genetic novelties thought lateral gene transfers. Taken together, these data support an accordion-like model of evolution in which GV genomes have undergone successive steps of gene gain and gene loss, accrediting the hypothesis that genome gigantism appears early, before the diversification of the different GV lineages.

  7. Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison

    Directory of Open Access Journals (Sweden)

    Saville Barry J

    2007-09-01

    Full Text Available Abstract Background Ustilago maydis is the basidiomycete fungus responsible for common smut of corn and is a model organism for the study of fungal phytopathogenesis. To aid in the annotation of the genome sequence of this organism, several expressed sequence tag (EST libraries were generated from a variety of U. maydis cell types. In addition to utility in the context of gene identification and structure annotation, the ESTs were analyzed to identify differentially abundant transcripts and to detect evidence of alternative splicing and anti-sense transcription. Results Four cDNA libraries were constructed using RNA isolated from U. maydis diploid teliospores (U. maydis strains 518 × 521 and haploid cells of strain 521 grown under nutrient rich, carbon starved, and nitrogen starved conditions. Using the genome sequence as a scaffold, the 15,901 ESTs were assembled into 6,101 contiguous expressed sequences (contigs; among these, 5,482 corresponded to predicted genes in the MUMDB (MIPS Ustilago maydis database, while 619 aligned to regions of the genome not yet designated as genes in MUMDB. A comparison of EST abundance identified numerous genes that may be regulated in a cell type or starvation-specific manner. The transcriptional response to nitrogen starvation was assessed using RT-qPCR. The results of this suggest that there may be cross-talk between the nitrogen and carbon signalling pathways in U. maydis. Bioinformatic analysis identified numerous examples of alternative splicing and anti-sense transcription. While intron retention was the predominant form of alternative splicing in U. maydis, other varieties were also evident (e.g. exon skipping. Selected instances of both alternative splicing and anti-sense transcription were independently confirmed using RT-PCR. Conclusion Through this work: 1 substantial sequence information has been provided for U. maydis genome annotation; 2 new genes were identified through the discovery of 619

  8. Close relationship of Plasmodium sequences detected from South American pampas deer (Ozotoceros bezoarticus to Plasmodium spp. in North American white-tailed deer

    Directory of Open Access Journals (Sweden)

    Masahito Asada

    2018-04-01

    Full Text Available We report, for the first time, the presence of ungulate malaria parasites in South America. We conducted PCR-based surveys of blood samples of multiple deer species and water buffalo from Brazil and detected Plasmodium sequences from pampas deer (Ozotoceros bezoarticus samples. Phylogenic analysis revealed that the obtained sequences are closely related to the Plasmodium odocoilei clade 2 sequence from North American white-tailed deer (Odocoileus virginianus. Nucleotide differences suggest that malaria parasites in South American pampas deer and North American P. odocoilei clade 2 branched more recently than the Great American Interchange. Keywords: Malaria, Pampas deer, South America, Plasmodium odocoilei, Brazil

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

    Science.gov (United States)

    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…

  10. SeqVISTA: a graphical tool for sequence feature visualization and comparison

    Directory of Open Access Journals (Sweden)

    Niu Tianhua

    2003-01-01

    Full Text Available Abstract Background Many readers will sympathize with the following story. You are viewing a gene sequence in Entrez, and you want to find whether it contains a particular sequence motif. You reach for the browser's "find in page" button, but those darn spaces every 10 bp get in the way. And what if the motif is on the opposite strand? Subsequently, your favorite sequence analysis software informs you that there is an interesting feature at position 13982–14013. By painstakingly counting the 10 bp blocks, you are able to examine the sequence at this location. But now you want to see what other features have been annotated close by, and this information is buried several screenfuls higher up the web page. Results SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet. Our viewer may be launched on a GenBank record by a single click of a button installed in the web browser. Conclusion SeqVISTA allows insights to be gained by viewing the totality of sequence annotations and predictions, which may be more revealing than the sum of their parts. SeqVISTA runs on any operating system with a Java 1.4 virtual machine. It is freely available to academic users at http://zlab.bu.edu/SeqVISTA.

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

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    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.

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

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

    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

  13. Cloning, characterization and sequence comparison of the gene coding for IMP dehydrogenase from Pyrococcus furiosus.

    Science.gov (United States)

    Collart, F R; Osipiuk, J; Trent, J; Olsen, G J; Huberman, E

    1996-10-03

    We have cloned and characterized the gene encoding inosine monophosphate dehydrogenase (IMPDH) from Pyrococcus furiosus (Pf), a hyperthermophillic archeon. Sequence analysis of the Pf gene indicated an open reading frame specifying a protein of 485 amino acids (aa) with a calculated M(r) of 52900. Canonical Archaea promoter elements, Box A and Box B, are located -49 and -17 nucleotides (nt), respectively, upstream of the putative start codon. The sequence of the putative active-site region conforms to the IMPDH signature motif and contains a putative active-site cysteine. Phylogenetic relationships derived by using all available IMPDH sequences are consistent with trees developed for other molecules; they do not precisely resolve the history of Pf IMPDH but indicate a close similarity to bacterial IMPDH proteins. The phylogenetic analysis indicates that a gene duplication occurred prior to the division between rodents and humans, accounting for the Type I and II isoforms identified in mice and humans.

  14. 3D representations of amino acids—applications to protein sequence comparison and classification

    Directory of Open Access Journals (Sweden)

    Jie Li

    2014-08-01

    Full Text Available 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.

  15. Testing statistical significance scores of sequence comparison methods with structure similarity

    Directory of Open Access Journals (Sweden)

    Leunissen Jack AM

    2006-10-01

    Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

  16. IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS

    Science.gov (United States)

    Sequence analysis of microbial genomes has provided biologists the opportunity to compare genetic differences between closely related microorganisms. While random sequencing has also been used to study natural microbial communities, metagenomic comparisons via sequencing analysis...

  17. Ribosomal DNA sequence analysis of different geographically distributed Aloe Vera plants: Comparison with clonally regenerated plants

    International Nuclear Information System (INIS)

    Yagi, A.; Sato, Y.; Miwa, Y.; Kabbash, A.; Moustafa, S.; Shimomura, K.; El-Bassuony, A.

    2006-01-01

    A comparison of the sequences in an internally transcribed spacer (ITS) 1 region of rDNA between clonally regenerated A.vera and same species in Japan, USA and Egypt revealed the presence of two types of nucleotide sequences, 252 and 254 bps. Based on the findings in the ITS 1 region, A.vera having 252 and 254 bps clearly showed a stable sequence similarity, suggesting high conversation of the base peak sequence in the ITS 1 region. However, frequent base substitutions in the 252 bps samples leaves that came from callus tissue and micropropagated plants were observed around the regions of nucleotide positions 66, 99 and 199-201. The minor deviation in clonally regenerated A.vera may be due to the stage of regeneration and cell specification in cases of the callus tissue. In the present study, the base peak sequence of the Its 1 region of rDNA was adopted as a molecular marker for differentiating A.vera plants from geographically distributed and clonally regenerated A.vera plants and it was suggested that the base peak substitutions in the ITS 1 region may arise from the different nutritional and environmental factors in cultivation and plant growth stages. (author)

  18. Reconsidering the generation time hypothesis based on nuclear ribosomal ITS sequence comparisons in annual and perennial angiosperms

    Directory of Open Access Journals (Sweden)

    Fiz-Palacios Omar

    2008-12-01

    Full Text Available Abstract Background Differences in plant annual/perennial habit are hypothesized to cause a generation time effect on divergence rates. Previous studies that compared rates of divergence for internal transcribed spacer (ITS1 and ITS2 sequences of nuclear ribosomal DNA (nrDNA in angiosperms have reached contradictory conclusions about whether differences in generation times (or other life history features are associated with divergence rate heterogeneity. We compared annual/perennial ITS divergence rates using published sequence data, employing sampling criteria to control for possible artifacts that might obscure any actual rate variation caused by annual/perennial differences. Results Relative rate tests employing ITS sequences from 16 phylogenetically-independent annual/perennial species pairs rejected rate homogeneity in only a few comparisons, with annuals more frequently exhibiting faster substitution rates. Treating branch length differences categorically (annual faster or perennial faster regardless of magnitude with a sign test often indicated an excess of annuals with faster substitution rates. Annuals showed an approximately 1.6-fold rate acceleration in nucleotide substitution models for ITS. Relative rates of three nuclear loci and two chloroplast regions for the annual Arabidopsis thaliana compared with two closely related Arabidopsis perennials indicated that divergence was faster for the annual. In contrast, A. thaliana ITS divergence rates were sometimes faster and sometimes slower than the perennial. In simulations, divergence rate differences of at least 3.5-fold were required to reject rate constancy in > 80 % of replicates using a nucleotide substitution model observed for the combination of ITS1 and ITS2. Simulations also showed that categorical treatment of branch length differences detected rate heterogeneity > 80% of the time with a 1.5-fold or greater rate difference. Conclusion Although rate homogeneity was not rejected

  19. Phylogeny of the genus Haemophilus as determined by comparison of partial infB sequences

    DEFF Research Database (Denmark)

    Hedegaard, J; Okkels, H; Bruun, B

    2001-01-01

    A 453 bp fragment of infB, the gene encoding translation initiation factor 2, was sequenced and compared from 66 clinical isolates and type strains of Haemophilus species and related bacteria. Analysis of the partial infB sequences obtained suggested that the human isolates dependent on X and V...... factor, H. influenzae, H. haemolyticus, H. aegyptius and some cryptic genospecies of H. influenzae, were closely related to each other. H. parainfluenzae constituted a heterogeneous group within the boundaries of the genus, whereas H. aphrophilus/paraphrophilus and Actinobacillus actinomycetemcomitans...... were only remotely related to the type species of the genus Haemophilus H. parahaemolyticus and H. paraphrohaemolyticus took up an intermediary position and may not belong in the genus Haemophilus sensu stricto. Ambiguous results were obtained with seven isolates tentatively identified as H. segnis...

  20. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+".

    Directory of Open Access Journals (Sweden)

    Markus H Antwerpen

    Full Text Available The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

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

    NARCIS (Netherlands)

    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

    2015-01-01

    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

  2. Depression, anxiety and quality of life in suicide survivors: a comparison of close and distant relationships.

    Science.gov (United States)

    Mitchell, Ann M; Sakraida, Teresa J; Kim, Yookyung; Bullian, Leann; Chiappetta, Laurel

    2009-02-01

    The study's purpose was to describe and compare depression, anxiety, and quality of life, by degree of relationship, between closely related and distantly related survivors (persons close to the suicide victim, or "suicide survivors"; N = 60) during the acute phase of bereavement (within 1 month of the death). The close relationship category included spouses, parents, children, and siblings, whereas the distant relationship category included in-laws, aunts/uncles, and nieces/nephews. Analysis of covariance examined differences between the two groups on the symptom measures. Results indicate that, after controlling for age and gender effects, closely related survivors had significantly higher mean levels of depression and anxiety and had lower levels of mental health quality of life. There were no statistically significant differences on the physical health quality of life subscale.

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

    Directory of Open Access Journals (Sweden)

    Andrea Vásquez

    2014-01-01

    Full Text Available 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.

  4. Comparison of static model and dynamic model for the evaluation of station blackout sequences

    International Nuclear Information System (INIS)

    Lee, Kwang-Nam; Kang, Sun-Koo; Hong, Sung-Yull.

    1992-01-01

    Station blackout is one of major contributors to the core damage frequency (CDF) in many PSA studies. Since station blackout sequence exhibits dynamic features, accurate calculation of CDF for the station blackout sequence is not possible with event tree/fault tree (ET/FT) method. Although the integral method can determine accurate CDF, it is time consuming and is difficult to evaluate various alternative AC source configuration and sensitivities. In this study, a comparison is made between static model and dynamic model and a new methodology which combines static model and dynamic model is provided for the accurate quantification of CDF and evaluation of improvement alternatives. Results of several case studies show that accurate calculation of CDF is possible by introducing equivalent mission time. (author)

  5. Modelling estimation and analysis of dynamic processes from image sequences using temporal random closed sets and point processes with application to the cell exocytosis and endocytosis

    OpenAIRE

    Díaz Fernández, Ester

    2010-01-01

    In this thesis, new models and methodologies are introduced for the analysis of dynamic processes characterized by image sequences with spatial temporal overlapping. The spatial temporal overlapping exists in many natural phenomena and should be addressed properly in several Science disciplines such as Microscopy, Material Sciences, Biology, Geostatistics or Communication Networks. This work is related to the Point Process and Random Closed Set theories, within Stochastic Ge...

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

    Science.gov (United States)

    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.

    2015-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Nathan D. Olson

    2015-03-01

    Full Text Available 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.

  8. Apophysomyces variabilis: draft genome sequence and comparison of predictive virulence determinants with other medically important Mucorales.

    Science.gov (United States)

    Prakash, Hariprasath; Rudramurthy, Shivaprakash Mandya; Gandham, Prasad S; Ghosh, Anup Kumar; Kumar, Milner M; Badapanda, Chandan; Chakrabarti, Arunaloke

    2017-09-18

    Apophysomyces species are prevalent in tropical countries and A. variabilis is the second most frequent agent causing mucormycosis in India. Among Apophysomyces species, A. elegans, A. trapeziformis and A. variabilis are commonly incriminated in human infections. The genome sequences of A. elegans and A. trapeziformis are available in public database, but not A. variabilis. We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. The whole genome of A. variabilis NCCPF 102052 was sequenced and the genomic structure of A. variabilis was compared with already available genome structures of A. elegans, A. trapeziformis and other medically important Mucorales. The total size of genome assembly of A. variabilis was 39.38 Mb with 12,764 protein-coding genes. The transposable elements (TEs) were low in Apophysomyces genome and the retrotransposon Ty3-gypsy was the common TE. Phylogenetically, Apophysomyces species were grouped closely with Phycomyces blakesleeanus. OrthoMCL analysis revealed 3025 orthologues proteins, which were common in those three pathogenic Apophysomyces species. Expansion of multiple gene families/duplication was observed in Apophysomyces genomes. Approximately 6% of Apophysomyces genes were predicted to be associated with virulence on PHIbase analysis. The virulence determinants included the protein families of CotH proteins (invasins), proteases, iron utilisation pathways, siderophores and signal transduction pathways. Serine proteases were the major group of proteases found in all Apophysomyces genomes. The carbohydrate active enzymes (CAZymes) constitute the majority of the secretory proteins. The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis. Together with available genome sequence of A. elegans and A. trapeziformis, the study helped to indicate the possible virulence determinants of

  9. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Czech Academy of Sciences Publication Activity Database

    Piednoël, M.; Aberer, A.J.; Schneeweiss, G. M.; Macas, Jiří; Novák, Petr; Gundlach, H.; Temsch, E.M.; Renner, S.S.

    2012-01-01

    Roč. 29, č. 11 (2012), s. 3601-3611 ISSN 0737-4038 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : next-generation sequencing * polyploidy * genome size * Ty3/Gypsy * transposable elements Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.353, year: 2012

  10. Synthesis of Heterocycles through a Ruthenium‐Catalyzed Tandem Ring‐Closing Metathesis/Isomerization/N‐Acyliminium Cyclization Sequence

    DEFF Research Database (Denmark)

    Ascic, Erhad; Jensen, Jakob Feldthusen; Nielsen, Thomas Eiland

    2011-01-01

    Tandem bicycle: In the title reaction double bonds created during ring-closing metathesis isomerize to generate reactive iminium intermediates that undergo intramolecular cyclization reactions with tethered heteroatom and carbon nucleophiles. In this way, a series of biologically interesting hete...... heterocyclic compounds can be made, including a known precursor for the total synthesis of the antiparasitic natural product harmicine....

  11. A Comparison of Selective Auditory Attention Abilities in Open-Space Versus Closed Classroom Students.

    Science.gov (United States)

    Reinertsen, Gloria M.

    A study compared performances on a test of selective auditory attention between students educated in open-space versus closed classroom environments. An open-space classroom environment was defined as having no walls separating it from hallways or other classrooms. It was hypothesized that the incidence of auditory figure-ground (ability to focus…

  12. A prospective comparison of the efficacy and safety of fully closed ...

    African Journals Online (AJOL)

    We conducted a within-group comparison of three modes of ventilation, ASV, Intellivent-ASV and SIMV, using a Hamilton S1 ventilator (Hamilton Medical, Switzerland). Subjects were ventilated for 2 hours on each mode, and at the end of each 2-hour period, parameters of ventilation and haemodynamics were measured.

  13. A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Wenyu Zhang

    Full Text Available 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.

  14. Computational complexity of algorithms for sequence comparison, short-read assembly and genome alignment.

    Science.gov (United States)

    Baichoo, Shakuntala; Ouzounis, Christos A

    A multitude of algorithms for sequence comparison, short-read assembly and whole-genome alignment have been developed in the general context of molecular biology, to support technology development for high-throughput sequencing, numerous applications in genome biology and fundamental research on comparative genomics. The computational complexity of these algorithms has been previously reported in original research papers, yet this often neglected property has not been reviewed previously in a systematic manner and for a wider audience. We provide a review of space and time complexity of key sequence analysis algorithms and highlight their properties in a comprehensive manner, in order to identify potential opportunities for further research in algorithm or data structure optimization. The complexity aspect is poised to become pivotal as we will be facing challenges related to the continuous increase of genomic data on unprecedented scales and complexity in the foreseeable future, when robust biological simulation at the cell level and above becomes a reality. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Fifty years of coiled-coils and alpha-helical bundles: a close relationship between sequence and structure.

    Science.gov (United States)

    Parry, David A D; Fraser, R D Bruce; Squire, John M

    2008-09-01

    alpha-Helical coiled coils are remarkable for the diversity of related conformations that they adopt in both fibrous and globular proteins, and for the range of functions that they exhibit. The coiled coils are based on a heptad (7-residue), hendecad (11-residue) or a related quasi-repeat of apolar residues in the sequences of the alpha-helical regions involved. Most of these, however, display one or more sequence discontinuities known as stutters or stammers. The resulting coiled coils vary in length, in the number of chains participating, in the relative polarity of the contributing alpha-helical regions (parallel or antiparallel), and in the pitch length and handedness of the supercoil (left- or right-handed). Functionally, the concept that a coiled coil can act only as a static rod is no longer valid, and the range of roles that these structures have now been shown to exhibit has expanded rapidly in recent years. An important development has been the recognition that the delightful simplicity that exists between sequence and structure, and between structure and function, allows coiled coils with specialized features to be designed de novo.

  16. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Science.gov (United States)

    Piednoël, Mathieu; Aberer, Andre J.; Schneeweiss, Gerald M.; Macas, Jiri; Novak, Petr; Gundlach, Heidrun; Temsch, Eva M.; Renner, Susanne S.

    2013-01-01

    We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types. PMID:22723303

  17. A comparison of Candle Auctions and Hard Close Auctions with Common Values

    OpenAIRE

    Sascha Füllbrunn

    2009-01-01

    With this study, we contribute to the literature of auction design by presenting a new auction format: the Candle auction, a popular auction in the Middle Ages. Considering a common value framework, we theoretically and experimentally point out that the Candle auction, where bidding is allowed until a stochastic deadline, yields a better outcome to the seller than the Hard Close auction, the popular eBay online auction format.

  18. Comparison of double-locus sequence typing (DLST) and multilocus sequence typing (MLST) for the investigation of Pseudomonas aeruginosa populations.

    Science.gov (United States)

    Cholley, Pascal; Stojanov, Milos; Hocquet, Didier; Thouverez, Michelle; Bertrand, Xavier; Blanc, Dominique S

    2015-08-01

    Reliable molecular typing methods are necessary to investigate the epidemiology of bacterial pathogens. Reference methods such as multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) are costly and time consuming. Here, we compared our newly developed double-locus sequence typing (DLST) method for Pseudomonas aeruginosa to MLST and PFGE on a collection of 281 isolates. DLST was as discriminatory as MLST and was able to recognize "high-risk" epidemic clones. Both methods were highly congruent. Not surprisingly, a higher discriminatory power was observed with PFGE. In conclusion, being a simple method (single-strand sequencing of only 2 loci), DLST is valuable as a first-line typing tool for epidemiological investigations of P. aeruginosa. Coupled to a more discriminant method like PFGE or whole genome sequencing, it might represent an efficient typing strategy to investigate or prevent outbreaks. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Comparison of Early and Delayed Open Reduction and Internal Fixation for Treating Closed Tibial Pilon Fractures.

    Science.gov (United States)

    Tang, Xin; Liu, Lei; Tu, Chong-qi; Li, Jian; Li, Qi; Pei, Fu-xing

    2014-07-01

    The timing of surgery for osteosynthesis of type C pilon (AO/OTA) fractures remains controversial. The aim of this study was to determine the outcome of early and delayed open reduction and internal fixation (ORIF) for treating closed type C pilon fractures. Forty-six patients with closed type C pilon fractures matched according to age, gender, soft tissue conditions, and fracture pattern were divided into group A (early group: underwent surgery within 36 hours of the injury) or group B (delayed group: underwent surgery 10 days to 3 weeks postinjury after the soft tissue swelling subsided). In the delayed group, 9 patients were treated first by temporary external fixation. All the closed fractures were managed by ORIF with locking plates. At follow-up, the clinical and radiographic results were retrospectively analyzed. The mean follow-up time was 25.8 months (range, 14 to 48 months) in group A and 26.0 months (range, 15 to 44 months) in group B. There was no significant difference (P > .05) between the 2 groups regarding the rate of soft tissue complication, the rate of fracture union, and the final functional score. The patients in group A had a significantly shorter mean time to fracture union (21.5 ± 4.0 weeks vs 23.3 ± 3.7 weeks, P fractures can be safe and effective, with similar rates of wound complication, fracture union, and final good functional recovery but shorter operative time, union time, and hospital stay. These results favorably compare with delayed ORIF treatment. Level III, retrospective comparative study. © The Author(s) 2014.

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

    Directory of Open Access Journals (Sweden)

    Quail Michael A

    2012-07-01

    Full Text Available Abstract 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.

  1. Comparison of closed-form and finite-element solutions of thick laminated anisotropic rectangular plates

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, J N; Chao, W C [Virginia Polytechnic Inst. and State Univ., Blacksburg (USA). Dept. of Engineering Science and Mechanics

    1981-04-01

    In this study the effects of reduced integration, mesh size, and element type (i.e. linear or quadratic) on the accuracy of a penalty-finite element based on the theory governing thick, laminated, anisotropic composite plates are investigated. In order to assess the accuracy of the present finite element, exact closed-form solutions are developed for cross-ply and antisymmetric angle-ply rectangular plates simply supported and subjected to sinusoidally distributed mechanical and/or thermal loadings, and free vibration.

  2. Comparison of open and closed techniques of haemorrhoidectomy in terms of post-operative complications

    International Nuclear Information System (INIS)

    Majeed, S.; Qamar, S.R.; Tariq, M.; Ali, M.A.

    2015-01-01

    Haemorrhoids have been diagnosed and treated since the dawn of civilization, yet their cause, nature, symptomatology and especially their treatment options, remain hotly debated. The general principle however is that treatment should be directed by symptoms and the degree of haemorrhoids. The objective of the study is to compare early and late complications and wound healing time in open versus closed methods of haemorrhoidectomy. Methods: This was a Randomized control trial conducted at Department of Surgery CMH Kharian for a period of 3 years. During the period of study, patients presenting in Surgical OPD (Age Range 20-72 Years) with 3rd or 4th degree haemorrhoids requiring haemorrhoidectomy (n=364) were divided in two groups:- Group-1 was subjected to haemorrhoidectomy by open (Milligan-Morgan) technique and Group-2 underwent closed (Ferguson) haemorrhoidectomy. All patients were followed up for 2 months post-operatively and assessed for duration of wound healing and post-operative complications. Results: In group-1 (Open haemorrhoidectomy) patients ages ranged from 21-70 years with a mean age of 43 years (SD1±2.51). Duration of wound healing in this group was on the average 22 days (SD±5.76). Incidence of early post-operative complications including haemorrhage, infection and urinary retention was 4.94%, 8.24% and 7.14% respectively. The only late complication observed was anal stenosis in one patient (0.55%). No fissure or faecal incontinence was observed in this group. In group-2 (subjected to closed haemorrhoidectomy), patients ages ranged from 20-72 years with a mean age of 42 years (SD±10.31). Duration of wound healing was on the average 14 days (SD±3.25). Incidence of early post- operative complications, i.e., haemorrhage, infection and urinary retention was 2.19%, 7.69% and 2.75% respectively. No late complications (stenosis, fissure or incontinence) were observed in this group. Conclusion: There is no statistical significant difference between open

  3. Genome sequence of the endosymbiont Rickettsia peacockii and comparison with virulent Rickettsia rickettsii: identification of virulence factors.

    Directory of Open Access Journals (Sweden)

    Roderick F Felsheim

    2009-12-01

    Full Text Available Rickettsia peacockii, also known as the East Side Agent, is a non-pathogenic obligate intracellular bacterium found as an endosymbiont in Dermacentor andersoni ticks in the western USA and Canada. Its presence in ticks is correlated with reduced prevalence of Rickettsia rickettsii, the agent of Rocky Mountain Spotted Fever. It has been proposed that a virulent SFG rickettsia underwent changes to become the East Side Agent. We determined the genome sequence of R. peacockii and provide a comparison to a closely related virulent R. rickettsii. The presence of 42 chromosomal copies of the ISRpe1 transposon in the genome of R. peacockii is associated with a lack of synteny with the genome of R. rickettsii and numerous deletions via recombination between transposon copies. The plasmid contains a number of genes from distantly related organisms, such as part of the glycosylation island of Pseudomonas aeruginosa. Genes deleted or mutated in R. peacockii which may relate to loss of virulence include those coding for an ankyrin repeat containing protein, DsbA, RickA, protease II, OmpA, ScaI, and a putative phosphoethanolamine transferase. The gene coding for the ankyrin repeat containing protein is especially implicated as it is mutated in R. rickettsii strain Iowa, which has attenuated virulence. Presence of numerous copies of the ISRpe1 transposon, likely acquired by lateral transfer from a Cardinium species, are associated with extensive genomic reorganization and deletions. The deletion and mutation of genes possibly involved in loss of virulence have been identified by this genomic comparison. It also illustrates that the introduction of a transposon into the genome can have varied effects; either correlating with an increase in pathogenicity as in Francisella tularensis or a loss of pathogenicity as in R. peacockii and the recombination enabled by multiple transposon copies can cause significant deletions in some genomes while not in others.

  4. Cluster based on sequence comparison of homologous proteins of 95 organism species - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Gclust Server Cluster based on sequence comparison of homologous proteins of 95 organism spe...cies Data detail Data name Cluster based on sequence comparison of homologous proteins of 95 organism specie...istory of This Database Site Policy | Contact Us Cluster based on sequence compariso

  5. Controlled heat flux measurement across a closing nanoscale gap and its comparison to theory

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Y.; Ghafari, A.; Budaev, B. V.; Bogy, D. B., E-mail: dbogy@berkeley.edu [Department of mechanical Engineering, Computer Mechanics Lab, University of California, Berkeley, California 94720 (United States)

    2016-05-23

    We present here a controlled measurement of heat flux across a closing gap that is initially less than 10 nm wide between two solid surfaces at different temperatures. The measured heat transfer is compared with our published theoretical analyses of this phenomenon that show thermal radiation dominates the heat transfer for gaps wider than about 1–2 nm, but phonon conduction dominates between 1 and 2 nm and contact. The experiments employ a thermal actuator mounted on a rocking base block for coarse positioning that supplies Joule heating to an embedded element to cause thermal expansion of a localized region for less than 10 nm spacing control, together with an embedded near-surface resistive temperature sensor to measure its temperature change due to the heat flux across the gap. The measured results are in general agreement with the theoretical predictions, and they also agree with common sense expectations. This paper not only shows nano-scale heat transfer measurement across a closing gap, it also lends additional strong support to the validity of the referenced theoretical developments. The proposed experimental approach can provide support to design of future devices for nano-scale heat transfer measurement.

  6. cDNA cloning and nucleotide sequence comparison of Chinese hamster metallothionein I and II mRNAs

    Energy Technology Data Exchange (ETDEWEB)

    Griffith, B B; Walters, R A; Enger, M D; Hildebrand, C E; Griffith, J K

    1983-01-01

    Polyadenylated RNA was extracted from a cadmium resistant Chinese hamster (CHO) cell line, enriched for metal-induced, abundant RNA sequences and cloned as double-stranded cDNA in the plasmid pBR322. Two cDNA clones, pCHMT1 and pCHMT2, encoding two Chinese hamster isometallothioneins were identified, and the nucleotide sequence of each insert was determined. The two Chinese hamster metallothioneins show nucleotide sequence homologies of 80% in the protein coding region and approximately 35% in both the 5' and 3' untranslated regions. Interestingly, an 8 nucleotide sequence (TGTAAATA) has been conserved in sequence and position in the 3' untranslated regions of each metallothionein mRNA sequenced thus far. Estimated nucleotide substitution rates derived from interspecies comparisons were used to calculate a metallothionein gene duplication time of 45 to 120 million years ago. 39 references, 1 figure, 1 table.

  7. Multilocus Sequence Typing Reveals a New Cluster of Closely Related Candida tropicalis Genotypes in Italian Patients With Neurological Disorders.

    Science.gov (United States)

    Scordino, Fabio; Giuffrè, Letterio; Barberi, Giuseppina; Marino Merlo, Francesca; Orlando, Maria Grazia; Giosa, Domenico; Romeo, Orazio

    2018-01-01

    Candida tropicalis is a pathogenic yeast that has emerged as an important cause of candidemia especially in elderly patients with hematological malignancies. Infections caused by this species are mainly reported from Latin America and Asian-Pacific countries although recent epidemiological data revealed that C. tropicalis accounts for 6-16.4% of the Candida bloodstream infections (BSIs) in Italy by representing a relevant issue especially for patients receiving long-term hospital care. The aim of this study was to describe the genetic diversity of C. tropicalis isolates contaminating the hands of healthcare workers (HCWs) and hospital environments and/or associated with BSIs occurring in patients with different neurological disorders and without hematological disease. A total of 28 C. tropicalis isolates were genotyped using multilocus sequence typing analysis of six housekeeping ( ICL1, MDR1, SAPT2, SAPT4, XYR1 , and ZWF1 ) genes and data revealed the presence of only eight diploid sequence types (DSTs) of which 6 (75%) were completely new. Four eBURST clonal complexes (CC2, CC10, CC11, and CC33) contained all DSTs found in this study and the CC33 resulted in an exclusive, well-defined, clonal cluster from Italy. In conclusion, C. tropicalis could represent an important cause of BSIs in long-term hospitalized patients with no underlying hematological disease. The findings of this study also suggest a potential horizontal transmission of a specific C. tropicalis clone through hands of HCWs and expand our understanding of the molecular epidemiology of this pathogen whose population structure is still far from being fully elucidated as its complexity increases as different categories of patients and geographic areas are examined.

  8. A multithreaded parallel implementation of a dynamic programming algorithm for sequence comparison.

    Science.gov (United States)

    Martins, W S; Del Cuvillo, J B; Useche, F J; Theobald, K B; Gao, G R

    2001-01-01

    This paper discusses the issues involved in implementing a dynamic programming algorithm for biological sequence comparison on a general-purpose parallel computing platform based on a fine-grain event-driven multithreaded program execution model. Fine-grain multithreading permits efficient parallelism exploitation in this application both by taking advantage of asynchronous point-to-point synchronizations and communication with low overheads and by effectively tolerating latency through the overlapping of computation and communication. We have implemented our scheme on EARTH, a fine-grain event-driven multithreaded execution and architecture model which has been ported to a number of parallel machines with off-the-shelf processors. Our experimental results show that the dynamic programming algorithm can be efficiently implemented on EARTH systems with high performance (e.g., speedup of 90 on 120 nodes), good programmability and reasonable cost.

  9. Comparison of pause predictions of two sequence-dependent transcription models

    International Nuclear Information System (INIS)

    Bai, Lu; Wang, Michelle D

    2010-01-01

    Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations

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

    Directory of Open Access Journals (Sweden)

    Michelle Klein Sercundes

    2016-03-01

    Full Text Available Abstract 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 genusHammondia 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.

  11. USE OF COMPETITIVE DNA HYBRIDIZATION TO IDENTIFY DIFFERENCES IN THE GENOMES OF TWO CLOSELY RELATED FECAL INDICATOR BACTERIA

    Science.gov (United States)

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, comparisons of closely related bacterial species and individual isolates by whole-genome sequencing approaches remains prohibitively expens...

  12. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments

    Directory of Open Access Journals (Sweden)

    Sadreyev Ruslan I

    2004-08-01

    Full Text Available Abstract Background Profile-based analysis of multiple sequence alignments (MSA allows for accurate comparison of protein families. Here, we address the problems of detecting statistically confident dissimilarities between (1 MSA position and a set of predicted residue frequencies, and (2 between two MSA positions. These problems are important for (i evaluation and optimization of methods predicting residue occurrence at protein positions; (ii detection of potentially misaligned regions in automatically produced alignments and their further refinement; and (iii detection of sites that determine functional or structural specificity in two related families. Results For problems (1 and (2, we propose analytical estimates of P-value and apply them to the detection of significant positional dissimilarities in various experimental situations. (a We compare structure-based predictions of residue propensities at a protein position to the actual residue frequencies in the MSA of homologs. (b We evaluate our method by the ability to detect erroneous position matches produced by an automatic sequence aligner. (c We compare MSA positions that correspond to residues aligned by automatic structure aligners. (d We compare MSA positions that are aligned by high-quality manual superposition of structures. Detected dissimilarities reveal shortcomings of the automatic methods for residue frequency prediction and alignment construction. For the high-quality structural alignments, the dissimilarities suggest sites of potential functional or structural importance. Conclusion The proposed computational method is of significant potential value for the analysis of protein families.

  13. Abdominal MR imaging using a HASTE sequence : image comparison on the different echo times

    International Nuclear Information System (INIS)

    Park, Kwang Bo; Lee, Moon Gyu; Lim, Tae Hwan; Jeong, Yoong Ki; Ha, Hyun Kwon; Kim, Pyo Nyun; Auh, Yong Ho

    1999-01-01

    To determine the optimal parameters of abdominal HASTE imaging by means of a comparison of intermediate and long TE (echo time). We evaluated 30 consecutive patients who had undergone liver MR during a three-month period. Twelve patients were diagnosed as normal, four as having liver cirrhosis, and 14 were found to be suffering form hepatic hemangioma. On the basis of measured signal intensity of the liver, spleen, pancreas and gallbladder, and of fat, muscle, hemangioma, and background, we calculated the ratios of signal to noise (S/N), signal difference to noise (SD/N), and signal intensity (SI). Image quality was compared using these three ratios, and using two HASTE sequences with TEs of 90 msec and 134 msec, images were qualitatively evaluated. S/N ratio of the liver was higher when TE was 90 msec(p<.05), though S/N, SD/N and SI rations of the spleen, gallbladder, and pancreas-and of hemangiom-were higher when TE was 134 msec (p<.05). However, in muscle, all these three ratios were higher at a TE of 90 msec. SD/N ratio and SI of fat were higher at a TE of 134 msec. Overall image quality was better at a TE of 134 msec than at one of 90msec. A HASTE sequence with a TE of 134msec showed greater tissue contrast and stronger T2-weighted images than one with a TE of 90msec

  14. Comparison of sequencing based CNV discovery methods using monozygotic twin quartets.

    Directory of Open Access Journals (Sweden)

    Marc-André Legault

    Full Text Available The advent of high throughput sequencing methods breeds an important amount of technical challenges. Among those is the one raised by the discovery of copy-number variations (CNVs using whole-genome sequencing data. CNVs are genomic structural variations defined as a variation in the number of copies of a large genomic fragment, usually more than one kilobase. Here, we aim to compare different CNV calling methods in order to assess their ability to consistently identify CNVs by comparison of the calls in 9 quartets of identical twin pairs. The use of monozygotic twins provides a means of estimating the error rate of each algorithm by observing CNVs that are inconsistently called when considering the rules of Mendelian inheritance and the assumption of an identical genome between twins. The similarity between the calls from the different tools and the advantage of combining call sets were also considered.ERDS and CNVnator obtained the best performance when considering the inherited CNV rate with a mean of 0.74 and 0.70, respectively. Venn diagrams were generated to show the agreement between the different algorithms, before and after filtering out familial inconsistencies. This filtering revealed a high number of false positives for CNVer and Breakdancer. A low overall agreement between the methods suggested a high complementarity of the different tools when calling CNVs. The breakpoint sensitivity analysis indicated that CNVnator and ERDS achieved better resolution of CNV borders than the other tools. The highest inherited CNV rate was achieved through the intersection of these two tools (81%.This study showed that ERDS and CNVnator provide good performance on whole genome sequencing data with respect to CNV consistency across families, CNV breakpoint resolution and CNV call specificity. The intersection of the calls from the two tools would be valuable for CNV genotyping pipelines.

  15. Sodium oxide aerosol behavior in a closed vessel. Comparison of computer modeling with aerosol experiments

    International Nuclear Information System (INIS)

    Fermandjian, Jean.

    1979-08-01

    Fast breeder reactor safety needs models validated to predict the behavior of sodium aerosols in the different reactor compartments during hypothetical sodium accident. Besides their chemical toxicity, the sodium aerosols are a transfer vector of radioactivity during a contaminated sodium fire. The purpose of this work is to validate models (HAARM 2 and PARDISEKO 3) with tests of sodium pool fires in a 400 m 3 concrete vessel in a confined atmosphere (CASSANDRE tests). The comparison between calculations and experimental results reveals that difficulties still exist, especially as to the selection of the values to be given to some input parameters (physical data of experimental origin, in particular the aerosols source function, the characteristics of the distribution of the emitted particles and the form factor of the agglomerated particles) [fr

  16. Complementary DNA and derived amino acid sequence of the β subunit of human complement protein C8: identification of a close structural and ancestral relationship to the α subunit and C9

    International Nuclear Information System (INIS)

    Howard, O.M.Z.; Rao, A.G.; Sodetz, J.M.

    1987-01-01

    A cDNA clone encoding the β subunit (M/sub r/ 64,000) of the eighth component of complement (C8) has been isolated from a human liver cDNA library. This clone has a cDNA insert of 1.95 kilobases (kb) and contains the entire β sequence [1608 base pairs (bp)]. Analysis of total cellular RNA isolated from the hepatoma cell line HepG2 revealed the mRNA for β to be ∼ 2.5 kb. This is similar to the message size for the α subunit of C8 and confirms the existence of different mRNAs for α and β. This finding supports genetic evidence that α and β are encoded at different loci. Analysis of the derived amino acid sequence revealed several membrane surface seeking segments that may facilitate β interaction with target membranes during complement-mediated cytolysis. Determined of the carbohydrate composition indicated 1 or 2 asparagine-linked but no O-linked oligosaccharide chains. Comparison of the β sequence to that reported earlier and to that of human C9 revealed a striking homology between all three proteins. For β and α, the overall homology is 33% on the basis of identity and 53% when conserved substitutions are allowed. For β and C9, the values are 26% and 47 5 , respectively. All three have a large internal domain that is nearly cysteine free and N- and C-termini that are cysteine-rich and homologous to the low-density lipoprotein receptor repeat and epidermal growth factor type sequences, respectively. The overall homology and similarities in size and structural organization are indicative of a close ancestral relationship. It is concluded that α, β and C9 are members of a family of structurally related proteins that are capable of interacting to produce a hydrophilic to amphiphilic transition and membrane association

  17. Partner cooperation with decode-and-forward: Closed-form outage analysis and comparison

    KAUST Repository

    Benjillali, Mustapha

    2013-01-01

    In this paper, we investigate the outage performance of "partner cooperation" based on opportunistic Decodeand- Forward with constrained partial selection and reactive relaying strategies in dual-hop cooperative Nakagami-m fading links. The source/destination, which is based on the unique knowledge of local channel state information, selects the best relay to increase the chances of cooperation in both uplink and downlink communications when the direct link is also available. After deriving new expressions for the cumulative distribution functions of the variables of interest, the outage probability of the system is obtained in closed-form. We also derive the ε-outage capacity in different particular cases, and the obtained results - when the channel model is reduced to a Rayleigh fading - either are new or correspond to those previously obtained in other works. Simulation results confirm the accuracy of our analysis for a large selection of system and fading parameters and provide a new insight into the design and optimization of cooperative configurations. © 2012 IEEE.

  18. Comparison of outcomes of permanently closed and periodically harvested coral reef reserves.

    Science.gov (United States)

    Bartlett, C Y; Manua, C; Cinner, J; Sutton, S; Jimmy, R; South, R; Nilsson, J; Raina, J

    2009-12-01

    In many areas of the developing world, the establishment of permanent marine reserves is inhibited by cultural norms or socioeconomic pressures. Community conserved areas that are periodically harvested are increasingly being implemented as fisheries management tools, but few researchers have empirically compared them with permanently closed reserves. We used a hierarchical control-impact experimental design to compare the abundance and biomass of reef fishes, invertebrates, and substrate composition in periodically harvested and permanent reserves and in openly fished (control sites) of the South Pacific island country of Vanuatu. Fished species had significantly higher biomass in periodically harvested reserves than in adjacent openly fished areas. We did not detect differences in substratum composition between permanent reserves and openly fished areas or between permanent reserves and periodically harvested reserves. Giant clams (tridacnids) and top shells (Trochus niloticus) were vulnerable to periodic harvest, and we suggest that for adequate management of these species, periodically harvested community conservation areas be used in conjunction with other management strategies. Periodic harvest within reserves is an example of adaptive and flexible management that may meet conservation goals and that is suited to the social, economic, and cultural contexts of many coastal communities in the developing world.

  19. Complete mitochondrial genome sequence of Indian medium carp, Labeo gonius (Hamilton, 1822) and its comparison with other related carp species.

    Science.gov (United States)

    Behera, Bijay Kumar; Kumari, Kavita; Baisvar, Vishwamitra Singh; Rout, Ajaya Kumar; Pakrashi, Sudip; Paria, Prasenjet; Jena, J K

    2017-01-01

    In the present study, the complete mitochondrial genome sequence of Labeo gonius is reported using PGM sequencer (Ion Torrent). The complete mitogenome of L. gonius is obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP) which is 16 614 bp in length. The mitogenome of L. gonius comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and D-loop as control region along with gene order and organization, being similar to most of other fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of Labeo fimbriatus, as reported earlier. The phylogenetic analysis of Cypriniformes depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of L. gonius would be helpful in understanding the population genetics, phylogenetics, and evolution of Indian Carps.

  20. Comparison of Intravenous Morphine with Sublingual Buprenorphine in Management of Postoperative Pain after Closed Reduction Orthopedic Surgery.

    Science.gov (United States)

    Soltani, Ghasem; Khorsand, Mahmood; Shamloo, Alireza Sepehri; Jarahi, Lida; Zirak, Nahid

    2015-10-01

    Postoperative pain is a common side effect following surgery that can significantly reduce surgical quality and patient's satisfaction. Treatment options are morphine and buprenorphine. We aimed to compare the efficacy of a single dose of intravenous morphine with sublingual buprenorphine in postoperative pain control following closed reduction surgery. This triple blind clinical trial was conducted on 90 patients referred for closed reduction orthopedic surgery. They were older than 18 years and in classes I and II of the American Society of Anesthesiologists (ASA) with an operation time of 30-90 minutes. Patients were divided into two groups of buprenorphine (4.5µg/kg sublingually) and morphine (0.2mg/kg intravenously). Baseline characteristics, vital signs, pain score, level of sedation and pharmacological side effects were recorded in the recovery room (at 0 and 30 minutes), and in the ward (at 3, 6 and 12 hours). SPSS version 19 software was used for data analysis and the significance level was set at P<0.05. Ninety patients were studied, 60 males and 30 females with a mean age of 37.7±16.2 years. There was no significant difference between the two groups in terms of baseline characteristics. Pain score in the morphine group was significantly higher than the buprenorphine group with an average score of 2.5 (P<0.001). Postoperative mean heart rate in the buprenorphine group was four beats lower than the morphine group (P<0.001). Also, in the buprenorphine 48.6% and in the morphine group 86.7% of cases were conscious in recovery (P=0.001) with a higher rate of pruritus in the latter group (P=0.001). Sublingual buprenorphine administration before anesthesia induction in closed reduction surgery can lead to better postoperative pain control in comparison to intravenous morphine. Due to simple usage and longer postoperative sedation, sublingual buprenorphine is recommended as a suitable drug in closed reduction surgery.

  1. A COMPARISON OF SPECTROSCOPIC VERSUS IMAGING TECHNIQUES FOR DETECTING CLOSE COMPANIONS TO KEPLER OBJECTS OF INTEREST

    International Nuclear Information System (INIS)

    Teske, Johanna K.; Everett, Mark E.; Hirsch, Lea; Furlan, Elise; Ciardi, David R.; Horch, Elliott P.; Howell, Steve B.; Gonzales, Erica; Crepp, Justin R.

    2015-01-01

    Kepler planet candidates require both spectroscopic and imaging follow-up observations to rule out false positives and detect blended stars. Traditionally, spectroscopy and high-resolution imaging have probed different host star companion parameter spaces, the former detecting tight binaries and the latter detecting wider bound companions as well as chance background stars. In this paper, we examine a sample of 11 Kepler host stars with companions detected by two techniques—near-infrared adaptive optics and/or optical speckle interferometry imaging, and a new spectroscopic deblending method. We compare the companion effective temperatures (T eff ) and flux ratios (F B /F A , where A is the primary and B is the companion) derived from each technique and find no cases where both companion parameters agree within 1σ errors. In 3/11 cases the companion T eff values agree within 1σ errors, and in 2/11 cases the companion F B /F A values agree within 1σ errors. Examining each Kepler system individually considering multiple avenues (isochrone mapping, contrast curves, probability of being bound), we suggest two cases for which the techniques most likely agree in their companion detections (detect the same companion star). Overall, our results support the advantage that the spectroscopic deblending technique has for finding very close-in companions (θ ≲ 0.″02–0.″05) that are not easily detectable with imaging. However, we also specifically show how high-contrast AO and speckle imaging observations detect companions at larger separations (θ ≥ 0.″02–0.″05) that are missed by the spectroscopic technique, provide additional information for characterizing the companion and its potential contamination (e.g., position angle, separation, magnitude differences), and cover a wider range of primary star effective temperatures. The investigation presented here illustrates the utility of combining the two techniques to reveal higher-order multiples in known

  2. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison.

    Science.gov (United States)

    Dai, Qi; Yang, Yanchun; Wang, Tianming

    2008-10-15

    Many proposed statistical measures can efficiently compare biological sequences to further infer their structures, functions and evolutionary information. They are related in spirit because all the ideas for sequence comparison try to use the information on the k-word distributions, Markov model or both. Motivated by adding k-word distributions to Markov model directly, we investigated two novel statistical measures for sequence comparison, called wre.k.r and S2.k.r. The proposed measures were tested by similarity search, evaluation on functionally related regulatory sequences and phylogenetic analysis. This offers the systematic and quantitative experimental assessment of our measures. Moreover, we compared our achievements with these based on alignment or alignment-free. We grouped our experiments into two sets. The first one, performed via ROC (receiver operating curve) analysis, aims at assessing the intrinsic ability of our statistical measures to search for similar sequences from a database and discriminate functionally related regulatory sequences from unrelated sequences. The second one aims at assessing how well our statistical measure is used for phylogenetic analysis. The experimental assessment demonstrates that our similarity measures intending to incorporate k-word distributions into Markov model are more efficient.

  3. A COMPARISON OF SPECTROSCOPIC VERSUS IMAGING TECHNIQUES FOR DETECTING CLOSE COMPANIONS TO KEPLER OBJECTS OF INTEREST

    Energy Technology Data Exchange (ETDEWEB)

    Teske, Johanna K. [Carnegie DTM, 5241 Broad Branch Road, NW, Washington, DC 20015 (United States); Everett, Mark E. [National Optical Astronomy Observatory, 950 N. Cherry Ave., Tucson, AZ 85719 (United States); Hirsch, Lea [Astronomy Department, University of California at Berkeley, Berkeley, CA 94720 (United States); Furlan, Elise; Ciardi, David R. [NASA Exoplanet Science Institute, California Institute of Technology, 770 South Wilson Ave., Pasadena, CA 91125 (United States); Horch, Elliott P. [Department of Physics, Southern Connecticut State University, 501 Crescent Street, New Haven, CT 06515 (United States); Howell, Steve B. [NASA Ames Research Center, Moffett Field, CA 94035 (United States); Gonzales, Erica; Crepp, Justin R., E-mail: jteske@carnegiescience.edu [Department of Physics, University of Notre Dame, 225 Nieuwland Science Hall, Notre Dame, IN 46556 (United States)

    2015-11-15

    Kepler planet candidates require both spectroscopic and imaging follow-up observations to rule out false positives and detect blended stars. Traditionally, spectroscopy and high-resolution imaging have probed different host star companion parameter spaces, the former detecting tight binaries and the latter detecting wider bound companions as well as chance background stars. In this paper, we examine a sample of 11 Kepler host stars with companions detected by two techniques—near-infrared adaptive optics and/or optical speckle interferometry imaging, and a new spectroscopic deblending method. We compare the companion effective temperatures (T{sub eff}) and flux ratios (F{sub B}/F{sub A}, where A is the primary and B is the companion) derived from each technique and find no cases where both companion parameters agree within 1σ errors. In 3/11 cases the companion T{sub eff} values agree within 1σ errors, and in 2/11 cases the companion F{sub B}/F{sub A} values agree within 1σ errors. Examining each Kepler system individually considering multiple avenues (isochrone mapping, contrast curves, probability of being bound), we suggest two cases for which the techniques most likely agree in their companion detections (detect the same companion star). Overall, our results support the advantage that the spectroscopic deblending technique has for finding very close-in companions (θ ≲ 0.″02–0.″05) that are not easily detectable with imaging. However, we also specifically show how high-contrast AO and speckle imaging observations detect companions at larger separations (θ ≥ 0.″02–0.″05) that are missed by the spectroscopic technique, provide additional information for characterizing the companion and its potential contamination (e.g., position angle, separation, magnitude differences), and cover a wider range of primary star effective temperatures. The investigation presented here illustrates the utility of combining the two techniques to reveal higher

  4. Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis.

    Science.gov (United States)

    Tsementzi, Despina; Castro Gordillo, Juan; Mahagna, Mustafa; Gottlieb, Yuval; Konstantinidis, Konstantinos T

    2018-05-01

    Understanding the symbiotic interaction between Coxiella-like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content. Both genomes encode numerous pseudogenes, consistent with an ongoing genome reduction process. In silico flux balance metabolic analysis (FBA) revealed the excess production of L-proline for both genomes, indicating a possible proline transport from Coxiella to the tick. Additionally, both CR genomes encode multiple copies of the proline/betaine transporter, proP gene. Modelling additional Coxiellaceae members including other tick CLE, did not identify proline as an excreted metabolite. Although both CRs and CRt genomes encode intact B vitamin synthesis pathway genes, which are presumed to underlay the mechanism of CLE-tick symbiosis, the FBA analysis indicated no changes for their products. Therefore, this study provides new testable hypotheses for the symbiosis mechanism and a better understanding of CLE genome evolution and diversity. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

  5. Microbial analysis of bite marks by sequence comparison of streptococcal DNA.

    Directory of Open Access Journals (Sweden)

    Darnell M Kennedy

    Full Text Available 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.

  6. Delineation of the genus Actinobacillus by comparison of partial infB sequences

    DEFF Research Database (Denmark)

    Nørskov-Lauritsen, Niels; Christensen, H; Okkels, H.

    2004-01-01

    A 426 bp fragment of infB, a housekeeping gene that encodes translation initiation factor 2, was sequenced from 59 clinical isolates and type strains of Actinobacillus species and sequences were compared. Partial sequences of 16S rRNA genes were also obtained. By comparing infB sequences, Actinob...

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

    Science.gov (United States)

    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. Copyright © 2015. Published by Elsevier Inc.

  8. a Comparison of Morphological Taxonomy and Next Generation DNA Sequencing for the Assessment of Zooplankton Diversity

    Science.gov (United States)

    Harvey, J.; Fisher, J. L.; Johnson, S.; Morgan, S.; Peterson, W. T.; Satterthwaite, E. V.; Vrijenhoek, R. C.

    2016-02-01

    Our ability to accurately characterize the diversity of planktonic organisms is affected by both the methods we use to collect water samples and our approaches to assessing sample contents. Plankton nets collect organisms from high volumes of water, but integrate sample contents along the net's path. In contrast, plankton pumps collect water from discrete depths. Autonomous underwater vehicles (AUVs) can collect water samples with pinpoint accuracy from physical features such as upwelling fronts or biological features such as phytoplankton blooms, but sample volumes are necessarily much smaller than those possible with nets. Characterization of plankton diversity and abundances in water samples may also vary with the assessment method we apply. Morphological taxonomy provides visual identification and enumeration of organisms via microscopy, but is labor intensive. Next generation DNA sequencing (NGS) shows great promise for assessing plankton diversity in water samples but accurate assessment of relative abundances may not be possible in all cases. Comparison of morphological taxonomy to molecular approaches is necessary to identify areas of overlap and also areas of disagreement between these methods. We have compared morphological taxonomic assessments to mitochondrial COI and nuclear 28S ribosomal RNA NGS results for plankton net samples collected in Monterey bay, California. We have made a similar comparison for plankton pump samples, and have also applied our NGS methods to targeted, small volume water samples collected by an AUV. Our goal is to communicate current results and lessons learned regarding application of traditional taxonomy and novel molecular approaches to the study of plankton diversity in spatially and temporally variable, coastal marine environments.

  9. Poecilia picta, a Close Relative to the Guppy, Exhibits Red Male Coloration Polymorphism: A System for Phylogenetic Comparisons.

    Directory of Open Access Journals (Sweden)

    Anna K Lindholm

    Full Text Available Studies on the evolution of female preference and male color polymorphism frequently focus on single species since traits and preferences are thought to co-evolve. The guppy, Poecilia reticulata, has long been a premier model for such studies because female preferences and orange coloration are well known to covary, especially in upstream/downstream pairs of populations. However, focused single species studies lack the explanatory power of the comparative method, which requires detailed knowledge of multiple species with known evolutionary relationships. Here we describe a red color polymorphism in Poecilia picta, a close relative to guppies. We show that this polymorphism is restricted to males and is maintained in natural populations of mainland South America. Using tests of female preference we show female P. picta are not more attracted to red males, despite preferences for red/orange in closely related species, such as P. reticulata and P. parae. Male color patterns in these closely related species are different from P. picta in that they occur in discrete patches and are frequently Y chromosome-linked. P. reticulata have an almost infinite number of male patterns, while P. parae males occur in discrete morphs. We show the red male polymorphism in P. picta extends continuously throughout the body and is not a Y-linked trait despite the theoretical prediction that sexually-selected characters should often be linked to the heterogametic sex chromosome. The presence/absence of red male coloration of P. picta described here makes this an ideal system for phylogenetic comparisons that could reveal the evolutionary forces maintaining mate choice and color polymorphisms in this speciose group.

  10. Comparison of variable region 3 sequences of human immunodeficiency virus type 1 from infected children with the RNA and DNA sequences of the virus populations of their mothers.

    Science.gov (United States)

    Scarlatti, G; Leitner, T; Halapi, E; Wahlberg, J; Marchisio, P; Clerici-Schoeller, M A; Wigzell, H; Fenyö, E M; Albert, J; Uhlén, M

    1993-01-01

    We have compared the variable region 3 sequences from 10 human immunodeficiency virus type 1 (HIV-1)-infected infants to virus sequences from the corresponding mothers. The sequences were derived from DNA of uncultured peripheral blood mononuclear cells (PBMC), DNA of cultured PBMC, and RNA from serum collected at or shortly after delivery. The infected infants, in contrast to the mothers, harbored homogeneous virus populations. Comparison of sequences from the children and clones derived from DNA of the corresponding mothers showed that the transmitted virus represented either a minor or a major virus population of the mother. In contrast to an earlier study, we found no evidence of selection of minor virus variants during transmission. Furthermore, the transmitted virus variant did not show any characteristic molecular features. In some cases the transmitted virus was more related to the virus RNA population of the mother and in other cases it was more related to the virus DNA population. This suggests that either cell-free or cell-associated virus may be transmitted. These data will help AIDS researchers to understand the mechanism of transmission and to plan strategies for prevention of transmission. PMID:8446584

  11. [Comparison research on two-stage sequencing batch MBR and one-stage MBR].

    Science.gov (United States)

    Yuan, Xin-Yan; Shen, Heng-Gen; Sun, Lei; Wang, Lin; Li, Shi-Feng

    2011-01-01

    Aiming at resolving problems in MBR operation, like low nitrogen and phosphorous removal efficiency, severe membrane fouling and etc, comparison research on two-stage sequencing batch MBR (TSBMBR) and one-stage aerobic MBR has been done in this paper. The results indicated that TSBMBR owned advantages of SBR in removing nitrogen and phosphorous, which could make up the deficiency of traditional one-stage aerobic MBR in nitrogen and phosphorous removal. During steady operation period, effluent average NH4(+) -N, TN and TP concentration is 2.83, 12.20, 0.42 mg/L, which could reach domestic scenic environment use. From membrane fouling control point of view, TSBMBR has lower SMP in supernatant, specific trans-membrane flux deduction rate, membrane fouling resistant than one-stage aerobic MBR. The sedimentation and gel layer resistant of TSBMBR was only 6.5% and 33.12% of one-stage aerobic MBR. Besides high efficiency in removing nitrogen and phosphorous, TSBMBR could effectively reduce sedimentation and gel layer pollution on membrane surface. Comparing with one-stage MBR, TSBMBR could operate with higher trans-membrane flux, lower membrane fouling rate and better pollutants removal effects.

  12. The optimal design of stepped wedge trials with equal allocation to sequences and a comparison to other trial designs.

    Science.gov (United States)

    Thompson, Jennifer A; Fielding, Katherine; Hargreaves, James; Copas, Andrew

    2017-12-01

    Background/Aims We sought to optimise the design of stepped wedge trials with an equal allocation of clusters to sequences and explored sample size comparisons with alternative trial designs. Methods We developed a new expression for the design effect for a stepped wedge trial, assuming that observations are equally correlated within clusters and an equal number of observations in each period between sequences switching to the intervention. We minimised the design effect with respect to (1) the fraction of observations before the first and after the final sequence switches (the periods with all clusters in the control or intervention condition, respectively) and (2) the number of sequences. We compared the design effect of this optimised stepped wedge trial to the design effects of a parallel cluster-randomised trial, a cluster-randomised trial with baseline observations, and a hybrid trial design (a mixture of cluster-randomised trial and stepped wedge trial) with the same total cluster size for all designs. Results We found that a stepped wedge trial with an equal allocation to sequences is optimised by obtaining all observations after the first sequence switches and before the final sequence switches to the intervention; this means that the first sequence remains in the control condition and the last sequence remains in the intervention condition for the duration of the trial. With this design, the optimal number of sequences is [Formula: see text], where [Formula: see text] is the cluster-mean correlation, [Formula: see text] is the intracluster correlation coefficient, and m is the total cluster size. The optimal number of sequences is small when the intracluster correlation coefficient and cluster size are small and large when the intracluster correlation coefficient or cluster size is large. A cluster-randomised trial remains more efficient than the optimised stepped wedge trial when the intracluster correlation coefficient or cluster size is small. A

  13. Comparison of single-shot fast spin-echo sequence and T2-weighted fast spin-echo sequence in MR imaging of the brain

    International Nuclear Information System (INIS)

    Cha, Sung Ho; Seo, Jeong Jin; Jeong, Gwang Woo; Kim, Jae Kyu; Kim, Yun Hyeon; Jeong, Yong Yeon; Kang, Heoung Keun; Oh, Hee Yeon; Yoon, Jong Hoon

    1998-01-01

    The purpose of this study was to evaluate the usefulness of the single-shot fast spinecho (SS-FSE) sequence in comparison with the T2-weighted fast spin-echo (T2-FSE) sequence in brain MR imaging. In 41 patients aged 15-75 years with intracranial lesion, both SS-FSE and T2-FES images were obtained using a 1.5-T MR system. Lesions included cerebral ischemia or infarcts (n=3D23), tumors (n=3D10), hemorrhages (n=3D3), inflammatory diseases (n=3D2), arachnoid cysts(n=3D2), and vascular disease (n=3D1), and the MR images were retrospectively evaluated. To calculate contrast-to-noise ratio (CNR), percentage contrast, and signal-to-noise ratio (SNR)-and thus make a quantitative comparison-the mean signal intensities of lesions, normal brain tissue, and noise out-side the patient were measured. For qualitative comparison, the visibility, margin, and extent of the lesions were rated using a five-grade system, and the degree of MR artifacts was also evaluated. Wilcoxon's signed ranks test was used for statistical analysis. The mean CNR of lesions was significantly higher on SS-FSE (31.3) than on T2-FSE images (27.5) (p=3D0.0131). Mean percentage contrast was also higher on SS-FSE (159.0) than on T2-FSE images (108.5) (p=3D0.0222), but mean SNR was higher on T2-FSE (80.3) than on SS-FSE images (53.5) (p=3D0.0000). No significant differences in lesion visibility were observed between the two imaging sequences, though margin and extent of the lesion were worse on SS-FSE images. For MR artifacts, no significant differences were demonstrated. For the evaluation of most intracranial lesions, MR imaging using the SS-FSE sequence appears to be slightly inferior to the T2-FSE sequence, but may be useful where patients are ill or uncooperative, or where children require sedation.=20

  14. Recent speciation in three closely related sympatric specialists: inferences using multi-locus sequence, post-mating isolation and endosymbiont data.

    Directory of Open Access Journals (Sweden)

    Huai-Jun Xue

    Full Text Available Shifting between unrelated host plants is relatively rare for phytophagous insects, and distinct host specificity may play crucial roles in reproductive isolation. However, the isolation status and the relationship between parental divergence and post-mating isolation among closely related sympatric specialists are still poorly understood. Here, multi-locus sequence were used to estimate the relationship among three host plant-specific closely related flea beetles, Altica cirsicola, A. fragariae and A. viridicyanea (abbreviated as AC, AF and AV respectively. The tree topologies were inconsistent using different gene or different combinations of gene fragments. The relationship of AF+(AC+AV was supported, however, by both gene tree and species tree based on concatenated data. Post-mating reproductive data on the results of crossing these three species are best interpreted in the light of a well established phylogeny. Nuclear-induced but not Wolbachia-induced unidirectional cytoplasmic incompatibility, which was detected in AC-AF and AF-AV but not in AC-AV, may also suggest more close genetic affinity between AC and AV. Prevalence of Wolbachia in these three beetles, and the endosymbiont in most individuals of AV and AC sharing a same wsp haplotype may give another evidence of AF+(AC+AV. Our study also suggested that these three flea beetles diverged in a relative short time (0.94 My, which may be the result of shifting between unrelated host plants and distinct host specificity. Incomplete post-mating isolation while almost complete lineage sorting indicated that effective pre-mating isolation among these three species should have evolved.

  15. Comparison of the phenomenology of SBO sequences with and without seals LOCA Westinghouse PWRs

    International Nuclear Information System (INIS)

    Mena Rosell, L.; Queral, C.; Jimenez Varas, G.

    2013-01-01

    SBO sequences have gained notoriety after the accident at Fukushima. Within this type of sequence the appearance or not of seals of the RCP LOCA determines the evolution of the accident. This work has been applied the methodology of integrated safety analysis (ISA), developed by the CSN, sequences of SBO. The objective is to compare the evolution of SBO sequences in a wide spectrum of conditions and recovery times of AC and DC loss. The simulations have been performed with the SCAIS tool coupled to MAAP. The set of simulations carried out, of the order of 2,000 sequences, clearly show the differences in the evolution of sequences with and without seals crazy. This type of analysis allows you to verify which would be the most appropriate management of sequence depending on the appearance or not of the MADWOMAN of seals.

  16. Experimental study on a comparison of typical premixed combustible gas-air flame propagation in a horizontal rectangular closed duct.

    Science.gov (United States)

    Jin, Kaiqiang; Duan, Qiangling; Liew, K M; Peng, Zhongjing; Gong, Liang; Sun, Jinhua

    2017-04-05

    Research surrounding premixed flame propagation in ducts has a history of more than one hundred years. Most previous studies focus on the tulip flame formation and flame acceleration in pure gas fuel-air flame. However, the premixed natural gas-air flame may show different behaviors and pressure dynamics due to its unique composition. Natural gas, methane and acetylene are chosen here to conduct a comparison study on different flame behaviors and pressure dynamics, and to explore the influence of different compositions on premixed flame dynamics. The characteristics of flame front and pressure dynamics are recorded using high-speed schlieren photography and a pressure transducer, respectively. The results indicate that the compositions of the gas mixture greatly influence flame behaviors and pressure. Acetylene has the fastest flame tip speed and the highest pressure, while natural gas has a faster flame tip speed and higher pressure than methane. The Bychkov theory for predicting the flame skirt motion is verified, and the results indicate that the experimental data coincide well with theory in the case of equivalence ratios close to 1.00. Moreover, the Bychkov theory is able to predict flame skirt motion for acetylene, even outside of the best suitable expansion ratio range of 6

  17. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing.

    Science.gov (United States)

    Chimukangara, Benjamin; Varyani, Bhavini; Shamu, Tinei; Mutsvangwa, Junior; Manasa, Justen; White, Elizabeth; Chimbetete, Cleophas; Luethy, Ruedi; Katzenstein, David

    2017-05-01

    HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant. Copyright © 2016 Elsevier B.V. All rights reserved.

  18. Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

    Directory of Open Access Journals (Sweden)

    Jonathan Z Li

    Full Text Available The impact of raltegravir-resistant HIV-1 minority variants (MVs on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs.A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser.Illumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001. Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454.In participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.

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

    Science.gov (United States)

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

    2014-01-01

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

  20. Nucleotide Sequences and Comparison of Two Large Conjugative Plasmids from Different Campylobacter species

    National Research Council Canada - National Science Library

    Batchelor, Roger A; Pearson, Bruce M; Friis, Lorna M; Guerry, Patricia; Wells, Jerry M

    2004-01-01

    .... Both plasmids are mosaic in structure, having homologues of genes found in a variety of different commensal and pathogenic bacteria, but nevertheless, showed striking similarities in DNA sequence...

  1. Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.

    Science.gov (United States)

    Zhang, Guoqiang; Wang, Jianfeng; Yang, Jin; Li, Wenjie; Deng, Yutian; Li, Jing; Huang, Jun; Hu, Songnian; Zhang, Bing

    2015-08-05

    To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer. Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3% in four samples, whereas the concordance of co-detected variant loci reached 99%. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5%) was higher than the SNPs specific to TargetSeq-Proton (60.0%) or specific to SureSelect-HiSeq (88.3%). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0%) and SureSelect-HiSeq-specific (89.6%) were higher than those of TargetSeq-Proton-specific (15.8%). In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the

  2. Comparison of MRI pulse sequences in defining prostate volume after permanent implantation

    International Nuclear Information System (INIS)

    McLaughlin, P.W.; Narayana, V.; Drake, D.G.; Miller, B.M.; Marsh, L.; Chan, J.; Gonda, R.; Winfield, R.J.; Roberson, P.L.

    2002-01-01

    Purpose: To determine the relative value of three MRI pulse sequences in defining the prostate volume after permanent implantation. Methods and Materials: A total of 45 patients who received a permanent 125 I implant were studied. Two weeks after implantation, an axial CT scan (2 mm thickness) and T 1 -weighted, T 1 -weighted fat saturation, and T 2 -weighted axial MRI (3-mm) studies were obtained. The prostate volumes were compared with the initial ultrasound planning volumes, and subsequently the CT, T 1 -weighted, and T 1 -weighted fat saturation MRI volumes were compared with the T 2 -weighted volumes. Discrepancies in volume were evaluated by visual inspection of the registered axial images and the registration of axial volumes on the sagittal T 2 -weighted volumes. In a limited set of patients, pre- and postimplant CT and T 2 -weighted MRI studies were available for comparison to determine whether prostate volume changes after implant were dependent on the imaging modality. Results: T 1 -weighted and T 1 -weighted fat saturation MRI and CT prostate volumes were consistently larger than the T 2 -weighted MRI prostate volumes, with a volume on average 1.33 (SD 0.24) times the T 2 -weighted volume. This discrepancy was due to the superiority of T 2 -weighted MRI for prostate definition at the following critical interfaces: membranous urethra, apex, and anterior base-bladder and posterior base-seminal vesicle interfaces. The differences in prostate definition in the anterior base region suggest that the commonly reported underdose may be due to overestimation of the prostate in this region by CT. The consistent difference in volumes suggests that the degree of swelling observed after implantation is in part a function of the imaging modality. In patients with pre- and postimplant CT and T 2 -weighted MRI images, swelling on the T 2 -weighted images was 1.1 times baseline and on CT was 1.3 times baseline, confirming the imaging modality dependence of prostate

  3. Sequence comparison of the rDNA introns from six different species of Tetrahymena

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engberg, J

    1985-01-01

    model for the intron RNA of Cech et al. (Proc. Natl. Acad. Sci. U.S.A. 80, 3903 (83)). Most of the sequence variation in the four new sequences reported here is found in single stranded loops in the model. However, in four cases we found nucleotide substitutions in duplex stem regions, two of them...

  4. Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing.

    Science.gov (United States)

    Monteiro, Rose A; Balsanelli, Eduardo; Tuleski, Thalita; Faoro, Helison; Cruz, Leonardo M; Wassem, Roseli; de Baura, Valter A; Tadra-Sfeir, Michelle Z; Weiss, Vinícius; DaRocha, Wanderson D; Muller-Santos, Marcelo; Chubatsu, Leda S; Huergo, Luciano F; Pedrosa, Fábio O; de Souza, Emanuel M

    2012-05-01

    Herbaspirillum rubrisubalbicans M1 causes the mottled stripe disease in sugarcane cv. B-4362. Inoculation of this cultivar with Herbaspirillum seropedicae SmR1 does not produce disease symptoms. A comparison of the genomic sequences of these closely related species may permit a better understanding of contrasting phenotype such as endophytic association and pathogenic life style. To achieve this goal, we constructed suppressive subtractive hybridization (SSH) libraries to identify DNA fragments present in one species and absent in the other. In a parallel approach, partial genomic sequence from H. rubrisubalbicans M1 was directly compared in silico with the H. seropedicae SmR1 genome. The genomic differences between the two organisms revealed by SSH suggested that lipopolysaccharide and adhesins are potential molecular factors involved in the different phenotypic behavior. The cluster wss probably involved in cellulose biosynthesis was found in H. rubrisubalbicans M1. Expression of this gene cluster was increased in H. rubrisubalbicans M1 cells attached to the surface of maize root, and knockout of wssD gene led to decrease in maize root surface attachment and endophytic colonization. The production of cellulose could be responsible for the maize attachment pattern of H. rubrisubalbicans M1 that is capable of outcompeting H. seropedicae SmR1. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. MR colonography with fecal tagging: comparison between 2D turbo FLASH and 3D FLASH sequences

    International Nuclear Information System (INIS)

    Papanikolaou, Nickolas; Grammatikakis, John; Maris, Thomas; Prassopoulos, Panos; Gourtsoyiannis, Nicholas; Lauenstein, Thomas

    2003-01-01

    The objective of this study was to compare inversion recovery turbo 2D fast low-angle shot (FLASH) and 3D FLASH sequences for fecal-tagged MR colonography studies. Fifteen consecutive patients with indications for colonoscopy underwent MR colonography with fecal tagging. An inversion recovery turbo-FLASH sequence was applied and compared in terms of artifacts presence, efficiency for masking residual stool, and colonic wall conspicuity with a fat-saturated 3D FLASH sequence. Both sequences were acquired following administration of paramagnetic contrast agent. Contrast-to-noise ratio and relative contrast between colonic wall and lumen were calculated and compared for both sequences. Turbo 2D FLASH provided fewer artifacts, higher efficiency for masking the residual stool, and colonic wall conspicuity equivalent to 3D FLASH. An inversion time of 10 ms provided homogeneously low signal intensity of the colonic lumen. Contrast to noise between colonic wall and lumen was significantly higher in the 3D FLASH images, whereas differences in relative contrast were not statistically significant. An optimized inversion-recovery 2D turbo-FLASH sequence provides better fecal tagging results and should be added to the 3D FLASH sequence when designing dark-lumen MR colonography examination protocols. (orig.)

  6. Resampling nucleotide sequences with closest-neighbor trimming and its comparison to other methods.

    Directory of Open Access Journals (Sweden)

    Kouki Yonezawa

    Full Text Available A large number of nucleotide sequences of various pathogens are available in public databases. The growth of the datasets has resulted in an enormous increase in computational costs. Moreover, due to differences in surveillance activities, the number of sequences found in databases varies from one country to another and from year to year. Therefore, it is important to study resampling methods to reduce the sampling bias. A novel algorithm-called the closest-neighbor trimming method-that resamples a given number of sequences from a large nucleotide sequence dataset was proposed. The performance of the proposed algorithm was compared with other algorithms by using the nucleotide sequences of human H3N2 influenza viruses. We compared the closest-neighbor trimming method with the naive hierarchical clustering algorithm and [Formula: see text]-medoids clustering algorithm. Genetic information accumulated in public databases contains sampling bias. The closest-neighbor trimming method can thin out densely sampled sequences from a given dataset. Since nucleotide sequences are among the most widely used materials for life sciences, we anticipate that our algorithm to various datasets will result in reducing sampling bias.

  7. [Comparison of rDNA internal transcribed spacer sequences in asparagus].

    Science.gov (United States)

    Ou, Li-Jun; Ye, Wei; Zeng, Gui-Ping; Jiang, Xiang-Hui; She, Chao-Wen; Xu, Dong; Yang, Jia-Qiang

    2010-10-01

    Using ITS sequence of nine species to identify counterfeiting medicine and analyse phylogenetic of Asparagus. Analysing ITS sequences by amplification, cloning,sequencing and alignment. The length range of ITS sequence of nine species was from 711 to 748 bp, the percentage of G + C content was about 60%. The phylogenetic tree constructed on the basis of the ITS sequences showed that nine species were divided into two branches: Asparagus cochinchinensis, Asparagus officinalis, Asparagus densiflorus, Asparagus densiflorus cv. Myers and Asparagus densiflorus cv. Sprengeri were a branch and the others were a branch. Asparagus densiflorus and Asparagus densflorus cv. Myers those were from Africa had priority to clustering and then clustering with Asparagus densiflorus cv. Sprengeri that was a variant of Asparagus densiflorus in the first branch. Asparagus setaceus had relatively distant genetic relationship with the others three materials in another branch. The ITS sequences could distinguish species of Asparagus to test the counterfeit. Division status in phylogenetic tree of some species were debatable and ITS sequence was combined with others analytical tools to analyze the realistic phylogeny.

  8. Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

    Science.gov (United States)

    Heydt, Carina; Fassunke, Jana; Künstlinger, Helen; Ihle, Michaela Angelika; König, Katharina; Heukamp, Lukas Carl; Schildhaus, Hans-Ulrich; Odenthal, Margarete; Büttner, Reinhard; Merkelbach-Bruse, Sabine

    2014-01-01

    Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3–24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for

  9. Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.

    Directory of Open Access Journals (Sweden)

    Carina Heydt

    Full Text Available Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA. No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can

  10. MRI in neuro-Behcet's syndrome: comparison of conventional spin-echo and FLAIR pulse sequences

    International Nuclear Information System (INIS)

    Jaeger, H.R.; Albrecht, T.; Curati-Alasonatti, W.L.; Williams, E.J.; Haskard, D.O.

    1999-01-01

    We compared the sensitivity of a fluid-attenuated inversion-recovery (FLAIR) sequence with that of a conventional dual-echo spin-echo (SE) sequence to brain lesions in 20 patients with Behcet's syndrome. They underwent 25 MRI examinations. The images were independently analysed for the number, type and anatomical location of lesions shown. There were 18 abnormal studies (13 initial and 5 follow-up). The FLAIR sequence detected significantly more lesions than the SE TE 80 (P < 0.05) and SE TE 20 (P < 0.01) sequences. It was particularly useful for demonstrating lesions in the juxtacortical white matter, which accounted for over half the lesions detected on the FLAIR images. Of patients presenting with nonspecific symptoms such as headache, seven had normal and five had abnormal studies. All patients presenting with focal neurological signs had abnormal imaging. We found supratentorial and, in particular, juxtacortical lesions to be more frequent than previously described. (orig.)

  11. Comparison of Human and Guinea Pig Acetylcholinesterase Sequences and Rates of Oxime-Assisted Reactivation

    Science.gov (United States)

    2010-01-01

    of appropriate animal model systems. For OP poisoning, the guinea pig (Cavia porcellus) is a commonly used animal model because guinea pigs more...endogenous bioscavenger in vivo. Although guinea pigs historically have been used to test OP poisoning therapies, it has been found recently that guinea pig AChE...transcribed mRNA encoding guinea pig AChE, amplified the resulting cDNA, and sequenced this product. The nucleotide and deduced amino acid sequences of

  12. Retrospective comparison of three-dimensional imaging sequences in the visualization of posterior fossa cranial nerves.

    Science.gov (United States)

    Ors, Suna; Inci, Ercan; Turkay, Rustu; Kokurcan, Atilla; Hocaoglu, Elif

    2017-12-01

    To compare efficancy of three-dimentional SPACE (sampling perfection with application-optimized contrasts using different flip-angle evolutions) and CISS (constructive interference in steady state) sequences in the imaging of the cisternal segments of cranial nerves V-XII. Temporal MRI scans from 50 patients (F:M ratio, 27:23; mean age, 44.5±15.9 years) admitted to our hospital with vertigo, tinnitus, and hearing loss were retrospectively analyzed. All patients had both CISS and SPACE sequences. Quantitative analysis of SPACE and CISS sequences was performed by measuring the ventricle-to-parenchyma contrast-to-noise ratio (CNR). Qualitative analysis of differences in visualization capability, image quality, and severity of artifacts was also conducted. A score ranging 'no artefact' to 'severe artefacts and unreadable' was used for the assessment of artifacts and from 'not visualized' to 'completely visualized' for the assesment of image quality, respectively. The distribution of variables was controlled by the Kolmogorov-Smirnov test. Samples t-test and McNemar's test were used to determine statistical significance. Rates of visualization of posterior fossa cranial nerves in cases of complete visualization were as follows: nerve V (100% for both sequences), nerve VI (94% in SPACE, 86% in CISS sequences), nerves VII-VIII (100% for both sequences), IX-XI nerve complex (96%, 88%); nerve XII (58%, 46%) (p<0.05). SPACE sequences showed fewer artifacts than CISS sequences (p<0.002). Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Comparison of MR sequences in early cerebral infarction at 0.5 T

    International Nuclear Information System (INIS)

    Saatci, I.; Baskan, O.; Cekirge, H.S.; Besim, A.

    2000-01-01

    To compare the diagnostic values of fluid-attenuated inversion recovery (FLAIR) and gradient spin-echo (GRASE) with those of conventional spin-echo (SE) and fast SE T2-weighted sequences in the evaluation of acute cerebrovascular lesions at 0.5 T. Material and Methods: Twenty-two consecutive patients with the clinical diagnosis of acute cerebrovascular accident were examined by MR imaging within the first 48 h of ictus. MR examination included 5-mm axial conventional SE and turbo SE (TSE) T2-weighted, dual-echo GRASE and FLAIR sequences. The patients also had pre- and postcontrast T1-weighted axial images. Two examiners evaluated the images and scored the conspicuity of the acute lesions. Results: Regardless of location, FLAIR provided the best lesion conspicuity in the detection of acute infarcts, followed by the GRASE sequence. In the posterior fossa, TSE and SE demonstrated the lesions better than GRASE and FLAIR techniques. In the detection of hemorrhagic elements within the ischemic region, TSE demonstrated statistically significant superiority over other sequences. Conclusion: In the detection of acute ischemic lesions in locations other than the posterior fossa, FLAIR provided the best lesion conspicuity among four T2-weighted sequences, including SE, TSE, GRASE and FLAIR. However, for the posterior fossa examination, preference of SE or TSE T2-weighted sequences is suggested

  14. Comparison of MR sequences in early cerebral infarction at 0.5 T

    Energy Technology Data Exchange (ETDEWEB)

    Saatci, I.; Baskan, O.; Cekirge, H.S.; Besim, A. [Hacettepe Univ. Hospital, Ankara (Turkey). Radiology Dept.

    2000-11-01

    To compare the diagnostic values of fluid-attenuated inversion recovery (FLAIR) and gradient spin-echo (GRASE) with those of conventional spin-echo (SE) and fast SE T2-weighted sequences in the evaluation of acute cerebrovascular lesions at 0.5 T. Material and Methods: Twenty-two consecutive patients with the clinical diagnosis of acute cerebrovascular accident were examined by MR imaging within the first 48 h of ictus. MR examination included 5-mm axial conventional SE and turbo SE (TSE) T2-weighted, dual-echo GRASE and FLAIR sequences. The patients also had pre- and postcontrast T1-weighted axial images. Two examiners evaluated the images and scored the conspicuity of the acute lesions. Results: Regardless of location, FLAIR provided the best lesion conspicuity in the detection of acute infarcts, followed by the GRASE sequence. In the posterior fossa, TSE and SE demonstrated the lesions better than GRASE and FLAIR techniques. In the detection of hemorrhagic elements within the ischemic region, TSE demonstrated statistically significant superiority over other sequences. Conclusion: In the detection of acute ischemic lesions in locations other than the posterior fossa, FLAIR provided the best lesion conspicuity among four T2-weighted sequences, including SE, TSE, GRASE and FLAIR. However, for the posterior fossa examination, preference of SE or TSE T2-weighted sequences is suggested.

  15. Sequence comparison for non-enhanced MRA of the lower extremity arteries at 7 Tesla.

    Directory of Open Access Journals (Sweden)

    Sören Johst

    Full Text Available In this study three sequences for non-contrast-enhanced MRA of the lower extremity arteries at 7T were compared. Cardiac triggering was used with the aim to reduce signal variations in the arteries. Two fast single-shot 2D sequences, a modified Ultrafast Spoiled Gradient Echo (UGRE sequence and a variant of the Quiescent-Interval Single-Shot (QISS sequence were triggered via phonocardiogram and compared in volunteer examinations to a non-triggered 2D gradient echo (GRE sequence. For image acquisition, a 16-channel transmit/receive coil and a manually positionable AngioSURF table were used. To tackle B1 inhomogeneities at 7T, Time-Interleaved Acquisition of Modes (TIAMO was integrated in GRE and UGRE. To compare the three sequences quantitatively, a vessel-to-background ratio (VBR was measured in all volunteers and stations. In conclusion, cardiac triggering was able to suppress flow artifacts satisfactorily. The modified UGRE showed only moderate image artifacts. Averaged over all volunteers and stations, GRE reached a VBR of 4.18±0.05, UGRE 5.20±0.06, and QISS 2.72±0.03. Using cardiac triggering and TIAMO imaging technique was essential to perform non-enhanced MRA of the lower extremities vessels at 7T. The modified UGRE performed best, as observed artifacts were only moderate and the highest average VBR was reached.

  16. Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II

    Directory of Open Access Journals (Sweden)

    Archer John

    2012-03-01

    Full Text Available Abstract Background Next generation sequencing provides detailed insight into the variation present within viral populations, introducing the possibility of treatment strategies that are both reactive and predictive. Current software tools, however, need to be scaled up to accommodate for high-depth viral data sets, which are often temporally or spatially linked. In addition, due to the development of novel sequencing platforms and chemistries, each with implicit strengths and weaknesses, it will be helpful for researchers to be able to routinely compare and combine data sets from different platforms/chemistries. In particular, error associated with a specific sequencing process must be quantified so that true biological variation may be identified. Results Segminator II was developed to allow for the efficient comparison of data sets derived from different sources. We demonstrate its usage by comparing large data sets from 12 influenza H1N1 samples sequenced on both the 454 Life Sciences and Illumina platforms, permitting quantification of platform error. For mismatches median error rates at 0.10 and 0.12%, respectively, suggested that both platforms performed similarly. For insertions and deletions median error rates within the 454 data (at 0.3 and 0.2%, respectively were significantly higher than those within the Illumina data (0.004 and 0.006%, respectively. In agreement with previous observations these higher rates were strongly associated with homopolymeric stretches on the 454 platform. Outside of such regions both platforms had similar indel error profiles. Additionally, we apply our software to the identification of low frequency variants. Conclusion We have demonstrated, using Segminator II, that it is possible to distinguish platform specific error from biological variation using data derived from two different platforms. We have used this approach to quantify the amount of error present within the 454 and Illumina platforms in

  17. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

    Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  18. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Science.gov (United States)

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

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  19. Comparison of Nucleotide Sequence of P2C Region in Diabetogenic and Non-Diabetogenic Coxsackie Virus B5 Isolates

    Directory of Open Access Journals (Sweden)

    Cheng-Chong Chou

    2004-11-01

    Full Text Available Enteroviruses are environmental triggers in the pathogenesis of type 1 diabetes mellitus (DM. A sequence of six identical amino acids (PEVKEK is shared by the 2C protein of Coxsackie virus B and the glutamic acid decarboxylase (GAD molecules. Between 1995 and 2002, we investigated 22 Coxsackie virus B5 (CVB5 isolates from southern Taiwan. Four of these isolates were obtained from four new-onset type 1 DM patients with diabetic ketoacidosis. We compared a 300 nucleotide sequence in the 2C protein gene (p2C in 24 CVB5 isolates (4 diabetogenic, 18 non-diabetogenic and 2 prototype. We found 0.3-10% nucleotide differences. In the four isolates from type 1 DM patients, there was only 2.4-3.4% nucleotide difference, and there was only 1.7-7.1% nucleotide difference between type 1 DM isolates and non-diabetogenic isolates. Comparison of the nucleotide sequence between prototype virus and 22 CVB5 isolates revealed 18.4-24.1% difference. Twenty-one CVB5 isolates from type 1 DM and non-type 1 DM patients contained the PEVKEK sequence, as shown by the p2C nucleotide sequence. Our data showed that the viral p2C sequence with homology with GAD is highly conserved in CVB5 isolates. There was no difference between diabetogenic and non-diabetogenic CVB5 isolates. All four type 1 DM patients had at least one of the genetic susceptibility alleles HLA-DR, DQA1, DQB1. Other genetic and autoimmune factors such as HLA genetic susceptibility and GAD may also play important roles in the pathogenesis in type 1 DM.

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

    Science.gov (United States)

    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

  1. Analysis and comparison of fragrant gene sequence in some rice cultivars

    Directory of Open Access Journals (Sweden)

    Karami Noushafarin

    2016-01-01

    Full Text Available It is known that the fragrant trait in rice (Oryza sativa L. is largely controlled by fgr gene on chromosome 8 and it has been specified that the existence of an 8 bp deletion and three single nucleotide polymorphism (SNP in exon 7 is effective on this trait. In this study, sequence alignment analysis of fgr exon7 on chromosome 8 for 11 different fragrant and non-fragrant cultivars revealed that 5 aromatic rice cultivars carried 3 SNPs and 8 bp deletion in exon7 which terminates prematurely at a TAA stop codon. However, 5 of the non-aromatics showed a sequence identical to the published Nipponbare, being non-fragrant Japonica variety sequence. An exception among them was Bejar, which had 8 bp deletion and 3SNPs but it was non-aromatic. Sequencing can determine nucleotide alignment of a gene and give beneficial information about gene function. In silico prediction showed proteins sequences alignment of fgr gene for Khazar and Domsiah genotypes were different. Betaine aldehyde dehydrogenase complete enzyme belongs to Khazar non-fragrant genotype that has complete length and 503 amino acids while non-functional BADH2 enzyme for Domsiah fragrant genotype has 251 amino acids that result in accumulate 2-acetyl-1-pyrroline (2AP and produces aroma in fragrant genotypes.

  2. Comparison of 3 T and 7 T MRI clinical sequences for ankle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Juras, Vladimir, E-mail: vladimir.juras@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Slovak Academy of Sciences, Institute of Measurement Science, Dubravska cesta 9, 84104 Bratislava (Slovakia); Welsch, Goetz, E-mail: welsch@bwh.harvard.edu [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Baer, Peter, E-mail: baerpeter@siemens.com [Siemens Healthcare, Richard-Strauss-Strasse 76, D81679 Munich (Germany); Kronnerwetter, Claudia, E-mail: claudia.kronnerwetter@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Fujita, Hiroyuki, E-mail: hiroyuki.fujita@qualedyn.com [Quality Electrodynamics, LCC, 777 Beta Dr, Cleveland, OH 44143-2336 (United States); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria)

    2012-08-15

    The purpose of this study was to compare 3 T and 7 T signal-to-noise and contrast-to noise ratios of clinical sequences for imaging of the ankles with optimized sequences and dedicated coils. Ten healthy volunteers were examined consecutively on both systems with three clinical sequences: (1) 3D gradient-echo, T{sub 1}-weighted; (2) 2D fast spin-echo, PD-weighted; and (3) 2D spin-echo, T{sub 1}-weighted. SNR was calculated for six regions: cartilage; bone; muscle; synovial fluid; Achilles tendon; and Kager's fat-pad. CNR was obtained for cartilage/bone, cartilage/fluid, cartilage/muscle, and muscle/fat-pad, and compared by a one-way ANOVA test for repeated measures. Mean SNR significantly increased at 7 T compared to 3 T for 3D GRE, and 2D TSE was 60.9% and 86.7%, respectively. In contrast, an average SNR decrease of almost 25% was observed in the 2D SE sequence. A CNR increase was observed in 2D TSE images, and in most 3D GRE images. There was a substantial benefit from ultra high-field MR imaging of ankles with routine clinical sequences at 7 T compared to 3 T. Higher SNR and CNR at ultra-high field MR scanners may be useful in clinical practice for ankle imaging. However, carefully optimized protocols and dedicated extremity coils are necessary to obtain optimal results.

  3. The Comparison of Biochemical and Sequencing 16S rDNA Gene Methods to Identify Nontuberculous Mycobacteria

    Directory of Open Access Journals (Sweden)

    Shafipour1, M.

    2014-11-01

    Full Text Available The identification of Mycobacteria in the species level has great medical importance. Biochemical tests are laborious and time-consuming, so new techniques could be used to identify the species. This research aimed to the comparison of biochemical and sequencing 16S rDNA gene methods to identify nontuberculous Mycobacteria in patients suspected to tuberculosis in Golestan province which is the most prevalent region of tuberculosis in Iran. Among 3336 patients suspected to tuberculosis referred to hospitals and health care centres in Golestan province during 2010-2011, 319 (9.56% culture positive cases were collected. Identification of species by using biochemical tests was done. On the samples recognized as nontuberculous Mycobacteria, after DNA extraction by boiling, 16S rDNA PCR was done and their sequencing were identified by NCBI BLAST. Of the 319 positive samples in Golestan Province, 300 cases were M.tuberculosis and 19 cases (5.01% were identified as nontuberculous Mycobacteria by biochemical tests. 15 out of 19 nontuberculous Mycobacteria were identified by PCR and sequencing method as similar by biochemical methods (similarity rate: 78.9%. But after PCR, 1 case known as M.simiae by biochemical test was identified as M. lentiflavum and 3 other cases were identified as Nocardia. Biochemical methods corresponded to the 16S rDNA PCR and sequencing in 78.9% of cases. However, in identification of M. lentiflavum and Nocaria sp. the molecular method is better than biochemical methods.

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

    International Nuclear Information System (INIS)

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

    1996-01-01

    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

  5. Comparison of the nucleotide sequence of wild-type hepatitis - A virus and its attenuated candidate vaccine derivative

    International Nuclear Information System (INIS)

    Cohen, J.I.; Rosenblum, B.; Ticehurst, J.R.; Daemer, R.; Feinstone, S.; Purcell, R.H.

    1987-01-01

    Development of attenuated mutants for use as vaccines is in progress for other viruses, including influenza, rotavirus, varicella-zoster, cytomegalovirus, and hepatitis-A virus (HAV). Attenuated viruses may be derived from naturally occurring mutants that infect human or nonhuman hosts. Alternatively, attenuated mutants may be generated by passage of wild-type virus in cell culture. Production of attenuated viruses in cell culture is a laborious and empiric process. Despite previous empiric successes, understanding the molecular basis for attenuation of vaccine viruses could facilitate future development and use of live-virus vaccines. Comparison of the complete nucleotide sequences of wild-type (virulent) and vaccine (attenuated) viruses has been reported for polioviruses and yellow fever virus. Here, the authors compare the nucleotide sequence of wild-type HAV HM-175 with that of a candidate vaccine derivative

  6. Hypercapnic normalization of BOLD fMRI: comparison across field strengths and pulse sequences

    DEFF Research Database (Denmark)

    Cohen, Eric R.; Rostrup, Egill; Sidaros, Karam

    2004-01-01

    to be more accurately localized and quantified based on changes in venous blood oxygenation alone. The normalized BOLD signal induced by the motor task was consistent across different magnetic fields and pulse sequences, and corresponded well with cerebral blood flow measurements. Our data suggest...... size, as well as experimental, such as pulse sequence and static magnetic field strength (B(0)). Thus, it is difficult to compare task-induced fMRI signals across subjects, field strengths, and pulse sequences. This problem can be overcome by normalizing the neural activity-induced BOLD fMRI response...... for global stimulation, subjects breathed a 5% CO(2) gas mixture. Under all conditions, voxels containing primarily large veins and those containing primarily active tissue (i.e., capillaries and small veins) showed distinguishable behavior after hypercapnic normalization. This allowed functional activity...

  7. Comparison of whole genome amplification techniques for human single cell exome sequencing.

    Science.gov (United States)

    Borgström, Erik; Paterlini, Marta; Mold, Jeff E; Frisen, Jonas; Lundeberg, Joakim

    2017-01-01

    Whole genome amplification (WGA) is currently a prerequisite for single cell whole genome or exome sequencing. Depending on the method used the rate of artifact formation, allelic dropout and sequence coverage over the genome may differ significantly. The largest difference between the evaluated protocols was observed when analyzing the target coverage and read depth distribution. These differences also had impact on the downstream variant calling. Conclusively, the products from the AMPLI1 and MALBAC kits were shown to be most similar to the bulk samples and are therefore recommended for WGA of single cells. In this study four commercial kits for WGA (AMPLI1, MALBAC, Repli-G and PicoPlex) were used to amplify human single cells. The WGA products were exome sequenced together with non-amplified bulk samples from the same source. The resulting data was evaluated in terms of genomic coverage, allelic dropout and SNP calling.

  8. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  9. Comparison of MRI pulse sequences for investigation of lesions of the cervical spinal cord

    International Nuclear Information System (INIS)

    Campi, A.; Pontesilli, S.; Gerevini, S.; Scotti, G.

    2000-01-01

    Small spinal cord lesions, even if clinically significant, can be due to the low sensitivity of some pulse sequences. We compared T2-weighted fast (FSE), and conventional (CSE) spin-echo and short-tau inversion-recovery (STIR)-FSE overlooked on MRI sequences to evaluate their sensitivity to and specificity for lesions of different types. We compared the three sequences in MRI of 57 patients with cervical spinal symptoms. The image sets were assessed by two of us individually for final diagnosis, lesion detectability and image quality. Both readers arrived at the same final diagnoses with all sequences, differentiating four groups of patients. Group 1 (30 patients, 53 %), with a final diagnosis of multiple sclerosis (MS). Demyelinating lesions were better seen on STIR-FSE images, on which the number of lesions was significantly higher than on FSE, while the FSE and CSE images showed approximately equal numbers of lesions; additional lesions were found in 9 patients. The contrast-to-noise ratio (CNR) of 17 demyelinating lesions was significantly higher on STIR-FSE images than with the other sequences. Group 2, 19 patients (33 %) with cervical pain, 15 of whom had disc protrusion or herniation: herniated discs were equally well delineated with all sequences, with better myelographic effect on FSE. In five patients with intrinsic spinal cord abnormalities, the conspicuity and demarcation of the lesions were similar with STIR-FSE and FSE. Group 3, 4 patients (7 %) with acute myelopathy of unknown aetiology. In two patients, STIR-FSE gave better demarcation of lesions and in one a questionable additional lesions. Group 4, 4 patients (7 %) with miscellaneous final diagnoses. STIR-FSE had high sensitivity to demyelinating lesions, can be considered quite specific and should be included in spinal MRI for assessment of suspected demyelinating disease. (orig.)

  10. COMPARISON BETWEEN MIXED INTEGER PROGRAMMING WITH HEURISTIC METHOD FOR JOB SHOP SCHEDULING WITH SEPARABLE SEQUENCE-DEPENDENT SETUPS

    Directory of Open Access Journals (Sweden)

    I Gede Agus Widyadana

    2001-01-01

    Full Text Available The decisions to choose appropriate tools for solving industrial problems are not just tools that achieve optimal solution only but it should consider computation time too. One of industrial problems that still difficult to achieve both criteria is scheduling problem. This paper discuss comparison between mixed integer programming which result optimal solution and heuristic method to solve job shop scheduling problem with separable sequence-dependent setup. The problems are generated and the result shows that the heuristic methods still cannot satisfy optimal solution.

  11. Magnetic resonance imaging of anterior cruciate ligament of the knee: a comparison of four sequences

    International Nuclear Information System (INIS)

    Casillas, C.; Marti-Bonmati, L.; Molla, E.; Ferrer, P.; Dosda, R.

    1999-01-01

    To compare the diagnostic efficacy of the four magnetic resonance imaging (MRI) sequences that compose the standard protocol for the study of the knee in our center when employed in the examination of anterior cruciate ligament (ACL). A prospective study was carried out based on MRI findings in the knees of 326 consecutive patients. Sagittal [proton density (PD w eighted turbo-spin-echo and T2*-weighted gradient echo], coronal (PD-weighted turbo-spin-echo with fat suppression) and transverse (T2*-weighted gradient echo with magnetization transfer) images were evaluated. Each sequence was analyzed independently by two radiologists, while another two assessed all the sequences together with the clinical findings. Four categories were established: normal ACL, partially torn, completely torn and synovialized. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) with respect to the definitive diagnosis were calculated for each sequence. The statistical analysis of the findings for each category was done using the chi-squared test and the Kappa test was employed to assess the degree of agreement. According to the final diagnosis, 263 ACL were normal, 29 were partially torn, 33 were completely torn and there was 1 case of synovialization associated with a completely torn ACL. The relationship between the analysis of the ACL according to each sequence and the definitive diagnosis was very significant (p<0.001) and the agreement was excellent. All the sequences presented similar levels of diagnostic precision. The coronal sequence had least number of diagnostic errors (2.1%). The combinations of imaging techniques that resulted in the lowest error rate with respect to the definitive diagnosis were coronal PD-weighted turbo-spin-echo with fat suppression and sagittal PD-weighted turbo-spin-echo. Coronal images are highly precise in the evaluation of ACL. Sagittal sequences are the most valid for diagnosis of torn ACL. Transverse

  12. Comparison of modern 3D and 2D MR imaging sequences of the wrist at 3 Tesla

    International Nuclear Information System (INIS)

    Rehnitz, C.; Klaan, B.; Amarteifio, E.; Kauczor, H.U.; Weber, M.A.; Stillfried, F. von; Burkholder, I.

    2016-01-01

    To compare the image quality of modern 3 D and 2 D sequences for dedicated wrist imaging at 3 Tesla (T) MRI. At 3 T MRI, 18 patients (mean age: 36.2 years) with wrist pain and 16 healthy volunteers (mean age: 26.4 years) were examined using 2 D proton density-weighted fat-saturated (PDfs), isotropic 3 D TrueFISP, 3 D MEDIC, and 3 D PDfs SPACE sequences. Image quality was rated on a five-point scale (0 - 4) including overall image quality (OIQ), visibility of important structures (cartilage, ligaments, TFCC) and degree of artifacts. Signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) of cartilage/bone/muscle/fluid as well as the mean overall SNR/CNR were calculated using region-of-interest analysis. ANOVA, paired t-, and Wilcoxon-signed-rank tests were applied. The image quality of all tested sequences was superior to 3 D PDfs SPACE (p < 0.01). 3 D TrueFISP had the highest combined cartilage score (mean: 3.4) and performed better in cartilage comparisons against 3 D PDfs SPACE in both groups and 2 D PDfs in volunteers (p < 0.05). 3 D MEDIC performed better in 7 of 8 comparisons (p < 0.05) regarding ligaments and TFCC. 2 D PDfs provided constantly high scores. The mean overall SNR/CNR for 2 D PDfs, 3 D PDfs SPACE, 3 D TrueFISP, and 3 D MEDIC were 68/65, 32/27, 45/47, and 57/45, respectively. 2 D PDfs performed best in most SNR/CNR comparisons (p < 0.05) and 3 D MEDIC performed best within the 3 D sequences (p < 0.05). Except 3 D PDfs SPACE, all tested 3 D and 2 D sequences provided high image quality. 3 D TrueFISP was best for cartilage imaging, 3 D MEDIC for ligaments and TFCC and 2 D PDfs for general wrist imaging.

  13. Closed Versus Open Supracondylar Fractures of the Humerus in Children: A Comparison of Clinical and Radiographic Presentation and Results.

    Science.gov (United States)

    Lewine, Eliza; Kim, Jaehon M; Miller, Patricia E; Waters, Peter M; Mahan, Susan T; Snyder, Brian; Hedequist, Daniel; Bae, Donald S

    2018-02-01

    The purpose of this investigation was to compare the presentation and postoperative results of children treated for open and closed, completely displaced type III supracondylar humerus fractures (SCFs). Thirty patients with open and 66 patients with closed, completely displaced type III SCFs were evaluated. Open fractures underwent irrigation and debridement, and all patients were treated by open or closed reduction and pin fixation. Medical records were reviewed to obtain demographic information as well as preoperative and postoperative clinical data regarding mechanism of injury, neurovascular status, associated injuries, postoperative range of motion, infections, and pain. Radiographs were evaluated to quantify displacement, Baumann's angle, humeral capitellar angle, position of the anterior humeral line, and adequacy of reduction. Outcomes were assessed using Flynn criteria. Mean clinical follow-up for the open and closed fracture groups was 8.9 and 5.7 months, respectively. Both groups were similar with respect to age, sex distribution, weight and body mass index, laterality of involvement, and mechanism of injury. At presentation, 35% of closed SCFs and 23% of open SCFs presented with abnormal neurovascular status. There was a higher prevalence of diminished/absent pulses or distal limb ischemia in patients with open injuries (27%) compared with closed fractures (18%). Conversely, severely displaced closed fractures were more commonly associated with nerve injury/palsy at presentation (35%) than those with open fractures (23%). Spontaneous nerve recovery was seen in 87% within 3 to 6 months. Postoperative loss of reduction and malunion were more common in the closed fracture group. However, 84% of patients achieved good-to-excellent results by Flynn criteria, with no appreciable difference based upon open versus closed fractures. With timely wound and fracture treatment, the clinical and radiographic results of children treated for open SCFs is similar to

  14. Comparison of microbial DNA enrichment tools for metagenomic whole genome sequencing.

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

    DEFF Research Database (Denmark)

    Yan, Guangmei; Zhang, Guojie; Fang, Xiaodong

    2011-01-01

    The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus...

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

    Science.gov (United States)

    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…

  17. Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences

    Directory of Open Access Journals (Sweden)

    Bhagwan N. Rekadwad

    2016-01-01

    Full Text Available A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709–AM260713. Genome-to-Genome Distance (GGDC showed high similarity to Pseudoalteromonas haloplanktis (X67024. The generated unique Quick Response (QR codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates using MEGA6 software. Principal Component Analysis (PCA was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.

  18. Comparison of two approaches for the classification of 16S rRNA gene sequences.

    Science.gov (United States)

    Chatellier, Sonia; Mugnier, Nathalie; Allard, Françoise; Bonnaud, Bertrand; Collin, Valérie; van Belkum, Alex; Veyrieras, Jean-Baptiste; Emler, Stefan

    2014-10-01

    The use of 16S rRNA gene sequences for microbial identification in clinical microbiology is accepted widely, and requires databases and algorithms. We compared a new research database containing curated 16S rRNA gene sequences in combination with the lca (lowest common ancestor) algorithm (RDB-LCA) to a commercially available 16S rDNA Centroid approach. We used 1025 bacterial isolates characterized by biochemistry, matrix-assisted laser desorption/ionization time-of-flight MS and 16S rDNA sequencing. Nearly 80 % of isolates were identified unambiguously at the species level by both classification platforms used. The remaining isolates were mostly identified correctly at the genus level due to the limited resolution of 16S rDNA sequencing. Discrepancies between both 16S rDNA platforms were due to differences in database content and the algorithm used, and could amount to up to 10.5 %. Up to 1.4 % of the analyses were found to be inconclusive. It is important to realize that despite the overall good performance of the pipelines for analysis, some inconclusive results remain that require additional in-depth analysis performed using supplementary methods. © 2014 The Authors.

  19. Molecular diagnosis of lyssaviruses and sequence comparison of Australian bat lyssavirus samples.

    Science.gov (United States)

    Foord, A J; Heine, H G; Pritchard, L I; Lunt, R A; Newberry, K M; Rootes, C L; Boyle, D B

    2006-07-01

    To evaluate and implement molecular diagnostic tests for the detection of lyssaviruses in Australia. A published hemi-nested reverse transcriptase polymerase chain reaction (RT-PCR) for the detection of all lyssavirus genotypes was modified to a fully nested RT-PCR format and compared with the original assay. TaqMan assays for the detection of Australian bat lyssavirus (ABLV) were compared with both the nested and hemi-nested RT-PCR assays. The sequences of RT-PCR products were determined to assess sequence variations of the target region (nucleocapsid gene) in samples of ABLV originating from different regions. The nested RT-PCR assay was highly analytically specific, and at least as analytically sensitive as the hemi-nested assay. The TaqMan assays were highly analytically specific and more analytically sensitive than either RT-PCR assay, with a detection level of approximately 10 genome equivalents per microl. Sequence of the first 544 nucleotides of the nucleocapsid protein coding sequence was obtained from all samples of ABLV received at Australian Animal Health Laboratory during the study period. The nested RT-PCR provided a means for molecular diagnosis of all tested genotypes of lyssavirus including classical rabies virus and Australian bat lyssavirus. The published TaqMan assay proved to be superior to the RT-PCR assays for the detection of ABLV in terms of analytical sensitivity. The TaqMan assay would also be faster and cross contamination is less likely. Nucleotide sequence analyses of samples of ABLV from a wide geographical range in Australia demonstrated the conserved nature of this region of the genome and therefore the suitability of this region for molecular diagnosis.

  20. The Complete Mitochondrial Genome Sequence of Bactericera cockerelli and Comparison with Three Other Psylloidea Species.

    Directory of Open Access Journals (Sweden)

    Fengnian Wu

    Full Text Available 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.

  1. XMM-NEWTON MONITORING OF THE CLOSE PRE-MAIN-SEQUENCE BINARY AK SCO. EVIDENCE OF TIDE-DRIVEN FILLING OF THE INNER GAP IN THE CIRCUMBINARY DISK

    Energy Technology Data Exchange (ETDEWEB)

    Gomez de Castro, Ana Ines [S. D. Astronomia y Geodesia and Instituto de Matematica Interdisciplinar, Fac. de CC Matematicas, Universidad Complutense, E-28040 Madrid (Spain); Lopez-Santiago, Javier [Departamento de Astrofisica, Fac de CC Fisicas, Universidad Complutense, E-28040 Madrid (Spain); Talavera, Antonio [European Space Astronomy Center, Villanueva de la Canada, E-28691, Madrid (Spain); Sytov, A. Yu.; Bisikalo, D. [Institute of Astronomy of the Russian Academy of Sciences, Pyatnitskaya St. 48, 109017 Moscow (Russian Federation)

    2013-03-20

    AK Sco stands out among pre-main-sequence binaries because of its prominent ultraviolet excess, the high eccentricity of its orbit, and the strong tides driven by it. AK Sco consists of two F5-type stars that get as close as 11 R{sub *} at periastron passage. The presence of a dense (n{sub e} {approx} 10{sup 11} cm{sup -3}) extended envelope has been unveiled recently. In this article, we report the results from an XMM-Newton-based monitoring of the system. We show that at periastron, X-ray and UV fluxes are enhanced by a factor of {approx}3 with respect to the apastron values. The X-ray radiation is produced in an optically thin plasma with T {approx} 6.4 Multiplication-Sign 10{sup 6} K and it is found that the N{sub H} column density rises from 0.35 Multiplication-Sign 10{sup 21} cm{sup -2} at periastron to 1.11 Multiplication-Sign 10{sup 21} cm{sup -2} at apastron, in good agreement with previous polarimetric observations. The UV emission detected in the Optical Monitor band seems to be caused by the reprocessing of the high-energy magnetospheric radiation on the circumstellar material. Further evidence of the strong magnetospheric disturbances is provided by the detection of line broadening of 278.7 km s{sup -1} in the N V line with Hubble Space Telescope/Space Telescope Imaging Spectrograph. Numerical simulations of the mass flow from the circumbinary disk to the components have been carried out. They provide a consistent scenario with which to interpret AK Sco observations. We show that the eccentric orbit acts like a gravitational piston. At apastron, matter is dragged efficiently from the inner disk border, filling the inner gap and producing accretion streams that end as ring-like structures around each component of the system. At periastron, the ring-like structures come into contact, leading to angular momentum loss, and thus producing an accretion outburst.

  2. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

    Directory of Open Access Journals (Sweden)

    Jovan Rebolledo-Mendez

    Full Text Available 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

  3. Comparison of Intravenous Morphine with Sublingual Buprenorphine in Management of Postoperative Pain after Closed Reduction Orthopedic Surgery

    OpenAIRE

    Ghasem Soltani; Mahmood Khorsand; ALireza Sepehri Shamloo; Lida Jarahi; Nahid Zirak

    2015-01-01

    Background: Postoperative pain is a common side effect following surgery that can significantly reduce surgical quality and patient’s satisfaction. Treatment options are morphine and buprenorphine. We aimed to compare the efficacy of a single dose of intravenous morphine with sublingual buprenorphine in postoperative pain control following closed reduction surgery. Methods: This triple blind clinical trial was conducted on 90 patients referred for closed reduction orthopedic surgery. They wer...

  4. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.

    Directory of Open Access Journals (Sweden)

    Jinhui Wang

    Full Text Available Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp and FIN111 (1.20 Mbp, were obtained from carrot psyllids (Trioza apicalis harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.

  5. The Comparison of Streptococcus agalactiae Isolated from Fish and Bovine using Multilocus Sequence Typing

    Directory of Open Access Journals (Sweden)

    ANGELA MARIANA LUSIASTUTI

    2013-12-01

    Full Text Available Multilocus sequence typing (MLST has greater utility for determining the recent ancestral lineage and the relatedness of individual strains. Group B streptococci (GBS is one of the major causes of subclinical mastitis of dairy cattle in several countries. GBS also sporadically causes epizootic infections in fish. The aim of this study was to compare the evolutionary lineage of fish and bovine isolates in relation to the S. agalactiae global population as a whole by comparing the MLST profiles. Twenty S. agalactiae isolates were obtained from dairy cattle and fish. PCR products were amplified with seven different oligonucleotide primer pairs designed from the NEM316 GBS genome sequence. Clone complexes demonstrated that bovine and fish isolates were separate populations. These findings lead us to conclude that fish S. agalactiae is not a zoonotic agent for bovine. MLST could help clarify the emergence of pathogenic clones and to decide whether the host acts as a reservoir for another pathogenic lineage.

  6. A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae: a traditional herbal medicinal genus

    Directory of Open Access Journals (Sweden)

    Hanghui Kong

    2017-11-01

    Full Text Available The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A. subgenus Lycoctonum and A. subg. Aconitum. The complete chloroplast (cp genome sequences were characterized in three species: A. angustius, A. finetianum, and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius, 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum, with each species possessing 126 genes with 84 protein coding genes (PCGs. While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψrps19 and Ψycf1 were in the LSC/IR/SSC boundaries, Ψrps16 and ΨinfA in the LSC region, and Ψycf15 in the IRb region. The nucleotide variability (Pi of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58–62 simple sequence repeats (SSRs were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum, respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum. Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

  7. A comparison of chloroplast genome sequences in Aconitum (Ranunculaceae): a traditional herbal medicinal genus.

    Science.gov (United States)

    Kong, Hanghui; Liu, Wanzhen; Yao, Gang; Gong, Wei

    2017-01-01

    The herbal medicinal genus Aconitum L., belonging to the Ranunculaceae family, represents the earliest diverging lineage within the eudicots. It currently comprises of two subgenera, A . subgenus Lycoctonum and A . subg. Aconitum . The complete chloroplast (cp) genome sequences were characterized in three species: A. angustius , A. finetianum , and A. sinomontanum in subg. Lycoctonum and compared to other Aconitum species to clarify their phylogenetic relationship and provide molecular information for utilization of Aconitum species particularly in Eastern Asia. The length of the chloroplast genome sequences were 156,109 bp in A. angustius , 155,625 bp in A. finetianum and 157,215 bp in A. sinomontanum , with each species possessing 126 genes with 84 protein coding genes (PCGs). While genomic rearrangements were absent, structural variation was detected in the LSC/IR/SSC boundaries. Five pseudogenes were identified, among which Ψ rps 19 and Ψ ycf 1 were in the LSC/IR/SSC boundaries, Ψ rps 16 and Ψ inf A in the LSC region, and Ψ ycf 15 in the IRb region. The nucleotide variability ( Pi ) of Aconitum was estimated to be 0.00549, with comparably higher variations in the LSC and SSC than the IR regions. Eight intergenic regions were revealed to be highly variable and a total of 58-62 simple sequence repeats (SSRs) were detected in all three species. More than 80% of SSRs were present in the LSC region. Altogether, 64.41% and 46.81% of SSRs are mononucleotides in subg. Lycoctonum and subg. Aconitum , respectively, while a higher percentage of di-, tri-, tetra-, and penta- SSRs were present in subg. Aconitum . Most species of subg. Aconitum in Eastern Asia were first used for phylogenetic analyses. The availability of the complete cp genome sequences of these species in subg. Lycoctonum will benefit future phylogenetic analyses and aid in germplasm utilization in Aconitum species.

  8. Mesoscopic modeling of DNA denaturation rates: Sequence dependence and experimental comparison

    Energy Technology Data Exchange (ETDEWEB)

    Dahlen, Oda, E-mail: oda.dahlen@ntnu.no; Erp, Titus S. van, E-mail: titus.van.erp@ntnu.no [Department of Chemistry, Norwegian University of Science and Technology (NTNU), Høgskoleringen 5, Realfagbygget D3-117 7491 Trondheim (Norway)

    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.

  9. Complete plastid genome sequence of goosegrass (Eleusine indica) and comparison with other Poaceae.

    Science.gov (United States)

    Zhang, Hui; Hall, Nathan; McElroy, J Scott; Lowe, Elijah K; Goertzen, Leslie R

    2017-02-05

    Eleusine indica, also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively. The plastome of goosegrass has 38.19% GC content and includes 108 unique genes, of which 76 are protein-coding, 28 are transfer RNA, and 4 are ribosomal RNA. The goosegrass plastome sequence was compared to eight other species of Poaceae. Although generally conserved with respect to Poaceae, this genomic resource will be useful for evolutionary studies within this weed species and the genus Eleusine. Copyright © 2016. Published by Elsevier B.V.

  10. Fast comparison of IS radar code sequences for lag profile inversion

    Directory of Open Access Journals (Sweden)

    M. S. Lehtinen

    2008-08-01

    Full Text Available A fast method for theoretically comparing the posteriori variances produced by different phase code sequences in incoherent scatter radar (ISR experiments is introduced. Alternating codes of types 1 and 2 are known to be optimal for selected range resolutions, but the code sets are inconveniently long for many purposes like ground clutter estimation and in cases where coherent echoes from lower ionospheric layers are to be analyzed in addition to standard F-layer spectra.

    The method is used in practice for searching binary code quads that have estimation accuracy almost equal to that of much longer alternating code sets. Though the code sequences can consist of as few as four different transmission envelopes, the lag profile estimation variances are near to the theoretical minimum. Thus the short code sequence is equally good as a full cycle of alternating codes with the same pulse length and bit length. The short code groups cannot be directly decoded, but the decoding is done in connection with more computationally expensive lag profile inversion in data analysis.

    The actual code searches as well as the analysis and real data results from the found short code searches are explained in other papers sent to the same issue of this journal. We also discuss interesting subtle differences found between the different alternating codes by this method. We assume that thermal noise dominates the incoherent scatter signal.

  11. MR of normal pancreas : comparison of five pulse sequences and enhancing patterns on dynamic imaging

    International Nuclear Information System (INIS)

    Jang, Hyun Jung; Kim, Tae Kyoung; Hong, Sung Hwan; Han, Joon Koo; Choi, Byung Ihn

    1997-01-01

    To compare T1-weighted FLASH and turbo spin echo (SE) T2-weighted sequences with conventional T1- and T2-weighted sequences in imaging normal pancreas and to describe the enhancing patterns on dynamic MR imging. Forty-four patients with presumed hepatic hemangiomas were studied at 1.0T or 1.5T by using conventional SE sequences (T1-weighted, T2-weighted, and heavily T2-weighted), turbo-SE T2-weighted sequences, and breath-hold T1-weighted FLASH sequences acquired before, immediately on, and at 1, 2, 3, and 5 or 10 minutes after injection of a bolus of gadopentetate dimeglumine. No patients had either a history or its clinical features of pancreatic disease. Images were quantitatively analyzed for signal-difference-to noise ratios (SD/Ns) between the pancreas and peripancreatic fat. Percentage enhancement of the pancreas was measured on each dynamic MR image. Conspicuity of the pancreatic border was qualitatively evaluated according to a consensus, reached by three radiologists. Turbo-SE T2-weighted images had a significantly higher SD/N ratio (p<0.001) and better conspicuity of the pancreatic border (p<0.001) than SE T2- and heavily T2-weighted images;T1-weighted SE images had a significantly higher SD/N ratio than T1-weighted FLASH images (p<0.001), but there was no significant difference between tham in qualitative analysis (p=0.346). Percentage enhancement immediately on and at 1, 2, 3, 5, and 10 minutes after administration of contrast material was 39.9%, 44.5%, 42.9%, 40.8%, 36.3%, 29.9%, respectively, with peak enhancement at 1 minute. In MR imaging of normal pancreas, turbo-SE T2-weighted imaging is superior to SE T2- and heavily T2- weighted imaging, and SE T1-weighted imaging is superior to T1-weighted FLASH imaging. On serial gadolinium-enhanced FLASH imaging, normal pancreas shows peak enhancement at 1 minute

  12. Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

    Science.gov (United States)

    Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

    2015-03-01

    The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

  13. Transcription factor IID in the Archaea: sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes

    Science.gov (United States)

    Marsh, T. L.; Reich, C. I.; Whitelock, R. B.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1994-01-01

    The first step in transcription initiation in eukaryotes is mediated by the TATA-binding protein, a subunit of the transcription factor IID complex. We have cloned and sequenced the gene for a presumptive homolog of this eukaryotic protein from Thermococcus celer, a member of the Archaea (formerly archaebacteria). The protein encoded by the archaeal gene is a tandem repeat of a conserved domain, corresponding to the repeated domain in its eukaryotic counterparts. Molecular phylogenetic analyses of the two halves of the repeat are consistent with the duplication occurring before the divergence of the archael and eukaryotic domains. In conjunction with previous observations of similarity in RNA polymerase subunit composition and sequences and the finding of a transcription factor IIB-like sequence in Pyrococcus woesei (a relative of T. celer) it appears that major features of the eukaryotic transcription apparatus were well-established before the origin of eukaryotic cellular organization. The divergence between the two halves of the archael protein is less than that between the halves of the individual eukaryotic sequences, indicating that the average rate of sequence change in the archael protein has been less than in its eukaryotic counterparts. To the extent that this lower rate applies to the genome as a whole, a clearer picture of the early genes (and gene families) that gave rise to present-day genomes is more apt to emerge from the study of sequences from the Archaea than from the corresponding sequences from eukaryotes.

  14. Computational Software to Fit Seismic Data Using Epidemic-Type Aftershock Sequence Models and Modeling Performance Comparisons

    Science.gov (United States)

    Chu, A.

    2016-12-01

    Modern earthquake catalogs are often analyzed using spatial-temporal point process models such as the epidemic-type aftershock sequence (ETAS) models of Ogata (1998). My work implements three of the homogeneous ETAS models described in Ogata (1998). With a model's log-likelihood function, my software finds the Maximum-Likelihood Estimates (MLEs) of the model's parameters to estimate the homogeneous background rate and the temporal and spatial parameters that govern triggering effects. EM-algorithm is employed for its advantages of stability and robustness (Veen and Schoenberg, 2008). My work also presents comparisons among the three models in robustness, convergence speed, and implementations from theory to computing practice. Up-to-date regional seismic data of seismic active areas such as Southern California and Japan are used to demonstrate the comparisons. Data analysis has been done using computer languages Java and R. Java has the advantages of being strong-typed and easiness of controlling memory resources, while R has the advantages of having numerous available functions in statistical computing. Comparisons are also made between the two programming languages in convergence and stability, computational speed, and easiness of implementation. Issues that may affect convergence such as spatial shapes are discussed.

  15. Cardiorespiratory Kinetics Determined by Pseudo-Random Binary Sequences - Comparisons between Walking and Cycling.

    Science.gov (United States)

    Koschate, J; Drescher, U; Thieschäfer, L; Heine, O; Baum, K; Hoffmann, U

    2016-12-01

    This study aims to compare cardiorespiratory kinetics as a response to a standardised work rate protocol with pseudo-random binary sequences between cycling and walking in young healthy subjects. Muscular and pulmonary oxygen uptake (V̇O 2 ) kinetics as well as heart rate kinetics were expected to be similar for walking and cycling. Cardiac data and V̇O 2 of 23 healthy young subjects were measured in response to pseudo-random binary sequences. Kinetics were assessed applying time series analysis. Higher maxima of cross-correlation functions between work rate and the respective parameter indicate faster kinetics responses. Muscular V̇O 2 kinetics were estimated from heart rate and pulmonary V̇O 2 using a circulatory model. Muscular (walking vs. cycling [mean±SD in arbitrary units]: 0.40±0.08 vs. 0.41±0.08) and pulmonary V̇O 2 kinetics (0.35±0.06 vs. 0.35±0.06) were not different, although the time courses of the cross-correlation functions of pulmonary V̇O 2 showed unexpected biphasic responses. Heart rate kinetics (0.50±0.14 vs. 0.40±0.14; P=0.017) was faster for walking. Regarding the biphasic cross-correlation functions of pulmonary V̇O 2 during walking, the assessment of muscular V̇O 2 kinetics via pseudo-random binary sequences requires a circulatory model to account for cardio-dynamic distortions. Faster heart rate kinetics for walking should be considered by comparing results from cycle and treadmill ergometry. © Georg Thieme Verlag KG Stuttgart · New York.

  16. Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing.

    Science.gov (United States)

    Eyre, David W; Fawley, Warren N; Rajgopal, Anu; Settle, Christopher; Mortimer, Kalani; Goldenberg, Simon D; Dawson, Susan; Crook, Derrick W; Peto, Tim E A; Walker, A Sarah; Wilcox, Mark H

    2017-08-01

    Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely. We used whole-genome sequencing (WGS) of consecutive C. difficile isolates from 6 English hospitals over 1 year (2013-14) to compare infection control performance. Fecal samples with a positive initial screen for C. difficile were sequenced. Within each hospital, we estimated the proportion of cases plausibly acquired from previous cases. Overall, 851/971 (87.6%) sequenced samples contained toxin genes, and 451 (46.4%) were fecal-toxin-positive. Of 652 potentially toxigenic isolates >90-days after the study started, 128 (20%, 95% confidence interval [CI] 17-23%) were genetically linked (within ≤2 single nucleotide polymorphisms) to a prior patient's isolate from the previous 90 days. Hospital 2 had the fewest linked isolates, 7/105 (7%, 3-13%), hospital 1, 9/70 (13%, 6-23%), and hospitals 3-6 had similar proportions of linked isolates (22-26%) (P ≤ .002 comparing hospital-2 vs 3-6). Results were similar adjusting for locally circulating ribotypes. Adjusting for hospital, ribotype-027 had the highest proportion of linked isolates (57%, 95% CI 29-81%). Fecal-toxin-positive and toxin-negative patients were similarly likely to be a potential transmission donor, OR = 1.01 (0.68-1.49). There was no association between the estimated proportion of linked cases and testing rates. WGS can be used as a novel surveillance tool to identify varying rates of C. difficile transmission between institutions and therefore to allow targeted efforts to reduce CDI incidence. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

  17. Comparison of the aflR gene sequences of strains in Aspergillus section Flavi.

    Science.gov (United States)

    Lee, Chao-Zong; Liou, Guey-Yuh; Yuan, Gwo-Fang

    2006-01-01

    Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus parasiticus, Aspergillus flavus, Aspergillus nomius and a few other species. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. Although Aspergillus oryzae and Aspergillus sojae, which are used in fermented foods and in ingredient manufacture, have no record of producing aflatoxin, they have been shown to possess an aflR gene. This study examined 34 strains of Aspergillus section Flavi. The aflR gene of 23 of these strains was successfully amplified and sequenced. No aflR PCR products were found in five A. sojae strains or six strains of A. oryzae. These PCR results suggested that the aflR gene is absent or significantly different in some A. sojae and A. oryzae strains. The sequenced aflR genes from the 23 positive strains had greater than 96.6 % similarity, which was particularly conserved in the zinc-finger DNA-binding domain. The aflR gene of A. sojae has two obvious characteristics: an extra CTCATG sequence fragment and a C to T transition that causes premature termination of AFLR protein synthesis. Differences between A. parasiticus/A. sojae and A. flavus/A. oryzae aflR genes were also identified. Some strains of A. flavus as well as A. flavus var. viridis, A. oryzae var. viridis and A. oryzae var. effuses have an A. oryzae-type aflR gene. For all strains with the A. oryzae-type aflR gene, there was no evidence of aflatoxin production. It is suggested that for safety reasons, the aflR gene could be examined to assess possible aflatoxin production by Aspergillus section Flavi strains.

  18. Comparison of closed-cell and hybrid-cell stent designs in carotid artery stenting: clinical and procedural outcomes

    Directory of Open Access Journals (Sweden)

    Ersan TatlI

    2017-05-01

    Full Text Available Introduction: Carotid artery stenting (CAS is a promising alternative to surgery in high-risk patients. However, the impact of stent cell design on outcomes in CAS is a matter of continued debate. Aim : To compare the periprocedural and clinical outcomes of different stent designs for CAS with distal protection devices. Material and methods : All CAS procedures with both closed- and hybrid-cell stents performed at our institution between February 2010 and December 2015 were analyzed retrospectively. Adverse events were defined as death, major stroke, minor stroke, transient ischemic attack and myocardial infarction. Periprocedural and 30-day adverse events and internal carotid artery (ICA vasospasm rates were compared between the closed-cell and hybrid-cell stent groups. Results : The study included 234 patients comprising 146 patients with a closed-cell stent (Xact stent, Abbott Vascular (mean age: 68.5 ±8.6; 67.1% male and 88 patients with a hybrid-cell stent (Cristallo Ideale, Medtronic (mean age: 67.2 ±12.8; 68.2% male. There was no significant difference between the groups with respect to periprocedural or 30-day adverse event rates. While there was no difference in terms of tortuosity index between the groups, there was a higher procedural ICA vasospasm rate in the closed-cell stent group (35 patients, 23% compared with the hybrid-cell stent group (10 patients, 11% (p = 0.017. Conclusions : The results of this study showed no significant difference in the clinical adverse event rates after CAS between the closed-cell stent group and the hybrid-cell stent group. However, procedural ICA vasospasm was more common in the closed-cell stent group.

  19. COMPARISON OF ROCURONIUM BROMIDE AND SUCCINYLCHOLINE CHLORIDE FOR USE DURING RAPID SEQUENCE INTUBATION IN ADULTS

    Directory of Open Access Journals (Sweden)

    Ch. Penchalaiah

    2015-08-01

    Full Text Available BACKGROUND AND OBJECTIVE : The goal of rapid sequence intubation is to secure the patients airway smoothly and quickly, minimizing the chances of regurgitation and aspiration of gastric contents. Traditionally succinylcholine chloride has been the neuromuscular blocking drug of choi ce for use in rapid sequence intubation because of its rapid onset of action and profound relaxation. Succinylcholine chloride remains unsurpassed in providing ideal intubating conditions. However the use of succinylcholine chloride is associated with many side effects like muscle pain, bradycardia, hyperkalaemia and rise in intragastric and intraocular pressure. Rocuronium bromide is the only drug currently available which has the rapidity of onset of action like succinylcholine chloride. Hence the present study was undertaken to compare rocuronium bromide with succinylcholine chloride for use during rapid sequence intubation in adult patients. METHODOLOGY : The study population consisted of 90 patients aged between 18 - 60 years posted for various elective su rgeries requiring general anaesthesia . S tudy population was randomly divided into 3 groups with 30 patients in each sub group. 1. Group I : Intubated with 1 mg kg - 1 of succinylcholine chloride (n=30 . 2. Grou p II : Intubated with rocuronium bromide 0.6 mg kg - 1 (n=30 . 3. Group III : Intubated with rocuronium bromide 0.9 mg kg - 1 (n=30 . Intubating conditions were assessed at 60 seconds based on the scale adopted by Toni Magorian et al. 1993. The haemodynamic para meters in the present study were compared using p - value obtained from student t - test . RESULTS : It was noted that succinylcholine chloride 1 mg kg - 1 body weight produced excellent intubating conditions in all patients. Rocuronium bromide 0.6 mg kg - 1 body we ight produced excellent intubating conditions in 53.33% of patients but produced good to excellent intubating conditions in 96.67% of patients. Rocuronium bromide 0.9 mg kg - 1

  20. Comparison of aftershock sequences between 1975 Haicheng earthquake and 1976 Tangshan earthquake

    Science.gov (United States)

    Liu, B.

    2017-12-01

    The 1975 ML 7.3 Haicheng earthquake and the 1976 ML 7.8 Tangshan earthquake occurred in the same tectonic unit. There are significant differences in spatial-temporal distribution, number of aftershocks and time duration for the aftershock sequence followed by these two main shocks. As we all know, aftershocks could be triggered by the regional seismicity change derived from the main shock, which was caused by the Coulomb stress perturbation. Based on the rate- and state- dependent friction law, we quantitative estimated the possible aftershock time duration with a combination of seismicity data, and compared the results from different approaches. The results indicate that, aftershock time durations from the Tangshan main shock is several times of that form the Haicheng main shock. This can be explained by the significant relationship between aftershock time duration and earthquake nucleation history, normal stressand shear stress loading rateon the fault. In fact the obvious difference of earthquake nucleation history from these two main shocks is the foreshocks. 1975 Haicheng earthquake has clear and long foreshocks, while 1976 Tangshan earthquake did not have clear foreshocks. In that case, abundant foreshocks may mean a long and active nucleation process that may have changed (weakened) the rocks in the source regions, so they should have a shorter aftershock sequences for the reason that stress in weak rocks decay faster.

  1. [Comparison of 2D and 3D sequences for MRCP. Clinical value of the different techniques].

    Science.gov (United States)

    Wallnoefer, A M; Herrmann, K A; Beuers, U; Zech, C J; Gourtsoyianni, S; Reiser, M F; Schoenberg, S O

    2005-11-01

    Magnetic resonance cholangio-pancreaticograpy (MRCP) is a non-invasive imaging modality of the pancreatico-biliary system which plays an increasingly important role in the clinical and diagnostic workup of patients with biliary or pancreatic diseases. The present review is designed to give an overview of the currently available and appropriate sequences, their technical background, as well as new developments and their relevance to the various clinical issues and challenges. The impact of the latest technical innovations, such as integrated parallel imaging techniques and navigator-based respiratory triggering, on the diagnostic capacities of MRCP is discussed. In this context, the individual value of RARE, T2w single shot turbo/fast spin echo (SSFSE) and the recently introduced 3D T2w turbo/fast spin echo sequences (T2w 3D-T/FSE) is reviewed. RARE imaging may be preferred in severely ill patients with limitations in cooperation, SSFSE is particularly effective in differentiating benign and malignant stenosis, and 3D-FSE offers additional advantages in the detection of small biliary concrements.

  2. Comparison of retreatment ability of full-sequence reciprocating instrumentation and 360° rotary instrumentation.

    Science.gov (United States)

    Capar, Ismail Davut; Gok, Tuba; Orhan, Ezgi

    2015-12-01

    The purpose of the present study was to investigate the amount of root canal filling material after root canal filling removal with 360° rotary instrumentation or reciprocating motion with the same file sequence. Root canals of the 36 mandibular premolars were shaped with ProTaper Universal instruments up to size F2 and filled with corresponding single gutta-percha cone and sealer. The teeth were assigned to two retreatment groups (n = 18): group 1 360° rotational motion and group 2 reciprocating motion of ATR Tecnika motors (1310° clockwise and 578° counterclockwise). Retreatment procedure was performed with ProTaper Universal retreatment files with a sequence of D1-3 and ProTaper Universal F3 instruments. Total time required to remove filling material were recorded. Remaining filling material was examined under stereomicroscope at ×8 magnification. The data were analysed statistically using the Mann-Whitney U test, and testing was performed at 95 % confidence level (p  0.05) in terms of remaining filling material. The total time required for retreatment was shorter in 360° rotational motion group compared to reciprocating motion group (p instruments with reciprocating motion of ATR motor and conventional rotary motion have similar efficacy in root canal filling removal.

  3. Sequence comparison of six human microRNAs genes between tuberculosis patients and healthy individuals.

    Science.gov (United States)

    Amila, A; Acosta, A; Sarmiento, M E; Suraiya, Siti; Zafarina, Z; Panneerchelvam, S; Norazmi, M N

    2015-12-01

    MicroRNAs (miRNAs) play an important role in diseases development. Therefore, human miRNAs may be able to inhibit the survival of Mycobacterium tuberculosis (Mtb) in the human host by targeting critical genes of the pathogen. Mutations within miRNAs can alter their target selection, thereby preventing them from inhibiting Mtb genes, thus increasing host susceptibility to the disease. This study was undertaken to investigate the genetic association of pulmonary tuberculosis (TB) with six human miRNAs genes, namely, hsa-miR-370, hsa-miR-520d, hsa-miR-154, hsa-miR-497, hsa-miR-758, and hsa-miR-593, which have been predicted to interact with Mtb genes. The objective of the study was to determine the possible sequence variation of selected miRNA genes that are potentially associated with the inhibition of critical Mtb genes in TB patients. The study did not show differences in the sequences compared with healthy individuals without antecedents of TB. This result could have been influenced by the sample size and the selection of miRNA genes, which need to be addressed in future studies. Copyright © 2015 Asian African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

  4. MR diffusion weighted imaging of gastric cancer: b-value determination and comparison with routine sequences

    International Nuclear Information System (INIS)

    Zhao Xiaopeng; Tang Lei; Sun Yingshi; Li Jie; Cao Kun

    2007-01-01

    Objective: To choose the optimal b-values for the DWI of gastric cancer (GC), and investigate the value of DWI in the diagnosis of GCs. Methods: MRI examinations (T 1 WI, T 2 WI, and DWI) were performed on 31 patients with gastric cancer. Three diffusion-weighted sequences were designed with different b values, including 300 s/mm 2 (low), 600 s/mm 2 (intermediate), and 1000 s/mm 2 (high). Free water grade was used to evaluate the suppression of content in gastric lumen. Background contrast grade was used to evaluate the discriminating ability of different sequences between GC and nearby tissues. The ADCs of GCs, nearby gastric wall region, and free water in gastric lumen were measured. SNR Ca , CNR Ca-GW and SIR CaGW of high b-value DWI and routine MRI sequences were evaluated and compared. Results: The signal intensity of free water in gastric lumen decreased as b-value increased, and the SIR were 8.11± 0.77 (b=300 s/mm 2 ), 2.70±0.35 (b=600 s/mm 2 ), and 1.13±0.22 (b=1000 s/mm 2 ) (F55.368, P 2 =16.692, P 2 =9.923, P -3 mm 2 /s, (1.43±0.41) x 10 -3 mm 2 /s, and (1.18±0.25) x 10 -3 mm 2 /s; (F=12.066, P 1 WI (CNR: 12.46 vs. 2.35, Z=-3.746, P 2 WI (CNR: 12.46 vs. 3.92, Z=-3.518, P 2 ) is reasonable for DWI of GCs, which can reflect diffusion condition of water molecules more accurately, suppress signal of content in gastric lumen, and possess higher contrast. DWI can be a supplementary method of routine MRI examination for better demonstration of gastric cancers. (authors)

  5. Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

    Directory of Open Access Journals (Sweden)

    Xue Ying

    2006-07-01

    Full Text Available Abstract Background Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features. To investigate the intra-species diversity of S. flexneri genomes further, we have sequenced the complete genome of S. flexneri 5b strain 8401 (abbreviated Sf8401 and compared it with S. flexneri 2a (Sf301. Results The Sf8401 chromosome is 4.5-Mb in size, a little smaller than that of Sf301, mainly because the former lacks the SHI-1 pathogenicity island (PAI. Compared with Sf301, there are 6 inversions and one translocation in Sf8401, which are probably mediated by insertion sequences (IS. There are clear differences in the known PAIs between these two genomes. The bacteriophage SfV segment remaining in SHI-O of Sf8401 is clearly larger than the remnants of bacteriophage SfII in Sf301. SHI-1 is absent from Sf8401 but a specific related protein is found next to the pheV locus. SHI-2 is involved in one intra-replichore inversion near the origin of replication, which may change the expression of iut/iuc genes. Moreover, genes related to the glycine-betaine biosynthesis pathway are present only in Sf8401 among the known Shigella genomes. Conclusion Our data show that the two S. flexneri genomes are very similar, which suggests a high level of structural and functional conservation between the two serotypes. The differences reflect different selection pressures during evolution. The ancestor of S. flexneri probably acquired SHI-1 and SHI-2 before SHI-O was integrated and the serotypes diverged. SHI-1 was subsequently deleted from the S. flexneri 5b genome by recombination, but stabilized in the S. flexneri 2a genome. These events may have contributed to the differences in pathogenicity and epidemicity between the two serotypes of S. flexneri.

  6. Murine mammary tumor virus pol-related sequences in human DNA: characterization and sequence comparison with the complete murine mammary tumor virus pol gene

    International Nuclear Information System (INIS)

    Deen, K.C.; Sweet, R.W.

    1986-01-01

    Sequences in the human genome with homology to the murine mammary tumor virus (MMTV) pol gene were isolated from a human phage library. Ten clones with extensive pol homology were shown to define five separate loci. These loci share common sequences immediately adjacent to the pol-like segments and, in addition, contain a related repeat element which bounds this region. This organization is suggestive of a proviral structure. The authors estimate that the human genome contains 30 to 40 copies of these pol-related sequences. The pol region of one of the cloned segments (HM16) and the complete MMTV pol gene were sequenced and compared. The nucleotide homology between these pol sequences is 52% and is concentrated in the terminal regions. The MMTV pol gene contains a single long open reading frame encoding 899 amino acids and is demarcated from the partially overlapping putative gag gene by termination codons and a shift in translational reading frame. The pol sequence of HM16 is multiply terminated but does contain open reading frames which encode 370, 105, and 112 amino acids residues in separate reading frames. The authors deduced a composite pol protein sequence for HM16 by aligning it to the MMTV pol gene and then compared these sequences with other retroviral pol protein sequences. Conserved sequences occur in both the amino and carboxyl regions which lie within the polymerase and endonuclease domains of pol, respectively

  7. Parallel computation for biological sequence comparison: comparing a portable model to the native model for the Intel Hypercube.

    Science.gov (United States)

    Nadkarni, P M; Miller, P L

    1991-01-01

    A parallel program for inter-database sequence comparison was developed on the Intel Hypercube using two models of parallel programming. One version was built using machine-specific Hypercube parallel programming commands. The other version was built using Linda, a machine-independent parallel programming language. The two versions of the program provide a case study comparing these two approaches to parallelization in an important biological application area. Benchmark tests with both programs gave comparable results with a small number of processors. As the number of processors was increased, the Linda version was somewhat less efficient. The Linda version was also run without change on Network Linda, a virtual parallel machine running on a network of desktop workstations.

  8. Combining real-time PCR and next-generation DNA sequencing to provide quantitative comparisons of fungal aerosol populations

    Science.gov (United States)

    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 0.70). 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 assessment.

  9. Comparison of two-staged ORIF and limited internal fixation with external fixator for closed tibial plafond fractures.

    Science.gov (United States)

    Wang, Cheng; Li, Ying; Huang, Lei; Wang, Manyi

    2010-10-01

    To compare the results of two-staged open reduction and internal fixation (ORIF) and limited internal fixation with external fixator (LIFEF) for closed tibial plafond fractures. From January 2005 to June 2007, 56 patients with closed type B3 or C Pilon fractures were randomly allocated into groups I and II. Two-staged ORIF was performed in group I and LIFEF in group II. The outcome measures included bone union, nonunion, malunion, pin-tract infection, wound infection, osteomyelitis, ankle joint function, etc. These postoperative data were analyzed with Statistical Package for Social Sciences (SPSS) 13.0. Incidence of superficial soft tissue infection (involved in wound infection or pin-tract infection) in group I was lower than that in group II (P delayed union, and arthritis symptoms, with no statistical significance. Both groups resulted similar ankle joint function. Logistic regression analysis indicated that smoking and fracture pattern were the two factors significantly influencing the final outcomes. In the treatment of closed tibial plafond fractures, both two-staged ORIF and LIFEF offer similar results. Patients undergo LIFEF carry significantly greater radiation exposure and higher superficial soft tissue infection rate (usually occurs on pin tract and does not affect the final outcomes).

  10. Ultrastructure and large subunit rDNA sequences of Lepidodinium viride reveal a close relationship to Lepidodinium chlorophorum comb. nov. (=Gymnodinium chlorophorum)

    DEFF Research Database (Denmark)

    Hansen, Gert; Botes, L.; DeSalas, M.

    2007-01-01

    . The flagellar apparatus was essentially identical to Gymnodinium chlorophorum Elbrächter et Schnepf, a species also containing chloroplasts of chlorophyte origin. Of particular interest was the connection of the flagellar apparatus to the nuclear envelope by means of both a fiber and a microtubular extension...... dinoflagellates, including both the 'type' culture and a new Tasmanian isolate of G. chlorophorum. These two isolates had identical sequences and differed from L. viride by only 3.75% of their partial LSU sequences, considerably less than the difference between other Gymnodinium species. Therefore, based...

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

    Science.gov (United States)

    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.

  12. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM sequencing platforms

    Directory of Open Access Journals (Sweden)

    Nagaraju Indugu

    2016-02-01

    Full Text Available 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.

  13. Comparison of ELISA, nested PCR and sequencing and a novel qPCR for detection of Giardia isolates from Jordan.

    Science.gov (United States)

    Hijjawi, Nawal; Yang, Rongchang; Hatmal, Ma'mon; Yassin, Yasmeen; Mharib, Taghrid; Mukbel, Rami; Mahmoud, Sameer Alhaj; Al-Shudifat, Abdel-Ellah; Ryan, Una

    2018-02-01

    Little is known about the prevalence of Giardia duodenalis in human patients in Jordan and all previous studies have used direct microscopy, which lacks sensitivity. The present study developed a novel quantitative PCR (qPCR) assay at the β-giardin (bg) locus and evaluated its use as a frontline test for the diagnosis of giardiasis in comparison with a commercially available ELISA using nested PCR and sequencing of the glutamate dehydrogenase (gdh) locus (gdh nPCR) as the gold standard. A total of 96 human faecal samples were collected from 96 patients suffering from diarrhoea from 5 regions of Jordan and were screened using the ELISA and qPCR. The analytical specificity of the bg qPCR assay revealed no cross-reactions with other genera and detected all the Giardia isolates tested. Analytical sensitivity was 1 Giardia cyst per μl of DNA extract. The overall prevalence of Giardia was 64.6%. The clinical sensitivity and specificity of the bg qPCR was 89.9% and 82.9% respectively compared to 76.5 and 68.0% for the ELISA. This study is the first to compare three different methods (ELISA, bg qPCR, nested PCR and sequencing at the gdh locus) to diagnose Jordanian patients suffering from giardiasis and to analyze their demographic data. Copyright © 2018 Elsevier Inc. All rights reserved.

  14. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  15. Chloroplast Genome Sequence of pigeonpea (Cajanus cajan (L. Millspaugh and Cajanus scarabaeoides: Genome organization and Comparison with other legumes

    Directory of Open Access Journals (Sweden)

    Tanvi Kaila

    2016-12-01

    Full Text Available Pigeonpea (Cajanus cajan (L. Millspaugh, a diploid (2n = 22 legume crop with a genome size of 852 Mbp, serves as an important source of human dietary protein especially in South East Asian and African regions. In this study, the draft chloroplast genomes of Cajanus cajan and Cajanus scarabaeoides were sequenced. Cajanus scarabaeoides is an important species of the Cajanus gene pool and has also been used for developing promising CMS system by different groups. A male sterile genotype harbouring the Cajanus scarabaeoides cytoplasm was used for sequencing the plastid genome. The cp genome of Cajanus cajan is 152,242bp long, having a quadripartite structure with LSC of 83,455 bp and SSC of 17,871 bp separated by IRs of 25,398 bp. Similarly, the cp genome of Cajanus scarabaeoides is 152,201bp long, having a quadripartite structure in which IRs of 25,402 bp length separates 83,423 bp of LSC and 17,854 bp of SSC. The pigeonpea cp genome contains 116 unique genes, including 30 tRNA, 4 rRNA, 78 predicted protein coding genes and 5 pseudogenes. A 50kb inversion was observed in the LSC region of pigeonpea cp genome, consistent with other legumes. Comparison of cp genome with other legumes revealed the contraction of IR boundaries due to the absence of rps19 gene in the IR region. Chloroplast SSRs were mined and a total of 280 and 292 cpSSRs were identified in Cajanus scarabaeoides and Cajanus cajan respectively. RNA editing was observed at 37 sites in both Cajanus scarabaeoides and Cajanus cajan, with maximum occurrence in the ndh genes. The pigeonpea cp genome sequence would be beneficial in providing informative molecular markers which can be utilized for genetic diversity analysis and aid in understanding the plant systematics studies among major grain legumes.

  16. Stress concentration during pellet cladding interaction: Comparison of closed-form solutions with 2D(r,θ) finite element simulations

    International Nuclear Information System (INIS)

    Sercombe, Jérôme; Masson, Renaud; Helfer, Thomas

    2013-01-01

    Highlights: • This paper presents closed-formed solutions concerning pellet cladding interaction. • First, the opening of a radial crack in a pellet fragment is estimated. • Second, the stresses in the cladding in front of the pellet crack are calculated. • The closed-formed solutions are found in good agreement with 2D FE simulations. • They are then used in the fuel code ALCYONE to model PCI during power ramps. -- Abstract: This paper presents two closed-form solutions that can be used to enrich the mechanical description of fuel pellets and cladding behavior in standard one-dimensional based fuel performance codes. The first one is concerned with the estimation of the opening of a radial crack in a pellet fragment induced by the radial thermal gradient in the pellet and limited by the pellet-clad contact pressure. The second one describes the stress distribution in a cladding bore in front of an opening pellet crack. A linear angular variation of the pellet-clad contact pressure and a constant prescribed radial displacement are considered. The closed-form solutions are checked by comparison to independent finite element models of the pellet fragment and of the cladding. Their ability to describe non-axisymmetric displacement and stress fields during loading histories representative of base irradiation and power ramps is then demonstrated by cross-comparison with the 2D pellet fragment-cladding model of the multi-dimensional fuel performance code ALCYONE. The calculated radial crack opening profiles at different times and the hoop stress concentration in the cladding at the top of the ramp are found in good agreement with ALCYONE

  17. Comparison of some characteristics of aerobic granules and sludge flocs from sequencing batch reactors.

    Science.gov (United States)

    Li, J; Garny, K; Neu, T; He, M; Lindenblatt, C; Horn, H

    2007-01-01

    Physical, chemical and biological characteristics were investigated for aerobic granules and sludge flocs from three laboratory-scale sequencing batch reactors (SBRs). One reactor was operated as normal SBR (N-SBR) and two reactors were operated as granular SBRs (G-SBR1 and G-SBR2). G-SBR1 was inoculated with activated sludge and G-SBR2 with granules from the municipal wastewater plant in Garching (Germany). The following major parameters and functions were measured and compared between the three reactors: morphology, settling velocity, specific gravity (SG), sludge volume index (SVI), specific oxygen uptake rate (SOUR), distribution of the volume fraction of extracellular polymeric substances (EPS) and bacteria, organic carbon and nitrogen removal. Compared with sludge flocs, granular sludge had excellent settling properties, good solid-liquid separation, high biomass concentration, simultaneous nitrification and denitrification. Aerobic granular sludge does not have a higher microbial activity and there are some problems including higher effluent suspended solids, lower ratio of VSS/SS and no nitrification at the beginning of cultivation. Measurement with CLSM and additional image analysis showed that EPS glycoconjugates build one main fraction inside the granules. The aerobic granules from G-SBR1 prove to be heavier, smaller and have a higher microbial activity compared with G-SBR2. Furthermore, the granules were more compact, with lower SVI and less filamentous bacteria.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

    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 13 C nuclear spins as qubits and an environment of 1 H 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.

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

    Science.gov (United States)

    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.

  20. Whole-Genome Sequences of Four Strains Closely Related to Members of the Mycobacterium chelonae Group, Isolated from Biofilms in a Drinking Water Distribution System Simulator

    Science.gov (United States)

    We report the draft genome sequences of four Mycobacterium chelonae group strains from biofilms obtained after a ‘chlorine burn’ in a chloraminated drinking water distribution system simulator. These opportunistic pathogens have been detected in drinking and hospital water distr...

  1. Whole-genome comparison of two Campylobacter jejuni isolates of the same sequence type reveals multiple loci of different ancestral lineage.

    Directory of Open Access Journals (Sweden)

    Patrick J Biggs

    Full Text Available Campylobacter jejuni ST-474 is the most important human enteric pathogen in New Zealand, and yet this genotype is rarely found elsewhere in the world. Insight into the evolution of this organism was gained by a whole genome comparison of two ST-474, flaA SVR-14 isolates and other available C. jejuni isolates and genomes. The two isolates were collected from different sources, human (H22082 and retail poultry (P110b, at the same time and from the same geographical location. Solexa sequencing of each isolate resulted in ~1.659 Mb (H22082 and ~1.656 Mb (P110b of assembled sequences within 28 (H22082 and 29 (P110b contigs. We analysed 1502 genes for which we had sequences within both ST-474 isolates and within at least one of 11 C. jejuni reference genomes. Although 94.5% of genes were identical between the two ST-474 isolates, we identified 83 genes that differed by at least one nucleotide, including 55 genes with non-synonymous substitutions. These covered 101 kb and contained 672 point differences. We inferred that 22 (3.3% of these differences were due to mutation and 650 (96.7% were imported via recombination. Our analysis estimated 38 recombinant breakpoints within these 83 genes, which correspond to recombination events affecting at least 19 loci regions and gives a tract length estimate of ~2 kb. This includes a ~12 kb region displaying non-homologous recombination in one of the ST-474 genomes, with the insertion of two genes, including ykgC, a putative oxidoreductase, and a conserved hypothetical protein of unknown function. Furthermore, our analysis indicates that the source of this recombined DNA is more likely to have come from C. jejuni strains that are more closely related to ST-474. This suggests that the rates of recombination and mutation are similar in order of magnitude, but that recombination has been much more important for generating divergence between the two ST-474 isolates.

  2. Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes.

    Science.gov (United States)

    Ari, Eszter; Ittzés, Péter; Podani, János; Thi, Quynh Chi Le; Jakó, Eena

    2012-04-01

    Boolean analysis (or BOOL-AN; Jakó et al., 2009. BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction. Mol. Phylogenet. Evol. 52, 887-97.), a recently developed method for sequence comparison uses the Iterative Canonical Form of Boolean functions. It considers sequence information in a way entirely different from standard phylogenetic methods (i.e. Maximum Parsimony, Maximum-Likelihood, Neighbor-Joining, and Bayesian analysis). The performance and reliability of Boolean analysis were tested and compared with the standard phylogenetic methods, using artificially evolved - simulated - nucleotide sequences and the 22 mitochondrial tRNA genes of the great apes. At the outset, we assumed that the phylogeny of Hominidae is generally well established, and the guide tree of artificial sequence evolution can also be used as a benchmark. These offer a possibility to compare and test the performance of different phylogenetic methods. Trees were reconstructed by each method from 2500 simulated sequences and 22 mitochondrial tRNA sequences. We also introduced a special re-sampling method for Boolean analysis on permuted sequence sites, the P-BOOL-AN procedure. Considering the reliability values (branch support values of consensus trees and Robinson-Foulds distances) we used for simulated sequence trees produced by different phylogenetic methods, BOOL-AN appeared as the most reliable method. Although the mitochondrial tRNA sequences of great apes are relatively short (59-75 bases long) and the ratio of their constant characters is about 75%, BOOL-AN, P-BOOL-AN and the Bayesian approach produced the same tree-topology as the established phylogeny, while the outcomes of Maximum Parsimony, Maximum-Likelihood and Neighbor-Joining methods were equivocal. We conclude that Boolean analysis is a promising alternative to existing methods of sequence comparison for phylogenetic reconstruction and congruence analysis. Copyright © 2012 Elsevier Inc. All

  3. The complete mitochondrial genome of Strongylus equinus (Chromadorea: Strongylidae): Comparison with other closely related species and phylogenetic analyses.

    Science.gov (United States)

    Xu, Wen-Wen; Qiu, Jian-Hua; Liu, Guo-Hua; Zhang, Yan; Liu, Ze-Xuan; Duan, Hong; Yue, Dong-Mei; Chang, Qiao-Cheng; Wang, Chun-Ren; Zhao, Xing-Cun

    2015-12-01

    The roundworms of genus Strongylus are the common parasitic nematodes in the large intestine of equine, causing significant economic losses to the livestock industries. In spite of its importance, the genetic data and epidemiology of this parasite are not entirely understood. In the present study, the complete S. equinus mitochondrial (mt) genome was determined. The length of S. equinus mt genome DNA sequence is 14,545 bp, containing 36 genes, of which 12 code for protein, 22 for transfer RNA, and two for ribosomal RNA, but lacks atp8 gene. All 36 genes are encoded in the same direction which is consistent with all other Chromadorea nematode mtDNAs published to date. Phylogenetic analysis based on concatenated amino acid sequence data of all 12 protein-coding genes showed that there were two large branches in the Strongyloidea nematodes, and S. equinus is genetically closer to S. vulgaris than to Cylicocyclus insignis in Strongylidae. This new mt genome provides a source of genetic markers for the molecular phylogeny and population genetics of equine strongyles. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  5. Comparison of Intravenous Morphine with Sublingual Buprenorphine in Management of Postoperative Pain after Closed Reduction Orthopedic Surgery

    Directory of Open Access Journals (Sweden)

    Ghasem Soltani

    2015-09-01

    Full Text Available Background: Postoperative pain is a common side effect following surgery that can significantly reduce surgical quality and patient’s satisfaction. Treatment options are morphine and buprenorphine. We aimed to compare the efficacy of a single dose of intravenous morphine with sublingual buprenorphine in postoperative pain control following closed reduction surgery. Methods: This triple blind clinical trial was conducted on 90 patients referred for closed reduction orthopedic surgery. They were older than 18 years and in classes I and II of the American Society of Anesthesiologists (ASA with an operation time of 30-90 minutes. Patients were divided into two groups of buprenorphine (4.5μg/kg sublingually and morphine (0.2mg/kg intravenously. Baseline characteristics, vital signs, pain score, level of sedation and pharmacological side effects were recorded in the recovery room (at 0 and 30 minutes, and in the ward (at 3, 6 and 12 hours. SPSS version 19 software was used for data analysis and the significance level was set at P Results: Ninety patients were studied, 60 males and 30 females with a mean age of 37.7±16.2 years. There was no significant difference between the two groups in terms of baseline characteristics.Pain score in the morphine group was significantly higher than the buprenorphine group with an average score of 2.5 (P

  6. Comparison of Intravenous Morphine with Sublingual Buprenorphine in Management of Postoperative Pain after Closed Reduction Orthopedic Surgery

    Directory of Open Access Journals (Sweden)

    Ghasem Soltani

    2015-10-01

    Full Text Available Background: Postoperative pain is a common side effect following surgery that can significantly reduce surgical quality and patient’s satisfaction. Treatment options are morphine and buprenorphine. We aimed to compare the efficacy of a single dose of intravenous morphine with sublingual buprenorphine in postoperative pain control following closed reduction surgery. Methods: This triple blind clinical trial was conducted on 90 patients referred for closed reduction orthopedic surgery. They were older than 18 years and in classes I and II of the American Society of Anesthesiologists (ASA with an operation time of 30-90 minutes. Patients were divided into two groups of buprenorphine (4.5μg/kg sublingually and morphine (0.2mg/kg intravenously. Baseline characteristics, vital signs, pain score, level of sedation and pharmacological side effects were recorded in the recovery room (at 0 and 30 minutes, and in the ward (at 3, 6 and 12 hours. SPSS version 19 software was used for data analysis and the significance level was set at P Results: Ninety patients were studied, 60 males and 30 females with a mean age of 37.7±16.2 years. There was no significant difference between the two groups in terms of baseline characteristics.Pain score in the morphine group was significantly higher than the buprenorphine group with an average score of 2.5 (P

  7. Characterisation of peacock (Pavo cristatus) mitochondrial 12S rRNA sequence and its use in differentiation from closely related poultry species.

    Science.gov (United States)

    Saini, M; Das, D K; Dhara, A; Swarup, D; Yadav, M P; Gupta, P K

    2007-04-01

    1. Poaching of peacocks, the national bird of India, is illegal. People kill this beautiful pheasant bird for tail feathers and mix the meat with chicken or turkey. Differentiation of the meat of these species is essential in order to address the ambiguity about the origin of the sample. 2. The present study was carried out to investigate the use of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of mitochondrial 12S rRNA gene for identification of these species. 3. Peacock mitochondrial 12S rRNA partial gene was amplified using universal primers, cloned and characterised. It was found to be 446 nucleotides long. 4. Sequence analysis revealed 86.8 and 84.1% similarity with reported turkey and chicken sequences, respectively. Sequence and phylogenetic analysis showed that the peacock is much closer to the turkey than the chicken. 5. PCR-RFLP of 446 bp amplicon using commonly available restriction enzymes AluI and Sau3AI produced a differential pattern for identifying these poultry species unambiguously.

  8. Comparison of {sup 99m}Tc-HMPAO SPECT and MRI after Acute and Subacute Closed-Head Injury

    Energy Technology Data Exchange (ETDEWEB)

    Yoo, Won Jong; Lee, Sang Hoon; Sohn, Hyung Sun; Lee, Han Jin; Park, Jeong Mi; Chung, Soo Kyo; Kim, Choon Yul; Bahk, Yong Whee; Shin, Kyung Sub [Catholic University College of Medicine, Seoul (Korea, Republic of)

    1994-10-15

    The purpose of this study was to compare {sup 99m}Tc-HMPAO SPECT with MRI after acute and subacute closed head injury. There were thirty two focal lesions in all cases of these, Fifteen lesions(47%) were seen on both MRI and SPECT. Fourteen lesions(44%) were seen only on MRI. Three lesions(9%) were seen only on SPECT. Of the 14 lesions seen only on MRl, one was epidural hematoma, two were subdural hematoma, three were subdural hygroma, one was intracerebral hematoma, four were contusion, and three were diffuse axonal injuries. SPECT detected 52% of the focal lesions found on MRI. For the detection of lesions, MRl was superior to SPECT in fourteen cases, while SPECT was superior to MRI in three cases. In conclusion, there was a tendency that detection rate of the traumatic lesions was higher on MRI, but the SPECT could delineate more wide extent of lesion.

  9. Comparison of detectable bleeding rates of radiopharmaceuticals for localization of gastrointestinal bleeding in sheep using a closed system

    Energy Technology Data Exchange (ETDEWEB)

    Owunwanne, A.; Sadek, S.; Yacoub, T.; Awdeh, M.; Abdel-Dayem, H.M. (Kuwait Univ. (Kuwait). Dept. of Nuclear Medicine); Al-Wafai, I.; Vallgren, S. (Kuwait Univ. (Kuwait). Dept. of Surgery)

    1989-06-01

    The closed experimental animal model system was used to compare the detectable gastrointestinal (GI) bleeding rates of {sup 99m}Tc-DTPA, {sup 99m}Tc-RBCs and {sup 99m}Tc tin colloid in sheep. The three radiopharmaceuticals were used to detect the upper GI bleeding sites at rates of 0.57 and 0.25 ml/min. At the lower bleeding rate of 0.1 ml/min, both {sup 99m}Tc-DTPA and {sup 99m}Tc-RBCs were successful in detecting the bleeding site. At the lowest rate of 0.07 ml/min only {sup 99m}Tc-DTPA was successful in detecting the bleeding site. The results indicate that {sup 99m}Tc-DTPA is the most useful {sup 99m}Tc radiopharmaceutical for detecting the upper GI bleeding site at the slowest bleeding rate studied. (orig.).

  10. Comparison of detectable bleeding rates of radiopharmaceuticals for localization of gastrointestinal bleeding in sheep using a closed system

    International Nuclear Information System (INIS)

    Owunwanne, A.; Sadek, S.; Yacoub, T.; Awdeh, M.; Abdel-Dayem, H.M.; Al-Wafai, I.; Vallgren, S.

    1989-01-01

    The closed experimental animal model system was used to compare the detectable gastrointestinal (GI) bleeding rates of 99m Tc-DTPA, 99m Tc-RBCs and 99m Tc tin colloid in sheep. The three radiopharmaceuticals were used to detect the upper GI bleeding sites at rates of 0.57 and 0.25 ml/min. At the lower bleeding rate of 0.1 ml/min, both 99m Tc-DTPA and 99m Tc-RBCs were successful in detecting the bleeding site. At the lowest rate of 0.07 ml/min only 99m Tc-DTPA was successful in detecting the bleeding site. The results indicate that 99m Tc-DTPA is the most useful 99m Tc radiopharmaceutical for detecting the upper GI bleeding site at the slowest bleeding rate studied. (orig.) [de

  11. Comparison of Open and Closed Hand Fractures and the Effect of Urgent Operative Intervention.

    Science.gov (United States)

    Minhas, Shobhit V; Catalano, Louis W

    2018-06-13

    To establish and compare the incidence of 30-day postoperative infection in surgically managed open and closed metacarpal and phalangeal fractures, and to determine whether open fractures treated urgently had a lower incidence of postoperative infection. We conducted a retrospective analysis of patient demographics, comorbidities, and 30-day infection rates of patients undergoing operative fixation of metacarpal, proximal, or middle phalanx fractures from 2008 to 2015 using the American College of Surgeons' National Surgical Quality Improvement Program database. A total of 3,506 patients were identified and patient variables and infection incidence were compared between open and closed injuries, as well as open injuries managed within 1 day of admission and those treated on an elective basis or treated more than 1 day after admission. Bivariate analysis was used to determine independent risk factors for postoperative infection. Although 34.2% of open hand fractures were taken urgently to the operating room, the diagnosis of open fractures along with nonurgent surgical treatment for open fractures was associated with a low incidence of postoperative infection. In addition, smoking was a risk factor for postoperative infection although anatomic location (phalanx vs metacarpal) was not. Patients undergoing surgery for metacarpal or proximal/middle phalangeal fractures are not at greater risk for infection based on the diagnosis of open fracture alone. In addition, patients with open fractures who are taken to the operating room more than 1 day from presentation did not have a higher incidence of infection. Smoking is associated with increased 30-day infection rates after surgery, and surgeons should identify these patients for preoperative risk stratification, counseling, and postoperative wound monitoring. Prognostic II. Copyright © 2018 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.

  12. In silico Coding Sequence Analysis of Walnut GAI and PIP2 Genes and Comparison with Different Plant Species

    Directory of Open Access Journals (Sweden)

    Mahdi Mohseniazar

    2017-02-01

    done with MEGA from aligned sequences. The motifs of protein sequences were found using the program of T-COFEE at website (http://www.ebi.ac.uk/Tools/msa/tcoffee/. The Neighbor-Joining (NJ method was used to designing the phylogenetic tree. The predicted exons and introns in mRNA sequences were done by http://genes.mit.edu/GENSCAN.html website. The secondary structure of proteins was predicted by PSIORED online on http://bioinf.cs.ucl.ac.uk/psipred/. Prediction of 3D model of protein was performed using the 3D alignment of protein structure by BLASTp and PDB database as source. Also, targeting prediction of proteins was done online by TargetP at (http://www.cbs.dtu.dk/services/TargetP/ website. Results and discussion: In phylogenetic investigation among 17 different species, Walnut species evolutionary stand in dicotyledonous and woody plants by both of GAI and PIP2 genes and protein sequence clustering. By multiple alignments and investigation in conserved sequence of these genes in plant revealed that despite differences in cDNA length, there were very similarities in conserved region, secondary and tertiary structure. Protein analysis in the GAI gene family showed that the following domains including DELLA, TVHYNP, VHIID, RKVATYFGEALARR, AVNSVFELH, RVER, and SAW were conserved in this proteins. In secondary structure of protein, β-sheets and α-helixes specified by PSIPRED software for both of GAI and PIP2 proteins. GAI protein had 9 β-sheets and 15 α-helixes in its structure, also PIP2 protein had2 β-sheet (at 180-188 and 248-253 and 8 α-helixes. In comparison of 3D structure, walnut PIP2 protein was very similar to chain A of PIP2 protein of spinach (Spinacia oleracea and GAI protein of walnut was similar to B-subunit of Arabidopsis GAI protein with 48% similarity. The length of GAI protein was varied from 636 aa in Malus baccata var. xiaojinensis to 336 aa in Physcomitrella patens among species. In walnut, the length of GAI and PIP2 protein was 613 aa and

  13. In silico Coding Sequence Analysis of Walnut GAI and PIP2 Genes and Comparison with Different Plant Species

    Directory of Open Access Journals (Sweden)

    Mahdi Mohseniazar

    2017-09-01

    done with MEGA from aligned sequences. The motifs of protein sequences were found using the program of T-COFEE at website (http://www.ebi.ac.uk/Tools/msa/tcoffee/. The Neighbor-Joining (NJ method was used to designing the phylogenetic tree. The predicted exons and introns in mRNA sequences were done by http://genes.mit.edu/GENSCAN.html website. The secondary structure of proteins was predicted by PSIORED online on http://bioinf.cs.ucl.ac.uk/psipred/. Prediction of 3D model of protein was performed using the 3D alignment of protein structure by BLASTp and PDB database as source. Also, targeting prediction of proteins was done online by TargetP at (http://www.cbs.dtu.dk/services/TargetP/ website. Results and discussion: In phylogenetic investigation among 17 different species, Walnut species evolutionary stand in dicotyledonous and woody plants by both of GAI and PIP2 genes and protein sequence clustering. By multiple alignments and investigation in conserved sequence of these genes in plant revealed that despite differences in cDNA length, there were very similarities in conserved region, secondary and tertiary structure. Protein analysis in the GAI gene family showed that the following domains including DELLA, TVHYNP, VHIID, RKVATYFGEALARR, AVNSVFELH, RVER, and SAW were conserved in this proteins. In secondary structure of protein, β-sheets and α-helixes specified by PSIPRED software for both of GAI and PIP2 proteins. GAI protein had 9 β-sheets and 15 α-helixes in its structure, also PIP2 protein had2 β-sheet (at 180-188 and 248-253 and 8 α-helixes. In comparison of 3D structure, walnut PIP2 protein was very similar to chain A of PIP2 protein of spinach (Spinacia oleracea and GAI protein of walnut was similar to B-subunit of Arabidopsis GAI protein with 48% similarity. The length of GAI protein was varied from 636 aa in Malus baccata var. xiaojinensis to 336 aa in Physcomitrella patens among species. In walnut, the length of GAI and PIP2 protein was 613 aa and

  14. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    International Nuclear Information System (INIS)

    Hopper, M.A.; Robinson, P.; Grainger, A.J.

    2011-01-01

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  15. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    Energy Technology Data Exchange (ETDEWEB)

    Hopper, M.A.; Robinson, P. [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom); Grainger, A.J., E-mail: andrew.grainger@leedsth.nhs.u [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom)

    2011-04-15

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  16. Comparison of spin echo T1-weighted sequences versus fast spin-echo proton density-weighted sequences for evaluation of meniscal tears at 1.5 T

    International Nuclear Information System (INIS)

    Wolff, Andrew B.; Pesce, Lorenzo L.; Wu, Jim S.; Smart, L.R.; Medvecky, Michael J.; Haims, Andrew H.

    2009-01-01

    At our institution, fast spin-echo (FSE) proton density (PD) imaging is used to evaluate articular cartilage, while conventional spin-echo (CSE) T1-weighted sequences have been traditionally used to characterize meniscal pathology. We sought to determine if FSE PD-weighted sequences are equivalent to CSE T1-weighted sequences in the detection of meniscal tears, obviating the need to perform both sequences. We retrospectively reviewed the records of knee arthroscopies performed by two arthroscopy-focused surgeons from an academic medical center over a 2-year period. The preoperative MRI images were interpreted independently by two fellowship-trained musculoskeletal radiologists who graded the sagittal CSE T1 and FSE PD sequences at different sittings with grades 1-5, where 1 = normal meniscus, 2 = probable normal meniscus, 3 indeterminate, 4 = probable torn meniscus, and 5 = torn meniscus. Each meniscus was divided into an anterior and posterior half, and these halves were graded separately. Operative findings provided the gold standard. Receiver operating characteristic (ROC) analysis was performed to compare the two sequences. There were 131 tears in 504 meniscal halves. Using ROC analysis, the reader 1 area under curve for FSE PD was significantly better than CSE T1 (0.939 vs. 0.902, >95% confidence). For reader 2, the difference met good criteria for statistical non-inferiority but not superiority (0.913 for FSE PD and 0.908 for CSE T1; >95% non-inferiority for difference at most of -0.027). FSE PD-weighted sequences, using our institutional protocol, are not inferior to CSE T1-weighted sequences for the detection of meniscal tears and may be superior. (orig.)

  17. Sequence comparisons of odorant receptors among tortricid moths reveal different rates of molecular evolution among family members.

    Directory of Open Access Journals (Sweden)

    Colm Carraher

    Full Text Available 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.

  18. Comparisons of Source Characteristics between Recent Inland Crustal Earthquake Sequences inside and outside of Niigata-Kobe Tectonic Zone, Japan

    Science.gov (United States)

    Somei, K.; Asano, K.; Iwata, T.; Miyakoshi, K.

    2012-12-01

    After the 1995 Kobe earthquake, many M7-class inland earthquakes occurred in Japan. Some of those events (e.g., the 2004 Chuetsu earthquake) occurred in a tectonic zone which is characterized as a high strain rate zone by the GPS observation (Sagiya et al., 2000) or dense distribution of active faults. That belt-like zone along the coast in Japan Sea side of Tohoku and Chubu districts, and north of Kinki district, is called as the Niigata-Kobe tectonic zone (NKTZ, Sagiya et al, 2000). We investigate seismic scaling relationship for recent inland crustal earthquake sequences in Japan and compare source characteristics between events occurring inside and outside of NKTZ. We used S-wave coda part for estimating source spectra. Source spectral ratio is obtained by S-wave coda spectral ratio between the records of large and small events occurring close to each other from nation-wide strong motion network (K-NET and KiK-net) and broad-band seismic network (F-net) to remove propagation-path and site effects. We carefully examined the commonality of the decay of coda envelopes between event-pair records and modeled the observed spectral ratio by the source spectral ratio function with assuming omega-square source model for large and small events. We estimated the corner frequencies and seismic moment (ratio) from those modeled spectral ratio function. We determined Brune's stress drops of 356 events (Mw: 3.1-6.9) in ten earthquake sequences occurring in NKTZ and six sequences occurring outside of NKTZ. Most of source spectra obey omega-square source spectra. There is no obvious systematic difference between stress drops of events in NKTZ zone and others. We may conclude that the systematic tendency of seismic source scaling of the events occurred inside and outside of NKTZ does not exist and the average source scaling relationship can be effective for inland crustal earthquakes. Acknowledgements: Waveform data were provided from K-NET, KiK-net and F-net operated by

  19. Comparison of three different fat graft preparation methods: gravity separation, centrifugation, and simultaneous washing with filtration in a closed system.

    Science.gov (United States)

    Zhu, Min; Cohen, Steven R; Hicok, Kevin C; Shanahan, Rob K; Strem, Brian M; Yu, Johnson C; Arm, Douglas M; Fraser, John K

    2013-04-01

    Successful long-term volume retention of an autologous fat graft is problematic. The presence of contaminating cells, tumescent fluid, and free lipid in the graft contributes to disparate outcomes. Better preparation methods for the fat graft before transplantation may significantly improve results. Subcutaneous fat from 22 donors was divided and processed using various graft preparation methods: (1) no manipulation control, (2) gravity separation, (3) Coleman centrifugation, and (4) simultaneous washing with filtration using a commercially available system (Puregraft; Cytori Therapeutics, Inc., San Diego, Calif.). Fat grafts from various preparation methods were examined for free lipid, aqueous liquid, viable tissue, and blood cell content. Adipose tissue viability was determined by measuring glycerol release after agonist induction of lipolysis. All test graft preparation methods exhibited significantly less aqueous fluid and blood cell content compared with the control. Grafts prepared by washing with filtration exhibited significantly reduced blood cell and free lipid content, with significantly greater adipose tissue viability than other methods. Washing with filtration within a closed system produces a fat graft with higher tissue viability and lower presence of contaminants compared with grafts prepared by alternate methods.

  20. Comparison of simulated and experimental results of temperature distribution in a closed two-phase thermosyphon cooling system

    Science.gov (United States)

    Shaanika, E.; Yamaguchi, K.; Miki, M.; Ida, T.; Izumi, M.; Murase, Y.; Oryu, T.; Yanamoto, T.

    2017-12-01

    Superconducting generators offer numerous advantages over conventional generators of the same rating. They are lighter, smaller and more efficient. Amongst a host of methods for cooling HTS machinery, thermosyphon-based cooling systems have been employed due to their high heat transfer rate and near-isothermal operating characteristics associated with them. To use them optimally, it is essential to study thermal characteristics of these cryogenic thermosyphons. To this end, a stand-alone neon thermosyphon cooling system with a topology resembling an HTS rotating machine was studied. Heat load tests were conducted on the neon thermosyphon cooling system by applying a series of heat loads to the evaporator at different filling ratios. The temperature at selected points of evaporator, adiabatic tube and condenser as well as total heat leak were measured. A further study involving a computer thermal model was conducted to gain further insight into the estimated temperature distribution of thermosyphon components and heat leak of the cooling system. The model employed boundary conditions from data of heat load tests. This work presents a comparison between estimated (by model) and experimental (measured) temperature distribution in a two-phase cryogenic thermosyphon cooling system. The simulation results of temperature distribution and heat leak compared generally well with experimental data.

  1. Variation in extragenic repetitive DNA sequences in Pseudomonas syringae and potential use of modified REP primers in the identification of closely related isolates

    Directory of Open Access Journals (Sweden)

    Elif Çepni

    2012-01-01

    Full Text Available In this study, Pseudomonas syringe pathovars isolated from olive, tomato and bean were identified by species-specific PCR and their genetic diversity was assessed by repetitive extragenic palindromic (REP-PCR. Reverse universal primers for REP-PCR were designed by using the bases of A, T, G or C at the positions of 1, 4 and 11 to identify additional polymorphism in the banding patterns. Binding of the primers to different annealing sites in the genome revealed additional fingerprint patterns in eight isolates of P. savastanoi pv. savastanoi and two isolates of P. syringae pv. tomato. The use of four different bases in the primer sequences did not affect the PCR reproducibility and was very efficient in revealing intra-pathovar diversity, particularly in P. savastanoi pv. savastanoi. At the pathovar level, the primer BOX1AR yielded shared fragments, in addition to five bands that discriminated among the pathovars P. syringae pv. phaseolicola, P. savastanoi pv. savastanoi and P. syringae pv. tomato. REP-PCR with a modified primer containing C produced identical bands among the isolates in a pathovar but separated three pathovars more distinctly than four other primers. Although REP-and BOX-PCRs have been successfully used in the molecular identification of Pseudomonas isolates from Turkish flora, a PCR based on inter-enterobacterial repetitive intergenic concensus (ERIC sequences failed to produce clear banding patterns in this study.

  2. The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida--evidence for close relationship to the T7 group

    International Nuclear Information System (INIS)

    Kovalyova, Irina V.; Kropinski, Andrew M.

    2003-01-01

    The genome of the lytic Pseudomonas putida bacteriophage gh-1 is linear double-stranded DNA containing 37,359 bp with 216-bp direct terminal repeats. Like other members of the T7 group, the gh-1 genome contains regions of high homology to T7 interspersed with nonhomologous regions that contain small open reading frames of unknown function. The genome shares 31 genes in common with other members of the T7 group, including RNA polymerase, and an additional 12 unique putative genes. A major difference between gh-1 and other members of this group is the absence of any open reading frames between the left direct terminal repeat and gene 1. Sequence analysis of the gh-1 genome also revealed the presence of 10 putative phage promoters with a consensus sequence similar to the promoters of T3 and phiYeO3-12 (consensus: TAAAAACCCTCACTRTGGCHSCM). P. putida mutants resistant to gh-1 were demonstrated to have an altered lipopolysaccharide structure, indicating that members of this group use lipopolysaccharide as their cellular receptor

  3. Close genetic relationship between Legionella pneumophila serogroup 1 isolates from sputum specimens and puddles on roads, as determined by sequence-based typing.

    Science.gov (United States)

    Kanatani, Jun-ichi; Isobe, Junko; Kimata, Keiko; Shima, Tomoko; Shimizu, Miwako; Kura, Fumiaki; Sata, Tetsutaro; Watahiki, Masanori

    2013-07-01

    We investigated the prevalence of Legionella species isolated from puddles on asphalt roads. In addition, we carried out sequence-based typing (SBT) analysis on the genetic relationship between L. pneumophila serogroup 1 (SG 1) isolates from puddles and from stock strains previously obtained from sputum specimens and public baths. Sixty-nine water samples were collected from puddles on roads at 6 fixed locations. Legionella species were detected in 33 samples (47.8%) regardless of season. Among the 325 isolates from puddles, strains of L. pneumophila SG 1, a major causative agent of Legionnaires' disease, were the most frequently isolated (n = 62, 19.1%). Sixty-two isolates of L. pneumophila SG 1 from puddles were classified into 36 sequence types (STs) by SBT. ST120 and ST48 were identified as major STs. Environmental ST120 strains from puddles were found for the first time in this study. Among the 14 STs of the clinical isolates (n = 19), 4 STs (n = 6, 31.6%), including ST120, were also detected in isolates from puddles on roads, and the sources of infection in these cases remained unclear. The lag-1 gene, a tentative marker for clinical isolates, was prevalent in puddle isolates (61.3%). Our findings suggest that puddles on asphalt roads serve as potential reservoirs for L. pneumophila in the environment.

  4. Detection of de novo single nucleotide variants in offspring of atomic-bomb survivors close to the hypocenter by whole-genome sequencing.

    Science.gov (United States)

    Horai, Makiko; Mishima, Hiroyuki; Hayashida, Chisa; Kinoshita, Akira; Nakane, Yoshibumi; Matsuo, Tatsuki; Tsuruda, Kazuto; Yanagihara, Katsunori; Sato, Shinya; Imanishi, Daisuke; Imaizumi, Yoshitaka; Hata, Tomoko; Miyazaki, Yasushi; Yoshiura, Koh-Ichiro

    2018-03-01

    Ionizing radiation released by the atomic bombs at Hiroshima and Nagasaki, Japan, in 1945 caused many long-term illnesses, including increased risks of malignancies such as leukemia and solid tumours. Radiation has demonstrated genetic effects in animal models, leading to concerns over the potential hereditary effects of atomic bomb-related radiation. However, no direct analyses of whole DNA have yet been reported. We therefore investigated de novo variants in offspring of atomic-bomb survivors by whole-genome sequencing (WGS). We collected peripheral blood from three trios, each comprising a father (atomic-bomb survivor with acute radiation symptoms), a non-exposed mother, and their child, none of whom had any past history of haematological disorders. One trio of non-exposed individuals was included as a control. DNA was extracted and the numbers of de novo single nucleotide variants in the children were counted by WGS with sequencing confirmation. Gross structural variants were also analysed. Written informed consent was obtained from all participants prior to the study. There were 62, 81, and 42 de novo single nucleotide variants in the children of atomic-bomb survivors, compared with 48 in the control trio. There were no gross structural variants in any trio. These findings are in accord with previously published results that also showed no significant genetic effects of atomic-bomb radiation on second-generation survivors.

  5. Cross-species comparison of the gut: Differential gene expression sheds light on biological differences in closely related tenebrionids.

    Science.gov (United States)

    Oppert, Brenda; Perkin, Lindsey; Martynov, Alexander G; Elpidina, Elena N

    2018-04-01

    The gut is one of the primary interfaces between an insect and its environment. Understanding gene expression profiles in the insect gut can provide insight into interactions with the environment as well as identify potential control methods for pests. We compared the expression profiles of transcripts from the gut of larval stages of two coleopteran insects, Tenebrio molitor and Tribolium castaneum. These tenebrionids have different life cycles, varying in the duration and number of larval instars. T. castaneum has a sequenced genome and has been a model for coleopterans, and we recently obtained a draft genome for T. molitor. We assembled gut transcriptome reads from each insect to their respective genomes and filtered mapped reads to RPKM>1, yielding 11,521 and 17,871 genes in the T. castaneum and T. molitor datasets, respectively. There were identical GO terms in each dataset, and enrichment analyses also identified shared GO terms. From these datasets, we compiled an ortholog list of 6907 genes; 45% of the total assembled reads from T. castaneum were found in the top 25 orthologs, but only 27% of assembled reads were found in the top 25 T. molitor orthologs. There were 2281 genes unique to T. castaneum, and 2088 predicted genes unique to T. molitor, although improvements to the T. molitor genome will likely reduce these numbers as more orthologs are identified. We highlight a few unique genes in T. castaneum or T. molitor that may relate to distinct biological functions. A large number of putative genes expressed in the larval gut with uncharacterized functions (36 and 68% from T. castaneum and T. molitor, respectively) support the need for further research. These data are the first step in building a comprehensive understanding of the physiology of the gut in tenebrionid insects, illustrating commonalities and differences that may be related to speciation and environmental adaptation. Published by Elsevier Ltd.

  6. Comparison of three optimized digestion methods for rapid determination of chemical oxygen demand: Closed microwaves, open microwaves and ultrasound irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Domini, Claudia E. [Departamento de Quimica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Hidalgo, Montserrat [Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidad de Alicante, Apdo. 99, 03080 Alicante (Spain); Marken, Frank [Department of Chemistry, University of Bath, Bath BA2 7AY (United Kingdom); Canals, Antonio [Departamento de Quimica Analitica, Nutricion y Bromatologia, Universidad de Alicante, Apdo. 99, 03080 Alicante (Spain)]. E-mail: a.canals@ua.es

    2006-03-02

    In the present work, experimental design was used for the fast optimization of three kinds of sample digestion procedures with the final aim of obtaining the COD value of wastewater samples. The digestion methods evaluated were 'closed microwave-assisted' (CMWD), 'open microwave-assisted' (OMWD) and 'ultrasound-assisted' (USD). Classical digestion was used as reference method. The optimum values for the different variables studied in each method were: 90 psi pressure, 475 W power and 4 min irradiation time (CMWD); 150 deg. C temperature and 4 min irradiation time (OMWD); 90% of maximum nominal power (180 W), 0.9 s (s{sup -1}) cycles and 1 min irradiation time (USD). In all cases, interference concentration that produces a deviation of 10% in COD values is 13.4, 23.4, 21.1 and 2819 mg/L for S{sup 2-}, Fe{sup 2+}, NO{sub 2} {sup -} and Cl{sup -}, respectively. Under optimum conditions, the proposed digestion methods have been successfully applied, with the exception of pyridine, to several pure organic compounds and COD recoveries for 10 real wastewater samples were ranged between 88 and 104% of the values obtained with the classical (open reflux) method used as reference, with R.S.D. lower than 4% in most cases. Thus, the use of ultrasound energy for COD determination seems to be an interesting and promising alternative to conventional open reflux and microwave-assisted digestion methods used for the same purpose since the instrumentation is simpler, cheaper and safer and the digestion step faster than the ones used for the same purpose.

  7. Calculation of T2 relaxation time from ultrafast single shot sequences for differentiation of liver tumors. Comparison of echo-planar, HASTE, and spin-echo sequences

    International Nuclear Information System (INIS)

    Abe, Yasuko; Yamashita, Yasuyuki; Tang, Yi; Namimoto, Tomohiro; Takahashi, Mutsumasa

    2000-01-01

    The purpose of this study was to evaluate the accuracy of T2 calculation from single shot imaging sequences such as echo-planar imaging (EPI) and half-Fourier single shot turbo spin-echo (HASTE) imaging. For the phantom study, we prepared vials containing different concentrations of agarose, copper sulfate, and nickel chloride. The temperature of the phantom was kept at 22 deg C. MR images were obtained with a 1.5-Tesla superconductive magnet. Spin-echo (SE)-type EPI and HASTE sequences with different TEs were obtained for T2 calculation, and the T2 values were compared with those obtained from the Carr-Purcell-Meiborm-Gill (CPMG) sequence. The clinical study group consisted of 30 consecutive patients referred for MR imaging to characterize focal liver lesions. A total of 40 focal liver lesions were evaluated, including 25 primary or metastatic solid masses and 15 non-solid lesions. Single shot SE-type EPI and HASTE were both performed with TEs of 64 and 90 msec. In the phantom study, the T2 values obtained from both single shot sequences showed significant correlations with those from the CPMG sequence (T2 on EPI vs. T2 on CPMG: r=0.98, p<0.01; T2 on HASTE vs. T2 on CPMG: r=0.99, p<0.01). In the clinical study, mean T2 values for liver calculated from EPI (42 msec) were significantly shorter than those calculated from the HASTE sequence (58 msec) (p<0.001). Mean T2 values for solid tumors were 95 msec with HASTE and 72 msec with EPI, and mean T2 values for non-solid lesions were 128 msec with HASTE and 159 msec with EPI. Although mean T2 values between solid and non-solid lesions were significantly different for both EPI and HASTE sequences (p=0.01 for HASTE, p<0.001 for EPI), the overlap of solid and non-solid lesions was less frequent in EPI than in HASTE. With single shot sequences, it is possible to obtain the T2 values that show excellent correlation with the CPMG sequence. Although both HASTE and EPI are useful to calculate T2 values, EPI appears to be more

  8. Comparison of 3D turbo spin-echo SPACE sequences with conventional 2D MRI sequences to assess the shoulder joint

    Energy Technology Data Exchange (ETDEWEB)

    Kloth, Jost Karsten, E-mail: jost.kloth@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Winterstein, Marianne, E-mail: marianne.winterstein@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Akbar, Michael, E-mail: michael.akbar@med.uni-heidelberg.de [Orthopedic and Trauma Surgery, University Hospital Heidelberg, Schlierbacher Landstraße 200a, D-69118 Heidelberg (Germany); Meyer, Esther, E-mail: esther.meyer@siemens.com [Siemens Healthcare, Erlangen (Germany); Paul, Dominik, E-mail: dominik.paul@siemens.com [Siemens Healthcare, Erlangen (Germany); Kauczor, Haus-Ulrich, E-mail: hans-ulrich.kauczor@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany); Weber, Marc-André, E-mail: marcandre.weber@med.uni-heidelberg.de [Diagnostic and Interventional Radiology, University Hospital Heidelberg, Im Neuenheimer Feld 110, D-69120 Heidelberg (Germany)

    2014-10-15

    Highlights: • 3D SPACE and conventional 2D TSE MRI for assessment of the shoulder joint were compared. • Concordance for most pathologys was substantial to almost perfect. • Examination time could be reduced up to 8 min (27%). • Regarding rotator cuff injuries an additional sagittal T2w TSE sequence in 3D protocol is recommended. - Abstract: Purpose: To determine the accuracy and reliability of three-dimensional (3D) T1- and proton density (PD)-weighted turbo spin-echo (TSE) sampling perfection with application-optimized contrasts using different flip-angle evolution (SPACE) compared with conventional 2D sequences in assessment of the shoulder-joint. Materials and methods: Ninety-three subjects were examined on a 3-T MRI system with both conventional 2D-TSE sequences in T1-, T2- and PD-weighting and 3D SPACE sequences in T1- and PD-weighting. All examinations were assessed independently by two reviewers for common pathologies of the shoulder-joint. Agreement between 2D- and 3D-sequences and inter-observer-agreement was evaluated using kappa-statistics. Results: Using conventional 2D TSE sequences as standard of reference, sensitivity, specificity, and accuracy values of 3D SPACE were 81.8%, 95.1%, and 93.5% for injuries of the supraspinatus-tendon (SSP), 81.3%, 93.5%, and 91.4% for the cartilage layer and 82.4%, 98.5%, and 97.5% for the long biceps tendon. Concordance between 2D and 3D was almost perfect for tendinopathies of the SSP (κ = 0.85), osteoarthritis (κ = 1), luxation of the biceps tendon (κ = 1) and adjacent bone marrow (κ = 0.92). Inter-observer-agreement was generally higher for conventional 2D TSE sequences (κ, 0.23–1.0), when compared to 3D SPACE sequences (κ, −0.33 to 1.0) except for disorders of the long biceps tendon and supraspinatus tendon rupture. Conclusion: Because of substantial and almost perfect concordance with conventional 2D TSE sequences for common shoulder pathologies, MRI examination-time can be reduced by nearly 40

  9. Quantitation of next generation sequencing library preparation protocol efficiencies using droplet digital PCR assays - a systematic comparison of DNA library preparation kits for Illumina sequencing.

    Science.gov (United States)

    Aigrain, Louise; Gu, Yong; Quail, Michael A

    2016-06-13

    The emergence of next-generation sequencing (NGS) technologies in the past decade has allowed the democratization of DNA sequencing both in terms of price per sequenced bases and ease to produce DNA libraries. When it comes to preparing DNA sequencing libraries for Illumina, the current market leader, a plethora of kits are available and it can be difficult for the users to determine which kit is the most appropriate and efficient for their applications; the main concerns being not only cost but also minimal bias, yield and time efficiency. We compared 9 commercially available library preparation kits in a systematic manner using the same DNA sample by probing the amount of DNA remaining after each protocol steps using a new droplet digital PCR (ddPCR) assay. This method allows the precise quantification of fragments bearing either adaptors or P5/P7 sequences on both ends just after ligation or PCR enrichment. We also investigated the potential influence of DNA input and DNA fragment size on the final library preparation efficiency. The overall library preparations efficiencies of the libraries show important variations between the different kits with the ones combining several steps into a single one exhibiting some final yields 4 to 7 times higher than the other kits. Detailed ddPCR data also reveal that the adaptor ligation yield itself varies by more than a factor of 10 between kits, certain ligation efficiencies being so low that it could impair the original library complexity and impoverish the sequencing results. When a PCR enrichment step is necessary, lower adaptor-ligated DNA inputs leads to greater amplification yields, hiding the latent disparity between kits. We describe a ddPCR assay that allows us to probe the efficiency of the most critical step in the library preparation, ligation, and to draw conclusion on which kits is more likely to preserve the sample heterogeneity and reduce the need of amplification.

  10. Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

    Science.gov (United States)

    Kimura, M; Kimura, J; Hatakeyama, T

    1988-11-21

    The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

  11. Comparison of the oropharyngeal cavity in the Starksiini (Teleostei: Blenniiformes: Labrisomidae): taste buds and teeth, including a comparison with closely-related genera.

    Science.gov (United States)

    Fishelson, Lev; Baldwin, Carole C; Hastings, Philip A

    2012-06-01

    The present study describes the distribution of taste buds and teeth in the oropharyngeal cavity of 13 species of adult (18-60 mm SL) Starksiini fishes inhabiting subtidal waters of the Neotropical region. Four types of taste buds described previously in other fish groups were observed within the oropharyngeal cavity, of which type I, situated on prominent protruding papillae, is the most common. The number of taste buds in this cavity varies considerably, ranging from ca. 202 in Starksia lepicoelia to ca. 770 in S. sluiteri. In all the studied species, taste buds are more numerous on the posterior (160-396) than on the anterior (42-294) part of the oropharyngeal cavity. The presence of different numbers of taste buds in different Starksiini species of the same standard length suggests that numbers of taste buds are not directly correlated with size and may be species-specific. Teeth are found on the premaxilla, dentary, vomer, palatine (in some species) and the upper and lower pharyngeal jaws (third pharyngobranchials and fifth ceratobranchials, respectively); the form and number of teeth and taste buds on each of these sites differs among the various species of Starksiini and between them and closely related species of the labrisomid tribes Labrisomini, Mnierpini, and Paraclinini. The results thus suggest potential systematic value in certain features of the oropharyngeal cavity for blenniiform fishes. It is also shown that benthic-feeding omnivorous fishes have higher densities of taste buds than piscivorous fishes. A possible correlation among numbers of taste buds, their positions in the oropharyngeal cavity, and other parameters is discussed. Copyright © 2012 Wiley Periodicals, Inc.

  12. Nucleotide and amino acid sequences of a coat protein of an Ukrainian isolate of Potato virus Y: comparison with homologous sequences of other isolates and phylogenetic analysis

    Directory of Open Access Journals (Sweden)

    Budzanivska I. G.

    2014-03-01

    Full Text Available Aim. Identification of the widespread Ukrainian isolate(s of PVY (Potato virus Y in different potato cultivars and subsequent phylogenetic analysis of detected PVY isolates based on NA and AA sequences of coat protein. Methods. ELISA, RT-PCR, DNA sequencing and phylogenetic analysis. Results. PVY has been identified serologically in potato cultivars of Ukrainian selection. In this work we have optimized a method for total RNA extraction from potato samples and offered a sensitive and specific PCR-based test system of own design for diagnostics of the Ukrainian PVY isolates. Part of the CP gene of the Ukrainian PVY isolate has been sequenced and analyzed phylogenetically. It is demonstrated that the Ukrainian isolate of Potato virus Y (CP gene has a higher percentage of homology with the recombinant isolates (strains of this pathogen (approx. 98.8– 99.8 % of homology for both nucleotide and translated amino acid sequences of the CP gene. The Ukrainian isolate of PVY is positioned in the separate cluster together with the isolates found in Syria, Japan and Iran; these isolates possibly have common origin. The Ukrainian PVY isolate is confirmed to be recombinant. Conclusions. This work underlines the need and provides the means for accurate monitoring of Potato virus Y in the agroecosystems of Ukraine. Most importantly, the phylogenetic analysis demonstrated the recombinant nature of this PVY isolate which has been attributed to the strain group O, subclade N:O.

  13. V(D)J recombination frequency is affected by the sequence interposed between a pair of recombination signals: sequence comparison reveals a putative recombinational enhancer element

    DEFF Research Database (Denmark)

    Roch, F A; Hobi, R; Berchtold, M W

    1997-01-01

    respectively, can markedly affect the frequency of V(D)J recombination. We report that the entire Emu, the Emu core as well as its flanking 5' and 3' matrix associated regions (5' and 3' MARs) upregulate V(D)J recombination while the downstream section of the 3' MAR of Emu does not. Also, prokaryotic sequences...

  14. Comparison of the complete genome sequences of Pseudomonassyringae pv. syringae B728a and pv. tomato DC3000.

    Energy Technology Data Exchange (ETDEWEB)

    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

  15. Complete plastid genome sequence of Primula sinensis (Primulaceae: structure comparison, sequence variation and evidence for accD transfer to nucleus

    Directory of Open Access Journals (Sweden)

    Tong-Jian Liu

    2016-06-01

    Full Text Available Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp were separated by a large single-copy region (82,064 bp and a small single-copy region (17,725 bp. The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. The accD and infA genes lacking intact open reading frames (ORF were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome of Primula sinensis, comparing with another available plastome of P. poissonii. The four most variable regions, rpl36–rps8, rps16–trnQ, trnH–psbA and ndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found from P. sinensis transcriptome showed a high similarity to plastid accD functional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastid accD has been functionally transferred to the nucleus in P. sinensis.

  16. Pattern recognition in complex activity travel patterns : comparison of Euclidean distance, signal-processing theoretical, and multidimensional sequence alignment methods

    NARCIS (Netherlands)

    Joh, C.H.; Arentze, T.A.; Timmermans, H.J.P.

    2001-01-01

    The application of a multidimensional sequence alignment method for classifying activity travel patterns is reported. The method was developed as an alternative to the existing classification methods suggested in the transportation literature. The relevance of the multidimensional sequence alignment

  17. Side-by-side comparison of an open-chamber (TM 300) and a closed-chamber (Vapometer™) transepidermal water loss meter.

    Science.gov (United States)

    Steiner, Markus; Aikman-Green, Sylvie; Prescott, Gordon J; Dick, Finlay D

    2011-08-01

    The measurement of transepidermal water loss (TEWL) is used to monitor changes in the stratum corneum's permeability to water vapor. This measurement is widely used in the cosmetics industry and in dermatology research. However, only limited work has been undertaken to assess the comparability of results from different TEWL meters over an extended range of measurements. This study compared the results of TEWL measurements between two commonly used open-chamber and closed-chamber TEWL devices. Five hundred and forty measurements were taken in 17 participants on the dorsum and palm of both hands on two different days and the order of the devices was randomized. The results showed that the open TEWL meter's capacity for measuring high values of TEWL was restricted, and that the closed-chamber TEWL meter was less sensitive to differences in the lower range of measurements. Both devices have their strengths for different applications, but their results cannot be directly compared. We were unable to find a statistical model that would allow us to transform the measurements made on one device for a comparison with the results generated by the other device. © 2011 John Wiley & Sons A/S.

  18. The cytoplasmic domain close to the transmembrane region of the glucagon-like peptide-1 receptor contains sequence elements that regulate agonist-dependent internalisation.

    Science.gov (United States)

    Vázquez, Patricia; Roncero, Isabel; Blázquez, Enrique; Alvarez, Elvira

    2005-07-01

    In order to gain better insight into the molecular events involved in the signal transduction generated through glucagon-like peptide-1 (GLP-1) receptors, we tested the effect of deletions and point mutations within the cytoplasmic tail of this receptor with a view to establishing relationships between signal transduction desensitisation and receptor internalisation. Wild-type and truncated (deletion of the last 27 amino acids (GLPR 435R) and deletion of 44 amino acids (GLPR 418R)) GLP-1 receptors bound the agonist with similar affinity. Deletion of the last 27 amino acids decreased the internalisation rate by 78%, while deletion of 44 amino acids containing all the phosphorylation sites hitherto described in this receptor decreased the internalisation rate by only 47%. Binding of the ligand to both receptors stimulated adenylyl cyclase. In contrast, deletion of the region containing amino acids 419 to 435 (GLPR 419delta435) increased the internalisation rate by 268%, and the replacement of EVQ(408-410) by alanine (GLPR A(408-410)) increased this process to 296%. In both receptors, the efficacy in stimulating adenylate cyclase was decreased. All the receptors studied were internalised by coated pits, except for the receptor with a deletion of the last 44 amino acids, which also had a faster resensitisation rate. Our findings indicate that the neighbouring trans-membrane domain of the carboxyl-terminal tail of the GLP-1 receptor contains sequence elements that regulate agonist-dependent internalisation and transmembrane signalling.

  19. Genetic divergence of Asiatic Bdellocephala (Turbellaria, Tricladida, Paludicola) as revealed by partial 18S rRNA gene sequence comparisons.

    Science.gov (United States)

    Kuznedelov, K D; Timoshkin, O A; Goldman, E

    1997-01-01

    Polymerase chain reaction (PCR) and direct sequencing of small ribosomal RNA genes were used for analysis of genetic differences among Asiatic species of freshwater triclad genus Bdellocephala. Representatives of four species and four subspecies of this genus were used to establish homology between nucleotides in the 5'-end portion of small ribosomal RNA gene sequences. Within 552 nucleotide sites of aligned sequences compared, six variable base positions were discovered, dividing Bdellocephala into five different genotypes. Sequence data allow to distinguish two groups of these genotypes. One of them unites species from Kamchatka and Japan, another one unites Baikalian taxa. Agreement between available morphological, cytological and sequence data is discussed.

  20. Intersampler field comparison of Respicon(R), IOM, and closed-face 25-mm personal aerosol samplers during primary production of aluminium.

    Science.gov (United States)

    Skaugset, Nils Petter; Ellingsen, Dag G; Notø, Hilde; Jordbekken, Lars; Thomassen, Yngvar

    2013-10-01

    Intersampler field comparison of Respicon(®), 25-mm closed-face 'total dust' cassette (CFC), and IOM inhalable aerosol sampler was conducted in pot rooms at seven aluminium smelters. The aerosol mass and water-soluble fluoride were selected as airborne contaminants for the comparisons. The aerosol masses of 889 sample pairs of IOM and Respicon(®) inhalable aerosol sub-fraction, 165 of IOM and 25-mm CFC, and 194 of CFC and Respicon(®) thoracic aerosol sub-fraction were compared. The number of sample pairs for the comparison of water-soluble fluoride was 906, 170, and 195, respectively. The geometric mean aerosol mass collected with the inhalable Respicon(®) was 2.91 mg m(-3) compared with 3.38 mg m(-3) with the IOM. The overall ratio between IOM and Respicon(®) inhalable sub-fraction was 1.16 [95% confidence interval (CI) = 1.11-1.21] for aerosol mass and 1.13 (95% CI = 1.08-1.18) for water-soluble fluoride. The results indicate that Respicon(®) undersampled the aerosol mass and water-soluble fluoride in the inhalable sub-fraction compared with the IOM. The results indicated undersampling of the Respicon(®) at mass concentrations higher than 1.35 mg m(-3) and oversampling at lower mass concentrations. The overall ratio between aerosol mass collected with IOM and CFC was 4.19 (95% CI = 3.79-4.64) and 1.61 (95% CI = 1.51-1.72) for water-soluble fluoride. Thus, for this industry, a correction factor of 4.2 is suggested for the conversion of CFC to inhalable aerosol masses and a conversion factor of 1.6 for water-soluble fluoride if wall deposits in the CFC are included. CFC and thoracic Respicon(®) collected similar aerosol masses (ratio = 1.04; 95% CI = 0.97-1.12), whereas the ratio was 1.19 (95% CI = 1.11-1.28) for water-soluble fluoride. The variability of the exposure is substantial; thus, large data sets are required in sampler performance field comparisons.

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

    Science.gov (United States)

    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. © 2015 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    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

  3. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa

    NARCIS (Netherlands)

    Choi, H.K.; Kim, D.; Uhm, T.; Limpens, E.H.M.; Lim, H.; Mun, J.H.; Kalo, P.; Penmetsa, R.V.; Seres, A.; Kulikova, O.; Roe, B.A.; Bisseling, T.; Kiss, G.B.; Cook, D.R.

    2004-01-01

    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene

  4. Comparison of different pulse sequences for in vivo determination of T1 relaxation times in the human brain

    DEFF Research Database (Denmark)

    Kjaer, L; Henriksen, O

    1988-01-01

    ). T1 measurements were performed on the human brain using a whole body MR scanner operating at 1.5 tesla. Three different pulse sequences were compared including two 6-points inversion recovery (IR) sequences with TR = 2.0 s and 4.0, respectively, and a 12-points partial saturation inversion recovery...

  5. Assessment of Cultivar Distinctness in Alfalfa: A Comparison of Genotyping-by-Sequencing, Simple-Sequence Repeat Marker, and Morphophysiological Observations

    Directory of Open Access Journals (Sweden)

    Paolo Annicchiarico

    2016-07-01

    Full Text Available Cultivar registration agencies typically require morphophysiological trait-based distinctness of candidate cultivars. This requirement is difficult to achieve for cultivars of major perennial forages because of their genetic structure and ever-increasing number of registered material, leading to possible rejection of agronomically valuable cultivars. This study aimed to explore the value of molecular markers applied to replicated bulked plants (three bulks of 100 independent plants each per cultivar to assess alfalfa ( L. subsp. cultivar distinctness. We compared genotyping-by-sequencing information based on 2902 polymorphic single-nucleotide polymorphism (SNP markers (>30 reads per DNA sample with morphophysiological information based on 11 traits and with simple-sequence repeat (SSR marker information from 41 polymorphic markers for their ability to distinguish 11 alfalfa landraces representative of the germplasm from northern Italy. Three molecular criteria, one based on cultivar differences for individual SSR bands and two based on overall SNP marker variation assessed either by statistically significant cultivar differences on principal component axes or discriminant analysis, distinctly outperformed the morphophysiological criterion. Combining the morphophysiological criterion with either molecular marker method increased discrimination among cultivars, since morphophysiological diversity was unrelated to SSR marker-based diversity ( = 0.04 and poorly related to SNP marker-based diversity ( = 0.23, < 0.15. The criterion based on statistically significant SNP allele frequency differences was less discriminating than morphophysiological variation. Marker-based distinctness, which can be assessed at low cost and without interactions with testing conditions, could validly substitute for (or complement morphophysiological distinctness in alfalfa cultivar registration schemes. It also has interest in sui generis registration systems aimed at

  6. Comparison of sequences of hypervariable region (HVR subunit S-1 gene of field isolate I-37 infectious bronchitis virus with Connecticut serotype

    Directory of Open Access Journals (Sweden)

    N.L.P Indi Dharmayanti

    2003-06-01

    Full Text Available Infectious Bronchitis is a contagious and acute respiratory disease in chickens caused by infectious bronchitis virus (IBV.Antigenic differences in IBV are associated with changes in the sequence of the spike glycoprotein (S. The subunit S1 which demonstrates more sequence variability than S-2 have been identified as hypervariable region (HVR-1 and 2. There were several IB virus field isolates included I-37 have been identified in Indonesia by serum neutralization method. However, gene sequence variation in HVR subunit S-1 had not yet been identified. Isolate I-37 was close to the serotype Connecticut 46 (Conn 46. The aim of this study is to identify sequence variation of HVR subunit S-1 gene of isolate I-37 produced by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR and sequencing. Several procedures were carried out in the study including virus titration, propagation and was concentrated from the allantoic fluid infected with IBV. Then, RNA was extracted for RTPCR. urther the product was sequnced and its homology with IBV references from GenBank was compared by GenMac version 8.0. Result showed that isolate I-37 produced 515 bp of amplification product. Isolate I-37 and Conn 46 are same serotype, yet their HVR subunit S-1 nucleotides and amino acids (protein differ by 6.9% and 15.6% respectively. It might be concluded that isolate I-37 was variant of Conn 46.

  7. A Comparison of Molecular Typing Methods Applied to Enterobacter cloacae complex: hsp60 Sequencing, Rep-PCR, and MLST

    Directory of Open Access Journals (Sweden)

    Roberto Viau

    2017-02-01

    Full Text Available Molecular typing using repetitive sequenced-based PCR (rep-PCR and hsp60 sequencing were applied to a collection of diverse Enterobacter cloacae complex isolates. To determine the most practical method for reference laboratories, we analyzed 71 E. cloacae complex isolates from sporadic and outbreak occurrences originating from 4 geographic areas. While rep-PCR was more discriminating, hsp60 sequencing provided a broader and a more objective geographical tracking method similar to multilocus sequence typing (MLST. In addition, we suggest that MLST may have higher discriminative power compared to hsp60 sequencing, although rep-PCR remains the most discriminative method for local outbreak investigations. In addition, rep-PCR can be an effective and inexpensive method for local outbreak investigation.

  8. Comparison of MRI sequences for evaluation of multiple sclerosis of the cervical spinal cord at 3 T

    International Nuclear Information System (INIS)

    Philpott, Cristina; Brotchie, Peter

    2011-01-01

    Purpose: Debate remains regarding the utility of the traditional STIR (short inversion time recovery) sequence in aiding MRI diagnosis of spinal cord lesions in patients with multiple sclerosis (MS) and this sequence is not included in the current imaging guidelines. A recent study proposed a T1 weighted STIR as a superior alternative to the traditional STIR and T2 fast spin echo (FSE). Thus, the aim of this study was to compare the sensitivity of T2, standard STIR and T1 weighted STIR sequences in the evaluation of MS plaques on our 3 T system. Methods and materials: A retrospective analysis of patients with multiple sclerosis who presented to our institution over a period of 5 months and who had cervical cord lesions was undertaken. Patients had been examined with our institutional protocol which included T2 FSE, STIR and the recommended T1 STIR. Quantitative analysis of the lesions versus background cord using sample T-tests was performed for each sequence, and comparative analysis of the lesion contrast:background cord ratios of the 3 sequences (using two-way ANOVA tests) was performed. Results: The T2 sequence was not as sensitive in detecting lesions versus the traditional STIR and T1 weighted STIR, with 10% of lesions not detected using statistical analysis (p < 0.05). The traditional STIR also demonstrated greater contrast ratios than the T2 sequence (p < 0.05) suggesting increased sensitivity. However, the T1 STIR demonstrated even greater contrast ratios than both the traditional STIR and T2 sequences (p < 0.05). Conclusion: This study confirms earlier findings of the traditional STIRs increased sensitivity versus the T2 sequence. However, the new “T1 weighted STIR” appears to be even more sensitive than both these sequences showing potential promise as an alternative method to monitor demyelinating plaques of MS.

  9. Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis

    Science.gov (United States)

    Diehn, Till A.; Pommerrenig, Benjamin; Bernhardt, Nadine; Hartmann, Anja; Bienert, Gerd P.

    2015-01-01

    Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of

  10. Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.

    Directory of Open Access Journals (Sweden)

    Johanna Rhodes

    Full Text Available The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina, along with two new kits: the TruSeq Nano DNA kit (Illumina and the NEBNext Ultra DNA kit (New England Biolabs to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality being considered when ultimately deciding on which library prep method to use.

  11. Illuminating choices for library prep: a comparison of library preparation methods for whole genome sequencing of Cryptococcus neoformans using Illumina HiSeq.

    Science.gov (United States)

    Rhodes, Johanna; Beale, Mathew A; Fisher, Matthew C

    2014-01-01

    The industry of next-generation sequencing is constantly evolving, with novel library preparation methods and new sequencing machines being released by the major sequencing technology companies annually. The Illumina TruSeq v2 library preparation method was the most widely used kit and the market leader; however, it has now been discontinued, and in 2013 was replaced by the TruSeq Nano and TruSeq PCR-free methods, leaving a gap in knowledge regarding which is the most appropriate library preparation method to use. Here, we used isolates from the pathogenic fungi Cryptococcus neoformans var. grubii and sequenced them using the existing TruSeq DNA v2 kit (Illumina), along with two new kits: the TruSeq Nano DNA kit (Illumina) and the NEBNext Ultra DNA kit (New England Biolabs) to provide a comparison. Compared to the original TruSeq DNA v2 kit, both newer kits gave equivalent or better sequencing data, with increased coverage. When comparing the two newer kits, we found little difference in cost and workflow, with the NEBNext Ultra both slightly cheaper and faster than the TruSeq Nano. However, the quality of data generated using the TruSeq Nano DNA kit was superior due to higher coverage at regions of low GC content, and more SNPs identified. Researchers should therefore evaluate their resources and the type of application (and hence data quality) being considered when ultimately deciding on which library prep method to use.

  12. MRI of the lumbar spine: comparison of 3D isotropic turbo spin-echo SPACE sequence versus conventional 2D sequences at 3.0 T.

    Science.gov (United States)

    Lee, Sungwon; Jee, Won-Hee; Jung, Joon-Yong; Lee, So-Yeon; Ryu, Kyeung-Sik; Ha, Kee-Yong

    2015-02-01

    Three-dimensional (3D) fast spin-echo sequence with variable flip-angle refocusing pulse allows retrospective alignments of magnetic resonance imaging (MRI) in any desired plane. To compare isotropic 3D T2-weighted (T2W) turbo spin-echo sequence (TSE-SPACE) with standard two-dimensional (2D) T2W TSE imaging for evaluating lumbar spine pathology at 3.0 T MRI. Forty-two patients who had spine surgery for disk herniation and had 3.0 T spine MRI were included in this study. In addition to standard 2D T2W TSE imaging, sagittal 3D T2W TSE-SPACE was obtained to produce multiplanar (MPR) images. Each set of MR images from 3D T2W TSE and 2D TSE-SPACE were independently scored for the degree of lumbar neural foraminal stenosis, central spinal stenosis, and nerve compression by two reviewers. These scores were compared with operative findings and the sensitivities were evaluated by McNemar test. Inter-observer agreements and the correlation with symptoms laterality were assessed with kappa statistics. The 3D T2W TSE and 2D TSE-SPACE had similar sensitivity in detecting foraminal stenosis (78.9% versus 78.9% in 32 foramen levels), spinal stenosis (100% versus 100% in 42 spinal levels), and nerve compression (92.9% versus 81.8% in 59 spinal nerves). The inter-observer agreements (κ = 0.849 vs. 0.451 for foraminal stenosis, κ = 0.809 vs. 0.503 for spinal stenosis, and κ = 0.681 vs. 0.429 for nerve compression) and symptoms correlation (κ = 0.449 vs. κ = 0.242) were better in 3D TSE-SPACE compared to 2D TSE. 3D TSE-SPACE with oblique coronal MPR images demonstrated better inter-observer agreements compared to 3D TSE-SPACE without oblique coronal MPR images (κ = 0.930 vs. κ = 0.681). Isotropic 3D T2W TSE-SPACE at 3.0 T was comparable to 2D T2W TSE for detecting foraminal stenosis, central spinal stenosis, and nerve compression with better inter-observer agreements and symptom correlation. © The Foundation Acta Radiologica 2014 Reprints and

  13. Comparison of PCR-RFLP pattern with sequencing analysis of the ITS region of Hyrcanain\\'s Tilia

    Directory of Open Access Journals (Sweden)

    Hamed Yousefzadeh

    2014-01-01

    T. hyrcana and T. rubra from Hyrcanian's origin, but it could not separate T. begonifloia from the other hyrcanian species. In this respect, derived results were similar to sequencing one. In conclusion, with regard to less expensive and less time consuming PCR-RFLP technique and high similarity between its result with sequencing, we recommend this method as a simple and economical method with relatively high efficiency studding plant phylogeny.

  14. Detection of hepatic VX2 carcinomas with ferucarbotran-enhanced magnetic resonance imaging in rabbits: Comparison of nine pulse sequences

    International Nuclear Information System (INIS)

    Kim, Seong Hyun; Choi, Dongil; Lim, Hyo K.; Kim, Min Ju; Jang, Kyung Mi; Kim, Seung Hoon; Lee, Won Jae; Lee, Jongmee; Jeon, Yong Hwan; Lim, Jae Hoon

    2006-01-01

    Objective: To compare the diagnostic performance of a variety of magnetic resonance imaging (MRI) sequences, in order to identify the most effective ferucarbotran-enhanced sequence for the detection of multiple small hepatic VX2 carcinomas in rabbits. Methods: Fifteen rabbits with experimentally induced 135 VX2 carcinomas in the liver underwent ferucarbotran-enhanced MRI using the following nine pulse sequences: a fat-suppressed fast spin-echo (FSE) sequence with two echo times (TE) (proton density- and T2-weighted images), four different T2*-weighted fast multiplanar GRASS (gradient-recalled acquisition in the steady state) (FMPGR) with the combination of three TEs (9, 12, 15 ms, respectively) and two flip angles (20 deg., 80 deg., respectively), T2*-weighted fast multiplanar spoiled GRASS (FMPSPGR), T1-weighted FMPSPGR, and dynamic T1-weighted FMPSPGR. All images were reviewed by three radiologists with quantitative and qualitative analysis. Results: Tumor-to-liver contrast-to-noise ratio of the proton density-weighted FSE sequence was significantly higher than those of the others (p o ) images were superior to those of the others and for the detection of very small hepatic tumors of less than 5 mm, the sensitivities of these sequences were less than 30%. Conclusion: Ferucarbotran-enhanced T2- and proton density-weighted FSE and T2*-weighed FMPGR (TE/flip angle, 12/20 o ) images were found to be the most effective pulse sequences for the detection of multiple small hepatic VX2 carcinomas but these sequences were limited in the detection of very small hepatic tumors of less than 5 mm in size

  15. Radiation-induced germ-line mutations detected by a direct comparison of parents and children DNA sequences containing SNPs

    International Nuclear Information System (INIS)

    Morimyo, M.; Hongo, E.; Higashi, T.; Wu, J.; Matsumoto, I.; Okamoto, M.; Kawano, A.; Tsuji, S.

    2003-01-01

    Full text: Germ-line mutation is detected in mice but not in humans. To estimate genetic risk of humans, a new approach to extrapolate from animal data to humans or to directly detect radiation-induced mutations in man is expected. We have developed a new method to detect germ-line mutations by directly comparing DNA sequences of parents and children. The nucleotide sequences among mouse strains are almost identical except SNP markers that are detected at 1/1000 frequency. When gamma-irradiated male mice are mated with female mice, heterogeneous nucleotide sequences induced in children DNA are a candidate of mutation, whose assignment can be done by SNP analysis. This system can easily detect all types of mutations such as transition, transversion, frameshift and deletion induced by radiation and can be applied to humans having genetically heterogeneous nucleotide sequences and many SNP markers. C3H male mice of 8 weeks of gestation were irradiated with gamma rays of 3 and 1 Gy and after 3 weeks, they were mated with the same aged C57BL female mice. After 3 weeks breeding, DNA was extracted from parents and children mice. The nucleotide sequences of 150 STS markers containing 300-900 bp and SNPs of parents and children DNA were determined by a direct sequencing; amplification of STS markers by Taq DNA polymerase, purification of PCR products, and DNA sequencing with a dye-terminator method. At each radiation dose, a total amount of 5 Mb DNA sequences were examined to detect radiation-induced mutations. We could find 6 deletions in 3 Gy irradiated mice but not in 1 Gy and control mice. The mutation frequency was about 4.0 x 10 -7 /bp/ Gy or 1.6 x 10 -4 /locus/Gy, and suggested the non-linear increase of mutation rate with dose

  16. Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers.

    Directory of Open Access Journals (Sweden)

    Xinzhong Li

    Full Text Available Molecular genetic testing is recommended for diagnosis of inherited cardiac disease, to guide prognosis and treatment, but access is often limited by cost and availability. Recently introduced high-throughput bench-top DNA sequencing platforms have the potential to overcome these limitations.We evaluated two next-generation sequencing (NGS platforms for molecular diagnostics. The protein-coding regions of six genes associated with inherited arrhythmia syndromes were amplified from 15 human samples using parallelised multiplex PCR (Access Array, Fluidigm, and sequenced on the MiSeq (Illumina and Ion Torrent PGM (Life Technologies. Overall, 97.9% of the target was sequenced adequately for variant calling on the MiSeq, and 96.8% on the Ion Torrent PGM. Regions missed tended to be of high GC-content, and most were problematic for both platforms. Variant calling was assessed using 107 variants detected using Sanger sequencing: within adequately sequenced regions, variant calling on both platforms was highly accurate (Sensitivity: MiSeq 100%, PGM 99.1%. Positive predictive value: MiSeq 95.9%, PGM 95.5%. At the time of the study the Ion Torrent PGM had a lower capital cost and individual runs were cheaper and faster. The MiSeq had a higher capacity (requiring fewer runs, with reduced hands-on time and simpler laboratory workflows. Both provide significant cost and time savings over conventional methods, even allowing for adjunct Sanger sequencing to validate findings and sequence exons missed by NGS.MiSeq and Ion Torrent PGM both provide accurate variant detection as part of a PCR-based molecular diagnostic workflow, and provide alternative platforms for molecular diagnosis of inherited cardiac conditions. Though there were performance differences at this throughput, platforms differed primarily in terms of cost, scalability, protocol stability and ease of use. Compared with current molecular genetic diagnostic tests for inherited cardiac arrhythmias

  17. [The use of the T2-weighted turbo-spin-echo sequence in studying the neurocranium. A comparison with the conventional T2-weighted spin-echo sequence].

    Science.gov (United States)

    Siewert, C; Hosten, N; Felix, R

    1994-07-01

    T2-weighted spin-echo imaging is the standard screening procedure in MR imaging of the neurocranium. We evaluated fast spin-echo T2-weighted imaging (TT2) of the neurocranium in comparison to conventional spin-echo T2-weighted imaging (T2). Signal-to-noise and contrast-to-noise ratio of normal brain tissues (basal ganglia, grey and white matter, CSF fluid) and different pathologies were calculated. Signal-to-noise ratio and contrast-to-noise ratio were significantly higher in TT2 than in T2 (with the exception of gray-to-white matter contrast). Tissues with increased content of water protons (mobile protons) showed the highest contrast to surrounding tissues. The increased signal intensity of fat must be given due attention in fatty lesions. Because the contrast-to-noise ratio between white matter and basal ganglia is less in TT2, Parkinson patients have to be examined by conventional T2. If these limitations are taken into account, fast spin-echo T2-weighted imaging is well appropriate for MR imaging of the neurocranium, resulting in heavy T2-weighting achieved in a short acquisition time.

  18. Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging

    Energy Technology Data Exchange (ETDEWEB)

    Nolte-Ernsting, C.C.A.; Tacke, J.; Adam, G.B.; Haage, P.; Guenther, R.W. [Univ. of Technology, Aachen (Germany). Dept. of Diagnostic Radiology; Jung, P.; Jakse, G. [Univ. of Technology, Aachen (Germany). Dept. of Urology

    2001-01-01

    The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. (orig.)

  19. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  20. A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

    Directory of Open Access Journals (Sweden)

    Bárbara Angulo

    Full Text Available The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry, with direct sequencing and to investigate the limit of detection (LOD of both PCR-based methods. We identified EGFR mutations in 21 (16% of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%, which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%. Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+ yielded similar results. Immunohistochemistry (IHC staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

  1. MR imaging of articular cartilage in the ankle: comparison of available imaging sequences and methods of measurement in cadavers

    Energy Technology Data Exchange (ETDEWEB)

    Tan, T.C.F. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)]|[Department of Radiology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan (Taiwan, Province of China); Wilcox, D.M. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Frank, L. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Shih, C. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)]|[Department of Radiology, Veterans General Hospital-Taipei (Taiwan, Province of China); Trudell, D.J. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Sartoris, D.J. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States); Resnick, D. [Department of Radiology, Veterans Administrative Medical Center, San Diego, CA (United States)]|[University of California Medical Center, San Diego, CA (United States)

    1996-11-01

    Objective. To assess hyaline cartilage of cadaveric ankles using different magnetic resonance (MR) imaging techniques and various methods of measurement. Design and patients. Cartilage thicknesses of the talus and tibia were measured in ten cadaveric ankles by naked eye and by digitized image analysis from MR images of fat-suppressed T1-weighted gradient recalled (FS-SPGR), sequences and pulsed transfer saturation sequences with (FS-STS) and without fat-suppression (STS); these measurements were compared with those derived from direct inspection of cadaveric sections. The accuracy and precision errors were evaluated statistically for each imaging technique as well as measuring method. Contrast-to-noise ratios of cartilage versus joint fluid and marrow were compared for each of the imaging sequences. Results. Statistically, measurements from FS-SPGR images were associated with the smallest estimation error. Precision error of measurements derived from digitized image analysis was found to be smaller than that derived from naked eye measurements. Cartilage thickness measurements in images from STS and FS-STS sequences revealed larger errors in both accuracy and precision. Interobserver variance was larger in naked eye assessment of the cartilage. Contrast-to-noise ratio of cartilage versus joint fluid and marrow was higher with FS-SPGR than with FS-STS or STS sequences. Conclusion. Of the sequences and measurement techniques studied, the FS-SPGR sequence combined with the use of digitized image analysis provides the most accurate method for the assessment of ankle hyaline cartilage. (orig.). With 3 figs., 2 tabs.

  2. Sequence of structures in fine-grained turbidites: Comparison of recent deep-sea and ancient flysch sediments

    Science.gov (United States)

    Stow, Dorrik A. V.; Shanmugam, Ganapathy

    1980-01-01

    A comparative study of the sequence of sedimentary structures in ancient and modern fine-grained turbidites is made in three contrasting areas. They are (1) Holocene and Pleistocene deep-sea muds of the Nova Scotian Slope and Rise, (2) Middle Ordovician Sevier Shale of the Valley and Ridge Province of the Southern Appalachians, and (3) Cambro-Ordovician Halifax Slate of the Meguma Group in Nova Scotia. A standard sequence of structures is proposed for fine-grained turbidites. The complete sequence has nine sub-divisions that are here termed T 0 to T 8. "The lower subdivision (T 0) comprises a silt lamina which has a sharp, scoured and load-cast base, internal parallel-lamination and cross-lamination, and a sharp current-lineated or wavy surface with 'fading-ripples' (= Type C etc. …)." (= Type C ripple-drift cross-lamination, Jopling and Walker, 1968). The overlying sequence shows textural and compositional grading through alternating silt and mud laminae. A convolute-laminated sub-division (T 1) is overlain by low-amplitude climbing ripples (T 2), thin regular laminae (T 3), thin indistinct laminae (T 4), and thin wipsy or convolute laminae (T 5). The topmost three divisions, graded mud (T 6), ungraded mud (T 7) and bioturbated mud (T 8), do not have silt laminae but rare patchy silt lenses and silt pseudonodules and a thin zone of micro-burrowing near the upper surface. The proposed sequence is analogous to the Bouma (1962) structural scheme for sandy turbidites and is approximately equivalent to Bouma's (C)DE divisions. The repetition of partial sequences characterizes different parts of the slope/base-of-slope/basin plain environment, and represents deposition from different stages of evolution of a large, muddy, turbidity flow. Microstructural detail and sequence are well preserved in ancient and even slightly metamorphosed sediments. Their recognition is important for determining depositional processes and for palaeoenvironmental interpretation.

  3. MR imaging of articular cartilage in the ankle: comparison of available imaging sequences and methods of measurement in cadavers

    International Nuclear Information System (INIS)

    Tan, T.C.F.; Wilcox, D.M.; Frank, L.; Shih, C.; Trudell, D.J.; Sartoris, D.J.; Resnick, D.

    1996-01-01

    Objective. To assess hyaline cartilage of cadaveric ankles using different magnetic resonance (MR) imaging techniques and various methods of measurement. Design and patients. Cartilage thicknesses of the talus and tibia were measured in ten cadaveric ankles by naked eye and by digitized image analysis from MR images of fat-suppressed T1-weighted gradient recalled (FS-SPGR), sequences and pulsed transfer saturation sequences with (FS-STS) and without fat-suppression (STS); these measurements were compared with those derived from direct inspection of cadaveric sections. The accuracy and precision errors were evaluated statistically for each imaging technique as well as measuring method. Contrast-to-noise ratios of cartilage versus joint fluid and marrow were compared for each of the imaging sequences. Results. Statistically, measurements from FS-SPGR images were associated with the smallest estimation error. Precision error of measurements derived from digitized image analysis was found to be smaller than that derived from naked eye measurements. Cartilage thickness measurements in images from STS and FS-STS sequences revealed larger errors in both accuracy and precision. Interobserver variance was larger in naked eye assessment of the cartilage. Contrast-to-noise ratio of cartilage versus joint fluid and marrow was higher with FS-SPGR than with FS-STS or STS sequences. Conclusion. Of the sequences and measurement techniques studied, the FS-SPGR sequence combined with the use of digitized image analysis provides the most accurate method for the assessment of ankle hyaline cartilage. (orig.). With 3 figs., 2 tabs

  4. Multishot versus single-shot pulse sequences in very high field fMRI: a comparison using retinotopic mapping.

    Directory of Open Access Journals (Sweden)

    Jascha D Swisher

    Full Text Available High-resolution functional MRI is a leading application for very high field (7 Tesla human MR imaging. Though higher field strengths promise improvements in signal-to-noise ratios (SNR and BOLD contrast relative to fMRI at 3 Tesla, these benefits may be partially offset by accompanying increases in geometric distortion and other off-resonance effects. Such effects may be especially pronounced with the single-shot EPI pulse sequences typically used for fMRI at standard field strengths. As an alternative, one might consider multishot pulse sequences, which may lead to somewhat lower temporal SNR than standard EPI, but which are also often substantially less susceptible to off-resonance effects. Here we consider retinotopic mapping of human visual cortex as a practical test case by which to compare examples of these sequence types for high-resolution fMRI at 7 Tesla. We performed polar angle retinotopic mapping at each of 3 isotropic resolutions (2.0, 1.7, and 1.1 mm using both accelerated single-shot 2D EPI and accelerated multishot 3D gradient-echo pulse sequences. We found that single-shot EPI indeed led to greater temporal SNR and contrast-to-noise ratios (CNR than the multishot sequences. However, additional distortion correction in postprocessing was required in order to fully realize these advantages, particularly at higher resolutions. The retinotopic maps produced by both sequence types were qualitatively comparable, and showed equivalent test/retest reliability. Thus, when surface-based analyses are planned, or in other circumstances where geometric distortion is of particular concern, multishot pulse sequences could provide a viable alternative to single-shot EPI.

  5. SU-F-T-189: Dosimetric Comparison of Spot-Scanning Proton Therapy Techniques for Liver Tumors Close to the Skin Surface

    International Nuclear Information System (INIS)

    Takao, S; Matsuzaki, Y; Matsuura, T; Umegaki, K; Fujii, Y; Fujii, T; Katoh, N; Shimizu, S; Shirato, H

    2016-01-01

    Purpose: Spot-scanning technique has been utilized to achieve conformal dose distribution to large and complicated tumors. This technique generally does not require patient-specific devices such as aperture and compensator. The commercially available spot-scanning proton therapy (SSPT) systems, however, cannot deliver proton beams to the region shallower than 4 g/cm2. Therefore some range compensation device is required to treat superficial tumors with SSPT. This study shows dosimetric comparison of the following treatment techniques: (i) with a tabletop bolus, (ii) with a nozzle-mounted applicator, and (iii) without any devices and using intensity-modulated proton therapy (IMPT) technique. Methods: The applicator composed of a combination of a mini-ridge filter and a range shifter has been manufactured by Hitachi, Ltd., and the tabletop bolus was made by .decimal, Inc. Both devices have been clinically implemented in our facility. Three patients with liver tumors close to the skin surface were examined in this study. Each treatment plan was optimized so that the prescription dose of 76 Gy(RBE) or 66 Gy(RBE) would be delivered to 99% of the clinical target volume in 20 fractions. Three beams were used for tabletop bolus plan and IMPT plan, whereas two beams were used in the applicator plan because the gantry angle available was limited due to potential collision to patient and couch. The normal liver, colon, and skin were considered as organs at risk (OARs). Results: The target heterogeneity index (HI = D_5/D_9_5) was 1.03 on average in each planning technique. The mean dose to the normal liver was considerably less than 20 Gy(RBE) in all cases. The dose to the skin could be reduced by 20 Gy(RBE) on average in the IMPT plan compared to the applicator plan. Conclusion: It has been confirmed that all treatment techniques met the dosimetric criteria for the OARs and could be implemented clinically.

  6. SU-F-T-189: Dosimetric Comparison of Spot-Scanning Proton Therapy Techniques for Liver Tumors Close to the Skin Surface

    Energy Technology Data Exchange (ETDEWEB)

    Takao, S; Matsuzaki, Y [Proton Beam Therapy Center, Hokkaido University Hospital, Sapporo, Hokkaido (Japan); Matsuura, T; Umegaki, K [Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido (Japan); Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido (Japan); Fujii, Y; Fujii, T [Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido (Japan); Katoh, N [Department of Radiation Oncology, Hokkaido University Hospital, Sapporo, Hokkaido (Japan); Shimizu, S; Shirato, H [Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Hokkaido (Japan); Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido (Japan)

    2016-06-15

    Purpose: Spot-scanning technique has been utilized to achieve conformal dose distribution to large and complicated tumors. This technique generally does not require patient-specific devices such as aperture and compensator. The commercially available spot-scanning proton therapy (SSPT) systems, however, cannot deliver proton beams to the region shallower than 4 g/cm2. Therefore some range compensation device is required to treat superficial tumors with SSPT. This study shows dosimetric comparison of the following treatment techniques: (i) with a tabletop bolus, (ii) with a nozzle-mounted applicator, and (iii) without any devices and using intensity-modulated proton therapy (IMPT) technique. Methods: The applicator composed of a combination of a mini-ridge filter and a range shifter has been manufactured by Hitachi, Ltd., and the tabletop bolus was made by .decimal, Inc. Both devices have been clinically implemented in our facility. Three patients with liver tumors close to the skin surface were examined in this study. Each treatment plan was optimized so that the prescription dose of 76 Gy(RBE) or 66 Gy(RBE) would be delivered to 99% of the clinical target volume in 20 fractions. Three beams were used for tabletop bolus plan and IMPT plan, whereas two beams were used in the applicator plan because the gantry angle available was limited due to potential collision to patient and couch. The normal liver, colon, and skin were considered as organs at risk (OARs). Results: The target heterogeneity index (HI = D{sub 5}/D{sub 95}) was 1.03 on average in each planning technique. The mean dose to the normal liver was considerably less than 20 Gy(RBE) in all cases. The dose to the skin could be reduced by 20 Gy(RBE) on average in the IMPT plan compared to the applicator plan. Conclusion: It has been confirmed that all treatment techniques met the dosimetric criteria for the OARs and could be implemented clinically.

  7. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Energy Technology Data Exchange (ETDEWEB)

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    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 shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  8. Comparisons between Arabidopsis thaliana and Drosophila melanogaster in relation to Coding and Noncoding Sequence Length and Gene Expression

    Directory of Open Access Journals (Sweden)

    Rachel Caldwell

    2015-01-01

    Full Text Available There is a continuing interest in the analysis of gene architecture and gene expression to determine the relationship that may exist. Advances in high-quality sequencing technologies and large-scale resource datasets have increased the understanding of relationships and cross-referencing of expression data to the large genome data. Although a negative correlation between expression level and gene (especially transcript length has been generally accepted, there have been some conflicting results arising from the literature concerning the impacts of different regions of genes, and the underlying reason is not well understood. The research aims to apply quantile regression techniques for statistical analysis of coding and noncoding sequence length and gene expression data in the plant, Arabidopsis thaliana, and fruit fly, Drosophila melanogaster, to determine if a relationship exists and if there is any variation or similarities between these species. The quantile regression analysis found that the coding sequence length and gene expression correlations varied, and similarities emerged for the noncoding sequence length (5′ and 3′ UTRs between animal and plant species. In conclusion, the information described in this study provides the basis for further exploration into gene regulation with regard to coding and noncoding sequence length.

  9. Phylogeny and Taxonomy of Archaea: A Comparison of the Whole-Genome-Based CVTree Approach with 16S rRNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Guanghong Zuo

    2015-03-01

    Full Text Available A tripartite comparison of Archaea phylogeny and taxonomy at and above the rank order is reported: (1 the whole-genome-based and alignment-free CVTree using 179 genomes; (2 the 16S rRNA analysis exemplified by the All-Species Living Tree with 366 archaeal sequences; and (3 the Second Edition of Bergey’s Manual of Systematic Bacteriology complemented by some current literature. A high degree of agreement is reached at these ranks. From the newly proposed archaeal phyla, Korarchaeota, Thaumarchaeota, Nanoarchaeota and Aigarchaeota, to the recent suggestion to divide the class Halobacteria into three orders, all gain substantial support from CVTree. In addition, the CVTree helped to determine the taxonomic position of some newly sequenced genomes without proper lineage information. A few discrepancies between the CVTree and the 16S rRNA approaches call for further investigation.

  10. Comparison of zero-sequence injection methods in cascaded H-bridge multilevel converters for large-scale photovoltaic integration

    DEFF Research Database (Denmark)

    Yu, Yifan; Konstantinou, Georgios; Townsend, Christopher David

    2017-01-01

    to maintain three-phase balanced grid currents with unbalanced power generation. This study theoretically compares power balance capabilities of various zero-sequence injection methods based on two metrics which can be easily generalised for all CHB applications to PV systems. Experimental results based......Photovoltaic (PV) power generation levels in the three phases of a multilevel cascaded H-bridge (CHB) converter can be significantly unbalanced, owing to different irradiance levels and ambient temperatures over a large-scale solar PV power plant. Injection of a zero-sequence voltage is required...... on a 430 V, 10 kW, three-phase, seven-level cascaded H-bridge converter prototype confirm superior performance of the optimal zero-sequence injection technique....

  11. SPIO-enhanced MR imaging for HCC detection in cirrhotic patient : comparison of various techniques for optimal sequence selection

    International Nuclear Information System (INIS)

    Kim, In Hwan; Lee, Jeong Min; Kwak, Hyo Sung; Kim, Chong Soo; Yu, Hee Chul; Kim, Tae Kon; Lee Soo Tiek

    2000-01-01

    To compare the efficacy of breathhold and non-breathhold sequences in the detection of hepatocellular carcinoma (HCC) in cirrhotic patients using superparamagnetic iron oxide (SPIO)-enhanced MR imaging, and to determine the optimal sequence combination. By means of unenhanced and iron-oxide-enhanced MRI, 29 patients with 49 nodular HCCs were evaluated for the presence of HCC nodules. Twenty-one were male and eight were female, and their ages ranged from 38 to 71 (mean, 56) years. Eight different MR sequences were used, including four non-breath-hold sequences and four breath-hold, and images were obtained before and after the administration of SPIO particles. Non-breath-hold sequences included T2-, proton density-weighted SE, and TSE imaging, while breath-hold sequences comprised T1-weighted fast low-angle shot (T1w FLASH), half-Fourier acquisition single shot turbo spine echo (HASTE), T2-weighted fast imaging with steady-state free precession (T2 * wFISP) and T2-weighted breath-hold TSE (T2wBHTSE). Image analysis involved both quantitative and qualitative analysis. The quantitative parameters calculated were signal-to noise (S/N) ratios for livers and tumors, contrast to noise (C/N) ratios for tumors seen on precontrast and postcontrast images, and percentage of signal intensity loss (PSIL) after SPIO injection. Images were analysed qualitatively in terms of image artifacts and lesion conspicuity, and prior to calculating sensitivity, the number of lesions detected using various pulse sequences were counted. SPIO had a marked effect on liver S/N ratio but a minimal effect on tumor S/N ratio. PSIL was best in T2 * wFISP images, while T2wSE images showed the second-best results (p less than 0.05). Tumor-to-liver C/N values were also highest with T2 * wFISP, while T2wTSE and HASTE images were next. Qualitative study showed that non-breath hold images and FISP were better than breath hold images in terms of lesion conspicuity. The latter, however, were much better

  12. Proton T2 relaxation effect of superparamagnetic iron oxide. Comparison between fast spin echo and conventional spin echo sequence

    International Nuclear Information System (INIS)

    Tanimoto, Akihiro; Satoh, Yoshinori; Higuchi, Nobuya; Izutsu, Mutsumu; Yuasa, Yuji; Hiramatsu, Kyoichi

    1995-01-01

    Superparamagnetic iron oxide (SPIO) particles have been known to show a great T 2 relaxation effect in the liver, which contributes to significant liver signal decrease and detection of hepatic neoplasms. Recently, fast spin echo (FSE) sequence with less scanning time than conventional spin echo (SE) sequence has been rapidly introduced in clinical MR imaging. To investigate whether SPIO would show decreased T 2 relaxation effect on FSE, we obtained T 2 relaxivity (R2) of SPIO in vitro and liver signal decrease caused by SPIO in vivo. SPIO showed 20% less R2 on Carr-Purcell-Meiboom-Gill (CPMG) sequence than on SE. Relative liver signal-to-noise ratio (SNR) decrease caused by SPIO was significantly smaller (p 2 relaxation effect on FSE than on SE. However, further studies will be required to assess the diagnostic capability of SPIO on FSE, in the detection of hepatic neoplasms. (author)

  13. Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes)

    Science.gov (United States)

    2011-01-01

    Background Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain are defensive and exhibit aggression to humans. To understand the genetic differences underlying these behavioral phenotypes fox-specific genomic resources are needed. Results cDNA from mRNA from pre-frontal cortex of a tame and an aggressive fox was sequenced using the Roche 454 FLX Titanium platform (> 2.5 million reads & 0.9 Gbase of tame fox sequence; >3.3 million reads & 1.2 Gbase of aggressive fox sequence). Over 80% of the fox reads were assembled into contigs. Mapping fox reads against the fox transcriptome assembly and the dog genome identified over 30,000 high confidence fox-specific SNPs. Fox transcripts for approximately 14,000 genes were identified using SwissProt and the dog RefSeq databases. An at least 2-fold expression difference between the two samples (p fox transcriptome. Conclusions Transcriptome sequencing significantly expanded genomic resources available for the fox, a species without a sequenced genome. In a very cost efficient manner this yielded a large number of fox-specific SNP markers for genetic studies and provided significant insights into the gene expression profile of the fox pre-frontal cortex; expression differences between the two fox samples; and a catalogue of potentially important gene-specific sequence variants. This result demonstrates the utility of this approach for developing genomic resources in species with limited genomic information. PMID:21967120

  14. Sequence comparison of prefrontal cortical brain transcriptome from a tame and an aggressive silver fox (Vulpes vulpes

    Directory of Open Access Journals (Sweden)

    Sun Qi

    2011-10-01

    Full Text Available Abstract Background Two strains of the silver fox (Vulpes vulpes, with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain are defensive and exhibit aggression to humans. To understand the genetic differences underlying these behavioral phenotypes fox-specific genomic resources are needed. Results cDNA from mRNA from pre-frontal cortex of a tame and an aggressive fox was sequenced using the Roche 454 FLX Titanium platform (> 2.5 million reads & 0.9 Gbase of tame fox sequence; >3.3 million reads & 1.2 Gbase of aggressive fox sequence. Over 80% of the fox reads were assembled into contigs. Mapping fox reads against the fox transcriptome assembly and the dog genome identified over 30,000 high confidence fox-specific SNPs. Fox transcripts for approximately 14,000 genes were identified using SwissProt and the dog RefSeq databases. An at least 2-fold expression difference between the two samples (p Conclusions Transcriptome sequencing significantly expanded genomic resources available for the fox, a species without a sequenced genome. In a very cost efficient manner this yielded a large number of fox-specific SNP markers for genetic studies and provided significant insights into the gene expression profile of the fox pre-frontal cortex; expression differences between the two fox samples; and a catalogue of potentially important gene-specific sequence variants. This result demonstrates the utility of this approach for developing genomic resources in species with limited genomic information.

  15. Recognition of hypoxyloid and xylarioid Entonaema species and allied Xylaria species from a comparison of holomorphic morphology, HPLC profiles, andribosomal DNA sequences

    DEFF Research Database (Denmark)

    Stadler, M.; Fournier, J.; Læssøe, Thomas

    2008-01-01

    pallidum is thus regarded as a later synonym of E. mesentericum. Therefore, the latter name is transferred to Xylaria. A key to entonaemoid Xylariaceae is provided. Colour reactions (NH3, KOH) of the ectostroma were applied to a limited number of Xylaria spp., but metabolite profiles of cultures appear......The genus Entonaema comprises Xylariaceae with hollow, gelatinous stromata that accumulate liquid. Some of its species, including the type species, appear related to Daldinia from a polyphasic approach, comprising morphological studies, comparisons of ribosomal DNA sequences, and high performance...

  16. A comparison of step-and-shoot leaf sequencing algorithms that eliminate tongue-and-groove effects

    International Nuclear Information System (INIS)

    Kamath, Srijit; Sahni, Sartaj; Ranka, Sanjay; Li, Jonathan; Palta, Jatinder

    2004-01-01

    The performances of three recently published leaf sequencing algorithms for step-and-shoot intensity-modulated radiation therapy delivery that eliminates tongue-and-groove underdosage are evaluated. Proofs are given to show that the algorithm of Que et al (2004 Phys. Med. Biol. 49 399-405) generates leaf sequences free of tongue-and-groove underdosage and interdigitation. However, the total beam-on times could be up to n times those of the sequences generated by the algorithms of Kamath et al (2004 Phys. Med. Biol. 49 N7-N19), which are optimal in beam-on time for unidirectional leaf movement under the same constraints, where n is the total number of involved leaf pairs. Using 19 clinical fluence matrices and 100 000 randomly generated 15 x 15 matrices, the average monitor units and number of segments of the leaf sequences generated using the algorithm of Que et al are about two to four times those generated by the algorithm of Kamath et al

  17. Complete mitochondrial genome sequence of black mustard (Brassica nigra; BB) and comparison with Brassica oleracea (CC) and Brassica carinata (BBCC).

    Science.gov (United States)

    Yamagishi, Hiroshi; Tanaka, Yoshiyuki; Terachi, Toru

    2014-11-01

    Crop species of Brassica (Brassicaceae) consist of three monogenomic species and three amphidiploid species resulting from interspecific hybridizations among them. Until now, mitochondrial genome sequences were available for only five of these species. We sequenced the mitochondrial genome of the sixth species, Brassica nigra (nuclear genome constitution BB), and compared it with those of Brassica oleracea (CC) and Brassica carinata (BBCC). The genome was assembled into a 232 145 bp circular sequence that is slightly larger than that of B. oleracea (219 952 bp). The genome of B. nigra contained 33 protein-coding genes, 3 rRNA genes, and 17 tRNA genes. The cox2-2 gene present in B. oleracea was absent in B. nigra. Although the nucleotide sequences of 52 genes were identical between B. nigra and B. carinata, the second exon of rps3 showed differences including an insertion/deletion (indel) and nucleotide substitutions. A PCR test to detect the indel revealed intraspecific variation in rps3, and in one line of B. nigra it amplified a DNA fragment of the size expected for B. carinata. In addition, the B. carinata lines tested here produced DNA fragments of the size expected for B. nigra. The results indicate that at least two mitotypes of B. nigra were present in the maternal parents of B. carinata.

  18. De-standardization of family-life trajectories of young adults: a cross-national comparison using sequence analysis

    NARCIS (Netherlands)

    Elzinga, C.; Liefbroer, A.C.

    2007-01-01

    We introduce a number of new methods based on sequence analysis to test hypotheses on the de-standardization of family-life trajectories in early adulthood, using Fertility and Family Survey data on 19 countries. Across cohorts, family-life trajectories of young adults have not become more

  19. Electron microscopic comparison of the sequences of single-stranded genomes of mammalian parvoviruses by heteroduplex mapping

    Energy Technology Data Exchange (ETDEWEB)

    Banerjee, P.T.; Olson, W.H.; Allison, D.P.; Bates, R.C.; Snyder, C.E.; Mitra, S.

    1983-01-01

    The sequence homologies among the linear single-stranded genomes of several mammalian parvoviruses have been studied by electron microscopic analysis of tthe heteroduplexes produced by reannealing the complementary strands of their DNAs. The genomes of Kilham rat virus, H-1, minute virus of ice and LuIII, which are antigenically distinct non-defective parvoviruses, have considerable homology: about 70% of their sequences are conserved. The homologous regions map at similar locations in the left halves (from the 3' ends) of the genomes. No sequence homology, however, is observed between the DNAs of these nondefective parvoviruses and that of bovine parvovirus, another non-defective virus, or that of defective adenoassociated virus, nor between the genomes of bovine parvovirus and adenoassociated virus. This suggests that only very short, if any, homologous regions are present. From these results, an evolutionary relationship among Kilham rat virus, H-1, minute virus of mice and LuIII is predicted. It is interesting to note that, although LuIII was originally isolated from a human cell line and is specific for human cells in vitro, its genome has sequences in common only with the rodent viruses Kilham rat virus, minute virus of mice and H-1, and not with the other two mammalian parvoviruses tested.

  20. De-standardization of family-life trajectories of young adults: A cross-national comparison using sequence analyses

    NARCIS (Netherlands)

    Elzinga, C.H.; Liefbroer, A.C.

    2007-01-01

    We introduce a number of new methods based on sequence analysis to test hypotheses on the de-standardization of family-life trajectories in early adulthood, using Fertility and Family Survey data on 19 countries. Across cohorts, family-life trajectories of young adults have not become more

  1. N-terminal amino acid sequence of Bacillus licheniformis alpha-amylase: comparison with Bacillus amyloliquefaciens and Bacillus subtilis Enzymes.

    OpenAIRE

    Kuhn, H; Fietzek, P P; Lampen, J O

    1982-01-01

    The thermostable, liquefying alpha-amylase from Bacillus licheniformis was immunologically cross-reactive with the thermolabile, liquefying alpha-amylase from Bacillus amyloliquefaciens. Their N-terminal amino acid sequences showed extensive homology with each other, but not with the saccharifying alpha-amylases of Bacillus subtilis.

  2. Comparison of complete mitochondrial DNA sequences between old and new world strains of the cowpea aphid, Aphis craccivora (Hemiptera: Aphididae)

    Science.gov (United States)

    Mitochondrial DNA provides useful tools for inferring population genetic structure within a species and phylogenetic relationships between species. The complete mitogenome sequences were assembled from strains of the cowpea aphids, Aphis craccivora, from the old (15,308 bp) and new world (15,305 bp...

  3. Comparison of Flow Injection MS, NMR, and DNA Sequencing: Methods for Identification and Authentication of Black Cohosh (Actaea racemosa)

    Science.gov (United States)

    Flow injection mass spectrometry (FIMS) and proton nuclear magnetic resonance spectrometry (1H-NMR), two metabolic fingerprinting methods, and DNA sequencing were used to identify and authenticate Actaea species. Initially, samples of Actaea racemosa L. from a single source were distinguished from ...

  4. A comparison of step-and-shoot leaf sequencing algorithms that eliminate tongue-and-groove effects

    Energy Technology Data Exchange (ETDEWEB)

    Kamath, Srijit [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Sahni, Sartaj [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Ranka, Sanjay [Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL (United States); Li, Jonathan [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States); Palta, Jatinder [Department of Radiation Oncology, University of Florida, Gainesville, FL (United States)

    2004-07-21

    The performances of three recently published leaf sequencing algorithms for step-and-shoot intensity-modulated radiation therapy delivery that eliminates tongue-and-groove underdosage are evaluated. Proofs are given to show that the algorithm of Que et al (2004 Phys. Med. Biol. 49 399-405) generates leaf sequences free of tongue-and-groove underdosage and interdigitation. However, the total beam-on times could be up to n times those of the sequences generated by the algorithms of Kamath et al (2004 Phys. Med. Biol. 49 N7-N19), which are optimal in beam-on time for unidirectional leaf movement under the same constraints, where n is the total number of involved leaf pairs. Using 19 clinical fluence matrices and 100 000 randomly generated 15 x 15 matrices, the average monitor units and number of segments of the leaf sequences generated using the algorithm of Que et al are about two to four times those generated by the algorithm of Kamath et al.

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

    Science.gov (United States)

    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

  6. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

    Full Text Available 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

  7. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L.) through plastome sequence comparison

    Science.gov (United States)

    2010-01-01

    Background The cultivated olive (Olea europaea L.) is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions discriminating among the agronomically and economically important olive cultivars have been identified. The objective of this study was to sequence the entire plastome of olive and analyze many potential polymorphic regions to develop new inter-cultivar genetic markers. Results The complete plastid genome of the olive cultivar Frantoio was determined by direct sequence analysis using universal and novel PCR primers designed to amplify all overlapping regions. The chloroplast genome of the olive has an organisation and gene order that is conserved among numerous Angiosperm species and do not contain any of the inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses that have been found in the chloroplast genomes of the genera Jasminum and Menodora, from the same family as Olea. The annotated sequence was used to evaluate the content of coding genes, the extent, and distribution of repeated and long dispersed sequences and the nucleotide composition pattern. These analyses provided essential information for structural, functional and comparative genomic studies in olive plastids. Furthermore, the alignment of the olive plastome sequence to those of other varieties and species identified 30 new organellar polymorphisms within the cultivated olive. Conclusions In addition to identifying mutations that may play a functional role in modifying the metabolism and adaptation of olive cultivars, the new chloroplast markers represent a valuable tool to assess the level of olive intercultivar plastome variation for use in population genetic analysis, phylogenesis, cultivar characterisation and DNA food tracking. PMID:20868482

  8. Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2004-05-01

    Full Text Available Abstract Background The elastin gene (ELN is implicated as a factor in both supravalvular aortic stenosis (SVAS and Williams Beuren Syndrome (WBS, two diseases involving pronounced complications in mental or physical development. Although the complete spectrum of functional roles of the processed gene product remains to be established, these roles are inferred to be analogous in human and mouse. This view is supported by genomic sequence comparison, in which there are no large-scale differences in the ~1.8 Mb sequence block encompassing the common region deleted in WBS, with the exception of an overall reversed physical orientation between human and mouse. Results Conserved synteny around ELN does not translate to a high level of conservation in the gene itself. In fact, ELN orthologs in mammals show more sequence divergence than expected for a gene with a critical role in development. The pattern of divergence is non-conventional due to an unusually high ratio of gaps to substitutions. Specifically, multi-sequence alignments of eight mammalian sequences reveal numerous non-aligning regions caused by species-specific insertions and deletions, in spite of the fact that the vast majority of aligning sites appear to be conserved and undergoing purifying selection. Conclusions The pattern of lineage-specific, in-frame insertions/deletions in the coding exons of ELN orthologous genes is unusual and has led to unique features of the gene in each lineage. These differences may indicate that the gene has a slightly different functional mechanism in mammalian lineages, or that the corresponding regions are functionally inert. Identified regions that undergo purifying selection reflect a functional importance associated with evolutionary pressure to retain those features.

  9. Value of fat-suppressed PD-weighted TSE-sequences for detection of anterior and posterior cruciate ligament lesions-Comparison to arthroscopy

    International Nuclear Information System (INIS)

    Schaefer, Fritz K.W.; Schaefer, Philipp J.; Brossmann, Joachim; Frahm, Christian; Muhle, Claus; Hilgert, Ralf Erik; Heller, Martin; Jahnke, Thomas

    2006-01-01

    Objective: To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging for the detection of anterior and posterior cruciate ligament lesions in comparison to arthroscopy. Materials and methods: In a prospective study 31 knee joints were imaged on a 1.5 T MR scanner (Vision[reg], Siemens, Erlangen) prior to arthroscopy using following sequences: (a) sagittal FS-PDw/T2w TSE (TR/TE: 4009/15/105 ms); (b) sagittal PDw/T2w TSE (TR/TE:3800/15/105 ms). Further imaging parameters: slice thickness 3 mm, FOV 160 mm, matrix 256 x 256. A total of 62 anterior and posterior cruciate ligaments (ACL/PCL) were evaluated, standard of reference was arthroscopy. Sensitivity, specificity, positive (ppv) and negative predictive value (npv) and accuracy were calculated. Results: Twenty-one cruciate ligament ruptures were detected in arthroscopy, 19 ACL- and 2 PCL-ruptures (on MRI 34/124, 25/62 ACL, 9/62 PCL lesions). For all four sequences in the 31 patients with arthroscopic correlation sensitivity, specificity, ppv, npv and accuracy were 86%, 98%, 95%, 93% and 94% for detection of tears, and 84%, 100%, 100%, 80% and 90% for ACL-ruptures respectively. The two PCL-ruptures were true positive in all sequences, one intact PCL was diagnosed as torn (false positive). Conclusions: Fat-suppressed PDw/T2w TSE-MR sequences are comparable to PDw TSE sequences for the detection of ACL/PCL-lesions

  10. A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map.

    Science.gov (United States)

    Solignac, Michel; Mougel, Florence; Vautrin, Dominique; Monnerot, Monique; Cornuet, Jean-Marie

    2007-01-01

    The honey bee is a key model for social behavior and this feature led to the selection of the species for genome sequencing. A genetic map is a necessary companion to the sequence. In addition, because there was originally no physical map for the honey bee genome project, a meiotic map was the only resource for organizing the sequence assembly on the chromosomes. We present the genetic (meiotic) map here and describe the main features that emerged from comparison with the sequence-based physical map. The genetic map of the honey bee is saturated and the chromosomes are oriented from the centromeric to the telomeric regions. The map is based on 2,008 markers and is about 40 Morgans (M) long, resulting in a marker density of one every 2.05 centiMorgans (cM). For the 186 megabases (Mb) of the genome mapped and assembled, this corresponds to a very high average recombination rate of 22.04 cM/Mb. Honey bee meiosis shows a relatively homogeneous recombination rate along and across chromosomes, as well as within and between individuals. Interference is higher than inferred from the Kosambi function of distance. In addition, numerous recombination hotspots are dispersed over the genome. The very large genetic length of the honey bee genome, its small physical size and an almost complete genome sequence with a relatively low number of genes suggest a very promising future for association mapping in the honey bee, particularly as the existence of haploid males allows easy bulk segregant analysis.

  11. Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile.

    Science.gov (United States)

    Li, Zhirong; Liu, Xiaolei; Zhao, Jianhong; Xu, Kaiyue; Tian, Tiantian; Yang, Jing; Qiang, Cuixin; Shi, Dongyan; Wei, Honglian; Sun, Suju; Cui, Qingqing; Li, Ruxin; Niu, Yanan; Huang, Bixing

    2018-04-01

    Clostridium difficile is the causative pathogen for antibiotic-related nosocomial diarrhea. For epidemiological study and identification of virulent clones, a new binary typing method was developed for C. difficile in this study. The usefulness of this newly developed optimized 10-loci binary typing method was compared with two widely used methods ribotyping and multilocus sequence typing (MLST) in 189 C. difficile samples. The binary typing, ribotyping and MLST typed the samples into 53 binary types (BTs), 26 ribotypes (RTs), and 33 MLST sequence types (STs), respectively. The typing ability of the binary method was better than that of either ribotyping or MLST expressed in Simpson Index (SI) at 0.937, 0.892 and 0.859, respectively. The ease of testing, portability and cost-effectiveness of the new binary typing would make it a useful typing alternative for outbreak investigations within healthcare facilities and epidemiological research. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing.

    Science.gov (United States)

    Yusrina, Falah; Chua, Cui Wen; Lee, Chun Kiat; Chiu, Lily; Png, Tracy Si-Yu; Khoo, Mui Joo; Yan, Gabriel; Lee, Guan Huei; Yan, Benedict; Lee, Hong Kai

    2018-05-01

    Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. The cobas showed similar or slightly higher accuracy (100%; 95% CI 94-100%) compared to the LiPA (99%; 95% CI 92-100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Prunus necrotic ringspot ilarvirus: nucleotide sequence of RNA3 and the relationship to other ilarviruses based on coat protein comparison.

    Science.gov (United States)

    Guo, D; Maiss, E; Adam, G; Casper, R

    1995-05-01

    The RNA3 of prunus necrotic ringspot ilarvirus (PNRSV) has been cloned and its entire sequence determined. The RNA3 consists of 1943 nucleotides (nt) and possesses two large open reading frames (ORFs) separated by an intergenic region of 74 nt. The 5' proximal ORF is 855 nt in length and codes for a protein of molecular mass 31.4 kDa which has homologies with the putative movement protein of other members of the Bromoviridae. The 3' proximal ORF of 675 nt is the cistron for the coat protein (CP) and has a predicted molecular mass of 24.9 kDa. The sequence of the 3' non-coding region (NCR) of PNRSV RNA3 showed a high degree of similarity with those of tobacco streak virus (TSV), prune dwarf virus (PDV), apple mosaic virus (ApMV) and also alfalfa mosaic virus (AIMV). In addition it contained potential stem-loop structures with interspersed AUGC motifs characteristic for ilar- and alfamoviruses. This conserved primary and secondary structure in all 3' NCRs may be responsible for the interaction with homologous and heterologous CPs and subsequent activation of genome replication. The CP gene of an ApMV isolate (ApMV-G) of 657 nt has also been cloned and sequenced. Although ApMV and PNRSV have a distant serological relationship, the deduced amino acid sequences of their CPs have an identity of only 51.8%. The N termini of PNRSV and ApMV CPs have in common a zinc-finger motif and the potential to form an amphipathic helix.

  14. Evaluation of pneumonia in children: comparison of MRI with fast imaging sequences at 1.5T with chest radiographs

    Energy Technology Data Exchange (ETDEWEB)

    Yikilmaz, Ali; Koc, Ali; Coskun, Abdulhakim (Dept. of Radiology, Erciyes Medical School, Kayseri (Turkey)); Ozturk, Mustafa K (Dept. of Pediatric Infectious Diseases, Erciyes Medical School, Kayseri (Turkey)); Mulkern, Robert V; Lee, Edward Y (Dept. of Radiology and Dept. of Medicine, Pulmonary Div., Children' s Hospital Boston and Harvard Medical School, Boston (United States)), email: Edward.lee@childrens.harvard.edu

    2011-10-15

    Background Although there has been a study aimed at magnetic resonance imaging (MRI) evaluation of pneumonia in children at a low magnetic field (0.2T), there is no study which assessed the efficacy of MRI, particularly with fast imaging sequences at 1.5T, for evaluating pneumonia in children. Purpose To investigate the efficacy of chest MRI with fast imaging sequences at 1.5T for evaluating pneumonia in children by comparing MRI findings with those of chest radiographs. Material and Methods This was an Institutional Review Board-approved, HIPPA-compliant prospective study of 40 consecutive pediatric patients (24 boys, 16 girls; mean age 7.3 years +- 6.6 years) with pneumonia, who underwent PA and lateral chest radiographs followed by MRI within 24 h. All MRI studies were obtained in axial and coronal planes with two different fast imaging sequences: T1-weighted FFE (Fast Field Echo) (TR/TE: 83/4.6) and T2-weighted B-FFE M2D (Balanced Fast Field Echo Multiple 2D Dimensional) (TR/TE: 3.2/1.6). Two experienced pediatric radiologists reviewed each chest radiograph and MRI for the presence of consolidation, necrosis/abscess, bronchiectasis, and pleural effusion. Chest radiograph and MRI findings were compared with Kappa statistics. Results All consolidation, lung necrosis/abscess, bronchiectasis, and pleural effusion detected with chest radiographs were also detected with MRI. There was statistically substantial agreement between chest radiographs and MRI in detecting consolidation (k = 0.78) and bronchiectasis (k = 0.72) in children with pneumonia. The agreement between chest radiographs and MRI was moderate for detecting necrosis/abscess (k = 0.49) and fair for detecting pleural effusion (k = 0.30). Conclusion MRI with fast imaging sequences is comparable to chest radiographs for evaluating underlying pulmonary consolidation, bronchiectasis, necrosis/abscess, and pleural effusion often associated with pneumonia in children

  15. Comparison of plastic single-use and metal reusable laryngoscope blades for orotracheal intubation during rapid sequence induction of anesthesia.

    Science.gov (United States)

    Amour, Julien; Marmion, Frédéric; Birenbaum, Aurélie; Nicolas-Robin, Armelle; Coriat, Pierre; Riou, Bruno; Langeron, Olivier

    2006-01-01

    Plastic single-use laryngoscope blades are inexpensive and carry a lower risk of infection compared with metal reusable blades, but their efficiency during rapid sequence induction remains a matter of debate. The authors therefore compared plastic and metal blades during rapid sequence induction in a prospective randomized trial. Two hundred eighty-four adult patients undergoing general anesthesia requiring rapid sequence induction were randomly assigned on a weekly basis to either plastic single-use or reusable metal blades (cluster randomization). After induction, a 60-s period was allowed to complete intubation. In the case of failed intubation, a second attempt was performed using metal blade. The primary endpoint of the study was the rate of failed intubations, and the secondary endpoint was the incidence of complications (oxygen desaturation, lung aspiration, and oropharynx trauma). Both groups were similar in their main characteristics, including risk factors for difficult intubation. On the first attempt, the rate of failed intubation was significantly increased in plastic blade group (17 vs. 3%; P < 0.01). In metal blade group, 50% of failed intubations were still difficult after the second attempt. In plastic blade group, all initial failed intubations were successfully intubated using metal blade, with an improvement in Cormack and Lehane grade. There was a significant increase in the complication rate in plastic group (15 vs. 6%; P < 0.05). In rapid sequence induction of anesthesia, the plastic laryngoscope blade is less efficient than a metal blade and thus should not be recommended for use in this clinical setting.

  16. Visualization of morphological parenchymal changes in emphysema: Comparison of different MRI sequences to 3D-HRCT

    International Nuclear Information System (INIS)

    Ley-Zaporozhan, Julia; Ley, Sebastian; Eberhardt, Ralf; Kauczor, Hans-Ulrich; Heussel, Claus Peter

    2010-01-01

    Purpose: Thin-section CT is the modality of choice for morphological imaging the lung parenchyma, while proton-MRI might be used for functional assessment. However, the capability of MRI to visualize morphological parenchymal alterations in emphysema is undetermined. Thus, the aim of the study was to compare different MRI sequences with CT. Materials and methods: 22 patients suffering from emphysema underwent thin-section MSCT serving as a reference. MRI (1.5 T) was performed using three different sequences: T2-HASTE in coronal and axial orientation, T1-GRE (VIBE) in axial orientation before and after application of contrast media (ce). All datasets were evaluated by four chest radiologists in consensus for each sequence separately independent from CT. The severity of emphysema, leading type, bronchial wall thickening, fibrotic changes and nodules was analyzed visually on a lobar level. Results: The sensitivity for correct categorization of emphysema severity was 44%, 48% and 41% and the leading type of emphysema was identical to CT in 68%, 55% and 60%, for T2-HASTE, T1-VIBE and T1-ce-VIBE respectively. A bronchial wall thickening was found in 43 lobes in CT and was correctly seen in MRI in 42%, 33% and 26%. Of those 74 lobes presented with fibrotic changes in CT were correctly identified by MRI in 39%, 35% and 58%. Small nodules were mostly underdiagnosed in MRI. Conclusion: MRI matched the CT severity classification and leading type of emphysema in half of the cases. All sequences showed a similar diagnostic performance, however a combination of HASTE and ce-VIBE should be recommended.

  17. Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I.

    Science.gov (United States)

    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. © 2016 Institute of Zoology, Chinese Academy of Sciences.

  18. Comparison of 16S ribosomal RNA gene sequence analysis and conventional culture in the environmental survey of a hospital

    OpenAIRE

    Manaka, Akihiro; Tokue, Yutaka; Murakami, Masami

    2017-01-01

    Background Nosocomial infection is one of the most common complications within health care facilities. Certain studies have reported outbreaks resulting from contaminated hospital environments. Although the identification of bacteria in the environment can readily be achieved using culturing methods, these methods detect live bacteria. Sequencing of the 16S ribosomal RNA (16S rRNA) gene is recognized to be effective for bacterial identification. In this study, we surveyed wards where drug-res...

  19. Legionella confirmation in cooling tower water. Comparison of culture, real-time PCR and next generation sequencing.

    Science.gov (United States)

    Farhat, Maha; Shaheed, Raja A; Al-Ali, Haider H; Al-Ghamdi, Abdullah S; Al-Hamaqi, Ghadeer M; Maan, Hawraa S; Al-Mahfoodh, Zainab A; Al-Seba, Hussain Z

    2018-02-01

    To investigate the presence of Legionella spp in cooling tower water. Legionella proliferation in cooling tower water has serious public health implications as it can be transmitted to humans via aerosols and cause Legionnaires' disease. Samples of cooling tower water were collected from King Fahd Hospital of the University (KFHU) (Imam Abdulrahman Bin Faisal University, 2015/2016). The water samples were analyzed by a standard Legionella culture method, real-time polymerase chain reaction (RT-PCR), and 16S rRNA next-generation sequencing. In addition, the bacterial community composition was evaluated. All samples were negative by conventional Legionella culture. In contrast, all water samples yielded positive results by real-time PCR (105 to 106 GU/L). The results of 16S rRNA next generation sequencing showed high similarity and reproducibility among the water samples. The majority of sequences were Alpha-, Beta-, and Gamma-proteobacteria, and Legionella was the predominant genus. The hydrogen-oxidizing gram-negative bacterium Hydrogenophaga was present at high abundance, indicating high metabolic activity. Sphingopyxis, which is known for its resistance to antimicrobials and as a pioneer in biofilm formation, was also detected. Our findings indicate that monitoring of Legionella in cooling tower water would be enhanced by use of both conventional culturing and molecular methods.

  20. Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

    Energy Technology Data Exchange (ETDEWEB)

    Van Leersum, M.D. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Schweitzer, M.E. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Gannon, F. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Vinitski, S. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Finkel, G. [Dept. of Pathology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States); Mitchell, D.G. [Dept. of Radiology, Thomas Jefferson Univ. Hospital, Philadelphia, PA (United States)

    1995-08-01

    This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

  1. Thickness of patellofemoral articular cartilage as measured on MR imaging: sequence comparison of accuracy, reproducibility, and interobserver variation

    International Nuclear Information System (INIS)

    Van Leersum, M.D.; Schweitzer, M.E.; Gannon, F.; Vinitski, S.; Finkel, G.; Mitchell, D.G.

    1995-01-01

    This study was undertaken to assess the accuracy, precision, and reliability of magnetic resonance (MR) measurements of articular cartilage. Fifteen cadaveric patellas were imaged in the axial plane at 1.5 T. Gradient echo and fat-suppressed FSE, T2-weighted, proton density, and T1-weighted sequences were performed. We measured each 5-mm section separately at three standardized positions, giving a total of 900 measurements. These findings were correlated with independently performed measurements of the corresponding anatomic sections. A hundred random measurements were also evaluated for reproducibility and interobserver variation. Although all sequences were highly accurate, the T1-weighted images were the most accurate, with a mean difference of 0.25 mm and a correlation coefficient of 0.85. All sequences were also highly reproducible with little inter-observer variation. In an attempt to improve the accuracy of the MR measurements further, we retrospectively evaluated all measurements with discrepancies greater than 1 mm from the specimen. All these differences were attributable to focal defects causing exaggeration of the thickness on MR imaging. (orig.)

  2. Nucleotide and deduced amino acid sequence of the envelope gene of the Vasilchenko strain of TBE virus; comparison with other flaviviruses.

    Science.gov (United States)

    Gritsun, T S; Frolova, T V; Pogodina, V V; Lashkevich, V A; Venugopal, K; Gould, E A

    1993-02-01

    A strain of tick-borne encephalitis virus known as Vasilchenko (Vs) exhibits relatively low virulence characteristics in monkeys, Syrian hamsters and humans. The gene encoding the envelope glycoprotein of this virus was cloned and sequenced. Alignment of the sequence with those of other known tick-borne flaviviruses and identification of the recognised amino acid genetic marker EHLPTA confirmed its identity as a member of the TBE complex. However, Vs virus was distinguishable from eastern and western tick-borne serotypes by the presence of the sequence AQQ at amino acid positions 232-234 and also by the presence of other specific amino acid substitutions which may be genetic markers for these viruses and could determine their pathogenetic characteristics. When compared with other tick-borne flaviviruses, Vs virus had 12 unique amino acid substitutions including an additional potential glycosylation site at position (315-317). The Vs virus strain shared closest nucleotide and amino acid homology (84.5% and 95.5% respectively) with western and far eastern strains of tick-borne encephalitis virus. Comparison with the far eastern serotype of tick-borne encephalitis virus, by cross-immunoelectrophoresis of Vs virions and PAGE analysis of the extracted virion proteins, revealed differences in surface charge and virus stability that may account for the different virulence characteristics of Vs virus. These results support and enlarge upon previous data obtained from molecular and serological analysis.

  3. A comparison of genotyping-by-sequencing analysis methods on low-coverage crop datasets shows advantages of a new workflow, GB-eaSy.

    Science.gov (United States)

    Wickland, Daniel P; Battu, Gopal; Hudson, Karen A; Diers, Brian W; Hudson, Matthew E

    2017-12-28

    Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are sequenced on short-read sequencing platforms. While cost-effective, this method produces extensive missing data and requires complex bioinformatics analysis. GBS is most commonly used on crop plant genomes, and because crop plants have highly variable ploidy and repeat content, the performance of GBS analysis software can vary by target organism. Here we focus our analysis on soybean, a polyploid crop with a highly duplicated genome, relatively little public GBS data and few dedicated tools. We compared the performance of five GBS pipelines using low-coverage Illumina sequence data from three soybean populations. To address issues identified with existing methods, we developed GB-eaSy, a GBS bioinformatics workflow that incorporates widely used genomics tools, parallelization and automation to increase the accuracy and accessibility of GBS data analysis. Compared to other GBS pipelines, GB-eaSy rapidly and accurately identified the greatest number of SNPs, with SNP calls closely concordant with whole-genome sequencing of selected lines. Across all five GBS analysis platforms, SNP calls showed unexpectedly low convergence but generally high accuracy, indicating that the workflows arrived at largely complementary sets of valid SNP calls on the low-coverage data analyzed. We show that GB-eaSy is approximately as good as, or better than, other leading software solutions in the accuracy, yield and missing data fraction of variant calling, as tested on low-coverage genomic data from soybean. It also performs well relative to other solutions in terms of the run time and disk space required. In addition, GB-eaSy is built from existing open-source, modular software packages that are regularly updated and commonly used, making it straightforward to install and maintain

  4. Evaluation of TSE- and T1-3D-GRE-sequences for focal cartilage lesions in vitro in comparison to ultrahigh resolution multi-slice CT

    International Nuclear Information System (INIS)

    Stork, A.; Schulze, D.; Koops, A.; Kemper, J.; Adam, G.

    2002-01-01

    Purpose: Evaluation of TSE- and T 1 -3D-GRE-sequences for focal cartilage lesions in vitro in comparison to ultrahigh resolution multi-slice CT. Materials and methods: Forty artificial cartilage lesions in ten bovine patellae were immersed in a solution of iodinated contrast medium and assessed with ultrahigh resolution multi-slice CT. Fat-suppressed TSE images with intermediate- and T 2 -weighting at a slice thickness of 2, 3 and 4 mm as well as fat-suppressed T 1 -weighted 3D-FLASH images with an effective slice thickness of 1, 2 and 3 mm were acquired at 1.5 T. After adding Gd-DTPA to the saline solution containing the patellae, the T 1 -weighted 3D-FLASH imaging was repeated. Results: All cartilage lesions were visualised and graded with ultrahigh resolution multi-slice CT. The TSE images had a higher sensitivity and a higher inter- and intraobserver kappa compared to the FLASH-sequences (TSE: 70-95%; 0.82-0.83; 0.85-0.9; FLASH: 57.5-85%; 0.53-0.72; 0.73-0.82, respectively). An increase in slice thickness decreased the sensitivity, whereby deep lesions were even reliably depicted on TSE images at a slice thickness of 3 and 4 mm. Adding Gd-DTPA to the saline solution increased the sensitivity by 10% with no detectable advantage over the T 2 -weighted TSE images. Conclusion: TSE sequences and application of Gd-DTPA seemed to be superior to T 1 -weighted 3D-FLASH sequences without Gd-DTPA in the detection of focal cartilage lesions. The ultrahigh resolution multi-slice CT can serve as in vitro reference standard for focal cartilage lesions. (orig.) [de

  5. Time-resolved echo-shared parallel MRA of the lung: observer preference study of image quality in comparison with non-echo-shared sequences

    International Nuclear Information System (INIS)

    Fink, C.; Puderbach, M.; Zaporozhan, J.; Plathow, C.; Kauczor, H.-U.; Ley, S.

    2005-01-01

    The aim of this study was to evaluate the image quality of time-resolved echo-shared parallel MRA of the lung. The pulmonary vasculature of nine patients (seven females, two males; median age: 44 years) with pulmonary disease was examined using a time-resolved MRA sequence combining echo sharing with parallel imaging (time-resolved echo-shared angiography technique, or TREAT). The sharpness of the vessel borders, conspicuousness of peripheral lung vessels, artifact level, and overall image quality of TREAT was assessed independently by four readers in a side-by-side comparison with non-echo-shared time-resolved parallel MRA data (pMRA) previously acquired in the same patients. Furthermore, the SNR of pulmonary arteries (PA) and veins (PV) achieved with both pulse sequences was compared. The mean voxel size of TREAT MRA was decreased by 24% compared with the non-echo-shared MRA. Regarding the sharpness of the vessel borders, conspicuousness of peripheral lung vessels, and overall image quality the TREAT sequence was rated superior in 75-76% of all cases. If the TREAT images were preferred over the pMRA images, the advantage was rated as major in 61-71% of all cases. The level of artifacts was not increased with the TREAT sequence. The mean interobserver agreement for all categories ranged between fair (artifact level) and good (overall image quality). The maximum SNR of TREAT did not differ from non-echo-shared parallel MRA (PA: TREAT: 273±45; pMRA: 280±71; PV: TREAT: 273±33; pMRA: 258±62). TREAT achieves a higher spatial resolution than non-echo-shared parallel MRA which is also perceived as an improved image quality. (orig.)

  6. Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains

    Science.gov (United States)

    Fagerlund, Annette; Langsrud, Solveig; Schirmer, Bjørn C. T.; Møretrø, Trond; Heir, Even

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen responsible for the disease listeriosis, and can be found throughout the environment, in many foods and in food processing facilities. The main cause of listeriosis is consumption of food contaminated from sources in food processing environments. Persistence in food processing facilities has previously been shown for the L. monocytogenes sequence type (ST) 8 subtype. In the current study, five ST8 strains were subjected to whole-genome sequencing and compared with five additionally available ST8 genomes, allowing comparison of strains from salmon, poultry and cheese industry, in addition to a human clinical isolate. Genome-wide analysis of single-nucleotide polymorphisms (SNPs) confirmed that almost identical strains were detected in a Danish salmon processing plant in 1996 and in a Norwegian salmon processing plant in 2001 and 2011. Furthermore, we show that L. monocytogenes ST8 was likely to have been transferred between two poultry processing plants as a result of relocation of processing equipment. The SNP data were used to infer the phylogeny of the ST8 strains, separating them into two main genetic groups. Within each group, the plasmid and prophage content was almost entirely conserved, but between groups, these sequences showed strong divergence. The accessory genome of the ST8 strains harbored genetic elements which could be involved in rendering the ST8 strains resilient to incoming mobile genetic elements. These included two restriction-modification loci, one of which was predicted to show phase variable recognition sequence specificity through site-specific domain shuffling. Analysis indicated that the ST8 strains harbor all important known L. monocytogenes virulence factors, and ST8 strains are commonly identified as the causative agents of invasive listeriosis. Therefore, the persistence of this L. monocytogenes subtype in food processing facilities poses a significant concern for food safety

  7. Comparison of the degree of homology of DNA and quantity of repeated sequences in an intact plant and cell structure

    International Nuclear Information System (INIS)

    Solov'yan, V.T.; Kunaleh, V.A.; Shumnyl, V.K.; Vershinin, A.V.

    1986-01-01

    This paper attempts to assess the quantity of repeated sequences and degree of homology of DNA in the intact plant and two lines of callus tissue of Rauwolfia serpentina Benth maintained for 20 years, which differ among themselves in the level of biosynthesis of the pharmacologically valuable alkaloid ajmaline. The tritium-labeled repeats of plants and calli were used in direct and reverse hybridization on nitrocellulose filters. Hybridization of H 3-labeled repeats with phage 17 DNA was used as control. The radioactivity of filters after washing was measured in a liquid scintillation counter

  8. Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

    Science.gov (United States)

    Yamagishi, Junya; Sato, Yukuto; Shinozaki, Natsuko; Ye, Bin; Tsuboi, Akito; Nagasaki, Masao; Yamashita, Riu

    2016-01-01

    The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field), QIAsymphony (a robotics method), and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.

  9. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny.

    Directory of Open Access Journals (Sweden)

    LaDeana W Hillier

    2007-07-01

    Full Text Available To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism-based genetic map to order and orient the whole genome shotgun assembly along the six C. briggsae chromosomes. Although these species are of the same genus, their most recent common ancestor existed 80-110 million years ago, and thus they are more evolutionarily distant than, for example, human and mouse. We found that, like C. elegans chromosomes, C. briggsae chromosomes exhibit high levels of recombination on the arms along with higher repeat density, a higher fraction of intronic sequence, and a lower fraction of exonic sequence compared with chromosome centers. Despite extensive intrachromosomal rearrangements, 1:1 orthologs tend to remain in the same region of the chromosome, and colinear blocks of orthologs tend to be longer in chromosome centers compared with arms. More strikingly, the two species show an almost complete conservation of synteny, with 1:1 orthologs present on a single chromosome in one species also found on a single chromosome in the other. The conservation of both chromosomal organization and synteny between these two distantly related species suggests roles for chromosome organization in the fitness of an organism that are only poorly understood presently.

  10. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

    Directory of Open Access Journals (Sweden)

    Zhang Guojie

    2011-07-01

    Full Text Available Abstract The recent publication of the draft genome sequences of the Neanderthal and a ~50,000-year-old archaic hominin from Denisova Cave in southern Siberia has ushered in a new age in molecular archaeology. We previously cross-compared the human, chimpanzee and Neanderthal genome sequences with respect to a set of disease-causing/disease-associated missense and regulatory mutations (Human Gene Mutation Database and succeeded in identifying genetic variants which, although apparently pathogenic in humans, may represent a 'compensated' wild-type state in at least one of the other two species. Here, in an attempt to identify further 'potentially compensated mutations' (PCMs of interest, we have compared our dataset of disease-causing/disease-associated mutations with their corresponding nucleotide positions in the Denisovan hominin, Neanderthal and chimpanzee genomes. Of the 15 human putatively disease-causing mutations that were found to be compensated in chimpanzee, Denisovan or Neanderthal, only a solitary F5 variant (Val1736Met was specific to the Denisovan. In humans, this missense mutation is associated with activated protein C resistance and an increased risk of thromboembolism and recurrent miscarriage. It is unclear at this juncture whether this variant was indeed a PCM in the Denisovan or whether it could instead have been associated with disease in this ancient hominin.

  11. Magnetic resonance cholangiography: comparison of two- and three-dimensional sequences for assessment of malignant biliary obstruction

    International Nuclear Information System (INIS)

    Choi, Jin-Young; Kim, Myeong-Jin; Lee, Jeong Min; Lee, Jae Young; Kim, Se Hyung; Han, Joon Koo; Choi, Byung Ihn; Kim, Ki Whang

    2008-01-01

    The purpose was to retrospectively compare two-dimensional (2D) magnetic resonance cholangiography (MRC) including breath-hold single-shot rapid acquisition with relaxation enhancement (RARE) and multislice half-Fourier RARE versus navigator-triggered 3D-RARE MRC in the evaluation of biliary malignancy. MRC findings were evaluated in 31 patients with malignant biliary obstruction, including biliary malignancy, gallbladder carcinoma, and ampullary cancer. Two observers independently reviewed the images to assess the overall image quality, artifacts, ductal conspicuity, extent of disease, diagnostic confidence of tumor extent, and origin of tumor. The results were compared with surgical and histopathologic findings. Studies obtained with 3D-MRC were of significantly higher technical quality than those obtained with 2D-MRC. However, the accuracy between two sequences for classification of tumor showed no statistical significance. There was no significant difference between the Az values of 2D- and 3D-MRC for overall tumor extent in bilateral second order branch, intrapancreatic common bile duct (CBD) involvement (Az = 0.889, 0.881 for 2D and Az = 0.903, 0.864 for 3D). Nor was there a significant difference between two sequences in the assessment of the origin of tumor. Although 3D-MRC has superior image quality over 2D-MRC, 3D-MRC showed no statistically significant difference in accuracy compared with 2D-MRC for evaluating the extent of disease in malignant biliary obstructions. (orig.)

  12. Comparison of Boiling and Robotics Automation Method in DNA Extraction for Metagenomic Sequencing of Human Oral Microbes.

    Directory of Open Access Journals (Sweden)

    Junya Yamagishi

    Full Text Available The rapid improvement of next-generation sequencing performance now enables us to analyze huge sample sets with more than ten thousand specimens. However, DNA extraction can still be a limiting step in such metagenomic approaches. In this study, we analyzed human oral microbes to compare the performance of three DNA extraction methods: PowerSoil (a method widely used in this field, QIAsymphony (a robotics method, and a simple boiling method. Dental plaque was initially collected from three volunteers in the pilot study and then expanded to 12 volunteers in the follow-up study. Bacterial flora was estimated by sequencing the V4 region of 16S rRNA following species-level profiling. Our results indicate that the efficiency of PowerSoil and QIAsymphony was comparable to the boiling method. Therefore, the boiling method may be a promising alternative because of its simplicity, cost effectiveness, and short handling time. Moreover, this method was reliable for estimating bacterial species and could be used in the future to examine the correlation between oral flora and health status. Despite this, differences in the efficiency of DNA extraction for various bacterial species were observed among the three methods. Based on these findings, there is no "gold standard" for DNA extraction. In future, we suggest that the DNA extraction method should be selected on a case-by-case basis considering the aims and specimens of the study.

  13. One-dimensional TRFLP-SSCP is an effective DNA fingerprinting strategy for soil Archaea that is able to simultaneously differentiate broad taxonomic clades based on terminal fragment length polymorphisms and closely related sequences based on single stranded conformation polymorphisms.

    Science.gov (United States)

    Swanson, Colby A; Sliwinski, Marek K

    2013-09-01

    DNA fingerprinting methods provide a means to rapidly compare microbial assemblages from environmental samples without the need to first cultivate species in the laboratory. The profiles generated by these techniques are able to identify statistically significant temporal and spatial patterns, correlations to environmental gradients, and biological variability to estimate the number of replicates for clone libraries or next generation sequencing (NGS) surveys. Here we describe an improved DNA fingerprinting technique that combines terminal restriction fragment length polymorphisms (TRFLP) and single stranded conformation polymorphisms (SSCP) so that both can be used to profile a sample simultaneously rather than requiring two sequential steps as in traditional two-dimensional (2-D) gel electrophoresis. For the purpose of profiling Archaeal 16S rRNA genes from soil, the dynamic range of this combined 1-D TRFLP-SSCP approach was superior to TRFLP and SSCP. 1-D TRFLP-SSCP was able to distinguish broad taxonomic clades with genetic distances greater than 10%, such as Euryarchaeota and the Thaumarchaeal clades g_Ca. Nitrososphaera (formerly 1.1b) and o_NRP-J (formerly 1.1c) better than SSCP. In addition, 1-D TRFLP-SSCP was able to simultaneously distinguish closely related clades within a genus such as s_SCA1145 and s_SCA1170 better than TRFLP. We also tested the utility of 1-D TRFLP-SSCP fingerprinting of environmental assemblages by comparing this method to the generation of a 16S rRNA clone library of soil Archaea from a restored Tallgrass prairie. This study shows 1-D TRFLP-SSCP fingerprinting provides a rapid and phylogenetically informative screen of Archaeal 16S rRNA genes in soil samples. © 2013.

  14. Intricate patterns of phylogenetic relationships in the olive family as inferred from multi-locus plastid and nuclear DNA sequence analyses: a close-up on Chionanthus and Noronhia (Oleaceae).

    Science.gov (United States)

    Hong-Wa, Cynthia; Besnard, Guillaume

    2013-05-01

    Noronhia represents the most successful radiation of the olive family (Oleaceae) in Madagascar with more than 40 named endemic species distributed in all ecoregions from sea level to high mountains. Its position within the subtribe Oleinae has, however, been largely unresolved and its evolutionary history has remained unexplored. In this study, we generated a dataset of plastid (trnL-F, trnT-L, trnS-G, trnK-matK) and nuclear (internal transcribed spacer [ITS]) DNA sequences to infer phylogenetic relationships within Oleinae and to examine evolutionary patterns within Noronhia. Our sample included most species of Noronhia and representatives of the ten other extant genera within the subtribe with an emphasis on Chionanthus. Bayesian inferences and maximum likelihood analyses of plastid and nuclear data indicated several instances of paraphyly and polyphyly within Oleinae, with some geographic signal. Both plastid and ITS data showed a polyphyletic Noronhia that included Indian Ocean species of Chionanthus. They also found close relationships between Noronhia and African Chionanthus. However, the plastid data showed little clear differentiation between Noronhia and the African Chionanthus whereas relationships suggested by the nuclear ITS data were more consistent with taxonomy and geography. We used molecular dating to discriminate between hybridization and lineage sorting/gene duplication as alternative explanations for these topological discordances and to infer the biogeographic history of Noronhia. Hybridization between African Chionanthus and Noronhia could not be ruled out. However, Noronhia has long been established in Madagascar after a likely Cenozoic dispersal from Africa, suggesting any hybridization between representatives of African and Malagasy taxa was ancient. In any case, the African and Indian Ocean Chionanthus and Noronhia together formed a strongly supported monophyletic clade distinct and distant from other Chionanthus, which calls for a revised

  15. High quality draft genome sequence of the moderately halophilic bacterium Pontibacillus yanchengensis Y32(T) and comparison among Pontibacillus genomes.

    Science.gov (United States)

    Huang, Jing; Qiao, Zi Xu; Tang, Jing Wei; Wang, Gejiao

    2015-01-01

    Pontibacillus yanchengensis Y32(T) is an aerobic, motile, Gram-positive, endospore-forming, and moderately halophilic bacterium isolated from a salt field. In this study, we describe the features of P. yanchengensis strain Y32(T) together with a comparison with other four Pontibacillus genomes. The 4,281,464 bp high-quality-draft genome of strain Y32(T) is arranged into 153 contigs containing 3,965 protein-coding genes and 77 RNA encoding genes. The genome of strain Y32(T) possesses many genes related to its halophilic character, flagellar assembly and chemotaxis to support its survival in a salt-rich environment.

  16. Comparison of lesion conspicuity of radiofrequency ablation zones among MR sequences according to time in the normal rabbit liver

    International Nuclear Information System (INIS)

    Ku, Myong Seo; Kim, Seung Kwon; Hong, Hyun Pyo; Kwag, Hyon Joo

    2007-01-01

    To compare the lesion conspicuity of radiofrequency ablation (RFA) zones among MR sequences according to time in the normal rabbit liver. RFA zones were created in 12 rabbit livers with a 17-gauge internally cooled electrode (1-cm active tip, 30 Watts, 3 minutes). Three rabbits were sacrificed immediately, three days, two weeks, and six weeks after the RFA procedure, respectively. Before sacrifice, T1-, T2-weighted images (WI), and gadolinium-enhanced (GE)-T1WI images were obtained. The lesion conspicuity of the RAF zone and the contrast-to-noise ratio (CNR) of the RFA zone to the liver parenchyma were analyzed and compared among the MR sequences according to time. On T1WI, the RFA zones were only clearly seen on acute phase. On T2WI, the RFA zones were clearly seen on all phases except the hyperacute phase. On GE T1WI, the RFA zones were clearly seen on all phases. The CNRs of the RFA zone to the liver parenchyma of GE-T1WI (8.1-12.4) were significantly higher than the CNRs of TIWI (1.6-2.7) and T2WI (1.7-6.3) on all phases (ρ < 0.05), but the visual lesion conspicuity between GE T1WI and T2WI were similar. On hyperacute phase, GE T1WI showed better lesion conspicuity of the RFA zone than T1WI and T2WI. On other phases, GE T1WI and T2WI showed similar lesion conspicuity

  17. Yeast diversity during the fermentation of Andean chicha: A comparison of high-throughput sequencing and culture-dependent approaches.

    Science.gov (United States)

    Mendoza, Lucía M; Neef, Alexander; Vignolo, Graciela; Belloch, Carmela

    2017-10-01

    Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species dominated the pre-fermentative steps and abounded in fermented samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with very few reads in the pyrosequencing analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Segmentation of Gait Sequences in Sensor-Based Movement Analysis: A Comparison of Methods in Parkinson’s Disease

    Directory of Open Access Journals (Sweden)

    Nooshin Haji Ghassemi

    2018-01-01

    Full Text Available Robust gait segmentation is the basis for mobile gait analysis. A range of methods have been applied and evaluated for gait segmentation of healthy and pathological gait bouts. However, a unified evaluation of gait segmentation methods in Parkinson’s disease (PD is missing. In this paper, we compare four prevalent gait segmentation methods in order to reveal their strengths and drawbacks in gait processing. We considered peak detection from event-based methods, two variations of dynamic time warping from template matching methods, and hierarchical hidden Markov models (hHMMs from machine learning methods. To evaluate the methods, we included two supervised and instrumented gait tests that are widely used in the examination of Parkinsonian gait. In the first experiment, a sequence of strides from instructed straight walks was measured from 10 PD patients. In the second experiment, a more heterogeneous assessment paradigm was used from an additional 34 PD patients, including straight walks and turning strides as well as non-stride movements. The goal of the latter experiment was to evaluate the methods in challenging situations including turning strides and non-stride movements. Results showed no significant difference between the methods for the first scenario, in which all methods achieved an almost 100% accuracy in terms of F-score. Hence, we concluded that in the case of a predefined and homogeneous sequence of strides, all methods can be applied equally. However, in the second experiment the difference between methods became evident, with the hHMM obtaining a 96% F-score and significantly outperforming the other methods. The hHMM also proved promising in distinguishing between strides and non-stride movements, which is critical for clinical gait analysis. Our results indicate that both the instrumented test procedure and the required stride segmentation algorithm have to be selected adequately in order to support and complement classical

  19. Comparison of multilocus sequence typing and pulsed-field gel electrophoresis for Salmonella spp. identification in surface water

    Science.gov (United States)

    Kuo, Chun Wei; Hao Huang, Kuan; Hsu, Bing Mu; Tsai, Hsien Lung; Tseng, Shao Feng; Kao, Po Min; Shen, Shu Min; Chou Chiu, Yi; Chen, Jung Sheng

    2013-04-01

    Salmonella is one of the most important pathogens of waterborne diseases with outbreaks from contaminated water reported worldwide. In addition, Salmonella spp. can survive for long periods in aquatic environments. To realize genotypes and serovars of Salmonella in aquatic environments, we isolated the Salmonella strains by selective culture plates to identify the serovars of Salmonella by serological assay, and identify the genotypes by Multilocus sequence typing (MLST) based on the sequence data from University College Cork (UCC), respectively. The results show that 36 stream water samples (30.1%) and 18 drinking water samples (23.3%) were confirmed the existence of Salmonella using culture method combined PCR specific invA gene amplification. In this study, 24 cultured isolates of Salmonella from water samples were classified to fifteen Salmonella enterica serovars. In addition, we construct phylogenetic analysis using phylogenetic tree and Minimum spanning tree (MST) method to analyze the relationship of clinical, environmental, and geographical data. Phylogenetic tree showed that four main clusters and our strains can be distributed in all. The genotypes of isolates from stream water are more biodiversity while comparing the Salmonella strains genotypes from drinking water sources. According to MST data, we can found the positive correlation between serovars and genotypes of Salmonella. Previous studies revealed that the result of Pulsed field gel electrophoresis (PFGE) method can predict the serovars of Salmonella strain. Hence, we used the MLST data combined phylogenetic analysis to identify the serovars of Salmonella strain and achieved effectiveness. While using the geographical data combined phylogenetic analysis, the result showed that the dominant strains were existed in whole stream area in rainy season. Keywords: Salmonella spp., MLST, phylogenetic analysis, PFGE

  20. Allelic diversity of the MHC class II DRB genes in brown bears (Ursus arctos) and a comparison of DRB sequences within the family Ursidae.

    Science.gov (United States)

    Goda, N; Mano, T; Kosintsev, P; Vorobiev, A; Masuda, R

    2010-11-01

    The allelic diversity of the DRB locus in major histocompatibility complex (MHC) genes was analyzed in the brown bear (Ursus arctos) from the Hokkaido Island of Japan, Siberia, and Kodiak of Alaska. Nineteen alleles of the DRB exon 2 were identified from a total of 38 individuals of U. arctos and were highly polymorphic. Comparisons of non-synonymous and synonymous substitutions in the antigen-binding sites of deduced amino acid sequences indicated evidence for balancing selection on the bear DRB locus. The phylogenetic analysis of the DRB alleles among three genera (Ursus, Tremarctos, and Ailuropoda) in the family Ursidae revealed that DRB allelic lineages were not separated according to species. This strongly shows trans-species persistence of DRB alleles within the Ursidae. © 2010 John Wiley & Sons A/S.

  1. Comparison of G protein sequences of South African street rabies viruses showing distinct progression of the disease in a mouse model of experimental rabies.

    Science.gov (United States)

    Seo, Wonhyo; Servat, Alexandre; Cliquet, Florence; Akinbowale, Jenkins; Prehaud, Christophe; Lafon, Monique; Sabeta, Claude

    Rabies is a fatal zoonotic disease and infections generally lead to a fatal encephalomyelitis in both humans and animals. In South Africa, domestic (dogs) and the wildlife (yellow mongoose) host species maintain the canid and mongoose rabies variants respectively. In this study, pathogenicity differences of South African canid and mongoose rabies viruses were investigated in a murine model, by assessing the progression of clinical signs and survivorship. Comparison of glycoprotein gene sequences revealed amino acid differences that may underpin the observed pathogenicity differences. Cumulatively, our results suggest that the canid rabies virus may be more neurovirulent in mice than the mongoose rabies variant. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  2. Diagnostic performance of the three-dimensional fast spin echo-Cube sequence in comparison with a conventional imaging protocol in evaluation of the lachrymal drainage system

    International Nuclear Information System (INIS)

    Zhang, Jing; Chen, Lang; Wang, Qiu-Xia; Zhu, Wen-Zhen; Luo, Xin; Peng, Li; Liu, Rong; Xiong, Wei

    2015-01-01

    To compare the three-dimensional (3D)-fast spin-echo (FSE)-Cube with a conventional imaging protocol in evaluation of dacryostenosis. Thirty-three patients with epiphora underwent examinations using Cube magnetic resonance dacryocystography (MRD) and a conventional protocol, which included 3D fast-recovery fast spin-echo (FRFSE) MRD and two-dimensional (2D)-FSE sequences at 3.0 T. Using lachrymal endoscopic findings as the reference standard, we calculated the sensitivity and specificity of both protocols for detecting lachrymal drainage system (LDS) obstruction and their accuracies in depicting the level of obstruction. Comparable coronal and axial images were selected for bot sequences. Two neuroradiologists graded paired images for blurring, artefacts, anatomic details, and overall image quality. The two methods showed no significant difference in sensitivity (89.5 % vs. 94.7 %; p =0.674), specificity (64.3 %; p =1) or accuracy (86.8 %; p =1) in detecting or depicting LDS obstruction. Blurring and artefacts were significantly better on 2D-FSE images (p 0.05). In comparison with the conventional protocol, Cube MRD demonstrates satisfactory image quality and similar diagnostic capability for cases of possible LDS disease. (orig.)

  3. Closing remarks

    International Nuclear Information System (INIS)

    Reig, J.

    2007-01-01

    Good afternoon. Before providing the closing remarks on behalf of the NEA, I would like to take this opportunity and make some personal reflections, if you allow me Mr. Chairman. I have had the opportunity to take part in the three workshops on public communication organised by the NEA. In the first one in Paris in 2000, representing my country, Spain, and in the two last ones in Ottawa in 2004 and Tokyo today, on behalf of the NEA. The topics for the three workshops follow a logical order, first the focus was on investing in trust in a time when public communication was becoming a big challenge for the regulators. Second, maintaining and measuring public confidence to assess how credible regulators are in front of the public; and finally here in Tokyo, transparency, which is a basic element to achieve trust and credibility. In my view, a regulatory decision has three main components, it has to be technically sound. legally correct and well communicated. The emphasis in the early years was in the technical matters, till legal issues became a key element to achieve the political acceptance from governments and local authorities. Finally the public communication aspects resulted into a major effort and challenge to achieve social acceptance. (author)

  4. Comparison of cluster-based and source-attribution methods for estimating transmission risk using large HIV sequence databases.

    Science.gov (United States)

    Le Vu, Stéphane; Ratmann, Oliver; Delpech, Valerie; Brown, Alison E; Gill, O Noel; Tostevin, Anna; Fraser, Christophe; Volz, Erik M

    2018-06-01

    Phylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission. A simulation study was conducted to assess error rates of clustering methods for detecting transmission risk factors. We modeled HIV epidemics among men having sex with men and generated phylogenies comparable to those that can be obtained from HIV surveillance data in the UK. Clustering and source attribution approaches were applied to evaluate their ability to identify patient attributes as transmission risk factors. We find that commonly used methods show a misleading association between cluster size or odds of clustering and covariates that are correlated with time since infection, regardless of their influence on transmission. Clustering methods usually have higher error rates and lower sensitivity than source attribution method for identifying transmission risk factors. But neither methods provide robust estimates of transmission risk ratios. Source attribution method can alleviate drawbacks from phylogenetic clustering but formal population genetic modeling may be required to estimate quantitative transmission risk factors. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  5. Ct shift: A novel and accurate real-time PCR quantification model for direct comparison of different nucleic acid sequences and its application for transposon quantifications.

    Science.gov (United States)

    Kolacsek, Orsolya; Pergel, Enikő; Varga, Nóra; Apáti, Ágota; Orbán, Tamás I

    2017-01-20

    There are numerous applications of quantitative PCR for both diagnostic and basic research. As in many other techniques the basis of quantification is that comparisons are made between different (unknown and known or reference) specimens of the same entity. When the aim is to compare real quantities of different species in samples, one cannot escape their separate precise absolute quantification. We have established a simple and reliable method for this purpose (Ct shift method) which combines the absolute and the relative approach. It requires a plasmid standard containing both sequences of amplicons to be compared (e.g. the target of interest and the endogenous control). It can serve as a reference sample with equal copies of templates for both targets. Using the ΔΔCt formula we can quantify the exact ratio of the two templates in each unknown sample. The Ct shift method has been successfully applied for transposon gene copy measurements, as well as for comparison of different mRNAs in cDNA samples. This study provides the proof of concept and introduces some potential applications of the method; the absolute nature of results even without the need for real reference samples can contribute to the universality of the method and comparability of different studies. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Cardiac MR tagging: optimization of sequence parameters and comparison at 1.5 T and 3.0 T in a volunteer study

    International Nuclear Information System (INIS)

    Kramer, U.; Fenchel, M.; Klumpp, B.; Claussen, C.D.; Miller, S.; Deshpande, V.; Laub, G.; Finn, J.P.

    2006-01-01

    Purpose: The aim of this study was the optimization of a gradient echo (GRE) MR tagging sequence at 3.0 T in comparison to 1.5 T in order to obtain the best image contrast between the myocardium, tag lines and blood signal. Theoretically expected improvements of signal-to-noise (SNR) and contrast-to-noise ratios (CNR) were also calculated. Materials and methods: 14 healthy volunteers (8 male, 6 female; mean age 43.4±10.3 years) were scanned using a 3.0 T as well as a 1.5 T whole-body system. A GRE flash-2 D tagging sequence was evaluated (midventricular short axis view) by varying the flip angle (8-16 ), slice thickness (4-8 mm; fixed flip angle 1.5/3.0 T: 12 /8 , tag size 8 mm) and tag size (4-8 mm, fixed flip angle 1.5/3.0 T: 12 /8 , slice thickness 6 mm). The field of view, acquisition time and temporal resolution (45 ms) were kept constant. Qualitative and quantitative image analysis was performed by calculating the SNR, CNR tag as well as the relative contrast between the myocardium and tag lines (RCMT). Results: Based on individual comparison, the best imaging protocol was found at a slice thickness of 6 mm, tag size of 8 mm, optimized flip angle of 8 (3.0 T) and 12 (1.5 T), respectively. Compared to 1.5 T, a significantly higher overall image score was determined (mean±sd; 3.2±0.2 vs 2.7±0.4) and a strong correlation between the CNR tag and RCMT for flip angle α and the slice thickness was found. A higher field strength resulted in an 80% increase in the CNR tag compared to 1.5 T (mean 10.7/6.1). Furthermore, the SNR was improved by 35% (mean 20.6/15.3) and the RCMT by 35% (mean 0.47/0.35). Conclusion: Myocardial tagging at 3.0 T has shown superior image quality in comparison to 1.5 T due to a higher baseline SNR and an improved CNR as well as RCMT. The suppressed fading of the tags enables the accessibility to the diastolic phase of the cardiac cycle. (orig.)

  7. Comparison of direct machine parameter optimization versus fluence optimization with sequential sequencing in IMRT of hypopharyngeal carcinoma

    International Nuclear Information System (INIS)

    Dobler, Barbara; Pohl, Fabian; Bogner, Ludwig; Koelbl, Oliver

    2007-01-01

    To evaluate the effects of direct machine parameter optimization in the treatment planning of intensity-modulated radiation therapy (IMRT) for hypopharyngeal cancer as compared to subsequent leaf sequencing in Oncentra Masterplan v1.5. For 10 hypopharyngeal cancer patients IMRT plans were generated in Oncentra Masterplan v1.5 (Nucletron BV, Veenendal, the Netherlands) for a Siemens Primus linear accelerator. For optimization the dose volume objectives (DVO) for the planning target volume (PTV) were set to 53 Gy minimum dose and 59 Gy maximum dose, in order to reach a dose of 56 Gy to the average of the PTV. For the parotids a median dose of 22 Gy was allowed and for the spinal cord a maximum dose of 35 Gy. The maximum DVO to the external contour of the patient was set to 59 Gy. The treatment plans were optimized with the direct machine parameter optimization ('Direct Step & Shoot', DSS, Raysearch Laboratories, Sweden) newly implemented in Masterplan v1.5 and the fluence modulation technique ('Intensity Modulation', IM) which was available in previous versions of Masterplan already. The two techniques were compared with regard to compliance to the DVO, plan quality, and number of monitor units (MU) required per fraction dose. The plans optimized with the DSS technique met the DVO for the PTV significantly better than the plans optimized with IM (p = 0.007 for the min DVO and p < 0.0005 for the max DVO). No significant difference could be observed for compliance to the DVO for the organs at risk (OAR) (p > 0.05). Plan quality, target coverage and dose homogeneity inside the PTV were superior for the plans optimized with DSS for similar dose to the spinal cord and lower dose to the normal tissue. The mean dose to the parotids was lower for the plans optimized with IM. Treatment plan efficiency was higher for the DSS plans with (901 ± 160) MU compared to (1151 ± 157) MU for IM (p-value < 0.05). Renormalization of the IM plans to the mean of the

  8. Microtomography-based comparison of reciprocating single-file F2 ProTaper technique versus rotary full sequence.

    Science.gov (United States)

    Paqué, Frank; Zehnder, Matthias; De-Deus, Gustavo

    2011-10-01

    A preparation technique with only 1 single instrument was proposed on the basis of the reciprocating movement of the F2 ProTaper instrument. The present study was designed to quantitatively assess canal preparation outcomes achieved by this technique. Twenty-five extracted human mandibular first molars with 2 separate mesial root canals were selected. Canals were randomly assigned to 1 of the 2 experimental groups: group 1, rotary conventional preparation by using ProTaper, and group 2, reciprocate instrumentation with 1 single ProTaper F2 instrument. Specimens were scanned initially and after root canal preparation with an isotropic resolution of 20 μm by using a micro-computed tomography system. The following parameters were assessed: changes in dentin volume, percentage of shaped canal walls, and degree of canal transportation. In addition, the time required to reach working length with the F2 instrument was recorded. Preoperatively, there were no differences regarding root canal curvature and volume between experimental groups. Overall, instrumentation led to enlarged canal shapes with no evidence of preparation errors. There were no statistical differences between the 2 preparation techniques in the anatomical parameters assessed (P > .01), except for a significantly higher canal transportation caused by the reciprocating file in the coronal canal third. On the other hand, preparation was faster by using the single-file technique (P ProTaper technique and conventional ProTaper full-sequence rotary approach were similar. However, the single-file F2 ProTaper technique was markedly faster in reaching working length. Copyright © 2011 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  9. Comparison of the effectivities of two-phase and single-phase anaerobic sequencing batch reactors during dairy wastewater treatment

    Energy Technology Data Exchange (ETDEWEB)

    Goebloes, Sz.; Portoero, P.; Bordas, D.; Kalman, M.; Kiss, I. [Institute for Biotechnology, Bay Zoltan Foundation for Applied Research, H-6726 Szeged (Hungary)

    2008-05-15

    The performances of anaerobic sequencing batch reactors fed with two different substrates were studied. The substrates were raw acid whey and acid whey fermented with Kluyveromyces lactis in order to investigate the suitability of ethanol for biogas production. The organic loading rates (OLRs) during the experiment ranged from 1.6 to 12.8 g COD dm{sup -3} d{sup -1} and the corresponding decreasing hydraulic retention times from 40 to 5 days for both reactor systems. The efficiency of each system depended on the OLR: the highest COD removal rate was observed at the lowest OLR applied (about 100% in both systems), and at maximum OLR the COD removal efficiency was 68% for the reactors fed with the raw whey and 80% for those fed with the pre-fermented whey. Under the same high OLR conditions the methane yield was 0.122 dm{sup -3} CH{sub 4} g{sup -1} COD{sub degraded} for the anaerobic digesters fed with the untreated whey, and 0.197 dm{sup -3} CH{sub 4} g{sup -1} COD{sub degraded} for those fed with the pre-fermented whey. The digesters functioned without pH control. At the maximum OLR the pH in the reactors fed with the raw acid whey was 5.1, while in those fed with the pre-fermented whey it was 7.15. The results demonstrate that the use of the pre-fermented acid whey as substrate for anaerobic digestion without pH control is feasible, especially at high OLR levels. This substrate is preferable to the raw acid whey, because of the ethanol formed as a non-acidic fermentation product of the yeast. (author)

  10. Analysis of normal anatomy of oral cavity in open-mouth view with CT and MRI; comparison with closed-mouth view

    International Nuclear Information System (INIS)

    Kim, Chan Ho; Kim, Seong Min; Cheon, Bont Jin; Huh, Jin Do; Joh, Young Duk

    2001-01-01

    When MRI and CT of the oral cavity utilize the traditional closed-mouth approach, direct contact between the tongue and surrounding structures may give rise to difficulty in recognizing the anatomy involved and demonstrating the possible presence of pathologic features. We describe a more appropriate scan technique, involving open-mouthed imaging, which may be used to demonstrate the anatomy of the oral cavity in detail. Axial and coronal MR imaging and axial CT scanning were performed in 14 healthy volunteers, using both the closed and open-mouth approach. For the latter, a mouth-piece was put in place prior to examination. In all volunteers, open-mouth MR and CT examinations involved the same parameters as the corresponding closed-mouth procedures. The CT and MR images obtained by each method were compared, particular attention being paid to the presence and symmetry of motion artifact of the tongue and the extent of air space in the oral cavity. Comparative imaging analysis was based on the recognition of 13 structures around the boundaries of the mouth. For statistical analysis, student's test was used and a p value<0.05 was considered significant. Due to symmetry of the tongue, a less severe motion artifact, and increased air space in the oral cavity, the open-mouth method produced excellent images. The axial and coronal MR images thus obtained were superior in terms of demarcation of the inferior surface and dortsum of the tongue, gingiva, buccal surface and buccal vestivule to those obtained with the mouth closed (p<0.05). In addition, axial MR images obtained with the mouth open showed better demarcation of structures at the lingual margin and anterior belly of the digastric muscle (p<0.05), while coronal MR images of the base of the tongue, surface of the hard palate, soft palate, and uvula, were also superior (p<0.05). Open-mouth CT provided better images at the lingual margin, dorsum of the tongue and buccal surface than the closed-mouth approach (p<0

  11. Comparison of Apical Extrusion of Debris by Using Single-File, Full-Sequence Rotary and Reciprocating Systems

    Directory of Open Access Journals (Sweden)

    Maryam Ehsani

    2017-01-01

    Full Text Available Objectives: During root canal preparation, apical extrusion of debris can cause inflammation, flare-ups, and delayed healing. Therefore, instrumentation techniques that cause the least extrusion of debris are desirable. This study aimed to compare apical extrusion of debris by five single-file, full-sequence rotary and reciprocating systems.Materials and Methods: One hundred twenty human mandibular premolars with similar root lengths, apical diameters, and canal curvatures were selected and randomly assigned to six groups (n=20: Reciproc R25 (25, 0.08, WaveOne Primary (25, 0.08, OneShape (25, 0.06, F360 (25, 0.04, Neoniti A1 (25, 0.08, and ProTaper Universal. Instrumentation of the root canals was performed in accordance with the manufacturers’ instructions. Each tooth's debris was collected in a pre-weighed vial. After drying the debris in an incubator, the mass was measured three times consecutively; the mean was then calculated. The preparation time by each system was also measured. For data analysis, one-way ANOVA and Games-Howell post hoc test were used.Results: The mean masses (±standard deviation of the apical debris were as follows: 2.071±1.38mg (ProTaper Universal, 1.702±1.306mg (Neoniti A1, 1.295±0.839mg (OneShape, 1.109±0.676mg (WaveOne, 0.976±0.478mg (Reciproc and 0.797±0.531mg (F360. Compared to ProTaper Universal, F360 generated significantly less debris (P=0.02. The ProTaper system required the longest preparation time (mean=88.6 seconds; the Reciproc (P=0.008, OneShape (P=0.006, and F360 (P=0.001 required significantly less time (P<0.05.Conclusions: All instruments caused extrusion of debris through the apex. The F360 produced significantly less debris than did the ProTaper Universal.Keywords: Dentistry; Endodontics; Root Canal Preparation; Instrumentation

  12. Comparison of Apical Extrusion of Debris by Using Single-File, Full-Sequence Rotary and Reciprocating Systems.

    Science.gov (United States)

    Ehsani, Maryam; Farhang, Robab; Harandi, Azadeh; Tavanafar, Saeid; Raoof, Maryam; Galledar, Saeedeh

    2016-11-01

    During root canal preparation, apical extrusion of debris can cause inflammation, flare-ups, and delayed healing. Therefore, instrumentation techniques that cause the least extrusion of debris are desirable. This study aimed to compare apical extrusion of debris by five single-file, full-sequence rotary and reciprocating systems. One hundred twenty human mandibular premolars with similar root lengths, apical diameters, and canal curvatures were selected and randomly assigned to six groups (n=20): Reciproc R25 (25, 0.08), WaveOne Primary (25, 0.08), OneShape (25, 0.06), F360 (25, 0.04), Neoniti A1 (25, 0.08), and ProTaper Universal. Instrumentation of the root canals was performed in accordance with the manufacturers' instructions. Each tooth's debris was collected in a pre-weighed vial. After drying the debris in an incubator, the mass was measured three times consecutively; the mean was then calculated. The preparation time by each system was also measured. For data analysis, one-way ANOVA and Games-Howell post hoc test were used. The mean masses (±standard deviation) of the apical debris were as follows: 2.071±1.38mg (ProTaper Universal), 1.702±1.306mg (Neoniti A1), 1.295±0.839mg (OneShape), 1.109±0.676mg (WaveOne), 0.976±0.478mg (Reciproc) and 0.797±0.531mg (F360). Compared to ProTaper Universal, F360 generated significantly less debris (P=0.02). The ProTaper system required the longest preparation time (mean=88.6 seconds); the Reciproc (P=0.008), OneShape (P=0.006), and F360 (P=0.001) required significantly less time (P<0.05). All instruments caused extrusion of debris through the apex. The F360 produced significantly less debris than did the ProTaper Universal.

  13. Comparison between autologous blood transfusion drainage and closed-suction drainage/no drainage in total knee arthroplasty: a meta-analysis.

    Science.gov (United States)

    Hong, Kun-Hao; Pan, Jian-Ke; Yang, Wei-Yi; Luo, Ming-Hui; Xu, Shu-Chai; Liu, Jun

    2016-08-01

    Autologous blood transfusion (ABT) drainage system is a new unwashed salvaged blood retransfusion system for total knee replacement (TKA). However, whether to use ABT drainage, closed-suction (CS) drainage or no drainage in TKA surgery remains controversial. This is the first meta-analysis to assess the clinical efficiency, safety and potential advantages regarding the use of ABT drains compared with closed-suction/no drainage. PubMed, Embase, and the Cochrane Library were comprehensively searched in March 2015. Fifteen randomized controlled trials (RCTs) were identified and pooled for statistical analysis. The primary outcome evaluated was homologous blood transfusion rate. The secondary outcomes were post-operative haemoglobin on days 3-5, length of hospital stay and wound infections after TKA surgery. The pooled data included 1,721 patients and showed that patients in the ABT drainage group might benefit from lower blood transfusion rates (16.59 % and 37.47 %, OR: 0.28 [0.14, 0.55]; 13.05 % and 16.91 %, OR: 0.73 [0.47,1.13], respectively). Autologous blood transfusion drainage and closed-suction drainage/no drainage have similar clinical efficacy and safety with regard to post-operative haemoglobin on days 3-5, length of hospital stay and wound infections. Autologous blood transfusion drainage offers a safe and efficient alternative to CS/no drainage with a lower blood transfusion rate. Future large-volume high-quality RCTs with extensive follow-up will affirm and update this system review.

  14. Value of Fat-Suppressed Proton-Density-Weighted Turbo Spin-Echo Sequences in Detecting Meniscal Lesions: Comparison with Arthroscopy

    International Nuclear Information System (INIS)

    Schaefer, F.K.W.; Schaefer, P.J.; Brossmann, J.; Frahm, C.; Hilgert, R.E.; Heller, M.; Jahnke, T.

    2006-01-01

    Purpose: To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging (MRI) compared to arthroscopy in the detection of meniscal lesions. Material and Methods: In a prospective study, 31 knee joints were imaged on a 1.5T MR scanner before arthroscopy using the following sequences: (a) coronal and sagittal FS-PDw TSE (TR/TE: 4009/15 ms); (b) coronal T1w SE (TR/TE: 722/20 ms), and sagittal PDw TSE (TR/TE: 3800/15 ms). Other imaging parameters were: slice thickness 3 mm, FOV 160 mm, matrix 256x256. A total of 186 meniscal regions (62 menisci; anterior horn, body, posterior horn) were evaluated. Standard of reference was arthroscopy. Sensitivity, specificity, negative predictive value (npv), positive predictive value (ppv), and accuracy were calculated. Results: Arthroscopically, meniscal lesions were detected in 55/186 segments (35 medial and 20 lateral meniscal lesions). Sensitivity, specificity, npv, ppv, and accuracy for combination of coronal and sagittal FS PDw TSE were 91.4%, 98.3%, 95%, 97%, and 93.5% for the medial meniscus, and 90%, 98.6%, 97.3%, 94.7%, and 96.8% for the lateral. The results were comparable to the combination of coronal T1w SE and sagittal PDw TSE for the medial (88.6%, 98.3%, 93.4%, 96.9%, 91.4%) and the lateral (90%, 95.9%, 97.2%, 85.7%, 92.5%) meniscus. Conclusion: FS PDw TSE-MR sequences are an excellent alternative for the detection of meniscal lesions in comparison with diagnostic arthroscopy

  15. Genome Sequence of Bivens Arm Virus, a Tibrovirus Belonging to the Species Tibrogargan virus (Mononegavirales: Rhabdoviridae).

    Science.gov (United States)

    Lauck, Michael; Yú, Shu Qìng; Caì, Yíngyún; Hensley, Lisa E; Chiu, Charles Y; O'Connor, David H; Kuhn, Jens H

    2015-03-19

    The new rhabdoviral genus Tibrovirus currently has two members, Coastal Plains virus and Tibrogargan virus. Here, we report the coding-complete genome sequence of a putative member of this genus, Bivens Arm virus. A genomic comparison reveals Bivens Arm virus to be closely related to, but distinct from, Tibrogargan virus. Copyright © 2015 Lauck et al.

  16. Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing.

    Science.gov (United States)

    Misyura, Maksym; Sukhai, Mahadeo A; Kulasignam, Vathany; Zhang, Tong; Kamel-Reid, Suzanne; Stockley, Tracy L

    2018-02-01

    A standard approach in test evaluation is to compare results of the assay in validation to results from previously validated methods. For quantitative molecular diagnostic assays, comparison of test values is often performed using simple linear regression and the coefficient of determination (R 2 ), using R 2 as the primary metric of assay agreement. However, the use of R 2 alone does not adequately quantify constant or proportional errors required for optimal test evaluation. More extensive statistical approaches, such as Bland-Altman and expanded interpretation of linear regression methods, can be used to more thoroughly compare data from quantitative molecular assays. We present the application of Bland-Altman and linear regression statistical methods to evaluate quantitative outputs from next-generation sequencing assays (NGS). NGS-derived data sets from assay validation experiments were used to demonstrate the utility of the statistical methods. Both Bland-Altman and linear regression were able to detect the presence and magnitude of constant and proportional error in quantitative values of NGS data. Deming linear regression was used in the context of assay comparison studies, while simple linear regression was used to analyse serial dilution data. Bland-Altman statistical approach was also adapted to quantify assay accuracy, including constant and proportional errors, and precision where theoretical and empirical values were known. The complementary application of the statistical methods described in this manuscript enables more extensive evaluation of performance characteristics of quantitative molecular assays, prior to implementation in the clinical molecular laboratory. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  17. Comparison and Efficacy of LigaSure and Rubber Band Ligature in Closing the Inflamed Cecal Stump in a Rat Model of Acute Appendicitis

    Directory of Open Access Journals (Sweden)

    Chun-Chieh Yeh

    2015-01-01

    Full Text Available Safety of either LigaSure or rubber band in closing inflamed appendiceal stump in acute appendicitis has been less investigated. In this study, cecal ligation followed by resecting inflamed cecum was performed to mimic appendectomy in a rat model of acute appendicitis. Rats were sacrificed immediately (Group A and 7 days (Group B after cecal resection, respectively. The cecal stumps were closed by silk ligature (S, 5 mm LigaSure (L, or rubber band (R. Seven days after cecal resection, the LigaSure (BL and silk subgroups (BS had significantly less intra-abdominal adhesion and better laparotomy wound healing than rubber band subgroup (BR. The initial bursting pressure at cecal stump was comparable among the three methods; along with tissue healing process, both BL and BS provided a higher bursting pressure than BR 7 days after appendectomy. BL subgroup had more abundant hydroxyproline deposition than BS and BR subgroup. Furthermore, serum TNF-α in BR group kept persistently increasing along with time after cecal resection. Thus, the finding that LigaSure but not rubber band is safe in sealing off the inflamed cecal stump in rat model of acute appendicitis suggests the possibility of applying LigaSure for appendectomy via single port procedure or natural orifice transluminal endoscopic surgery (NOTES.

  18. Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes

    Directory of Open Access Journals (Sweden)

    Yamada Mari

    2010-03-01

    Full Text Available Abstract Background Plant mitochondrial genomes are known for their complexity, and there is abundant evidence demonstrating that this organelle is important for plant sexual reproduction. Cytoplasmic male sterility (CMS is a phenomenon caused by incompatibility between the nucleus and mitochondria that has been discovered in various plant species. As the exact sequence of steps leading to CMS has not yet been revealed, efforts should be made to elucidate the factors underlying the mechanism of this important trait for crop breeding. Results Two CMS mitochondrial genomes, LD-CMS, derived from Oryza sativa L. ssp. indica (434,735 bp, and CW-CMS, derived from Oryza rufipogon Griff. (559,045 bp, were newly sequenced in this study. Compared to the previously sequenced Nipponbare (Oryza sativa L. ssp. japonica mitochondrial genome, the presence of 54 out of 56 protein-encoding genes (including pseudo-genes, 22 tRNA genes (including pseudo-tRNAs, and three rRNA genes was conserved. Two other genes were not present in the CW-CMS mitochondrial genome, and one of them was present as part of the newly identified chimeric ORF, CW-orf307. At least 12 genomic recombination events were predicted between the LD-CMS mitochondrial genome and Nipponbare, and 15 between the CW-CMS genome and Nipponbare, and novel genetic structures were formed by these genomic rearrangements in the two CMS lines. At least one of the genomic rearrangements was completely unique to each CMS line and not present in 69 rice cultivars or 9 accessions of O. rufipogon. Conclusion Our results demonstrate novel mitochondrial genomic rearrangements that are unique in CMS cytoplasm, and one of the genes that is unique in the CW mitochondrial genome, CW-orf307, appeared to be the candidate most likely responsible for the CW-CMS event. Genomic rearrangements were dynamic in the CMS lines in comparison with those of rice cultivars, suggesting that 'death' and possible 'birth' processes of the

  19. Comparison of traditional phenotypic identification methods with partial 5' 16S rRNA gene sequencing for species-level identification of nonfermenting Gram-negative bacilli.

    Science.gov (United States)

    Cloud, Joann L; Harmsen, Dag; Iwen, Peter C; Dunn, James J; Hall, Gerri; Lasala, Paul Rocco; Hoggan, Karen; Wilson, Deborah; Woods, Gail L; Mellmann, Alexander

    2010-04-01

    Correct identification of nonfermenting Gram-negative bacilli (NFB) is crucial for patient management. We compared phenotypic identifications of 96 clinical NFB isolates with identifications obtained by 5' 16S rRNA gene sequencing. Sequencing identified 88 isolates (91.7%) with >99% similarity to a sequence from the assigned species; 61.5% of sequencing results were concordant with phenotypic results, indicating the usability of sequencing to identify NFB.

  20. A comparison of linear speed, closed-skill agility, and open-skill agility qualities between backcourt and frontcourt adult semiprofessional male basketball players.

    Science.gov (United States)

    Scanlan, Aaron T; Tucker, Patrick S; Dalbo, Vincent J

    2014-05-01

    The measurement of fitness qualities relevant to playing position is necessary to inform basketball coaching and conditioning staff of role-related differences in playing groups. To date, sprinting and agility performance have not been compared between playing positions in adult male basketball players. Therefore, the purpose of this study was to describe and compare linear speed, closed-skill agility, and open-skill agility qualities between backcourt (point guard and shooting guard positions) and frontcourt (small forward, power forward, and center positions) semiprofessional basketball players. Six backcourt (mean ± SD: age, 24.3 ± 7.9 years; stature, 183.4 ± 4.0 cm; body mass, 85.5 ± 12.3 kg; VO2max, 51.9 ± 4.8 ml·kg(-1)·min(-1)) and 6 frontcourt (mean ± SD: age, 27.5 ± 5.5 years; stature, 194.4 ± 7.1 cm; body mass, 109.4 ± 8.8 kg; VO2max, 47.1 ± 5.0 ml·kg(-1)·min(-1)) adult male basketball players completed 20-m sprint, closed-skill agility, and open-skill agility performance tests. Magnitude-based inferences revealed that backcourt players (5 m, 1.048 ± 0.027 seconds; 10 m, 1.778 ± 0.048 seconds; 20 m, 3.075 ± 0.121 seconds) possessed likely quicker linear sprint times than frontcourt players (5 m, 1.095 ± 0.085 seconds; 10 m, 1.872 ± 0.127 seconds; 20 m, 3.242 ± 0.221 seconds). Conversely, frontcourt players (1.665 ± 0.096 seconds) held possible superior closed-skill agility performance than backcourt players (1.613 ± 0.111 seconds). In addition, unclear positional differences were apparent for open-skill agility qualities. These findings indicate that linear speed and change of direction speed might be differently developed across playing positions. Furthermore, position-related functions might similarly depend on the aspects of open-skill agility performance across backcourt and frontcourt players. Basketball coaching and conditioning staff should consider the development of position-targeted training drills to improve speed, agility

  1. Intra-individual comparison of CAIPIRINHA VIBE technique with conventional VIBE sequences in contrast-enhanced MRI of focal liver lesions

    Energy Technology Data Exchange (ETDEWEB)

    Albrecht, M.H., E-mail: MoritzAlbrecht@gmx.net [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Bodelle, B., E-mail: boris.bodelle@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Varga-Szemes, A., E-mail: vargaasz@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Dewes, P., E-mail: patricia.dewes@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Bucher, A.M., E-mail: andreas.bucher@kgu.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Ball, B.D., E-mail: BallBr@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); De Cecco, C.N., E-mail: dececco@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Schoepf, U.J., E-mail: schoepf@musc.edu [Medical University of South Carolina, Department of Radiology and Radiological Science, Charleston, SC (United States); Zhu, X., E-mail: zhuxun@shzu.edu.cn [Shihezi University, Department of Psychology, Beisi Road, Xinjiang (China); Zangos, S., E-mail: Zangos@em.uni-frankfurt.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Gruber-Rouh, T., E-mail: tatjanagruber2004@yahoo.de [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); Wichmann, J.L., E-mail: dochwichmann@gmail.com [University Hospital Frankfurt, Department of Diagnostic and Interventional Radiology, Frankfurt (Germany); and others

    2017-01-15

    Purpose: To evaluate the impact of controlled aliasing in parallel imaging results in higher acceleration (CAIPIRINHA) volume interpolated breath-hold examination (VIBE) magnetic resonance imaging (MRI) technique on image quality, reader confidence, and inter-observer agreement for the assessment of focal liver lesions in comparison with the standard VIBE approach. Material and methods: In this IRB-approved intra-individual comparison study, abdominal arterial and portal-venous contrast-enhanced MRI studies were retrospectively analyzed in 38 patients with malignant liver lesions. Each patient underwent both CAIPIRINHA and conventional VIBE 3 T MRI within 3 months, showing stable disease. Images were evaluated using 5-point rating scales by two blinded radiologists with more than 20 and 5 years of experience in MRI, respectively. Readers scored dignity of liver lesions and assessed which liver segments were affected by malignancy (ranging from 1 = definitely benign/not affected to 5 = definitely malignant/affected by malignancy). Readers also rated overall image quality, sharpness of intrahepatic veins, and diagnostic confidence (ranging from 1 = poor to 5 = excellent). Results: Reviewers achieved a higher inter-observer reliability using CAIPIRINHA when they reported which liver segments were affected by malignancy compared to traditional VIBE series (κ = 0.62 and 0.54, respectively, p < 0.05). Similarly, CAIPIRINHA showed a slightly higher inter-rater agreement for the dignity of focal liver lesions versus the standard VIBE images (κ = 0.50 and 0.49, respectively, p < 0.05). CAIPIRINHA series also scored higher in comparison to standard VIBE sequences (mean scores: image quality, 4.2 and 3.5; sharpness of intrahepatic vessels, 3.8 and 3.2, respectively, p < 0.05) for both reviewers and allowed for higher subjective diagnostic confidence (ratings, 3.8 and 3.2, respectively, p < 0.05). Conclusion: Compared to the standard VIBE approach, CAIPIRINHA VIBE technique

  2. Comparison of the live attenuated yellow fever vaccine 17D-204 strain to its virulent parental strain Asibi by deep sequencing.

    Science.gov (United States)

    Beck, Andrew; Tesh, Robert B; Wood, Thomas G; Widen, Steven G; Ryman, Kate D; Barrett, Alan D T

    2014-02-01

    The first comparison of a live RNA viral vaccine strain to its wild-type parental strain by deep sequencing is presented using as a model the yellow fever virus (YFV) live vaccine strain 17D-204 and its wild-type parental strain, Asibi. The YFV 17D-204 vaccine genome was compared to that of the parental strain Asibi by massively parallel methods. Variability was compared on multiple scales of the viral genomes. A modeled exploration of small-frequency variants was performed to reconstruct plausible regions of mutational plasticity. Overt quasispecies diversity is a feature of the parental strain, whereas the live vaccine strain lacks diversity according to multiple independent measurements. A lack of attenuating mutations in the Asibi population relative to that of 17D-204 was observed, demonstrating that the vaccine strain was derived by discrete mutation of Asibi and not by selection of genomes in the wild-type population. Relative quasispecies structure is a plausible correlate of attenuation for live viral vaccines. Analyses such as these of attenuated viruses improve our understanding of the molecular basis of vaccine attenuation and provide critical information on the stability of live vaccines and the risk of reversion to virulence.

  3. Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

    Science.gov (United States)

    Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

    2014-01-01

    Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

  4. Detection of hepatitis A virus by the nucleic acid sequence-based amplification technique and comparison with reverse transcription-PCR.

    Science.gov (United States)

    Jean, J; Blais, B; Darveau, A; Fliss, I

    2001-12-01

    A nucleic acid sequence-based amplification (NASBA) technique for the detection of hepatitis A virus (HAV) in foods was developed and compared to the traditional reverse transcription (RT)-PCR technique. Oligonucleotide primers targeting the VP1 and VP2 genes encoding the major HAV capsid proteins were used for the amplification of viral RNA in an isothermal process resulting in the accumulation of RNA amplicons. Amplicons were detected by hybridization with a digoxigenin-labeled oligonucleotide probe in a dot blot assay format. Using the NASBA, as little as 0.4 ng of target RNA/ml was detected per comparison to 4 ng/ml for RT-PCR. When crude HAV viral lysate was used, a detection limit of 2 PFU (4 x 10(2) PFU/ml) was obtained with NASBA, compared to 50 PFU (1 x 10(4) PFU/ml) obtained with RT-PCR. No interference was encountered in the amplification of HAV RNA in the presence of excess nontarget RNA or DNA. The NASBA system successfully detected HAV recovered from experimentally inoculated samples of waste water, lettuce, and blueberries. Compared to RT-PCR and other amplification techniques, the NASBA system offers several advantages in terms of sensitivity, rapidity, and simplicity. This technique should be readily adaptable for detection of other RNA viruses in both foods and clinical samples.

  5. Studies of CdS/CdTe interface: Comparison of CdS films deposited by close space sublimation and chemical bath deposition techniques

    Energy Technology Data Exchange (ETDEWEB)

    Han, Jun-feng, E-mail: pkuhjf@bit.edu.cn [Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3 (France); Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Fu, Gan-hua; Krishnakumar, V.; Schimper, Hermann-Josef [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Liao, Cheng [Department of Physics, Peking University, Beijing 100871 (China); Jaegermann, Wolfram [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Besland, M.P. [Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3 (France)

    2015-05-01

    The CdS layers were deposited by two different methods, close space sublimation (CSS) and chemical bath deposition (CBD) technique. The CdS/CdTe interface properties were investigated by transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS). The TEM images showed a large CSS-CdS grain size in the range of 70-80 nm. The interface between CSS-CdS and CdTe were clear and sharp, indicating an abrupt hetero-junction. On the other hand, CBD-CdS layer had much smaller grain size in the 5-10 nm range. The interface between CBD-CdS and CdTe was not as clear as CSS-CdS. With the stepwise coverage of CdTe layer, the XPS core levels of Cd 3d and S 2p in CSS-CdS had a sudden shift to lower binding energies, while those core levels shifted gradually in CBD-CdS. In addition, XPS depth profile analyses indicated a strong diffusion in the interface between CBD-CdS and CdTe. The solar cells prepared using CSS-CdS yielded better device performance than the CBD-CdS layer. The relationships between the solar cell performances and properties of CdS/CdTe interfaces were discussed. - Highlights: • Studies of CdS deposited by close space sublimation and chemical bath deposition • An observation of CdS/CdTe interface by transmission electron microscope • A careful investigation of CdS/CdTe interface by X ray photoelectron spectra • An easier diffusion at the chemical bath deposition CdS and CdTe interface.

  6. Transauricular embolization of the rabbit coronary artery for experimental myocardial infarction: comparison of a minimally invasive closed-chest model with open-chest surgery

    Directory of Open Access Journals (Sweden)

    Katsanos Konstantinos

    2012-02-01

    Full Text Available Abstract Introduction To date, most animal studies of myocardial ischemia have used open-chest models with direct surgical coronary artery ligation. We aimed to develop a novel, percutaneous, minimally-invasive, closed-chest model of experimental myocardial infarction (EMI in the New Zealand White rabbit and compare it with the standard open-chest surgical model in order to minimize local and systemic side-effects of major surgery. Methods New Zealand White rabbits were handled in conformity with the "Guide for the Care and Use of Laboratory Animals" and underwent EMI under intravenous anesthesia. Group A underwent EMI with an open-chest method involving surgical tracheostomy, a mini median sternotomy incision and left anterior descending (LAD coronary artery ligation with a plain suture, whereas Group B underwent EMI with a closed-chest method involving fluoroscopy-guided percutaneous transauricular intra-arterial access, superselective LAD catheterization and distal coronary embolization with a micro-coil. Electrocardiography (ECG, cardiac enzymes and transcatheter left ventricular end-diastolic pressure (LVEDP measurements were recorded. Surviving animals were euthanized after 4 weeks and the hearts were harvested for Hematoxylin-eosin and Masson-trichrome staining. Results In total, 38 subjects underwent EMI with a surgical (n = 17 or endovascular (n = 21 approach. ST-segment elevation (1.90 ± 0.71 mm occurred sharply after surgical LAD ligation compared to progressive ST elevation (2.01 ± 0.84 mm;p = 0.68 within 15-20 min after LAD micro-coil embolization. Increase of troponin and other cardiac enzymes, abnormal ischemic Q waves and LVEDP changes were recorded in both groups without any significant differences (p > 0.05. Infarct area was similar in both models (0.86 ± 0.35 cm in the surgical group vs. 0.92 ± 0.54 cm in the percutaneous group;p = 0.68. Conclusion The proposed model of transauricular coronary coil embolization avoids

  7. Modification of the cranial closing wedge ostectomy technique for the treatment of canine cruciate disease. Description and comparison with standard technique.

    Science.gov (United States)

    Wallace, A M; Addison, E S; Smith, B A; Radke, H; Hobbs, S J

    2011-01-01

    To describe a modification of the cranial closing wedge ostectomy (CCWO) technique and to compare its efficacy to the standard technique on cadaveric specimens. The standard and modified CCWO technique were applied to eight pairs of cadaveric tibiae. The following parameters were compared following the ostectomy: degrees of plateau levelling achieved (degrees), tibial long axis shift (degrees), reduction in tibial length (mm), area of bone wedge removed (cm²), and the area of proximal fragment (cm²). The size of the removed wedge of bone and the reduction in tibial length were significantly less with the modified CCWO technique. The modified CCWO has two main advantages. Firstly a smaller wedge is removed, allowing a greater preservation of bone stock in the proximal tibia, which is advantageous for implant placement. Secondly, the tibia is shortened to a lesser degree, which might reduce the risk of recurvatum, fibular fracture and patella desmitis. These factors are particularly propitious for the application of this technique to Terrier breeds with excessive tibial plateau angle, where large angular corrections are required. The modified CCWO is equally effective for plateau levelling and results in an equivalent tibial long-axis shift. A disadvantage with the modified technique is that not all of the cross sectional area of the distal fragment contributes to load sharing at the osteotomy.

  8. Comparison of net CO2 fluxes measured with open- and closed-path infrared gas analyzers in an urban complex environment

    DEFF Research Database (Denmark)

    Järvi, L.; Mammarella, I.; Eugster, W.

    2009-01-01

    and their suitability to accurately measure CO2 exchange in such non-ideal landscape. In addition, this study examined the effect of open-path sensor heating on measured fluxes in urban terrain, and these results were compared with similar measurements made above a temperate beech forest in Denmark. The correlation...... between the two fluxes was good (R2 = 0.93) at the urban site, but during the measurement period the open-path net surface exchange (NSE) was 17% smaller than the closed-path NSE, indicating apparent additional uptake of CO2 by open-path measurements. At both sites, sensor heating corrections evidently...... improved the performance of the open-path analyzer by reducing discrepancies in NSE at the urban site to 2% and decreasing the difference in NSE from 67% to 7% at the forest site. Overall, the site-specific approach gave the best results at both sites and, if possible, it should be preferred in the sensor...

  9. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  10. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    Energy Technology Data Exchange (ETDEWEB)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C. [Medical University of Innsbruck, Department of Radiology, Innsbruck (Austria); Zoller, H. [Medical University of Innsbruck, Department of Internal Medicine, Innsbruck (Austria); Kannengiesser, S. [Siemens AG, Healthcare Sector, MR Applications Development, Erlangen (Germany); Zhong, X. [Siemens Healthcare, MR R and D Collaborations, Atlanta, GA (United States); Reiter, G. [Siemens AG, Healthcare Sector, MR R and D Collaborations, Graz (Austria)

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  11. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    International Nuclear Information System (INIS)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C.; Zoller, H.; Kannengiesser, S.; Zhong, X.; Reiter, G.

    2015-01-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  12. Transformation of topologically close-packed β-W to body-centered cubic α-W: Comparison of experiments and computations.

    Science.gov (United States)

    Barmak, Katayun; Liu, Jiaxing; Harlan, Liam; Xiao, Penghao; Duncan, Juliana; Henkelman, Graeme

    2017-10-21

    The enthalpy and activation energy for the transformation of the metastable form of tungsten, β-W, which has the topologically close-packed A15 structure (space group Pm3¯n), to equilibrium α-W, which is body-centered cubic (A2, space group Im3¯m), was measured using differential scanning calorimetry. The β-W films were 1 μm-thick and were prepared by sputter deposition in argon with a small amount of nitrogen. The transformation enthalpy was measured as -8.3 ± 0.4 kJ/mol (-86 ± 4 meV/atom) and the transformation activation energy as 2.2 ± 0.1 eV. The measured enthalpy was found to agree well with the difference in energies of α and β tungsten computed using density functional theory, which gave a value of -82 meV/atom for the transformation enthalpy. A calculated concerted transformation mechanism with a barrier of 0.4 eV/atom, in which all the atoms in an A15 unit cell transform into A2, was found to be inconsistent with the experimentally measured activation energy for any critical nucleus larger than two A2 unit cells. Larger calculations of eight A15 unit cells spontaneously relax to a mechanism in which part of the supercell first transforms from A15 to A2, creating a phase boundary, before the remaining A15 transforms into the A2 phase. Both calculations indicate that a nucleation and growth mechanism is favored over a concerted transformation. More consistent with the experimental activation energy was that of a calculated local transformation mechanism at the A15-A2 phase boundary, computed as 1.7 eV using molecular dynamics simulations. This calculated phase transformation mechanism involves collective rearrangements of W atoms in the disordered interface separating the A15 and A2 phases.

  13. Comparison of Reef Fish Survey Data Gathered by Open and Closed Circuit SCUBA Divers Reveals Differences in Areas With Higher Fishing Pressure.

    Directory of Open Access Journals (Sweden)

    Andrew E Gray

    Full Text Available Visual survey by divers using open-circuit (OC SCUBA is the most widely used approach to survey coral reef fishes. Therefore, it is important to quantify sources of bias in OC surveys, such as the possibility that avoidance of OC divers by fishes can lead to undercounting in areas where targeted species have come to associate divers with a risk of being speared. One potential way to reduce diver avoidance is to utilize closed circuit rebreathers (CCRs, which do not produce the noise and bubbles that are a major source of disturbance associated with OC diving. For this study, we conducted 66 paired OC and CCR fish surveys in the Main Hawaiian Islands at locations with relatively high, moderate, and light fishing pressure. We found no significant differences in biomass estimates between OC and CCR surveys when data were pooled across all sites, however there were differences at the most heavily fished location, Oahu. There, biomass estimates from OC divers were significantly lower for several targeted fish groups, including surgeonfishes, targeted wrasses, and snappers, as well as for all targeted fishes combined, with mean OC biomass between 32 and 68% of mean CCR biomass. There were no clear differences between OC and CCR biomass estimates for these groups at sites with moderate or low fishing pressure, or at any location for other targeted fish groups, including groupers, parrotfishes, and goatfishes. Bias associated with avoidance of OC divers at heavily fished locations could be substantially reduced, or at least calibrated for, by utilization of CCR. In addition to being affected by fishing pressure, the extent to which avoidance of OC divers is problematic for visual surveys varies greatly among taxa, and is likely to be highly influenced by the survey methodology and dimensions used.

  14. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  15. Closing the gender leadership gap: a multi-centre cross-country comparison of women in management and leadership in academic health centres in the European Union.

    Science.gov (United States)

    Kuhlmann, Ellen; Ovseiko, Pavel V; Kurmeyer, Christine; Gutiérrez-Lobos, Karin; Steinböck, Sandra; von Knorring, Mia; Buchan, Alastair M; Brommels, Mats

    2017-01-06

    Women's participation in medicine and the need for gender equality in healthcare are increasingly recognised, yet little attention is paid to leadership and management positions in large publicly funded academic health centres. This study illustrates such a need, taking the case of four large European centres: Charité - Universitätsmedizin Berlin (Germany), Karolinska Institutet (Sweden), Medizinische Universität Wien (Austria), and Oxford Academic Health Science Centre (United Kingdom). The percentage of female medical students and doctors in all four countries is now well within the 40-60% gender balance zone. Women are less well represented among specialists and remain significantly under-represented among senior doctors and full professors. All four centres have made progress in closing the gender leadership gap on boards and other top-level decision-making bodies, but a gender leadership gap remains relevant. The level of achieved gender balance varies significantly between the centres and largely mirrors country-specific welfare state models, with more equal gender relations in Sweden than in the other countries. Notably, there are also similar trends across countries and centres: gender inequality is stronger within academic enterprises than within hospital enterprises and stronger in middle management than at the top level. These novel findings reveal fissures in the 'glass ceiling' effects at top-level management, while the barriers for women shift to middle-level management and remain strong in academic positions. The uneven shifts in the leadership gap are highly relevant and have policy implications. Setting gender balance objectives exclusively for top-level decision-making bodies may not effectively promote a wider goal of gender equality. Academic health centres should pay greater attention to gender equality as an issue of organisational performance and good leadership at all levels of management, with particular attention to academic enterprises

  16. Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.

    Directory of Open Access Journals (Sweden)

    Koen M Verstappen

    Full Text Available Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74 and non-pseudintermedius genomes (n = 138. Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt. One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54, and eight other staphylococcal species (n = 43. In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

  17. Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses.

    Science.gov (United States)

    Li, Jing; Zheng, Yi; Xu, Haiyan; Xi, Xiaoxia; Hou, Qiangchuan; Feng, Shuzhen; Wuri, Laga; Bian, Yanfei; Yu, Zhongjie; Kwok, Lai-Yu; Sun, Zhihong; Sun, Tiansong

    2017-01-09

    In Kazakhstan, traditional artisanal cheeses have a long history and are widely consumed. The unique characteristics of local artisanal cheeses are almost completely preserved. However, their microbial communities have rarely been reported. The current study firstly generated the Single Molecule, Real-Time (SMRT) sequencing bacterial diversity profiles of 6 traditional artisanal cheese samples of Kazakhstan origin, followed by comparatively analyzed the microbiota composition between the current dataset and those from cheeses originated from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy. Across the Kazakhstan cheese samples, a total of 238 bacterial species belonging to 14 phyla and 140 genera were identified. Lactococcus lactis (28.93%), Lactobacillus helveticus (26.43%), Streptococcus thermophilus (12.18%) and Lactobacillus delbrueckii (12.15%) were the dominant bacterial species for these samples. To further evaluate the cheese bacterial diversity of Kazakhstan cheeses in comparison with those from other geographic origins, 16S rRNA datasets of 36 artisanal cheeses from Belgium, Russian Republic of Kalmykia (Kalmykia) and Italy were retrieved from public databases. The cheese bacterial microbiota communities were largely different across sample origins. By principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA), the structure of the Kazakhstan artisanal cheese samples was found to be different from those of the other geographic origins. Furthermore, the redundancy analysis (RDA) identified 16 bacterial OTUs as the key variables responsible for such microbiota structural difference. Our results together suggest that the diversity of bacterial communities in different groups is stratified by geographic region. This study does not only provide novel information on the bacterial microbiota of traditional artisanal cheese of Kazakhstan at species level, but also interesting insights into the bacterial diversity of artisanal

  18. Harnessing Whole Genome Sequencing in Medical Mycology.

    Science.gov (United States)

    Cuomo, Christina A

    2017-01-01

    Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

  19. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C

    2006-07-01

    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  20. Whole-body magnetic resonance imaging for staging and follow-up of pediatric patients with Hodgkin's lymphoma: comparison of different sequences

    International Nuclear Information System (INIS)

    Nava, Daniel; Oliveira, Heverton Cesar de

    2011-01-01

    Objective: to compare the performance of the T1, T2, STIR and DWIBS (diffusion-weighted whole-body imaging with background body signal suppression) sequences in the staging and follow-up of pediatric patients with Hodgkin's lymphoma in lymph node chains, parenchymal organs and bone marrow, and to evaluate interobserver agreement. Materials and methods: the authors studied 12 patients with confirmed diagnosis of Hodgkin's lymphoma. The patients were referred for whole body magnetic resonance imaging with T1-weighted, T2-weighted, STIR and DWIBS sequences. Results: the number of lymph node sites characterized as affected by the disease on T1- and T2-weighted sequences showed similar results (8 sites for both sequences), but lower than DWIBS and STIR sequences (11 and 12 sites, respectively). The bone marrow involvement by lymphoma showed the same values for the T1-, T2-weighted and DWIBS sequences (17 lesions), higher than the value found on STIR (13 lesions). A high rate of interobserver agreement was observed as the four sequences were analyzed. Conclusion: STIR and DWIBS sequences detected the highest number of lymph node sites characterized as affected by the disease. Similar results were demonstrated by all the sequences in the evaluation of parenchymal organs and bone marrow. A high interobserver agreement was observed as the four sequences were analyzed. (author)

  1. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2-relaxometry and chemical shift-based sequences.

    Science.gov (United States)

    Henninger, B; Zoller, H; Rauch, S; Schocke, M; Kannengiesser, S; Zhong, X; Reiter, G; Jaschke, W; Kremser, C

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm ("screening" sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. • MRI plays a major role in the clarification of diffuse liver disease. • The screening sequence was introduced for the assessment of diffuse liver disease. • It is a fast and automated algorithm for the evaluation of hepatic iron and fat. • It is capable of estimating the amount of hepatic fat and iron.

  2. Classification of domains of closed operators

    International Nuclear Information System (INIS)

    Lassner, G.; Timmermann, W.

    1975-01-01

    The structure of domains of determining closed operators in the Hilbert space by means of sequence spaces is investigated. The final classification provides three classes of these domains. Necessary and sufficient conditions of equivalence of these domains are obtained in the form of equivalency of corresponding sequences of natural numbers. Connection with the perturbation theory is mentioned [ru

  3. Whole-genome in-silico subtractive hybridization (WISH - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Parrinello Hugues

    2010-06-01

    Full Text Available Abstract Background Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison. We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni. Results Genomic DNA was extracted from male and female (heterogametic S. mansoni adults and sequenced with a Genome Analyzer (Illumina. Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome. The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome. Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite. Conclusion Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex. It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars or even closely related species.

  4. The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea.

    Science.gov (United States)

    Zhao, Fumei; Lim, Seungmo; Yoo, Ran Hee; Igori, Davaajargal; Kim, Sang-Min; Kwak, Do Yeon; Kim, Sun Lim; Lee, Bong Choon; Moon, Jae Sun

    2016-07-01

    The complete nucleotide sequence of a new barley polerovirus, tentatively named barley virus G (BVG), which was isolated in Gimje, South Korea, has been determined using an RNA sequencing technique combined with polymerase chain reaction methods. The viral genomic RNA of BVG is 5,620 nucleotides long and contains six typical open reading frames commonly observed in other poleroviruses. Sequence comparisons revealed that BVG is most closely related to maize yellow dwarf virus-RMV, with the highest amino acid identities being less than 90 % for all of the corresponding proteins. These results suggested that BVG is a member of a new species in the genus Polerovirus.

  5. MRI of the wrist: Comparison of high resolution pulse sequences and different fat-suppression techniques; Magnetresonanztomographie des Handgelenks - Vergleich hochaufloesender Pulssequenzen und unterschiedlicher Fettsignalunterdrueckungen an Leichenpraeparaten

    Energy Technology Data Exchange (ETDEWEB)

    Staebler, A.; Spieker, A.; Bonel, H.; Glaser, C.; Reiser, M. [Klinikum Grosshadern, Muenchen (Germany). Inst. fuer Radiologische Diagnostik; Schrank, C.; Putz, R. [Muenchen Univ. (Germany). Anatomische Anstalt; Petsch, R. [Siemens AG, Erlangen (Germany). Unternehmensbereich Medizinische Technik

    2000-02-01

    Purpose: To evaluate high resolution sequences with and without fat-suppression techniques for MR imaging of the wrist. Results: The highest homogeneity and the least artifacts were achieved by the T{sub 1}-w SE sequence. For the STIR and PD-FS TSE sequence high rankings were found for the detection of free water. The PD FS sequence had high ranking also for visualization of the SL ligament and the triangular fibrocartilage. The best sequence for the assessment of hyaline cartilage was the FLASH-FS sequence. For detailed analysis of bony structures the CISS sequence performed best. Conclusion: The isolated use of a PD-FS-TSE sequence enables for evaluation of all clinically relevant structures at the wrist. Dedicated questions for hyaline cartilage are answered best by the use of a FLASH 3D-FS sequence. Selective water excitation reduces acquisition time to 60%, nevertheless FS sequences are still diagnostically superior to WE sequences. (orig./AJ) [German] Ziel: Beurteilung der Wertigkeit hochaufloesender MRT-Sequenzen ohne und mit Fettsignalunterdrueckung (FS) und selektiver Wasseranregung (WE) fuer Untersuchungen des Handgelenkes. Ergebnisse: SE-T{sub 1} zeigte die hoechste Signalhomogenitaet bei geringsten Artefakten. Die STIR und PD FS-Sequenz stellten Signal von freiem Wasser am besten dar. Die beste Knorpeldarstellung erreicht die FLASH 3D-FS-Sequenz. Die Kortikalis und die Spongiosa konnten am besten mit der CISS-Sequenz beurteilt werden. Die FS-Sequenzen waren den WE-Sequenzen diagnostisch ueberlegen. Schlussfolgerungen: Mit der PD FS TSE-Sequenz mit verlaengerter Echozeit ist eine gute Beurteilung aller klinisch wichtigen Strukturen moeglich. Die beste Darstellung des hyalinen Knorpels wird mit der FLASH-3D-FS-, des Knochens mit der CISS-Sequenz erreicht. Die selektive Wasseranregung bei FLASH- und DESS-Sequenzen reduziert die Aufnahmezeit, ohne die diagnostische Aussagekraft der FS-Sequenzen zu erreichen. (orig./AJ)

  6. Three-dimensional isotropic T2-weighted cervical MRI at 3 T: Comparison with two-dimensional T2-weighted sequences

    International Nuclear Information System (INIS)

    Kwon, J.W.; Yoon, Y.C.; Choi, S.-H.

    2012-01-01

    Aim: To compare three-dimensional (3D) isotropic T2-weighted magnetic resonance imaging (MRI) sequences and reformation with two-dimensional (2D) T2-weighted sequences regarding image quality of the cervical spine at 3 T. Materials and methods: A phantom study was performed using a water-filled cylinder. The signal-to-noise and image homogeneity were evaluated. Fourteen (n = 14) volunteers were examined at 3 T using 3D isotropic T2-weighted sagittal and conventional 2D T2-weighted sagittal, axial, and oblique sagittal MRI. Multiplanar reformation (MPR) of the 3D T2-weighted sagittal dataset was performed simultaneously with image evaluation. In addition to artefact assessment, the visibility of anatomical structures in the 3D and 2D sequences was qualitatively assessed by two radiologists independently. Cohen’s kappa and Wilcoxon signed rank test were used for the statistical analysis. Result: The 3D isotropic T2-weighted sequence resulted in the highest signal-to-noise ratio (SNR) and lowest non-uniformity (NU) among the sequences in the phantom study. Quantitative evaluation revealed lower NU values of the cerebrospinal fluid (CSF) and muscles in 2D T2-weighted sagittal sequences compared to the 3D volume isotropic turbo spin-echo acquisition (VISTA) sequence. The other NU values revealed no statistically significant difference between the 2D turbo spin-echo (TSE) and 3D VISTA sequences (0.059 < p < 0.959). 3D VISTA images showed significantly fewer CSF flow artefacts (p < 0.001) and better delineated intradural nerve rootlets (p = 0.001) and neural foramina (p = 0.016) compared to 2D sequences. Conclusion: A 3D T2 weighted sequence is superior to conventional 2D sequences for the delineation of intradural nerve rootlets and neural foramina and is less affected by CSF flow artefacts.

  7. Metal artefact suppression at 3 T MRI: comparison of MAVRIC-SL with conventional fast spin echo sequences in patients with Hip joint arthroplasty

    International Nuclear Information System (INIS)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M.; Koch, Kevin M.

    2015-01-01

    The aim of our study was to evaluate the clinical feasibility and diagnostic value of a new MRI metal artefact reduction pulse sequence called MAVRIC-SL in a 3 T MRI environment. Two MAVRIC-SL sequences obtained in 61 patients with symptomatic total hip replacement were compared with standard FSE-STIR sequences optimized for imaging around metal. Artefact size was measured on the slice of greatest extent. Image quality, fat saturation, image distortion, visibility of anatomical structures, and detectability of joint abnormalities were visually assessed and graded on qualitative scales. Differences between MAVRIC-SL and FSE sequences were tested with the Wilcoxon signed-rank test. MAVRIC-SL sequences at 3 T showed significantly smaller metal artefacts compared to FSE-STIR sequences (p < 0.0001). The general image quality of MAVRIC-SL sequences was reduced with regard to spatial resolution, noise and contrast (p = 0.001), and fat saturation (p < 0.0001). The reduction of artefact size and image distortion significantly improved visualization of joint anatomy (p < 0.0001) and diagnostic confidence regarding implant-associated abnormalities (p = 0.0075 to <0.0001). Although the image quality of MAVRIC-SL sequences is limited at 3 T, its clinical application is feasible and provides important additional diagnostic information for the workup of patients with symptomatic hip replacement through substantially reduced metal artefacts. (orig.)

  8. Metal artefact suppression at 3 T MRI: comparison of MAVRIC-SL with conventional fast spin echo sequences in patients with Hip joint arthroplasty

    Energy Technology Data Exchange (ETDEWEB)

    Kretzschmar, Martin; Nardo, Lorenzo; Han, Misung M.; Heilmeier, Ursula; Sam, Craig; Joseph, Gabby B.; Krug, Roland; Link, Thomas M. [University of California San Francisco, Musculoskeletal Quantitative Imaging Research Group, Department of Radiology and Biomedical Imaging, San Francisco, CA (United States); Koch, Kevin M. [Medical Collage of Wisconsin, Departments of Biophysics and Radiology, Milwaukee, WI (United States)

    2015-08-15

    The aim of our study was to evaluate the clinical feasibility and diagnostic value of a new MRI metal artefact reduction pulse sequence called MAVRIC-SL in a 3 T MRI environment. Two MAVRIC-SL sequences obtained in 61 patients with symptomatic total hip replacement were compared with standard FSE-STIR sequences optimized for imaging around metal. Artefact size was measured on the slice of greatest extent. Image quality, fat saturation, image distortion, visibility of anatomical structures, and detectability of joint abnormalities were visually assessed and graded on qualitative scales. Differences between MAVRIC-SL and FSE sequences were tested with the Wilcoxon signed-rank test. MAVRIC-SL sequences at 3 T showed significantly smaller metal artefacts compared to FSE-STIR sequences (p < 0.0001). The general image quality of MAVRIC-SL sequences was reduced with regard to spatial resolution, noise and contrast (p = 0.001), and fat saturation (p < 0.0001). The reduction of artefact size and image distortion significantly improved visualization of joint anatomy (p < 0.0001) and diagnostic confidence regarding implant-associated abnormalities (p = 0.0075 to <0.0001). Although the image quality of MAVRIC-SL sequences is limited at 3 T, its clinical application is feasible and provides important additional diagnostic information for the workup of patients with symptomatic hip replacement through substantially reduced metal artefacts. (orig.)

  9. Detection of Subarachnoid Hemorrhage at Acute and Subacute/Chronic Stages: Comparison of Four Magnetic Resonance Imaging Pulse Sequences and Computed Tomography

    Directory of Open Access Journals (Sweden)

    Mei-Kang Yuan

    2005-03-01

    Conclusion: FLAIR and GE T2* MRI pulse sequences, and CT scans, are all statistically significant indicators of acute SAH. GE T2*-weighted images are statistically significant indicators of subacute-to-chronic SAH, whereas other MRI pulse sequences, and CT scans, are not.

  10. Comparison between two.magnetic resonance sequences (spin-echo and gradient-echo) in the analysis of lesions of the knee joint meniscus

    International Nuclear Information System (INIS)

    Marti-Bonati, L.; Casillas, C.

    1999-01-01

    To compare the diagnostic reliability, the proportion of common diagnoses and the degree of agreement between the results of two magnetic resonance (MR) sequences in the diagnosis of lesions of the meniscus of the knee. One hundred consecutive patients were studied prospectively by MR (1,5 Teslas). All of them underwent T1-weighted spin-echo and T1 and T2-weighted gradient-echo sequences. The final diagnosis was based on the combined results of four imaging sequences. The sensitivity, specificity, positive predictive value (PPV) and negative predictive (NPV) in terms of the final diagnosis were calculated for each meniscus and MR technique. The chi.squared test and kappa test were employed for the statistical analysis. There were discrepancies between the final diagnosis and the spin-echo sequence in 4 cases and between the final diagnosis and the gradient-echo sequences in 5 Both spin-echo and gradient-echo sequences showed the same diagnostic reliabilities: sensitivity of 0.98, specificity of 0.99, PPV of 0.98 and NPV of 0.99. The correlation between the two sequences was highly significant (chi-squared, p < 0.001) with a very high rate of agreement (kappa=0.84). The two sequences can be considered equally reliable in the study of meniscal lesions. (Author) 7 refs

  11. Comparison of Burrows-Wheeler transform-based mapping algorithms used in high-throughput whole-genome sequencing: application to Illumina data for livestock genomes

    Science.gov (United States)

    Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Eff...

  12. Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

    Science.gov (United States)

    Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

    2018-06-12

    This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

  13. Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

    Science.gov (United States)

    Budak, Hikmet; Kantar, Melda

    2015-07-01

    MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

  14. Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir.

    Science.gov (United States)

    Muangkram, Yuttamol; Amano, Akira; Wajjwalku, Worawidh; Pinyopummintr, Tanu; Thongtip, Nikorn; Kaolim, Nongnid; Sukmak, Manakorn; Kamolnorranath, Sumate; Siriaroonrat, Boripat; Tipkantha, Wanlaya; Maikaew, Umaporn; Thomas, Warisara; Polsrila, Kanda; Dongsaard, Kwanreaun; Sanannu, Saowaphang; Wattananorrasate, Anuwat

    2017-07-01

    The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.

  15. Comparison of the Diversity of Basidiomycetes from Dead Wood of the Manchurian fir (Abies holophylla) as Evaluated by Fruiting Body Collection, Mycelial Isolation, and 454 Sequencing.

    Science.gov (United States)

    Jang, Yeongseon; Jang, Seokyoon; Min, Mihee; Hong, Joo-Hyun; Lee, Hanbyul; Lee, Hwanhwi; Lim, Young Woon; Kim, Jae-Jin

    2015-10-01

    In this study, three different methods (fruiting body collection, mycelial isolation, and 454 sequencing) were implemented to determine the diversity of wood-inhabiting basidiomycetes from dead Manchurian fir (Abies holophylla). The three methods recovered similar species richness (26 species from fruiting bodies, 32 species from mycelia, and 32 species from 454 sequencing), but Fisher's alpha, Shannon-Wiener, Simpson's diversity indices of fungal communities indicated fruiting body collection and mycelial isolation displayed higher diversity compared with 454 sequencing. In total, 75 wood-inhabiting basidiomycetes were detected. The most frequently observed species were Heterobasidion orientale (fruiting body collection), Bjerkandera adusta (mycelial isolation), and Trichaptum fusco-violaceum (454 sequencing). Only two species, Hymenochaete yasudae and Hypochnicium karstenii, were detected by all three methods. This result indicated that Manchurian fir harbors a diverse basidiomycetous fungal community and for complete estimation of fungal diversity, multiple methods should be used. Further studies are required to understand their ecology in the context of forest ecosystems.

  16. Next-generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis.

    Science.gov (United States)

    Webb, Kristen M; Rosenthal, Benjamin M

    2011-01-01

    The mitochondrial genome's non-recombinant mode of inheritance and relatively rapid rate of evolution has promoted its use as a marker for studying the biogeographic history and evolutionary interrelationships among many metazoan species. A modest portion of the mitochondrial genome has been defined for 12 species and genotypes of parasites in the genus Trichinella, but its adequacy in representing the mitochondrial genome as a whole remains unclear, as the complete coding sequence has been characterized only for Trichinella spiralis. Here, we sought to comprehensively describe the extent and nature of divergence between the mitochondrial genomes of T. spiralis (which poses the most appreciable zoonotic risk owing to its capacity to establish persistent infections in domestic pigs) and Trichinella murrelli (which is the most prevalent species in North American wildlife hosts, but which poses relatively little risk to the safety of pork). Next generation sequencing methodologies and scaffold and de novo assembly strategies were employed. The entire protein-coding region was sequenced (13,917 bp), along with a portion of the highly repetitive non-coding region (1524 bp) of the mitochondrial genome of T. murrelli with a combined average read depth of 250 reads. The accuracy of base calling, estimated from coding region sequence was found to exceed 99.3%. Genome content and gene order was not found to be significantly different from that of T. spiralis. An overall inter-species sequence divergence of 9.5% was estimated. Significant variation was identified when the amount of variation between species at each gene is compared to the average amount of variation between species across the coding region. Next generation sequencing is a highly effective means to obtain previously unknown mitochondrial genome sequence. Particular to parasites, the extremely deep coverage achieved through this method allows for the detection of sequence heterogeneity between the multiple

  17. A Comparison of the Effects of Temporary Hippocampal Lesions on Single and Dual Context Versions of the Olfactory Sequence Memory Task

    OpenAIRE

    Sill, Orriana C.; Smith, David M.

    2012-01-01

    In recent years, many animal models of memory have focused on one or more of the various components of episodic memory. For example, the odor sequence memory task requires subjects to remember individual items and events (the odors) and the temporal aspects of the experience (the sequence of odor presentation). The well-known spatial context coding function of the hippocampus, as exemplified by place cell firing, may reflect the ‘where’ component of episodic memory. In the present study, we a...

  18. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae

    Directory of Open Access Journals (Sweden)

    Samuel E. Fox

    2013-03-01

    Full Text Available Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis, 104,950 (Spain, and 177,682 (Greece transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs and >20,000 simple sequence repeat (SSR DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.

  19. MRI evaluation of myometrial invasion by endometrial carcinoma. Comparison between fast-spin-echo T2W and coronal FMPSPGR Gadolinium-Dota-Enhanced Sequences

    International Nuclear Information System (INIS)

    Nasi, Francesca; Fiocchi, Federica; Pecchi, Annarita; Torricelli, Pietro; Rivasi, Francesco

    2005-01-01

    Purpose. The depth of myometrial invasion by endometrial carcinoma strongly affects the incidence of metastasis to regional nodes and influences the surgical strategies. The aim of this paper is to compare the results of FSE T2-w and Gadolinium-enhanced FMPSGR MR sequences in assessing the depth of myometrial invasion by endometrial cancer. Materials and methods. Forty-five women with histopathologically-proven endometrial carcinoma underwent preoperative MRI. Axial SE TI w, axial, sagittal and para-coronal FSE T2w and para-coronal Gadolinium enhanced FMPSGR sequences were performed using a high field strength magnet (1.5T). Within one month of MR all patients underwent hysterectomy, and anatomical evaluation of the surgical specimen was done sectioning the uterus along the short axis. Based upon the results of the histological evaluation the results of the FSE T2w and Gadolinium-enhanced sequences were compared and the statistical difference between the results obtained was statistically evaluated. Results. The histological evaluation showed intra mucosal neoplasm in 11 patients, myometrial infiltration less than 50% in 31 patients, myometrial infiltration more than 50% in 12 patients and transmural cancer 1 patient. Statistical evaluation showed that the FSE T2w sequence had a global sensitivity and specificity of 80.6% and 87.6%, respectively, with a mean Negative Predictive Value of 92.6% and a mean Positive Predictive Value of 86%. Gadolinium-enhanced FMPSPGR sequence had a global sensitivity and specificity of 90.6% and 93.3%, respectively, with a mean Negative Predictive Value of 96,3% and a mean Positive Predictive Value of 88%. The staging accuracy (χ 2 test) on FMPSPGR images (95%) was higher than that on FSE T2w images (78%). Conclusions. In our experience Gadolinium-enhanced dynamic sequences increase the accuracy of MR imaging in diagnosing the depth of myometrial invasion. In particular they improve the visualisation of the inner myometrium, the so

  20. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  1. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    International Nuclear Information System (INIS)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar

    2017-01-01

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol

  2. Qualitative and quantitative comparison of contrast-enhanced fluid-attenuated inversion recovery, magnetization transfer spin echo, and fat-saturation T1-weighted sequences in infectious meningitis

    Energy Technology Data Exchange (ETDEWEB)

    Azad, Rajiv; Tayal, Mohit; Azad, Sheenam; Sharma, Garima; Srivastava, Rajendra Kumar [SGRR Institute of Medical and Health Sciences, Patel Nagar, Dehradun (India)

    2017-11-15

    To compare the contrast-enhanced fluid-attenuated inversion recovery (CE-FLAIR), the CE T1-weighted (CE-T1W) sequence with fat suppression (FS) and magnetization transfer (MT) for early detection and characterization of infectious meningitis. Fifty patients and 10 control subjects were evaluated with the CE-FLAIR and the CE-T1W sequences with FS and MT. Qualitative assessment was done by two observers for presence and grading of abnormal leptomeningeal enhancement. Quantitative assessment included computation of net meningeal enhancement, using single pixel signal intensity software. A newly devised FLAIR based scoring system, based on certain imaging features including ventricular dilatation, ependymal enhancement, infarcts and subdural effusions was used to indicate the etiology. Data were analysed using the Student's t test, Cohen's Kappa coefficient, Pearson's correlation coefficient, the intraclass correlation coefficient, one way analysis of variance, and Fisher's exact test with Bonferroni correction as the post hoc test. The CE-FLAIR sequence demonstrated a better sensitivity (100%), diagnostic accuracy (95%), and a stronger correlation with the cerebrospinal fluid, total leukocyte count (r = 0.75), protein (r = 0.77), adenosine deaminase (r = 0.81) and blood glucose (r = -0.6) values compared to the CE-T1W sequences. Qualitative grades and quantitative meningeal enhancement on the CE-FLAIR sequence were also significantly greater than those on the other sequences. The FLAIR based scoring system yielded a diagnostic accuracy of 91.6% and a sensitivity of 96%. A strong inverse Pearson's correlation (r = -0.95) was found between the assigned score and patient's Glasgow Coma Scale at the time of admission. The CE-FLAIR sequence is better suited for evaluating infectious meningitis and could be included as a part of the routine MR imaging protocol.

  3. A comparison of parallel pyrosequencing and sanger clone-based sequencing and its impact on the characterization of the genetic diversity of HIV-1.

    Directory of Open Access Journals (Sweden)

    Binhua Liang

    Full Text Available BACKGROUND: Pyrosequencing technology has the potential to rapidly sequence HIV-1 viral quasispecies without requiring the traditional approach of cloning. In this study, we investigated the utility of ultra-deep pyrosequencing to characterize genetic diversity of the HIV-1 gag quasispecies and assessed the possible contribution of pyrosequencing technology in studying HIV-1 biology and evolution. METHODOLOGY/PRINCIPAL FINDINGS: HIV-1 gag gene was amplified from 96 patients using nested PCR. The PCR products were cloned and sequenced using capillary based Sanger fluorescent dideoxy termination sequencing. The same PCR products were also directly sequenced using the 454 pyrosequencing technology. The two sequencing methods were evaluated for their ability to characterize quasispecies variation, and to reveal sites under host immune pressure for their putative functional significance. A total of 14,034 variations were identified by 454 pyrosequencing versus 3,632 variations by Sanger clone-based (SCB sequencing. 11,050 of these variations were detected only by pyrosequencing. These undetected variations were located in the HIV-1 Gag region which is known to contain putative cytotoxic T lymphocyte (CTL and neutralizing antibody epitopes, and sites related to virus assembly and packaging. Analysis of the positively selected sites derived by the two sequencing methods identified several differences. All of them were located within the CTL epitope regions. CONCLUSIONS/SIGNIFICANCE: Ultra-deep pyrosequencing has proven to be a powerful tool for characterization of HIV-1 genetic diversity with enhanced sensitivity, efficiency, and accuracy. It also improved reliability of downstream evolutionary and functional analysis of HIV-1 quasispecies.

  4. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

    Science.gov (United States)

    Dobrijevic, Dragana; Abraham, Anne-Laure; Jamet, Alexandre; Maguin, Emmanuelle; van de Guchte, Maarten

    2016-01-01

    The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

  5. Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.

    Directory of Open Access Journals (Sweden)

    Dragana Dobrijevic

    Full Text Available The human GI tract is a complex and still poorly understood environment, inhabited by one of the densest microbial communities on earth. The gut microbiota is shaped by millennia of evolution to co-exist with the host in commensal or symbiotic relationships. Members of the gut microbiota perform specific molecular functions important in the human gut environment. This can be illustrated by the presence of a highly expanded repertoire of proteins involved in carbohydrate metabolism, in phase with the large diversity of polysaccharides originating from the diet or from the host itself that can be encountered in this environment. In order to identify other bacterial functions that are important in the human gut environment, we investigated the distribution of functional groups of proteins in a group of human gut bacteria and their close non-gut relatives. Complementary to earlier global comparisons between different ecosystems, this approach should allow a closer focus on a group of functions directly related to the gut environment while avoiding functions related to taxonomically divergent microbiota composition, which may or may not be relevant for gut homeostasis. We identified several functions that are overrepresented in the human gut bacteria which had not been recognized in a global approach. The observed under-representation of certain other functions may be equally important for gut homeostasis. Together, these analyses provide us with new information about this environment so critical to our health and well-being.

  6. A comparison of the effects of temporary hippocampal lesions on single and dual context versions of the olfactory sequence memory task.

    Science.gov (United States)

    Sill, Orriana C; Smith, David M

    2012-08-01

    In recent years, many animal models of memory have focused on one or more of the various components of episodic memory. For example, the odor sequence memory task requires subjects to remember individual items and events (the odors) and the temporal aspects of the experience (the sequence of odor presentation). The well-known spatial context coding function of the hippocampus, as exemplified by place cell firing, may reflect the "where" component of episodic memory. In the present study, we added a contextual component to the odor sequence memory task by training rats to choose the earlier odor in one context and the later odor in another context and we compared the effects of temporary hippocampal lesions on performance of the original single context task and the new dual context task. Temporary lesions significantly impaired the single context task, although performance remained significantly above chance levels. In contrast, performance dropped all the way to chance when temporary lesions were used in the dual context task. These results demonstrate that rats can learn a dual context version of the odor sequence learning task that requires the use of contextual information along with the requirement to remember the "what" and "when" components of the odor sequence. Moreover, the addition of the contextual component made the task fully dependent on the hippocampus.

  7. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects.

    Science.gov (United States)

    Hong, Mee Yeon; Lee, Eun Mee; Jo, Yong Hun; Park, Hae Chul; Kim, Seong Ryul; Hwang, Jae Sam; Jin, Byung Rae; Kang, Pil Don; Kim, Ki-Gyoung; Han, Yeon Soo; Kim, Iksoo

    2008-04-30

    The 15,360-bp long complete mitogenome of Caligula boisduvalii possesses a gene arrangement and content identical to other completely sequenced lepidopteran mitogenomes, but different from the common arrangement found in most insect order, as the result of the movement of tRNA(Met) to a position 5'-upstream of tRNA Ile. The 330-bp A+T-rich region is apparently capable of forming a stem-and-loop structure, which harbors the conserved flanking sequences at both ends. Dissimilar to what has been seen in other sequenced lepidopteran insects, the initiation codon for C. boisduvalii COI appears to be TTG, which is a rare, but apparently possible initiation codon. The ATP8, ATP6, ND4L, and ND6 genes, which neighbor another PCG at their 3' end, all harbored potential sequences for the formation of a hairpin structure. This is suggestive of the importance of such structures for the precise cleavage of the mRNA of mature PCGs. Phylogenetic analyses of available sequenced species of Bombycoidea, Pyraloidea, and Tortricidea supported the morphology-based current hypothesis that Bombycoidea and Pyraloidea are monophyletic (Obtectomera). As previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (Antheraea pernyi and C. boisduvalii) formed a reciprocal monophyletic group.

  8. Comparison of Muscle Onset Activation Sequences between a Golf or Tennis Swing and Common Training Exercises Using Surface Electromyography: A Pilot Study

    Directory of Open Access Journals (Sweden)

    John M. Vasudevan

    2016-01-01

    Full Text Available Aim. The purpose of this pilot study is to use surface electromyography to determine an individual athlete’s typical muscle onset activation sequence when performing a golf or tennis forward swing and to use the method to assess to what degree the sequence is reproduced with common conditioning exercises and a machine designed for this purpose. Methods. Data for 18 healthy male subjects were collected for 15 muscles of the trunk and lower extremities. Data were filtered and processed to determine the average onset of muscle activation for each motion. A Spearman correlation estimated congruence of activation order between the swing and each exercise. Correlations of each group were pooled with 95% confidence intervals using a random effects meta-analytic strategy. Results. The averaged sequences differed among each athlete tested, but pooled correlations demonstrated a positive association between each exercise and the participants’ natural muscle onset activation sequence. Conclusion. The selected training exercises and Turning Point™ device all partially reproduced our athletes’ averaged muscle onset activation sequences for both sports. The results support consideration of a larger, adequately powered study using this method to quantify to what degree each of the selected exercises is appropriate for use in both golf and tennis.

  9. Determination of vitality in myocardial infarction. Comparison of single- and multi-slice MRI techniques with TurboFlash and TrueFISP sequences

    International Nuclear Information System (INIS)

    Huber, A.; Schoenberg, S.O.; Spannagl, B.; Rieber, J.; Klauss, V.; Reiser, M.F.

    2004-01-01

    The aim of the study was to compare the diagnostic accuracy in imaging viability of the myocardium with a multislice inversions recovery 2D single shot TrueFISP sequence and an established inversion recovery TurboFlash sequence. Twelve patients with myocardial infarction were examined at a 1.5 tesla MR system (Sonata, Siemens, Medical Systems) 10 min after application of a single dose multihance (0,1 mmol/kg body weight) with a 2D multislice technique (inversion recovery single shot TrueFISP), that allows to image the entire short axis during one breathhold and a 2D single slice technique (inversion recovery TurboFlash), that requires one breathhold per slice. Signal intensity was determined in normal myocardium, in the infarcted myocardium and in the left ventricle. The contrast/noise ratio of normal and infarcted myocardium was determined. The areas of hyperintense infarction were compared for both sequence techniques. The multislice single shot 2D IR-TrueFisp sequence has a lower contrast/noise ratio than the IR-TurboFlash sequence (mean values 6.9 vs. 12.5) for viable and non viable myocardium. The assessment of the volume of the infarction is possible with excellent correlation of both techniques (r=0.97, p [de

  10. Added value of diffusion-weighted MRI in detection of cervical cancer recurrence: comparison with morphologic and dynamic contrast-enhanced MRI sequences.

    Science.gov (United States)

    Lucas, Rita; Lopes Dias, João; Cunha, Teresa Margarida

    2015-01-01

    We aimed to evaluate the added value of diffusion-weighted imaging (DWI) to standard magnetic resonance imaging (MRI) for detecting post-treatment cervical cancer recurrence. The detection accuracy of T2-weighted (T2W) images was compared with that of T2W MRI combined with either dynamic contrast-enhanced (DCE) MRI or DWI. Thirty-eight women with clinically suspected uterine cervical cancer recurrence more than six months after treatment completion were examined with 1.5 Tesla MRI including T2W, DCE, and DWI sequences. Disease was confirmed histologically and correlated with MRI findings. The diagnostic performance of T2W imaging and its combination with either DCE or DWI were analyzed. Sensitivity, positive predictive value, and accuracy were calculated. Thirty-six women had histologically proven recurrence. The accuracy for recurrence detection was 80% with T2W/DCE MRI and 92.1% with T2W/DWI. The addition of DCE sequences did not significantly improve the diagnostic ability of T2W imaging, and this sequence combination misclassified two patients as falsely positive and seven as falsely negative. The T2W/DWI combination revealed a positive predictive value of 100% and only three false negatives. The addition of DWI to T2W sequences considerably improved the diagnostic ability of MRI. Our results support the inclusion of DWI in the initial MRI protocol for the detection of cervical cancer recurrence, leaving DCE sequences as an option for uncertain cases.

  11. Comparison between quantitative nucleic acid sequence-based amplification, real-time reverse transcriptase PCR, and real-time PCR for quantification of Leishmania parasites

    NARCIS (Netherlands)

    van der Meide, Wendy; Guerra, Jorge; Schoone, Gerard; Farenhorst, Marit; Coelho, Leila; Faber, William; Peekel, Inge; Schallig, Henk

    2008-01-01

    DNA or RNA amplification methods for detection of Leishmania parasites have advantages regarding sensitivity and potential quantitative characteristics in comparison with conventional diagnostic methods but are often still not routinely applied. However, the use and application of molecular assays

  12. Detection of aneurysmal subarachnoid hemorrhage 3 months after initial bleeding: evaluation of T2* and FLAIR MR sequences at 3 T in comparison with initial non-enhanced CT as a gold standard.

    Science.gov (United States)

    Mulé, Sébastien; Soize, Sébastien; Benaissa, Azzedine; Portefaix, Christophe; Pierot, Laurent

    2016-08-01

    To investigate the ability of T2* and fluid-attenuated inversion recovery (FLAIR) MR sequences to detect hemosiderin deposition 3 months after aneurysmal subarachnoid hemorrhage (SAH) in comparison with early non-enhanced CT (NECT) as a gold standard. From September 2008 through May 2013, patients with aneurysmal SAH were included if a NECT less than 24 h after the onset of symptoms showed a SAH, and MRI, including T2* and FLAIR sequences, was performed 3 months later. All aneurysms were treated endovascularly. NECT and MR sequences were blindly analyzed for the presence of SAH (NECT) or hemosiderin deposition (MRI). When positive, details of the spatial distribution of SAH or hemosiderin deposits were noted. Sensitivities were calculated for each patient. Sensitivities, specificities, and positive predictive values (PPVs) were calculated for each location. Forty-nine patients (mean age 52.9 years) were included. Bleeding-related patterns were identified in 43 patients (87.8%) on T2* and 10 patients (20.4%) on FLAIR. T2* was highly predictive of the location of the initial hemorrhage, especially in the Sylvian cisterns (PPVs 95% and 100%) and the anterior interhemispheric fissure (PPV 90%). The T2* sequence can detect and localize a previous SAH a few months after aneurysmal bleeding. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  13. Molecular Cloning and Sequence Analysis of the Sta58 Major Antigen Gene of Rickettsia tsutsugamushi: Sequence homology and Antigenic Comparison of Sta58 to the 60-Kilodalton Family of Stress Proteins

    Science.gov (United States)

    1990-05-01

    encoding the animals have shown that both cellular and humoral immune Sta58 protein antigen in E. coli. DNA sequence analysis of a responses occur after...infection, with the cellular immune 2.9-kilobase (kb) HindIl fragment carrying the Sta58 gene response being required for protection (16, 19, 25, 42...The first evidence of a 60-kDa common HtpB antigen) reacted strongly with protein antigens in the antigen family (Hsp6O) among procaryotes was based

  14. Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation.

    Science.gov (United States)

    Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie; Kück, Ulrich

    2004-03-01

    One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.

  15. Openings and Closings in Telephone Conversations between Native Spanish Speakers.

    Science.gov (United States)

    Coronel-Molina, Serafin M.

    1998-01-01

    A study analyzed the opening and closing sequences of 11 dyads of native Spanish-speakers in natural telephone conversations conducted in Spanish. The objective was to determine how closely Hispanic cultural patterns of conduct for telephone conversations follow the sequences outlined in previous research. It is concluded that Spanish…

  16. Three monoclonal antibodies to the VHS virus glycoprotein: comparison of reactivity in relation to differences in immunoglobulin variable domain gene sequences

    DEFF Research Database (Denmark)

    Lorenzen, Niels; Cupit, P.M.; Secombes, C.J.

    2000-01-01

    and their neutralising activity was evident. Binding kinetic analyses by plasmon resonance identified differences in the dissociation rate constant (kd) as a possible explanation for the different reactivity levels of the MAbs. The Ig variable heavy (VH) and light (V kappa) domain gene sequences of the three hybridomas...... were compared. The inferred amino acid sequence of the two neutralising antibody VH domains differed by three amino acid residues (97% identity) and only one residue difference was evident in the Vk. domains. In contrast, IP1H3 shared only 38 and 39% identity with the 3F1A2 and 3F1H10 VH domains...... respectively and 49 and 50% identity with the 3F1A2 and 3F1H10 VK domains respectively. The neutralising antibodies were produced by hybridomas originating from the same fusion and the high nucleotide sequence homology of the variable Ig gene regions indicated that the plasma cell partners of the hybridomas...

  17. Comparison of a conventional cardiac-triggered dual spin-echo and a fast STIR sequence in detection of spinal cord lesions in multiple sclerosis

    International Nuclear Information System (INIS)

    Bot, J.C.J.; Barkhof, F.; Lycklama a Nijeholt, G.J.; Bergers, E.; Castelijns, J.A.; Polman, C.H.; Ader, H.J.

    2000-01-01

    The current optimal imaging protocol in spinal cord MR imaging in patients with multiple sclerosis includes a long TR conventional spin-echo (CSE) sequence, requiring long acquisition times. Using short tau inversion recovery fast spin-echo (fast STIR) sequences both acquisition time can be shortened and sensitivity in the detection of multiple sclerosis (MS) abnormalities can be increased. This study compares both sequences for the potential to detect both focal and diffuse spinal abnormalities. Spinal cords of 5 volunteers and 20 MS patients were studied at 1.0 T. Magnetic resonance imaging included cardiac-gated sagittal dual-echo CSE and a cardiac-gated fast STIR sequence. Images were scored regarding number, size, and location of focal lesions, diffuse abnormalities and presence/hindrance of artifacts by two experienced radiologists. Examinations were scored as being definitely normal, indeterminate, or definitely abnormal. Interobserver agreement regarding focal lesions was higher for CSE (κ=0.67) than for fast STIR (κ=0.57) but did not differ significantly. Of all focal lesions scored in consensus, 47 % were scored on both sequences, 31 % were only detected by fast STIR, and 22 % only by dual-echo CSE (n. s.). Interobserver agreement for diffuse abnormalities was lower with fast STIR (κ=0.48) than dual-echo CSE (κ=0.65; n. s.). After consensus, fast STIR showed in 10 patients diffuse abnormalities and dual-echo CSE in 3. After consensus, in 19 of 20 patients dual-echo CSE scans were considered as definitely abnormal compared with 17 for fast STIR. The fast STIR sequence is a useful adjunct to dual-echo CSE in detecting focal abnormalities and is helpful in detecting diffuse MS abnormalities in the spinal cord. Due to the frequent occurrence of artifacts and the lower observer concordance, fast STIR cannot be used alone. (orig.)

  18. Comparison of cDNA-derived protein sequences of the human fibronectin and vitronectin receptor α-subunits and platelet glycoprotein IIb

    International Nuclear Information System (INIS)

    Fitzgerald, L.A.; Poncz, M.; Steiner, B.; Rall, S.C. Jr.; Bennett, J.S.; Phillips, D.R.

    1987-01-01

    The fibronectin receptor (FnR), the vitronectin receptor (VnR), and the platelet membrane glycoprotein (GP) IIb-IIIa complex are members of a family of cell adhesion receptors, which consist of noncovalently associated α- and β-subunits. The present study was designed to compare the cDNA-derived protein sequences of the α-subunits of human FnR, VnR, and platelet GP IIb. cDNA clones for the α-subunit of the FnR (FnR/sub α/) were obtained from a human umbilical vein endothelial (HUVE) cell library by using an oligonucleotide probe designed from a peptide sequence of platelet GP IIb. cDNA clones for platelet GP IIb were isolated from a cDNA expression library of human erythroleukemia cells by using antibodies. cDNA clones of the VnR α-subunit (VnR/sub α/) were obtained from the HUVE cell library by using an oligonucleotide probe from the partial cDNA sequence for the VnR/sub α/. Translation of these sequences showed that the FNR/sub α/, the VnR/sub α/, and GP IIb are composed of disulfide-linked large (858-871 amino acids) and small (137-158 amino acids) chains that are posttranslationally processed from a single mRNA. A single hydrophobic segment located near the carboxyl terminus of each small chain appears to be a transmembrane domain. The large chains appear to be entirely extracellular, and each contains four repeated putative Ca 2+ -binding domains of about 30 amino acids that have sequence similarities to other Ca 2+ -binding proteins. The identity among the protein sequences of the three receptor α-subunits ranges from 36.1% to 44.5%, with the Ca 2+ -binding domains having the greatest homology. These proteins apparently evolved by a process of gene duplication

  19. Repetitive DNA in the pea (Pisum sativum L. genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Navrátilová Alice

    2007-11-01

    Full Text Available Abstract Background Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum. Results Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. Conclusion We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35–48% of the genome. These data

  20. 3D MR cisternography to identify distal dural rings. Comparison of 3D-CISS and 3D-SPACE sequences

    International Nuclear Information System (INIS)

    Watanabe, Yoshiyuki; Makidono, Akari; Nakamura, Miho; Saida, Yukihisa

    2011-01-01

    The distal dural ring (DDR) is an anatomical landmark used to distinguish intra- and extradural aneurysms. We investigated identification of the DDR using 2 three-dimensional (3D) magnetic resonance (MR) cisternography sequences-3D constructive interference in steady state (CISS) and 3D sampling perfection with application optimized contrasts using different flip angle evolutions (SPACE)-at 3.0 tesla. Ten healthy adult volunteers underwent imaging with 3D-CISS, 3D-SPACE, and time-of-flight (TOF) MR angiography (TOF-MRA) sequences at 3.0T. We analyzed DDR identification and internal carotid artery (ICA) signal intensity and classified the shape of the carotid cave. We identified the DDR using both 3D-SPACE and 3D-CISS, with no significant difference between the sequences. Visualization of the outline of the ICA in the cavernous sinus (CS) was significantly clearer with 3D-SPACE than 3D-CISS. In the CS and petrous portions, signal intensity was lower with 3D-SPACE, and the flow void was poor with 3D-CISS in some subjects. We identified the DDR with both 3D-SPACE and 3D-CISS, but the superior contrast of the ICA in the CS using 3D-SPACE suggests the superiority of this sequence for evaluating the DDR. (author)

  1. ACE-Inhibitors and the Risk of Urinary Tract Infections : Comparison of a Case-Crossover and Prescription Sequence Symmetry Design

    NARCIS (Netherlands)

    Pouwels, Koen B.; Bos, Jens H.J.; Hak, Eelko

    2014-01-01

    Background: In a post-hoc analysis of a randomized controlled trial (RCT) (HR 1.82, 95%CI, 1.16-2.88) and a prescription sequence symmetry analysis (PSSA) (SR 1.56, 95%CI 1.11-2.20), we observed that angiotensin-converting enzyme inhibitor (ACEi) use was associated with an increased risk of urinary

  2. Complete primary structure of a Lolium perenne (perennial rye grass) pollen allergen, Lol p III: comparison with known Lol p I and II sequences.

    Science.gov (United States)

    Ansari, A A; Shenbagamurthi, P; Marsh, D G

    1989-10-17

    The complete amino acid sequence of a Lolium perenne (rye grass) pollen allergen, Lol p III, determined by the automated Edman degradation of the protein and its selected fragments, is reported in this paper. Cleavage by enzymatic and chemical techniques established unambiguously the sequence for this 97-residue protein (Mr = 10,909), which lacks cysteine and shows no evidence of glycosylation. The sequence of Lol p III is very similar to that of another L. perenne allergen, Lol p II, which was sequenced recently; of the 97 positions in the two proteins, 57 are occupied by identical amino acids (59% identity). In addition, both allergens share a similar structure with an antibody-binding fragment of a third L. perenne allergen, Lol p I. Since human antibody responsiveness to all these three allergens is associated with HLA-DR3, and since the structure common to the three molecules shows high degrees of amphipathicity in Lol p II and III, we speculate that this common segment in the three molecules might contain or contribute to the respectively Ia/T-cell sites.

  3. Comparison of the Sequences of the Internal Transcribed Spacer Regions and PbGP43 Genes of Paracoccidioides brasiliensis from Patients and Armadillos (Dasypus novemcinctus)

    Science.gov (United States)

    Hebeler-Barbosa, Flavia; Morais, Flavia V.; Montenegro, Mario R.; Kuramae, Eiko E.; Montes, Beatriz; McEwen, Juan G.; Bagagli, Eduardo; Puccia, Rosana

    2003-01-01

    Paracoccidioides brasiliensis isolates from 10 nine-banded armadillos (Dasypus novemcinctus) were comparable with 19 clinical isolates by sequence analysis of the PbGP43 gene and ribosomal internal transcribed spacer 1 (ITS1) and ITS2 and by random amplified polymorphic DNA. In this original ITS study, eight isolates differed by one or three sites among five total substitution sites. PMID:14662970

  4. Detection and volume estimation of artificial hematomas in the subcutaneous fatty tissue: comparison of different MR sequences at 3.0 T.

    Science.gov (United States)

    Ogris, Kathrin; Petrovic, Andreas; Scheicher, Sylvia; Sprenger, Hanna; Urschler, Martin; Hassler, Eva Maria; Yen, Kathrin; Scheurer, Eva

    2017-06-01

    In legal medicine, reliable localization and analysis of hematomas in subcutaneous fatty tissue is required for forensic reconstruction. Due to the absence of ionizing radiation, magnetic resonance imaging (MRI) is particularly suited to examining living persons with forensically relevant injuries. However, there is limited experience regarding MRI signal properties of hemorrhage in soft tissue. The aim of this study was to evaluate MR sequences with respect to their ability to show high contrast between hematomas and subcutaneous fatty tissue as well as to reliably determine the volume of artificial hematomas. Porcine tissue models were prepared by injecting blood into the subcutaneous fatty tissue to create artificial hematomas. MR images were acquired at 3T and four blinded observers conducted manual segmentation of the hematomas. To assess segmentability, the agreement of measured volume with the known volume of injected blood was statistically analyzed. A physically motivated normalization taking into account partial volume effect was applied to the data to ensure comparable results among differently sized hematomas. The inversion recovery sequence exhibited the best segmentability rate, whereas the T1T2w turbo spin echo sequence showed the most accurate results regarding volume estimation. Both sequences led to reproducible volume estimations. This study demonstrates that MRI is a promising forensic tool to assess and visualize even very small amounts of blood in soft tissue. The presented results enable the improvement of protocols for detection and volume determination of hemorrhage in forensically relevant cases and also provide fundamental knowledge for future in-vivo examinations.

  5. Lung MRI of invasive fungal infection at 3 Tesla: evaluation of five different pulse sequences and comparison with multidetector computed tomography (MDCT)

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Chenggong; Tan, Xiangliang; Li, Caixia; Wu, Yuankui; Hao, Peng; Xiong, Wei; Xu, Yikai [Southern Medical University, Department of Medical Imaging Center, Nanfang Hospital, Guangzhou, Guangdong (China); Wei, Qi; Feng, Ru; Xu, Jun [Southern Medical University, Department of Hematology, Nanfang Hospital, Guangzhou (China); Chan, Queenie [Philips Healthcare, New Territories (China)

    2014-09-18

    To evaluate the diagnostic performance of five MR sequences to detect pulmonary infectious lesions in patients with invasive fungal infection (IFI), using multidetector computed tomography (MDCT) as the reference standard. Thirty-four immunocompromised patients with suspected IFI underwent MDCT and MRI. The MR studies were performed using five pulse sequences at 3.0 T: T2-weighted turbo spin echo (TSE), short-tau inversion recovery (STIR), spectrally selective attenuated inversion recovery (SPAIR), T1-weighted high resolution isotropic volume excitation (e-THRIVE) and T1-weighted fast field echo (T1-FFE). The size, lesion-to-lung contrast ratio and the detectability of pulmonary lesions on MR images were assessed. Image quality and artefacts on different sequences were also rated. A total of 84 lesions including nodules (n = 44) and consolidation (n = 40) were present in 75 lobes. SPAIR and e-THRIVE images achieved high overall lesion-related sensitivities for the detection of pulmonary abnormalities (90.5 % and 86.9 %, respectively). STIR showed the highest lesion-to-lung contrast ratio for nodules (21.8) and consolidation (17.0), whereas TSE had the fewest physiological artefacts. MRI at 3.0 T can depict clinically significant pulmonary IFI abnormalities with high accuracy compared to MDCT. SPAIR and e-THRIVE are preferred sequences for the detection of infectious lesions of 5 mm and larger. (orig.)

  6. The complete mitochondrial genome sequence of the world's largest fish, the whale shark (Rhincodon typus), and its comparison with those of related shark species.

    Science.gov (United States)

    Alam, Md Tauqeer; Petit, Robert A; Read, Timothy D; Dove, Alistair D M

    2014-04-10

    The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a "vulnerable" species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes it an important species for conservation efforts. We report here the first complete sequence of the mitochondrial genome (mitogenome) of the whale shark obtained by next-generation sequencing methods. The assembled mitogenome is a 16,875 bp circle, comprising of 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region. We also performed comparative analysis of the whale shark mitogenome to the available mitogenome sequences of 17 other shark species, four from the order Orectolobiformes, five from Lamniformes and eight from Carcharhiniformes. The nucleotide composition, number and arrangement of the genes in whale shark mitogenome are the same as found in the mitogenomes of the other members of the order Orectolobiformes and its closest orders Lamniformes and Carcharhiniformes, although the whale shark mitogenome had a slightly longer control region. The availability of mitogenome sequence of whale shark will aid studies of molecular systematics, biogeography, genetic differentiation, and conservation genetics in this species. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Comparison of multi-echo and single-echo gradient-recalled echo sequences for SPIO-enhanced Liver MRI at 3 T

    International Nuclear Information System (INIS)

    Choi, J.S.; Kim, M.-J.; Kim, J.H.; Choi, J.-Y.; Chung, Y.E.; Park, M.-S.; Kim, K.W.

    2010-01-01

    Aim: To assess the utility of a T2*-weighted, multi-echo data imaging combination sequenced on superparamagnetic iron oxide (SPIO)-enhanced liver magnetic resonance imaging (MRI) using a 3 T system. Materials and methods: Fifty patients underwent SPIO-enhanced MRI at 3 T using T2*-weighted, single-echo, gradient-recalled echo (GRE) sequences [fast imaging with steady precession; repetition time (TR)/echo time (TE), 126 ms/9 ms; flip angle, 30 o ] and multi-echo GRE (multi-echo data image combination) sequences (TR/TE, 186 ms/9 ms; flip angle, 30 o ). Three radiologists independently reviewed the images in a random order. The sensitivity and accuracy for the detection of focal hepatic lesions (a total of 76 lesions in 33 patients; 48 solid lesions, 28 non-solid lesions) were compared by analysing the area under the receiver operating characteristic curves. Image artefacts (flow artefacts, susceptibility artefacts, dielectric artefacts, and motion artefacts), lesion conspicuity, and overall image quality were evaluated according to a four-point scale: 1, poor; 2, fair; 3, good; 4, excellent. The signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) of the lesions were compared. Results: Image artefacts were more frequent with single-echo GRE (p < 0.05). The mean scale of image quality assessment for flow, susceptibility, dielectric, and motion artefacts were 2.76, 3.13, 3.42, and 2.89 with singe-echo, respectively, compared with 3.47, 3.43, 3.47, and 3.39, respectively, with multi-echo GRE. There was no significant difference in lesion conspicuity between single-echo (3.15) and multi-echo (3.30) GRE sequences. The overall image quality was significantly (p < 0.05) better with multi-echo (3.37) than with single-echo GRE (2.89). The mean SNR and CNR of the lesions were significantly (p < 0.05) higher on multi-echo (79 ± 23 and 128 ± 59, respectively) images than on single-echo (38 ± 11 and 102 ± 44, respectively) images. Lesion detection accuracy and

  8. Diagnosing lung nodules on oncologic MR/PET imaging: Comparison of fast T1-weighted sequences and influence of image acquisition in inspiration and expiration breath-hold

    Energy Technology Data Exchange (ETDEWEB)

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios; Brendle, Cornelia; Schmidt, Holger; Pfannenberg, Christina A; LaFougère, Christian; Nikolaou, Konstantin; Schraml, Christina [University Hospital of Tuebingen, Tuebingen (Germany)

    2016-09-15

    First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

  9. Diagnosing Lung Nodules on Oncologic MR/PET Imaging: Comparison of Fast T1-Weighted Sequences and Influence of Image Acquisition in Inspiration and Expiration Breath-Hold

    Energy Technology Data Exchange (ETDEWEB)

    Schwenzer, Nina F.; Seith, Ferdinand; Gatidis, Sergios [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Brendle, Cornelia [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Department of Diagnostic and Interventional Neuroradiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Schmidt, Holger; Pfannenberg, Christina A. [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Fougère, Christian la [Department of Nuclear Medicine, University Hospital of Tuebingen, Tuebingen 72076 (Germany); Nikolaou, Konstantin; Schraml, Christina [Department of Diagnostic and Interventional Radiology, University Hospital of Tuebingen, Tuebingen 72076 (Germany)

    2016-11-01

    First, to investigate the diagnostic performance of fast T1-weighted sequences for lung nodule evaluation in oncologic magnetic resonance (MR)/positron emission tomography (PET). Second, to evaluate the influence of image acquisition in inspiration and expiration breath-hold on diagnostic performance. The study was approved by the local Institutional Review Board. PET/CT and MR/PET of 44 cancer patients were evaluated by 2 readers. PET/CT included lung computed tomography (CT) scans in inspiration and expiration (CTin, CTex). MR/PET included Dixon sequence for attenuation correction and fast T1-weighted volumetric interpolated breath-hold examination (VIBE) sequences (volume interpolated breath-hold examination acquired in inspiration [VIBEin], volume interpolated breath-hold examination acquired in expiration [VIBEex]). Diagnostic performance was analyzed for lesion-, lobe-, and size-dependence. Diagnostic confidence was evaluated (4-point Likert-scale; 1 = high). Jackknife alternative free-response receiver-operating characteristic (JAFROC) analysis was performed. Seventy-six pulmonary lesions were evaluated. Lesion-based detection rates were: CTex, 77.6%; VIBEin, 53.3%; VIBEex, 51.3%; and Dixon, 22.4%. Lobe-based detection rates were: CTex, 89.6%; VIBEin, 58.3%; VIBEex, 60.4%; and Dixon, 31.3%. In contrast to CT, inspiration versus expiration did not alter diagnostic performance in VIBE sequences. Diagnostic confidence was best for VIBEin and CTex and decreased in VIBEex and Dixon (1.2 ± 0.6; 1.2 ± 0.7; 1.5 ± 0.9; 1.7 ± 1.1, respectively). The JAFROC figure-of-merit of Dixon was significantly lower. All patients with malignant lesions were identified by CTex, VIBEin, and VIBEex, while 3 patients were false-negative in Dixon. Fast T1-weighted VIBE sequences allow for identification of patients with malignant pulmonary lesions. The Dixon sequence is not recommended for lung nodule evaluation in oncologic MR/PET patients. In contrast to CT, inspiration versus

  10. Driven equilibrium (drive) MR imaging of the cranial nerves V-VIII: comparison with the T2-weighted 3D TSE sequence

    Energy Technology Data Exchange (ETDEWEB)

    Ciftci, E. E-mail: eciftcis7@hotmail.com; Anik, Yonca; Arslan, Arzu; Akansel, Gur; Sarisoy, Tahsin; Demirci, Ali

    2004-09-01

    Purpose: The aim of this study is to evaluate the efficacy of the driven equilibrium radio frequency reset pulse (DRIVE) on image quality and nerve detection when used in adjunction with T2-weighted 3D turbo spin-echo (TSE) sequence. Materials and methods: Forty-five patients with cranial nerve symptoms referable to the cerebellopontine angle (CPA) were examined using a T2-weighted 3D TSE pulse sequence with and without DRIVE. MR imaging was performed on a 1.5-T MRI scanner. In addition to the axial resource images, reformatted oblique sagittal, oblique coronal and maximum intensity projection (MIP) images of the inner ear were evaluated. The nerve identification and image quality were graded for the cranial nerves V-VIII as well as inner ear structures. These structures were chosen because fluid-solid interfaces existed due to the CSF around (the cranial nerves V-VIII) or the endolymph within (the inner ear structures). Statistical analysis was performed using the Wilcoxon test. P<0.05 was considered significant. Results: The addition of the DRIVE pulse shortens the scan time by 25%. T2-weighted 3D TSE sequence with DRIVE performed slightly better than the T2-weighted 3D TSE sequence without DRIVE in identifying the individual nerves. The image quality was also slightly better with DRIVE. Conclusion: The addition of the DRIVE pulse to the T2-weighted 3D TSE sequence is preferable when imaging the cranial nerves surrounded by the CSF, or fluid-filled structures because of shorter scan time and better image quality due to reduced flow artifacts.

  11. Driven equilibrium (drive) MR imaging of the cranial nerves V-VIII: comparison with the T2-weighted 3D TSE sequence

    International Nuclear Information System (INIS)

    Ciftci, E.; Anik, Yonca; Arslan, Arzu; Akansel, Gur; Sarisoy, Tahsin; Demirci, Ali

    2004-01-01

    Purpose: The aim of this study is to evaluate the efficacy of the driven equilibrium radio frequency reset pulse (DRIVE) on image quality and nerve detection when used in adjunction with T2-weighted 3D turbo spin-echo (TSE) sequence. Materials and methods: Forty-five patients with cranial nerve symptoms referable to the cerebellopontine angle (CPA) were examined using a T2-weighted 3D TSE pulse sequence with and without DRIVE. MR imaging was performed on a 1.5-T MRI scanner. In addition to the axial resource images, reformatted oblique sagittal, oblique coronal and maximum intensity projection (MIP) images of the inner ear were evaluated. The nerve identification and image quality were graded for the cranial nerves V-VIII as well as inner ear structures. These structures were chosen because fluid-solid interfaces existed due to the CSF around (the cranial nerves V-VIII) or the endolymph within (the inner ear structures). Statistical analysis was performed using the Wilcoxon test. P<0.05 was considered significant. Results: The addition of the DRIVE pulse shortens the scan time by 25%. T2-weighted 3D TSE sequence with DRIVE performed slightly better than the T2-weighted 3D TSE sequence without DRIVE in identifying the individual nerves. The image quality was also slightly better with DRIVE. Conclusion: The addition of the DRIVE pulse to the T2-weighted 3D TSE sequence is preferable when imaging the cranial nerves surrounded by the CSF, or fluid-filled structures because of shorter scan time and better image quality due to reduced flow artifacts

  12. School Closings in Philadelphia

    Science.gov (United States)

    Jack, James; Sludden, John

    2013-01-01

    In 2012, the School District of Philadelphia closed six schools. In 2013, it closed 24. The closure of 30 schools has occurred amid a financial crisis, headlined by the district's $1.35 billion deficit. School closures are one piece of the district's plan to cut expenditures and close its budget gap. The closures are also intended to make…

  13. A measure of the denseness of a phylogenetic network. [by sequenced proteins from extant species

    Science.gov (United States)

    Holmquist, R.

    1978-01-01

    An objective measure of phylogenetic denseness is developed to examine various phylogenetic criteria: alpha- and beta-hemoglobin, myoglobin, cytochrome c, and the parvalbumin family. Attention is given to the number of nucleotide replacements separating homologous sequences, and to the topology of the network (in other words, to the qualitative nature of the network as defined by how closely the studied species are related). Applications include quantitative comparisons of species origin, relation, and rates of evolution.

  14. Comparison of hydrodynamically closed isotachophoresis-capillary zone electrophoresis with hydrodynamically open capillary zone electrophoresis hyphenated with tandem mass spectrometry in drug analysis: pheniramine, its metabolite and phenylephrine in human urine.

    Science.gov (United States)

    Piešťanský, Juraj; Maráková, Katarína; Kovaľ, Marián; Mikuš, Peter

    2014-09-05

    The advanced two dimensional isotachophoresis (ITP)-capillary zone electrophoresis (CZE) hyphenated with tandem mass spectrometry (MS/MS, here triple quadrupole, QqQ) was developed in this work to demonstrate analytical potentialities of this approach in the analysis of drugs in multicomponent ionic matrices. Pheniramine (PHM), phenylephrine (PHE), paracetamol (PCM) and their potential metabolic products were taken for the analysis by the ITP-CZE-ESI-QqQ technique working in hydrodynamically closed CE separation system and then a comparison with the conventional (hydrodynamically open) CZE-ESI-QqQ technique was made. The ITP-CZE-ESI-QqQ method was favorable in terms of obtainable selectivity (due to highly effective heart-cut analysis), concentration limits of detection (LOD at pgmL(-1) levels due to enhanced sample load capacity and ITP preconcentration), sample handling (on-line sample pretreatment, i.e. clean-up, preconcentration, preseparation), and, by that, possibilities for future automation and miniaturization. On the other hand, this experimental arrangement, in contrast to the CZE-ESI-QqQ arrangement supported by an electroosmotic flow, is principally limited to the analysis of uniformly (i.e. positively or negatively) charged analytes in one run without any possibilities to analyze neutral compounds (here, PCM and neutral or acidic metabolites of the drugs had to be excluded from the analysis). Hence, these general characteristics should be considered when choosing a proper analytical CE-MS approach for a given biomedical application. Here, the analytical potential of the ITP-CZE-ESI-QqQ method was demonstrated showing the real time profiles of excreted targeted drugs and metabolite (PHM, PHE, M-PHM) in human urine after the administration of one dose of Theraflu(®) to the volunteers. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch.) and comparison with related species of Rosaceae.

    Science.gov (United States)

    Cheng, Hui; Li, Jinfeng; Zhang, Hong; Cai, Binhua; Gao, Zhihong; Qiao, Yushan; Mi, Lin

    2017-01-01

    Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F . ×  ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the F . ×  ananassa 'Benihoppe' chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria , particularly among three octoploid strawberries which were F . ×  ananassa 'Benihoppe', F . chiloensis (GP33) and F . virginiana (O477). However, when the sequences of the coding and non-coding regions of F . ×  ananassa 'Benihoppe' were compared in detail with those of F . chiloensis (GP33) and F . virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions ( trnK - matK , trnS - trnG , atpF - atpH , trnC - petN , trnT - psbD and trnP - psaJ ) with a percentage of variable sites greater than

  16. The complete chloroplast genome sequence of strawberry (Fragaria  × ananassa Duch. and comparison with related species of Rosaceae

    Directory of Open Access Journals (Sweden)

    Hui Cheng

    2017-10-01

    Full Text Available Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa ‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp separated by large (LSC, 85,531 bp and small (SSC, 18,146 bp single-copy (SC regions. The length of the F. × ananassa ‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria, particularly among three octoploid strawberries which were F. × ananassa ‘Benihoppe’, F. chiloensis (GP33 and F. virginiana (O477. However, when the sequences of the coding and non-coding regions of F. × ananassa ‘Benihoppe’ were compared in detail with those of F. chiloensis (GP33 and F. virginiana (O477, a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ with a percentage of variable sites greater than 1

  17. Partial characterization of the lettuce infectious yellows virus genomic RNAs, identification of the coat protein gene and comparison of its amino acid sequence with those of other filamentous RNA plant viruses.

    Science.gov (United States)

    Klaassen, V A; Boeshore, M; Dolja, V V; Falk, B W

    1994-07-01

    Purified virions of lettuce infectious yellows virus (LIYV), a tentative member of the closterovirus group, contained two RNAs of approximately 8500 and 7300 nucleotides (RNAs 1 and 2 respectively) and a single coat protein species with M(r) of approximately 28,000. LIYV-infected plants contained multiple dsRNAs. The two largest were the correct size for the replicative forms of LIYV virion RNAs 1 and 2. To assess the relationships between LIYV RNAs 1 and 2, cDNAs corresponding to the virion RNAs were cloned. Northern blot hybridization analysis showed no detectable sequence homology between these RNAs. A partial amino acid sequence obtained from purified LIYV coat protein was found to align in the most upstream of four complete open reading frames (ORFs) identified in a LIYV RNA 2 cDNA clone. The identity of this ORF was confirmed as the LIYV coat protein gene by immunological analysis of the gene product expressed in vitro and in Escherichia coli. Computer analysis of the LIYV coat protein amino acid sequence indicated that it belongs to a large family of proteins forming filamentous capsids of RNA plant viruses. The LIYV coat protein appears to be most closely related to the coat proteins of two closteroviruses, beet yellows virus and citrus tristeza virus.

  18. A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

    DEFF Research Database (Denmark)

    Davis, Jerrold I.; Stevenson, Dennis W.; Petersen, Gitte

    2004-01-01

    elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR...

  19. Boosting antibody developability through rational sequence optimization.

    Science.gov (United States)

    Seeliger, Daniel; Schulz, Patrick; Litzenburger, Tobias; Spitz, Julia; Hoerer, Stefan; Blech, Michaela; Enenkel, Barbara; Studts, Joey M; Garidel, Patrick; Karow, Anne R

    2015-01-01

    The application of monoclonal antibodies as commercial therapeutics poses substantial demands on stability and properties of an antibody. Therapeutic molecules that exhibit favorable properties increase the success rate in development. However, it is not yet fully understood how the protein sequences of an antibody translates into favorable in vitro molecule properties. In this work, computational design strategies based on heuristic sequence analysis were used to systematically modify an antibody that exhibited a tendency to precipitation in vitro. The resulting series of closely related antibodies showed improved stability as assessed by biophysical methods and long-term stability experiments. As a notable observation, expression levels also improved in comparison with the wild-type candidate. The methods employed to optimize the protein sequences, as well as the biophysical data used to determine the effect on stability under conditions commonly used in the formulation of therapeutic proteins, are described. Together, the experimental and computational data led to consistent conclusions regarding the effect of the introduced mutations. Our approach exemplifies how computational methods can be used to guide antibody optimization for increased stability.

  20. Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature

    DEFF Research Database (Denmark)

    Guðnason, Haukur; Dufva, Hans Martin; Bang, Dang Duong

    2007-01-01

    investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit......The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include...... the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we...

  1. Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR.

    Science.gov (United States)

    Nilyanimit, Pornjarim; Chansaenroj, Jira; Poomipak, Witthaya; Praianantathavorn, Kesmanee; Payungporn, Sunchai; Poovorawan, Yong

    2018-03-01

    Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations. © The Korean Society for Laboratory Medicine

  2. Intraspecific sequence comparisons reveal similar rates of non-collinear gene insertion in the B and D genomes of bread wheat

    Czech Academy of Sciences Publication Activity Database

    Bartoš, Jan; Vlček, Čestmír; Choulet, F.; Džunková, Mária; Cviková, Kateřina; Šafář, Jan; Šimková, Hana; Pačes, Jan; Strnad, Hynek; Sourdille, P.; Berges, H.; Cattonaro, F.; Feuillet, C.; Doležel, Jaroslav

    2012-01-01

    Roč. 12, č. 155 (2012), s. 1-10 ISSN 1471-2229 R&D Projects: GA ČR GAP501/10/1778 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511; CEZ:AV0Z50520514 Keywords : Wheat * BAC sequencing * Homoeologous genomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.354, year: 2012

  3. Nucleotide sequence analysis of HTLV-I isolated from cerebrospinal fluid of a patient with TSP/HAM: comparison to other HTLV-I isolates.

    Science.gov (United States)

    Mukhopadhyaya, R; Sadaie, M R

    1993-02-01

    Human T-cell leukemia virus type I (HTLV-I) has been associated with adult T-cell leukemia/lymphoma and the chronic neurologic disorder tropical spastic paraparesis/HTLV-I-associated myelopathy (TSP/HAM). To study the genetic structure of the virus associated with TSP/HAM, we have obtained and sequenced a partial genomic clone from an HTLV-I-positive cell line established from cerebrospinal fluid (CSF) of a Jamaican patient with TSP/HAM. This clone consisted of a 4.3-kb viral sequence containing the 5' long terminal repeat (LTR), gag, and N-terminal portion of the pol gene, with an overall 1.3% sequence variation resulting from mostly nucleotide substitutions, as compared to the prototype HTLV-I ATK-1. The gag and pol regions showed only 1.4% and 1.2% nucleotide variations, respectively. However, the U3 region of the LTR showed the highest sequence variation (3.6%), where several changes appear to be common among certain TSP/HAM isolates. Several of these changes reside within the 21-bp boundaries and the Tax-responsive element. It would be important to determine if the observed changes are sufficient to cause neurologic disorders similar to the murine leukemia virus system or simply reflect the divergent pool of HTLV-I from different geographic locations. At this time, we cannot rule out the possibility that the observed changes have either direct or indirect significance for the HTLV-I pathogenesis in TSP/HAM.

  4. MR contrast of ferritin and hemosiderin in the brain: comparison among gradient-echo, conventional spin-echo and fast spin-echo sequences

    Energy Technology Data Exchange (ETDEWEB)

    Haque, Tabassum Laz; Miki, Yukio; Kanagaki, Mitsunori; Takahashi, Takahiro; Yamamoto, Akira; Konishi, Junya; Nozaki, Kazuhiko; Hashimoto, Nobuo; Konishi, Junji

    2003-12-01

    Objective: To compare the magnetic resonance image contrasts due to ferritin and hemosiderin in the brain tissue among different pulse sequences. Materials and methods: Fourteen patients with cavernous hemangioma in the brain prospectively underwent MR imaging with T2*-weighted gradient-echo (GRE), T2-weighted conventional spin-echo (SE) and fast spin-echo (FSE) sequences. The relative contrast ratios (CRs) of the hypointense part of cavernous hemangioma, globus pallidus and putamen to the deep frontal white matter were measured on each pulse sequence and statistically analyzed using analysis of variance followed by paired t-test. Results: In the hypointense part of cavernous hemangioma, relative CRs were significantly lower on T2*-weighted GRE than on T2-weighted SE images (P=0.0001), and on T2-weighted SE than on T2-weighted FSE images (P=0.0001). In the globus pallidus, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.002), and on T2*-weighted GRE than on T2-weighted FSE images (P=0.0002). In the putamen, relative CRs were significantly lower on T2-weighted SE than on T2*-weighted GRE images (P=0.001), and there was no significant difference between CRs on T2-weighted FSE and T2*-weighted GRE images (P=0.90). Conclusion: Hemosiderin showed best image contrast on T2*-weighted GRE images but ferritin showed more prominent image contrast on T2-weighted SE than on T2*-weighted GRE images, which may help to determine an appropriate pulse sequence in neurological diseases associated with excessive ferritin accumulation.

  5. MR contrast of ferritin and hemosiderin in the brain: comparison among gradient-echo, conventional spin-echo and fast spin-echo sequences

    International Nuclear Information System (INIS)

    Haque, Tabassum Laz; Miki, Yukio; Kanagaki, Mitsunori; Takahashi, Takahiro; Yamamoto, Akira; Konishi, Junya; Nozaki, Kazuhiko; Hashimoto, Nobuo; Konishi, Junji

    2003-01-01

    Objective: To compare the magnetic resonance image contrasts due to ferritin and hemosiderin in the brain tissue among different pulse sequences. Materials and methods: Fourteen patients with cavernous hemangioma in the brain prospectively underwent MR imaging with T2*-weighted gradient-echo (GRE), T2-weighted conventional spin-echo (SE) and fast spin-echo (FSE) sequences. The relative contrast ratios (CRs) of the hypointense part of cavernous hemangioma, globus pallidus and putamen to the deep frontal white matter were measured on each pulse sequence and statistically analyzed using analysis of variance followed by paired t-test. Results: In the hypointense part of cavernous hemangioma, relative CRs were significantly lower on T2*-weighted GRE than on T2-we