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Sample records for dsrna genomic segments

  1. In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

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    Zhang, Xing; Ding, Ke; Yu, Xuekui; Chang, Winston; Sun, Jingchen; Hong Zhou, Z.

    2015-11-01

    Viruses in the Reoviridae, like the triple-shelled human rotavirus and the single-shelled insect cytoplasmic polyhedrosis virus (CPV), all package a genome of segmented double-stranded RNAs (dsRNAs) inside the viral capsid and carry out endogenous messenger RNA synthesis through a transcriptional enzyme complex (TEC). By direct electron-counting cryoelectron microscopy and asymmetric reconstruction, we have determined the organization of the dsRNA genome inside quiescent CPV (q-CPV) and the in situ atomic structures of TEC within CPV in both quiescent and transcribing (t-CPV) states. We show that the ten segmented dsRNAs in CPV are organized with ten TECs in a specific, non-symmetric manner, with each dsRNA segment attached directly to a TEC. The TEC consists of two extensively interacting subunits: an RNA-dependent RNA polymerase (RdRP) and an NTPase VP4. We find that the bracelet domain of RdRP undergoes marked conformational change when q-CPV is converted to t-CPV, leading to formation of the RNA template entry channel and access to the polymerase active site. An amino-terminal helix from each of two subunits of the capsid shell protein (CSP) interacts with VP4 and RdRP. These findings establish the link between sensing of environmental cues by the external proteins and activation of endogenous RNA transcription by the TEC inside the virus.

  2. Generation of full-length cDNA of the two genomic dsRNA segments of infectious bursal disease virus

    NARCIS (Netherlands)

    Boot, H.J.; Huurne, ter A.H.M.; Peeters, B.P.H.

    2000-01-01

    To determine the complete nucleotide sequence of Infectious Bursal Disease virus (IBDV) isolates, an efficient method was developed to generate full-length cDNA of both the genomic A- and B-segments. Reverse transcription was carried out at the highest possible temperature (50°C) for the reverse

  3. Separation and isolation of BTV dsRNA segments and viral proteins.

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    Li, Joseph K-K; Huang, I-Jen; Hayama, Emiko

    2012-05-01

    Bluetongue virus (BTV) genome contains ten double-stranded RNA segments. The sequence of the plus strand of each of the BTV genomic double-stranded RNAs is the same as that of its mRNA, which encodes for a single viral protein, except the smallest S4 segment which can encode for two nonstructural proteins, primarily for the release assistance of the viral progeny. The separation and isolation of each BTV dsRNA segment and viral protein have provided extensive data related to its viral infection, pathology, suppression of host cellular functions, and eventual apoptosis of the infected host cells. This cytoplasmic virus is also an animal killer that costs the U.S. livestock industry at least $125 million yearly. However, this virus has no known effect on humans. Thus, it is very safe to carry out investigation with the virus, preferably in a BSL-2 laboratory.

  4. Assortment and packaging of the segmented rotavirus genome.

    Science.gov (United States)

    McDonald, Sarah M; Patton, John T

    2011-03-01

    The rotavirus (RV) genome comprises 11 segments of double-stranded RNA (dsRNA) and is contained within a non-enveloped, icosahedral particle. During assembly, a highly coordinated selective packaging mechanism ensures that progeny RV virions contain one of each genome segment. Cis-acting signals thought to mediate assortment and packaging are associated with putative panhandle structures formed by base-pairing of the ends of RV plus-strand RNAs (+RNAs). Viral polymerases within assembling core particles convert the 11 distinct +RNAs to dsRNA genome segments. It remains unclear whether RV +RNAs are assorted before or during encapsidation, and the functions of viral proteins during these processes are not resolved. However, as reviewed here, recent insights gained from the study of RV and two other segmented RNA viruses, influenza A virus and bacteriophage Φ6, reveal potential mechanisms of RV assortment and packaging.

  5. Functional genomics tool: Gene silencing in Ixodes scapularis eggs and nymphs by electroporated dsRNA

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    Troiano Emily

    2010-01-01

    Full Text Available Abstract Background Ticks are blood-sucking arthropods responsible for transmitting a wide variety of disease-causing agents, and constitute important public health threats globally. Ixodes scapularis is the primary vector of the Lyme disease agent in the eastern and central U.S. RNAi is a mechanism by which gene-specific double-stranded RNA (dsRNA triggers degradation of homologous mRNA transcripts. Here, we describe an optimized protocol for effectively suppressing gene expression in the egg and nymphal stages of I. scapularis by electroporation. Results The genes encoding the putative Phospholipase A2 (PLA2, cytoplasmic Cystatin, Syntaxin-5, β-Actin and Calreticulin were targeted by delivering the dsRNA encoding the specific gene coding regions in the unfed nymphs. Silencing was measured using real time qRT-PCR. Electroporation as a mode of dsRNA delivery appears to be substantially efficient and less traumatic to the tick than dsRNA microinjection in the unfed nymphs. Using Cy3-labeled dsRNA to monitor the movement, electroporated dsRNA entered the nymphs and spread to salivary glands and other tissues. The significant disruption of β-actin and cytoplasmic Cystatin transcripts in tick eggs demonstrate the applicability of this technique. The PLA2, cytoplasmic Cystatin, Syntaxin-5, β-Actin and Calreticulin genes were also significantly silenced, suggesting that this method has the potential to introduce dsRNA in eggs and unfed nymphs. Conclusions Our study demonstrates that electroporation can be used as a simple dsRNA delivery tool in assessing the functional role of tick genes in the vector-host interactions. This technique represents a novel approach for specific gene suppression in immature stages of ticks.

  6. Exogenously applied dsRNA molecules deriving from the Zucchini yellow mosaic virus (ZYMV) genome move systemically and protect cucurbits against ZYMV.

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    Kaldis, Athanasios; Berbati, Margarita; Melita, Ourania; Reppa, Chrysavgi; Holeva, Maria; Otten, Patricia; Voloudakis, Andreas

    2017-06-16

    Zucchini yellow mosaic virus (ZYMV) causes serious damage in a large number of cucurbits, and control measures are necessary. Transgenic cucurbits expressing parts of the ZYMV genome have been shown to be resistant to the cognate virus. A non-transgenic approach involving the exogenous application of double-stranded RNA (dsRNA) has also been shown to induce resistance in tobacco against Cucumber mosaic virus (CMV) and Tobacco mosaic virus (TMV). In the present study, dsRNA molecules derived from the helper component-proteinase (HC-Pro) and coat protein (CP) genes of the ZYMV_DE_2014 isolate were produced in vitro. On exogenous dsRNA application in cucumber, watermelon and squash plants, dsRNA HC-Pro conferred resistance of 82%, 50% and 18%, and dsRNA CP molecules of 70%, 43% and 16%, respectively. On deep sequencing analysis of ZYMV-infected watermelon, hot-spot regions for viral small interfering RNAs (vsiRNAs) in the genome of ZYMV were identified. Stem-loop reverse transcription-polymerase chain reaction (RT-PCR) detection of selected 21-nucleotide-long vsiRNAs in plants that received only dsRNA molecules suggested that the dsRNAs exogenously applied onto plants were successfully diced, thus initiating RNA silencing. dsRNA molecules were found to be progressively degraded in planta, and strongly detected by semi-quantitative RT-PCR for at least 9 days after exogenous application. Moreover, dsRNA molecules were detected in systemic tissue of watermelon and squash, showing that dsRNA is transported long distances in these plants. © 2017 BSPP AND JOHN WILEY & SONS LTD.

  7. Isolation and Identification of Virus dsRNA from Strawberry Plants

    Institute of Scientific and Technical Information of China (English)

    LI He; DAI Hong-yan; ZHANG Zhi-hong; GAO Xiu-yan; DU Guo-dong; ZHANG Xin-yu

    2007-01-01

    The analysis of virus genome is based on nucleic acid isolation. The aims of this study were to develop a method for isolation and identification of virus double-stranded ribonucleic acid (dsRNA) and to elucidate the nucleotide sequences of strawberry virus. Using the modified method, virus dsRNA was extracted from strawberry virus indicator plants and cultivated strawberry plants and detected using agarose gel electrophoresis with ethidium bromide staining and reverse transcription-polymerase chain reaction (RT-PCR). The quantity of virus dsRNA varied among strawberry cultivars. The quantity of dsRNA from in vitro plantlets was higher than that from the young leaves of field plants. For the field-grown plants, there was more dsRNA in the young leaves. Virus dsRNA extracted from strawberry plants was resistant to deoxyribonuclease Ⅰ (DNase Ⅰ ), but evidently, it became resistant to ribonuclease A (RNase A) only in the presence of 0.5 M NaCl. Its bands in agarose gel could be readily recycled using an agarose gel DNA purification kit. With RT-PCR, the segments of both strawberry mottle virus and Strawberry mild yellow edge virus genomes were amplified by using the virus dsRNA recycled from gel or treated with DNase Ⅰ /RNase A as templates. The system developed for dsRNA isolation and identification in strawberry plants laid a sound foundation for the work on genome analysis of strawberry virus isolates in China.

  8. Competition between influenza A virus genome segments.

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    Ivy Widjaja

    Full Text Available Influenza A virus (IAV contains a segmented negative-strand RNA genome. How IAV balances the replication and transcription of its multiple genome segments is not understood. We developed a dual competition assay based on the co-transfection of firefly or Gaussia luciferase-encoding genome segments together with plasmids encoding IAV polymerase subunits and nucleoprotein. At limiting amounts of polymerase subunits, expression of the firefly luciferase segment was negatively affected by the presence of its Gaussia luciferase counterpart, indicative of competition between reporter genome segments. This competition could be relieved by increasing or decreasing the relative amounts of firefly or Gaussia reporter segment, respectively. The balance between the luciferase expression levels was also affected by the identity of the untranslated regions (UTRs as well as segment length. In general it appeared that genome segments displaying inherent higher expression levels were more efficient competitors of another segment. When natural genome segments were tested for their ability to suppress reporter gene expression, shorter genome segments generally reduced firefly luciferase expression to a larger extent, with the M and NS segments having the largest effect. The balance between different reporter segments was most dramatically affected by the introduction of UTR panhandle-stabilizing mutations. Furthermore, only reporter genome segments carrying these mutations were able to efficiently compete with the natural genome segments in infected cells. Our data indicate that IAV genome segments compete for available polymerases. Competition is affected by segment length, coding region, and UTRs. This competition is probably most apparent early during infection, when limiting amounts of polymerases are present, and may contribute to the regulation of segment-specific replication and transcription.

  9. Metabolic engineering of the baculovirus-expression system via inverse "shotgun" genomic analysis and RNA interference (dsRNA) increases product yield and cell longevity.

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    Kim, Eun Jeong; Kramer, Shannon F; Hebert, Colin G; Valdes, James J; Bentley, William E

    2007-10-15

    RNA interference (RNAi) is as powerful tool for characterizing gene function in eukaryotic organisms and cultured cell lines. Its use in metabolic engineering has been limited and few reports have targeted protein expression systems to increase yield. In this work, we examine the use of in vitro synthesized double stranded RNA (dsRNA) in the baculovirus expression vector system (BEVS), using commercially relevant cultured cells (Spodoptera frugiperda, Sf-9) and larvae (Trichoplusia ni) as hosts. First, we employed an inverse "shotgun" genomic analysis to "find" an array of 16 putative insect gene targets. We then synthesized dsRNA in vitro targeting these genes and investigated the effects of injected dsRNA on larval growth, development, and product yield. Growth and development was at times stunted and in several cases, the effects were lethal. However, dsRNA targeting an acidic juvenile hormone-suppressible protein (AJHSP1), and translational elongation factor 2 (Ef-2) resulted in significantly increased yield of model product, GFP. Next, we targeted known genes, v-cath and apoptosis inducer, sf-caspase 1, in cultured Sf-9 cells. We confirm RNAi-mediated sf-caspase 1 suppression in Sf-9 cells, but not in baculovirus-infected cells, likely due to the overriding effects of inhibitor of apoptosis protein, p35. We also demonstrate suppression of v-cath in infected cells, which leads to a approximately 3-fold increase in product yield. Overall, our results support the application of RNAi in metabolic engineering, specifically for enhancing protein productivity in the baculovirus expression vector system.

  10. Segmenting the Human Genome into Isochores.

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    Cozzi, Paolo; Milanesi, Luciano; Bernardi, Giorgio

    2015-01-01

    The human genome is a mosaic of isochores, which are long (>200 kb) DNA sequences that are fairly homogeneous in base composition and can be assigned to five families comprising 33%-59% of GC composition. Although the compartmentalized organization of the mammalian genome has been investigated for more than 40 years, no satisfactory automatic procedure for segmenting the genome into isochores is available so far. We present a critical discussion of the currently available methods and a new approach called isoSegmenter which allows segmenting the genome into isochores in a fast and completely automatic manner. This approach relies on two types of experimentally defined parameters, the compositional boundaries of isochore families and an optimal window size of 100 kb. The approach represents an improvement over the existing methods, is ideally suited for investigating long-range features of sequenced and assembled genomes, and is publicly available at https://github.com/bunop/isoSegmenter.

  11. Sequence Analysis of dsRNA Segments from Infected Maize from Hangzhou China%杭州地区玉米病毒病dsRNA序列分析

    Institute of Scientific and Technical Information of China (English)

    赵洪斌; 唐香山; 陈集双

    2011-01-01

    Natural-infected maize with strip mosaic symptoms were collected from Hangzhou,China. Double stranded RNAs were amplified using SPAT(single primer amplification technique,SPAT) and viral genomie segments were cloned.Sequence analysis revealed that three segments (1801bp 、2193bp and 3164bp,respectively )shared 98% identity, at nucleotide level, with the tenth (AF227205),the seventh (AJ297428) and the fifth (AJ409147) segments of rice blackstreaked dwarf virus (RBSDV),and their similarity were less than 88% with Maize rough dwarf fijivirus (MRDV). They showed higher homology with RBSDV than MRDV at amino acid level, too. Results for sequence homology analysis indicated that the three segments obtained from dsRNA sequencing originated from RBSDV,which is regarded as the main virus infecting maize in this area.%从杭州地区采集花叶症状的玉米,抽提双链RNA(double-stranded RNA,dsRNA).用单引物扩增方法(Single primer amplification technique,SPAT)对dsRNA进行RT-PCR扩增,获得了三条dsRNA片段的cDNA克隆并测定全序列.核苷酸水平上,三条片段(长度分别为1801 bp、2193 bp和3164 bp)分别与水稻黑条矮缩病毒(Rice black-streaked dwarf virus,RBSDV)的第十(AF227205)、第七(AJ297428)和第五(AJ409147)号片段序列存在高达98%的同源性,与玉米粗缩病毒(Maize rough dwarf fijivirus,MRDV)相应片段序列同源性最高为88%.在氨基酸水平上,推测的氨基酸序列也与RBSDV相似性较高,而与MRDV的相似性较低.序列同源性分析结果表明:三条片段来源于RBSDV.因此,该地区发生的玉米病毒病病原是水稻黑条矮缩病毒而不是玉米粗缩病毒.

  12. Dynamics of dsRNA mycoviruses in black Aspergillus population.

    NARCIS (Netherlands)

    Diepeningen, van A.D.; Debets, A.J.M.; Hoekstra, R.F.

    2006-01-01

    Approximately 10% of all examined 668 representatives of black Aspergillus species, independent of worldwide location, were infected with double-stranded RNA (dsRNA) mycoviruses. These isometric viruses (25-40 nm diameter) contained a variety of often multiple segments of different dsRNA sizes rangi

  13. Reovirus genome segment assortment into progeny genomes studied by the use of monoclonal antibodies directed against reovirus proteins.

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    Antczak, J B; Joklik, W K

    1992-04-01

    Using a panel of monoclonal antibodies (MABs) against reovirus proteins, we have identified proteins that associate with reovirus messenger RNA molecules prior to the generation of progeny double-stranded (ds) genome segments and proteins that are components of the structures within which progeny ds genome segments are generated. The following conclusions can be drawn from the results obtained. (1) Three proteins rapidly become associated with mRNA molecules to form single-stranded RNA-containing complexes (ssRCCs): the nonstructural protein microNS, the nonstructural protein sigma NS, and protein sigma 3. (2) Analysis of populations of ssRCCs in density gradients and by sequential exposure to various MABs indicates that some ssRCCs contain only microNS, others microNS and sigma NS or sigma 3, and others all three proteins. Each ssRCC contains one RNA molecule and, depending on the size of the RNA, 10-30 protein molecules. (3) The relative proportions of the individual RNA species in the ssRCC populations reflect the composition of the total mRNA population present in infected cells (which differs substantially from equimolarity). (4) RCCs that contain dsRNA, which become detectable as early as 4 hr after infection, contain not only microNS, sigma NS, and sigma 3, but also lambda 2. (5) The relative proportions of the 10 genome segments in dsRCCs are equimolar. This suggests that genome segment assortment into progeny genomes is linked to the transcription of plus strands into minus strands.

  14. Comparative genomic hybridization: Detection of segmental aneusomies

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    Cronin, J.E.; Magrane, G.G.; Gray, J.W. [Univ. of California, San Francisco, CA (United States)] [and others

    1994-09-01

    Comparative genomic hybridization (CGH) has been used successfully to detect whole chromosome and segmental aneusomies. However, its sensitivity for detection of segmental aneusomies is still not well known. We present here an analysis of CGH sensitivity with emphasis on detection of abnormalities commonly found during pre-and neo-natal diagnosis. CGH is performed by hybridizing green and red fluorescing test and normal DNA samples, respectively, to normal metaphase spreads and measuring green:red fluorescence ratios along all chromosomes. The ratios are normalized such that 2 copies of a normal chromosome region in the test sample gives a ratio of 1.0. Alterations in test vs. control gene copy number range from 1.5 [trisomy] to 0.5 [monosomy]. Clinical samples analyzed included Wolf Hirschhorn (4p-), Cri du Chat (5p-) and DiGeorge (22q-). In addition, 7 cell lines with chromosome 21 segmental aneusomies were analyzed. These included 3 with terminal duplications, 1 with a terminal deletion, 1 with an interstitial deletion and 2 with interstitial amplifications. The DiGeorge deletion was the only deletion not deleted by CGH. This is not surprising as standard G banding does not routinely detect this 1-2 megabase deletion. The 4p- and 5p- monosomies were detected and breakpoints correctly assigned prospectively. Proximal alterations involving 21q22.11 are unambiguously defined. Specifically, two interstitial aneusomies involving this region are detected. Studies involving late prophase chromosome normal spreads gave identical breakpoints. Thus, analysis of extended chromosomes did not improve the sensitivity of the technique. Taken together, these data suggest that CGH can detect segmental aneusomies greater than 8 megabases in extent. Smaller aneusomies can, at times, be detected. Work is now underway to modify the analysis software to increase sensitivity and to decrease the amount of material needed for analysis.

  15. Molecular characterization of the genome segments S4, S6 and S7 of rice gall dwarf virus.

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    Zhang, H M; Yang, J; Xin, X; Chen, J P; Adams, M J

    2007-01-01

    Rice gall dwarf virus (RGDV) is a member of the genus Phytoreovirus within the family Reovirdae. Its genome has 12 segments of double-stranded RNA (dsRNA), of which the nucleotide sequences of segments S4, S6, and S7 were determined, providing the first complete genome sequence of RGDV. Each of the segments S4, S6, and S7 contained conserved terminal sequences conforming to the RGDV consensus, 5'-GGXA ... UGAU-3' (X = U or C). Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of 79.8, 58.6, and 53.3 kDa. These proteins appeared to be homologous to those encoded by the corresponding segments of rice dwarf virus and wound tumor virus, the other known members of the same genus, having about 20-30% amino acid identity to them. It is therefore likely that RGDV S4 and S6 encode non-structural proteins and S7 an inner core protein. Probable homologies between the segments of all known phytoreoviruses are summarized. Beyond these similarities, the RGDV proteins displayed no significant similarity to any other reported viral proteins.

  16. Molecular characterization of eight segments of Scylla serrata reovirus (SsRV) provides the complete genome sequence.

    Science.gov (United States)

    Chen, Jigang; Xiong, Juan; Cui, Bojing; Yang, Jifang; Li, Wenchen; Mao, Zhijuan

    2012-08-01

    Scylla serrata reovirus (SsRV) is one of the most prevalent viral pathogens of mud crabs (S. serrata). Of the 12 double-stranded RNA (dsRNA) genomic segments (S1-S12), the three largest (S1-S3) and S7 were sequenced previously and were shown to have no or only low sequence homology to known members within the family Reoviridae. The sequences of the remaining segments, S4-S6 and S8-S12, are reported here. With the exception of S4, all have single open reading frames (ORFs) on their positive strands, and the terminal sequences 5'-AUAAA(U)/(C) (A)/(U)…G(A)/(G) (A)/(U) (A)/(C)AAC(G)/(U)AU-3' are conserved among currently and previously sequenced segments. S4 contains two out-of-phase ORFs on the positive strand, suggesting that this segment is bicistronic. The ORFs of segments S4-S6 and S8-S12 have low or no homology to other reovirus genes, with the exception that all of the SsRV segments have high sequence similarity to those of mud crab reovirus (MCRV) and share the same 5'- and 3'-terminal nucleotide sequences, suggesting that the two viruses belong to the same species in the family Reoviridae. Analysis of virion proteins revealed that SsRV contains at least eight structural proteins, with sizes ranging from 25 to 160 kDa.

  17. Balance of RNA sequence requirement and NS3/NS3a expression of segment 10 of orbiviruses

    NARCIS (Netherlands)

    Feenstra, Femke; Gennip, Van René G.P.; Schreuder, Myrte; Rijn, van Piet A.

    2016-01-01

    Orbiviruses are insect-transmitted, non-enveloped viruses with a ten-segmented dsRNA genome of which the bluetongue virus (BTV) is the prototype. Viral non-structural protein NS3/NS3a is encoded by genome segment 10 (Seg-10), and is involved in different virus release mechanisms. This protein ind

  18. The Feat of Packaging Eight Unique Genome Segments

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    Sebastian Giese

    2016-06-01

    Full Text Available Influenza A viruses (IAVs harbor a segmented RNA genome that is organized into eight distinct viral ribonucleoprotein (vRNP complexes. Although a segmented genome may be a major advantage to adapt to new host environments, it comes at the cost of a highly sophisticated genome packaging mechanism. Newly synthesized vRNPs conquer the cellular endosomal recycling machinery to access the viral budding site at the plasma membrane. Genome packaging sequences unique to each RNA genome segment are thought to be key determinants ensuring the assembly and incorporation of eight distinct vRNPs into progeny viral particles. Recent studies using advanced fluorescence microscopy techniques suggest the formation of vRNP sub-bundles (comprising less than eight vRNPs during their transport on recycling endosomes. The formation of such sub-bundles might be required for efficient packaging of a bundle of eight different genomes segments at the budding site, further highlighting the complexity of IAV genome packaging.

  19. Analysis of recent segmental duplications in the bovine genome

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    Li Congjun

    2009-12-01

    Full Text Available Abstract Background Duplicated sequences are an important source of gene innovation and structural variation within mammalian genomes. We performed the first systematic and genome-wide analysis of segmental duplications in the modern domesticated cattle (Bos taurus. Using two distinct computational analyses, we estimated that 3.1% (94.4 Mb of the bovine genome consists of recently duplicated sequences (≥ 1 kb in length, ≥ 90% sequence identity. Similar to other mammalian draft assemblies, almost half (47% of 94.4 Mb of these sequences have not been assigned to cattle chromosomes. Results In this study, we provide the first experimental validation large duplications and briefly compared their distribution on two independent bovine genome assemblies using fluorescent in situ hybridization (FISH. Our analyses suggest that the (75-90% of segmental duplications are organized into local tandem duplication clusters. Along with rodents and carnivores, these results now confidently establish tandem duplications as the most likely mammalian archetypical organization, in contrast to humans and great ape species which show a preponderance of interspersed duplications. A cross-species survey of duplicated genes and gene families indicated that duplication, positive selection and gene conversion have shaped primates, rodents, carnivores and ruminants to different degrees for their speciation and adaptation. We identified that bovine segmental duplications corresponding to genes are significantly enriched for specific biological functions such as immunity, digestion, lactation and reproduction. Conclusion Our results suggest that in most mammalian lineages segmental duplications are organized in a tandem configuration. Segmental duplications remain problematic for genome and assembly and we highlight genic regions that require higher quality sequence characterization. This study provides insights into mammalian genome evolution and generates a valuable

  20. Structural constraints in the packaging of bluetongue virus genomic segments.

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    Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C; Roy, Polly

    2014-10-01

    The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5' and 3' ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment.

  1. Use of bacterially expressed dsRNA to downregulate Entamoeba histolytica gene expression.

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    Carlos F Solis

    Full Text Available BACKGROUND: Modern RNA interference (RNAi methodologies using small interfering RNA (siRNA oligonucleotide duplexes or episomally synthesized hairpin RNA are valuable tools for the analysis of gene function in the protozoan parasite Entamoeba histolytica. However, these approaches still require time-consuming procedures including transfection and drug selection, or costly synthetic molecules. PRINCIPAL FINDINGS: Here we report an efficient and handy alternative for E. histolytica gene down-regulation mediated by bacterial double-stranded RNA (dsRNA targeting parasite genes. The Escherichia coli strain HT115 which is unable to degrade dsRNA, was genetically engineered to produce high quantities of long dsRNA segments targeting the genes that encode E. histolytica beta-tubulin and virulence factor KERP1. Trophozoites cultured in vitro were directly fed with dsRNA-expressing bacteria or soaked with purified dsRNA. Both dsRNA delivery methods resulted in significant reduction of protein expression. In vitro host cell-parasite assays showed that efficient downregulation of kerp1 gene expression mediated by bacterial dsRNA resulted in significant reduction of parasite adhesion and lytic capabilities, thus supporting a major role for KERP1 in the pathogenic process. Furthermore, treatment of trophozoites cultured in microtiter plates, with a repertoire of eighty-five distinct bacterial dsRNA segments targeting E. histolytica genes with unknown function, led to the identification of three genes potentially involved in the growth of the parasite. CONCLUSIONS: Our results showed that the use of bacterial dsRNA is a powerful method for the study of gene function in E. histolytica. This dsRNA delivery method is also technically suitable for the study of a large number of genes, thus opening interesting perspectives for the identification of novel drug and vaccine targets.

  2. The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats.

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    van der Weide, Robin H; Simonis, Marieke; Hermsen, Roel; Toonen, Pim; Cuppen, Edwin; de Ligt, Joep

    2016-01-01

    Unmapped next-generation sequencing reads are typically ignored while they contain biologically relevant information. We systematically analyzed unmapped reads from whole genome sequencing of 33 inbred rat strains. High quality reads were selected and enriched for biologically relevant sequences; similarity-based analysis revealed clustering similar to previously reported phylogenetic trees. Our results demonstrate that on average 20% of all unmapped reads harbor sequences that can be used to improve reference genomes and generate hypotheses on potential genotype-phenotype relationships. Analysis pipelines would benefit from incorporating the described methods and reference genomes would benefit from inclusion of the genomic segments obtained through these efforts.

  3. In vitro packaging of individual genomic segments of bacteriophage phi 6 RNA: serial dependence relationships.

    OpenAIRE

    Qiao, X; Casini, G.; Qiao, J; Mindich, L

    1995-01-01

    Bacteriophage phi 6 has a genome of three segments of double-stranded RNA enclosed in a procapsid composed of four different proteins. The preformed procapsid is capable of packaging plus-strand transcripts of the genomic segments in an in vitro reaction. The packaging of the three segments shows a strong order of dependence in that segment S packages alone, but segment M requires S and and segment L requires S and M for efficient packaging. Packaging of individual segments is dependent on un...

  4. Polymorphism of viral dsRNA in Xanthophyllomyces dendrorhous strains isolated from different geographic areas

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    Libkind Diego

    2009-10-01

    Full Text Available Abstract Background Strains of the astaxanthin producing yeast Xanthophyllomyces dendrorhous have been isolated from different cold regions around the earth, and the presence of double stranded RNA (dsRNA elements was described in some isolates. This kind of viruses is widely distributed among yeasts and filamentous fungi and, although generally are cryptic in function, their studies have been a key factor in the knowledge of important fungi. In this work, the characterization and genetic relationships among dsRNA elements were determined in strains representatives of almost all regions of the earth where X. dendrorhous have been isolated. Results Almost all strains of X. dendrorhous analyzed carry one, two or four dsRNA elements, of molecular sizes in the range from 0.8 to 5.0 kb. Different dsRNA-patterns were observed in strains with different geographic origin, being L1 (5.0 kb the common dsRNA element. By hybridization assays a high genomic polymorphism was observed among L1 dsRNAs of different X. dendrorhous strains. Contrary, hybridization was observed between L1 and L2 dsRNAs of strains from same or different regions, while the dsRNA elements of minor sizes (M, S1, and S2 present in several strains did not show hybridization with neither L1 or L2 dsRNAs. Along the growth curve of UCD 67-385 (harboring four dsRNAs an increase of L2 relative to L1 dsRNA was observed, whiles the S1/L1 ratio remains constant, as well as the M/L1 ratio of Patagonian strain. Strains cured of S2 dsRNA were obtained by treatment with anisomycin, and comparison of its dsRNA contents with uncured strain, revealed an increase of L1 dsRNA while the L2 and S1 dsRNA remain unaltered. Conclusion The dsRNA elements of X. dendrorhous are highly variable in size and sequence, and the dsRNA pattern is specific to the geographic region of isolation. Each L1 and L2 dsRNA are viral elements able to self replicate and to coexist into a cell, and L1 and S2 dsRNAs elements could

  5. Viral genome segmentation can result from a trade-off between genetic content and particle stability.

    Science.gov (United States)

    Ojosnegros, Samuel; García-Arriaza, Juan; Escarmís, Cristina; Manrubia, Susanna C; Perales, Celia; Arias, Armando; Mateu, Mauricio García; Domingo, Esteban

    2011-03-01

    The evolutionary benefit of viral genome segmentation is a classical, yet unsolved question in evolutionary biology and RNA genetics. Theoretical studies anticipated that replication of shorter RNA segments could provide a replicative advantage over standard size genomes. However, this question has remained elusive to experimentalists because of the lack of a proper viral model system. Here we present a study with a stable segmented bipartite RNA virus and its ancestor non-segmented counterpart, in an identical genomic nucleotide sequence context. Results of RNA replication, protein expression, competition experiments, and inactivation of infectious particles point to a non-replicative trait, the particle stability, as the main driver of fitness gain of segmented genomes. Accordingly, measurements of the volume occupation of the genome inside viral capsids indicate that packaging shorter genomes involves a relaxation of the packaging density that is energetically favourable. The empirical observations are used to design a computational model that predicts the existence of a critical multiplicity of infection for domination of segmented over standard types. Our experiments suggest that viral segmented genomes may have arisen as a molecular solution for the trade-off between genome length and particle stability. Genome segmentation allows maximizing the genetic content without the detrimental effect in stability derived from incresing genome length.

  6. Viral genome segmentation can result from a trade-off between genetic content and particle stability.

    Directory of Open Access Journals (Sweden)

    Samuel Ojosnegros

    2011-03-01

    Full Text Available The evolutionary benefit of viral genome segmentation is a classical, yet unsolved question in evolutionary biology and RNA genetics. Theoretical studies anticipated that replication of shorter RNA segments could provide a replicative advantage over standard size genomes. However, this question has remained elusive to experimentalists because of the lack of a proper viral model system. Here we present a study with a stable segmented bipartite RNA virus and its ancestor non-segmented counterpart, in an identical genomic nucleotide sequence context. Results of RNA replication, protein expression, competition experiments, and inactivation of infectious particles point to a non-replicative trait, the particle stability, as the main driver of fitness gain of segmented genomes. Accordingly, measurements of the volume occupation of the genome inside viral capsids indicate that packaging shorter genomes involves a relaxation of the packaging density that is energetically favourable. The empirical observations are used to design a computational model that predicts the existence of a critical multiplicity of infection for domination of segmented over standard types. Our experiments suggest that viral segmented genomes may have arisen as a molecular solution for the trade-off between genome length and particle stability. Genome segmentation allows maximizing the genetic content without the detrimental effect in stability derived from incresing genome length.

  7. Viral Genome Segmentation Can Result from a Trade-Off between Genetic Content and Particle Stability

    Science.gov (United States)

    Ojosnegros, Samuel; García-Arriaza, Juan; Escarmís, Cristina; Manrubia, Susanna C.; Perales, Celia; Arias, Armando; Mateu, Mauricio García; Domingo, Esteban

    2011-01-01

    The evolutionary benefit of viral genome segmentation is a classical, yet unsolved question in evolutionary biology and RNA genetics. Theoretical studies anticipated that replication of shorter RNA segments could provide a replicative advantage over standard size genomes. However, this question has remained elusive to experimentalists because of the lack of a proper viral model system. Here we present a study with a stable segmented bipartite RNA virus and its ancestor non-segmented counterpart, in an identical genomic nucleotide sequence context. Results of RNA replication, protein expression, competition experiments, and inactivation of infectious particles point to a non-replicative trait, the particle stability, as the main driver of fitness gain of segmented genomes. Accordingly, measurements of the volume occupation of the genome inside viral capsids indicate that packaging shorter genomes involves a relaxation of the packaging density that is energetically favourable. The empirical observations are used to design a computational model that predicts the existence of a critical multiplicity of infection for domination of segmented over standard types. Our experiments suggest that viral segmented genomes may have arisen as a molecular solution for the trade-off between genome length and particle stability. Genome segmentation allows maximizing the genetic content without the detrimental effect in stability derived from incresing genome length. PMID:21437265

  8. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

    Directory of Open Access Journals (Sweden)

    Xu Wanhong

    2008-12-01

    Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV

  9. Analysis Of Segmental Duplications In The Pig Genome Based On Next-Generation Sequencing

    DEFF Research Database (Denmark)

    Fadista, João; Bendixen, Christian

    extensively studied in other organisms, its analysis in pig has been hampered by the lack of a complete pig genome assembly. By measuring the depth of coverage of Illumina whole-genome shotgun sequencing reads of the Tabasco animal aligned to the latest pig genome assembly (Sus scrofa 10 – based also...... on Tabasco), led us to the detection of a high-resolution map of segmental duplications in the pig genome. Comparing these segments with four other Duroc animals sequenced at our institute, supplied the resources needed to describe the first genome-wide and systematic analysis of segmental duplications...

  10. Delivery of dsRNA for RNAi in insects: an overview and future directions.

    Science.gov (United States)

    Yu, Na; Christiaens, Olivier; Liu, Jisheng; Niu, Jinzhi; Cappelle, Kaat; Caccia, Silvia; Huvenne, Hanneke; Smagghe, Guy

    2013-02-01

    RNA interference (RNAi) refers to the process of exogenous double-stranded RNA (dsRNA) silencing the complementary endogenous messenger RNA. RNAi has been widely used in entomological research for functional genomics in a variety of insects and its potential for RNAi-based pest control has been increasingly emphasized mainly because of its high specificity. This review focuses on the approaches of introducing dsRNA into insect cells or insect bodies to induce effective RNAi. The three most common delivery methods, namely, microinjection, ingestion, and soaking, are illustrated in details and their advantages and limitations are summarized for purpose of feasible RNAi research. In this review, we also briefly introduce the two possible dsRNA uptake machineries, other dsRNA delivery methods and the history of RNAi in entomology. Factors that influence the specificity and efficiency of RNAi such as transfection reagents, selection of dsRNA region, length, and stability of dsRNA in RNAi research are discussed for further studies.

  11. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D.

    Science.gov (United States)

    Gonzalez, Gabriel; Koyanagi, Kanako O; Aoki, Koki; Kitaichi, Nobuyoshi; Ohno, Shigeaki; Kaneko, Hisatoshi; Ishida, Susumu; Watanabe, Hidemi

    2014-08-15

    Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Identification of the Genome Segments of Bluetongue Virus Serotype 26 (Isolate KUW2010/02 that Restrict Replication in a Culicoides sonorensis Cell Line (KC Cells.

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    Gillian D Pullinger

    Full Text Available Bluetongue virus (BTV can infect most ruminant species and is usually transmitted by adult, vector-competent biting midges (Culicoides spp.. Infection with BTV can cause severe clinical signs and can be fatal, particularly in naïve sheep and some deer species. Although 24 distinct BTV serotypes were recognized for several decades, additional 'types' have recently been identified, including BTV-25 (from Switzerland, BTV-26 (from Kuwait and BTV-27 from France (Corsica. Although BTV-25 has failed to grow in either insect or mammalian cell cultures, BTV-26 (isolate KUW2010/02, which can be transmitted horizontally between goats in the absence of vector insects, does not replicate in a Culicoides sonorensis cell line (KC cells but can be propagated in mammalian cells (BSR cells. The BTV genome consists of ten segments of linear dsRNA. Mono-reassortant viruses were generated by reverse-genetics, each one containing a single BTV-26 genome segment in a BTV-1 genetic-background. However, attempts to recover a mono-reassortant containing genome-segment 2 (Seg-2 of BTV-26 (encoding VP2, were unsuccessful but a triple-reassortant was successfully generated containing Seg-2, Seg-6 and Seg-7 (encoding VP5 and VP7 respectively of BTV-26. Reassortants were recovered and most replicated well in mammalian cells (BSR cells. However, mono-reassortants containing Seg-1 or Seg-3 of BTV-26 (encoding VP1, or VP3 respectively and the triple reassortant failed to replicate, while a mono-reassortant containing Seg-7 of BTV-26 only replicated slowly in KC cells.

  13. Exploration of sequence space as the basis of viral RNA genome segmentation.

    Science.gov (United States)

    Moreno, Elena; Ojosnegros, Samuel; García-Arriaza, Juan; Escarmís, Cristina; Domingo, Esteban; Perales, Celia

    2014-05-06

    The mechanisms of viral RNA genome segmentation are unknown. On extensive passage of foot-and-mouth disease virus in baby hamster kidney-21 cells, the virus accumulated multiple point mutations and underwent a transition akin to genome segmentation. The standard single RNA genome molecule was replaced by genomes harboring internal in-frame deletions affecting the L- or capsid-coding region. These genomes were infectious and killed cells by complementation. Here we show that the point mutations in the nonstructural protein-coding region (P2, P3) that accumulated in the standard genome before segmentation increased the relative fitness of the segmented version relative to the standard genome. Fitness increase was documented by intracellular expression of virus-coded proteins and infectious progeny production by RNAs with the internal deletions placed in the sequence context of the parental and evolved genome. The complementation activity involved several viral proteins, one of them being the leader proteinase L. Thus, a history of genetic drift with accumulation of point mutations was needed to allow a major variation in the structure of a viral genome. Thus, exploration of sequence space by a viral genome (in this case an unsegmented RNA) can reach a point of the space in which a totally different genome structure (in this case, a segmented RNA) is favored over the form that performed the exploration.

  14. dsRNA interference on expression of a RNA-dependent RNA polymerase gene of Bombyx mori cytoplasmic polyhedrosis virus.

    Science.gov (United States)

    Pan, Zhong-Hua; Gao, Kun; Hou, Cheng-Xiang; Wu, Ping; Qin, Guang-Xing; Geng, Tao; Guo, Xi-Jie

    2015-07-01

    Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) is one of the major viral pathogens in silkworm. Its infection often results in significant losses to sericulture. Studies have demonstrated that RNAi is one of the important anti-viral mechanisms in organisms. In this study, three dsRNAs targeting the RNA-dependent RNA polymerase (RDRP) gene of BmCPV were designed and synthesized with 2'-F modification to explore their interference effects on BmCPV replication in silkworm larvae. The results showed that injecting dsRNA in the dosage of 4-6 ng per mg body weight into the 5th instar larvae can interfere with the BmCPV-RDRP expression by 93% after virus infection and by 99.9% before virus infection. In addition, the expression of two viral structural protein genes (genome RNA segments 1 and 5) was also decreased with the decrease of RDRP expression, suggesting that RNAi interference of BmCPV-RDRP expression could affect viral replication. The study provides an effective method for investigating virus replication as well as the virus-host interactions in the silkworm larvae using dsRNA.

  15. Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method.

    Science.gov (United States)

    Zhang, Ren; Ou, Hong-Yu; Gao, Feng; Luo, Hao

    2014-04-01

    The nucleotide composition of genomes undergoes dramatic variations among all three kingdoms of life. GC content, an important characteristic for a genome, is related to many important functions, and therefore GC content and its distribution are routinely reported for sequenced genomes. Traditionally, GC content distribution is assessed by computing GC contents in windows that slide along the genome. Disadvantages of this routinely used window-based method include low resolution and low sensitivity. Additionally, different window sizes result in different GC content distribution patterns within the same genome. We proposed a windowless method, the GC profile, for displaying GC content variations across the genome. Compared to the window-based method, the GC profile has the following advantages: 1) higher sensitivity, because of variation-amplifying procedures; 2) higher resolution, because boundaries between domains can be determined at one single base pair; 3) uniqueness, because the GC profile is unique for a given genome and 4) the capacity to show both global and regional GC content distributions. These characteristics are useful in identifying horizontally-transferred genomic islands and homogenous GC-content domains. Here, we review the applications of the GC profile in identifying genomic islands and genome segmentation points, and in serving as a platform to integrate with other algorithms for genome analysis. A web server generating GC profiles and implementing relevant genome segmentation algorithms is available at: www.zcurve.net.

  16. RNA structural constraints in the evolution of the influenza A virus genome NP segment

    NARCIS (Netherlands)

    A.P. Gultyaev (Alexander); A. Tsyganov-Bodounov (Anton); M.I. Spronken (Monique); S. Van Der Kooij (Sander); R.A.M. Fouchier (Ron); R.C.L. Olsthoorn (René)

    2014-01-01

    textabstractConserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, includi

  17. The word landscape of the non-coding segments of the Arabidopsis thaliana genome

    Directory of Open Access Journals (Sweden)

    Geisler Matt

    2009-10-01

    Full Text Available Abstract Background Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression. Results Using an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of Arabidopsis thaliana. Focusing on promoter regions, introns, and 3' and 5' untranslated regions (3'UTRs and 5'UTRs, we compared word frequencies in these segments to genome-wide frequencies. The statistically interesting words in each segment were clustered with similar words to generate motif logos. We investigated whether words were clustered at particular locations or were distributed randomly within each genomic segment, and we classified the words using gene expression information from public repositories. Finally, we investigated whether particular sets of words appeared together more frequently than others. Conclusion Our studies provide a detailed view of the word composition of several segments of the non-coding portion of the Arabidopsis genome. Each segment contains a unique word-based signature. The respective signatures consist of the sets of enriched words, 'unwords', and word pairs within a segment, as well as the preferential locations and functional classifications for the signature words. Additionally, the positional distributions of enriched words within the segments highlight possible functional elements, and the co-associations of words in promoter regions likely represent the formation of higher order regulatory modules. This work is an important step toward fully cataloguing the functional elements of the Arabidopsis genome.

  18. Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes.

    Science.gov (United States)

    Khaja, Razi; MacDonald, Jeffrey R; Zhang, Junjun; Scherer, Stephen W

    2006-01-01

    The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

  19. Unusual assortment of segments in 2 rare human rotavirus genomes.

    Science.gov (United States)

    De Grazia, Simona; Giammanco, Giovanni M; Potgieter, Christiaan A; Matthijnssens, Jelle; Banyai, Krisztian; Platia, Maria A; Colomba, Claudia; Martella, Vito

    2010-05-01

    Using full-length genome sequence analysis, we investigated 2 rare G3P[9] human rotavirus strains isolated from children with diarrhea. The genomes were recognized as assortments of genes closely related to rotaviruses originating from cats, ruminants, and humans. Results suggest multiple transmissions of genes from animal to human strains of rotaviruses.

  20. Transmission of dsRNA in Cryphonectria parasitica and it's Affecting Factors%栗疫菌弱毒力特征的传递及其影响因素

    Institute of Scientific and Technical Information of China (English)

    王克荣; 周而勋; 姜爱萍; 成桂英

    2004-01-01

    dsRNA in Cryphonectria parasitica could be transmitted to progeny through conidia with varying efficiency in culture. Both light and prolonging cultural time could reduce the transmission efficiency, but the effect of light was more efficient. No dsRNA segments were found to be loss after 30 generations subculture, indicating that dsRNA could transmitted stably through subculture. Vegetative incompatibility was a barrier for the transfer of dsRNA from one isolate to another, and hypovirulence conversion reduced as the number of different VC genes between donor and recipient isolates increased.

  1. Analysis of high-identity segmental duplications in the grapevine genome

    Directory of Open Access Journals (Sweden)

    Carelli Francesco N

    2011-08-01

    Full Text Available Abstract Background Segmental duplications (SDs are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera genome (PN40024. Results We demonstrate that recent SDs (> 94% identity and >= 10 kb in size are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence. We detected mitochondrial and plastid DNA and genes (10% of gene annotation in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress. Conclusions These data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.

  2. Detection of Maize rough dwarf virus in Spain: a survey of susceptible host genotypes and molecular characterization of two genomic segments of the virus

    Directory of Open Access Journals (Sweden)

    Vilma ORTIZ

    2014-05-01

    Full Text Available An increase in the number of plants infected with Maize rough dwarf disease (MRDD has been reported recently in Spain. The disease was presumed to be caused by Maize rough dwarf virus (MRDV, but there was no conclusive evidence for this assumption. Two viruses have been associated with MRDD: Rice black streaked dwarf virus (RBSDV and MRDV. In this study, maize plants showing MRDD in the Ebro zone province of Lerida, Spain were assessed using common primers for MRDV and RBSDV. Molecular characterization of one isolate and phylogenetic analysis were also carried out. Polyacrylamide electrophoretic profiles of genome segments of dsRNA, the size of PCR amplified fragments and the nucleotide sequence comparison matched closely with Maize rough dwarf virus Italian isolate (MRDV accession no. L76561, confirming that MRDV is present in maize plants showing MRDD in Spain. The phylogenetic analysis made with segments S9 and S10 from Fijivirus and the MRDV-Sp isolate obtained in the present study, showed that: i MRDV is closely related to RBSDV; ii there is high variability within isolates clustering as RBSDV in S9, especially in the ORF1 at the amino acid level, which allowed grouping one isolate close to MRDV; and iii the grouping of RBSDV isolates at the 3’NCR of S9 was correlated with the host. The incidence of MRDD varied between two locations sampled, probably associated with sowing date, the presence of the winged form of the MRDV vector Laodelphax striatellus and differences in the abundance of virus reservoir plants.

  3. Segmenting the human genome based on states of neutral genetic divergence.

    Science.gov (United States)

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-03

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  4. RNA editing by ADAR1 prevents MDA5 sensing of endogenous dsRNA as nonself.

    Science.gov (United States)

    Liddicoat, Brian J; Piskol, Robert; Chalk, Alistair M; Ramaswami, Gokul; Higuchi, Miyoko; Hartner, Jochen C; Li, Jin Billy; Seeburg, Peter H; Walkley, Carl R

    2015-09-04

    Adenosine-to-inosine (A-to-I) editing is a highly prevalent posttranscriptional modification of RNA, mediated by ADAR (adenosine deaminase acting on RNA) enzymes. In addition to RNA editing, additional functions have been proposed for ADAR1. To determine the specific role of RNA editing by ADAR1, we generated mice with an editing-deficient knock-in mutation (Adar1(E861A), where E861A denotes Glu(861)→Ala(861)). Adar1(E861A/E861A) embryos died at ~E13.5 (embryonic day 13.5), with activated interferon and double-stranded RNA (dsRNA)-sensing pathways. Genome-wide analysis of the in vivo substrates of ADAR1 identified clustered hyperediting within long dsRNA stem loops within 3' untranslated regions of endogenous transcripts. Finally, embryonic death and phenotypes of Adar1(E861A/E861A) were rescued by concurrent deletion of the cytosolic sensor of dsRNA, MDA5. A-to-I editing of endogenous dsRNA is the essential function of ADAR1, preventing the activation of the cytosolic dsRNA response by endogenous transcripts. Copyright © 2015, American Association for the Advancement of Science.

  5. Molecular epidemiology of bovine rotaviruses. Characterization of rotaviruses isolated from diarrhoeic calves by genome profile analysis.

    Science.gov (United States)

    Legrottaglie, R; Rizzi, V; Agrimi, P

    1995-04-01

    Fifteen bovine rotavirus group A strains were isolated in several Italian regions over the period 1981-1989 from calves in ten neonatal diarrhoea outbreaks. The electrophoretical analysis of the genoma showed genomic variations and five different profiles were observed, including one with thirteen dsRNA segments. The finding of extra RNA fragments, with respect to the regular eleven genome segments, suggests the possibility of simultaneous or sequential infection by more than one electropherotype or a modification in the length of RNA segments during infection.

  6. Evidence that avian reovirus σNS is an RNA chaperone: implications for genome segment assortment.

    Science.gov (United States)

    Borodavka, Alexander; Ault, James; Stockley, Peter G; Tuma, Roman

    2015-08-18

    Reoviruses are important human, animal and plant pathogens having 10-12 segments of double-stranded genomic RNA. The mechanisms controlling the assortment and packaging of genomic segments in these viruses, remain poorly understood. RNA-protein and RNA-RNA interactions between viral genomic segment precursors have been implicated in the process. While non-structural viral RNA-binding proteins, such as avian reovirus σNS, are essential for virus replication, the mechanism by which they assist packaging is unclear. Here we demonstrate that σNS assembles into stable elongated hexamers in vitro, which bind single-stranded nucleic acids with high affinity, but little sequence specificity. Using ensemble and single molecule fluorescence spectroscopy, we show that σNS also binds to a partially double-stranded RNA, resulting in gradual helix unwinding. The hexamer can bind multiple RNA molecules and exhibits strand-annealing activity, thus mediating conversion of metastable, intramolecular stem-loops into more stable heteroduplexes. We demonstrate that the ARV σNS acts as an RNA chaperone facilitating specific RNA-RNA interactions between genomic precursors during segment assortment and packaging.

  7. Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence.

    Science.gov (United States)

    Kotta-Loizou, Ioly; Coutts, Robert H A

    2017-01-01

    The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests. Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely. Here we show that 21.3% of a collection of B. bassiana isolates sourced from worldwide locations, harbor dsRNA elements. Molecular characterization of these elements revealed the prevalence of mycoviruses belonging to the Partitiviridae and Totiviridae families, the smallest reported virus to date, belonging to the family Narnaviridae, and viruses unassigned to a family or genus. Of particular importance is the discovery of members of a newly proposed family Polymycoviridae in B. bassiana. Polymycoviruses, previously designated as tetramycoviruses, consist of four non-conventionally encapsidated capped dsRNAs. The presence of additional non-homologous genomic segments in B. bassiana polymycoviruses and other fungi illustrates the unprecedented dynamic nature of the viral genome. Finally, a comparison of virus-free and virus-infected isogenic lines derived from an exemplar B. bassiana isolate revealed a mild hypervirulent effect of mycoviruses on the growth of their host isolate and on its pathogenicity against the greater wax moth Galleria mellonella, highlighting for the first time the potential of mycoviruses as enhancers of biocontrol agents.

  8. Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease.

    Directory of Open Access Journals (Sweden)

    Kathryn M Hastie

    Full Text Available Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA. dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by "relocation" of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.

  9. Structural basis for the dsRNA specificity of the Lassa virus NP exonuclease.

    Science.gov (United States)

    Hastie, Kathryn M; King, Liam B; Zandonatti, Michelle A; Saphire, Erica Ollmann

    2012-01-01

    Lassa virus causes hemorrhagic fever characterized by immunosuppression. The nucleoprotein of Lassa virus, termed NP, binds the viral genome. It also has an additional enzymatic activity as an exonuclease that specifically digests double-stranded RNA (dsRNA). dsRNA is a strong signal to the innate immune system of viral infection. Digestion of dsRNA by the NP exonuclease activity appears to cause suppression of innate immune signaling in the infected cell. Although the fold of the NP enzyme is conserved and the active site completely conserved with other exonucleases in its DEDDh family, NP is atypical among exonucleases in its preference for dsRNA and its strict specificity for one substrate. Here, we present the crystal structure of Lassa virus NP in complex with dsRNA. We find that unlike the exonuclease in Klenow fragment, the double-stranded nucleic acid in complex with Lassa NP remains base-paired instead of splitting, and that binding of the paired complementary strand is achieved by "relocation" of a basic loop motif from its typical exonuclease position. Further, we find that just one single glycine that contacts the substrate strand and one single tyrosine that stacks with a base of the complementary, non-substrate strand are responsible for the unique substrate specificity. This work thus provides templates for development of antiviral drugs that would be specific for viral, rather than host exonucleases of similar fold and active site, and illustrates how a very few amino acid changes confer alternate specificity and biological phenotype to an enzyme.

  10. POLAR MODELLING AND SEGMENTATION OF GENOMIC MICROARRAY SPOTS USING MATHEMATICAL MORPHOLOGY

    Directory of Open Access Journals (Sweden)

    Jesús Angulo

    2011-05-01

    Full Text Available Robust image analysis of spots in microarrays (quality control + spot segmentation + quantification is a requirement for automated software which is of fundamental importance for a high-throughput analysis of genomics microarray-based data. This paper deals with the development of model-based image processing algorithms for qualifying/segmenting/quantifying adaptively each spot according to its morphology. A series of morphologicalmodels for spot intensities are introduced. The spot typologies representmost of the possible qualitative cases identified from a large database (different routines, techniques, etc.. Then, based on these spot models, a classification framework has been developed. The spot feature extraction and classification (without segmenting is based on converting the spot image to polar coordinates and, after computing the radial/angular projections, the calculation of granulometric curves and derived parameters from these projections. Spot contour segmentation can also be solved by working in polar coordinates, calculating the up/downminimal path, which is easily obtained with the generalized distance function. With this model-based technique, the segmentation can be regularised by controlling different elements of the algorithm. According to the spot typology (e.g., doughnut-like or egg-like spots, several minimal paths can be computed to obtain a multi-region segmentation. Moreover, this segmentation is more robust and sensible to weak spots, improving the previous approaches.

  11. Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis

    Directory of Open Access Journals (Sweden)

    Paterson Andrew H

    2009-11-01

    Full Text Available Abstract Background The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level. Results We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events. Conclusion Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions

  12. The genomic architecture of segmental duplications and associated copy number variants in dogs.

    Science.gov (United States)

    Nicholas, Thomas J; Cheng, Ze; Ventura, Mario; Mealey, Katrina; Eichler, Evan E; Akey, Joshua M

    2009-03-01

    Structural variation is an important and abundant source of genetic and phenotypic variation. Here we describe the first systematic and genome-wide analysis of segmental duplications and associated copy number variants (CNVs) in the modern domesticated dog, Canis familiaris, which exhibits considerable morphological, physiological, and behavioral variation. Through computational analyses of the publicly available canine reference sequence, we estimate that segmental duplications comprise approximately 4.21% of the canine genome. Segmental duplications overlap 841 genes and are significantly enriched for specific biological functions such as immunity and defense and KRAB box transcription factors. We designed high-density tiling arrays spanning all predicted segmental duplications and performed aCGH in a panel of 17 breeds and a gray wolf. In total, we identified 3583 CNVs, approximately 68% of which were found in two or more samples that map to 678 unique regions. CNVs span 429 genes that are involved in a wide variety of biological processes such as olfaction, immunity, and gene regulation. Our results provide insight into mechanisms of canine genome evolution and generate a valuable resource for future evolutionary and phenotypic studies.

  13. Mechanisms of dsRNA uptake in insects and potential of RNAi for pest control: a review.

    Science.gov (United States)

    Huvenne, Hanneke; Smagghe, Guy

    2010-03-01

    RNA interference already proved its usefulness in functional genomic research on insects, but it also has considerable potential for the control of pest insects. For this purpose, the insect should be able to autonomously take up the dsRNA, for example through feeding and digestion in its midgut. In this review we bring together current knowledge on the uptake mechanisms of dsRNA in insects and the potential of RNAi to affect pest insects. At least two pathways for dsRNA uptake in insects are described: the transmembrane channel-mediated uptake mechanism based on Caenorhabditis elegans' SID-1 protein and an 'alternative' endocytosis-mediated uptake mechanism. In the second part of the review dsRNA feeding experiments on insects are brought together for the first time, highlighting the achievement of implementing RNAi in insect control with the first successful experiments in transgenic plants and the diversity of successfully tested insect orders/species and target genes. We conclude with points of discussion and concerns regarding further research on dsRNA uptake mechanisms and the promising application possibilities for RNAi in insect control.

  14. Assignment of simian rotavirus SA11 temperature-sensitive mutant groups B and E to genome segments

    Energy Technology Data Exchange (ETDEWEB)

    Gombold, J.L.; Estes, M.K.; Ramig, R.F.

    1985-05-01

    Recombinant (reassortant) viruses were selected from crosses between temperature-sensitive (ts) mutants of simian rotavirus SA11 and wild-type human rotavirus Wa. The double-stranded genome RNAs of the reassortants were examined by electrophoresis in Tris-glycine-buffered polyacrylamide gels and by dot hybridization with a cloned DNA probe for genome segment 2. Analysis of replacements of genome segments in the reassortants allowed construction of a map correlating genome segments providing functions interchangeable between SA11 and Wa. The reassortants revealed a functional correspondence in order of increasing electrophoretic mobility of genome segments. Analysis of the parental origin of genome segments in ts+ SA11/Wa reassortants derived from the crosses SA11 tsB(339) X Wa and SA11 tsE(1400) X Wa revealed that the group B lesion of tsB(339) was located on genome segment 3 and the group E lesion of tsE(1400) was on segment 8.

  15. Complete nucleotide sequence of wound tumor virus genomic segments encoding nonstructural polypeptides.

    Science.gov (United States)

    Anzola, J V; Dall, D J; Xu, Z K; Nuss, D L

    1989-07-01

    Sequence analysis of the genomic segments which encode the five wound tumor virus nonstructural polypeptides has been completed. The complete nucleotide sequence of segments S4 (2565 bp), S6 (1700 bp), S9 (1182 bp), and S10 (1172 bp) are presented in this report while the sequence of segment S12 (851 bp) has been described previously (T. Asamizu, D. Summers, M. B. Motika, J. V. Anzola, and D. L. Nuss, 1985, Virology 144, 398-409). Comparison of the only published sequence for another member of the genus Phytoreovirus, that of rice dwarf virus segment S10, with the combined available wound tumor virus sequence data revealed similarity with WTV segment S10: 54.9 and 30.6% at the nucleotide and amino acid level, respectively. Although wound tumor virus and rice dwarf virus differ in plant host range, tissue specificity, vector range, and disease symptom expression, the level of sequence similarity shared by the two segments suggests a common origin for these viruses. The potential use of a phytoreovirus sequence database for predicting functions of viral encoded gene products is considered.

  16. Inhibiting DNA methylation causes an interferon response in cancer via dsRNA including endogenous retroviruses

    Science.gov (United States)

    Chiappinelli, Katherine B.; Strissel, Pamela L.; Desrichard, Alexis; Li, Huili; Henke, Christine; Akman, Benjamin; Hein, Alexander; Rote, Neal S.; Cope, Leslie M.; Snyder, Alexandra; Makarov, Vladimir; Buhu, Sadna; Slamon, Dennis J.; Wolchok, Jedd D.; Pardoll, Drew M.; Beckmann, Matthias W.; Zahnow, Cynthia A.; Mergoub, Taha; Chan, Timothy A.; Baylin, Stephen B.; Strick, Reiner

    2015-01-01

    Summary We show that DNA methyltransferase inhibitors (DNMTis) upregulate immune signaling in cancer through the viral defense pathway. In ovarian cancer (OC), DNMTis trigger cytosolic sensing of double-stranded RNA (dsRNA) causing a Type I Interferon response and apoptosis. Knocking down dsRNA sensors TLR3 and MAVS reduces this response twofold, and blocking interferon beta or its receptor abrogates it. Upregulation of hypermethylated endogenous retrovirus (ERV) genes accompanies the response and ERV overexpression activates the response. Basal levels of ERV and viral defense gene expression significantly correlate in primary OC and the latter signature separates primary samples for multiple tumor types from The Cancer Genome Atlas into low versus high expression groups. In melanoma patients treated with an immune checkpoint therapy, high viral defense signature expression in tumors significantly associates with durable clinical response and DNMTi treatment sensitizes to anti-CTLA4 therapy in a pre-clinical melanoma model. PMID:26317466

  17. Genetic modification of Bluetongue virus by uptake of "synthetic" genome segments

    Directory of Open Access Journals (Sweden)

    van de Water Sandra GP

    2010-10-01

    Full Text Available Abstract Since 1998, several serotypes of Bluetongue virus (BTV have invaded several southern European countries. In 2006, the unknown BTV serotype 8 (BTV8/net06 unexpectedly invaded North-West Europe and has resulted in the largest BT-outbreak ever recorded. More recently, in 2008 BTV serotype 6 was reported in the Netherlands and Germany. This virus, BTV6/net08, is closely related to modified-live vaccine virus serotype 6, except for genome segment S10. This genome segment is closer related to that of vaccine virus serotype 2, and therefore BTV6/net08 is considered as a result of reassortment. Research on orbiviruses has been hampered by the lack of a genetic modification method. Recently, reverse genetics has been developed for BTV based on ten in vitro synthesized genomic RNAs. Here, we describe a targeted single-gene modification system for BTV based on the uptake of a single in vitro synthesized viral positive-stranded RNA. cDNAs corresponding to BTV8/net06 genome segments S7 and S10 were obtained by gene synthesis and cloned downstream of the T7 RNA-polymerase promoter and upstream of a unique site for a restriction enzyme at the 3'-terminus for run-off transcription. Monolayers of BSR cells were infected by BTV6/net08, and subsequently transfected with purified in vitro synthesized, capped positive-stranded S7 or S10 RNA from BTV8/net06 origin. "Synthetic" reassortants were rescued by endpoint dilutions, and identified by serotype-specific PCR-assays for segment 2, and serogroup-specific PCRs followed by restriction enzyme analysis or sequencing for S7 and S10 segments. The targeted single-gene modification system can also be used to study functions of viral proteins by uptake of mutated genome segments. This method is also useful to generate mutant orbiviruses for other serogroups of the genus Orbivirus for which reverse genetics has not been developed yet.

  18. Stochastic segmentation models for array-based comparative genomic hybridization data analysis.

    Science.gov (United States)

    Lai, Tze Leung; Xing, Haipeng; Zhang, Nancy

    2008-04-01

    Array-based comparative genomic hybridization (array-CGH) is a high throughput, high resolution technique for studying the genetics of cancer. Analysis of array-CGH data typically involves estimation of the underlying chromosome copy numbers from the log fluorescence ratios and segmenting the chromosome into regions with the same copy number at each location. We propose for the analysis of array-CGH data, a new stochastic segmentation model and an associated estimation procedure that has attractive statistical and computational properties. An important benefit of this Bayesian segmentation model is that it yields explicit formulas for posterior means, which can be used to estimate the signal directly without performing segmentation. Other quantities relating to the posterior distribution that are useful for providing confidence assessments of any given segmentation can also be estimated by using our method. We propose an approximation method whose computation time is linear in sequence length which makes our method practically applicable to the new higher density arrays. Simulation studies and applications to real array-CGH data illustrate the advantages of the proposed approach.

  19. Analysis of segmental duplications reveals a distinct pattern of continuation-of-synteny between human and mouse genomes.

    Science.gov (United States)

    Mehan, Michael R; Almonte, Maricel; Slaten, Erin; Freimer, Nelson B; Rao, P Nagesh; Ophoff, Roel A

    2007-03-01

    About 5% of the human genome consists of large-scale duplicated segments of almost identical sequences. Segmental duplications (SDs) have been proposed to be involved in non-allelic homologous recombination leading to recurrent genomic variation and disease. It has also been suggested that these SDs are associated with syntenic rearrangements that have shaped the human genome. We have analyzed 14 members of a single family of closely related SDs in the human genome, some of which are associated with common inversion polymorphisms at chromosomes 8p23 and 4p16. Comparative analysis with the mouse genome revealed syntenic inversions for these two human polymorphic loci. In addition, 12 of the 14 SDs, while absent in the mouse genome, occur at the breaks of synteny; suggesting a non-random involvement of these sequences in genome evolution. Furthermore, we observed a syntenic familial relationship between 8 and 12 breakpoint-loci, where broken synteny that ends at one family member resumes at another, even across different chromosomes. Subsequent genome-wide assessment revealed that this relationship, which we named continuation-of-synteny, is not limited to the 8p23 family and occurs 46 times in the human genome with high frequency at specific chromosomes. Our analysis supports a non-random breakage model of genomic evolution with an active involvement of segmental duplications for specific regions of the human genome.

  20. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

    LENUS (Irish Health Repository)

    OhEigeartaigh, Sean S

    2011-07-26

    Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

  1. Concatemeric intermediates of equine herpesvirus type 1 DNA replication contain frequent inversions of adjacent long segments of the viral genome.

    Science.gov (United States)

    Slobedman, B; Simmons, A

    1997-03-17

    In common with other alpha-herpesviruses, the genome of equine herpesvirus type-1 (EHV-1) comprises covalently linked long and short unique sequences of DNA, each flanked by inverted repeats. Equimolar amounts of two genomic isomers, generated by free inversion of the short segment, relative to the long segment, are packaged into EHV-1 virions. In contrast with herpes simplex virus (HSV), inversion of genomic long segments has not been described. In the current work, the structures of high molecular weight intermediates of EHV-1 DNA replication were studied by field inversion gel electrophoresis. It is shown that adjacent long segments of the viral genome are frequently inverted in concatemeric intermediates of EHV-1 DNA replication. Further, like HSV concatemers, high molecular weight intermediates of EHV-1 replication are flanked exclusively by the long segment of the viral genome. Hence, despite the fact that only two, rather than four, isomers of EHV-1 DNA are packaged into virions, the intermediates of EHV-1 DNA replication closely resemble those of herpes simplex virus type 1 in structure. These data have implications relating to the mechanisms involved in packaging of alpha-herpesvirus DNA.

  2. Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans.

    Directory of Open Access Journals (Sweden)

    Mohammed Uddin

    Full Text Available The primary objective of this study was to create a genome-wide high resolution map (i.e., >100 bp of 'rearrangement hotspots' which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a 'seed and extend' approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (18× coverage, including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs. These regions are correlated with increased non-allelic homologous recombination (NAHR event frequency which presumably represents the origin of copy number variations (CNVs and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of 'rearrangement hotspots', which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s for development of constitutional and acquired diseases.

  3. Characterization of gene expression on genomic segment 7 of infectious salmon anaemia virus

    Directory of Open Access Journals (Sweden)

    Qian Biao

    2007-03-01

    Full Text Available Abstract Background Infectious salmon anaemia (ISA virus (ISAV, an important pathogen of fish that causes disease accompanied by high mortality in marine-farmed Atlantic salmon, is the only species in the genus Isavirus, one of the five genera of the Orthomyxoviridae family. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; haemagglutinin-esterase (HE protein encoded on segment 6 and fusion (F protein encoded on segment 5. Based on the initial demonstration of two 5'-coterminal mRNA transcripts by RT-PCR, ISAV genomic segment 7 was suggested to share a similar coding strategy with segment 7 of influenza A virus, encoding two proteins. However, there appears to be confusion as to the protein sizes predicted from the two open reading frames (ORFs of ISAV segment 7 which has in turn led to confusion of the predicted protein functions. The primary goal of the present work was to clone and express these two ORFs in order to assess whether the predicted protein sizes match those of the expressed proteins so as to clarify the coding assignments, and thereby identify any additional structural proteins of ISAV. Results In the present study we show that ISAV segment 7 encodes 3 proteins with estimated molecular masses of 32, 18, and 9.5 kDa. The 18-kDa and 9.5-kDa products are based on removal of an intron each from the primary transcript (7-ORF1 so that the translation continues in the +2 and +3 reading frames, respectively. The segment 7-ORF1/3 product is variably truncated in the sequence of ISAV isolates of the European genotype. All three proteins are recognized by rabbit antiserum against the 32-kDa product of the primary transcript, as they all share the N-terminal 22 amino acids. This antiserum detected a single 35-kDa protein in Western blots of purified virus, and immunoprecipitated a 32-kDa protein in ISAV-infected TO cells. Immunofluorescence staining of infected cells with the

  4. Shared genomic segment analysis: the power to find rare disease variants.

    Science.gov (United States)

    Knight, Stacey; Abo, Ryan P; Abel, Haley J; Neklason, Deborah W; Tuohy, Therese M; Burt, Randall W; Thomas, Alun; Camp, Nicola J

    2012-11-01

    Shared genomic segment (SGS) analysis uses dense single nucleotide polymorphism genotyping in high-risk (HR) pedigrees to identify regions of sharing between cases. Here, we illustrate the power of SGS to identify dominant rare risk variants. Using simulated pedigrees, we consider 12 disease models based on disease prevalence, minor allele frequency and penetrance to represent disease loci that explain 0.2-99.8% of total disease risk. Pedigrees were required to contain ≥ 15 meioses between all cases and to be HR based on significant excess of disease (P power for a single pedigree ranged widely. Nonetheless, fewer than 10 pedigrees were sufficient for excellent power in the majority of models. Power increased with the risk attributable to the disease locus, penetrance and the excess of disease in the pedigree. Sharing allowing for one sporadic case was uniformly more powerful than sharing using all cases. Furthermore, an SGS analysis using a large attenuated familial adenomatous polyposis pedigree identified a 1.96 Mb region containing the known causal APC gene with genome-wide significance. SGS is a powerful method for detecting rare variants and a valuable complement to genome-wide association studies and linkage analysis.

  5. Sequencing of the bicistronic genome segments S7 and S9 of Mal de Río Cuarto virus (Fijivirus, Reoviridae) completes the genome of this virus.

    Science.gov (United States)

    Guzmán, F A; Distéfano, A J; Arneodo, J D; Hopp, H E; Lenardon, S L; del Vas, M; Conci, L R

    2007-01-01

    The nucleotide sequences of genomic segments S7 and S9 of Mal de Río Cuarto virus (MRCV, Fijivirus group II) have been determined, thus completing the entire genome sequence of the virus. These segments showed a non-overlapping bicistronic structure, as in other members of the genus. MRCV S7 ORF-1 had a length of 1086 bp and encoded a 41.5 kDa putative polypeptide, whereas MRCV S7 ORF-2 had a length of 930 bp and encoded a 36.8 kDa putative polypeptide. Proteins of 39 and 20.5 kDa were predicted for the 1014 bp long MRCV S9 ORF-1 and the 537 bp long MRCV S9 ORF-2, respectively. The terminal 5' and 3' sequences of both segments were 5'AAGUUUUU3' and 5'CAGCUnnnGUC3', respectively. Specific imperfect inverted repeats of each segment were identified. Comparison of the predicted proteins with those of related virus genome segments counterparts in maize rough dwarf virus (MRDV) and rice black streaked dwarf virus (RBSDV), showed 64.5-44.3% identities. These values are lower than those resulting from comparisons between MRDV and RBSDV. The topology of the trees obtained using the complete nucleotide and amino acid sequences of MRCV S7 and MRCV S9 was consistent with the analysis of the other MRCV segments previously published.

  6. Assessment of Recombination in the S-segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Iran

    OpenAIRE

    Sadegh Chinikar; Nariman Shah-Hosseini; Saeid Bouzari; MohammadAli Shokrgozar; Ehsan Mostafavi; Tahmineh Jalali; Sahar Khakifirouz; Groschup, Martin H.; Matthias Niedrig

    2015-01-01

     Background: Crimean-Congo Hemorrhagic Fever Virus (CCHFV) belongs to genus Nairovirus and family Bunyaviridae. The main aim of this study was to investigate the extent of recombination in S-segment genome of CCHFV in Iran.Methods: Samples were isolated from Iranian patients and those available in GenBank, and analyzed by phyloge­netic and bootscan methods.Results: Through comparison of the phylogenetic trees based on full length sequences and partial fragments in the S-segment genome of CCHF...

  7. An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments.

    Science.gov (United States)

    Marshall, Spencer H; Adegbola, Raphael O; Adkins, Scott; Naidu, Rayapati A

    2017-04-01

    Tospoviruses (genus Tospovirus, family Bunyaviridae) are responsible for major losses in an extensive range of crops worldwide. New species of these single-stranded, ambisense RNA viruses regularly emerge and have been shown to maintain heterogeneous populations with individual isolates having quite variable biological and virulence characteristics. Most tospovirus phylogenetic studies have focused on analysis of a single gene, most often the nucleocapsid protein gene. Complete genomic RNA segment amplification as a single fragment would facilitate more detailed analyses of genome-wide sequence variability, but obtaining such sequences for a large number of tospovirus isolates using traditional methods of amplification and cloning of small overlapping fragments is tedious, time consuming and expensive. In this study, protocols were optimized to amplify, clone and sequence full-length M- and S-RNA genome segments of Tomato spotted wilt virus and Impatiens necrotic spot virus. The strategy presented here is straightforward, scalable and offers several advantages over the previously commonplace and overlapping amplicon-based approach. Use of whole genome segments, instead of individual gene sequences or defined portions of genome segments, will facilitate a better understanding of the underlying molecular diversity of tospoviruses in mixed infections.

  8. Effects of the Number of Genome Segments on Primary and Systemic Infections with a Multipartite Plant RNA Virus

    OpenAIRE

    Sánchez-Navarro, Jesús A.; Zwart, Mark P.; Elena, Santiago F

    2013-01-01

    Multipartite plant viruses were discovered because of discrepancies between the observed dose response and predictions of the independent-action hypothesis (IAH) model. Theory suggests that the number of genome segments predicts the shape of the dose-response curve, but a rigorous test of this hypothesis has not been reported. Here, Alfalfa mosaic virus (AMV), a tripartite Alfamovirus, and transgenic Nicotianatabacum plants expressing no (wild type), one (P2), or two (P12) viral genome seg...

  9. The most conserved genome segments for life detection on Earth and other planets.

    Science.gov (United States)

    Isenbarger, Thomas A; Carr, Christopher E; Johnson, Sarah Stewart; Finney, Michael; Church, George M; Gilbert, Walter; Zuber, Maria T; Ruvkun, Gary

    2008-12-01

    On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets.

  10. dsRNA provides sequence-dependent protection against infectious myonecrosis virus in Litopenaeus vannamei.

    Science.gov (United States)

    Loy, J Dustin; Mogler, Mark A; Loy, Duan S; Janke, Bruce; Kamrud, Kurt; Scura, Edward D; Harris, D L Hank; Bartholomay, Lyric C

    2012-04-01

    Viral diseases are significant impediments to the sustainability of shrimp aquaculture. In addition to endemic disease, new viral diseases continue to emerge and cause significant impact on the shrimp industry. Disease caused by infectious myonecrosis virus (IMNV) has caused tremendous losses in farmed Pacific white shrimp (Litopenaeus vannamei) since it emerged in Brazil and translocated to Indonesia. There are no existing antiviral interventions, outside of pathogen exclusion, to mitigate disease in commercial shrimp operations. Here, we describe an iterative process of panning the genome of IMNV to discover RNA interference trigger sequences that initiate a robust and long-lasting protective response against IMNV in L. vannamei. Using this process, a single, low dose (0.02 µg) of an 81 or 153 bp fragment, with sequence corresponding to putative cleavage protein 1 in ORF1, protected 100 % of animals from disease and mortality caused by IMNV. Furthermore, animals that were treated with highly efficacious dsRNA survived an initial infection and were resistant to subsequent infections over 50 days later with a 100-fold greater dose of virus. This protection is probably sequence dependent, because targeting the coding regions for the polymerase or structural genes of IMNV conferred lesser or no protection. Interestingly, non-sequence specific dsRNA did not provide any degree of protection to animals as had been described for other shrimp viruses. Our data indicate that the targeted region for dsRNA is a crucial factor in maximizing the degree of protection and lowering the dose required to induce a protective effect against IMNV infection in shrimp.

  11. Genome-wide mapping of IBD segments in an Ashkenazi PD cohort identifies associated haplotypes.

    Science.gov (United States)

    Vacic, Vladimir; Ozelius, Laurie J; Clark, Lorraine N; Bar-Shira, Anat; Gana-Weisz, Mali; Gurevich, Tanya; Gusev, Alexander; Kedmi, Merav; Kenny, Eimear E; Liu, Xinmin; Mejia-Santana, Helen; Mirelman, Anat; Raymond, Deborah; Saunders-Pullman, Rachel; Desnick, Robert J; Atzmon, Gil; Burns, Edward R; Ostrer, Harry; Hakonarson, Hakon; Bergman, Aviv; Barzilai, Nir; Darvasi, Ariel; Peter, Inga; Guha, Saurav; Lencz, Todd; Giladi, Nir; Marder, Karen; Pe'er, Itsik; Bressman, Susan B; Orr-Urtreger, Avi

    2014-09-01

    The recent series of large genome-wide association studies in European and Japanese cohorts established that Parkinson disease (PD) has a substantial genetic component. To further investigate the genetic landscape of PD, we performed a genome-wide scan in the largest to date Ashkenazi Jewish cohort of 1130 Parkinson patients and 2611 pooled controls. Motivated by the reduced disease allele heterogeneity and a high degree of identical-by-descent (IBD) haplotype sharing in this founder population, we conducted a haplotype association study based on mapping of shared IBD segments. We observed significant haplotype association signals at three previously implicated Parkinson loci: LRRK2 (OR = 12.05, P = 1.23 × 10(-56)), MAPT (OR = 0.62, P = 1.78 × 10(-11)) and GBA (multiple distinct haplotypes, OR > 8.28, P = 1.13 × 10(-11) and OR = 2.50, P = 1.22 × 10(-9)). In addition, we identified a novel association signal on chr2q14.3 coming from a rare haplotype (OR = 22.58, P = 1.21 × 10(-10)) and replicated it in a secondary cohort of 306 Ashkenazi PD cases and 2583 controls. Our results highlight the power of our haplotype association method, particularly useful in studies of founder populations, and reaffirm the benefits of studying complex diseases in Ashkenazi Jewish cohorts.

  12. Seed-borne viral dsRNA elements in three cultivated Raphanus and Brassica plants suggest three cryptoviruses.

    Science.gov (United States)

    Li, Liqiang; Liu, Jianning; Zhang, Qiong; Fu, Runying; Zhu, Xiwu; Li, Chao; Chen, Jishuang

    2016-04-01

    Since the 1970s, several dsRNA viruses, including Radish yellow edge virus, Raphanus sativus virus 1, Raphanus sativus virus 2, and Raphanus sativus virus 3, have been identified and reported as infecting radish. In the present study, in conjunction with a survey of seed-borne viruses in cultivated Brassica and Raphanus using the dsRNA diagnostic method, we discovered 3 novel cryptoviruses that infect Brassica and Raphanus: Raphanus sativus partitivirus 1, which infects radish (Raphanus sativus); Sinapis alba cryptic virus 1, which infects Sinapis alba; and Brassica rapa cryptic virus 1 (BrCV1), which infects Brassica rapa. The genomic organization of these cryptoviruses was analyzed and characterized. BrCV1 might represent the first plant partitivirus found in Gammapartitivirus. Additionally, the evolutionary relationships among all of the partitiviruses reported in Raphanus and Brassica were analyzed.

  13. Discovery of novel dsRNA viral sequences by in silico cloning and implications for viral diversity, host range and evolution.

    Directory of Open Access Journals (Sweden)

    Huiquan Liu

    Full Text Available Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. Therefore, the EST databases may include numerous unknown viral sequences. In this study, we performed in silico cloning, a procedure for obtaining full or partial cDNA sequence of a gene by bioinformatics analysis, using known dsRNA viral sequences as queries to search against NCBI Expressed Sequence Tag (EST database. From this analysis, we obtained 119 novel virus-like sequences related to members of the families, Endornaviridae, Chrysoviridae, Partitiviridae, and Totiviridae. Many of them were identified in cDNA libraries of eukaryotic lineages, which were not known to be hosts for these viruses. Furthermore, comprehensive phylogenetic analysis of these newly discovered virus-like sequences with known dsRNA viruses revealed that these dsRNA viruses may have co-evolved with respective host supergroups over a long evolutionary time while potential horizontal transmissions of viruses between different host supergroups also is possible. We also found that some of the plant partitiviruses may have originated from fungal viruses by horizontal transmissions. These findings extend our knowledge of the diversity and possible host range of dsRNA viruses and offer insight into the origin and evolution of relevant viruses with

  14. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis.

    Science.gov (United States)

    Herman, Emily K; Greninger, Alexander L; Visvesvara, Govinda S; Marciano-Cabral, Francine; Dacks, Joel B; Chiu, Charles Y

    2013-01-01

    Naegleria fowleri is a unicellular eukaryote causing primary amoebic meningoencephalitis, a neuropathic disease killing 99% of those infected, usually within 7-14 days. Naegleria fowleri is found globally in regions including the US and Australia. The genome of the related nonpathogenic species Naegleria gruberi has been sequenced, but the genetic basis for N. fowleri pathogenicity is unclear. To generate such insight, we sequenced and assembled the mitochondrial genome and a 60-kb segment of nuclear genome from N. fowleri. The mitochondrial genome is highly similar to its counterpart in N. gruberi in gene complement and organization, while distinct lack of synteny is observed for the nuclear segments. Even in this short (60-kb) segment, we identified examples of potential factors for pathogenesis, including ten novel N. fowleri-specific genes. We also identified a homolog of cathepsin B; proteases proposed to be involved in the pathogenesis of diverse eukaryotic pathogens, including N. fowleri. Finally, we demonstrate a likely case of horizontal gene transfer between N. fowleri and two unrelated amoebae, one of which causes granulomatous amoebic encephalitis. This initial look into the N. fowleri nuclear genome has revealed several examples of potential pathogenesis factors, improving our understanding of a neglected pathogen of increasing global importance.

  15. Assessment of Recombination in the S-segment Genome of Crimean-Congo Hemorrhagic Fever Virus in Iran

    Directory of Open Access Journals (Sweden)

    Sadegh Chinikar

    2015-10-01

    Full Text Available  Background: Crimean-Congo Hemorrhagic Fever Virus (CCHFV belongs to genus Nairovirus and family Bunyaviridae. The main aim of this study was to investigate the extent of recombination in S-segment genome of CCHFV in Iran.Methods: Samples were isolated from Iranian patients and those available in GenBank, and analyzed by phyloge­netic and bootscan methods.Results: Through comparison of the phylogenetic trees based on full length sequences and partial fragments in the S-segment genome of CCHFV, genetic switch was evident, due to recombination event. Moreover, evidence of multi­ple recombination events was detected in query isolates when bootscan analysis was used by SimPlot software.Conclusion: Switch of different genomic regions between different strains by recombination could contribute to CCHFV diversification and evolution. The occurrence of recombination in CCHFV has a critical impact on epidemi­ological investigations and vaccine design. 

  16. Molecular characterization of L class genome segments of a newly isolated turkey arthritis reovirus.

    Science.gov (United States)

    Mor, Sunil K; Sharafeldin, Tamer A; Porter, Robert E; Goyal, Sagar M

    2014-10-01

    Seven strains of turkey arthritis reovirus (TARV) isolated from cases of turkey arthritis were characterized on the basis of their L class genome segment sequences, which were then compared with those of turkey enteric reovirus (TERV) and chicken reovirus (CRV). All three L class gene segments of TARVs and TERVs and their encoded proteins λA, λB, and λC were similar in size to those of CRV reference strain S1133. The conserved motifs such as C2H2 zinc-binding motif and conserved polymerase region were present in λA and λB, respectively. A conserved motif for ATP/GTP-binding site and an S-adenosyl-l-methionine (SAM)-binding pocket for methyltransferase were observed in λC protein of TARVs and TERVs with only one substitution as compared to that in CRV. We propose a new genotype classification system for avian reoviruses (ARVs) based on the nt identity cut-off value for each of the L class. Based on this new genotype classification, all ARVs were divided into six, seven and eight genotypes in L1, L2 and L3 genes, respectively. Interestingly TARVs and TERVs grouped with three CRVs (two arthritic strains from Taiwan and one enteritic strain from Japan) in genotype L1-I and formed a different genotypes (L2-I, L3-I) from CRVs in L2 and L3 genes. The maximum nucleotide divergence was observed in genotypes of L1 and L2 genes but less at amino acid level indicates mostly changes were synonymous type. Compared to L1 and L2 genes, the nonsynonymous changes were more in L3 gene. Point mutations and possible reassortments among TARVs, TERVs and CRVs were also observed. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Occurrence of dsRNA Mycovirus (LeV-FMRI0339 in the Edible Mushroom Lentinula edodes and Meiotic Stability of LeV-FMRI0339 among Monokaryotic Progeny

    Directory of Open Access Journals (Sweden)

    Jung-Mi Kim

    2013-12-01

    Full Text Available dsRNA was found in malformed cultures of Lentinula edodes strain FMRI0339, one of the three most popular sawdust cultivated commercial strains of shiitake, and was also found in healthy-looking fruiting bodies and actively growing mycelia. Cloning of the partial genome of the dsRNA revealed the presence of the RdRp sequence of a novel L. edodes mycovirus (LeV, and sequence comparison of the cloned amplicon showed identical sequences sequence to known RNA-dependent RNA polymerase genes of LeV found in strain HKA. The meiotic stability of dsRNA was examined by measuring the ratio of the presence of dsRNA among sexual monokaryotic progeny. More than 40% of the monokaryotic progeny still contained the dsRNA, indicating the persistence of dsRNA during sexual reproduction. Comparing the mycelia growth of monokaryotic progeny suggested that there appeared to be a tendency toward a lower frequency of virus incidence in actively growing progeny.

  18. Analysis of segmental duplications, mouse genome synteny and recurrent cancer-associated amplicons in human chromosome 6p21-p12.

    Science.gov (United States)

    Martin, J W; Yoshimoto, M; Ludkovski, O; Thorner, P S; Zielenska, M; Squire, J A; Nuin, P A S

    2010-06-01

    It has been proposed that regions of microhomology in the human genome could facilitate genomic rearrangements, copy number transitions, and rapid genomic change during tumor progression. To investigate this idea, this study examines the role of repetitive sequence elements, and corresponding syntenic mouse genomic features, in targeting cancer-associated genomic instability of specific regions of the human genome. Automated database-mining algorithms designed to search for frequent copy number transitions and genomic breakpoints were applied to 2 publicly-available online databases and revealed that 6p21-p12 is one of the regions of the human genome most frequently involved in tumor-specific alterations. In these analyses, 6p21-p12 exhibited the highest frequency of genomic amplification in osteosarcomas. Analysis of repetitive elements in regions of homology between human chromosome 6p and the syntenic regions of the mouse genome revealed a strong association between the location of segmental duplications greater than 5 kilobase-pairs and the position of discontinuities at the end of the syntenic region. The presence of clusters of segmental duplications flanking these syntenic regions also correlated with a high frequency of amplification and genomic alteration. Collectively, the experimental findings, in silico analyses, and comparative genomic studies presented here suggest that segmental duplications may facilitate cancer-associated copy number transitions and rearrangements at chromosome 6p21-p12. This process may involve homology-dependent DNA recombination and/or repair, which may also contribute towards the overall plasticity of the human genome.

  19. CHSE-214: A model for studying extracellular dsRNA sensing in vitro.

    Science.gov (United States)

    Monjo, A L; Poynter, S J; DeWitte-Orr, S J

    2017-09-01

    Double-stranded RNA (dsRNA) is produced by almost all viruses during their replicative cycle and is a potent inducer of the innate antiviral immune response including inducing expression of type I interferons (IFNs) and interferon-stimulated genes (ISGs). During lytic virus infections intracellular dsRNA can escape into the extracellular space, where surface pattern recognition receptors, such as class A scavenger receptors (SR-As) facilitate its binding and entry into neighbouring cells. Studying extracellular dsRNA entry is difficult due to the ubiquitous expression profile and compensatory dsRNA binding characteristics of SR-As; a SR-A deficient cell line has yet to be identified. The present study suggests the Chinook salmon embryonic cell line, CHSE-214, as a model for studying extracellular dsRNA sensing in vitro. CHSE-214 is unable to bind and respond to extracellular dsRNA, can only respond to dsRNA when it is transfected into the cells, and is able to bind dsRNA when overexpressing human SR-AI. The applications for this model could include elucidating: dsRNA binding and entry mechanisms, including sequence and length effects, as well as SR-A and other putative surface dsRNA receptor ligand binding studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus.

    Directory of Open Access Journals (Sweden)

    Aaron M Collier

    2016-04-01

    Full Text Available During the replication cycle of double-stranded (ds RNA viruses, the viral RNA-dependent RNA polymerase (RdRP replicates and transcribes the viral genome from within the viral capsid. How the RdRP molecules are packaged within the virion and how they function within the confines of an intact capsid are intriguing questions with answers that most likely vary across the different dsRNA virus families. In this study, we have determined a 2.4 Å resolution structure of an RdRP from the human picobirnavirus (hPBV. In addition to the conserved polymerase fold, the hPBV RdRP possesses a highly flexible 24 amino acid loop structure located near the C-terminus of the protein that is inserted into its active site. In vitro RNA polymerization assays and site-directed mutagenesis showed that: (1 the hPBV RdRP is fully active using both ssRNA and dsRNA templates; (2 the insertion loop likely functions as an assembly platform for the priming nucleotide to allow de novo initiation; (3 RNA transcription by the hPBV RdRP proceeds in a semi-conservative manner; and (4 the preference of virus-specific RNA during transcription is dictated by the lower melting temperature associated with the terminal sequences. Co-expression of the hPBV RdRP and the capsid protein (CP indicated that, under the conditions used, the RdRP could not be incorporated into the recombinant capsids in the absence of the viral genome. Additionally, the hPBV RdRP exhibited higher affinity towards the conserved 5'-terminal sequence of the viral RNA, suggesting that the RdRP molecules may be encapsidated through their specific binding to the viral RNAs during assembly.

  1. A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

    National Research Council Canada - National Science Library

    Tran Thi Ngoc Dung; Pham Thanh Duy; October M Sessions; Uma K Sangumathi; Voong Vinh Phat; Pham Thi Thanh Tam; Nguyen Thi Nguyen To; Tran My Phuc; Tran Thi Hong Chau; Nguyen Ngoc Minh Chau; Ngoc Nguyen Minh; Guy E Thwaites; Maia A Rabaa; Stephen Baker

    2017-01-01

    Background Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material...

  2. Comparative genome analysis of the major histocompatibility complex (MHC) class I B/C segments in primates elucidated by genomic sequencing in common marmoset (Callithrix jacchus).

    Science.gov (United States)

    Shiina, Takashi; Kono, Azumi; Westphal, Nico; Suzuki, Shingo; Hosomichi, Kazuyoshi; Kita, Yuki F; Roos, Christian; Inoko, Hidetoshi; Walter, Lutz

    2011-08-01

    Common marmoset monkeys (Callithrix jacchus) have emerged as important animal models for biomedical research, necessitating a more extensive characterization of their major histocompatibility complex (MHC) region. However, the genomic information of the marmoset MHC (Caja) is still lacking. The MHC-B/C segment represents the most diverse MHC region among primates. Therefore, in this paper, to elucidate the detailed gene organization and evolutionary processes of the Caja class I B (Caja-B) segment, we determined two parts of the Caja-B sequences with 1,079 kb in total, ranging from H6orf15 to BAT1 and compared the structure and phylogeny with that of other primates. This segment contains 54 genes in total, nine Caja-B genes (Caja-B1 to Caja-B9), two MIC genes (MIC1 and MIC2), eight non-MHC genes, two non-coding genes, and 33 non-MHC pseudogenes that have not been observed in other primate MHC-B/C segments. Caja-B3, Caja-B4, and Caja-B7 encode proper MHC class I proteins according to amino acid structural characteristics. Phylogenetic relationships based on 48 MHC-I nucleotide sequences in primates suggested (1) species-specific divergence for Caja, Mamu, and HLA/Patr/Gogo lineages, (2) independent generation of the "seven coding exon" type MHC-B genes in Mamu and HLA/Patr/Gogo lineages from an ancestral "eight coding exon" type MHC-I gene, (3) parallel correlation with the long and short segmental duplication unit length in Caja and Mamu lineages. These findings indicate that the MHC-B/C segment has been under permanent selective pressure in the evolution of primates.

  3. Transfection of exogenous rotavirus rearranged RNA segments in cells infected with a WT rotavirus results in subsequent gene rearrangements.

    Science.gov (United States)

    Duponchel, Sarah; Troupin, Cécile; Vu, Lan Trang; Schnuriger, Aurélie; Trugnan, Germain; Garbarg-Chenon, Antoine

    2014-09-01

    Group A rotaviruses, members of the family Reoviridae, are a major cause of infantile acute gastroenteritis. The rotavirus genome consists of 11 dsRNA segments. In some cases, an RNA segment is replaced by a rearranged RNA segment, which is derived from its standard counterpart by partial sequence duplication. It has been shown that some rearranged segments are preferentially encapsidated into viral progenies after serial passages in cell culture. Based on this characteristic, a reverse genetics system was used previously to introduce exogenous segment 7 rearrangements into an infectious rotavirus. This study extends this reverse genetics system to RNA segments 5 and 11. Transfection of exogenous rotavirus rearranged RNA segment 5 or 11 into cells infected with a WT helper rotavirus (bovine strain RF) resulted in subsequent gene rearrangements in the viral progeny. Whilst recombinant viruses were rescued with an exogenous rearranged segment 11, the exogenous segment was modified by a secondary rearrangement. The occurrence of spontaneous rearrangements of WT or exogenous segments is a major hindrance to the use of this reverse genetics approach. © 2014 The Authors.

  4. Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-03-01

    Full Text Available Abstract The plant-infecting members of the genus Fijivirus (family Reoviridae have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons that overlaps the 3' end of the major ORF (~920–940 codons in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.

  5. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

    Directory of Open Access Journals (Sweden)

    Abdulahi Alfonso-Morales

    Full Text Available Infectious bursal disease (IBD is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV strains worldwide.Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for

  6. cDNA cloning and sequence analysis of genome segments S8 from rice black-streaked dwarf virus

    Institute of Scientific and Technical Information of China (English)

    张恒木; 陈剑平; 薛庆中; 雷娟利

    2002-01-01

    Genome segments S8 of two Chinese isolates of rice black-streaked dwarf virus (RBSDV), one from Zhejiang Province and another from Hebei Province, were amplified by RT-PCR and sequenced. Both segments consisted of 1936 nts in full length (EMBL accession numbers were AJ297431 and AJ297432, respectively) and contained only one big open reading frame which encoded a polypeptide with molecular weight of 68kD. The two Chinese isolates shared 94.0% and 96.5% identity at nucleotide and amino acid level, respectively. They shared 94.5-94.9% and 92.5-92.9% homology with S8 of RBSDV Japanese isolate at nucleotide and amino acid level, respectively; shared 85.1-87.6% and 91.7-91.9% homology with S7 of Italian MRDV (maize rough dwarf virus).

  7. Genomic sequence analysis of the MHC class I G/F segment in common marmoset (Callithrix jacchus).

    Science.gov (United States)

    Kono, Azumi; Brameier, Markus; Roos, Christian; Suzuki, Shingo; Shigenari, Atsuko; Kametani, Yoshie; Kitaura, Kazutaka; Matsutani, Takaji; Suzuki, Ryuji; Inoko, Hidetoshi; Walter, Lutz; Shiina, Takashi

    2014-04-01

    The common marmoset (Callithrix jacchus) is a New World monkey that is used frequently as a model for various human diseases. However, detailed knowledge about the MHC is still lacking. In this study, we sequenced and annotated a total of 854 kb of the common marmoset MHC region that corresponds to the HLA-A/G/F segment (Caja-G/F) between the Caja-G1 and RNF39 genes. The sequenced region contains 19 MHC class I genes, of which 14 are of the MHC-G (Caja-G) type, and 5 are of the MHC-F (Caja-F) type. Six putatively functional Caja-G and Caja-F genes (Caja-G1, Caja-G3, Caja-G7, Caja-G12, Caja-G13, and Caja-F4), 13 pseudogenes related either to Caja-G or Caja-F, three non-MHC genes (ZNRD1, PPPIR11, and RNF39), two miscRNA genes (ZNRD1-AS1 and HCG8), and one non-MHC pseudogene (ETF1P1) were identified. Phylogenetic analysis suggests segmental duplications of units consisting of basically five (four Caja-G and one Caja-F) MHC class I genes, with subsequent expansion/deletion of genes. A similar genomic organization of the Caja-G/F segment has not been observed in catarrhine primates, indicating that this genomic segment was formed in New World monkeys after the split of New World and Old World monkeys.

  8. Evolutionary relationship of the L- and M-class genome segments of bat-borne fusogenic orthoreoviruses in Malaysia and Australia.

    Science.gov (United States)

    Voon, Kenny; Chua, Kaw Bing; Yu, Meng; Crameri, Gary; Barr, Jennifer A; Malik, Yasmin; Wang, Lin-Fa

    2011-12-01

    We previously described three new Malaysian orthoreoviruses designated Pulau virus, Melaka virus and Kampar virus. Melaka and Kampar viruses were shown to cause respiratory disease in humans. These viruses, together with Nelson Bay virus, isolated from Australian bats, are tentatively classified as different strains within the species Pteropine orthoreovirus (PRV), formerly known as Nelson Bay orthoreovirus, based on the small (S) genome segments. Here we report the sequences of the large (L) and medium (M) segments, thus completing the whole-genome characterization of the four PRVs. All L and M segments were highly conserved in size and sequence. Conserved functional motifs previously identified in other orthoreovirus gene products were also found in the deduced proteins encoded by the cognate segments of these viruses. Detailed sequence analysis identified two genetic lineages divided into the Australian and Malaysian PRVs, and potential genetic reassortment among the M and S segments of the three Malaysian viruses.

  9. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  10. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean

    Science.gov (United States)

    Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean (Glycine max (L.) Merrill) pl...

  11. Efifciency of Different Methods for dsRNA Delivery in Cotton Bollworm (Helicoverpa armigera)

    Institute of Scientific and Technical Information of China (English)

    YANG Jing; HAN Zhao-jun

    2014-01-01

    RNAi trigged by dsRNA not only facilitates the development of molecular biology, but also initiates a new way for pest control by silence of fatal genes. However, one of the key limitations in pest control is lack of the convenient and efifcient method for dsRNA delivery. In this study, different dsRNA delivery methods at their own optimum conditions were evaluated comparatively for their efifciency with Helicoverpa armigera as test animal. It was found that the popular one-time injection of larvae with dsRNA could reduce the pupation rate by 43.0%and enhance larva mortality by 11.7%. One-time ingestion of dsRNA did not result in any signiifcant effect on phenotype. Continuous ingestion of in vitro synthesized dsRNA by refreshing the bait diet every day caused 40.4% decrease in successful pupation and 10.0% increase in larval mortality, which was similar as one-time injection. The most efifcient method was found to be the continuous ingestion of the bacteria containing dsRNA expressed, which reduced the rate of pupation by 68.7%and enhanced the larval mortality by 34.1%. Further analysis found that dsRNA was degraded faster in midgut juice than in hemolymph. However, the cell of bacteria could protect dsRNA and delay the degradation in the midgut juice of H. armigera. These results throw light on the application of dsRNA in pest management with proper ways.

  12. Rice black-streaked dwarf virus genome segment S5 is a bicistronic mRNA in infected plants.

    Science.gov (United States)

    Yang, Jian; Zhang, Heng-Mu; Ying, Lu; Li, Jing; Lv, Ming-Fang; Xie, Li; Li, Pei-Pei; Liu, Xiao-Ya; Liang-Ying, Dai; Chen, Jian-Ping

    2014-02-01

    Rice black-streaked dwarf virus (RBSDV) is a recognized member of the genus Fijivirus, family Reoviridae. Genome segment S5 has a putative second ORF partially overlapping the major ORF but in a different reading frame. This putative ORF is present in a published sequence and in two Chinese isolates now sequenced. Antibodies were raised against purified P5-1 and P5-2 fusion proteins expressed in a prokaryotic system. In western blots, these antibodies reacted with proteins of about 106 and 27 kDa, respectively, as predicted by sequence analysis. In immunoelectron microscopy, antibodies to P5-1 reacted with viroplasms, indicating that P5-1 is a component of viroplasms, but no labeling was observed with P5-2 antisera. Northern blot assays showed that the genome segment S5 was transcribed as a single mRNA with no subgenomic RNA. These results show that S5 is functionally bicistronic in infected plants. Possible translational mechanisms for P5-2 are discussed.

  13. The dsRNA Virus Papaya Meleira Virus and an ssRNA Virus Are Associated with Papaya Sticky Disease.

    Directory of Open Access Journals (Sweden)

    Tathiana Ferreira Sá Antunes

    Full Text Available Papaya sticky disease, or "meleira", is one of the major diseases of papaya in Brazil and Mexico, capable of causing complete crop loss. The causal agent of sticky disease was identified as an isometric virus with a double stranded RNA (dsRNA genome, named papaya meleira virus (PMeV. In the present study, PMeV dsRNA and a second RNA band of approximately 4.5 kb, both isolated from latex of papaya plants with severe symptoms of sticky disease, were deep-sequenced. The nearly complete sequence obtained for PMeV dsRNA is 8,814 nucleotides long and contains two putative ORFs; the predicted ORF1 and ORF2 display similarity to capsid proteins and RdRp's, respectively, from mycoviruses tentatively classified in the family Totiviridae. The sequence obtained for the second RNA is 4,515 nucleotides long and contains two putative ORFs. The predicted ORFs 1 and 2 display 48% and 73% sequence identity, respectively, with the corresponding proteins of papaya virus Q, an umbravirus recently described infecting papaya in Ecuador. Viral purification in a sucrose gradient allowed separation of particles containing each RNA. Mass spectrometry analysis indicated that both PMeV and the second RNA virus (named papaya meleira virus 2, PMeV2 were encapsidated in particles formed by the protein encoded by PMeV ORF1. The presence of both PMeV and PMeV2 was confirmed in field plants showing typical symptoms of sticky disease. Interestingly, PMeV was detected alone in asymptomatic plants. Together, our results indicate that sticky disease is associated with double infection by PMeV and PMeV2.

  14. Nucleotide sequences of genome segments S6, S7 and S10 of Dendrolimus punctatus cypovirus 1.

    Science.gov (United States)

    Hong, J J; Duan, J L; Zhao, S L; Xu, H G; Peng, H Y

    2004-01-01

    The nucleotide sequences of genome segments S6, S7 and S10 of Dendrolimus punctatus cypovirus 1 Hunan I (DpCPV-HN(I)) and DpCPV-HN(I)-Se(3) (DpCPV-HN(I) passed three times in Spodoptera exigua) were determined. Segment S10 was 944 nucleotides in length and encoded a polyhedrin of 248 amino acids (28,439 Da). Only two nucleotide mutations were found between DpCPV-HN(I) S10 and DpCPV-HN(I)-Se3 S10, and the deduced amino acid sequences of the polyhedrin proteins were identical. Segment S7, 1 501 nucleotides, encoded a protein of 448 amino acids ( approximately 50 kDa; p50). Thirty-one nucleotide mutations were found between DpCPV-HN(I) S7 and DpCPV-HN(I)-Se3 S7, but these resulted in only four amino acid changes. DpCPV-HN(I) S6 encoded a protein of 561 amino acids (63,688 Da; p64). The amino acid sequence of p64, had a high leucine content (10%), and contained a leucine zipper motif and one ATP/GTP-binding site motif.

  15. Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

    DEFF Research Database (Denmark)

    Harms, Klaus; Lunnan, Asbjørn; Hülter, Nils;

    2016-01-01

    In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules...... to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal...... gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome....

  16. Structural basis for dsRNA recognition and interferon antagonism by Ebola VP35

    Energy Technology Data Exchange (ETDEWEB)

    Leung, Daisy W.; Prins, Kathleen C.; Borek, Dominika M.; Farahbakhsh, Mina; Tufariello, JoAnn M.; Ramanan, Parameshwaran; Nix, Jay C.; Helgeson, Luke A.; Otwinowski, Zbyszek; Honzatko, Richard B.; Basler, Christopher F.; Amarasinghe, Gaya K. (Sinai); (Iowa State); (LBNL); (UTSMC)

    2010-03-12

    Ebola viral protein 35 (VP35), encoded by the highly pathogenic Ebola virus, facilitates host immune evasion by antagonizing antiviral signaling pathways, including those initiated by RIG-I-like receptors. Here we report the crystal structure of the Ebola VP35 interferon inhibitory domain (IID) bound to short double-stranded RNA (dsRNA), which together with in vivo results reveals how VP35-dsRNA interactions contribute to immune evasion. Conserved basic residues in VP35 IID recognize the dsRNA backbone, whereas the dsRNA blunt ends are 'end-capped' by a pocket of hydrophobic residues that mimic RIG-I-like receptor recognition of blunt-end dsRNA. Residues critical for RNA binding are also important for interferon inhibition in vivo but not for viral polymerase cofactor function of VP35. These results suggest that simultaneous recognition of dsRNA backbone and blunt ends provides a mechanism by which Ebola VP35 antagonizes host dsRNA sensors and immune responses.

  17. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae.

    Science.gov (United States)

    Kaboli, Saeed; Miyamoto, Tetsuya; Sunada, Keisuke; Sasano, Yu; Sugiyama, Minetaka; Harashima, Satoshi

    2016-06-01

    Saccharomyces cerevisiae strains from industrial and natural geographical environments are reported to show great variation in copy number of chromosomal regions. Such variation contributes to the mechanisms underlying adaptation to different environments. Here, we created and phenotypically analyzed segmentally haploidized strains, each harboring a deletion of one copy of approximately 100-300 kb of the left or right terminal region of 16 chromosomes in a diploid strain by using a PCR-mediated chromosomal deletion method. No haploidized strain of the 158-kb deleted right terminal region of chromosome III or the 172-kb deleted right terminal region of chromosome VI was produced; however, segmentally haploidized strains of the remaining 30 terminal regions were obtained. Among these 30 strains, two exhibited higher lactic acid resistance and two displayed higher thermo-tolerance at 41°C versus the host diploid strain. By contrast, four and two segmentally haploidized strains showed sensitivity to 6% lactic acid and low temperature at 13°C, respectively. The effect of the decreased copy number of the chromosomal terminal regions on ethanol production was analyzed. As compared with the host diploid strain, a 3.8% and 4.3% improvement in ethanol production in 10% glucose medium was observed for two strains in which one of two copies of the 197-kb left terminal region of chromosome V and one of two copies of the 195-kb left terminal region of chromosome X was deleted, respectively. These results indicate that artificial segmental haploidization might contribute to improvement of industrially important phenotypes and provide a new approach to breeding superior yeast strains. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  18. Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan

    Science.gov (United States)

    Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be easily seen by analyzing the unexpected behaviour of the linkage disequilibrium (LD) decay. A heuristic process was proposed to identify those misassembly signatures and presented the ones found in ...

  19. Leishmania aethiopica field isolates bearing an endosymbiontic dsRNA virus induce pro-inflammatory cytokine response.

    Directory of Open Access Journals (Sweden)

    Haroun Zangger

    2014-04-01

    Full Text Available BACKGROUND: Infection with Leishmania parasites causes mainly cutaneous lesions at the site of the sand fly bite. Inflammatory metastatic forms have been reported with Leishmania species such as L. braziliensis, guyanensis and aethiopica. Little is known about the factors underlying such exacerbated clinical presentations. Leishmania RNA virus (LRV is mainly found within South American Leishmania braziliensis and guyanensis. In a mouse model of L. guyanensis infection, its presence is responsible for an hyper-inflammatory response driven by the recognition of the viral dsRNA genome by the host Toll-like Receptor 3 leading to an exacerbation of the disease. In one instance, LRV was reported outside of South America, namely in the L. major ASKH strain from Turkmenistan, suggesting that LRV appeared before the divergence of Leishmania subgenera. LRV presence inside Leishmania parasites could be one of the factors implicated in disease severity, providing rationale for LRV screening in L. aethiopica. METHODOLOGY/PRINCIPAL FINDINGS: A new LRV member was identified in four L. aethiopica strains (LRV-Lae. Three LRV-Lae genomes were sequenced and compared to L. guyanensis LRV1 and L. major LRV2. LRV-Lae more closely resembled LRV2. Despite their similar genomic organization, a notable difference was observed in the region where the capsid protein and viral polymerase open reading frames overlap, with a unique -1 situation in LRV-Lae. In vitro infection of murine macrophages showed that LRV-Lae induced a TLR3-dependent inflammatory response as previously observed for LRV1. CONCLUSIONS/SIGNIFICANCE: In this study, we report the presence of an immunogenic dsRNA virus in L. aethiopica human isolates. This is the first observation of LRV in Africa, and together with the unique description of LRV2 in Turkmenistan, it confirmed that LRV was present before the divergence of the L. (Leishmania and (Viannia subgenera. The potential implication of LRV-Lae on

  20. Evolutionary break point analysis between the proximal half of bovine chromosome 27 and conserved segments of the human genome.

    Science.gov (United States)

    Goldammer, T; Kuehn, C; Brunner, R M; Weikard, R

    2009-01-01

    The proximal half of Bos taurus chromosome 27 (BTA27prox) delimited by microsatellite markers BM3507 and CSSM043 reveals complex rearrangements compared to its corresponding Homo sapiens chromosome (HSA) fragments. A comparative mapping approach combining somatic and radiation hybrid cell mapping techniques and related cytogenetic data resulted in an improved physical map for BTA27prox, which provides candidate genes for several important economic traits. The generated comprehensive map includes anchor loci for 103 genes and microsatellite markers. Mapping of genes proximal to BM3507 matching a region from 0.60 to 2.78 megabase pairs (Mb) of HSA8 confirmed recent sequence annotations on BTA27. Assignments of loci predicted to be on BTA27 to BTA1, BTA8, and BTA17 narrowed down evolutionary chromosome break points compared with corresponding chromosome segments in human. New physical anchors obtained in this study confirm in more detail the described evolutionary conservation between the proximal half of BTA27 and homologous segments of HSA4 and HSA8 and will contribute to the completion of the cattle DNA genome sequence.

  1. Molecular cloning, sequence analysis and expression of genome segment 7 (S7) of Antheraea mylitta cypovirus (AmCPV) that encodes a viral structural protein.

    Science.gov (United States)

    Chavali, Venkata Ramana Murthy; Ghosh, Ananta K

    2007-10-01

    The Genome segment 7 (S7) of the 11 double stranded RNA genomes from Antheraea mylitta cypovirus (AmCPV) was converted to cDNA, cloned and sequenced. The nucleotide sequence showed that segment 7 consisted of 1789 nucleotides with an ORF of 530 amino acids and could encode a protein of approximately 61 kDa, termed P61. The 5' terminal sequence, AGTAAT and the 3' terminal sequence, AGAGC of the plus strand was found to be the same as genome segment 10 of AmCPV encoding polyhedrin. No sequence similarity was found by searching nucleic acid and protein sequence databases using BLAST. The secondary structure prediction showed the presence of 17 alpha-helices, 18 extended beta-sheets along the entire length of P61. The ORF of segment 7 was expressed in E. coli as His-tagged fusion protein, purified through Ni-NTA chromatography, and polyclonal antibody was raised in rabbit indicating that P61 is immunogenic. Immunoblot analysis using this antibody on viral infected cells as well as purified polyhedra showed that P61 is a viral structural protein. Motif scan search showed some similarity of P61 with Inosine monophosphate dehydrogenase (IMPDH) cystathionine-beta-synthase (CBS) domain at the C-terminus and it was hypothesized that by binding to single stranded viral RNA through its CBS domain P61 may help in virus replication or transcription.

  2. dsRNA sensing during viral infection: lessons from plants, worms, insects, and mammals.

    Science.gov (United States)

    de Faria, Isaque João da Silva; Olmo, Roenick Proveti; Silva, Emanuele Guimarães; Marques, João Trindade

    2013-05-01

    Host defense systems often rely on direct and indirect pattern recognition to sense the presence of invading pathogens. Patterns can be molecules directly produced by the pathogen or indirectly generated by changes in host parameters as a consequence of infection. Viruses are intracellular pathogens that hijack the cellular machinery to synthesize their own molecules making direct recognition of viral molecules a great challenge. Antiviral systems in prokaryotes and eukaryotes commonly exploit aberrant nucleic acid sensing to recognize virus infection as host and viral nucleic acid metabolism can greatly differ. Indeed, the generation of dsRNA is often associated with viral infection. In this review, we discuss current knowledge on the mechanisms of viral dsRNA sensing utilized by 2 important antiviral defense systems, RNA interference (RNAi) and the vertebrate immune system. The major viral sensors of the vertebrate immune systems are RIG-like receptors, while RNAi pathways depend on Dicer proteins. These 2 families of sensors share a similar helicase domain with high specificity for dsRNA, which is necessary, but not sufficient for efficient recognition by these receptors. Additional intrinsic features to the dsRNA molecule are also necessary for activation of antiviral systems. Studies utilizing synthetic ligands, in vitro biochemistry and reporter systems have greatly helped increase our knowledge on intrinsic features of dsRNA recognition. However, characteristics such as subcellular localization are extrinsic to the dsRNA itself, but certainly influence the recognition in vivo. Thus, mechanisms of viral dsRNA recognition must address how cellular sensors are recruited to nucleic acids or vice versa. Accessory proteins are likely important for in vivo recognition of extrinsic features of viral RNA, but have mostly remained undiscovered due to the limitations of previous strategies. Hence, the identification of novel components of antiviral systems must take

  3. Purification and characterisation of dsRNA using ion pair reverse phase chromatography and mass spectrometry.

    Science.gov (United States)

    Nwokeoji, Alison O; Kung, An-Wen; Kilby, Peter M; Portwood, David E; Dickman, Mark J

    2017-02-10

    RNA interference has provided valuable insight into a wide range of biological systems and is a powerful tool for the analysis of gene function. The exploitation of this pathway to block the expression of specific gene targets holds considerable promise for the development of novel RNAi-based insect management strategies. In addition, there are a wide number of future potential applications of RNAi to control agricultural insect pests as well as its use for prevention of diseases in beneficial insects. The potential to synthesise large quantities of dsRNA by in-vitro transcription or in bacterial systems for RNA interference applications has generated significant demand for the development and application of high throughput analytical tools for the rapid extraction, purification and analysis of dsRNA. Here we have developed analytical methods that enable the rapid purification of dsRNA from associated impurities from bacterial cells in conjunction with downstream analyses. We have optimised TRIzol extractions in conjunction with a single step protocol to remove contaminating DNA and ssRNA, using RNase T1/DNase I digestion under high-salt conditions in combination with solid phase extraction to purify the dsRNA. In addition, we have utilised and developed IP RP HPLC for the rapid, high resolution analysis of the dsRNA. Furthermore, we have optimised base-specific cleavage of dsRNA by RNase A and developed a novel method utilising RNase T1 for RNase mass mapping approaches to further characterise the dsRNA using liquid chromatography interfaced with mass spectrometry. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  4. Inducing RNAi in Caenorhabditis elegans by Injection of dsRNA.

    Science.gov (United States)

    Hammell, Christopher M; Hannon, Gregory J

    2016-01-04

    In Caenorhabditis elegans, long double-stranded RNAs (dsRNAs) are overwhelmingly the trigger of choice for inducing RNA interference (RNAi). Although injection of dsRNA into the somatic or germline tissues of animals requires both specific equipment and technical skills, the ability of C. elegans to amplify the initial dsRNA trigger and to transmit the RNAi activity to other somatic tissues and to the progeny of injected animals is one of the main advantages of using C. elegans as a model system. The direct injection of dsRNA into parental animals is the most reliable method for RNAi and also presents the least experiment-to-experiment and animal-to-animal variability.

  5. Design and testing of multiplex RT-PCR primers for the rapid detection of influenza A virus genomic segments: Application to equine influenza virus.

    Science.gov (United States)

    Lee, EunJung; Kim, Eun-Ju; Shin, Yeun-Kyung; Song, Jae-Young

    2016-02-01

    The avian influenza A virus causes respiratory infections in animal species. It can undergo genomic recombination with newly obtained genetic material through an interspecies transmission. However, the process is an unpredictable event, making it difficult to predict the emergence of a new pandemic virus and distinguish its origin, especially when the virus is the result of multiple infections. Therefore, identifying a novel influenza is entirely dependent on sequencing its whole genome. Occasionally, however, it can be time-consuming, costly, and labor-intensive when sequencing many influenza viruses. To compensate for the difficulty, we developed a rapid, cost-effective, and simple multiplex RT-PCR to identify the viral genomic segments. As an example to evaluate its performance, H3N8 equine influenza virus (EIV) was studied for the purpose. In developing this protocol to amplify the EIV eight-segments, a series of processes, including phylogenetic analysis based on different influenza hosts, in silico analyses to estimate primer specificity, coverage, and variation scores, and investigation of host-specific amino acids, were progressively conducted to reduce or eliminate the negative factors that might affect PCR amplification. Selectively, EIV specific primers were synthesized with dual priming oligonucleotides (DPO) system to increase primer specificity. As a result, 16 primer pairs were selected to screen the dominantly circulating H3N8 EIV 8 genome segments: PA (3), PB2 (1), PA (3), NP (3), NA8 (2), HA3 (1), NS (1), and M (2). The diagnostic performance of the primers was evaluated with eight sets composing of four segment combinations using viral samples from various influenza hosts. The PCR results suggest that the multiplex RT-PCR has a wide range of applications in detection and diagnosis of newly emerging EIVs. Further, the proposed procedures of designing multiplex primers are expected to be used for detecting other animal influenza A viruses

  6. Comparison of human rotaviruses isolated in Mexico City and in Santiago, Chile, by electrophoretic migration of their double-stranded ribonucleic acid genome segments.

    Science.gov (United States)

    Espejo, R T; Avendaño, L F; Muñoz, O; Romero, P; Eternod, J G; Lopez, S; Moncaya, J

    1980-11-01

    During the period October to December 1979, rotaviruses were obtained from infants and young children hospitalized with acute gastroenteritis in Mexico City and were compared by analysis of the migration of their double-stranded ribonucleic acid (RNA) genome segments in gel electrophoresis. Comparison of the results of this analysis and of those of similar studies carried out in 1977 and 1978 showed that the two rotavirus electropherotypes designated 2s and 21 have been continuously present and that the proportion in which these two types have been found in hospitalized patients has varied greatly year to year. The RNAs from rotaviruses 2s and 21 differed in the electrophoretic migraton of at least eight genome segments. However, RNAs from virus assigned to the same electrophoreotypes were not necessarily identical: on the basis of small but significant differences in the migration of segment 7, 8, or 9, isolates of types 2s and 21 could be assigned to two and three different subtypes, respectively. Human rotaviruses obtained in a distant geographical region, Santiago, Chile, in July 1979 had RNA electrophoretic patterns similar to that of electropherotype 21 but different from it in the migration of one or two of the larger RNA segments.

  7. Rapid mapping of functional cis-acting RNA elements by recovery of virus from a degenerate RNA population: application to genome segment 10 of bluetongue virus.

    Science.gov (United States)

    Boyce, M; McCrae, M A

    2015-10-01

    The regulatory elements which control the processes of virus replication and gene expression in the Orbivirus genus are uncharacterized in terms of both their locations within genome segments and their specific functions. The reverse genetics system for the type species, Bluetongue virus, has been used in combination with RNA secondary structure prediction to identify and map the positions of cis-acting regions within genome segment 10. Through the simultaneous introduction of variability at multiple nucleotide positions in the rescue RNA population, the functional contribution of these positions was used to map regions containing cis-acting elements essential for virus viability. Nucleotides that were individually lethal when varied mapped within a region of predicted secondary structure involving base pairing between the 5' and 3' ends of the transcript. An extended region of predicted perfect base pairing located within the 3' untranslated region of the genome segment was also found to be required for virus viability. In contrast to the identification of individually lethal mutations, gross alteration of the composition of this predicted stem region was possible, providing the base-pairing potential between the two strands was maintained, identifying a structural feature predicted to be conserved throughout the Orbivirus genus. The approach of identifying cis-acting sequences through sequencing the recovered virus following the rescue of a degenerate RNA population is broadly applicable to viruses where reverse genetics is available.

  8. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

    2015-11-15

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  9. A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection.

    Science.gov (United States)

    Dung, Tran Thi Ngoc; Duy, Pham Thanh; Sessions, October M; Sangumathi, Uma K; Phat, Voong Vinh; Tam, Pham Thi Thanh; To, Nguyen Thi Nguyen; Phuc, Tran My; Hong Chau, Tran Thi; Chau, Nguyen Ngoc Minh; Minh, Ngoc Nguyen; Thwaites, Guy E; Rabaa, Maia A; Baker, Stephen

    2017-04-24

    Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. Our approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct RoV characterization and could be scaled-up for use in global RoV surveillance systems. Current Controlled Trials ISRCTN88101063 . Date of registration: 14/06/2012.

  10. Diverged Copies of the Seed Regulatory Opaque-2 Gene by a Segmental Duplication in the Progenitor Genome of Rice,Sorghum,and Maize

    Institute of Scientific and Technical Information of China (English)

    Jian-Hong Xu; Joachim Messing

    2008-01-01

    Comparative analyses of the sequence of entire genomes have shown that gene duplications,chromosomal segmental duplications.or even whole genome duplications(WGD)have played prominent roles in the evolution of many eukaryotic species.Here,we used the ancient duplication of a well known transcription factor in maize,encoded by the Opaque-2(02)IOCUS,to examine the generaI features of divergences of chromosomaI segmentaI duplications in a lineagespecific manner.We took advantage of contiguous chromosomal sequence information in rice(Oryza sativa,Nipponbare).sorghum(Sorghum bicoloc Btx623),and maize(Zea mays,B73)that were aligned by conserved gene order(synteny).This analysis showed that the maize O2 locus is contained within a 1.25 million base-pair(Mb)segment on chromosome 7.which was duplicated≈56 million years ago(mya)before the split of rice and maize 50 mya.The duplicated region on chromosome 1 is only half the size and contains the maize OHP gene.which does not restore the o2 mutation although it encodes a protein with the same DNA and protein binding properties in endosperm.The segmental duplication iS not only found in rice,but also in sorghum,which split from maize 11.9 mya.A detailed analysis of the duplicated regions provided examples for complex rearrangements including deletions.duplications,conversions,inversions,and translocations.Furthermore,the rice and sorghum genomes appeared to be more stable than the maize genome,probably because maize underwent allotetraploidization and then diploidization.

  11. The Diversity of Sequence and Chromosomal Distribution of New Transposable Element-Related Segments in the Rye Genome Revealed by FISH and Lineage Annotation

    Directory of Open Access Journals (Sweden)

    Yingxin Zhang

    2017-10-01

    Full Text Available Transposable elements (TEs in plant genomes exhibit a great variety of structure, sequence content and copy number, making them important drivers for species diversity and genome evolution. Even though a genome-wide statistic summary of TEs in rye has been obtained using high-throughput DNA sequencing technology, the accurate diversity of TEs in rye, as well as their chromosomal distribution and evolution, remains elusive due to the repetitive sequence assembling problems and the high dynamic and nested nature of TEs. In this study, using genomic plasmid library construction combined with dot-blot hybridization and fluorescence in situ hybridization (FISH analysis, we successfully isolated 70 unique FISH-positive TE-related sequences including 47 rye genome specific ones: 30 showed homology or partial homology with previously FISH characterized sequences and 40 have not been characterized. Among the 70 sequences, 48 sequences carried Ty3/gypsy-derived segments, 7 sequences carried Ty1/copia-derived segments and 15 sequences carried segments homologous with multiple TE families. 26 TE lineages were found in the 70 sequences, and among these lineages, Wilma was found in sequences dispersed in all chromosome regions except telomeric positions; Abiba was found in sequences predominantly located at pericentromeric and centromeric positions; Wis, Carmilla, and Inga were found in sequences displaying signals dispersed from distal regions toward pericentromeric positions; except DNA transposon lineages, all the other lineages were found in sequences displaying signals dispersed from proximal regions toward distal regions. A high percentage (21.4% of chimeric sequences were identified in this study and their high abundance in rye genome suggested that new TEs might form through recombination and nested transposition. Our results also gave proofs that diverse TE lineages were arranged at centromeric and pericentromeric positions in rye, and lineages like

  12. A genome-wide survey of hybrid incompatibility factors by the introgression of marked segments of Drosophila mauritiana chromosomes into Drosophila simulans

    Energy Technology Data Exchange (ETDEWEB)

    True, J.R.; Laurie, C.C. [Duke Univ., Durham, NC (United States); Weir, B.S. [North Carolina State Univ., Raleigh, NC (United States)

    1996-03-01

    In hybrids between Drosophila simulans and D. mauritiana, males are sterile and females are fertile, in compliance with HALDANE`s rule. The genetic basis of this phenomenon was investigated by introgression of segments of the mauritiana genome into a simulans background. A total of 87 positions throughout the mauritiana genome were marked with P-element insertions and replicate introgressions were made by repeated backcrossing to simulans for 15 generations. The fraction of hemizygous X chromosomal introgressions that are male sterile is {approximately}50% greater than the fraction of homozygous autosomal segments. This result suggests that male sterility factors have evolved at a higher rate on the X, but chromosomal differences in segment length cannot be ruled out. The fraction of homozygous autosomal introgressions that are male sterile is several times greater than the fraction that are either female sterile or inviable. This observation strongly indicates that male sterility factors have evolved more rapidly than either female sterility or inviability factors. These results, combined with previous work on these and other species, suggest that HALDANE`s rule has at least two causes: recessivity of incompatibility factors and differential accumulation of sterility factors affecting males and females. 50 refs., 4 figs., 3 tabs.

  13. Effects of ced-9 dsRNA on Caenorhabditis elegans and Meloidogyne incognita

    Directory of Open Access Journals (Sweden)

    Robert T. Gaeta

    2011-01-01

    Full Text Available Problem Statement: In metazoans Programmed Cell Death (PCD is essential for proper development. Suppression of PCD is needed to guarantee cell survival and in the nematode Caenorhabditis elegans the regulation of PCD is accomplished by the function of the ced-9 gene. Approach: In this work the use of double stranded RNA (dsRNA to knock-down ced-9 gene function was tested as means to induce PCD. Results: Our results indicate that dsRNA targeting the cell death protection gene ced-9 is effective at decreasing the fecundity of C. elegans by up to 21%. The decreased fecundity correlated with an increased presence of cell corpses in developing embryos. Endogenous ced-9 transcript levels were reduced in progeny of ced-3 mutant nematodes fed bacteria expressing ced-9 dsRNA. These data suggest that nematode fecundity can be reduced by ingestion and exposure to dsRNAs targeting regulation of the cell death pathway. In an attempt to determine if plant parasitic nematodes are susceptible to the targeting of the PCD regulatory pathway we exposed Meloidogyne incognita, a plant parasitic nematode, to ced-9 dsRNA; here we show that this exposure results in decreased gall formation in the tobacco plants. Conclusion/Recommendations: Our results provide the first steps toward using RNAi technologies to attempt nematode control by targeting cell death pathways. Ongoing research with transgenic plants designed to express dsRNA for ced-9-like sequences will further test the feasibility of generating plants with RNAi-based resistance to parasitic nematodes.

  14. Genome Editing of Wnt-1, a Gene Associated with Segmentation, via CRISPR/Cas9 in the Pine Caterpillar Moth, Dendrolimus punctatus

    Science.gov (United States)

    Liu, Huihui; Liu, Qun; Zhou, Xuguo; Huang, Yongping; Zhang, Zhen

    2017-01-01

    The pine caterpillar moth, Dendrolimus punctatus, is a devastating forest pest. Genetic manipulation of this insect pest is limited due to the lack of genomic and functional genomic toolsets. Recently, CRISPR/Cas9 technology has been demonstrated to be a promising approach to modify the genome. To investigate gene functions during the embryogenesis, we introduced CRISPR/Cas9 system in D. punctatus to precisely and effectively manipulate gene expressions inmutant embryos. Compared to controls, knocking out of DpWnt-1, a gene well known for its role in the early body planning, led to high embryonic mortality. Among these mutants, 32.9% of the embryos and larvae showed an abnormal development. DpWnt-1 mutants predominantly exhibited abnormal posterior segments. In addition, multiple phenotypes were observed, including the loss of limbs and the head deformation, suggesting that DpWnt-1 signaling pathway is necessary for anterior segmentation and appendage development. Overall, our results demonstrate that CRISPR/Cas9 system is feasible and efficient in inducing mutations at a specific locus in D. punctatus. This study not only lays the foundation for characterizing gene functions in a non-model species, but also facilitates the future development of pest control alternatives for a major defoliator. PMID:28111552

  15. Genomic and biological characterization of a new cypovirus isolated from Dendrolimus punctatus.

    Science.gov (United States)

    Zhou, Yin; Qin, Tongcheng; Xiao, Yuzhou; Qin, Fujun; Lei, Chengfeng; Sun, Xiulian

    2014-01-01

    A novel cypovirus (designated DpCPV-MC) was isolated from the pine moth Dendrolimus punctatus using serial in vivo cloning procedures. DpCPV-MC occurs in typical polyhedral occlusion bodies, containing a number of spherical virions. Laboratory bioassays indicated that the infectivity of DpCPV-MC against second-instar Spodoptera exigua larvae does not differ significantly from that of Dendrolimus punctatus cypovirus 1. Full-length amplification of the DpCPV-MC cDNAs identified 16 dsRNA genome segments. Each segment encodes one open reading frame with unique conserved terminal sequences at the 5' and 3' ends, which differ from those of all previously reported cypoviruses. On a phylogenetic tree based on the amino acid sequences of the polyhedrin of 19 cypovirus species, DpCPV-MC was closest to the type-4 cypoviruses. Homology searches showed that ten segments of DpCPV-MC (S1, S2, S3, S4, S5, S7, S8, S9, S12, and S13) encode putative CPV structural and nonstructural proteins, three segments (S6, S10 and S14) encode putative insect proteins or other viral proteins, and the other three segments (S11, S15, and S16) encode proteins that have no obvious sequence similarity to any known protein. Based on RNA secondary structures analysis, two segments of them (S11 and S16) were predicted to possibly transcript less efficiently than the other segments. We speculate that DpCPV-MC is composed of several genotypes. The ten CPV-related segments constantly exist in all genotypes, and one or two of the six CPV-unrelated segments co-exist with the ten CPV-related segments in one DpCPV-MC genotype, thus each virion contains no more than 12 segments. Based on our results and the literature, DpCPV-MC is a new cypovirus (Cypovirus 22, strain DpCPV-22).

  16. Genomic and biological characterization of a new cypovirus isolated from Dendrolimus punctatus.

    Directory of Open Access Journals (Sweden)

    Yin Zhou

    Full Text Available A novel cypovirus (designated DpCPV-MC was isolated from the pine moth Dendrolimus punctatus using serial in vivo cloning procedures. DpCPV-MC occurs in typical polyhedral occlusion bodies, containing a number of spherical virions. Laboratory bioassays indicated that the infectivity of DpCPV-MC against second-instar Spodoptera exigua larvae does not differ significantly from that of Dendrolimus punctatus cypovirus 1. Full-length amplification of the DpCPV-MC cDNAs identified 16 dsRNA genome segments. Each segment encodes one open reading frame with unique conserved terminal sequences at the 5' and 3' ends, which differ from those of all previously reported cypoviruses. On a phylogenetic tree based on the amino acid sequences of the polyhedrin of 19 cypovirus species, DpCPV-MC was closest to the type-4 cypoviruses. Homology searches showed that ten segments of DpCPV-MC (S1, S2, S3, S4, S5, S7, S8, S9, S12, and S13 encode putative CPV structural and nonstructural proteins, three segments (S6, S10 and S14 encode putative insect proteins or other viral proteins, and the other three segments (S11, S15, and S16 encode proteins that have no obvious sequence similarity to any known protein. Based on RNA secondary structures analysis, two segments of them (S11 and S16 were predicted to possibly transcript less efficiently than the other segments. We speculate that DpCPV-MC is composed of several genotypes. The ten CPV-related segments constantly exist in all genotypes, and one or two of the six CPV-unrelated segments co-exist with the ten CPV-related segments in one DpCPV-MC genotype, thus each virion contains no more than 12 segments. Based on our results and the literature, DpCPV-MC is a new cypovirus (Cypovirus 22, strain DpCPV-22.

  17. Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region.

    Science.gov (United States)

    Ando, Asako; Shigenari, Atsuko; Kulski, Jerzy K; Renard, Christine; Chardon, Patrick; Shiina, Takashi; Inoko, Hidetoshi

    2005-12-01

    Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block.

  18. Accumulation of point mutations and reassortment of genomic RNA segments are involved in the microevolution of Puumala hantavirus in a bank vole (Myodes glareolus) population.

    Science.gov (United States)

    Razzauti, Maria; Plyusnina, Angelina; Henttonen, Heikki; Plyusnin, Alexander

    2008-07-01

    The genetic diversity of Puumala hantavirus (PUUV) was studied in a local population of its natural host, the bank vole (Myodes glareolus). The trapping area (2.5 x 2.5 km) at Konnevesi, Central Finland, included 14 trapping sites, at least 500 m apart; altogether, 147 voles were captured during May and October 2005. Partial sequences of the S, M and L viral genome segments were recovered from 40 animals. Seven, 12 and 17 variants were detected for the S, M and L sequences, respectively; these represent new wild-type PUUV strains that belong to the Finnish genetic lineage. The genetic diversity of PUUV strains from Konnevesi was 0.2-4.9 % for the S segment, 0.2-4.8 % for the M segment and 0.2-9.7 % for the L segment. Most nucleotide substitutions were synonymous and most deduced amino acid substitutions were conservative, probably due to strong stabilizing selection operating at the protein level. Based on both sequence markers and phylogenetic clustering, the S, M and L sequences could be assigned to two groups, 'A' and 'B'. Notably, not all bank voles carried S, M and L sequences belonging to the same group, i.e. S(A)M(A)L(A) or S(B)M(B)L(B). A substantial proportion (8/40, 20 %) of the newly characterized PUUV strains possessed reassortant genomes such as S(B)M(A)L(A), S(A)M(B)L(B) or S(B)M(A)L(B). These results suggest that at least some of the PUUV reassortants are viable and can survive in the presence of their parental strains.

  19. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India.

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    Sushila Maan

    Full Text Available Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV. Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp. and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV 'topotype'. However, genome-segment 5 (Seg-5 encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03 are closely related (>99% identity to a South African BTV-2 vaccine-strain (western topotype. Similarly BTV-10 isolates (IND2003/06; IND2005/04 show >99% identity in all genome segments, to the prototype BTV-10 (CA-8 strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of 'live' South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies.

  20. Isolation of bluetongue virus serotype 1 from Culicoides vector captured in livestock farms and sequence analysis of the viral genome segment-2.

    Science.gov (United States)

    Dadawala, A I; Biswas, S K; Rehman, W; Chand, K; De, A; Mathapati, B S; Kumar, P; Chauhan, H C; Chandel, B S; Mondal, B

    2012-08-01

    Bluetongue virus serotype-1 (BTV-1) was isolated from Culicoides oxystoma vectors captured on livestock farms in two places of Gujarat, India. The viruses were isolated on BHK-21 cells, which produced characteristic BTV-related cytopathic effects between 24 and 48 h post-infection. Virus antigen was demonstrated in infected cells at different passage by a BTV-specific sandwich ELISA. Further, polyacrylamide gel electrophoresis and silver staining of viral genomic RNA revealed ten double-stranded RNA segments characteristic of BTV. Serotype of the isolates was identified by virus neutralization and PCR coupled with sequencing. The isolates were designated as SKN-7 and SKN-8 and their genome segment-2 (VP2) were sequenced. Phylogenetic analyses revealed very close relationship between them although they are not identical. SKN-8 showed closer relationship with a recently isolated BTV-1 from goat. Bluetongue virus was earlier isolated from Culicoides in adjacent state more than 20 years ago, although the serotype of the virus was not determined.

  1. Non-Invasive Delivery of dsRNA into De-Waxed Tick Eggs by Electroporation

    Science.gov (United States)

    Ruiz, Newton; de Abreu, Leonardo Araujo; Parizi, Luís Fernando; Kim, Tae Kwon; Mulenga, Albert; Braz, Gloria Regina Cardoso; Vaz, Itabajara da Silva; Logullo, Carlos

    2015-01-01

    RNA interference-mediated gene silencing was shown to be an efficient tool for validation of targets that may become anti-tick vaccine components. Here, we demonstrate the application of this approach in the validation of components of molecular signaling cascades, such as the Protein Kinase B (AKT) / Glycogen Synthase Kinase (GSK) axis during tick embryogenesis. It was shown that heptane and hypochlorite treatment of tick eggs can remove wax, affecting corium integrity and but not embryo development. Evidence of AKT and GSK dsRNA delivery into de-waxed eggs of via electroporation is provided. Primers designed to amplify part of the dsRNA delivered into the electroporated eggs dsRNA confirmed its entry in eggs. In addition, it was shown that electroporation is able to deliver the fluorescent stain, 4',6-diamidino-2-phenylindole (DAPI). To confirm gene silencing, a second set of primers was designed outside the dsRNA sequence of target gene. In this assay, the suppression of AKT and GSK transcripts (approximately 50% reduction in both genes) was demonstrated in 7-day-old eggs. Interestingly, silencing of GSK in 7-day-old eggs caused 25% reduction in hatching. Additionally, the effect of silencing AKT and GSK on embryo energy metabolism was evaluated. As expected, knockdown of AKT, which down regulates GSK, the suppressor of glycogen synthesis, decreased glycogen content in electroporated eggs. These data demonstrate that electroporation of de-waxed R. microplus eggs could be used for gene silencing in tick embryos, and improve the knowledge about arthropod embryogenesis. PMID:26091260

  2. Mosquito and Drosophila entomobirnaviruses suppress dsRNA- and siRNA-induced RNAi.

    Science.gov (United States)

    van Cleef, Koen W R; van Mierlo, Joël T; Miesen, Pascal; Overheul, Gijs J; Fros, Jelke J; Schuster, Susan; Marklewitz, Marco; Pijlman, Gorben P; Junglen, Sandra; van Rij, Ronald P

    2014-07-01

    RNA interference (RNAi) is a crucial antiviral defense mechanism in insects, including the major mosquito species that transmit important human viruses. To counteract the potent antiviral RNAi pathway, insect viruses encode RNAi suppressors. However, whether mosquito-specific viruses suppress RNAi remains unclear. We therefore set out to study RNAi suppression by Culex Y virus (CYV), a mosquito-specific virus of the Birnaviridae family that was recently isolated from Culex pipiens mosquitoes. We found that the Culex RNAi machinery processes CYV double-stranded RNA (dsRNA) into viral small interfering RNAs (vsiRNAs). Furthermore, we show that RNAi is suppressed in CYV-infected cells and that the viral VP3 protein is responsible for RNAi antagonism. We demonstrate that VP3 can functionally replace B2, the well-characterized RNAi suppressor of Flock House virus. VP3 was found to bind long dsRNA as well as siRNAs and interfered with Dicer-2-mediated cleavage of long dsRNA into siRNAs. Slicing of target RNAs by pre-assembled RNA-induced silencing complexes was not affected by VP3. Finally, we show that the RNAi-suppressive activity of VP3 is conserved in Drosophila X virus, a birnavirus that persistently infects Drosophila cell cultures. Together, our data indicate that mosquito-specific viruses may encode RNAi antagonists to suppress antiviral RNAi.

  3. Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.

    Science.gov (United States)

    Zhou, Degui; Chen, Wei; Lin, Zechuan; Chen, Haodong; Wang, Chongrong; Li, Hong; Yu, Renbo; Zhang, Fengyun; Zhen, Gang; Yi, Junliang; Li, Kanghuo; Liu, Yaoguang; Terzaghi, William; Tang, Xiaoyan; He, Hang; Zhou, Shaochuan; Deng, Xing Wang

    2016-02-01

    Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  4. Molecular analysis of the genome segments S1, S4, S6, S7 and S12 of a Rice gall dwarf virus isolate from Thailand; completion of the genomic sequence.

    Science.gov (United States)

    Moriyasu, Y; Maruyama-Funatsuki, W; Kikuchi, A; Ichimi, K; Zhong, B; Yan, J; Zhu, Y; Suga, H; Watanabe, Y; Ichiki-Uehara, T; Shimizu, T; Hagiwara, K; Kamiunten, H; Akutsu, K; Omura, T

    2007-01-01

    The complete nucleotide sequences of the double-stranded RNA segments S1, S4, S6, S7 and S12 of the genome of a Rice gall dwarf virus (RGDV) isolate from Thailand were determined. The segments consisted of 4505, 2622, 1648, 1652 and 853 nucleotides, encoding putative proteins of 1458, 725, 489, 511 and 206 amino acids with molecular masses of approximately 166, 80, 53, 59 and 24 kDa, respectively. Homology searches indicated that each of the putative proteins has a counterpart in isolates of Rice dwarf virus (RDV) and Wound tumor virus, two other species in the genus Phytoreovirus. However, no similarities were found to other registered sequences, including those of other viruses that belong to the family Reoviridae. The identities between homologous structural proteins of RGDV and RDV ranged from 34 to 51% and were thus higher than those between homologous non-structural proteins of RGDV and RDV (16-37%). Among the nonstructural proteins, the highest amino acid sequence identity (37%) was observed for RGDV Pns11 and RDV Pns10, a constituent of tubular inclusions. This observation suggests that a specific amino acid backbone might be required for maintaining not only the three-dimensional structure of virions but also that of inclusions. The entire sequence of the RGDV genome is now available.

  5. Variation in RNAi efficacy among insect species is attributable to dsRNA degradation in vivo.

    Science.gov (United States)

    Wang, Kangxu; Peng, Yingchuan; Pu, Jian; Fu, Wenxi; Wang, Jiale; Han, Zhaojun

    2016-10-01

    RNA interference (RNAi) has become an essential technique in entomology research. However, RNAi efficiency appears to vary significantly among insect species. Here, the sensitivity of four insect species from different orders to RNAi was compared to understand the reason for this variation. A previously reported method was modified to monitor trace amounts of double-stranded RNA (dsRNA). After the administration of dsRNA, the dynamics of its content was determined in the hemolymph, in addition to the capability of its degradation in both the hemolymph and the midgut juice. The results showed that injection of dsRNA targeting the homologous chitinase gene in Periplaneta americana, Zophobas atratus, Locusta migratoria, and Spodoptera litura, with doses (1.0, 2.3, 11.5, and 33.0 μg, respectively) resulting in the same initial hemolymph concentration, caused 82%, 78%, 76%, and 20% depletion, respectively, whereas feeding doses based on body weight (24, 24, 36, and 30 μg) accounted for 47%, 28%, 5%, and 1% depletion. The sensitivity of insects to RNAi was observed to be as follows: P. americana > Z. atratus >L. migratoria >S. litura. In vivo monitoring revealed that RNAi effects among these insect species were highly correlated with the hemolymph dsRNA contents. Furthermore, in vitro experiments demonstrated that the hemolymph contents after dsRNA injection were dependent on hemolymph degradation capacities, and on the degradation capabilities in the midgut juice, when dsRNA was fed. In conclusion, the RNAi efficacy in different insect species was observed to depend on the enzymatic degradation of dsRNA, which functions as the key factor determining the inner target exposure dosages. Thus, enzymatic degradation in vivo should be taken into consideration for efficient use of RNAi in insects.

  6. Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges

    Science.gov (United States)

    Kolliopoulou, Anna; Taning, Clauvis N. T.; Smagghe, Guy; Swevers, Luc

    2017-01-01

    RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed. PMID:28659820

  7. Reduced stability and intracellular transport of dsRNA contribute to poor RNAi response in lepidopteran insects.

    Science.gov (United States)

    Shukla, Jayendra Nath; Kalsi, Megha; Sethi, Amit; Narva, Kenneth E; Fishilevich, Elane; Singh, Satnam; Mogilicherla, Kanakachari; Palli, Subba Reddy

    2016-07-02

    RNA interference (RNAi) has become a widely used reverse genetic tool to study gene function in eukaryotic organisms and is being developed as a technology for insect pest management. The efficiency of RNAi varies among organisms. Insects from different orders also display differential efficiency of RNAi, ranging from highly efficient (coleopterans) to very low efficient (lepidopterans). We investigated the reasons for varying RNAi efficiency between lepidopteran and coleopteran cell lines and also between the Colorado potato beetle, Leptinotarsa decemlineata and tobacco budworm, Heliothis virescens. The dsRNA either injected or fed was degraded faster in H. virescens than in L. decemlineata. Both lepidopteran and coleopteran cell lines and tissues efficiently took up the dsRNA. Interestingly, the dsRNA administered to coleopteran cell lines and tissues was taken up and processed to siRNA whereas the dsRNA was taken up by lepidopteran cell lines and tissues but no siRNA was detected in the total RNA isolated from these cell lines and tissues. The data included in this paper showed that the degradation and intracellular transport of dsRNA are the major factors responsible for reduced RNAi efficiency in lepidopteran insects.

  8. Effect of PEG biofunctional spacers and TAT peptide on dsRNA loading on gold nanoparticles

    Science.gov (United States)

    Sanz, Vanesa; Conde, João; Hernández, Yulán; Baptista, Pedro V.; Ibarra, M. R.; de la Fuente, Jesús M.

    2012-06-01

    The surface chemistry of gold nanoparticles (AuNPs) plays a critical role in the self-assembly of thiolated molecules and in retaining the biological function of the conjugated biomolecules. According to the well-established gold-thiol interaction the undefined ionic species on citrate-reduced gold nanoparticle surface can be replaced with a self-assembled monolayer of certain thiolate derivatives and other biomolecules. Understanding the effect of such derivatives in the functionalization of several types of biomolecules, such as PEGs, peptides or nucleic acids, has become a significant challenge. Here, an approach to attach specific biomolecules to the AuNPs ( 14 nm) surface is presented together with a study of their effect in the functionalization with other specific derivatives. The effect of biofunctional spacers such as thiolated poly(ethylene glycol) (PEG) chains and a positive peptide, TAT, in dsRNA loading on AuNPs is reported. Based on the obtained data, we hypothesize that loading of oligonucleotides onto the AuNP surface may be controlled by ionic and weak interactions positioning the entry of the oligo through the PEG layer. We demonstrate that there is a synergistic effect of the TAT peptide and PEG chains with specific functional groups on the enhancement of dsRNA loading onto AuNPs.

  9. Effect of PEG biofunctional spacers and TAT peptide on dsRNA loading on gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, Vanesa; Conde, Joao; Hernandez, Yulan [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain); Baptista, Pedro V. [Universidade Nova de Lisboa, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Centro de Investigacao em Genetica Molecular Humana (Portugal); Ibarra, M. R.; Fuente, Jesus M. de la, E-mail: jmfuente@unizar.es [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain)

    2012-06-15

    The surface chemistry of gold nanoparticles (AuNPs) plays a critical role in the self-assembly of thiolated molecules and in retaining the biological function of the conjugated biomolecules. According to the well-established gold-thiol interaction the undefined ionic species on citrate-reduced gold nanoparticle surface can be replaced with a self-assembled monolayer of certain thiolate derivatives and other biomolecules. Understanding the effect of such derivatives in the functionalization of several types of biomolecules, such as PEGs, peptides or nucleic acids, has become a significant challenge. Here, an approach to attach specific biomolecules to the AuNPs ({approx}14 nm) surface is presented together with a study of their effect in the functionalization with other specific derivatives. The effect of biofunctional spacers such as thiolated poly(ethylene glycol) (PEG) chains and a positive peptide, TAT, in dsRNA loading on AuNPs is reported. Based on the obtained data, we hypothesize that loading of oligonucleotides onto the AuNP surface may be controlled by ionic and weak interactions positioning the entry of the oligo through the PEG layer. We demonstrate that there is a synergistic effect of the TAT peptide and PEG chains with specific functional groups on the enhancement of dsRNA loading onto AuNPs.

  10. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome.

    Science.gov (United States)

    Ohshima, Kazusato; Matsumoto, Kosuke; Yasaka, Ryosuke; Nishiyama, Mai; Soejima, Kenta; Korkmaz, Savas; Ho, Simon Y W; Gibbs, Adrian J; Takeshita, Minoru

    2016-01-01

    Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and Japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550-2600 years ago, but that the population mostly radiated 295-545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world.

  11. DNM1DN: a new class of paralogous genomic segments (duplicons) with highly conserved copies on chromosomes Y and 15.

    Science.gov (United States)

    Makrinou, E; Fox, M; Wolfe, J; Cameron, J; Taylor, K; Edwards, Y H

    2004-03-01

    Screening a testis cDNA selection library for Y-linked genes yielded 79 cDNAs. Of these, 9 matched the 3' region of the dynamin 1 gene (DNM1) on chromosome 9q34 with >90% identity. Fluoresence in situ hybridisation and PCR amplification were used to localise a large number of DNM1-like sequences to human chromosomes 15 and Y. PCR amplification of overlapping Y-linked YACs allowed a more accurate mapping of the Y-linked DNM1-like cDNAs to a euchromatic locus in close proximity to heterochromatin at Yq11.23. A search of the genome database identified 64 highly homologous copies of the DNM1 fragment. Most of these copies were localised to chromosomes 15 and Y, but others mapped to chromosomes 5, 8, 10, 12, 19 and 22. These sequences exhibit all the major features of a duplicon and have been designated DNM1DN (DNM1 duplicon). Evolutionary studies using fluorescence in situ hybridisation indicate that transposition of the DNM1DN sequence to chromosome 15 took place earlier in primate evolution than the transposition to the Y chromosome. The translocation to the Y took place at a time following the divergence of a common ancestor from gorilla, approximately 4-7 million years ago.

  12. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, Kazusato, E-mail: ohshimak@cc.saga-u.ac.jp [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima (Japan); Matsumoto, Kosuke [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); Yasaka, Ryosuke [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima (Japan); Nishiyama, Mai; Soejima, Kenta [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); Korkmaz, Savas [Department of Plant Protection, Faculty of Agriculture, University of Canakkale Onsekiz Mart, Canakkale (Turkey); Ho, Simon Y.W. [School of Biological Sciences, University of Sydney, Sydney, New South Wales (Australia); Gibbs, Adrian J. [Emeritus Faculty, Australian National University, Canberra (Australia); Takeshita, Minoru [Laboratory of Plant Pathology, Faculty of Agriculture, University of Miyazaki, Miyazaki (Japan)

    2016-01-15

    Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and Japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550–2600 years ago, but that the population mostly radiated 295–545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world. - Highlights: • Present-day CMV lineages had a most recent common ancestor 1550–2600 years ago. • The CMV population mostly radiated less than 295–545 years ago. • No reassortant found in the present populations is more than 251 years old. • The open-reading frames evolve at around 2.3–4.7×10{sup −4} substitutions/site/year. • Synonymous codons of CMV seem to have a more precise temporal signal than all codons.

  13. Umatilla virus genome sequencing and phylogenetic analysis: identification of stretch lagoon orbivirus as a new member of the Umatilla virus species.

    Directory of Open Access Journals (Sweden)

    Manjunatha N Belaganahalli

    Full Text Available The genus Orbivirus, family Reoviridae, includes 22 species of viruses with genomes composed of ten segments of linear dsRNA that are transmitted between their vertebrate hosts by insects or ticks, or with no identified vectors. Full-genome sequence data are available for representative isolates of the insect borne mammalian orbiviruses (including bluetongue virus, as well as a tick borne avian orbivirus (Great Island virus. However, no sequence data are as yet available for the mosquito borne avian orbiviruses.We report full-length, whole-genome sequence data for Umatilla virus (UMAV, a mosquito borne avian orbivirus from the USA, which belongs to the species Umatilla virus. Comparisons of conserved genome segments 1, 2 and 8 (Seg-1, Seg-2 and Seg-8 - encoding the polymerase-VP1, sub-core 'T2' protein and core-surface 'T13' protein, respectively, show that UMAV groups with the mosquito transmitted mammalian orbiviruses. The highest levels of sequence identity were detected between UMAV and Stretch Lagoon orbivirus (SLOV from Australia, showing that they belong to the same virus species (with nt/aa identity of 76.04%/88.07% and 77.96%/95.36% in the polymerase and T2 genes and protein, respectively. The data presented here has assisted in identifying the SLOV as a member of the Umatilla serogroup. This sequence data reported here will also facilitate identification of new isolates, and epidemiological studies of viruses belonging to the species Umatilla virus.

  14. GENOME-WIDE INVESTIGATION OF HSF GENES IN SESAME REVEALS THEIR SEGMENTAL DUPLICATION EXPANSION AND THEIR ACTIVE ROLE IN DROUGHT STRESS RESPONSE

    Directory of Open Access Journals (Sweden)

    Komivi Dossa

    2016-10-01

    Full Text Available Sesame is a survivor crop cultivated for ages in arid areas under high temperatures and limited water conditions. Since its entire genome has been sequenced, revealing evolution and functional characterization of its abiotic stress genes became a hot topic. In this study, we performed a whole-genome identification and analysis of Hsf gene family in sesame. Thirty genes encoding Hsf domain were found and classified into 3 major classes A, B and C. The class A members were the most representative one and Hsf genes were distributed in 12 of the 16 linkage groups (except the LG 8, 9, 13 and 16. Evolutionary analysis revealed that, segmental duplication events which occurred around 67 MYA, were the primary force underlying Hsf genes expansion in sesame. Comparative analysis also suggested that sesame has retained most of its Hsf genes while its relatives viz. tomato and potato underwent extensive gene losses during evolution. Continuous purifying selection has played a key role in the maintenance of Hsf genes in sesame. Expression analysis of the Hsf genes in sesame revealed their putative involvement in multiple tissue-/developmental stages. Time-course expression profiling of Hsf genes in response to drought stress showed that 90% Hsfs are drought responsive. We infer that classes B-Hsfs might be the primary regulators of drought response in sesame by cooperating with some class A genes. This is the first insight into this gene family and the results provide some gene resources for future gene cloning and functional studies towards the improvement in stress tolerance of sesame.

  15. Evaluation of deoxynivalenol production in dsRNA Carrying and Cured Fusarium graminearum isolates by AYT1 expressing transformed tobacco

    Directory of Open Access Journals (Sweden)

    Mohammad Hasan shahhosseiny

    2015-12-01

    Full Text Available Introduction: Fusarium head blight (FHB, is the most destructive disease of wheat, producing the mycotoxin deoxynivalenol, a protein synthesis inhibitor, which is harmful to humans and livestock. dsRNAmycoviruses-infected-isolates of Fusariumgraminearum, showed changes in morphological and pathogenicity phenotypes including reduced virulence towards wheat and decreased production of trichothecene mycotoxin (deoxynivalenol: DON. Materials and methods: Previous studies indicated that over expression of yeast acetyl transferase gene (ScAYT1 encoding a 3-O trichothecene acetyl transferase that converts deoxynivalenol to a less toxic acetylated form, leads to suppression of the deoxynivalenol sensitivity in pdr5 yeast mutants. To identify whether ScAYT1 over-expression in transgenic tobacco plants can deal with mycotoxin (deoxynivalenol in fungal extract and studying the effect of dsRNA contamination on detoxification and resistance level, we have treated T1 AYT1 transgenic tobacco seedlings with complete extraction of normal F. graminearum isolate carrying dsRNA metabolites. First, we introduced AYT1into the model tobacco plants through Agrobacterium-mediated transformation in an attempt to detoxify deoxynivalenol. Results: In vitro tests with extraction of dsRNA carrying and cured isolates of F. graminearum and 10 ppm of deoxynivalenol indicated variable resistance levels in transgenic plants. Discussion and conclusion: The results of this study indicate that the transgene expression AYT1 and Fusarium infection to dsRNA can induce tolerance to deoxynivalenol, followed by increased resistance to Fusarium head blight disease of wheat.

  16. Advances in RNA interference: dsRNA treatment in trees and grapevines for insect pest population suppression

    Science.gov (United States)

    RNA interference (RNAi) is a breakthrough technology that has significantly impacted contemporary approaches to control the damage caused by insect pests. Most well-known RNAi studies continue to rely on injecting the dsRNA molecules directly into the organism; this approach is not suitable for use...

  17. Differential responses of normal human melanocytes to intra- and extracellular dsRNA.

    Science.gov (United States)

    Wang, Suiquan; Liu, Dongyin; Jin, Rong; Zhu, Yiping; Xu, Aie

    2015-06-01

    Viral factor has been implicated in the etiopathogenesis of vitiligo. To elucidate the effects of viral double-stranded RNA (dsRNA) on melanocytes and to explore the underlying mechanisms, primary cultured normal human melanocytes were treated with synthetic viral dsRNA analog poly(I:C). The results demonstrated that poly(I:C)-triggered apoptosis when transfected into melanocytes, while extracellular poly(I:C) did not have that effect. Intracellular poly(I:C)-induced melanocyte death was decreased by RIG-I or MDA5 siRNA, but not by TLR3 siRNA. Both intracellular and extracellular poly(I:C) induced the expression of IFNB, TNF, IL6, and IL8. However, extracellular poly(I:C) demonstrated a much weaker induction capacity of cytokine genes than intracellular poly(I:C). Further analysis revealed that phosphorylation of TBK1, IRF3, IRF7, and TAK1 was differentially induced by intra- or extracellular poly(I:C). NFκB inhibitor Bay 11-7082 decreased the induction of all the cytokines by poly(I:C), suggesting the ubiquitous role of NFκB in the process. Poly(I:C) treatment also induced the phosphorylation of p38 and JNK in melanocytes. Both JNK and p38 inhibitors showed suppression on the cytokine induction by intra- or extracellular poly(I:C). However, only the JNK inhibitor decreased the intracellular poly(I:C)-induced melanocyte death. Taken together, this study provides the possible mechanism of viral factor in the pathogenesis of vitiligo.

  18. Whole-Genome Resequencing of a Cucumber Chromosome Segment Substitution Line and Its Recurrent Parent to Identify Candidate Genes Governing Powdery Mildew Resistance

    Science.gov (United States)

    Yu, Ting; Xu, Xuewen; Yan, Yali; Qi, Xiaohua; Chen, Xuehao

    2016-01-01

    Cucumber is an economically important vegetable crop worldwide. Powdery mildew (PM) is one of the most severe diseases that can affect cucumber crops. There have been several research efforts to isolate PM resistance genes for breeding PM-resistant cucumber. In the present study, we used a chromosome segment substitution line, SSL508-28, which carried PM resistance genes from the donor parent, JIN5-508, through twelve generations of backcrossing with a PM-susceptible inbred line, D8. We performed whole-genome resequencing of SSL508-28 and D8 to identify single nucleotide polymorphisms (SNPs), and insertions and deletions (indels). When compared against the reference genome of the inbred cucumber line 9930, a total of 468,616 SNPs and 67,259 indels were identified in SSL508-28, and 537,352 SNPs and 91,698 indels were identified in D8. Of these, 3,014 non-synonymous SNPs and 226 frameshift indels in SSL508-28, and 3,104 non-synonymous SNPs and 251 frameshift indels in D8, were identified. Bioinformatics analysis of these variations revealed a total of 15,682 SNPs and 6,262 indels between SSL508-28 and D8, among which 120 non-synonymous SNPs and 30 frameshift indels in 94 genes were detected between SSL508-28 and D8. Finally, out of these 94 genes, five resistance genes with nucleotide-binding sites and leucine-rich repeat domains were selected for qRT-PCR analysis. This revealed an upregulation of two transcripts, Csa2M435460.1 and Csa5M579560.1, in SSL508-28. Furthermore, the results of qRT-PCR analysis of these two genes in ten PM resistant and ten PM susceptible cucumber lines showed that when exposed to PM, Csa2M435460.1 and Csa5M579560.1 exhibited a higher expression level of resistant lines than susceptible lines. This indicates that Csa2M435460.1 and Csa5M579560.1 are candidate genes for PM resistance in cucumber. In addition, the non-synonymous SNPs in Csa2M435460.1 and Csa5M579560.1, identified in SSL508-28 and D8, might be the key to high PM-resistance in

  19. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  20. Identification of the 3' and 5' terminal sequences of the 8 rna genome segments of european and north american genotypes of infectious salmon anemia virus (an orthomyxovirus and evidence for quasispecies based on the non-coding sequences of transcripts

    Directory of Open Access Journals (Sweden)

    Riveroll Angela

    2010-11-01

    Full Text Available Abstract Background Infectious salmon anemia (ISA virus (ISAV is a pathogen of marine-farmed Atlantic salmon (Salmo salar; a disease first diagnosed in Norway in 1984. This virus, which was first characterized following its isolation in cell culture in 1995, belongs to the family Orthomyxoviridae, genus, Isavirus. The Isavirus genome consists of eight single-stranded RNA segments of negative sense, each with one to three open reading frames flanked by 3' and 5' non-coding regions (NCRs. Although the terminal sequences of other members of the family Orthomyxoviridae such as Influenzavirus A have been extensively analyzed, those of Isavirus remain largely unknown, and the few reported are from different ISAV strains and on different ends of the different RNA segments. This paper describes a comprehensive analysis of the 3' and 5' end sequences of the eight RNA segments of ISAV of both European and North American genotypes, and evidence of quasispecies of ISAV based on sequence variation in the untranslated regions (UTRs of transcripts. Results Two different ISAV strains and two different RNA preparations were used in this study. ISAV strain ADL-PM 3205 ISAV-07 (ADL-ISAV-07 of European genotype was the source of total RNA extracted from ISAV-infected TO cells, which contained both viral mRNA and cRNA. ISAV strain NBISA01 of North American genotype was the source of vRNA extracted from purified virus. The NCRs of each segment were identified by sequencing cDNA prepared by three different methods, 5' RACE (Rapid amplification of cDNA ends, 3' RACE, and RNA ligation mediated PCR. Sequence analysis of five clones each derived from one RT-PCR product from each NCR of ISAV transcripts of segments 1 to 8 revealed significant heterogeneity among the clones of the same segment end, providing unequivocal evidence for presence of intra-segment ISAV quasispecies. Both RNA preparations (mRNA/cRNA and vRNA yielded complementary sequence information, allowing the

  1. Copy number variation at the HvCBF4-HvCBF2 genomic segment is a major component of frost resistance in barley.

    Science.gov (United States)

    Francia, Enrico; Morcia, Caterina; Pasquariello, Marianna; Mazzamurro, Valentina; Milc, Justyna Anna; Rizza, Fulvia; Terzi, Valeria; Pecchioni, Nicola

    2016-09-01

    A family of CBF transcription factors plays a major role in reconfiguring the plant transcriptome in response to low-freezing temperature in temperate cereals. In barley, more than 13 HvCBF genes map coincident with the major QTL FR-H2 suggesting them as candidates to explain the function of the locus. Variation in copy number (CNV) of specific HvCBFs was assayed in a panel of 41 barley genotypes using RT-qPCR. Taking advantage of an accurate phenotyping that combined Fv/Fm and field survival, resistance-associated variants within FR-H2 were identified. Genotypes with an increased copy number of HvCBF4 and HvCBF2 (at least ten and eight copies, respectively) showed greater frost resistance. A CAPS marker able to distinguish the CBF2A, CBF2B and CBF2A/B forms was developed and showed that all the higher-ranking genotypes in term of resistance harbour only CBF2A, while other resistant winter genotypes harbour also CBF2B, although at a lower CNV. In addition to the major involvement of the HvCBF4-HvCBF2 genomic segment in the proximal cluster of CBF elements, a negative role of HvCBF3 in the distal cluster was identified. Multiple linear regression models taking into account allelic variation at FR-H1/VRN-H1 explained 0.434 and 0.550 (both at p < 0.001) of the phenotypic variation for Fv/Fm and field survival respectively, while no interaction effect between CNV at the HvCBFs and FR-H1/VRN-H1 was found. Altogether our data suggest a major involvement of the CBF genes located in the proximal cluster, with no apparent involvement of the central cluster contrary to what was reported for wheat.

  2. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    Directory of Open Access Journals (Sweden)

    Jeffrey W Habig

    Full Text Available C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  3. Inhibition of BmNPV replication in Bombyx mori cell by dsRNA triggered RNA interference

    Institute of Scientific and Technical Information of China (English)

    XU Ying; ZHU Chenggang; JIN Yongfeng; ZHANG Yaozhou

    2004-01-01

    RNA interference (RNAi) causes degradation of targeted endogenous RNA in many diverse organisms, To investigate the effect of dsRNA on silkworm cells, we transfected three kinds of synthetic dsRNAs of 435 bp(Ap1), 300bp(Ape) and 399 bp(Au) in length against the various regions of BmNPV's DNA polymerase gene and DNA helicase gene,which are indispensable for viral replication in silkworm cells by TransMessengerTM transfection Reagent. Results indicated that in the experiment where silkworm cells were infected with wild-strain BmNPV of the three dsRNAs, Ap2 and AH can effectively suppress the replication of virus, but Ap1 had no effect on the inhibition of viral replication. Ap2 and Au can reduce the infective titer of BmNPV with a peak change of approximately 3-4 logs on day 4 post-infection.The results of reverse transcript polylnerase chain reaction (RT-PCR) and DNA dot blotting also indicated that the expression level of the two target genes and the quantity of viral DNA both distinctly decreased under the influence of Ap2 or Au. Furthermore, using fluorescence microscopy we analyzed the distribution patterns of dsRNA. Our studies revealed that a majority of dsRNA was localized in the nuclear periphery discontinuously after 24 h of transfection.

  4. Knockdown of RNA Interference Pathway Genes in Western Corn Rootworms (Diabrotica virgifera virgifera Le Conte Demonstrates a Possible Mechanism of Resistance to Lethal dsRNA.

    Directory of Open Access Journals (Sweden)

    Ana María Vélez

    Full Text Available RNA interference (RNAi is being developed as a potential tool for insect pest management. Increased understanding of the RNAi pathway in target insect pests will provide information to use this technology effectively and to inform decisions related to resistant management strategies for RNAi based traits. Dicer 2 (Dcr2, an endonuclease responsible for formation of small interfering RNA's and Argonaute 2 (Ago2, an essential catalytic component of the RNA-induced silencing complex (RISC have both been associated with the RNAi pathway in a number of different insect species including the western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae. We identified both genes from a transcriptome library generated from different tissues and developmental stages of the western corn rootworm, an important target pest for transgenic plants expressing dsRNA targeting essential genes. The expression of these genes was suppressed by more than 90% after injecting gene specific dsRNA into adult rootworms. The injected beetles were then fed vATPase A dsRNA which has previously been demonstrated to cause mortality in western corn rootworm adults. The suppression of both RNAi pathway genes resulted in reduced mortality after subsequent exposure to lethal concentrations of vATPase A dsRNA as well as increased vATPase A expression relative to control treatments. Injections with dsRNA for a non-lethal target sequence (Laccase 2 did not affect mortality or expression caused by vATPase A dsRNA indicating that the results observed with Argo and Dicer dsRNA were not caused by simple competition among different dsRNA's. These results confirm that both genes play an important role in the RNAi pathway for western corn rootworms and indicate that selection pressures that potentially affect the expression of these genes may provide a basis for future studies to understand potential mechanisms of resistance.

  5. Application of YHV-protease dsRNA for protection and therapeutic treatment against yellow head virus infection in Litopenaeus vannamei.

    Science.gov (United States)

    Assavalapsakul, Wanchai; Chinnirunvong, Wanlop; Panyim, Sakol

    2009-04-06

    While farming of the Pacific white shrimp Litopenaeus vannamei is well established in North and South America, the industry has more recently been introduced to Asia, and the Pacific white shrimp is now the most commonly farmed species in Thailand. However, outbreaks of yellow head virus (YHV) disease in the Pacific white shrimp have caused severe economic losses and currently there is no effective prevention or treatment of YHV infections. The YHV-protease double-stranded RNA (YHV-Pro dsRNA) can act as both a prophylactic agent and as a treatment to inhibit YHV replication in infected black tiger shrimp Penaeus monodon. The utility of this methodology to other shrimp species has not, however, been established. The purpose of this study was to determine whether YHV-Pro dsRNA can be applied to the Pacific white shrimp. To assess prophylactic efficiency, YHV-Pro dsRNA was injected into juvenile shrimp 24 h prior to challenge with YHV. Subsequent YHV replication was inhibited by YHV-Pro dsRNA as compared with injection of an unrelated dsRNA. For therapeutic treatment of YHV-infected shrimp, shrimp were challenged with YHV before dsRNA injection. Injection of YHV-Pro dsRNA up to 6 h post-infection resulted in the almost complete elimination of YHV replication. These results suggest that YHV-Pro dsRNA can also be broadly applied as a prophylactic agent to inhibit YHV replication and therapeutic treatment of YHV-infected Pacific white shrimp.

  6. Segmentation: Identification of consumer segments

    DEFF Research Database (Denmark)

    Høg, Esben

    2005-01-01

    It is very common to categorise people, especially in the advertising business. Also traditional marketing theory has taken in consumer segments as a favorite topic. Segmentation is closely related to the broader concept of classification. From a historical point of view, classification has its...... and analysed possible segments in the market. Results show that the statistical model used identified two segments - a segment of so-called "fish lovers" and another segment called "traditionalists". The "fish lovers" are very fond of eating fish and they actually prefer fish to other dishes...... origin in other sciences as for example biology, anthropology etc. From an economic point of view, it is called segmentation when specific scientific techniques are used to classify consumers to different characteristic groupings. What is the purpose of segmentation? For example, to be able to obtain...

  7. Improvement of pest resistance in transgenic tobacco plants expressing dsRNA of an insect-associated gene EcR.

    Directory of Open Access Journals (Sweden)

    Jin-Qi Zhu

    Full Text Available The adoption of pest-resistant transgenic plants to reduce yield loss and pesticide utilization has been successful in the past three decades. Recently, transgenic plant expressing double-stranded RNA (dsRNA targeting pest genes emerges as a promising strategy for improving pest resistance in crops. The steroid hormone, 20-hydroxyecdysone (20E, predominately controls insect molting via its nuclear receptor complex, EcR-USP. Here we report that pest resistance is improved in transgenic tobacco plants expressing dsRNA of EcR from the cotton bollworm, Helicoverpa armigera, a serious lepidopteran pest for a variety of crops. When H. armigera larvae were fed with the whole transgenic tobacco plants expressing EcR dsRNA, resistance to H. armigera was significantly improved in transgenic plants. Meanwhile, when H. armigera larvae were fed with leaves of transgenic tobacco plants expressing EcR dsRNA, its EcR mRNA level was dramatically decreased causing molting defects and larval lethality. In addition, the transgenic tobacco plants expressing H. armigera EcR dsRNA were also resistant to another lepidopteran pest, the beet armyworm, Spodoptera exigua, due to the high similarity in the nucleotide sequences of their EcR genes. This study provides additional evidence that transgenic plant expressing dsRNA targeting insect-associated genes is able to improve pest resistance.

  8. dsRNA uptake and persistence account for tissue-dependent susceptibility to RNA interference in the migratory locust, Locusta migratoria.

    Science.gov (United States)

    Ren, D; Cai, Z; Song, J; Wu, Z; Zhou, S

    2014-04-01

    RNA interference (RNAi) by introducing double-stranded RNA (dsRNA) is a powerful approach to the analysis of gene function in insects; however, RNAi responses vary dramatically in different insect species and tissues, and the underlying mechanisms remain poorly understood. The migratory locust, a destructive insect pest and a hemimetabolic insect with panoistic ovaries, is considered to be a highly susceptible species to RNAi via dsRNA injection, but its ovary appears to be completely insensitive. In the present study, we showed that dsRNA persisted only briefly in locust haemolymph. The ovariole sheath was permeable to dsRNA, but injected dsRNA was not present in the follicle cells and oocytes. The lack of dsRNA uptake into the follicle cells and oocytes is likely to be the primary factor that contributes to the ineffective RNAi response in locust ovaries. These observations provide insights into tissue-dependent variability of RNAi and help in achieving successful gene silencing in insensitive tissues.

  9. Sequence analysis of genome segments S4 and S8 of Mal de Río Cuarto virus (MRCV): evidence that the virus should be a separate Fijivirus species.

    Science.gov (United States)

    Distéfano, A J; Conci, L R; Muñoz Hidalgo, M; Guzmán, F A; Hopp, H E; del Vas, M

    2002-09-01

    This is the first sequence-based characterization of Mal de Río Cuarto virus (MRCV), currently classified as a variant of Maize rough dwarf virus (MRDV) and exclusively found in South America. We sequenced and analyzed genome segments S4 and S8. MRCV S4 coded for a putative 131.67 kDa protein while MRCV S8 coded for a putative 68.26 kDa protein containing an ATP/GTP-binding motif. The 5' and 3' ends of MRCV segments, were 5'AAGUUUUU3' and 5'CAGCUnnnGUC3', respectively. Prediction of secondary structure of both segments coding strands showed that terminal regions were able to form structures that are proposed to be replication and packaging signals. MRCV S4 showed identity to members of Fijivirus as well as to two other genera of the Reoviridae family. MRCV S8 revealed identity with Rice black streaked dwarf virus (RBSDV) S8, MRDV S7, Oat sterile dwarf virus (OSDV) S9 and Nilaparvata lugens reovirus (NLRV) S7. While MRDV and RBSDV segments are highly homologous between each other, MRCV identity levels with them was considerably lower. We discussed the evolutionary relationships of MRCV to other Reoviridae, and based on phylogenetic analysis we proposed that although MRCV is related to MRDV, it could be regarded as a new species of the Fijivirus genus.

  10. Cucumis melo endornavirus: Genome organization, host range and codivergence with the host

    Science.gov (United States)

    A high molecular weight dsRNA was isolated from a Cucumis melo plant (referred to as“CL01”) of an unknown cultivar and completely sequenced. Sequence analyses showed similarities with members of the Endornaviridae. The name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consis...

  11. Crude extracts of bacterially expressed dsRNA can be used to protect plants against virus infections

    Directory of Open Access Journals (Sweden)

    Vargas Marisol

    2003-03-01

    Full Text Available Abstract Background Double-stranded RNA (dsRNA is a potent initiator of gene silencing in a diverse group of organisms that includes plants, Caenorhabditis elegans, Drosophila and mammals. We have previously shown and patented that mechanical inoculation of in vitro-transcribed dsRNA derived from viral sequences specifically prevents virus infection in plants. The approach required the in vitro synthesis of large amounts of RNA involving high cost and considerable labour. Results We have developed an in vivo expression system to produce large amounts of virus-derived dsRNAs in bacteria, with a view to providing a practical control of virus diseases in plants. Partially purified bacterial dsRNAs promoted specific interference with the infection in plants by two viruses belonging to the tobamovirus and potyvirus groups. Furthermore, we have demonstrated that easy to obtain, crude extracts of bacterially expressed dsRNAs are equally effective protecting plants against virus infections when sprayed onto plant surfaces by a simple procedure. Virus infectivity was significantly abolished when plants were sprayed with French Press lysates several days before virus inoculation. Conclusion Our approach provides an alternative to genetic transformation of plant species with dsRNA-expressing constructs capable to interfere with plant viruses. The main advantage of this mode of dsRNA production is its simplicity and its extremely low cost compared with the requirements for regenerating transgenic plants. This approach provides a reliable and potential tool, not only for plant protection against virus diseases, but also for the study of gene silencing mechanisms in plant virus infections.

  12. Complete Genome Sequence of a Double-Stranded RNA Virus from Avocado

    Science.gov (United States)

    Villanueva, Francisco; Sabanadzovic, Sead; Valverde, Rodrigo A.

    2012-01-01

    A number of avocado (Persea americana) cultivars are known to contain high-molecular-weight double-stranded RNA (dsRNA) molecules for which a viral nature has been suggested, although sequence data are not available. Here we report the cloning and complete sequencing of a 13.5-kbp dsRNA virus isolated from avocado and show that it corresponds to the genome of a new species of the genus Endornavirus (family Endornaviridae), tentatively named Persea americana endornavirus (PaEV). PMID:22205720

  13. DsRNA degradation in the pea aphid (Acyrthosiphon pisum) associated with lack of response in RNAi feeding and injection assay.

    Science.gov (United States)

    Christiaens, Olivier; Swevers, Luc; Smagghe, Guy

    2014-03-01

    Over the past decade, RNA interference (RNAi), the sequence-specific suppression of gene expression, has proven very promising for molecular research in many species, including model insects as Tribolium castaneum and Apis mellifera. It showed its usefulness to analyze gene function and its potential to manage pest populations and reduce disease pathogens. However, in several insects, the efficiency of RNAi is low or very variable at best. One of the factors that could influence RNAi efficiency in insects is degradation of dsRNA after administration to the insect. In this paper, we report on the importance of dsRNA breakdown in the pea aphid (Acyrthosiphon pisum) associated with the absence of an RNAi response upon oral feeding and injection with dsRNA targeting different genes such as the ecdysone hormone receptor and ultraspiracle. In essence, we discovered that both the salivary secretions of aphids and the hemolymph were able to degrade the dsRNA. In parallel, introduction of dsRNA in the aphid body was not able to provoke a response in the expression of the siRNA core machinery genes.

  14. The exonuclease ISG20 is directly induced by synthetic dsRNA via NF-kappaB and IRF1 activation.

    Science.gov (United States)

    Espert, Lucile; Rey, Clémence; Gonzalez, Laure; Degols, Geneviève; Chelbi-Alix, Mounira Kmar; Mechti, Nadir; Gongora, Céline

    2004-06-03

    Many interferon (IFN)-stimulated genes are also induced by double-stranded RNA (dsRNA), a component closely associated with the IFN system in the context of virus-host interactions. Recently, we demonstrated that the IFN-induced 3' --> 5' exonuclease ISG20 possesses antiviral activities against RNA viruses. Here we show that ISG20 induction by synthetic dsRNA (pIpC) is stronger and faster than its induction by IFN. Two families of transcription factors are implicated in the transcriptional activation of ISG20 by dsRNA. Initially, the NF-kappaB factors p50 and p65 bind and activate the kappaB element of the Isg20 promoter. This is followed by IRF1 binding to the ISRE. As pIpC often induces protein movements in the cells, we questioned whether it could influence ISG20 localization. Interestingly and contrary to IFN, dsRNA induces a nuclear matrix enrichment of the ISG20 protein. dsRNA induction of ISG20 via NF-kappaB and its antiviral activity led us to suggest that ISG20 could participate in the cellular response to virus infection.

  15. The Human dsRNA binding protein PACT is unable to functionally substitute for the Drosophila dsRNA binding protein R2D2 [v1; ref status: indexed, http://f1000r.es/201

    Directory of Open Access Journals (Sweden)

    Benjamin K Dickerman

    2013-10-01

    Full Text Available The primary function of the dsRNA binding protein (dsRBP PACT/RAX is to activate the dsRNA dependent protein kinase PKR in response to stress signals.  Additionally, it has been identified as a component of the small RNA processing pathway.  A role for PACT/RAX in this pathway represents an important interplay between two modes of post-transcriptional gene regulation.  The function of PACT/RAX in this context is poorly understood.  Thus, additional models are required to clarify the mechanism by which PACT/RAX functions.  In this study, Drosophila melanogaster was employed to identify functionally orthologous dsRNA-binding proteins.  Transgenic Drosophila expressing human PACT were generated to determine whether PACT is capable of functionally substituting for the Drosophila dsRBP R2D2, which has a well-defined role in small RNA biogenesis.  Results presented here indicate that PACT is unable to substitute for R2D2 at the whole organism level.

  16. Fingerprint Segmentation

    OpenAIRE

    Jomaa, Diala

    2009-01-01

    In this thesis, a new algorithm has been proposed to segment the foreground of the fingerprint from the image under consideration. The algorithm uses three features, mean, variance and coherence. Based on these features, a rule system is built to help the algorithm to efficiently segment the image. In addition, the proposed algorithm combine split and merge with modified Otsu. Both enhancements techniques such as Gaussian filter and histogram equalization are applied to enhance and improve th...

  17. [Familial Focal Segmental Glomerulosclerosis, a vademecum for clinical nephrologist].

    Science.gov (United States)

    Caridi, Gianluca; Lugani, Francesca; Bonanni, Elisa; Rossi, Roberta; Carrea, Alba; Ghiggeri, Gian Marco

    2015-01-01

    The new genomic technologies (Next Generation Sequencing, NGS) are opening a new era in Genomic Medicine. This simple guide gives a state-of-the-art description of the genes that cause Focal Segmental Glomerulosclerosis and nephrotic syndrome.

  18. BNYVV-derived dsRNA confers resistance to rhizomania disease of sugar beet as evidenced by a novel transgenic hairy root approach

    NARCIS (Netherlands)

    Pavli, R.; Panopoulos, N.J.; Goldbach, R.W.; Skaracis, G.N.

    2010-01-01

    Agrobacterium rhizogenes-transformed sugar beet hairy roots, expressing dsRNA from the Beet necrotic yellow vein virus replicase gene, were used as a novel approach to assess the efficacy of three intron-hairpin constructs at conferring resistance to rhizomania disease. Genetically engineered roots

  19. BNYVV-derived dsRNA confers resistance to rhizomania disease of sugar beet as evidenced by a novel transgenic hairy root approach

    NARCIS (Netherlands)

    Pavli, R.; Panopoulos, N.J.; Goldbach, R.W.; Skaracis, G.N.

    2010-01-01

    Agrobacterium rhizogenes-transformed sugar beet hairy roots, expressing dsRNA from the Beet necrotic yellow vein virus replicase gene, were used as a novel approach to assess the efficacy of three intron-hairpin constructs at conferring resistance to rhizomania disease. Genetically engineered roots

  20. A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System.

    Directory of Open Access Journals (Sweden)

    Justine M Pompey

    Full Text Available Dicer enzymes process double-stranded RNA (dsRNA into small RNAs that target gene silencing through the RNA interference (RNAi pathway. Dicer enzymes are complex, multi-domain RNaseIII proteins, however structural minimalism of this protein has recently emerged in parasitic and fungal systems. The most minimal Dicer, Saccharomyces castellii Dicer1, has a single RNaseIII domain and two double stranded RNA binding domains. In the protozoan parasite Entamoeba histolytica 27nt small RNAs are abundant and mediate silencing, yet no canonical Dicer enzyme has been identified. Although EhRNaseIII does not exhibit robust dsRNA cleavage in vitro, it can process dsRNA in the RNAi-negative background of Saccharomyces cerevisiae, and in conjunction with S. castellii Argonaute1 can partially reconstitute the RNAi pathway. Thus, although EhRNaseIII lacks the domain architecture of canonical or minimal Dicer enzymes, it has dsRNA processing activity that contributes to gene silencing via RNAi. Our data advance the understanding of small RNA biogenesis in Entamoeba as well as broaden the spectrum of non-canonical Dicer enzymes that contribute to the RNAi pathway.

  1. A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System.

    Science.gov (United States)

    Pompey, Justine M; Foda, Bardees; Singh, Upinder

    2015-01-01

    Dicer enzymes process double-stranded RNA (dsRNA) into small RNAs that target gene silencing through the RNA interference (RNAi) pathway. Dicer enzymes are complex, multi-domain RNaseIII proteins, however structural minimalism of this protein has recently emerged in parasitic and fungal systems. The most minimal Dicer, Saccharomyces castellii Dicer1, has a single RNaseIII domain and two double stranded RNA binding domains. In the protozoan parasite Entamoeba histolytica 27nt small RNAs are abundant and mediate silencing, yet no canonical Dicer enzyme has been identified. Although EhRNaseIII does not exhibit robust dsRNA cleavage in vitro, it can process dsRNA in the RNAi-negative background of Saccharomyces cerevisiae, and in conjunction with S. castellii Argonaute1 can partially reconstitute the RNAi pathway. Thus, although EhRNaseIII lacks the domain architecture of canonical or minimal Dicer enzymes, it has dsRNA processing activity that contributes to gene silencing via RNAi. Our data advance the understanding of small RNA biogenesis in Entamoeba as well as broaden the spectrum of non-canonical Dicer enzymes that contribute to the RNAi pathway.

  2. Knock-down of OsDCL2 in rice negatively affects maintenance of the endogenous dsRNA virus, Oryza sativa endornavirus.

    Science.gov (United States)

    Urayama, Syunichi; Moriyama, Hiromitsu; Aoki, Nanako; Nakazawa, Yukihiro; Okada, Ryo; Kiyota, Eri; Miki, Daisuke; Shimamoto, Ko; Fukuhara, Toshiyuki

    2010-01-01

    An endogenous double-stranded RNA (dsRNA), which has recently been recognized as the dsRNA virus Oryza sativa endornavirus (OsEV), is found in many strains of cultivated rice (Oryza sativa). Small RNAs derived from OsEV dsRNA were detected, indicating that the RNA silencing machinery recognizes OsEV dsRNA. The existence of OsEV in knock-down (KD) lines of five genes of RNA-dependent RNA polymerase (OsRDR1-OsRDR5) or two genes of Dicer-like protein (OsDCL2 or OsDCL3a) was examined to characterize the relationship between the host RNA silencing system and the propagation of this dsRNA virus. OsEV was not detected in OsRDR4-KD or OsDCL2-KD T(1) lines. We attempted to introduce OsEV into these KD lines by crossing them with OsEV-carrying plants because of the efficient transmission of OsEV to F(1) plants via pollen or ova. All OsRDR4-KD but only some OsDCL2-KD F(1) plants contained OsEV. Some OsDCL2-KD F(1) plants consisted of OsEV-carrying and OsEV-free cells. These results suggest that the maintenance of OsEV is unstable in OsDCL2-KD plants. Furthermore, the amount of OsEV-derived small interfering RNA (vsiRNA) in the OsDCL2-KD plants increased relative to the wild type. This increased level of vsiRNA may cause OsEV instability during cell division.

  3. [Segmental neurofibromatosis].

    Science.gov (United States)

    Zulaica, A; Peteiro, C; Pereiro, M; Pereiro Ferreiros, M; Quintas, C; Toribio, J

    1989-01-01

    Four cases of segmental neurofibromatosis (SNF) are reported. It is a rare entity considered to be a localized variant of neurofibromatosis (NF)-Riccardi's type V. Two cases are male and two female. The lesions are located to the head in a patient and the other three cases in the trunk. No family history nor transmission to progeny were manifested. The rest of the organs are undamaged.

  4. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

    Directory of Open Access Journals (Sweden)

    Bruggmann Rémy

    2007-05-01

    Full Text Available Abstract Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL. To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions

  5. Storage conditions affect the toxicity of E. coli expressing S-adenosyl-L-homocysteine hydrolase (SAHase) gene dsRNA to potato beetles%储存条件对表达马铃薯甲虫腺苷高半胱氨酸水解酶基因 dsRNA 的大肠杆菌生物活性的影响

    Institute of Scientific and Technical Information of China (English)

    李晓旭; 付开赟; 李国清; 王刚; 吐尔逊; 何江; 郭文超

    2015-01-01

    【目的】将 RNA 干扰应用于害虫防治领域,通过饲喂表达 dsRNA 的转基因植物或表达 dsRNA的细菌,可沉默特定基因进而控制害虫,为农业害虫防治开辟一个新领域。而表达 dsRNA 的细菌能否有效储存是决定此项技术实际应用的关键。【方法】用﹣20℃冻存的表达马铃薯甲虫腺苷高半胱氨酸水解酶(SAHase)dsRNA 的大肠杆菌 E.coli,饲喂马铃薯甲虫 Leptinotarsa decemlineata(Say)2龄幼虫,检测不同时间储存、灭活与否的活性变化,明确其储存条件。【结果】大肠杆菌﹣20℃储存24 h 后生物活性优于新鲜菌,储存48 h 后效果减弱,而载体大肠杆菌是否灭活对活性影响不大。【结论】 dsRNA 大肠杆菌发酵液在﹣20℃条件下可以短暂储存。%Objectives] By expressing double stranded RNA (dsRNA) in transgenic plants and in prokaryotic cells, RNA interference has potential applications in pest control. Determination of the influence of storage conditions on the toxic effects of dsRNA expressing E. coli is therefore of great importance for determining the effectiveness of such methods. [Methods] We stored living, or sterile, dsRNA expressing E. coli at ﹣20℃ for different periods, and compared their toxicity to Leptinotarsa decemlineata larvae. [Result] E. coli that had been stored for 24 h had higher biological activity than fresh E. coli, however, this difference sharply decreased after 48 h. No significant difference was found between living and sterile dsRNA expressing E. coli. [Conclusion] Twenty-four hours storage under ﹣20℃ has little influence on toxic effects of dsRNA expressing E. coli.

  6. Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on chromosome 3p21.3

    National Research Council Canada - National Science Library

    Daigo, Y; Isomura, M; Nishiwaki, T; Suzuki, K; Maruyama, O; Takeuchi, K; Yamane, Y; Hayashi, R; Minami, M; Hojo, Y; Uchiyama, I; Takagi, T; Nakamura, Y

    1999-01-01

    ... 3p21.3 corresponding to an R-band region. The two segments were significantly different with respect to the frequency of transcriptional units, the types and numbers of repetitive elements present, their GC content, and the number of CpG islands...

  7. Mixed segmentation

    DEFF Research Database (Denmark)

    Bonde, Anders; Aagaard, Morten; Hansen, Allan Grutt

    This book is about using recent developments in the fields of data analytics and data visualization to frame new ways of identifying target groups in media communication. Based on a mixed-methods approach, the authors combine psychophysiological monitoring (galvanic skin response) with textual...... content analysis and audience segmentation in a single-source perspective. The aim is to explain and understand target groups in relation to, on the one hand, emotional response to commercials or other forms of audio-visual communication and, on the other hand, living preferences and personality traits...

  8. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

    Science.gov (United States)

    Ogiwara, Ikuo; Miya, Masaki; Ohshima, Kazuhiko; Okada, Norihiro

    2002-02-01

    We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5'-end tRNA-related region and followed by a potentially recombinogenic (TG)(n) tract, with a 3' tail derived from the 3' untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be approximately 550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3' tails of V-SINEs differ from one another, it is possible that the original 3' tail might have been replaced, via recombination, by the 3' tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates.

  9. Rotavirus structural proteins and dsRNA are required for the human primary plasmacytoid dendritic cell IFNalpha response.

    Directory of Open Access Journals (Sweden)

    Emily M Deal

    Full Text Available Rotaviruses are the leading cause of severe dehydrating diarrhea in children worldwide. Rotavirus-induced immune responses, especially the T and B cell responses, have been extensively characterized; however, little is known about innate immune mechanisms involved in the control of rotavirus infection. Although increased levels of systemic type I interferon (IFNalpha and beta correlate with accelerated resolution of rotavirus disease, multiple rotavirus strains, including rhesus rotavirus (RRV, have been demonstrated to antagonize type I IFN production in a variety of epithelial and fibroblast cell types through several mechanisms, including degradation of multiple interferon regulatory factors by a viral nonstructural protein. This report demonstrates that stimulation of highly purified primary human peripheral plasmacytoid dendritic cells (pDCs with either live or inactivated RRV induces substantial IFNalpha production by a subset of pDCs in which RRV does not replicate. Characterization of pDC responses to viral stimulus by flow cytometry and Luminex revealed that RRV replicates in a small subset of human primary pDCs and, in this RRV-permissive small subset, IFNalpha production is diminished. pDC activation and maturation were observed independently of viral replication and were enhanced in cells in which virus replicates. Production of IFNalpha by pDCs following RRV exposure required viral dsRNA and surface proteins, but neither viral replication nor activation by trypsin cleavage of VP4. These results demonstrate that a minor subset of purified primary human peripheral pDCs are permissive to RRV infection, and that pDCs retain functionality following RRV stimulus. Additionally, this study demonstrates trypsin-independent infection of primary peripheral cells by rotavirus, which may allow for the establishment of extraintestinal viremia and antigenemia. Importantly, these data provide the first evidence of IFNalpha induction in primary

  10. A novel monopartite dsRNA virus isolated from the phytopathogenic fungus Ustilaginoidea virens and ancestrally related to a mitochondria-associated dsRNA in the green alga Bryopsis.

    Science.gov (United States)

    Zhang, Tingting; Jiang, Yinhui; Dong, Wubei

    2014-08-01

    In this study, we describe a novel mycovirus isolated from Ustilaginoidea virens, which was designated Ustilaginoidea virens nonsegmented virus 1 (UvNV-1). The sequence analysis revealed that UvNV-1 has two open reading frames (ORFs). ORF1 encodes an unknown protein, which is similar to the hypothetical protein BN7_5177 of Wickerhamomyces ciferrii. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp), which is most closely related to Bryopsis mitochondria-associated dsRNA (BDRM) and is likely expressed by a +1 ribosomal frameshift within the sequence CCC_UUU_CGA. The phylogenetic analysis of the RdRp of UvNV-1 showed that UvNV-1 represents a new virus taxon of mycoviruses with a partitivirus-like lineage that is classified into the family of picorna-like viruses. Based on northern hybridization, UvNV-1 was found to be common to U. virens from different geographic locations in China. The biological comparison of virus-free and infected fungal strains revealed that UvNV-1 is likely to be cryptic to its host.

  11. dsRNA sensors and plasmacytoid dendritic cells in host defense and autoimmunity.

    Science.gov (United States)

    Wang, Yaming; Swiecki, Melissa; McCartney, Stephen A; Colonna, Marco

    2011-09-01

    The innate immune system detects viruses through molecular sensors that trigger the production of type I interferons (IFN-I) and inflammatory cytokines. As viruses vary tremendously in size, structure, genomic composition, and tissue tropism, multiple sensors are required to detect their presence in various cell types and tissues. In this review, we summarize current knowledge of the diversity, specificity, and signaling pathways downstream of viral sensors and ask whether two distinct sensors that recognize the same viral component are complementary, compensatory, or simply redundant. We also discuss why viral sensors are differentially distributed in distinct cell types and whether a particular cell type dominates the IFN-I response during viral infection. Finally, we review evidence suggesting that inappropriate signaling through viral sensors may induce autoimmunity. The picture emerging from these studies is that disparate viral sensors in different cell types form a dynamic and integrated molecular network that can be exploited for improving vaccination and therapeutic strategies for infectious and autoimmune diseases.

  12. Segmented blockcopolymers with uniform amide segments

    NARCIS (Netherlands)

    Husken, D.; Krijgsman, J.; Gaymans, R.J.

    2004-01-01

    Segmented blockcopolymers based on poly(tetramethylene oxide) (PTMO) soft segments and uniform crystallisable tetra-amide segments (TxTxT) are made via polycondensation. The PTMO soft segments, with a molecular weight of 1000 g/mol, are extended with terephthalic groups to a molecular weight of 6000

  13. Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein.

    Science.gov (United States)

    Meier, Doreen; Kruse, Janis; Buttlar, Jann; Friedrich, Michael; Zenk, Fides; Boesler, Benjamin; Förstner, Konrad U; Hammann, Christian; Nellen, Wolfgang

    2016-06-01

    We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class.

  14. BNYVV-derived dsRNA confers resistance to rhizomania disease of sugar beet as evidenced by a novel transgenic hairy root approach

    OpenAIRE

    Pavli, R.; Panopoulos, N J; Goldbach, R.W.; Skaracis, G.N.

    2010-01-01

    Agrobacterium rhizogenes-transformed sugar beet hairy roots, expressing dsRNA from the Beet necrotic yellow vein virus replicase gene, were used as a novel approach to assess the efficacy of three intron-hairpin constructs at conferring resistance to rhizomania disease. Genetically engineered roots were similar in morphology to wild type roots but were characterized by a profound abundancy, rapid growth rate and, in some cases, plagiotropic development. Upon challenge inoculation, seedlings s...

  15. Intracellular delivery of poly(I:C) induces apoptosis of fibroblast-like synoviocytes via an unknown dsRNA sensor

    Energy Technology Data Exchange (ETDEWEB)

    Karpus, Olga N.; Hsiao, Cheng-Chih; Kort, Hanneke de; Tak, Paul P.; Hamann, Jörg, E-mail: j.hamann@amc.uva.nl

    2016-08-26

    Fibroblast-like synoviocytes (FLS) express functional membranous and cytoplasmic sensors for double-stranded (ds)RNA. Notably, FLS undergo apoptosis upon transfection with the synthetic dsRNA analog poly(I:C). We here studied the mechanism of intracellular poly(I:C) recognition and subsequent cell death in FLS. FLS responded similarly to poly(I:C) or 3pRNA transfection; however, only intracellular delivery of poly(I:C) induced significant cell death, accompanied by upregulation of pro-apoptotic proteins Puma and Noxa, caspase 3 cleavage, and nuclear segregation. Knockdown of the DExD/H-box helicase MDA5 did not affect the response to intracellular poly(I:C); in contrast, knockdown of RIG-I abrogated the response to 3pRNA. Knockdown of the downstream adaptor proteins IPS, STING, and TRIF or inhibition of TBK1 did not affect the response to intracellular poly(I:C), while knockdown of IFNAR blocked intracellular poly(I:C)-mediated signaling and cell death. We conclude that a so far unknown intracellular sensor recognizes linear dsRNA and induces apoptosis in FLS. - Highlights: • Intracellular poly(I:C) and 3pRNA evoke immune responses in FLS. • Only intracellular delivery of poly(I:C) induces FLS apoptosis. • FLS do not require MDA5 for their response to intracellular poly(I:C). • FLS respond to intracellular poly(I:C) independent of IPS and STING. • An unknown intracellular sensor recognizes linear dsRNA in FLS.

  16. Sequence and phylogenetic analysis of genome segments S1, S2, S3 and S6 of Mal de Río Cuarto virus, a newly accepted Fijivirus species.

    Science.gov (United States)

    Distéfano, Ana J; Conci, Luis R; Muñoz Hidalgo, Marianne; Guzmán, Fabiana A; Hopp, Horacio E; del Vas, Mariana

    2003-03-01

    Mal de Río Cuarto virus (MRCV) is a newly described species of the genus Fijivirus, family Reoviridae. The nucleotide sequence of four MRCV genome segments was determined. MRCV S1, S2, S3 and S6 were predicted to encode proteins of 168.4, 134.4, 141.7 and 90 kDa, respectively. MRCV S1 encodes a basic protein that contains conserved RNA-dependent RNA polymerase motifs, and is homologous to Rice black streaked dwarf virus (RBSDV), Fiji disease virus (FDV) and Nilaparvata lugens reovirus (NLRV) polymerases as well as to corresponding proteins of members of other genera of the Reoviridae. MRCV S2 codes for a protein with intermediate homology to the ones coded by RBSDV S4 and FDV S3 'B' spike, which is presumably the B-spike protein. MRCV S3 most probably encodes the major core protein and is highly homologous to corresponding proteins of RBSDV S2 and FDV S3. MRCV S6-encoded protein has low homology to the proteins of unknown function coded by RBSDV S6 and FDV S6. The identity levels between all analyzed MRCV coded proteins and their RBSDV counterparts varied between 84.5 and 44.8%. The analysis of the reported sequences allowed a phylogenetic comparison of MRCV with other reovirus and supported its taxonomic status within the genus.

  17. Exposure to the viral by-product dsRNA or Coxsackievirus B5 triggers pancreatic beta cell apoptosis via a Bim / Mcl-1 imbalance.

    Directory of Open Access Journals (Sweden)

    Maikel L Colli

    2011-09-01

    Full Text Available The rise in type 1 diabetes (T1D incidence in recent decades is probably related to modifications in environmental factors. Viruses are among the putative environmental triggers of T1D. The mechanisms regulating beta cell responses to viruses, however, remain to be defined. We have presently clarified the signaling pathways leading to beta cell apoptosis following exposure to the viral mimetic double-stranded RNA (dsRNA and a diabetogenic enterovirus (Coxsackievirus B5. Internal dsRNA induces cell death via the intrinsic mitochondrial pathway. In this process, activation of the dsRNA-dependent protein kinase (PKR promotes eIF2α phosphorylation and protein synthesis inhibition, leading to downregulation of the antiapoptotic Bcl-2 protein myeloid cell leukemia sequence 1 (Mcl-1. Mcl-1 decrease results in the release of the BH3-only protein Bim, which activates the mitochondrial pathway of apoptosis. Indeed, Bim knockdown prevented both dsRNA- and Coxsackievirus B5-induced beta cell death, and counteracted the proapoptotic effects of Mcl-1 silencing. These observations indicate that the balance between Mcl-1 and Bim is a key factor regulating beta cell survival during diabetogenic viral infections.

  18. Cry3Bb1-Resistant Western Corn Rootworm, Diabrotica virgifera virgifera (LeConte) Does Not Exhibit Cross-Resistance to DvSnf7 dsRNA

    Science.gov (United States)

    Khajuria, Chitvan; Pleau, Michael; Ilagan, Oliver; Chen, Mao; Jiang, Changjian; Price, Paula; McNulty, Brian; Clark, Thomas; Head, Graham

    2017-01-01

    Background and Methodology There is a continuing need to express new insect control compounds in transgenic maize against western corn rootworm, Diabrotica virgifera virgifera (LeConte) (WCR). In this study three experiments were conducted to determine cross-resistance between the new insecticidal DvSnf7 dsRNA, and Bacillus thuringiensis (Bt) Cry3Bb1; used to control WCR since 2003, with field-evolved resistance being reported. Laboratory susceptible and Cry3Bb1-resistant WCR were evaluated against DvSnf7 dsRNA in larval diet-incorporation bioassays. Additionally, the susceptibility of seven field and one field-derived WCR populations to DvSnf7 (and Cry3Bb1) was assessed in larval diet-overlay bioassays. Finally, beetle emergence of laboratory susceptible and Cry3Bb1-resistant WCR was evaluated with maize plants in the greenhouse expressing Cry3Bb1, Cry34Ab1/Cry35Ab1, or DvSnf7 dsRNA singly, or in combination. Principal Findings and Conclusions The Cry3Bb1-resistant colony had slight but significantly (2.7-fold; PIRM tool against WCR that will increase the durability of these Bt proteins. These results also illustrate the importance of using appropriate bioassay methods when characterizing field-evolved resistant WCR populations. PMID:28060922

  19. Exposure to the viral by-product dsRNA or Coxsackievirus B5 triggers pancreatic beta cell apoptosis via a Bim / Mcl-1 imbalance.

    Directory of Open Access Journals (Sweden)

    Maikel L Colli

    2011-09-01

    Full Text Available The rise in type 1 diabetes (T1D incidence in recent decades is probably related to modifications in environmental factors. Viruses are among the putative environmental triggers of T1D. The mechanisms regulating beta cell responses to viruses, however, remain to be defined. We have presently clarified the signaling pathways leading to beta cell apoptosis following exposure to the viral mimetic double-stranded RNA (dsRNA and a diabetogenic enterovirus (Coxsackievirus B5. Internal dsRNA induces cell death via the intrinsic mitochondrial pathway. In this process, activation of the dsRNA-dependent protein kinase (PKR promotes eIF2α phosphorylation and protein synthesis inhibition, leading to downregulation of the antiapoptotic Bcl-2 protein myeloid cell leukemia sequence 1 (Mcl-1. Mcl-1 decrease results in the release of the BH3-only protein Bim, which activates the mitochondrial pathway of apoptosis. Indeed, Bim knockdown prevented both dsRNA- and Coxsackievirus B5-induced beta cell death, and counteracted the proapoptotic effects of Mcl-1 silencing. These observations indicate that the balance between Mcl-1 and Bim is a key factor regulating beta cell survival during diabetogenic viral infections.

  20. Schizophrenia as segmental progeria

    Science.gov (United States)

    Papanastasiou, Evangelos; Gaughran, Fiona; Smith, Shubulade

    2011-01-01

    Schizophrenia is associated with a variety of physical manifestations (i.e. metabolic, neurological) and despite psychotropic medication being blamed for some of these (in particular obesity and diabetes), there is evidence that schizophrenia itself confers an increased risk of physical disease and early death. The observation that schizophrenia and progeroid syndromes share common clinical features and molecular profiles gives rise to the hypothesis that schizophrenia could be conceptualized as a whole body disorder, namely a segmental progeria. Mammalian cells employ the mechanisms of cellular senescence and apoptosis (programmed cell death) as a means to control inevitable DNA damage and cancer. Exacerbation of those processes is associated with accelerated ageing and schizophrenia and this warrants further investigation into possible underlying biological mechanisms, such as epigenetic control of the genome. PMID:22048679

  1. Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function

    Directory of Open Access Journals (Sweden)

    St-Laurent Georges

    2006-11-01

    Full Text Available Abstract Background The HIV Rev protein is known to facilitate export of incompletely spliced and unspliced viral transcripts to the cytoplasm, a necessary step in virus life cycle. The Rev-mediated nucleo-cytoplasmic transport of nascent viral transcripts, dependents on interaction of Rev with the RRE RNA structural element present in the target RNAs. The C-terminal variant of dsRNA-binding nuclear protein 90 (NF90ctv has been shown to markedly attenuate viral replication in stably transduced HIV-1 target cell line. Here we examined a mechanism of interference of viral life cycle involving Rev-NF90ctv interaction. Results Since Rev:RRE complex formations depend on protein:RNA and protein:protein interactions, we investigated whether the expression of NF90ctv might interfere with Rev-mediated export of RRE-containing transcripts. When HeLa cells expressed both NF90ctv and Rev protein, we observed that NF90ctv inhibited the Rev-mediated RNA transport. In particular, three regions of NF90ctv protein are involved in blocking Rev function. Moreover, interaction of NF90ctv with the RRE RNA resulted in the expression of a reporter protein coding sequences linked to the RRE structure. Moreover, Rev influenced the subcellular localization of NF90ctv, and this process is leptomycin B sensitive. Conclusion The dsRNA binding protein, NF90ctv competes with HIV Rev function at two levels, by competitive protein:protein interaction involving Rev binding to specific domains of NF90ctv, as well as by its binding to the RRE-RNA structure. Our results are consistent with a model of Rev-mediated HIV-1 RNA export that envisions Rev-multimerization, a process interrupted by NF90ctv.

  2. The genomic and biological characterization of Citrullus lanatus cryptic virus infecting watermelon in China.

    Science.gov (United States)

    Xin, Min; Cao, Mengji; Liu, Wenwen; Ren, Yingdang; Lu, Chuantao; Wang, Xifeng

    2017-03-15

    A dsRNA virus was detected in the watermelon (Citrullus lanatus) samples collected from Kaifeng, Henan province, China through the use of next generation sequencing of small RNAs. The complete genome of this virus is comprised of dsRNA-1 (1603nt) and dsRNA-2 (1466nt), both of which are single open reading frames and potentially encode a 54.2kDa RNA-dependent RNA polymerase (RdRp) and a 45.9kDa coat protein (CP), respectively. The RdRp and CP share the highest amino acid identities 85.3% and 75.4% with a previously reported Israeli strain Citrullus lanatus cryptic virus (CiLCV), respectively. Genome comparisons indicate that this virus is the same species with CiLCV, whereas the reported sequences of the Israeli strain of CiLCV are partial, and our newly identified sequences can represent the complete genome of CiLCV. Futhermore, phylogenetic tree analyses based on the RdRp sequences suggest that CiLCV is one member in the genus Deltapartitivirus, family Partitiviridae. In addition, field investigation and seed-borne bioassays show that CiLCV commonly occurs in many varieties and is transmitted though seeds at a very high rate. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Selective amplification of cDNA sequence from total RNA by cassette-ligation mediated polymerase chain reaction (PCR): application to sequencing 6.5 kb genome segment of hantavirus strain B-1.

    Science.gov (United States)

    Isegawa, Y; Sheng, J; Sokawa, Y; Yamanishi, K; Nakagomi, O; Ueda, S

    1992-12-01

    A method, referred to as cassette-ligation mediated polymerase chain reaction (PCR), has been developed to permit selective and specific amplification of cDNA sequence from total cellular RNA. This technique comprises (i) digestion of cDNA with multiple restriction enzymes, (ii) ligation of cleavage products to double-stranded DNA cassettes possessing a corresponding restriction site and (iii) amplification of cassette-ligated restriction fragments containing a short, known sequence (but not all the other ligation products) by PCR using the specific and cassette primers; the specific primer is designed to prime synthesis from the known sequence of the cDNA whereas the cassette primer anneals to one strand of the cassette. Sequencing from the cassette primer provides information to design a new primer for the next walking step. The amplified cDNA fragments are often larger than the maximum DNA fragments (500-600 bp) that can be sequenced without the need of synthesizing internal sequencing primer. Each of such large cDNA fragments is dissected into smaller DNA fragments by repeating cassette-ligation mediated PCR exploiting different restriction sites and different sets of cassette primers. This dissection process reduces the number of specific primers to a minimum, thereby increasing the speed of sequencing and minimizing the overall cost. We have successfully applied this cDNA walking and sequencing by the cassette-ligation mediated PCR to the sequencing of an entire 6.5 kb genome segment of hantavirus strain B-1.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Strategic market segmentation

    National Research Council Canada - National Science Library

    Maričić Branko R; Đorđević Aleksandar

    2015-01-01

    ..., requires segmented approach to the market that appreciates differences in expectations and preferences of customers. One of significant activities in strategic planning of marketing activities is market segmentation...

  5. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  6. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    NARCIS (Netherlands)

    H.W.M. van de Ven (Marieke); J.-O. Andressoo (Jaan-Olle); V.B. Holcomb (Valerie); M.M. von Lindern (Marieke); W.M.C. Jong (Willeke); C.I. de Zeeuw (Chris); Y. Suh (Yousin); P. Hasty (Paul); J.H.J. Hoeijmakers (Jan); G.T.J. van der Horst (Gijsbertus); J.R. Mitchell (James)

    2006-01-01

    textabstractHow congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular senes

  7. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    NARCIS (Netherlands)

    H.W.M. van de Ven (Marieke); J.-O. Andressoo (Jaan-Olle); V.B. Holcomb (Valerie); M.M. von Lindern (Marieke); W.M.C. Jong (Willeke); C.I. de Zeeuw (Chris); Y. Suh (Yousin); P. Hasty (Paul); J.H.J. Hoeijmakers (Jan); G.T.J. van der Horst (Gijsbertus); J.R. Mitchell (James)

    2006-01-01

    textabstractHow congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular senes

  8. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    NARCIS (Netherlands)

    H.W.M. van de Ven (Marieke); J.-O. Andressoo (Jaan-Olle); V.B. Holcomb (Valerie); M.M. von Lindern (Marieke); W.M.C. Jong (Willeke); C.I. de Zeeuw (Chris); Y. Suh (Yousin); P. Hasty (Paul); J.H.J. Hoeijmakers (Jan); G.T.J. van der Horst (Gijsbertus); J.R. Mitchell (James)

    2006-01-01

    textabstractHow congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular

  9. Triggering of the dsRNA sensors TLR3, MDA5, and RIG-I induces CD55 expression in synovial fibroblasts.

    Directory of Open Access Journals (Sweden)

    Olga N Karpus

    Full Text Available BACKGROUND: CD55 (decay-accelerating factor is a complement-regulatory protein highly expressed on fibroblast-like synoviocytes (FLS. CD55 is also a ligand for CD97, an adhesion-type G protein-coupled receptor abundantly present on leukocytes. Little is known regarding the regulation of CD55 expression in FLS. METHODS: FLS isolated from arthritis patients were stimulated with pro-inflammatory cytokines and Toll-like receptor (TLR ligands. Transfection with polyinosinic-polycytidylic acid (poly(I:C and 5'-triphosphate RNA were used to activate the cytoplasmic double-stranded (dsRNA sensors melanoma differentiation-associated gene 5 (MDA5 and retinoic acid-inducible gene-I (RIG-I. CD55 expression, cell viability, and binding of CD97-loaded beads were quantified by flow cytometry. RESULTS: CD55 was expressed at equal levels on FLS isolated from patients with rheumatoid arthritis (RA, osteoarthritis, psoriatic arthritis and spondyloarthritis. CD55 expression in RA FLS was significantly induced by IL-1β and especially by the TLR3 ligand poly(I:C. Activation of MDA5 and RIG-I also enhanced CD55 expression. Notably, activation of MDA5 dose-dependently induced cell death, while triggering of TLR3 or RIG-I had a minor effect on viability. Upregulation of CD55 enhanced the binding capacity of FLS to CD97-loaded beads, which could be blocked by antibodies against CD55. CONCLUSIONS: Activation of dsRNA sensors enhances the expression of CD55 in cultured FLS, which increases the binding to CD97. Our findings suggest that dsRNA promotes the interaction between FLS and CD97-expressing leukocytes.

  10. Influence of Bxpel1 Gene Silencing by dsRNA Interference on the Development and Pathogenicity of the Pine Wood Nematode, Bursaphelenchus xylophilus

    Directory of Open Access Journals (Sweden)

    Xiu-Wen Qiu

    2016-01-01

    Full Text Available As the causal agent of pine wilt disease (PWD, the pine wood nematode (PWN, Bursaphelenchus xylophilus, causes huge economic losses by devastating pine forests worldwide. The pectate lyase gene is essential for successful invasion of their host plants by plant-parasitic nematodes. To demonstrate the role of pectate lyase gene in the PWD process, RNA interference (RNAi is used to analyze the function of the pectate lyase 1 gene in B. xylophilus (Bxpel1. The efficiency of RNAi was detected by real-time PCR. The result demonstrated that the quantity of B. xylophilus propagated with control solution treatment was 62 times greater than that soaking in double-stranded RNA (dsRNA after B. xylophilus inoculation in Botrytis cinerea for the first generation (F1. The number of B. xylophilus soaking in control solution was doubled compared to that soaking in Bxpel1 dsRNA four days after inoculation in Pinus thunbergii. The quantity of B. xylophilus was reduced significantly (p < 0.001 after treatment with dsRNAi compared with that using a control solution treatment. Bxpel1 dsRNAi reduced the migration speed and reproduction of B. xylophilus in pine trees. The pathogenicity to P. thunbergii seedling of B. xylophilus was weaker after soaking in dsRNA solution compared with that after soaking in the control solution. Our results suggest that Bxpel1 gene is a significant pathogenic factor in the PWD process and this basic information may facilitate a better understanding of the molecular mechanism of PWD.

  11. Segmentation Similarity and Agreement

    CERN Document Server

    Fournier, Chris

    2012-01-01

    We propose a new segmentation evaluation metric, called segmentation similarity (S), that quantifies the similarity between two segmentations as the proportion of boundaries that are not transformed when comparing them using edit distance, essentially using edit distance as a penalty function and scaling penalties by segmentation size. We propose several adapted inter-annotator agreement coefficients which use S that are suitable for segmentation. We show that S is configurable enough to suit a wide variety of segmentation evaluations, and is an improvement upon the state of the art. We also propose using inter-annotator agreement coefficients to evaluate automatic segmenters in terms of human performance.

  12. Three-Dimensional Structure of the Enveloped Bacteriophage Φ12: An Incomplete T = 13 Lattice Is Superposed on an Enclosed T = 1 Shell

    OpenAIRE

    Wei, Hui; Cheng, R. Holland; Berriman, John; Rice, William J; Stokes, David L.; Katz, A.; Morgan, David Gene; Gottlieb, Paul

    2009-01-01

    Background Bacteriophage φ12 is a member of the Cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen Pseudomonas syringae pv. phaseolicola. The genomes of the virus species contain three double-stranded (dsRNA) segments, and the virus capsid itself is organized in multiple protein shells. The segmented dsRNA genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the Cystoviridae s...

  13. Molecular characterization of a new monopartite dsRNA mycovirus from mycorrhizal Thelephora terrestris (Ehrh.) and its detection in soil oribatid mites (Acari: Oribatida)

    Energy Technology Data Exchange (ETDEWEB)

    Petrzik, Karel, E-mail: petrzik@umbr.cas.cz [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); Sarkisova, Tatiana [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); Starý, Josef [Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice (Czech Republic); Koloniuk, Igor [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); and others

    2016-02-15

    A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris (Ehrh.) and sequenced. This virus, named Thelephora terrestris virus 1 (TtV1), contains two reading frames in different frames but with the possibility that ORF2 could be translated as a fusion polyprotein after ribosomal -1 frameshifting. Picornavirus 2A-like motif, nudix hydrolase, phytoreovirus S7, and RdRp domains were found in a unique arrangement on the polyprotein. A new genus named Phlegivirus and containing TtV1, PgLV1, RfV1 and LeV is therefore proposed. Twenty species of oribatid mites were identified in soil material in the vicinity of T. terrestris. TtV1 was detected in large amounts in Steganacarus (Tropacarus) carinatus (C.L. Koch, 1841) and in much smaller amounts in Nothrus silvestris (Nicolet). This is the first description of mycovirus presence in oribatid mites. - Highlights: • A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris. • A new virus genus Phlegivirus is proposed. • The mycovirus was firstly detected in oribatid mites.

  14. BNYVV-derived dsRNA confers resistance to rhizomania disease of sugar beet as evidenced by a novel transgenic hairy root approach.

    Science.gov (United States)

    Pavli, Ourania I; Panopoulos, Nicholas J; Goldbach, Rob; Skaracis, George N

    2010-10-01

    Agrobacterium rhizogenes-transformed sugar beet hairy roots, expressing dsRNA from the Beet necrotic yellow vein virus replicase gene, were used as a novel approach to assess the efficacy of three intron-hairpin constructs at conferring resistance to rhizomania disease. Genetically engineered roots were similar in morphology to wild type roots but were characterized by a profound abundancy, rapid growth rate and, in some cases, plagiotropic development. Upon challenge inoculation, seedlings showed a considerable delay in symptom development compared to untransformed or vector-transformed seedlings, expressing dsRNA from an unrelated source. The transgenic root system of almost all seedlings contained no or very low virus titer while the non-transformed aerial parts of the same plants were found infected, leading to the conclusion that the hairy roots studied were effectively protected against the virus. This readily applicable novel method forms a plausible approach to preliminarily evaluate transgenic rhizomania resistance before proceeding in transformation and whole plant regeneration of sugar beet, a tedious and time consuming process for such a recalcitrant crop species.

  15. Pituitary Adenoma Segmentation

    CERN Document Server

    Egger, Jan; Kuhnt, Daniela; Freisleben, Bernd; Nimsky, Christopher

    2011-01-01

    Sellar tumors are approximately 10-15% among all intracranial neoplasms. The most common sellar lesion is the pituitary adenoma. Manual segmentation is a time-consuming process that can be shortened by using adequate algorithms. In this contribution, we present a segmentation method for pituitary adenoma. The method is based on an algorithm we developed recently in previous work where the novel segmentation scheme was successfully used for segmentation of glioblastoma multiforme and provided an average Dice Similarity Coefficient (DSC) of 77%. This scheme is used for automatic adenoma segmentation. In our experimental evaluation, neurosurgeons with strong experiences in the treatment of pituitary adenoma performed manual slice-by-slice segmentation of 10 magnetic resonance imaging (MRI) cases. Afterwards, the segmentations were compared with the segmentation results of the proposed method via the DSC. The average DSC for all data sets was 77.49% +/- 4.52%. Compared with a manual segmentation that took, on the...

  16. New stopping criteria for segmenting DNA sequences

    CERN Document Server

    Li, W

    2001-01-01

    We propose a solution on the stopping criterion in segmenting inhomogeneous DNA sequences with complex statistical patterns. This new stopping criterion is based on Bayesian Information Criterion (BIC) in the model selection framework. When this stopping criterion is applied to a left telomere sequence of yeast Saccharomyces cerevisiae and the complete genome sequence of bacterium Escherichia coli, borders of biologically meaningful units were identified (e.g. subtelomeric units, replication origin, and replication terminus), and a more reasonable number of domains was obtained. We also introduce a measure called segmentation strength which can be used to control the delineation of large domains. The relationship between the average domain size and the threshold of segmentation strength is determined for several genome sequences.

  17. Avances y limitaciones en el uso de los dsRNA como estrategias de control y prevención de enfermedades virales en sistemas acuícolas

    Directory of Open Access Journals (Sweden)

    Ljubomir Papic

    2015-07-01

    Full Text Available El desarrollo de la acuicultura sustentable es acorde con la demanda creciente de nuevas metodologías que aseguren la salud de las diversas especies acuícolas. Dentro de ellas, el uso de terapias revolucionarias basadas en RNA de doble cadena (dsRNA ha abierto una amplia gama de posibilidades en el progreso de las estrategias de control y prevención de enfermedades. El sistema de silenciamiento génico mediante RNA de interferencia (RNAi presenta un interesante potencial para el control de enfermedades infecciosas en sistemas de acuicultura. Por otro lado, se ha visto que los dsRNA pueden tener un importante efecto inmunomodulador en células de peces activando mecanismos de defensa inmune innata. La definición de un adecuado sistema de suministro para asegurar el ingreso de los dsRNA a la célula objetivo ha resultado en pruebas medianamente exitosas. Sin embargo, el cómo suministrar el dsRNA para asegurar el ingreso al organismo en su hábitat natural, se presenta como la principal dificultad de esta tecnología. Este trabajo presenta una completa revisión del potencial del silenciamiento post-transcripcional mediado por dsRNA, como estrategia antiviral en peces de cultivo y de su potencial uso como inmunoestimulante, enfatizando la necesidad de buscar metodologías que permitan suministrar el dsRNA al organismo objetivo, considerando las limitaciones y particularidades de un sistema de cultivo intensivo.

  18. GPS Control Segment

    Science.gov (United States)

    2015-04-29

    Luke J. Schaub Chief, GPS Control Segment Division 29 Apr 15 GPS Control Segment Report Documentation Page Form ApprovedOMB No. 0704-0188...00-2015 4. TITLE AND SUBTITLE GPS Control Segment 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...Center, GPS Control Segment Division,Los Angeles AFB, El Segundo,CA,90245 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S

  19. Sipunculans and segmentation

    DEFF Research Database (Denmark)

    Wanninger, Andreas; Kristof, Alen; Brinkmann, Nora

    2009-01-01

    Comparative molecular, developmental and morphogenetic analyses show that the three major segmented animal groups- Lophotrochozoa, Ecdysozoa and Vertebrata-use a wide range of ontogenetic pathways to establish metameric body organization. Even in the life history of a single specimen, different...... plasticity and potential evolutionary lability of segmentation nourishes the controversy of a segmented bilaterian ancestor versus multiple independent evolution of segmentation in respective metazoan lineages....

  20. Automatic Melody Segmentation

    NARCIS (Netherlands)

    Rodríguez López, Marcelo

    2016-01-01

    The work presented in this dissertation investigates music segmentation. In the field of Musicology, segmentation refers to a score analysis technique, whereby notated pieces or passages of these pieces are divided into “units” referred to as sections, periods, phrases, and so on. Segmentation analy

  1. What is a segment?

    Science.gov (United States)

    Hannibal, Roberta L; Patel, Nipam H

    2013-12-17

    Animals have been described as segmented for more than 2,000 years, yet a precise definition of segmentation remains elusive. Here we give the history of the definition of segmentation, followed by a discussion on current controversies in defining a segment. While there is a general consensus that segmentation involves the repetition of units along the anterior-posterior (a-p) axis, long-running debates exist over whether a segment can be composed of only one tissue layer, whether the most anterior region of the arthropod head is considered segmented, and whether and how the vertebrate head is segmented. Additionally, we discuss whether a segment can be composed of a single cell in a column of cells, or a single row of cells within a grid of cells. We suggest that 'segmentation' be used in its more general sense, the repetition of units with a-p polarity along the a-p axis, to prevent artificial classification of animals. We further suggest that this general definition be combined with an exact description of what is being studied, as well as a clearly stated hypothesis concerning the specific nature of the potential homology of structures. These suggestions should facilitate dialogue among scientists who study vastly differing segmental structures.

  2. Myxoma Virus dsRNA Binding Protein M029 Inhibits the Type I IFN-Induced Antiviral State in a Highly Species-Specific Fashion

    Science.gov (United States)

    Rahman, Masmudur M.; McFadden, Grant

    2017-01-01

    Myxoma virus (MYXV) is a Leporipoxvirus that possesses a specific rabbit-restricted host tropism but exhibits a much broader cellular host range in cultured cells. MYXV is able to efficiently block all aspects of the type I interferon (IFN)-induced antiviral state in rabbit cells, partially in human cells and very poorly in mouse cells. The mechanism(s) of this species-specific inhibition of type I IFN-induced antiviral state is not well understood. Here we demonstrate that MYXV encoded protein M029, a truncated relative of the vaccinia virus (VACV) E3 double-stranded RNA (dsRNA) binding protein that inhibits protein kinase R (PKR), can also antagonize the type I IFN-induced antiviral state in a highly species-specific manner. In cells pre-treated with type I IFN prior to infection, MYXV exploits M029 to overcome the induced antiviral state completely in rabbit cells, partially in human cells, but not at all in mouse cells. However, in cells pre-infected with MYXV, IFN-induced signaling is fully inhibited even in the absence of M029 in cells from all three species, suggesting that other MYXV protein(s) apart from M029 block IFN signaling in a species-independent manner. We also show that the antiviral state induced in rabbit, human or mouse cells by type I IFN can inhibit M029-knockout MYXV even when PKR is genetically knocked-out, suggesting that M029 targets other host proteins for this antiviral state inhibition. Thus, the MYXV dsRNA binding protein M029 not only antagonizes PKR from multiple species but also blocks the type I IFN antiviral state independently of PKR in a highly species-specific fashion. PMID:28157174

  3. Feasibility of dsRNA treatment for post-clearing SPF shrimp stocks of newly discovered viral infections using Laem Singh virus (LSNV) as a model.

    Science.gov (United States)

    Saksmerprome, Vanvimon; Charoonnart, Patai; Flegel, Timothy W

    2017-05-02

    Using post-larvae derived from specific pathogen free (SPF) stocks in penaeid shrimp farming has led to a dramatic increase in production. At the same time, new pathogens of farmed shrimp are continually being discovered. Sometimes these pathogens are carried by shrimp and other crustaceans as persistent infections without gross signs of disease. Thus it is that a 5-generation stock of Penaeus monodon SPF for several pathogens was found, post-stock-development, to be persistently-infected with newly-discovered Laem Singh virus (LSNV). In this situation, the stock developers were faced with destroying their existing stock (developed over a long period at considerable cost) and starting the whole stock development process anew in order to add LSNV to its SPF list. As an alternative, it was hypothesized that injection of complementary dsRNA into viral-infected broodstock prior to mating might inhibit replication of the target virus sufficiently to reduce or eliminate its transmission to their offspring. Subsequent selection of uninfected offspring would allow for post-clearing of LSNV from the existing stock and for conversion of the stock to LSNV-free status. Testing this hypothesis using the LSNV-infected stock described above, we found that transmission was substantially reduced in several treated broodstock compared to much higher transmission in buffer-injected broodstock. Based on these results, the model is proposed for post-clearing of SPF stocks using dsRNA treatment. The model may also be applicable to post-clearing of exceptional, individual performers from grow-out ponds for return to a nucleus breeding center. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Comparative testing of DNA segmentation algorithms using benchmark simulations.

    Science.gov (United States)

    Elhaik, Eran; Graur, Dan; Josic, Kresimir

    2010-05-01

    Numerous segmentation methods for the detection of compositionally homogeneous domains within genomic sequences have been proposed. Unfortunately, these methods yield inconsistent results. Here, we present a benchmark consisting of two sets of simulated genomic sequences for testing the performances of segmentation algorithms. Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability. The sequences in the second set are composed of a mosaic of many short domains and a few long ones, distinguished by sharp GC content boundaries between neighboring domains. We use these sets to test the performance of seven segmentation algorithms in the literature. Our results show that recursive segmentation algorithms based on the Jensen-Shannon divergence outperform all other algorithms. However, even these algorithms perform poorly in certain instances because of the arbitrary choice of a segmentation-stopping criterion.

  5. Keypoint Transfer Segmentation

    OpenAIRE

    Wachinger, C.; Toews, M.; Langs, G.; Wells, W.; Golland, P.

    2015-01-01

    We present an image segmentation method that transfers label maps of entire organs from the training images to the novel image to be segmented. The transfer is based on sparse correspondences between keypoints that represent automatically identified distinctive image locations. Our segmentation algorithm consists of three steps: (i) keypoint matching, (ii) voting-based keypoint labeling, and (iii) keypoint-based probabilistic transfer of organ label maps. We introduce generative models for th...

  6. Universal Numeric Segmented Display

    CERN Document Server

    Azad, Md Abul kalam; Kamruzzaman, S M

    2010-01-01

    Segmentation display plays a vital role to display numerals. But in today's world matrix display is also used in displaying numerals. Because numerals has lots of curve edges which is better supported by matrix display. But as matrix display is costly and complex to implement and also needs more memory, segment display is generally used to display numerals. But as there is yet no proposed compact display architecture to display multiple language numerals at a time, this paper proposes uniform display architecture to display multiple language digits and general mathematical expressions with higher accuracy and simplicity by using a 18-segment display, which is an improvement over the 16 segment display.

  7. GENOMIC FEATURES OF COTESIA PLUTELLAE POLYDNAVIRUS

    Institute of Scientific and Technical Information of China (English)

    LIUCai-ling; ZHUXiang-xiong; FuWen-jun; ZHAOMu-jun

    2003-01-01

    Polydnavirus was purified from the calyx fluid of Cotesia plutellae ovary. The genomic features of C. plutellae polydnavirus (CpPDV) were investigated. The viral genome consists of at least 12 different segments and the aggregate genome size is a lower estimate of 80kbp. By partial digestion of CpPDV DNA with BamHI and subsequent ligation with BamHI-cut plasmid Bluescript, a representative library of CpPDV genome was obtained.

  8. From interpretation to segmentation

    NARCIS (Netherlands)

    Koning, A.R.; Lier, R.J. van

    2005-01-01

    In visual perception, part segmentation of an object is considered to be guided by image-based properties, such as occurrences of deep concavities in the outer contour. However, object-based properties can also provide information regarding segmentation. In this study, outer contours and interpretat

  9. Segmentation, advertising and prices

    NARCIS (Netherlands)

    Galeotti, Andrea; Moraga González, José

    This paper explores the implications of market segmentation on firm competitiveness. In contrast to earlier work, here market segmentation is minimal in the sense that it is based on consumer attributes that are completely unrelated to tastes. We show that when the market is comprised by two

  10. Segmentation, advertising and prices

    NARCIS (Netherlands)

    Galeotti, Andrea; Moraga González, José

    2008-01-01

    This paper explores the implications of market segmentation on firm competitiveness. In contrast to earlier work, here market segmentation is minimal in the sense that it is based on consumer attributes that are completely unrelated to tastes. We show that when the market is comprised by two consume

  11. Benign segmental bronchial obstruction

    Energy Technology Data Exchange (ETDEWEB)

    Loercher, U.

    1988-09-01

    The benigne segmental bronchial obstruction - mostly discovered on routine chest films - can well be diagnosed by CT. The specific findings in CT are the site of the bronchial obstruction, the mucocele and the localized empysema of the involved segment. Furthermore CT allows a better approach to the underlying process.

  12. Hospital benefit segmentation.

    Science.gov (United States)

    Finn, D W; Lamb, C W

    1986-12-01

    Market segmentation is an important topic to both health care practitioners and researchers. The authors explore the relative importance that health care consumers attach to various benefits available in a major metropolitan area hospital. The purposes of the study are to test, and provide data to illustrate, the efficacy of one approach to hospital benefit segmentation analysis.

  13. : a database of ciliate genome rearrangements.

    Science.gov (United States)

    Burns, Jonathan; Kukushkin, Denys; Lindblad, Kelsi; Chen, Xiao; Jonoska, Nataša; Landweber, Laura F

    2016-01-01

    Ciliated protists exhibit nuclear dimorphism through the presence of somatic macronuclei (MAC) and germline micronuclei (MIC). In some ciliates, DNA from precursor segments in the MIC genome rearranges to form transcriptionally active genes in the mature MAC genome, making these ciliates model organisms to study the process of somatic genome rearrangement. Similar broad scale, somatic rearrangement events occur in many eukaryotic cells and tumors. The (http://oxytricha.princeton.edu/mds_ies_db) is a database of genome recombination and rearrangement annotations, and it provides tools for visualization and comparative analysis of precursor and product genomes. The database currently contains annotations for two completely sequenced ciliate genomes: Oxytricha trifallax and Tetrahymena thermophila.

  14. Keypoint Transfer Segmentation.

    Science.gov (United States)

    Wachinger, C; Toews, M; Langs, G; Wells, W; Golland, P

    2015-01-01

    We present an image segmentation method that transfers label maps of entire organs from the training images to the novel image to be segmented. The transfer is based on sparse correspondences between keypoints that represent automatically identified distinctive image locations. Our segmentation algorithm consists of three steps: (i) keypoint matching, (ii) voting-based keypoint labeling, and (iii) keypoint-based probabilistic transfer of organ label maps. We introduce generative models for the inference of keypoint labels and for image segmentation, where keypoint matches are treated as a latent random variable and are marginalized out as part of the algorithm. We report segmentation results for abdominal organs in whole-body CT and in contrast-enhanced CT images. The accuracy of our method compares favorably to common multi-atlas segmentation while offering a speed-up of about three orders of magnitude. Furthermore, keypoint transfer requires no training phase or registration to an atlas. The algorithm's robustness enables the segmentation of scans with highly variable field-of-view.

  15. Pancreas and cyst segmentation

    Science.gov (United States)

    Dmitriev, Konstantin; Gutenko, Ievgeniia; Nadeem, Saad; Kaufman, Arie

    2016-03-01

    Accurate segmentation of abdominal organs from medical images is an essential part of surgical planning and computer-aided disease diagnosis. Many existing algorithms are specialized for the segmentation of healthy organs. Cystic pancreas segmentation is especially challenging due to its low contrast boundaries, variability in shape, location and the stage of the pancreatic cancer. We present a semi-automatic segmentation algorithm for pancreata with cysts. In contrast to existing automatic segmentation approaches for healthy pancreas segmentation which are amenable to atlas/statistical shape approaches, a pancreas with cysts can have even higher variability with respect to the shape of the pancreas due to the size and shape of the cyst(s). Hence, fine results are better attained with semi-automatic steerable approaches. We use a novel combination of random walker and region growing approaches to delineate the boundaries of the pancreas and cysts with respective best Dice coefficients of 85.1% and 86.7%, and respective best volumetric overlap errors of 26.0% and 23.5%. Results show that the proposed algorithm for pancreas and pancreatic cyst segmentation is accurate and stable.

  16. Segmentation of consumer's markets and evaluation of market's segments

    OpenAIRE

    ŠVECOVÁ, Iveta

    2013-01-01

    The goal of this bachelor thesis was to explain a possibly segmentation of consumer´s markets for a chosen company, and to present a suitable goods offer, so it would be suitable to the needs of selected segments. The work is divided into theoretical and practical part. First part describes marketing, segmentation, segmentation of consumer's markets, consumer's market, market's segments a other terms. Second part describes an evaluation of questionnaire survey, discovering of market's segment...

  17. Recurring genomic breaks in independent lineages support genomic fragility

    Directory of Open Access Journals (Sweden)

    Hannenhalli Sridhar

    2006-11-01

    Full Text Available Abstract Background Recent findings indicate that evolutionary breaks in the genome are not randomly distributed, and that certain regions, so-called fragile regions, are predisposed to breakages. Previous approaches to the study of genomic fragility have examined the distribution of breaks, as well as the coincidence of breaks with segmental duplications and repeats, within a single species. In contrast, we investigate whether this regional fragility is an inherent genomic characteristic and is thus conserved over multiple independent lineages. Results We do this by quantifying the extent to which certain genomic regions are disrupted repeatedly in independent lineages. Our investigation, based on Human, Chimp, Mouse, Rat, Dog and Chicken, suggests that the propensity of a chromosomal region to break is significantly correlated among independent lineages, even when covariates are considered. Furthermore, the fragile regions are enriched for segmental duplications. Conclusion Based on a novel methodology, our work provides additional support for the existence of fragile regions.

  18. Targeting polyIC to EGFR over-expressing cells using a dsRNA binding protein domain tethered to EGF

    Science.gov (United States)

    Edinger, Nufar; Lebendiker, Mario; Klein, Shoshana; Zigler, Maya; Langut, Yael; Levitzki, Alexander

    2016-01-01

    Selective delivery of drugs to tumor cells can increase potency and reduce toxicity. In this study, we describe a novel recombinant chimeric protein, dsRBEC, which can bind polyIC and deliver it selectively into EGFR over-expressing tumor cells. dsRBEC, comprises the dsRNA binding domain (dsRBD) of human PKR (hPKR), which serves as the polyIC binding moiety, fused to human EGF (hEGF), the targeting moiety. dsRBEC shows high affinity towards EGFR and triggers ligand-induced endocytosis of the receptor, thus leading to the selective internalization of polyIC into EGFR over-expressing tumor cells. The targeted delivery of polyIC by dsRBEC induced cellular apoptosis and the secretion of IFN-β and other pro-inflammatory cytokines. dsRBEC-delivered polyIC is much more potent than naked polyIC and is expected to reduce the toxicity caused by systemic delivery of polyIC. PMID:27598772

  19. Herpes simplex virus type 2 virion host shutoff protein suppresses innate dsRNA antiviral pathways in human vaginal epithelial cells.

    Science.gov (United States)

    Yao, Xiao-Dan; Rosenthal, Kenneth Lee

    2011-09-01

    Viruses that establish persistent infections have evolved numerous strategies to evade host innate antiviral responses. We functionally assessed the role of herpes simplex virus type 2 (HSV-2) virion host shutoff (vhs) protein on innate immune sensing pathways in human vaginal epithelial cells (VK2 ECs). Infection of cells with wild-type (WT) HSV-2 significantly decreased expression of innate immune sensors of viral infection, Toll-like receptor (TLR)2, TLR3, retinoic acid inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (Mda-5), relative to cells infected with a mutant that lacks vhs (vhsB) or mock-infected cells. Transfection with HSV-2 vhs similarly decreased expression of TLR2, TLR3, RIG-I and Mda-5, which was also confirmed in human embryonic kidney (HEK) 293 cells. vhsB infection of VK2 cells caused robust increases in the active form of interferon regulatory factor (IRF)3 and its translocation to the nucleus compared with the WT. Additionally, IRF3 activation by Sendai virus and polyinosinic : polycytidylic acid-induced stimulation of beta interferon (IFN-β) was significantly inhibited in vhs-transfected cells. Overall, our findings provide the first evidence that HSV-2 vhs plays roles in selectively inhibiting TLR3 and RIG-I/Mda-5, as well as TLR2-mediated antiviral pathways for sensing dsRNA and effectively suppresses IFN-β antiviral responses in human vaginal ECs.

  20. Segmentation of antiperspirants and deodorants

    OpenAIRE

    KRÁL, Tomáš

    2009-01-01

    The goal of Master's Thesis on topic Segmentation of antiperspirants and deodorants is to discover differences in consumer's behaviour, determinate and describe segments of consumers based on these differences and propose marketing strategy for the most attractive segments. Theoretical part describes market segmentation in general, process of segmentation and segmentation criteria. Analytic part characterizes Czech market of antiperspirants and deodorants, analyzes ACNielsen market data and d...

  1. Modulation of the transcriptional response of innate immune and RNAi genes upon exposure to dsRNA and LPS in silkmoth-derived Bm5 cells overexpressing BmToll9-1 receptor.

    Science.gov (United States)

    Liu, Jisheng; Kolliopoulou, Anna; Smagghe, Guy; Swevers, Luc

    2014-07-01

    Injection or feeding of dsRNA is commonly used to induce specific gene silencing by RNAi in insects but very little research has been carried out to investigate non-specific effects on gene expression of dsRNA as pathogen-associated molecular pattern (PAMP). This study focuses on the potential role of the BmToll9-1 receptor to modulate the transcriptional response of innate immune and RNAi genes to dsRNA and lipopolysaccharide (LPS), which was used for comparison. To study this role, we took advantage of the silkmoth-derived Bm5 cell line, which does not express BmToll9-1 endogenously, and engineered a transformed cell line that permanently expresses BmToll9-1. Quantitative mRNA expression studies showed that BmToll9-1 can significantly alter the transcriptional response to dsRNA and LPS: (1) BmToll9-1 promotes the transcriptional response of Dicer2, encoding a key component of the RNAi machinery, and, to a lesser extent, that of transcription factors in the Jak-STAT and Toll pathways; and (2) BmToll9-1 represses the transcriptional induction of the IMD and Jak-STAT pathway genes, as well as the antimicrobial peptide (AMP) effector genes, by LPS. Thus, BmToll9-1 was identified as a modulator of innate immune and RNAi machinery gene expression that could be related to its preferential expression in the larval gut, the major barrier of pathogen entry. While BmToll9-1 was found to modulate RNAi-related gene expression, a reporter-based RNAi assay established no evidence for a direct interaction of BmToll9-1 with the intracellular RNAi machinery.

  2. a segmentation approach

    African Journals Online (AJOL)

    kirstam

    a visitor survey was conducted at the Cape Town International Jazz ... 13Key words: dining motives, tipping, black diners, market segmentation, South .... and tipping behaviour as well as the findings from cross-cultural tipping and market.

  3. Segmental tuberculosis verrucosa cutis

    Directory of Open Access Journals (Sweden)

    Hanumanthappa H

    1994-01-01

    Full Text Available A case of segmental Tuberculosis Verrucosa Cutis is reported in 10 year old boy. The condition was resembling the ascending lymphangitic type of sporotrichosis. The lesions cleared on treatment with INH 150 mg daily for 6 months.

  4. Market segmentation: venezuelan adrs

    OpenAIRE

    Urbi Garay; Maximiliano González

    2012-01-01

    The foreign exchange controls imposed by Venezuela in 2003, constitute a natural experiment that allows researchers to observe the effects of exchange controls on stock market segmentation. This paper provides empirical evidence that, although the Venezuelan capital market as a whole was highly segmented before the controls were imposed, shares in the firm CANTV were, through its American Depositary Receipts (ADRs), partially integrated with the global market. Following the imposition of the ...

  5. Adjacent segment disease.

    Science.gov (United States)

    Virk, Sohrab S; Niedermeier, Steven; Yu, Elizabeth; Khan, Safdar N

    2014-08-01

    EDUCATIONAL OBJECTIVES As a result of reading this article, physicians should be able to: 1. Understand the forces that predispose adjacent cervical segments to degeneration. 2. Understand the challenges of radiographic evaluation in the diagnosis of cervical and lumbar adjacent segment disease. 3. Describe the changes in biomechanical forces applied to adjacent segments of lumbar vertebrae with fusion. 4. Know the risk factors for adjacent segment disease in spinal fusion. Adjacent segment disease (ASD) is a broad term encompassing many complications of spinal fusion, including listhesis, instability, herniated nucleus pulposus, stenosis, hypertrophic facet arthritis, scoliosis, and vertebral compression fracture. The area of the cervical spine where most fusions occur (C3-C7) is adjacent to a highly mobile upper cervical region, and this contributes to the biomechanical stress put on the adjacent cervical segments postfusion. Studies have shown that after fusion surgery, there is increased load on adjacent segments. Definitive treatment of ASD is a topic of continuing research, but in general, treatment choices are dictated by patient age and degree of debilitation. Investigators have also studied the risk factors associated with spinal fusion that may predispose certain patients to ASD postfusion, and these data are invaluable for properly counseling patients considering spinal fusion surgery. Biomechanical studies have confirmed the added stress on adjacent segments in the cervical and lumbar spine. The diagnosis of cervical ASD is complicated given the imprecise correlation of radiographic and clinical findings. Although radiological and clinical diagnoses do not always correlate, radiographs and clinical examination dictate how a patient with prolonged pain is treated. Options for both cervical and lumbar spine ASD include fusion and/or decompression. Current studies are encouraging regarding the adoption of arthroplasty in spinal surgery, but more long

  6. Reassortment in segmented RNA viruses: mechanisms and outcomes.

    Science.gov (United States)

    McDonald, Sarah M; Nelson, Martha I; Turner, Paul E; Patton, John T

    2016-07-01

    Segmented RNA viruses are widespread in nature and include important human, animal and plant pathogens, such as influenza viruses and rotaviruses. Although the origin of RNA virus genome segmentation remains elusive, a major consequence of this genome structure is the capacity for reassortment to occur during co-infection, whereby segments are exchanged among different viral strains. Therefore, reassortment can create viral progeny that contain genes that are derived from more than one parent, potentially conferring important fitness advantages or disadvantages to the progeny virus. However, for segmented RNA viruses that package their multiple genome segments into a single virion particle, reassortment also requires genetic compatibility between parental strains, which occurs in the form of conserved packaging signals, and the maintenance of RNA and protein interactions. In this Review, we discuss recent studies that examined the mechanisms and outcomes of reassortment for three well-studied viral families - Cystoviridae, Orthomyxoviridae and Reoviridae - and discuss how these findings provide new perspectives on the replication and evolution of segmented RNA viruses.

  7. Strategic market segmentation

    Directory of Open Access Journals (Sweden)

    Maričić Branko R.

    2015-01-01

    Full Text Available Strategic planning of marketing activities is the basis of business success in modern business environment. Customers are not homogenous in their preferences and expectations. Formulating an adequate marketing strategy, focused on realization of company's strategic objectives, requires segmented approach to the market that appreciates differences in expectations and preferences of customers. One of significant activities in strategic planning of marketing activities is market segmentation. Strategic planning imposes a need to plan marketing activities according to strategically important segments on the long term basis. At the same time, there is a need to revise and adapt marketing activities on the short term basis. There are number of criteria based on which market segmentation is performed. The paper will consider effectiveness and efficiency of different market segmentation criteria based on empirical research of customer expectations and preferences. The analysis will include traditional criteria and criteria based on behavioral model. The research implications will be analyzed from the perspective of selection of the most adequate market segmentation criteria in strategic planning of marketing activities.

  8. Skin Images Segmentation

    Directory of Open Access Journals (Sweden)

    Ali E. Zaart

    2010-01-01

    Full Text Available Problem statement: Image segmentation is a fundamental step in many applications of image processing. Skin cancer has been the most common of all new cancers detected each year. At early stage detection of skin cancer, simple and economic treatment can cure it mostly. An accurate segmentation of skin images can help the diagnosis to define well the region of the cancer. The principal approach of segmentation is based on thresholding (classification that is lied to the problem of the thresholds estimation. Approach: The objective of this study is to develop a method to segment the skin images based on a mixture of Beta distributions. We assume that the data in skin images can be modeled by a mixture of Beta distributions. We used an unsupervised learning technique with Beta distribution to estimate the statistical parameters of the data in skin image and then estimate the thresholds for segmentation. Results: The proposed method of skin images segmentation was implemented and tested on different skin images. We obtained very good results in comparing with the same techniques with Gamma distribution. Conclusion: The experiment showed that the proposed method obtained very good results but it requires more testing on different types of skin images.

  9. The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase.

    Directory of Open Access Journals (Sweden)

    Heng-Chi Lee

    Full Text Available The production of aberrant RNA (aRNA is the initial step in several RNAi pathways. How aRNA is produced and specifically recognized by RNA-dependent RNA polymerases (RdRPs to generate double-stranded RNA (dsRNA is not clear. We previously showed that in the filamentous fungus Neurospora, the RdRP QDE-1 is required for rDNA-specific aRNA production, suggesting that QDE-1 may be important in aRNA synthesis. Here we show that a recombinant QDE-1 is both an RdRP and a DNA-dependent RNA polymerase (DdRP. Its DdRP activity is much more robust than the RdRP activity and occurs on ssDNA but not dsDNA templates. We further show that Replication Protein A (RPA, a single-stranded DNA-binding complex that interacts with QDE-1, is essential for aRNA production and gene silencing. In vitro reconstitution assays demonstrate that QDE-1 can produce dsRNA from ssDNA, a process that is strongly promoted by RPA. Furthermore, the interaction between QDE-1 and RPA requires the RecQ DNA helicase QDE-3, a homolog of the human Werner/Bloom Syndrome proteins. Together, these results suggest a novel small RNA biogenesis pathway in Neurospora and a new mechanism for the production of aRNA and dsRNA in RNAi pathways.

  10. Molecular analysis of six segments of tobacco leaf enation virus, a novel phytoreovirus from tobacco.

    Science.gov (United States)

    Picton, Anabela; Potgieter, Christiaan; Rey, Marie Emma Christine

    2007-10-01

    Tobacco leaf enation virus (TLEV) is a putative member of the genus Phytoreovirus within the family Reoviridae. Previous western blot analysis of structural viral proteins (apparent molecular weights of 93 kDa; 58 kDa; 48 kDa; 39 kDa and 36 kDa) associated with TLEV, isolated from infected tobacco in South Africa, suggested that these proteins may correspond to structural Wound tumor virus (WTV) proteins. To further establish the nature of this novel virus disease phenotype in tobacco, molecular characterization of six dsRNA components was undertaken. Full-length cDNA clones were obtained by an optimized modified single-primer amplification sequence-independent dsRNA cloning method. Results of this study revealed the conserved terminal sequence: 5'GG(U/C)...UGAU 3' of segments S6-S12, while adjacent to these conserved terminal sequences are imperfect inverted repeats (7-15 bp in length), both features being common to reoviruses. The complete nucleotide sequences of segments S5 (2,610 bp), S7 (1,740 bp), S8 (1,439 bp), S10 (1,252 bp), S11 (1,187 bp) and S12 (836 bp) were determined. Comparison of full-length nucleotide sequences with corresponding segments of other phytoreoviruses, Rice gall dwarf virus (RGDV), Rice dwarf virus (RDV) and WTV has shown nucleotide and predicted amino acid identities within the range of 30-60%. TLEV consistently shows a higher identity to WTV than to other phytoreovirus species where sequence data is available. Each segment had a single predicted open reading frame encoding proteins with calculated molecular weights of S5 (90.6 kDa); S7 (58.1 kDa); S8 (47.7 kDa); S10 (39.8 kDa); S11 (35 kDa) and S12 (19.5 kDa). The relatively low nucleotide and amino acid identity to other members of the genus demonstrates that TLEV is a novel phytoreovirus, distinct from the only other reported dicotyledenous-infecting WTV and is the first phytoreovirus reported to emerge in Africa.

  11. Rediscovering market segmentation.

    Science.gov (United States)

    Yankelovich, Daniel; Meer, David

    2006-02-01

    In 1964, Daniel Yankelovich introduced in the pages of HBR the concept of nondemographic segmentation, by which he meant the classification of consumers according to criteria other than age, residence, income, and such. The predictive power of marketing studies based on demographics was no longer strong enough to serve as a basis for marketing strategy, he argued. Buying patterns had become far better guides to consumers' future purchases. In addition, properly constructed nondemographic segmentations could help companies determine which products to develop, which distribution channels to sell them in, how much to charge for them, and how to advertise them. But more than 40 years later, nondemographic segmentation has become just as unenlightening as demographic segmentation had been. Today, the technique is used almost exclusively to fulfill the needs of advertising, which it serves mainly by populating commercials with characters that viewers can identify with. It is true that psychographic types like "High-Tech Harry" and "Joe Six-Pack" may capture some truth about real people's lifestyles, attitudes, self-image, and aspirations. But they are no better than demographics at predicting purchase behavior. Thus they give corporate decision makers very little idea of how to keep customers or capture new ones. Now, Daniel Yankelovich returns to these pages, with consultant David Meer, to argue the case for a broad view of nondemographic segmentation. They describe the elements of a smart segmentation strategy, explaining how segmentations meant to strengthen brand identity differ from those capable of telling a company which markets it should enter and what goods to make. And they introduce their "gravity of decision spectrum", a tool that focuses on the form of consumer behavior that should be of the greatest interest to marketers--the importance that consumers place on a product or product category.

  12. Segmentation of Color Images Based on Different Segmentation Techniques

    Directory of Open Access Journals (Sweden)

    Purnashti Bhosale

    2013-03-01

    Full Text Available In this paper, we propose an Color image segmentation algorithm based on different segmentation techniques. We recognize the background objects such as the sky, ground, and trees etc based on the color and texture information using various methods of segmentation. The study of segmentation techniques by using different threshold methods such as global and local techniques and they are compared with one another so as to choose the best technique for threshold segmentation. Further segmentation is done by using clustering method and Graph cut method to improve the results of segmentation.

  13. A conserved segmental duplication within ELA.

    Science.gov (United States)

    Brinkmeyer-Langford, C L; Murphy, W J; Childers, C P; Skow, L C

    2010-12-01

    The assembled genomic sequence of the horse major histocompatibility complex (MHC) (equine lymphocyte antigen, ELA) is very similar to the homologous human HLA, with the notable exception of a large segmental duplication at the boundary of ELA class I and class III that is absent in HLA. The segmental duplication consists of a ∼ 710 kb region of at least 11 repeated blocks: 10 blocks each contain an MHC class I-like sequence and the helicase domain portion of a BAT1-like sequence, and the remaining unit contains the full-length BAT1 gene. Similar genomic features were found in other Perissodactyls, indicating an ancient origin, which is consistent with phylogenetic analyses. Reverse-transcriptase PCR (RT-PCR) of mRNA from peripheral white blood cells of healthy and chronically or acutely infected horses detected transcription from predicted open reading frames in several of the duplicated blocks. This duplication is not present in the sequenced MHCs of most other mammals, although a similar feature at the same relative position is present in the feline MHC (FLA). Striking sequence conservation throughout Perissodactyl evolution is consistent with a functional role for at least some of the genes included within this segmental duplication.

  14. Gene conversion in the rice genome

    DEFF Research Database (Denmark)

    Xu, Shuqing; Clark, Terry; Zheng, Hongkun;

    2008-01-01

    BACKGROUND: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes...... is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less...

  15. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    Sybesma, W.; Molenaar, D.; IJcken, W. van; Venema, K.; Korta, R.

    2013-01-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the

  16. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    W. Sybesma (Wilbert); D. Molenaar (Douwe); W.F.J. van IJcken (Wilfred); K. Venema (Koen); R. Kort (Remco)

    2013-01-01

    textabstractWe describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing

  17. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    W. Sybesma (Wilbert); D. Molenaar (Douwe); W.F.J. van IJcken (Wilfred); K. Venema (Koen); R. Kort (Remco)

    2013-01-01

    textabstractWe describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing f

  18. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    Sybesma, W.; Molenaar, D.; IJcken, W. van; Venema, K.; Korta, R.

    2013-01-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the geno

  19. Segmented conjugated polymers

    Indian Academy of Sciences (India)

    G Padmanaban; S Ramakrishnan

    2003-08-01

    Segmented conjugated polymers, wherein the conjugation is randomly truncated by varying lengths of non-conjugated segments, form an interesting class of polymers as they not only represent systems of varying stiffness, but also ones where the backbone can be construed as being made up of chromophores of varying excitation energies. The latter feature, especially when the chromophores are fluorescent, like in MEHPPV, makes these systems particularly interesting from the photophysics point of view. Segmented MEHPPV- samples, where x represents the mole fraction of conjugated segments, were prepared by a novel approach that utilizes a suitable precursor wherein selective elimination of one of the two eliminatable groups is affected; the uneliminated units serve as conjugation truncations. Control of the composition x of the precursor therefore permits one to prepare segmented MEHPPV- samples with varying levels of conjugation (elimination). Using fluorescence spectroscopy, we have seen that even in single isolated polymer chains, energy migration from the shorter (higher energy) chromophores to longer (lower energy) ones occurs – the extent of which depends on the level of conjugation. Further, by varying the solvent composition, it is seen that the extent of energy transfer and the formation of poorly emissive inter-chromophore excitons are greatly enhanced with increasing amounts of non-solvent. A typical S-shaped curve represents the variation of emission yields as a function of composition suggestive of a cooperative collapse of the polymer coil, reminiscent of conformational transitions seen in biological macromolecules.

  20. Scorpion image segmentation system

    Science.gov (United States)

    Joseph, E.; Aibinu, A. M.; Sadiq, B. A.; Bello Salau, H.; Salami, M. J. E.

    2013-12-01

    Death as a result of scorpion sting has been a major public health problem in developing countries. Despite the high rate of death as a result of scorpion sting, little report exists in literature of intelligent device and system for automatic detection of scorpion. This paper proposed a digital image processing approach based on the floresencing characteristics of Scorpion under Ultra-violet (UV) light for automatic detection and identification of scorpion. The acquired UV-based images undergo pre-processing to equalize uneven illumination and colour space channel separation. The extracted channels are then segmented into two non-overlapping classes. It has been observed that simple thresholding of the green channel of the acquired RGB UV-based image is sufficient for segmenting Scorpion from other background components in the acquired image. Two approaches to image segmentation have also been proposed in this work, namely, the simple average segmentation technique and K-means image segmentation. The proposed algorithm has been tested on over 40 UV scorpion images obtained from different part of the world and results obtained show an average accuracy of 97.7% in correctly classifying the pixel into two non-overlapping clusters. The proposed 1system will eliminate the problem associated with some of the existing manual approaches presently in use for scorpion detection.

  1. Segmented heterochromia in scalp hair.

    Science.gov (United States)

    Yoon, Kyeong Han; Kim, Daehwan; Sohn, Seonghyang; Lee, Won Soo

    2003-12-01

    Segmented heterochromia of scalp hair is characterized by the irregularly alternating segmentation of hair into dark and light bands and is known to be associated with iron deficiency anemia. The authors report the case of an 11-year-old boy with segmented heterochromia associated with iron deficiency anemia. After 11 months of iron replacement, the boy's segmented heterochromic hair recovered completely.

  2. Optimally segmented magnetic structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bahl, Christian; Bjørk, Rasmus;

    ], or are applicable only to analytically solvable geometries[4]. In addition, some questions remained fundamentally unanswered, such as how to segment a given design into N uniformly magnetized pieces.Our method calculates the globally optimal shape and magnetization direction of each segment inside a certain......We present a semi-analytical algorithm for magnet design problems, which calculates the optimal way to subdivide a given design region into uniformly magnetized segments.The availability of powerful rare-earth magnetic materials such as Nd-Fe-B has broadened the range of applications of permanent...... designarea with an optional constraint on the total amount of magnetic material. The method can be applied to any objective functional which is linear respect to the field, and with any combination of linear materials. Being based on an analytical-optimization approach, the algorithm is not computationally...

  3. Segmentation of complex document

    Directory of Open Access Journals (Sweden)

    Souad Oudjemia

    2014-06-01

    Full Text Available In this paper we present a method for segmentation of documents image with complex structure. This technique based on GLCM (Grey Level Co-occurrence Matrix used to segment this type of document in three regions namely, 'graphics', 'background' and 'text'. Very briefly, this method is to divide the document image, in block size chosen after a series of tests and then applying the co-occurrence matrix to each block in order to extract five textural parameters which are energy, entropy, the sum entropy, difference entropy and standard deviation. These parameters are then used to classify the image into three regions using the k-means algorithm; the last step of segmentation is obtained by grouping connected pixels. Two performance measurements are performed for both graphics and text zones; we have obtained a classification rate of 98.3% and a Misclassification rate of 1.79%.

  4. Microscopic Halftone Image Segmentation

    Institute of Scientific and Technical Information of China (English)

    WANG Yong-gang; YANG Jie; DING Yong-sheng

    2004-01-01

    Microscopic halftone image recognition and analysis can provide quantitative evidence for printing quality control and fault diagnosis of printing devices, while halftone image segmentation is one of the significant steps during the procedure. Automatic segmentation on microscopic dots by the aid of the Fuzzy C-Means (FCM) method that takes account of the fuzziness of halftone image and utilizes its color information adequately is realized. Then some examples show the technique effective and simple with better performance of noise immunity than some usual methods. In addition, the segmentation results obtained by the FCM in different color spaces are compared, which indicates that the method using the FCM in the f1f2f3 color space is superior to the rest.

  5. Viral Effects of a dsRNA Mycovirus (PoV-ASI2792) on the Vegetative Growth of the Edible Mushroom Pleurotus ostreatus

    Science.gov (United States)

    Song, Ha-Yeon; Choi, Hyo-Jin; Jeong, Hansaem; Choi, Dahye

    2016-01-01

    A double-stranded RNA (dsRNA) mycovirus was detected in malformed fruiting bodies of Pleurotus ostreatus strain ASI2792, one of bottle cultivated commercial strains of the edible oyster mushroom. The partial RNA-dependent RNA polymerase (RdRp) gene of the P. ostreatus ASI2792 mycovirus (PoV-ASI2792) was cloned, and a cDNA sequences alignment revealed that the sequence was identical to the RdRp gene of a known PoSV found in the P. ostreatus strain. To investigate the symptoms of PoV-ASI2792 infection by comparing the isogenic virus-free P. ostreatus strains with a virus-infected strain, isogenic virus-cured P. ostreatus strains were obtained by the mycelial fragmentation method for virus curing. The absence of virus was verified with gel electrophoresis after dsRNA-specific virus purification and Northern blot analysis using a partial RdRp cDNA of PoV-ASI2792. The growth rate and mycelial dry weight of virus-infected P. ostreatus strain with PoV-ASI2792 mycovirus were compared to those of three virus-free isogenic strains on 10 different media. The virus-cured strains showed distinctly higher mycelial growth rates and dry weights on all kinds of experimental culture media, with at least a 2.2-fold higher mycelial growth rate on mushroom complete media (MCM) and Hamada media, and a 2.7-fold higher mycelial dry weight on MCM and yeastmalt-glucose agar media than those of the virus-infected strain. These results suggest that the infection of PoV mycovirus has a deleterious effect on the vegetative growth of P. ostreatus.

  6. Development of a walleye spleen stromal cell line sensitive to viral hemorrhagic septicemia virus (VHSV IVb) and to protection by synthetic dsRNA.

    Science.gov (United States)

    Vo, Nguyen T K; Bender, Aaron W; Ammendolia, Dustin A; Lumsden, John S; Dixon, Brian; Bols, Niels C

    2015-07-01

    A cell line, WE-spleen6, has been developed from the stromal layer of primary spleen cell cultures. On conventional plastic, WE-spleen6 cells had a spindle-shaped morphology at low cell density but grew to become epithelial-like at confluency. On the commercial extracellular matrix (ECM), Matrigel, the cells remained spindle-shaped and formed lumen-like structures. WE-spleen6 cells had intermediate filament protein, vimentin and the ECM protein, collagen I, but not smooth muscle α-actin (SMA) and von Willebrand factor (vWF) and lacked alkaline phosphatase and phagocytic activities. WE-spleen6 was more susceptible to infection with VHSV IVb than a fibroblast and epithelial cell lines from the walleye caudal fin, WE-cfin11f and WE-cfin11e, respectively. Viral transcripts and proteins appeared earlier in WE-spleen6 cultures as did cytopathic effect (CPE) and significant virus production. The synthetic double-stranded RNA (dsRNA), polyinosinic: polycytidylic acid (pIC), induced the antiviral protein Mx in both cell lines. Treating WE-spleen6 cultures with pIC prior to infection with VHSV IVb inhibited the early accumulation of viral transcripts and proteins and delayed the appearance of CPE and significant viral production. Of particular note, pIC caused the disappearance of viral P protein 2 days post infection. WE-spleen6 should be useful for investigating the impact of VHSV IVb on hematopoietic organs and the actions of pIC on the rhabdovirus life cycle.

  7. Immune responses of whiteleg shrimp, Litopenaeus vannamei (Boone, 1931), to bacterially expressed dsRNA specific to VP28 gene of white spot syndrome virus.

    Science.gov (United States)

    Taju, G; Madan, N; Abdul Majeed, S; Kumar, T Raj; Thamizhvanan, S; Otta, S K; Sahul Hameed, A S

    2015-05-01

    In this study, dsRNA specific to VP28 gene of white spot syndrome virus (WSSV) of shrimp was synthesized in Escherichia coli in large scale and studied the immune response of shrimp to dsRNA-VP28. The haematological parameters such as clotting time and total haemocytes counts, and immunological parameters such as prophenoloxidase (proPO), superoxide dismutase (SOD), superoxide anion (SOA) and malondialdehyde content, as well as the mRNA expression of ten immune-related genes were examined to estimate the effect of dsRNA-VP28 on the innate immunity of Litopenaeus vannamei. The activities of proPO, SOA and SOD significantly increased in haemocyte after dsRNA-VP28 treatment, whereas MDA content did not change significantly. Among the ten immune-related genes examined, only the mRNA expression of proPO, cMnSOD, haemocyanin, crustin, BGBP, lipopolysaccharides (LPs), lectin and lysozyme in haemocytes, gill and hepatopancreas of L. vannamei, was significantly upregulated at 12 h after dsRNA-VP28 treatment, while no significant expression changes were observed in Toll receptor and tumour receptor genes. The increase of proPO and SOD activities, and SOA level and mRNA expression level of proPO, cMnSOD, haemocyanin, crustin, BGBP, LPs, lectin and lysozyme after dsRNA-VP28 stimulation indicate that these immune-related genes were involved in dsRNA-VP28-induced innate immunity in shrimp.

  8. Viral Effects of a dsRNA Mycovirus (PoV-ASI2792) on the Vegetative Growth of the Edible Mushroom Pleurotus ostreatus.

    Science.gov (United States)

    Song, Ha-Yeon; Choi, Hyo-Jin; Jeong, Hansaem; Choi, Dahye; Kim, Dae-Hyuk; Kim, Jung-Mi

    2016-12-01

    A double-stranded RNA (dsRNA) mycovirus was detected in malformed fruiting bodies of Pleurotus ostreatus strain ASI2792, one of bottle cultivated commercial strains of the edible oyster mushroom. The partial RNA-dependent RNA polymerase (RdRp) gene of the P. ostreatus ASI2792 mycovirus (PoV-ASI2792) was cloned, and a cDNA sequences alignment revealed that the sequence was identical to the RdRp gene of a known PoSV found in the P. ostreatus strain. To investigate the symptoms of PoV-ASI2792 infection by comparing the isogenic virus-free P. ostreatus strains with a virus-infected strain, isogenic virus-cured P. ostreatus strains were obtained by the mycelial fragmentation method for virus curing. The absence of virus was verified with gel electrophoresis after dsRNA-specific virus purification and Northern blot analysis using a partial RdRp cDNA of PoV-ASI2792. The growth rate and mycelial dry weight of virus-infected P. ostreatus strain with PoV-ASI2792 mycovirus were compared to those of three virus-free isogenic strains on 10 different media. The virus-cured strains showed distinctly higher mycelial growth rates and dry weights on all kinds of experimental culture media, with at least a 2.2-fold higher mycelial growth rate on mushroom complete media (MCM) and Hamada media, and a 2.7-fold higher mycelial dry weight on MCM and yeastmalt-glucose agar media than those of the virus-infected strain. These results suggest that the infection of PoV mycovirus has a deleterious effect on the vegetative growth of P. ostreatus.

  9. GPS Control Segment Improvements

    Science.gov (United States)

    2015-04-29

    Systems Center GPS Control Segment Improvements Mr. Tim McIntyre GPS Product Support Manager GPS Ops Support and Sustainment Division Peterson...DATE 29 APR 2015 2. REPORT TYPE 3. DATES COVERED 00-00-2015 to 00-00-2015 4. TITLE AND SUBTITLE GPS Control Segment Improvements 5a. CONTRACT...ORGANIZATION NAME(S) AND ADDRESS(ES) Air Force Space Command,Space and Missile Systems Center, GPS Ops Support and Sustainment Division,Peterson AFB,CO,80916 8

  10. Statistical Images Segmentation

    Directory of Open Access Journals (Sweden)

    Corina Curilă

    2008-05-01

    Full Text Available This paper deals with fuzzy statistical imagesegmentation. We introduce a new hierarchicalMarkovian fuzzy hidden field model, which extends to thefuzzy case the classical Pérez and Heitz hard model. Twofuzzy statistical segmentation methods related with themodel proposed are defined in this paper and we show viasimulations that they are competitive with, in some casesthan, the classical Maximum Posterior Mode (MPMbased methods. Furthermore, they are faster, which willshould facilitate extensions to more than two hard classesin future work. In addition, the model proposed isapplicable to the multiscale segmentation andmultiresolution images fusion problems.

  11. Sipunculans and segmentation

    DEFF Research Database (Denmark)

    Wanninger, Andreas; Kristof, Alen; Brinkmann, Nora

    2009-01-01

    Comparative molecular, developmental and morphogenetic analyses show that the three major segmented animal groups- Lophotrochozoa, Ecdysozoa and Vertebrata-use a wide range of ontogenetic pathways to establish metameric body organization. Even in the life history of a single specimen, different m...

  12. [Segmental testicular infarction].

    Science.gov (United States)

    Ripa Saldías, L; Guarch Troyas, R; Hualde Alfaro, A; de Pablo Cárdenas, A; Ruiz Ramo, M; Pinós Paul, M

    2006-02-01

    We report the case of a 47 years old man previously diagnosed of left hidrocele. After having a recent mild left testicular pain, an ultrasonografic study revealed a solid hipoecoic testicular lesion rounded by a big hidrocele, suggesting a testicular neoplasm. Radical inguinal orchiectomy was made and pathologic study showed segmental testicular infarction. No malignancy was found. We review the literature of the topic.

  13. Dictionary Based Image Segmentation

    DEFF Research Database (Denmark)

    Dahl, Anders Bjorholm; Dahl, Vedrana Andersen

    2015-01-01

    We propose a method for weakly supervised segmentation of natural images, which may contain both textured or non-textured regions. Our texture representation is based on a dictionary of image patches. To divide an image into separated regions with similar texture we use an implicit level sets...

  14. Potential for La Crosse virus segment reassortment in nature

    Science.gov (United States)

    Reese, Sara M; Blitvich, Bradley J; Blair, Carol D; Geske, Dave; Beaty, Barry J; Black, William C

    2008-01-01

    The evolutionary success of La Crosse virus (LACV, family Bunyaviridae) is due to its ability to adapt to changing conditions through intramolecular genetic changes and segment reassortment. Vertical transmission of LACV in mosquitoes increases the potential for segment reassortment. Studies were conducted to determine if segment reassortment was occurring in naturally infected Aedes triseriatus from Wisconsin and Minnesota in 2000, 2004, 2006 and 2007. Mosquito eggs were collected from various sites in Wisconsin and Minnesota. They were reared in the laboratory and adults were tested for LACV antigen by immunofluorescence assay. RNA was isolated from the abdomen of infected mosquitoes and portions of the small (S), medium (M) and large (L) viral genome segments were amplified by RT-PCR and sequenced. Overall, the viral sequences from 40 infected mosquitoes and 5 virus isolates were analyzed. Phylogenetic and linkage disequilibrium analyses revealed that approximately 25% of infected mosquitoes and viruses contained reassorted genome segments, suggesting that LACV segment reassortment is frequent in nature. PMID:19114023

  15. Potential for La Crosse virus segment reassortment in nature

    Directory of Open Access Journals (Sweden)

    Geske Dave

    2008-12-01

    Full Text Available Abstract The evolutionary success of La Crosse virus (LACV, family Bunyaviridae is due to its ability to adapt to changing conditions through intramolecular genetic changes and segment reassortment. Vertical transmission of LACV in mosquitoes increases the potential for segment reassortment. Studies were conducted to determine if segment reassortment was occurring in naturally infected Aedes triseriatus from Wisconsin and Minnesota in 2000, 2004, 2006 and 2007. Mosquito eggs were collected from various sites in Wisconsin and Minnesota. They were reared in the laboratory and adults were tested for LACV antigen by immunofluorescence assay. RNA was isolated from the abdomen of infected mosquitoes and portions of the small (S, medium (M and large (L viral genome segments were amplified by RT-PCR and sequenced. Overall, the viral sequences from 40 infected mosquitoes and 5 virus isolates were analyzed. Phylogenetic and linkage disequilibrium analyses revealed that approximately 25% of infected mosquitoes and viruses contained reassorted genome segments, suggesting that LACV segment reassortment is frequent in nature.

  16. Family genome browser: visualizing genomes with pedigree information.

    Science.gov (United States)

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Segmentation in Tardigrada and diversification of segmental patterns in Panarthropoda.

    Science.gov (United States)

    Smith, Frank W; Goldstein, Bob

    2016-10-31

    The origin and diversification of segmented metazoan body plans has fascinated biologists for over a century. The superphylum Panarthropoda includes three phyla of segmented animals-Euarthropoda, Onychophora, and Tardigrada. This superphylum includes representatives with relatively simple and representatives with relatively complex segmented body plans. At one extreme of this continuum, euarthropods exhibit an incredible diversity of serially homologous segments. Furthermore, distinct tagmosis patterns are exhibited by different classes of euarthropods. At the other extreme, all tardigrades share a simple segmented body plan that consists of a head and four leg-bearing segments. The modular body plans of panarthropods make them a tractable model for understanding diversification of animal body plans more generally. Here we review results of recent morphological and developmental studies of tardigrade segmentation. These results complement investigations of segmentation processes in other panarthropods and paleontological studies to illuminate the earliest steps in the evolution of panarthropod body plans.

  18. Organizational heterogeneity of vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  19. Organizational heterogeneity of vertebrate genomes.

    Science.gov (United States)

    Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

    2012-01-01

    Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  20. Market segmentation: Venezuelan ADRs

    Directory of Open Access Journals (Sweden)

    Urbi Garay

    2012-12-01

    Full Text Available The control on foreign exchange imposed by Venezuela in 2003 constitute a natural experiment that allows researchers to observe the effects of exchange controls on stock market segmentation. This paper provides empirical evidence that although the Venezuelan capital market as a whole was highly segmented before the controls were imposed, the shares in the firm CANTV were, through their American Depositary Receipts (ADRs, partially integrated with the global market. Following the imposition of the exchange controls this integration was lost. Research also documents the spectacular and apparently contradictory rise experienced by the Caracas Stock Exchange during the serious economic crisis of 2003. It is argued that, as it happened in Argentina in 2002, the rise in share prices occurred because the depreciation of the Bolívar in the parallel currency market increased the local price of the stocks that had associated ADRs, which were negotiated in dollars.

  1. Segmentation Using Symmetry Deviation

    DEFF Research Database (Denmark)

    Hollensen, Christian; Højgaard, L.; Specht, L.;

    2011-01-01

    segmentations on manual contours was evaluated using concordance index and sensitivity for the hypopharyngeal patients. The resulting concordance index and sensitivity was compared with the result of using a threshold of 3 SUV using a paired t-test. Results: The anatomical and symmetrical atlas was constructed...... and sensitivity of respectively 0.43±0.15 and 0.56±0.18 was acquired. It was compared to the concordance index of segmentation using absolute threshold of 3 SUV giving respectively 0.41±0.16 and 0.51±0.19 for concordance index and sensitivity yielding p-values of 0.33 and 0.01 for a paired t-test respectively....

  2. Connecting textual segments

    DEFF Research Database (Denmark)

    Brügger, Niels

    2017-01-01

    In “Connecting textual segments: A brief history of the web hyperlink” Niels Brügger investigates the history of one of the most fundamental features of the web: the hyperlink. Based on the argument that the web hyperlink is best understood if it is seen as another step in a much longer and broader......-alone computers and in local and global digital networks....

  3. Cloning of genomic sequences of three crustacean hyperglycemic hormone superfamily genes and elucidation of their roles of regulating insulin-like androgenic gland hormone gene.

    Science.gov (United States)

    Li, Fajun; Bai, Hongkun; Zhang, Wenyi; Fu, Hongtuo; Jiang, Fengwei; Liang, Guoxia; Jin, Shubo; Sun, Shengming; Qiao, Hui

    2015-04-25

    The insulin-like androgenic gland hormone (IAG) gene in crustaceans plays an important role in male sexual differentiation, metabolism, and growth. However, the upstream regulation of IAG signaling schemes remains poorly studied. In the present study, we cloned the 5' flanking sequence of IAG and full-length genomic sequences of gonad-inhibiting hormone (Mn-GIH), molt-inhibiting hormone (Mn-MIH) and crustacean hyperglycemic hormone (Mn-CHH) in Macrobrachium nipponense. We identified the transcription factor-binding sites in the 5' flanking sequence of IAG and investigated the exon-intron patterns of the three CHH superfamily genes. Each CHH superfamily gene consisted of two introns separating three exons. Mn-GIH and Mn-MIH shared the same intron insertion sites, which differed from Mn-CHH. We provided DNA-level evidence for the type definition. We also identified two cAMP response elements in the 5' untranslated region. We further investigated the regulatory relationships between Mn-GIH, Mn-MIH, and Mn-CHH and IAG at the transcriptional level by injection of double-stranded RNA (dsRNA). IAG transcription levels were significantly increased to 660.2%, 472.9%, and 112.4% of control levels in the Mn-GIH dsRNA, Mn-MIH dsRNA, and Mn-CHH dsRNA groups, respectively. The results clearly demonstrated that Mn-GIH and Mn-MIH, but not Mn-CHH, negatively regulate the expression of the IAG gene. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Market segmentation in behavioral perspective.

    OpenAIRE

    Wells, V.K.; Chang, S. W.; Oliveira-Castro, J.M.; Pallister, J.

    2010-01-01

    A segmentation approach is presented using both traditional demographic segmentation bases (age, social class/occupation, and working status) and a segmentation by benefits sought. The benefits sought in this case are utilitarian and informational reinforcement, variables developed from the Behavioral Perspective Model (BPM). Using data from 1,847 consumers and from a total of 76,682 individual purchases, brand choice and price and reinforcement responsiveness were assessed for each segment a...

  5. Market Segmentation for Information Services.

    Science.gov (United States)

    Halperin, Michael

    1981-01-01

    Discusses the advantages and limitations of market segmentation as strategy for the marketing of information services made available by nonprofit organizations, particularly libraries. Market segmentation is defined, a market grid for libraries is described, and the segmentation of information services is outlined. A 16-item reference list is…

  6. Segmenting the Adult Education Market.

    Science.gov (United States)

    Aurand, Tim

    1994-01-01

    Describes market segmentation and how the principles of segmentation can be applied to the adult education market. Indicates that applying segmentation techniques to adult education programs results in programs that are educationally and financially satisfying and serve an appropriate population. (JOW)

  7. Market Segmentation for Information Services.

    Science.gov (United States)

    Halperin, Michael

    1981-01-01

    Discusses the advantages and limitations of market segmentation as strategy for the marketing of information services made available by nonprofit organizations, particularly libraries. Market segmentation is defined, a market grid for libraries is described, and the segmentation of information services is outlined. A 16-item reference list is…

  8. Segmenting the Adult Education Market.

    Science.gov (United States)

    Aurand, Tim

    1994-01-01

    Describes market segmentation and how the principles of segmentation can be applied to the adult education market. Indicates that applying segmentation techniques to adult education programs results in programs that are educationally and financially satisfying and serve an appropriate population. (JOW)

  9. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  10. Signs of segmentation?

    DEFF Research Database (Denmark)

    Ilsøe, Anna

    2012-01-01

    This article addresses the contribution of decentralized collective bargaining to the development of different forms of flexicurity for different groups of employees on the Danish labour market. Based on five case studies of company-level bargaining on flexible working hours in Danish industry...... the text of the agreements. On the other hand, less flexible employees often face difficulties in meeting the demands of the agreements and may ultimately be forced to leave the company and rely on unemployment benefits and active labour market policies. In a flexicurity perspective, this development seems...... to imply a segmentation of the Danish workforce regarding hard and soft versions of flexicurity....

  11. Noncooperative Iris Segmentation

    Directory of Open Access Journals (Sweden)

    Elsayed Mostafa

    2012-01-01

    Full Text Available In noncooperative iris recognition one should deal with uncontrolled behavior of the subject as well as uncontrolled lighting conditions. That means eyelids and eyelashes occlusion, non uniform intensities, reflections, imperfect focus, and orientation among the others are to be considered. To cope with this situation a noncooperative iris segmentation algorithm based on numerically stable direct least squares fitting of ellipses model and modified Chan-Vese model (local binary fitting energy with variational level set formulation is to be proposed. The proposed algorithm is tested using CASIA-IrisV3.

  12. The LOFT Ground Segment

    DEFF Research Database (Denmark)

    Bozzo, E.; Antonelli, A.; Argan, A.;

    2014-01-01

    targets per orbit (~90 minutes), providing roughly ~80 GB of proprietary data per day (the proprietary period will be 12 months). The WFM continuously monitors about 1/3 of the sky at a time and provides data for about ~100 sources a day, resulting in a total of ~20 GB of additional telemetry. The LOFT...... we summarize the planned organization of the LOFT ground segment (GS), as established in the mission Yellow Book 1 . We describe the expected GS contributions from ESA and the LOFT consortium. A review is provided of the planned LOFT data products and the details of the data flow, archiving...

  13. The complete nucleotide sequence and genome organization of pea streak virus (genus Carlavirus).

    Science.gov (United States)

    Su, Li; Li, Zhengnan; Bernardy, Mike; Wiersma, Paul A; Cheng, Zhihui; Xiang, Yu

    2015-10-01

    Pea streak virus (PeSV) is a member of the genus Carlavirus in the family Betaflexiviridae. Here, the first complete genome sequence of PeSV was determined by deep sequencing of a cDNA library constructed from dsRNA extracted from a PeSV-infected sample and Rapid Amplification of cDNA Ends (RACE) PCR. The PeSV genome consists of 8041 nucleotides excluding the poly(A) tail and contains six open reading frames (ORFs). The putative peptide encoded by the PeSV ORF6 has an estimated molecular mass of 6.6 kDa and shows no similarity to any known proteins. This differs from typical carlaviruses, whose ORF6 encodes a 12- to 18-kDa cysteine-rich nucleic-acid-binding protein.

  14. Genomic disorders: A window into human gene and genome evolution

    Science.gov (United States)

    Carvalho, Claudia M. B.; Zhang, Feng; Lupski, James R.

    2010-01-01

    Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events. PMID:20080665

  15. Segmented Target Design

    Science.gov (United States)

    Merhi, Abdul Rahman; Frank, Nathan; Gueye, Paul; Thoennessen, Michael; MoNA Collaboration

    2013-10-01

    A proposed segmented target would improve decay energy measurements of neutron-unbound nuclei. Experiments like this have been performed at the National Superconducting Cyclotron Laboratory (NSCL) located at Michigan State University. Many different nuclei are produced in such experiments, some of which immediately decay into a charged particle and neutron. The charged particles are bent by a large magnet and measured by a suite of charged particle detectors. The neutrons are measured by the Modular Neutron Array (MoNA) and Large Multi-Institutional Scintillation Array (LISA). With the current target setup, a nucleus in a neutron-unbound state is produced with a radioactive beam impinged upon a beryllium target. The resolution of these measurements is very dependent on the target thickness since the nuclear interaction point is unknown. In a segmented target using alternating layers of silicon detectors and Be-targets, the Be-target in which the nuclear reaction takes place would be determined. Thus the experimental resolution would improve. This poster will describe the improvement over the current target along with the status of the design. Work supported by Augustana College and the National Science Foundation grant #0969173.

  16. Localizing introgression on the chromosome of rice by genomic in ...

    African Journals Online (AJOL)

    USER

    2010-07-26

    Jul 26, 2010 ... 1Department of Genetics, Hazara University, Garden Campus, Mansehra, Pakistan. ... Genomic in situ hybridization was used to detect introgressed segment .... Gene transfer and molecular characterization of introgression.

  17. Segmentation of the Infant Food Market

    OpenAIRE

    Hrůzová, Daniela

    2015-01-01

    The theoretical part covers general market segmentation, namely the marketing importance of differences among consumers, the essence of market segmentation, its main conditions and the process of segmentation, which consists of four consecutive phases - defining the market, determining important criteria, uncovering segments and developing segment profiles. The segmentation criteria, segmentation approaches, methods and techniques for the process of market segmentation are also described in t...

  18. Segmentation of the Infant Food Market

    OpenAIRE

    Hrůzová, Daniela

    2015-01-01

    The theoretical part covers general market segmentation, namely the marketing importance of differences among consumers, the essence of market segmentation, its main conditions and the process of segmentation, which consists of four consecutive phases - defining the market, determining important criteria, uncovering segments and developing segment profiles. The segmentation criteria, segmentation approaches, methods and techniques for the process of market segmentation are also described in t...

  19. Cucumis melo endornavirus: Genome organization, host range and co-divergence with the host.

    Science.gov (United States)

    Sabanadzovic, Sead; Wintermantel, William M; Valverde, Rodrigo A; McCreight, James D; Aboughanem-Sabanadzovic, Nina

    2016-03-02

    A high molecular weight dsRNA was isolated from a Cucumis melo L. plant (referred to as 'CL01') of an unknown cultivar and completely sequenced. Sequence analyses showed that dsRNA is associated with an endornavirus for which a name Cucumis melo endornavirus (CmEV) is proposed. The genome of CmEV-CL01 consists of 15,078 nt, contains a single, 4939 codons-long ORF and terminates with a stretch of 10 cytosine residues. Comparisons of the putative CmEV-encoded polyprotein with available references in protein databases revealed a unique genome organization characterized by the presence of the following domains: viral helicase Superfamily 1 (Hel-1), three glucosyltransferases (doublet of putative capsular polysaccharide synthesis proteins and a putative C_28_Glycosyltransferase), and an RNA-dependent RNA polymerase (RdRp). The presence of three glycome-related domains of different origin makes the genome organization of CmEV unique among endornaviruses. Phylogenetic analyses of viral RdRp domains showed that CmEV belongs to a specific lineage within the family Endornaviridae made exclusively of plant-infecting endornaviruses. An RT-PCR based survey demonstrated high incidence of CmEV among melon germplasm accession (>87% of tested samples). Analyses of partial genome sequences of CmEV isolates from 26 different melon genotypes suggest fine-tuned virus adaptation and co-divergence with the host. Finally, results of the present study revealed that CmEV is present in plants belonging to three different genera in the family Cucurbitaceae. Such diverse host range is unreported for known endornaviruses and suggests a long history of CmEV association with cucurbits predating their speciation.

  20. Segmented heat exchanger

    Science.gov (United States)

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  1. Probabilistic retinal vessel segmentation

    Science.gov (United States)

    Wu, Chang-Hua; Agam, Gady

    2007-03-01

    Optic fundus assessment is widely used for diagnosing vascular and non-vascular pathology. Inspection of the retinal vasculature may reveal hypertension, diabetes, arteriosclerosis, cardiovascular disease and stroke. Due to various imaging conditions retinal images may be degraded. Consequently, the enhancement of such images and vessels in them is an important task with direct clinical applications. We propose a novel technique for vessel enhancement in retinal images that is capable of enhancing vessel junctions in addition to linear vessel segments. This is an extension of vessel filters we have previously developed for vessel enhancement in thoracic CT scans. The proposed approach is based on probabilistic models which can discern vessels and junctions. Evaluation shows the proposed filter is better than several known techniques and is comparable to the state of the art when evaluated on a standard dataset. A ridge-based vessel tracking process is applied on the enhanced image to demonstrate the effectiveness of the enhancement filter.

  2. Automated medical image segmentation techniques

    Directory of Open Access Journals (Sweden)

    Sharma Neeraj

    2010-01-01

    Full Text Available Accurate segmentation of medical images is a key step in contouring during radiotherapy planning. Computed topography (CT and Magnetic resonance (MR imaging are the most widely used radiographic techniques in diagnosis, clinical studies and treatment planning. This review provides details of automated segmentation methods, specifically discussed in the context of CT and MR images. The motive is to discuss the problems encountered in segmentation of CT and MR images, and the relative merits and limitations of methods currently available for segmentation of medical images.

  3. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    Directory of Open Access Journals (Sweden)

    Gendrault-Jacquemard A

    2005-07-01

    Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

  4. Automatic segmentation of pulmonary segments from volumetric chest CT scans.

    NARCIS (Netherlands)

    Rikxoort, E.M. van; Hoop, B. de; Vorst, S. van de; Prokop, M.; Ginneken, B. van

    2009-01-01

    Automated extraction of pulmonary anatomy provides a foundation for computerized analysis of computed tomography (CT) scans of the chest. A completely automatic method is presented to segment the lungs, lobes and pulmonary segments from volumetric CT chest scans. The method starts with lung segmenta

  5. Shape-Memory Properties of Segmented Polymers Containing Aramid Hard Segments and Polycaprolactone Soft Segments

    Directory of Open Access Journals (Sweden)

    Arno Kraft

    2010-06-01

    Full Text Available A series of segmented multiblock copolymers containing aramid hard segments and extended polycaprolactone soft segments (with an Mn of 4,200 or 8,200 g mol–1 was prepared and tested for their shape-memory properties. Chain extenders were essential to raise the hard segment concentration so that an extended rubbery plateau could be observed. Dynamic mechanical thermal analysis provided a useful guide in identifying (i the presence of a rubbery plateau, (ii the flow temperature, and (iii the temperature when samples started to deform irreversibly.

  6. Electronic transport in double-strand DNA segments

    Science.gov (United States)

    Albuquerque, E. L.; Mauriz, P. W.; Moreira, D. A.

    2008-03-01

    We report in this work a numerical study of the electronic density of states in π-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  7. Electronic transport in double-strand DNA segments

    Energy Technology Data Exchange (ETDEWEB)

    Albuquerque, E L; Moreira, D A [Departamento de Fisica, Universidade Federal do Rio Grande do Norte 59072-970 Natal-RN (Brazil); Mauriz, P W [Departamento de Ciencias Exatas, Centro Federal de Educacao Tecnologica do Maranhao 65025-001 Sao Luis-MA (Brazil)], E-mail: eudenilson@dfte.ufrn.br

    2008-03-15

    We report in this work a numerical study of the electronic density of states in {pi}-stacked arrays of DNA double-strand segments made up from the nucleotides guanine G, adenine A, cytosine C and thymine T. In order to reveal the relevance of the underlying correlations in the nucleotides distribution, we compare the results for a genomic DNA sequence, considering a segment of the first sequenced human chromosome 22 (Ch 22), with those of two artificial sequences forming a Rudin-Shapiro (RS) as well as a Fibonacci (FB) polyGC quasiperiodic sequences. Our theoretical method uses an electronic tight-binding Hamiltonian suitable to describe the DNA segments modeled by the quasiperiodic chains.

  8. Optimally segmented permanent magnet structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bjørk, Rasmus; Smith, Anders

    2016-01-01

    We present an optimization approach which can be employed to calculate the globally optimal segmentation of a two-dimensional magnetic system into uniformly magnetized pieces. For each segment the algorithm calculates the optimal shape and the optimal direction of the remanent flux density vector...

  9. Upper medium segment cooling down

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    <正>The sluggish growth of the passenger car market in top provinces was also reflected in a depression of the upper medium segment. In Jan-Apr, 2008, the top 3 upper medium models accounting for nearly 40% of this segment performed poorly, with the Passat-Lingyu and the Accord decreasing. The Camry also saw a decrease in three top provinces: Guangdong,

  10. Essays in International Market Segmentation

    NARCIS (Netherlands)

    Hofstede, ter F.

    1999-01-01

    The primary objective of this thesis is to develop and validate new methodologies to improve the effectiveness of international segmentation strategies. The current status of international market segmentation research is reviewed in an introductory chapter, which provided a number of methodological

  11. Adaptive Segmentation for Scientific Databases

    NARCIS (Netherlands)

    Ivanova, M.G.; Kersten, M.L.; Nes, N.J.

    2008-01-01

    In this paper we explore database segmentation in the context of a column-store DBMS targeted at a scientific database. We present a novel hardware- and scheme-oblivious segmentation algorithm, which learns and adapts to the workload immediately. The approach taken is to capitalize on (intermediate)

  12. Dermatology case: segmental lichen aureus

    OpenAIRE

    Fernandes, I.; S. Carvalho; Machado, S.; Alves,R.; Selores, M.

    2012-01-01

    ABSTRACT The authors describe a clinical case of a six-year-old boy with history of a segmental brownish maculopapular skin eruption on his left thoracic and lumbar wall, since the last four months. Based on clinical and histological findings he was diagnosed with segmental lichen aureus.

  13. Essays in international market segmentation

    NARCIS (Netherlands)

    Hofstede, ter F.

    1999-01-01

    The primary objective of this thesis is to develop and validate new methodologies to improve the effectiveness of international segmentation strategies. The current status of international market segmentation research is reviewed in an introductory chapter, which provided a number of

  14. Adaptive segmentation for scientific databases

    NARCIS (Netherlands)

    Ivanova, M.; Kersten, M.L.; Nes, N.

    2008-01-01

    In this paper we explore database segmentation in the context of a column-store DBMS targeted at a scientific database. We present a novel hardware- and scheme-oblivious segmentation algorithm, which learns and adapts to the workload immediately. The approach taken is to capitalize on (intermediate)

  15. Market segmentation using perceived constraints

    Science.gov (United States)

    Jinhee Jun; Gerard Kyle; Andrew Mowen

    2008-01-01

    We examined the practical utility of segmenting potential visitors to Cleveland Metroparks using their constraint profiles. Our analysis identified three segments based on their scores on the dimensions of constraints: Other priorities--visitors who scored the highest on 'other priorities' dimension; Highly Constrained--visitors who scored relatively high on...

  16. The Importance of Marketing Segmentation

    Science.gov (United States)

    Martin, Gillian

    2011-01-01

    The rationale behind marketing segmentation is to allow businesses to focus on their consumers' behaviors and purchasing patterns. If done effectively, marketing segmentation allows an organization to achieve its highest return on investment (ROI) in turn for its marketing and sales expenses. If an organization markets its products or services to…

  17. Market Segmentation: An Instructional Module.

    Science.gov (United States)

    Wright, Peter H.

    A concept-based introduction to market segmentation is provided in this instructional module for undergraduate and graduate transportation-related courses. The material can be used in many disciplines including engineering, business, marketing, and technology. The concept of market segmentation is primarily a transportation planning technique by…

  18. Segmentation: Slicing the Urban Pie.

    Science.gov (United States)

    Keim, William A.

    1981-01-01

    Explains market segmentation and defines undifferentiated, concentrated, and differentiated marketing strategies. Describes in detail the marketing planning process at the Metropolitan Community Colleges. Focuses on the development and implementation of an ongoing recruitment program designed for the market segment composed of business employees.…

  19. Adaptive segmentation for scientific databases

    NARCIS (Netherlands)

    Ivanova, M.; Kersten, M.L.; Nes, N.

    2008-01-01

    In this paper we explore database segmentation in the context of a column-store DBMS targeted at a scientific database. We present a novel hardware- and scheme-oblivious segmentation algorithm, which learns and adapts to the workload immediately. The approach taken is to capitalize on (intermediate)

  20. The LOFT Ground Segment

    CERN Document Server

    Bozzo, E; Argan, A; Barret, D; Binko, P; Brandt, S; Cavazzuti, E; Courvoisier, T; Herder, J W den; Feroci, M; Ferrigno, C; Giommi, P; Götz, D; Guy, L; Hernanz, M; Zand, J J M in't; Klochkov, D; Kuulkers, E; Motch, C; Lumb, D; Papitto, A; Pittori, C; Rohlfs, R; Santangelo, A; Schmid, C; Schwope, A D; Smith, P J; Webb, N A; Wilms, J; Zane, S

    2014-01-01

    LOFT, the Large Observatory For X-ray Timing, was one of the ESA M3 mission candidates that completed their assessment phase at the end of 2013. LOFT is equipped with two instruments, the Large Area Detector (LAD) and the Wide Field Monitor (WFM). The LAD performs pointed observations of several targets per orbit (~90 minutes), providing roughly ~80 GB of proprietary data per day (the proprietary period will be 12 months). The WFM continuously monitors about 1/3 of the sky at a time and provides data for about ~100 sources a day, resulting in a total of ~20 GB of additional telemetry. The LOFT Burst alert System additionally identifies on-board bright impulsive events (e.g., Gamma-ray Bursts, GRBs) and broadcasts the corresponding position and trigger time to the ground using a dedicated system of ~15 VHF receivers. All WFM data are planned to be made public immediately. In this contribution we summarize the planned organization of the LOFT ground segment (GS), as established in the mission Yellow Book 1 . We...

  1. Evolution of segmented strings

    CERN Document Server

    Gubser, Steven S

    2016-01-01

    I explain how to evolve segmented strings in de Sitter and anti-de Sitter spaces of any dimension in terms of forward-directed null displacements. The evolution is described entirely in terms of discrete hops which do not require a continuum spacetime. Moreover, the evolution rule is purely algebraic, so it can be defined not only on ordinary real de Sitter and anti-de Sitter, but also on the rational points of the quadratic equations that define these spaces. For three-dimensional anti-de Sitter space, a simpler evolution rule is possible that descends from the Wess-Zumino-Witten equations of motion. In this case, one may replace three-dimensional anti-de Sitter space by a non-compact discrete subgroup of SL(2,R) whose structure is related to the Pell equation. A discrete version of the BTZ black hole can be constructed as a quotient of this subgroup. This discrete black hole avoids the firewall paradox by a curious mechanism: even for large black holes, there are no points inside the horizon until one reach...

  2. Segment Based Camera Calibration

    Institute of Scientific and Technical Information of China (English)

    马颂德; 魏国庆; 等

    1993-01-01

    The basic idea of calibrating a camera system in previous approaches is to determine camera parmeters by using a set of known 3D points as calibration reference.In this paper,we present a method of camera calibration in whih camera parameters are determined by a set of 3D lines.A set of constraints is derived on camea parameters in terms of perspective line mapping.Form these constraints,the same perspective transformation matrix as that for point mapping can be computed linearly.The minimum number of calibration lines is 6.This result generalizes that of Liu,Huang and Faugeras[12] for camera location determination in which at least 8 line correspondences are required for linear computation of camera location.Since line segments in an image can be located easily and more accurately than points,the use of lines as calibration reference tends to ease the computation in inage preprocessing and to improve calibration accuracy.Experimental results on the calibration along with stereo reconstruction are reported.

  3. The CGView Server: a comparative genomics tool for circular genomes.

    Science.gov (United States)

    Grant, Jason R; Stothard, Paul

    2008-07-01

    The CGView Server generates graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots. Sequences can be supplied in raw, FASTA, GenBank or EMBL format. Additional feature or analysis information can be submitted in the form of GFF (General Feature Format) files. The server uses BLAST to compare the primary sequence to up to three comparison genomes or sequence sets. The BLAST results and feature information are converted to a graphical map showing the entire sequence, or an expanded and more detailed view of a region of interest. Several options are included to control which types of features are displayed and how the features are drawn. The CGView Server can be used to visualize features associated with any bacterial, plasmid, chloroplast or mitochondrial genome, and can aid in the identification of conserved genome segments, instances of horizontal gene transfer, and differences in gene copy number. Because a collection of sequences can be used in place of a comparison genome, maps can also be used to visualize regions of a known genome covered by newly obtained sequence reads. The CGView Server can be accessed at http://stothard.afns.ualberta.ca/cgview_server/

  4. Signals of historical interlocus gene conversion in human segmental duplications.

    Directory of Open Access Journals (Sweden)

    Beth L Dumont

    Full Text Available Standard methods of DNA sequence analysis assume that sequences evolve independently, yet this assumption may not be appropriate for segmental duplications that exchange variants via interlocus gene conversion (IGC. Here, we use high quality multiple sequence alignments from well-annotated segmental duplications to systematically identify IGC signals in the human reference genome. Our analysis combines two complementary methods: (i a paralog quartet method that uses DNA sequence simulations to identify a statistical excess of sites consistent with inter-paralog exchange, and (ii the alignment-based method implemented in the GENECONV program. One-quarter (25.4% of the paralog families in our analysis harbor clear IGC signals by the quartet approach. Using GENECONV, we identify 1477 gene conversion tracks that cumulatively span 1.54 Mb of the genome. Our analyses confirm the previously reported high rates of IGC in subtelomeric regions and Y-chromosome palindromes, and identify multiple novel IGC hotspots, including the pregnancy specific glycoproteins and the neuroblastoma breakpoint gene families. Although the duplication history of a paralog family is described by a single tree, we show that IGC has introduced incredible site-to-site variation in the evolutionary relationships among paralogs in the human genome. Our findings indicate that IGC has left significant footprints in patterns of sequence diversity across segmental duplications in the human genome, out-pacing the contributions of single base mutation by orders of magnitude. Collectively, the IGC signals we report comprise a catalog that will provide a critical reference for interpreting observed patterns of DNA sequence variation across duplicated genomic regions, including targets of recent adaptive evolution in humans.

  5. Full Genome Sequence of Giant Panda Rotavirus Strain CH-1

    Science.gov (United States)

    Guo, Ling; Yang, Shaolin; Wang, Chengdong; Chen, Shijie; Yang, Xiaonong; Hou, Rong; Quan, Zifang; Hao, Zhongxiang

    2013-01-01

    We report here the complete genomic sequence of the giant panda rotavirus strain CH-1. This work is the first to document the complete genomic sequence (segments 1 to 11) of the CH-1 strain, which offers an effective platform for providing authentic research experiences to novice scientists. PMID:23469354

  6. Genomics of Escherichia and Shigella

    Science.gov (United States)

    Perna, Nicole T.

    The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

  7. Sometimes spelling is easier than phonemic segmentation

    NARCIS (Netherlands)

    Bon, W.H.J. van; Duighuisen, H.C.M.

    1995-01-01

    Poor spellers from the Netherlands segmented and spelled the same words on different occasions. If they base their spellings on the segmentations that they produce in the segmentation task, the correlation between segmentation and spelling scores should be high, and segmentation should not be more d

  8. A Segmental Framework for Representing Signs Phonetically

    Science.gov (United States)

    Johnson, Robert E.; Liddell, Scott K.

    2011-01-01

    The arguments for dividing the signing stream in signed languages into sequences of phonetic segments are compelling. The visual records of instances of actually occurring signs provide evidence of two basic types of segments: postural segments and trans-forming segments. Postural segments specify an alignment of articulatory features, both manual…

  9. Genetic modification of mammalian genome at chromosome level

    Directory of Open Access Journals (Sweden)

    OLEG L. SEROV

    2000-09-01

    Full Text Available The review is concerned with a progress in genetic modification of a mammalian genome in vitro and in vivo at chromosomal level. Recently three new approaches for the chromosome biotechnology have been developed: Using Cre/loxP-system a researcher is able to produce targeted rearrangements of whole chromosomes or their segments or particular genes within the genome, and therefore to modify the set, position and copy number of the endogenous elements of the genome. Mammalian artificial chromosomes (MACs provide a possibility to introduce into genome relatively large segments of alien chromosome material, either artificially constructed or derived from the genome of different species. Using ES-somatic cell hybrids allows to transfer whole chromosomes or their fragments between different genomes within and between species. Advantages and limitations of these approaches are discussed.

  10. Forces shaping the fastest evolving regions in the human genome

    DEFF Research Database (Denmark)

    Pollard, Katherine S; Salama, Sofie R; King, Bryan;

    2006-01-01

    Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202 gen...... contributed to accelerated evolution of the fastest evolving elements in the human genome.......Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202...... genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements...

  11. Multiatlas segmentation as nonparametric regression.

    Science.gov (United States)

    Awate, Suyash P; Whitaker, Ross T

    2014-09-01

    This paper proposes a novel theoretical framework to model and analyze the statistical characteristics of a wide range of segmentation methods that incorporate a database of label maps or atlases; such methods are termed as label fusion or multiatlas segmentation. We model these multiatlas segmentation problems as nonparametric regression problems in the high-dimensional space of image patches. We analyze the nonparametric estimator's convergence behavior that characterizes expected segmentation error as a function of the size of the multiatlas database. We show that this error has an analytic form involving several parameters that are fundamental to the specific segmentation problem (determined by the chosen anatomical structure, imaging modality, registration algorithm, and label-fusion algorithm). We describe how to estimate these parameters and show that several human anatomical structures exhibit the trends modeled analytically. We use these parameter estimates to optimize the regression estimator. We show that the expected error for large database sizes is well predicted by models learned on small databases. Thus, a few expert segmentations can help predict the database sizes required to keep the expected error below a specified tolerance level. Such cost-benefit analysis is crucial for deploying clinical multiatlas segmentation systems.

  12. Antarctic Genomics

    Directory of Open Access Journals (Sweden)

    Alex D. Rogers

    2006-03-01

    Full Text Available With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies.

  13. Iris Pattern Segmentation using Automatic Segmentation and Window Technique

    OpenAIRE

    Swati Pandey; Prof. Rajeev Gupta

    2013-01-01

    A Biometric system is an automatic identification of an individual based on a unique feature or characteristic. Iris recognition has great advantage such as variability, stability and security. In thispaper, use the two methods for iris segmentation -An automatic segmentation method and Window method. Window method is a novel approach which comprises two steps first finds pupils' center andthen two radial coefficients because sometime pupil is not perfect circle. The second step extract the i...

  14. Principles of Video Segmentation Scenarios

    Directory of Open Access Journals (Sweden)

    M. R. KHAMMAR

    2013-05-01

    Full Text Available Video segmentation is the first step toward automatic video processing such as browsing, retrieval, and indexing. Many algorithms and techniques have been proposed a few years ago. They can cover the topic of video segmentation from different angles and it is beneficial to review the most important properties of them in brief in order to clarify the subject and find out the latest challenges and drawbacks. In this paper, the important parameters which are involved in video segmentation are discussed and video shot detection systems are compared together.

  15. Multiple Segmentation of Image Stacks

    DEFF Research Database (Denmark)

    Smets, Jonathan; Jaeger, Manfred

    2014-01-01

    We propose a method for the simultaneous construction of multiple image segmentations by combining a recently proposed “convolution of mixtures of Gaussians” model with a multi-layer hidden Markov random field structure. The resulting method constructs for a single image several, alternative...... segmentations that capture different structural elements of the image. We also apply the method to collections of images with identical pixel dimensions, which we call image stacks. Here it turns out that the method is able to both identify groups of similar images in the stack, and to provide segmentations...

  16. CHSMiner: a GUI tool to identify chromosomal homologous segments

    Directory of Open Access Journals (Sweden)

    Liu Lei

    2009-01-01

    Full Text Available Abstract Background The identification of chromosomal homologous segments (CHS within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs. Results Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source. Conclusion CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.

  17. An Active Contour for Range Image Segmentation

    OpenAIRE

    Khaldi Amine; Merouani Hayet Farida

    2012-01-01

    In this paper a new classification of range image segmentation method is proposed according to the criterion of homogeneity which obeys the segmentation, then, a deformable model-type active contour “Snake” is applied to segment range images.

  18. Ensemble segmentation using efficient integer linear programming.

    Science.gov (United States)

    Alush, Amir; Goldberger, Jacob

    2012-10-01

    We present a method for combining several segmentations of an image into a single one that in some sense is the average segmentation in order to achieve a more reliable and accurate segmentation result. The goal is to find a point in the "space of segmentations" which is close to all the individual segmentations. We present an algorithm for segmentation averaging. The image is first oversegmented into superpixels. Next, each segmentation is projected onto the superpixel map. An instance of the EM algorithm combined with integer linear programming is applied on the set of binary merging decisions of neighboring superpixels to obtain the average segmentation. Apart from segmentation averaging, the algorithm also reports the reliability of each segmentation. The performance of the proposed algorithm is demonstrated on manually annotated images from the Berkeley segmentation data set and on the results of automatic segmentation algorithms.

  19. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  20. Image Segmentation Based on Support Vector Machine

    Institute of Scientific and Technical Information of China (English)

    XU Hai-xiang; ZHU Guang-xi; TIAN Jin-wen; ZHANG Xiang; PENG Fu-yuan

    2005-01-01

    Image segmentation is a necessary step in image analysis. Support vector machine (SVM) approach is proposed to segment images and its segmentation performance is evaluated.Experimental results show that: the effects of kernel function and model parameters on the segmentation performance are significant; SVM approach is less sensitive to noise in image segmentation; The segmentation performance of SVM approach is better than that of back-propagation multi-layer perceptron (BP-MLP) approach and fuzzy c-means (FCM) approach.

  1. Accurate and Fast Iris Segmentation

    Directory of Open Access Journals (Sweden)

    G. AnnaPoorani,

    2010-06-01

    Full Text Available A novel iris segmentation approach for noisy iris is proposed in this paper. The proposed approach comprises of specular reflection removal, pupil localization, iris localization and eyelid localization. Reflection map computation is devised to get the reflection ROI of eye image using adaptive threshold technique. Bilinear interpolation is used to fill these reflection points in the eye image. Variant of edge-based segmentation technique is adopted to detect the pupil boundary from the eye image. Gradient based heuristic approach is devised to detect the iris boundary from theeye image. Eyelid localization is designed to detect the eyelids using the edge detection and curve fitting. Feature sequence combined into spatial domain segments the iris texture patterns properly. Empirical results show that the proposed approach is effective and suitable to deal with the noisy eye image for iris segmentation.

  2. Metrology of IXO Mirror Segments

    Science.gov (United States)

    Chan, Kai-Wing

    2011-01-01

    For future x-ray astrophysics mission that demands optics with large throughput and excellent angular resolution, many telescope concepts build around assembling thin mirror segments in a Wolter I geometry, such as that originally proposed for the International X-ray Observatory. The arc-second resolution requirement posts unique challenges not just for fabrication, mounting but also for metrology of these mirror segments. In this paper, we shall discuss the metrology of these segments using normal incidence metrological method with interferometers and null lenses. We present results of the calibration of the metrology systems we are currently using, discuss their accuracy and address the precision in measuring near-cylindrical mirror segments and the stability of the measurements.

  3. Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Lu Xin-Yan

    2009-11-01

    Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

  4. The Envisat-1 ground segment

    Science.gov (United States)

    Harris, Ray; Ashton, Martin

    1995-03-01

    The European Space Agency (ESA) Earth Remote Sensing Satellite (ERS-1 and ERS-2) missions will be followed by the Polar Orbit Earth Mission (POEM) program. The first of the POEM missions will be Envisat-1. ESA has completed the design phase of the ground segment. This paper presents the main elements of that design. The main part of this paper is an overview of the Payload Data Segment (PDS) which is the core of the Envisat-1 ground segment, followed by two further sections which describe in more detail the facilities to be offered by the PDS for archiving and for user servcies. A further section describes some future issues for ground segment development. Logica was the prime contractor of a team of 18 companies which undertook the ESA financed architectural design study of the Envisat-1 ground segment. The outputs of the study included detailed specifications of the components that will acquire, process, archive and disseminate the payload data, together with the functional designs of the flight operations and user data segments.

  5. Neural network for image segmentation

    Science.gov (United States)

    Skourikhine, Alexei N.; Prasad, Lakshman; Schlei, Bernd R.

    2000-10-01

    Image analysis is an important requirement of many artificial intelligence systems. Though great effort has been devoted to inventing efficient algorithms for image analysis, there is still much work to be done. It is natural to turn to mammalian vision systems for guidance because they are the best known performers of visual tasks. The pulse- coupled neural network (PCNN) model of the cat visual cortex has proven to have interesting properties for image processing. This article describes the PCNN application to the processing of images of heterogeneous materials; specifically PCNN is applied to image denoising and image segmentation. Our results show that PCNNs do well at segmentation if we perform image smoothing prior to segmentation. We use PCNN for obth smoothing and segmentation. Combining smoothing and segmentation enable us to eliminate PCNN sensitivity to the setting of the various PCNN parameters whose optimal selection can be difficult and can vary even for the same problem. This approach makes image processing based on PCNN more automatic in our application and also results in better segmentation.

  6. Medical image segmentation by MDP model

    Science.gov (United States)

    Lu, Yisu; Chen, Wufan

    2011-11-01

    MDP (Dirichlet Process Mixtures) model is applied to segment medical images in this paper. Segmentation can been automatically done without initializing segmentation class numbers. The MDP model segmentation algorithm is used to segment natural images and MR (Magnetic Resonance) images in the paper. To demonstrate the accuracy of the MDP model segmentation algorithm, many compared experiments, such as EM (Expectation Maximization) image segmentation algorithm, K-means image segmentation algorithm and MRF (Markov Field) image segmentation algorithm, have been done to segment medical MR images. All the methods are also analyzed quantitatively by using DSC (Dice Similarity Coefficients). The experiments results show that DSC of MDP model segmentation algorithm of all slices exceed 90%, which show that the proposed method is robust and accurate.

  7. Communicative functions integrate segments in prosodies and prosodies in segments.

    Science.gov (United States)

    Kohler, Klaus J

    2011-01-01

    This paper takes a new look at the traditionally established divide between sounds and prosodies, viewing it as a useful heuristics in language descriptions that focus on the segmental make- up of words. It pleads for a new approach that bridges this reified compartmentalization of speech in a more global communicative perspective. Data are presented from a German perception experiment in the framework of the Semantic Differential that shows interdependence of f0 contours and the spectral characteristics of a following fricative segment, for the expression of semantic functions along the scales questioning - asserting, excited - calm, forceful - not forceful, contrary - agreeable. The results lead to the conclusion that segments shape prosodies and are shaped by them in varying ways in the coding of semantic functions. This implies that the analysis of sentence prosodies needs to integrate the manifestation of segments, just as the analysis of segments needs to consider their prosodic embedding. In communicative interaction, speakers set broad prosodic time windows of varying sizes, and listeners respond to them. So, future phonetic research needs to concentrate on speech analysis in such windows.

  8. Genome-Wide Characterization and Expression Profiling of Sugar Transporter Family in the Whitefly, Bemisia tabaci (Gennadius (Hemiptera: Aleyrodidae

    Directory of Open Access Journals (Sweden)

    Zezhong Yang

    2017-05-01

    Full Text Available Sugar transporters (STs play pivotal roles in the growth, development, and stress responses of phloem-sucking insects, such as the whitefly, Bemisia tabaci. In this study, 137 sugar transporters (STs were identified based on analysis of the genome and transcriptome of B. tabaci MEAM1. B. tabaci MEAM1 encodes a larger number of STs than other selected insects. Phylogenetic and molecular evolution analysis showed that the 137 STs formed three expanded clades and that the genes in Sternorrhyncha expanded clades had accelerated rates of evolution. B. tabaci sugar transporters (BTSTs were divided into three groups based on their expression profiles across developmental stages; however, no host-specific BTST was found in B. tabaci fed on different host plants. Feeding of B. tabaci adults with feeding diet containing dsRNA significantly reduced the transcript level of the target genes in B. tabaci and mortality was significantly improved in B. tabaci fed on dsRNA compared to the control, which indicates the sugar transporters may be used as potential RNAi targets for B. tabaci bio-control. These results provide a foundation for further studies of STs in B. tabaci.

  9. Genome-Wide Characterization and Expression Profiling of Sugar Transporter Family in the Whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae).

    Science.gov (United States)

    Yang, Zezhong; Xia, Jixing; Pan, Huipeng; Gong, Cheng; Xie, Wen; Guo, Zhaojiang; Zheng, Huixin; Yang, Xin; Yang, Fengshan; Wu, Qingjun; Wang, Shaoli; Zhang, Youjun

    2017-01-01

    Sugar transporters (STs) play pivotal roles in the growth, development, and stress responses of phloem-sucking insects, such as the whitefly, Bemisia tabaci. In this study, 137 sugar transporters (STs) were identified based on analysis of the genome and transcriptome of B. tabaci MEAM1. B. tabaci MEAM1 encodes a larger number of STs than other selected insects. Phylogenetic and molecular evolution analysis showed that the 137 STs formed three expanded clades and that the genes in Sternorrhyncha expanded clades had accelerated rates of evolution. B. tabaci sugar transporters (BTSTs) were divided into three groups based on their expression profiles across developmental stages; however, no host-specific BTST was found in B. tabaci fed on different host plants. Feeding of B. tabaci adults with feeding diet containing dsRNA significantly reduced the transcript level of the target genes in B. tabaci and mortality was significantly improved in B. tabaci fed on dsRNA compared to the control, which indicates the sugar transporters may be used as potential RNAi targets for B. tabaci bio-control. These results provide a foundation for further studies of STs in B. tabaci.

  10. Genome databases

    Energy Technology Data Exchange (ETDEWEB)

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  11. Methods of evaluating segmentation characteristics and segmentation of major faults

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kie Hwa; Chang, Tae Woo; Kyung, Jai Bok [Seoul National Univ., Seoul (Korea, Republic of)] (and others)

    2000-03-15

    Seismological, geological, and geophysical studies were made for reasonable segmentation of the Ulsan fault and the results are as follows. One- and two- dimensional electrical surveys revealed clearly the fault fracture zone enlarges systematically northward and southward from the vicinity of Mohwa-ri, indicating Mohwa-ri is at the seismic segment boundary. Field Geological survey and microscope observation of fault gouge indicates that the Quaternary faults in the area are reactivated products of the preexisting faults. Trench survey of the Chonbuk fault Galgok-ri revealed thrust faults and cumulative vertical displacement due to faulting during the late Quaternary with about 1.1-1.9 m displacement per event; the latest event occurred from 14000 to 25000 yrs. BP. The seismic survey showed the basement surface os cut by numerous reverse faults and indicated the possibility that the boundary between Kyeongsangbukdo and Kyeongsannamdo may be segment boundary.

  12. 玉米矮花叶病毒CP基因dsRNA的原核表达与分离%Prokaryotic Expression and Extraction of dsRNA Based on the CP Gene of Maize Dwarf Mosaic Virus

    Institute of Scientific and Technical Information of China (English)

    甘德芳; 张姣; 赵阳; 朱苏文; 程备久

    2011-01-01

    根据玉米矮花叶病毒CP基因序列设计特异性引物,RT-PCR扩增玉米矮花叶病毒CP基因特异性干涉片段,将干涉片段及pUCCRNAi载体分别用BamH I及Sal I双酶切,然后将干涉片段分别正反向插入pUC- CRNAi载体中,构建CP基因反向重复克隆载体pUCCRNAi+2 F.再利用Pst I-Sal I位点插入到L4440质粒中构建原核表达载体LMCP.利用IPTG进行诱导表达并对诱导表达条件进行优化.结果表明,经过IPTG诱导,LMCP在大肠杆菌HT115(DE3)菌株中可表达产生预期大小的核酸片段,经DNase I和RNase A消化处理,证实为dsRNA.同时IPTG浓度为0.4~0.6 mmol/L,诱导表达4 h,dsRNA的表达量最高.另外,溶解于ddH2O中的dsRNA稳定性要高于溶解在NaCl中的,且随着放置时间的延长,dsRNA将出现明显的降解.%MDMV CP gene fragments were amplified by RT-PCR from extracted MDMV mRNA. To prepare a hairpin RNA, MDMV CP gene fragments and the pUCCRNAi cloning vector were digested by BamH I-Sal I respectively, First,the BamH I-Sal I fragment from MDMV RNA was cloned in the positive orientation into pUCCRNAi to generate pUCCRNAi + F. And then, the other BamH I-Sal I fragment was cloned in the reverse orientation into Bgl II-Xho I digested pUCCRNAi + F to generate an inverted repeat sequence of pUCCRNAi + 2 F ( sense orientation fragment and antisense orientation fragment were separated by an intron). Thirdly, L4440 and pUCCRNAi + 2 F plasmids were digested with Pst I-Sal I and subsequently joined to generate LMCP. And the recombinant plasmid was induced by IPTG. The results showed that the expression product was the dsRNA by treating with RNase A or DNase I to remove single-stranded RNA or DNA, respectively. Meanwhile, an IPTG concentration of 0.4 ~ 0.6 mmol/L and induction time of 4 h was the most optimal expression condition. The stability of the dsRNA in ddH20 is higher than that of in NaCl, and the dsRNA appeares to he dissolved with the time extending.

  13. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  14. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  15. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  16. Plugin procedure in segmentation and application to hyperspectral image segmentation

    CERN Document Server

    Girard, R

    2010-01-01

    In this article we give our contribution to the problem of segmentation with plug-in procedures. We give general sufficient conditions under which plug in procedure are efficient. We also give an algorithm that satisfy these conditions. We give an application of the used algorithm to hyperspectral images segmentation. Hyperspectral images are images that have both spatial and spectral coherence with thousands of spectral bands on each pixel. In the proposed procedure we combine a reduction dimension technique and a spatial regularisation technique. This regularisation is based on the mixlet modelisation of Kolaczyck and Al.

  17. Automatic segmentation of psoriasis lesions

    Science.gov (United States)

    Ning, Yang; Shi, Chenbo; Wang, Li; Shu, Chang

    2014-10-01

    The automatic segmentation of psoriatic lesions is widely researched these years. It is an important step in Computer-aid methods of calculating PASI for estimation of lesions. Currently those algorithms can only handle single erythema or only deal with scaling segmentation. In practice, scaling and erythema are often mixed together. In order to get the segmentation of lesions area - this paper proposes an algorithm based on Random forests with color and texture features. The algorithm has three steps. The first step, the polarized light is applied based on the skin's Tyndall-effect in the imaging to eliminate the reflection and Lab color space are used for fitting the human perception. The second step, sliding window and its sub windows are used to get textural feature and color feature. In this step, a feature of image roughness has been defined, so that scaling can be easily separated from normal skin. In the end, Random forests will be used to ensure the generalization ability of the algorithm. This algorithm can give reliable segmentation results even the image has different lighting conditions, skin types. In the data set offered by Union Hospital, more than 90% images can be segmented accurately.

  18. Identifying Benefit Segments among College Students.

    Science.gov (United States)

    Brown, Joseph D.

    1991-01-01

    Using concept of market segmentation (dividing market into distinct groups requiring different product benefits), surveyed 398 college students to determine benefit segments among students selecting a college to attend and factors describing each benefit segment. Identified one major segment of students (classroomers) plus three minor segments…

  19. U.S. Army Custom Segmentation System

    Science.gov (United States)

    2007-06-01

    segmentation is individual or intergroup differences in response to marketing - mix variables. Presumptions about segments: •different demands in a...product or service category, •respond differently to changes in the marketing mix Criteria for segments: •The segments must exist in the environment

  20. Discourse segmentation and ambiguity in discourse structure

    NARCIS (Netherlands)

    Hoek, J.; Evers-Vermeul, J.; Sanders, T.J.M.

    2016-01-01

    Discourse relations hold between two or more text segments. The process of discourse annotation not only involves determining what type of relation holds between segments, but also indicating the segments themselves. Often, segmentation and annotation are treated as individual steps, and separate gu

  1. An interactive segmentation method based on superpixel

    DEFF Research Database (Denmark)

    Yang, Shu; Zhu, Yaping; Wu, Xiaoyu

    2015-01-01

    This paper proposes an interactive image-segmentation method which is based on superpixel. To achieve fast segmentation, the method is used to establish a Graphcut model using superpixels as nodes, and a new energy function is proposed. Experimental results demonstrate that the authors' method has...... excellent performance in terms of segmentation accuracy and computation efficiency compared with other segmentation algorithm based on pixels....

  2. 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...

  3. Study on effect of segments erection tolerance and wedge-shaped segment on segment ring in shield tunnel

    Institute of Scientific and Technical Information of China (English)

    CHEN Jun-sheng; MO Hai-hong

    2006-01-01

    Deformation and dislocations of segments of shield tunnel in construction stage have apparent effect on tunnel structure stress and even cause local cracks and breakage in tunnel. 3D finite element method was used to analyze two segment ring models under uniform injected pressure: (1) segment ring without wedge-shaped segment, which has 16 types of preinstall erection tolerance; (2) segment ring with wedge-shaped segment, which has no preinstall erection tolerance. The analysis results indicate that different erection tolerances can cause irregular deformation in segment ring under uniform injected pressure, and that the tolerance values are enlarged further. Wedge-shaped segment apparently affects the overall deformation of segment ring without erection tolerances. The uniform injected pressure can cause deformation of ring with wedge-shaped segment irregular,and dislocations also appear in this situation. The stress of segment with erection tolerances is much larger than that of segment without erection tolerances. Enlarging the central angle of wedge-shaped segment can make the irregular deformation and dislocations of segments smaller. The analysis results also provide basis for erection tolerance control and improvement of segment constitution.

  4. Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

    Directory of Open Access Journals (Sweden)

    Sathish Sankar

    Full Text Available Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments.A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC, codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments.All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution.There is a dichotomy among evolutionary pressures shaping a the relative abundance of different dinucleotides in hantavirus genomes b the evolution of the three hantavirus segments.

  5. Novel Insights on Hantavirus Evolution: The Dichotomy in Evolutionary Pressures Acting on Different Hantavirus Segments.

    Science.gov (United States)

    Sankar, Sathish; Upadhyay, Mohita; Ramamurthy, Mageshbabu; Vadivel, Kumaran; Sagadevan, Kalaiselvan; Nandagopal, Balaji; Vivekanandan, Perumal; Sridharan, Gopalan

    2015-01-01

    Hantaviruses are important emerging zoonotic pathogens. The current understanding of hantavirus evolution is complicated by the lack of consensus on co-divergence of hantaviruses with their animal hosts. In addition, hantaviruses have long-term associations with their reservoir hosts. Analyzing the relative abundance of dinucleotides may shed new light on hantavirus evolution. We studied the relative abundance of dinucleotides and the evolutionary pressures shaping different hantavirus segments. A total of 118 sequences were analyzed; this includes 51 sequences of the S segment, 43 sequences of the M segment and 23 sequences of the L segment. The relative abundance of dinucleotides, effective codon number (ENC), codon usage biases were analyzed. Standard methods were used to investigate the relative roles of mutational pressure and translational selection on the three hantavirus segments. All three segments of hantaviruses are CpG depleted. Mutational pressure is the predominant evolutionary force leading to CpG depletion among hantaviruses. Interestingly, the S segment of hantaviruses is GpU depleted and in contrast to CpG depletion, the depletion of GpU dinucleotides from the S segment is driven by translational selection. Our findings also suggest that mutational pressure is the primary evolutionary pressure acting on the S and the M segments of hantaviruses. While translational selection plays a key role in shaping the evolution of the L segment. Our findings highlight how different evolutionary pressures may contribute disproportionally to the evolution of the three hantavirus segments. These findings provide new insights on the current understanding of hantavirus evolution. There is a dichotomy among evolutionary pressures shaping a) the relative abundance of different dinucleotides in hantavirus genomes b) the evolution of the three hantavirus segments.

  6. Unsupervised segmentation with dynamical units.

    Science.gov (United States)

    Rao, A Ravishankar; Cecchi, Guillermo A; Peck, Charles C; Kozloski, James R

    2008-01-01

    In this paper, we present a novel network to separate mixtures of inputs that have been previously learned. A significant capability of the network is that it segments the components of each input object that most contribute to its classification. The network consists of amplitude-phase units that can synchronize their dynamics, so that separation is determined by the amplitude of units in an output layer, and segmentation by phase similarity between input and output layer units. Learning is unsupervised and based on a Hebbian update, and the architecture is very simple. Moreover, efficient segmentation can be achieved even when there is considerable superposition of the inputs. The network dynamics are derived from an objective function that rewards sparse coding in the generalized amplitude-phase variables. We argue that this objective function can provide a possible formal interpretation of the binding problem and that the implementation of the network architecture and dynamics is biologically plausible.

  7. Compliance with Segment Disclosure Initiatives

    DEFF Research Database (Denmark)

    Arya, Anil; Frimor, Hans; Mittendorf, Brian

    2013-01-01

    Regulatory oversight of capital markets has intensified in recent years, with a particular emphasis on expanding financial transparency. A notable instance is efforts by the Financial Accounting Standards Board that push firms to identify and report performance of individual business units...... (segments). This paper seeks to address short-run and long-run consequences of stringent enforcement of and uniform compliance with these segment disclosure standards. To do so, we develop a parsimonious model wherein a regulatory agency promulgates disclosure standards and either permits voluntary...... compliance or mandates strict compliance from firms. Under voluntary compliance, a firm is able to credibly withhold individual segment information from its competitors by disclosing data only at the aggregate firm level. Consistent with regulatory hopes, we show that mandatory compliance enhances welfare...

  8. Vehicle License Plate Character Segmentation

    Institute of Scientific and Technical Information of China (English)

    Mei-Sen Pan; Jun-Biao Yan; Zheng-Hong Xiao

    2008-01-01

    Vehicle license plate (VLP) character segmentation is an important part of the vehicle license plate recognition system (VLPRS). This paper proposes a least square method (LSM) to treat horizontal tilt and vertical tilt in VLP images. Auxiliary lines are added into the image (or the tilt-corrected image) to make the separated parts of each Chinese character to be an interconnected region. The noise regions will be eliminated after two fusing images are merged according to the minimum principle of gray values.Then, the characters are segmented by projection method (PM) and the final character images are obtained. The experimental results show that this method features fast processing and good performance in segmentation.

  9. Segmental Rescoring in Text Recognition

    Science.gov (United States)

    2014-02-04

    ttm № tes/m, m* tmvr mowm* a Smyrna Of l δrtA£ACf02S’ A w m - y i p m AmiKSiS € f № ) C № № m .. sg6#?«rA fiθN ; Atφ h Sft№’·’Spxn mm m fim f№b t&m&mm...applying a Hidden Markov Model (HMM) recognition approach. Generating the plurality text hypotheses for the image forming includes generating a first...image. Applying segmental analysis to a segmentation determined by a first OCR engine, such as a segmentation determined by a Hidden Markov Model (HMM

  10. A Novel Iris Segmentation Scheme

    Directory of Open Access Journals (Sweden)

    Chen-Chung Liu

    2014-01-01

    Full Text Available One of the key steps in the iris recognition system is the accurate iris segmentation from its surrounding noises including pupil, sclera, eyelashes, and eyebrows of a captured eye-image. This paper presents a novel iris segmentation scheme which utilizes the orientation matching transform to outline the outer and inner iris boundaries initially. It then employs Delogne-Kåsa circle fitting (instead of the traditional Hough transform to further eliminate the outlier points to extract a more precise iris area from an eye-image. In the extracted iris region, the proposed scheme further utilizes the differences in the intensity and positional characteristics of the iris, eyelid, and eyelashes to detect and delete these noises. The scheme is then applied on iris image database, UBIRIS.v1. The experimental results show that the presented scheme provides a more effective and efficient iris segmentation than other conventional methods.

  11. Segmentation in dermatological hyperspectral images: dedicated methods

    OpenAIRE

    Koprowski, Robert; Olczyk, Paweł

    2016-01-01

    Background Segmentation of hyperspectral medical images is one of many image segmentation methods which require profiling. This profiling involves either the adjustment of existing, known image segmentation methods or a proposal of new dedicated methods of hyperspectral image segmentation. Taking into consideration the size of analysed data, the time of analysis is of major importance. Therefore, the authors proposed three new dedicated methods of hyperspectral image segmentation with special...

  12. Segmentation by Large Scale Hypothesis Testing - Segmentation as Outlier Detection

    DEFF Research Database (Denmark)

    Darkner, Sune; Dahl, Anders Lindbjerg; Larsen, Rasmus

    2010-01-01

    locally. We propose a method based on large scale hypothesis testing with a consistent method for selecting an appropriate threshold for the given data. By estimating the background distribution we characterize the segment of interest as a set of outliers with a certain probability based on the estimated...

  13. SExSeg: SExtractor segmentation

    Science.gov (United States)

    Coe, Dan

    2015-08-01

    SExSeg forces SExtractor (ascl:1010.064) to run using a pre-defined segmentation map (the definition of objects and their borders). The defined segments double as isophotal apertures. SExSeg alters the detection image based on a pre-defined segmenation map while preparing your "analysis image" by subtracting the background in a separate SExtractor run (using parameters you specify). SExtractor is then run in "double-image" mode with the altered detection image and background-subtracted analysis image.

  14. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  15. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  16. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  17. MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

    Science.gov (United States)

    Chiapello, Hélène; Gendrault, Annie; Caron, Christophe; Blum, Jérome; Petit, Marie-Agnès; El Karoui, Meriem

    2008-11-27

    The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at the nucleotide level but their use and the biological interpretation of results are not straightforward. It is therefore necessary to develop new resources to access, analyze, and visualize genome comparisons. Here we present recent developments on MOSAIC, a generalist comparative bacterial genome database. This database provides the bacteriologist community with easy access to comparisons of complete bacterial genomes at the intra-species level. The strategy we developed for comparison allows us to define two types of regions in bacterial genomes: backbone segments (i.e., regions conserved in all compared strains) and variable segments (i.e., regions that are either specific to or variable in one of the aligned genomes). Definition of these segments at the nucleotide level allows precise comparative and evolutionary analyses of both coding and non-coding regions of bacterial genomes. Such work is easily performed using the MOSAIC Web interface, which allows browsing and graphical visualization of genome comparisons. The MOSAIC database now includes 493 pairwise comparisons and 35 multiple maximal comparisons representing 78 bacterial species. Genome conserved regions (backbones) and variable segments are presented in various formats for further analysis. A graphical interface allows visualization of aligned genomes and functional annotations. The MOSAIC database is available online at http://genome.jouy.inra.fr/mosaic.

  18. Genetics in Ophthalmology II–Anterior Segment Diseases

    Directory of Open Access Journals (Sweden)

    Canan Aslı Utine

    2012-10-01

    Full Text Available Genetic diseases are congenital or acquired hereditary diseases that result from structural/functional disorders of the human genome. Today, the genetic factors that play a role in many diseases are being highlighted with the rapid progress in the field of genetics science. It becomes increasingly important that physicians from all disciplines have knowledge about the basic principles of genetics, patterns of inheritance, etc., so that they can follow the new developments. In genetic eye diseases, ophthalmologists should know the basic clinical and recently rapidly developing genetic characteristics of these diseases in order to properly approach the diagnosis and treatment and to provide genetic counseling. In this paper, anterior segment eye diseases of genetic origin are reviewed, and aniridia, anterior segment dysgenesis, glaucoma, corneal dystrophies, cataract, ectopia lentis, myopia, and other refractive errors are covered. (Turk J Ophthalmol 2012; 42: 378-85

  19. Three-Dimensional Genome Organization and Function in Drosophila.

    Science.gov (United States)

    Schwartz, Yuri B; Cavalli, Giacomo

    2017-01-01

    Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques. Copyright © 2017 Schwartz and Cavalli.

  20. Three-Dimensional Genome Organization and Function in Drosophila

    Science.gov (United States)

    Schwartz, Yuri B.; Cavalli, Giacomo

    2017-01-01

    Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques. PMID:28049701

  1. Research Progress on Image Segmentation

    Science.gov (United States)

    1981-06-01

    AUTHOR. HANON A.R. AND RISEMAM E- 𔃻. TITLE G SE MENTATION OF NATURA’ CNIE PAGE 6 REFERENCES FOR< IMAGE...PUBLICAIION-DAIA : 1976 KEY-WORDS : IMAGE SEGMENTATION AU’ihOR I KRUGER K. P., THOMPSON W. B, AND TURNER A. F, TITLE COMPUTER DIAGNOSIS OF TNEUMOCONIOSIS

  2. Increasing Enrollment through Benefit Segmentation.

    Science.gov (United States)

    Goodnow, Betty

    1982-01-01

    The applicability of benefit segmentation, a market research technique which groups people according to benefits expected from a program offering, was tested at the College of DuPage. Preferences and demographic characteristics were analyzed and program improvements adopted, increasing enrollment by 20 percent. (Author/SK)

  3. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape cha

  4. Age Differences in Language Segmentation.

    Science.gov (United States)

    Stine-Morrow, Elizabeth A L; Payne, Brennan R

    2016-01-01

    Reading bears the evolutionary footprint of spoken communication. Prosodic contour in speech helps listeners parse sentences and establish semantic focus. Readers' regulation of input mirrors the segmentation patterns of prosody, such that reading times are longer for words at the ends of syntactic constituents. As reflected in these "micropauses," older readers are often found to segment text into smaller chunks. The mechanisms underlying these micropauses are unclear, with some arguing that they derive from the mental simulation of prosodic contour and others arguing they reflect higher-level language comprehension mechanisms (e.g., conceptual integration, consolidation with existing knowledge, ambiguity resolution) that are common across modality and support the consolidation of the memory representation. The authors review evidence based on reading time and comprehension performance to suggest that (a) age differences in segmentation derive both from age-related declines in working memory, as well as from crystallized ability and knowledge, which have the potential to grow in adulthood, and that (b) shifts in segmentation patterns may be a pathway through which language comprehension is preserved in late life.

  5. XRA image segmentation using regression

    Science.gov (United States)

    Jin, Jesse S.

    1996-04-01

    Segmentation is an important step in image analysis. Thresholding is one of the most important approaches. There are several difficulties in segmentation, such as automatic selecting threshold, dealing with intensity distortion and noise removal. We have developed an adaptive segmentation scheme by applying the Central Limit Theorem in regression. A Gaussian regression is used to separate the distribution of background from foreground in a single peak histogram. The separation will help to automatically determine the threshold. A small 3 by 3 widow is applied and the modal of the local histogram is used to overcome noise. Thresholding is based on local weighting, where regression is used again for parameter estimation. A connectivity test is applied to the final results to remove impulse noise. We have applied the algorithm to x-ray angiogram images to extract brain arteries. The algorithm works well for single peak distribution where there is no valley in the histogram. The regression provides a method to apply knowledge in clustering. Extending regression for multiple-level segmentation needs further investigation.

  6. Multiple Segment Factorial Vignette Designs

    Science.gov (United States)

    Ganong, Lawrence H.; Coleman, Marilyn

    2006-01-01

    The multiple segment factorial vignette design (MSFV) combines elements of experimental designs and probability sampling with the inductive, exploratory approach of qualitative research. MSFVs allow researchers to investigate topics that may be hard to study because of ethical or logistical concerns. Participants are presented with short stories…

  7. Segmental Colitis Complicating Diverticular Disease

    Directory of Open Access Journals (Sweden)

    Guido Ma Van Rosendaal

    1996-01-01

    Full Text Available Two cases of idiopathic colitis affecting the sigmoid colon in elderly patients with underlying diverticulosis are presented. Segmental resection has permitted close review of the histopathology in this syndrome which demonstrates considerable similarity to changes seen in idiopathic ulcerative colitis. The reported experience with this syndrome and its clinical features are reviewed.

  8. Body segments and growth hormone.

    OpenAIRE

    Bundak, R; Hindmarsh, P C; Brook, C. G.

    1988-01-01

    The effects of human growth hormone treatment for five years on sitting height and subischial leg length of 35 prepubertal children with isolated growth hormone deficiency were investigated. Body segments reacted equally to treatment with human growth hormone; this is important when comparing the effect of growth hormone on the growth of children with skeletal dysplasias or after spinal irradiation.

  9. Increasing Enrollment through Benefit Segmentation.

    Science.gov (United States)

    Goodnow, Betty

    1982-01-01

    The applicability of benefit segmentation, a market research technique which groups people according to benefits expected from a program offering, was tested at the College of DuPage. Preferences and demographic characteristics were analyzed and program improvements adopted, increasing enrollment by 20 percent. (Author/SK)

  10. Segmenting Trajectories by Movement States

    NARCIS (Netherlands)

    Buchin, M.; Kruckenberg, H.; Kölzsch, A.; Timpf, S.; Laube, P.

    2013-01-01

    Dividing movement trajectories according to different movement states of animals has become a challenge in movement ecology, as well as in algorithm development. In this study, we revisit and extend a framework for trajectory segmentation based on spatio-temporal criteria for this purpose. We adapt

  11. Multiple Segment Factorial Vignette Designs

    Science.gov (United States)

    Ganong, Lawrence H.; Coleman, Marilyn

    2006-01-01

    The multiple segment factorial vignette design (MSFV) combines elements of experimental designs and probability sampling with the inductive, exploratory approach of qualitative research. MSFVs allow researchers to investigate topics that may be hard to study because of ethical or logistical concerns. Participants are presented with short stories…

  12. Dictionary Based Segmentation in Volumes

    DEFF Research Database (Denmark)

    Emerson, Monica Jane; Jespersen, Kristine Munk; Jørgensen, Peter Stanley

    Method for supervised segmentation of volumetric data. The method is trained from manual annotations, and these annotations make the method very flexible, which we demonstrate in our experiments. Our method infers label information locally by matching the pattern in a neighborhood around a voxel ...... to a dictionary, and hereby accounts for the volume texture....

  13. Copy number variation in the bovine genome

    DEFF Research Database (Denmark)

    Fadista, João; Thomsen, Bo; Holm, Lars-Erik;

    2010-01-01

    to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation...... in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental...

  14. Joint shape segmentation with linear programming

    KAUST Repository

    Huang, Qixing

    2011-01-01

    We present an approach to segmenting shapes in a heterogenous shape database. Our approach segments the shapes jointly, utilizing features from multiple shapes to improve the segmentation of each. The approach is entirely unsupervised and is based on an integer quadratic programming formulation of the joint segmentation problem. The program optimizes over possible segmentations of individual shapes as well as over possible correspondences between segments from multiple shapes. The integer quadratic program is solved via a linear programming relaxation, using a block coordinate descent procedure that makes the optimization feasible for large databases. We evaluate the presented approach on the Princeton segmentation benchmark and show that joint shape segmentation significantly outperforms single-shape segmentation techniques. © 2011 ACM.

  15. Small RNA in rice genome

    Institute of Scientific and Technical Information of China (English)

    王凯; 朱小蓬; 钟兰; 陈润生

    2002-01-01

    Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.

  16. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    Full Text Available Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings

  17. Ancient genomics.

    Science.gov (United States)

    Der Sarkissian, Clio; Allentoft, Morten E; Ávila-Arcos, María C; Barnett, Ross; Campos, Paula F; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D; Moreno-Mayar, J Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M Thomas P; Willerslev, Eske; Orlando, Ludovic

    2015-01-19

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

  18. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  19. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  20. Genome architecture: domain organization of interphase chromosomes.

    Science.gov (United States)

    Bickmore, Wendy A; van Steensel, Bas

    2013-03-14

    The architecture of interphase chromosomes is important for the regulation of gene expression and genome maintenance. Chromosomes are linearly segmented into hundreds of domains with different protein compositions. Furthermore, the spatial organization of chromosomes is nonrandom and is characterized by many local and long-range contacts among genes and other sequence elements. A variety of genome-wide mapping techniques have made it possible to chart these properties at high resolution. Combined with microscopy and computational modeling, the results begin to yield a more coherent picture that integrates linear and three-dimensional (3D) views of chromosome organization in relation to gene regulation and other nuclear functions.

  1. Incorporation of the influenza A virus NA segment into virions does not require cognate non-coding sequences

    Science.gov (United States)

    Crescenzo-Chaigne, Bernadette; Barbezange, Cyril V. S.; Léandri, Stéphane; Roquin, Camille; Berthault, Camille; van der Werf, Sylvie

    2017-01-01

    For each influenza virus genome segment, the coding sequence is flanked by non-coding (NC) regions comprising shared, conserved sequences and specific, non-conserved sequences. The latter and adjacent parts of the coding sequence are involved in genome packaging, but the precise role of the non-conserved NC sequences is still unclear. The aim of this study is to better understand the role of the non-conserved non-coding sequences in the incorporation of the viral segments into virions. The NA-segment NC sequences were systematically replaced by those of the seven other segments. Recombinant viruses harbouring two segments with identical NC sequences were successfully rescued. Virus growth kinetics and serial passages were performed, and incorporation of the viral segments was tested by real-time RT-PCR. An initial virus growth deficiency correlated to a specific defect in NA segment incorporation. Upon serial passages, growth properties were restored. Sequencing revealed that the replacing 5′NC sequence length drove the type of mutations obtained. With sequences longer than the original, point mutations in the coding region with or without substitutions in the 3′NC region were detected. With shorter sequences, insertions were observed in the 5′NC region. Restoration of viral fitness was linked to restoration of the NA segment incorporation. PMID:28240311

  2. Polyp Segmentation in NBI Colonoscopy

    Science.gov (United States)

    Gross, Sebastian; Kennel, Manuel; Stehle, Thomas; Wulff, Jonas; Tischendorf, Jens; Trautwein, Christian; Aach, Til

    Endoscopic screening of the colon (colonoscopy) is performed to prevent cancer and to support therapy. During intervention colon polyps are located, inspected and, if need be, removed by the investigator. We propose a segmentation algorithm as a part of an automatic polyp classification system for colonoscopic Narrow-Band images. Our approach includes multi-scale filtering for noise reduction, suppression of small blood vessels, and enhancement of major edges. Results of the subsequent edge detection are compared to a set of elliptic templates and evaluated. We validated our algorithm on our polyp database with images acquired during routine colonoscopic examinations. The presented results show the reliable segmentation performance of our method and its robustness to image variations.

  3. Spatial localization of speech segments

    DEFF Research Database (Denmark)

    Karlsen, Brian Lykkegaard

    1999-01-01

    angle the target is likely to have originated from. The model is trained on the experimental data. On the basis of the experimental results, it is concluded that the human ability to localize speech segments in adverse noise depends on the speech segment as well as its point of origin in space...... the task of the experiment. The psychoacoustical experiment used naturally-spoken Danish consonant-vowel combinations as targets presented in diffuse speech-shaped noise at a peak SNR of -10 dB. The subjects were normal hearing persons. The experiment took place in an anechoic chamber where eight...... loudspeakers were suspended so that they surrounded the subjects in the horizontal plane. The subjects were required to push a button on a pad indicating where they had localized the target to in the horizontal plane. The response pad had twelve buttons arranged uniformly in a circle and two further buttons so...

  4. Aorta Segmentation for Stent Simulation

    CERN Document Server

    Egger, Jan; Setser, Randolph; Renapuraar, Rahul; Biermann, Christina; O'Donnell, Thomas

    2011-01-01

    Simulation of arterial stenting procedures prior to intervention allows for appropriate device selection as well as highlights potential complications. To this end, we present a framework for facilitating virtual aortic stenting from a contrast computer tomography (CT) scan. More specifically, we present a method for both lumen and outer wall segmentation that may be employed in determining both the appropriateness of intervention as well as the selection and localization of the device. The more challenging recovery of the outer wall is based on a novel minimal closure tracking algorithm. Our aortic segmentation method has been validated on over 3000 multiplanar reformatting (MPR) planes from 50 CT angiography data sets yielding a Dice Similarity Coefficient (DSC) of 90.67%.

  5. Text Segmentation Using Exponential Models

    CERN Document Server

    Beeferman, D; Lafferty, G D; Beeferman, Doug; Berger, Adam; Lafferty, John

    1997-01-01

    This paper introduces a new statistical approach to partitioning text automatically into coherent segments. Our approach enlists both short-range and long-range language models to help it sniff out likely sites of topic changes in text. To aid its search, the system consults a set of simple lexical hints it has learned to associate with the presence of boundaries through inspection of a large corpus of annotated data. We also propose a new probabilistically motivated error metric for use by the natural language processing and information retrieval communities, intended to supersede precision and recall for appraising segmentation algorithms. Qualitative assessment of our algorithm as well as evaluation using this new metric demonstrate the effectiveness of our approach in two very different domains, Wall Street Journal articles and the TDT Corpus, a collection of newswire articles and broadcast news transcripts.

  6. Dictionary Based Segmentation in Volumes

    DEFF Research Database (Denmark)

    Emerson, Monica Jane; Jespersen, Kristine Munk; Jørgensen, Peter Stanley

    2015-01-01

    We present a method for supervised volumetric segmentation based on a dictionary of small cubes composed of pairs of intensity and label cubes. Intensity cubes are small image volumes where each voxel contains an image intensity. Label cubes are volumes with voxelwise probabilities for a given...... label. The segmentation process is done by matching a cube from the volume, of the same size as the dictionary intensity cubes, to the most similar intensity dictionary cube, and from the associated label cube we get voxel-wise label probabilities. Probabilities from overlapping cubes are averaged...... and hereby we obtain a robust label probability encoding. The dictionary is computed from labeled volumetric image data based on weighted clustering. We experimentally demonstrate our method using two data sets from material science – a phantom data set of a solid oxide fuel cell simulation for detecting...

  7. Older People's Mobility: Segments, Factors, Trends

    DEFF Research Database (Denmark)

    Haustein, Sonja; Siren, Anu

    2015-01-01

    demographic, health-related, or transport-related factors. This paper reviews these studies and compares the segments of older people that different studies have identified. First, as a result of a systematic comparison, we identified four generic segments: (1) an active car-oriented segment; (2) a car......The expanding older population is increasingly diverse with regard to, for example, age, income, location, and health. Within transport research, this diversity has recently been addressed in studies that segment the older population into homogeneous groups based on combinations of various......-dependent segment, restricted in mobility; (3) a mobile multimodal segment; (4) and a segment depending on public transport and other services. Second, we examined the single factors used in the reviewed segmentation studies, with focus on whether there is evidence in the literature for the factors’ effect on older...

  8. Vibration damping for the Segmented Mirror Telescope

    Science.gov (United States)

    Maly, Joseph R.; Yingling, Adam J.; Griffin, Steven F.; Agrawal, Brij N.; Cobb, Richard G.; Chambers, Trevor S.

    2012-09-01

    The Segmented Mirror Telescope (SMT) at the Naval Postgraduate School (NPS) in Monterey is a next-generation deployable telescope, featuring a 3-meter 6-segment primary mirror and advanced wavefront sensing and correction capabilities. In its stowed configuration, the SMT primary mirror segments collapse into a small volume; once on location, these segments open to the full 3-meter diameter. The segments must be very accurately aligned after deployment and the segment surfaces are actively controlled using numerous small, embedded actuators. The SMT employs a passive damping system to complement the actuators and mitigate the effects of low-frequency (operating deflection shapes of the mirror and to quantify segment edge displacements; relative alignment of λ/4 or better was desired. The TMDs attenuated the vibration amplitudes by 80% and reduced adjacent segment phase mismatches to acceptable levels.

  9. HF Transverse Segmentation and Tagging Jet Capability

    CERN Document Server

    Doroshkevich, E A; Kuleshov, Sergey

    1998-01-01

    So called tagging jets and pile-up were simulated for the optimisation of the HF segmentation. The energy resolution, angular resolution and efficiency of jet reconstruction are defined for different calorimeter segmentation.

  10. Human Segmentation Using Haar-Classifier

    Directory of Open Access Journals (Sweden)

    Dharani S

    2014-07-01

    Full Text Available Segmentation is an important process in many aspects of multimedia applications. Fast and perfect segmentation of moving objects in video sequences is a basic task in many computer visions and video investigation applications. Particularly Human detection is an active research area in computer vision applications. Segmentation is very useful for tracking and recognition the object in a moving clip. The motion segmentation problem is studied and reviewed the most important techniques. We illustrate some common methods for segmenting the moving objects including background subtraction, temporal segmentation and edge detection. Contour and threshold are common methods for segmenting the objects in moving clip. These methods are widely exploited for moving object segmentation in many video surveillance applications, such as traffic monitoring, human motion capture. In this paper, Haar Classifier is used to detect humans in a moving video clip some features like face detection, eye detection, full body, upper body and lower body detection.

  11. Segmentation in local hospital markets.

    Science.gov (United States)

    Dranove, D; White, W D; Wu, L

    1993-01-01

    This study examines evidence of market segmentation on the basis of patients' insurance status, demographic characteristics, and medical condition in selected local markets in California in the years 1983 and 1989. Substantial differences exist in the probability patients may be admitted to particular hospitals based on insurance coverage, particularly Medicaid, and race. Segmentation based on insurance and race is related to hospital characteristics, but not the characteristics of the hospital's community. Medicaid patients are more likely to go to hospitals with lower costs and fewer service offerings. Privately insured patients go to hospitals offering more services, although cost concerns are increasing. Hispanic patients also go to low-cost hospitals, ceteris paribus. Results indicate little evidence of segmentation based on medical condition in either 1983 or 1989, suggesting that "centers of excellence" have yet to play an important role in patient choice of hospital. The authors found that distance matters, and that patients prefer nearby hospitals, moreso for some medical conditions than others, in ways consistent with economic theories of consumer choice.

  12. Segmentation-based video coding

    Energy Technology Data Exchange (ETDEWEB)

    Lades, M. [Lawrence Livermore National Lab., CA (United States); Wong, Yiu-fai; Li, Qi [Texas Univ., San Antonio, TX (United States). Div. of Engineering

    1995-10-01

    Low bit rate video coding is gaining attention through a current wave of consumer oriented multimedia applications which aim, e.g., for video conferencing over telephone lines or for wireless communication. In this work we describe a new segmentation-based approach to video coding which belongs to a class of paradigms appearing very promising among the various proposed methods. Our method uses a nonlinear measure of local variance to identify the smooth areas in an image in a more indicative and robust fashion: First, the local minima in the variance image are identified. These minima then serve as seeds for the segmentation of the image with a watershed algorithm. Regions and their contours are extracted. Motion compensation is used to predict the change of regions between previous frames and the current frame. The error signal is then quantized. To reduce the number of regions and contours, we use the motion information to assist the segmentation process, to merge regions, resulting in a further reduction in bit rate. Our scheme has been tested and good results have been obtained.

  13. Primary mirror segment fabrication for CELT

    Science.gov (United States)

    Mast, Terry S.; Nelson, Jerry E.; Sommargren, Gary E.

    2000-07-01

    The primary mirror of the proposed California Extremely Large Telescope is a 30-meter diameter mosaic of hexagonal segments. An initial design calls for about a thousand segments with a hexagon side length of 0.5 meters, a primary-mirror focal ratio of 1.5, and a segment surface quality of about 20 nanometers rms. We describe concepts for fabricating these segments.

  14. Perfect and Dynamic Segmentation via the Internet

    OpenAIRE

    Matthias Huehn

    2007-01-01

    The paper starts from the hypothesis that traditional approaches to segmentation are seriously flawed because the object of segmentation, the consumer, has dramatically changed over the past 30 years. The New Consumer actively defies segmentation attempts by marketing professionals and thus makes a new approach to marketing strategy necessary. The paper suggests to let the consumers segment themselves instead of doing market research. Thereby the filter between consumer and company is dropped...

  15. Multi-strategy Segmentation of Melodies

    NARCIS (Netherlands)

    Rodríguez López, M.E.; Volk, Anja; Bountouridis, D.

    2014-01-01

    Melodic segmentation is a fundamental yet unsolved problem in automatic music processing. At present most melody segmentation models rely on a ‘single strategy’ (i.e. they model a single perceptual segmentation cue). However, cognitive studies suggest that multiple cues need to be considered. In thi

  16. Market Segmentation from a Behavioral Perspective

    Science.gov (United States)

    Wells, Victoria K.; Chang, Shing Wan; Oliveira-Castro, Jorge; Pallister, John

    2010-01-01

    A segmentation approach is presented using both traditional demographic segmentation bases (age, social class/occupation, and working status) and a segmentation by benefits sought. The benefits sought in this case are utilitarian and informational reinforcement, variables developed from the Behavioral Perspective Model (BPM). Using data from 1,847…

  17. The Process of Marketing Segmentation Strategy Selection

    OpenAIRE

    Ionel Dumitru

    2007-01-01

    The process of marketing segmentation strategy selection represents the essence of strategical marketing. We present hereinafter the main forms of the marketing statategy segmentation: undifferentiated marketing, differentiated marketing, concentrated marketing and personalized marketing. In practice, the companies use a mix of these marketing segmentation methods in order to maximize the proffit and to satisfy the consumers’ needs.

  18. Segmenting the mental health care market.

    Science.gov (United States)

    Stone, T R; Warren, W E; Stevens, R E

    1990-03-01

    The authors report the results of a segmentation study of the mental health care market. A random sample of 387 residents of a western city were interviewed by telephone. Cluster analysis of the data identified six market segments. Each is described according to the mental health care services to which it is most sensitive. Implications for targeting the segments are discussed.

  19. An Active Contour for Range Image Segmentation

    Directory of Open Access Journals (Sweden)

    Khaldi Amine

    2012-06-01

    Full Text Available In this paper a new classification of range image segmentation method is proposed according to the criterion of homogeneity which obeys the segmentation, then, a deformable model-type active contour “Snake” is applied to segment range images.

  20. Market Segmentation from a Behavioral Perspective

    Science.gov (United States)

    Wells, Victoria K.; Chang, Shing Wan; Oliveira-Castro, Jorge; Pallister, John

    2010-01-01

    A segmentation approach is presented using both traditional demographic segmentation bases (age, social class/occupation, and working status) and a segmentation by benefits sought. The benefits sought in this case are utilitarian and informational reinforcement, variables developed from the Behavioral Perspective Model (BPM). Using data from 1,847…

  1. LIFE-STYLE SEGMENTATION WITH TAILORED INTERVIEWING

    NARCIS (Netherlands)

    KAMAKURA, WA; WEDEL, M

    1995-01-01

    The authors present a tailored interviewing procedure for life-style segmentation. The procedure assumes that a life-style measurement instrument has been designed. A classification of a sample of consumers into life-style segments is obtained using a latent-class model. With these segments, the tai

  2. Quick Dissection of the Segmental Bronchi

    Science.gov (United States)

    Nakajima, Yuji

    2010-01-01

    Knowledge of the three-dimensional anatomy of the bronchopulmonary segments is essential for respiratory medicine. This report describes a quick guide for dissecting the segmental bronchi in formaldehyde-fixed human material. All segmental bronchi are easy to dissect, and thus, this exercise will help medical students to better understand the…

  3. The Process of Marketing Segmentation Strategy Selection

    OpenAIRE

    Ionel Dumitru

    2007-01-01

    The process of marketing segmentation strategy selection represents the essence of strategical marketing. We present hereinafter the main forms of the marketing statategy segmentation: undifferentiated marketing, differentiated marketing, concentrated marketing and personalized marketing. In practice, the companies use a mix of these marketing segmentation methods in order to maximize the proffit and to satisfy the consumers’ needs.

  4. Mora or syllable? Speech segmentation in Japanese

    NARCIS (Netherlands)

    Otake, T.; Hatano, G.; Cutler, A.; Mehler, J.

    1993-01-01

    Four experiments examined segmentation of spoken Japanese words by native and non-native listeners. Previous studies suggested that language rhythm determines the segmentation unit most natural to native listeners: French has syllabic rhythm, and French listeners use the syllable in segmentation, wh

  5. Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis.

    Science.gov (United States)

    Christen, Matthias; Deutsch, Samuel; Christen, Beat

    2015-08-21

    Recent advances in synthetic biology have resulted in an increasing demand for the de novo synthesis of large-scale DNA constructs. Any process improvement that enables fast and cost-effective streamlining of digitized genetic information into fabricable DNA sequences holds great promise to study, mine, and engineer genomes. Here, we present Genome Calligrapher, a computer-aided design web tool intended for whole genome refactoring of bacterial chromosomes for de novo DNA synthesis. By applying a neutral recoding algorithm, Genome Calligrapher optimizes GC content and removes obstructive DNA features known to interfere with the synthesis of double-stranded DNA and the higher order assembly into large DNA constructs. Subsequent bioinformatics analysis revealed that synthesis constraints are prevalent among bacterial genomes. However, a low level of codon replacement is sufficient for refactoring bacterial genomes into easy-to-synthesize DNA sequences. To test the algorithm, 168 kb of synthetic DNA comprising approximately 20 percent of the synthetic essential genome of the cell-cycle bacterium Caulobacter crescentus was streamlined and then ordered from a commercial supplier of low-cost de novo DNA synthesis. The successful assembly into eight 20 kb segments indicates that Genome Calligrapher algorithm can be efficiently used to refactor difficult-to-synthesize DNA. Genome Calligrapher is broadly applicable to recode biosynthetic pathways, DNA sequences, and whole bacterial genomes, thus offering new opportunities to use synthetic biology tools to explore the functionality of microbial diversity. The Genome Calligrapher web tool can be accessed at https://christenlab.ethz.ch/GenomeCalligrapher  .

  6. Detection of chromosomal abnormalities by comparative genomic hybridization.

    Science.gov (United States)

    Lapierre, Jean-Michel; Tachdjian, Gérard

    2005-04-01

    Comparative genomic hybridization (CGH) is a modified in-situ hybridization technique. In this type of analysis, two differentially labeled genomic DNAs (study and reference) are cohybridized to normal metaphase spreads or to microarray. Chromosomal locations of copy number changes in the DNA segments of the study genome are revealed by a variable fluorescence intensity ratio along each target chromosome. Thus, CGH allows detection and mapping of DNA sequence copy differences between two genomes in a single experiment. Since its development, comparative genomic hybridization has been applied mostly as a research tool in the field of cancer cytogenetics to identify genetic changes in many previously unknown regions. It is also a powerful tool for detection and identification of unbalanced chromosomal abnormalities in prenatal, postnatal and preimplantation diagnostics. The development of comparative genomic hybridization and increase in resolution analysis by using the microarray-based technique offer new information on chromosomal pathologies and thus better management of patients.

  7. Surface properties of poly(ethylene oxide)-based segmented block copolymers with monodisperse hard segments

    NARCIS (Netherlands)

    Husken, D.; Feijen, Jan; Gaymans, R.J.

    2009-01-01

    The surface properties of segmented block copolymers based on poly(ethylene oxide) (PEO) segments and monodisperse crystallizable tetra-amide segments were studied. The monodisperse crystallizable segments (T6T6T) were based on terephthalate (T) and hexamethylenediamine (6). Due to the crystallinity

  8. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    Science.gov (United States)

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-05

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago.

  9. Unfolding Implementation in Industrial Market Segmentation

    DEFF Research Database (Denmark)

    Bøjgaard, John; Ellegaard, Chris

    2011-01-01

    of implementing industrial market segmentation is discussed and unfolded in this article. Extant literature has identified segmentation implementation as a core challenge for marketers, but also one, which has received limited empirical attention. Future research opportunities are formulated in this article......Market segmentation is an important method of strategic marketing and constitutes a cornerstone of the marketing literature. It has undergone extensive scientific inquiry during the past 50 years. Reporting on an extensive review of the market segmentation literature, the challenging task...... for marketing management. Three key elements and challenges connected to execution of market segmentation are identified — organization, motivation, and adaptation....

  10. Segmental patterning of the vertebrate embryonic axis.

    Science.gov (United States)

    Dequéant, Mary-Lee; Pourquié, Olivier

    2008-05-01

    The body axis of vertebrates is composed of a serial repetition of similar anatomical modules that are called segments or metameres. This particular mode of organization is especially conspicuous at the level of the periodic arrangement of vertebrae in the spine. The segmental pattern is established during embryogenesis when the somites--the embryonic segments of vertebrates--are rhythmically produced from the paraxial mesoderm. This process involves the segmentation clock, which is a travelling oscillator that interacts with a maturation wave called the wavefront to produce the periodic series of somites. Here, we review our current understanding of the segmentation process in vertebrates.

  11. Automatic Speech Segmentation Based on HMM

    Directory of Open Access Journals (Sweden)

    M. Kroul

    2007-06-01

    Full Text Available This contribution deals with the problem of automatic phoneme segmentation using HMMs. Automatization of speech segmentation task is important for applications, where large amount of data is needed to process, so manual segmentation is out of the question. In this paper we focus on automatic segmentation of recordings, which will be used for triphone synthesis unit database creation. For speech synthesis, the speech unit quality is a crucial aspect, so the maximal accuracy in segmentation is needed here. In this work, different kinds of HMMs with various parameters have been trained and their usefulness for automatic segmentation is discussed. At the end of this work, some segmentation accuracy tests of all models are presented.

  12. Unsupervised Performance Evaluation of Image Segmentation

    Directory of Open Access Journals (Sweden)

    Chabrier Sebastien

    2006-01-01

    Full Text Available We present in this paper a study of unsupervised evaluation criteria that enable the quantification of the quality of an image segmentation result. These evaluation criteria compute some statistics for each region or class in a segmentation result. Such an evaluation criterion can be useful for different applications: the comparison of segmentation results, the automatic choice of the best fitted parameters of a segmentation method for a given image, or the definition of new segmentation methods by optimization. We first present the state of art of unsupervised evaluation, and then, we compare six unsupervised evaluation criteria. For this comparative study, we use a database composed of 8400 synthetic gray-level images segmented in four different ways. Vinet's measure (correct classification rate is used as an objective criterion to compare the behavior of the different criteria. Finally, we present the experimental results on the segmentation evaluation of a few gray-level natural images.

  13. Metric Learning for Hyperspectral Image Segmentation

    Science.gov (United States)

    Bue, Brian D.; Thompson, David R.; Gilmore, Martha S.; Castano, Rebecca

    2011-01-01

    We present a metric learning approach to improve the performance of unsupervised hyperspectral image segmentation. Unsupervised spatial segmentation can assist both user visualization and automatic recognition of surface features. Analysts can use spatially-continuous segments to decrease noise levels and/or localize feature boundaries. However, existing segmentation methods use tasks-agnostic measures of similarity. Here we learn task-specific similarity measures from training data, improving segment fidelity to classes of interest. Multiclass Linear Discriminate Analysis produces a linear transform that optimally separates a labeled set of training classes. The defines a distance metric that generalized to a new scenes, enabling graph-based segmentation that emphasizes key spectral features. We describe tests based on data from the Compact Reconnaissance Imaging Spectrometer (CRISM) in which learned metrics improve segment homogeneity with respect to mineralogical classes.

  14. Image Segmentation Using Hierarchical Merge Tree

    Science.gov (United States)

    Liu, Ting; Seyedhosseini, Mojtaba; Tasdizen, Tolga

    2016-10-01

    This paper investigates one of the most fundamental computer vision problems: image segmentation. We propose a supervised hierarchical approach to object-independent image segmentation. Starting with over-segmenting superpixels, we use a tree structure to represent the hierarchy of region merging, by which we reduce the problem of segmenting image regions to finding a set of label assignment to tree nodes. We formulate the tree structure as a constrained conditional model to associate region merging with likelihoods predicted using an ensemble boundary classifier. Final segmentations can then be inferred by finding globally optimal solutions to the model efficiently. We also present an iterative training and testing algorithm that generates various tree structures and combines them to emphasize accurate boundaries by segmentation accumulation. Experiment results and comparisons with other very recent methods on six public data sets demonstrate that our approach achieves the state-of-the-art region accuracy and is very competitive in image segmentation without semantic priors.

  15. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

    OpenAIRE

    Hirokawa Takatsugu; Ikeda Kazuyoshi; Higo Junichi; Tomii Kentaro

    2008-01-01

    Abstract Background Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-l...

  16. An efficient iris segmentation approach

    Science.gov (United States)

    Gomai, Abdu; El-Zaart, A.; Mathkour, H.

    2011-10-01

    Iris recognition system became a reliable system for authentication and verification tasks. It consists of five stages: image acquisition, iris segmentation, iris normalization, feature encoding, and feature matching. Iris segmentation stage is one of the most important stages. It plays an essential role to locate the iris efficiently and accurately. In this paper, we present a new approach for iris segmentation using image processing technique. This approach is composed of four main parts. (1) Eliminating reflections of light on the eye image based on inverting the color of the grayscale image, filling holes in the intensity image, and inverting the color of the intensity image to get the original grayscale image without any reflections. (2) Pupil boundary detection based on dividing an eye image to nine sub-images and finding the minimum value of the mean intensity for each sub-image to get a suitable threshold value of pupil. (3) Enhancing the contrast of outer iris boundary using exponential operator to have sharp variation. (4) Outer iris boundary localization based on applying a gray threshold and morphological operations on the rectangular part of an eye image including the pupil and the outer boundaries of iris to find the small radius of outer iris boundary from the center of pupil. The proposed approach has been tested on CASIA v1.0 iris image database and other collected iris image database. The experimental results show that the approach is able to detect pupil and outer iris boundary with high accuracy results approximately 100% and reduce time consuming.

  17. Heterologous Packaging Signals on Segment 4, but Not Segment 6 or Segment 8, Limit Influenza A Virus Reassortment.

    Science.gov (United States)

    White, Maria C; Steel, John; Lowen, Anice C

    2017-06-01

    Influenza A virus (IAV) RNA packaging signals serve to direct the incorporation of IAV gene segments into virus particles, and this process is thought to be mediated by segment-segment interactions. These packaging signals are segment and strain specific, and as such, they have the potential to impact reassortment outcomes between different IAV strains. Our study aimed to quantify the impact of packaging signal mismatch on IAV reassortment using the human seasonal influenza A/Panama/2007/99 (H3N2) and pandemic influenza A/Netherlands/602/2009 (H1N1) viruses. Focusing on the three most divergent segments, we constructed pairs of viruses that encoded identical proteins but differed in the packaging signal regions on a single segment. We then evaluated the frequency with which segments carrying homologous versus heterologous packaging signals were incorporated into reassortant progeny viruses. We found that, when segment 4 (HA) of coinfecting parental viruses was modified, there was a significant preference for the segment containing matched packaging signals relative to the background of the virus. This preference was apparent even when the homologous HA constituted a minority of the HA segment population available in the cell for packaging. Conversely, when segment 6 (NA) or segment 8 (NS) carried modified packaging signals, there was no significant preference for homologous packaging signals. These data suggest that movement of NA and NS segments between the human H3N2 and H1N1 lineages is unlikely to be restricted by packaging signal mismatch, while movement of the HA segment would be more constrained. Our results indicate that the importance of packaging signals in IAV reassortment is segment dependent.IMPORTANCE Influenza A viruses (IAVs) can exchange genes through reassortment. This process contributes to both the highly diverse population of IAVs found in nature and the formation of novel epidemic and pandemic IAV strains. Our study sought to determine the

  18. Novel Facial Features Segmentation Algorithm

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An efficient algorithm for facial features extractions is proposed. The facial features we segment are the two eyes, nose and mouth. The algorithm is based on an improved Gabor wavelets edge detector, morphological approach to detect the face region and facial features regions, and an improved T-shape face mask to locate the extract location of facial features. The experimental results show that the proposed method is robust against facial expression, illumination, and can be also effective if the person wearing glasses, and so on.

  19. Operational Gesture Segmentation and Recognition

    Institute of Scientific and Technical Information of China (English)

    马赓宇; 林学訚

    2003-01-01

    Gesture analysis by computer is an important part of the human computer interface (HCI) and agesture analysis method was developed using a skin-color-based method to extract the area representing thehand in a single image with a distribution feature measurement designed to describe the hand shape in theimages. A hidden Markov model (HMM) based method was used to analyze the temporal variation andsegmentation of continuous operational gestures. Furthermore, a transition HMM was used to represent theperiod between gestures, so the method could segment continuous gestures and eliminate non-standardgestures. The system can analyze 2 frames per second, which is sufficient for real time analysis.

  20. Interferon Induced Focal Segmental Glomerulosclerosis

    Science.gov (United States)

    Bayram Kayar, Nuket; Alpay, Nadir; Hamdard, Jamshid; Emegil, Sebnem; Bag Soydas, Rabia; Baysal, Birol

    2016-01-01

    Behçet's disease is an inflammatory disease of unknown etiology which involves recurring oral and genital aphthous ulcers and ocular lesions as well as articular, vascular, and nervous system involvement. Focal segmental glomerulosclerosis (FSGS) is usually seen in viral infections, immune deficiency syndrome, sickle cell anemia, and hyperfiltration and secondary to interferon therapy. Here, we present a case of FSGS identified with kidney biopsy in a patient who had been diagnosed with Behçet's disease and received interferon-alpha treatment for uveitis and presented with acute renal failure and nephrotic syndrome associated with interferon. PMID:27847659

  1. A contrario line segment detection

    CERN Document Server

    von Gioi, Rafael Grompone

    2014-01-01

    The reliable detection of low-level image structures is an old and still challenging problem in computer vision. This?book leads a detailed tour through the LSD algorithm, a line segment detector designed to be fully automatic. Based on the a contrario framework, the algorithm works efficiently without the need of any parameter tuning. The design criteria are thoroughly explained and the algorithm's good and bad results are illustrated on real and synthetic images. The issues involved, as well as the strategies used, are common to many geometrical structure detection problems and some possible

  2. Segmentation of DNA into Coding and Noncoding Regions Based on Recursive Entropic Segmentation and Stop-Codon Statistics

    Directory of Open Access Journals (Sweden)

    Daniel Nicorici

    2004-01-01

    Full Text Available Heterogeneous DNA sequences can be partitioned into homogeneous domains that are comprised of the four nucleotides A, C, G, and T and the stop-codons. Recursively, we apply a new entropic segmentation method on DNA sequences using Jensen-Shannon and Jensen-Rényi divergences in order to find the borders between coding and noncoding DNA regions. We have chosen 12- and 18-symbol alphabets that capture (i the differential nucleotide composition in codons, and (ii the differential stop-codon composition along all the three phases in both strands of the DNA. The new segmentation method is based on the Jensen-Rényi divergence measure, nucleotide statistics, and stop-codon statistics in both DNA strands. The recursive segmentation process requires no prior training on known datasets. Consequently, for three entire genomes of bacteria, we find that the use of nucleotide composition, stop-codon composition, and Jensen-Rényi divergence improve the accuracy of finding the borders between coding and noncoding regions in DNA sequences.

  3. Genome instability in Lactobacillus rhamnosus GG.

    Science.gov (United States)

    Sybesma, Wilbert; Molenaar, Douwe; van IJcken, Wilfred; Venema, Koen; Kort, Remco

    2013-04-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the genomic islands LGGISL1,2. The deleted DNA segments consist of 34 genes in one isolate and 84 genes in the other and are flanked by identical insertion elements. Among the missing genes are the spaCBA genes, which encode pilin subunits involved in adhesion to mucus and persistence of the strains in the human intestinal tract. Subsequent quantitative PCR analyses of six commercial probiotic products confirmed that two more products contain a heterogeneous population of L. rhamnosus GG variants, including genotypes with or without spaC. These results underline the relevance for quality assurance and control measures targeting genome stability in probiotic strains and justify research assessing the effect of genetic rearrangements in probiotics on the outcome of in vitro and in vivo efficacy studies.

  4. Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

    Science.gov (United States)

    Uchiyama, Ikuo

    2008-10-31

    Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs) that maximally retains the conserved gene orders. The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

  5. Multiple genome alignment for identifying the core structure among moderately related microbial genomes

    Directory of Open Access Journals (Sweden)

    Uchiyama Ikuo

    2008-10-01

    Full Text Available Abstract Background Identifying the set of intrinsically conserved genes, or the genomic core, among related genomes is crucial for understanding prokaryotic genomes where horizontal gene transfers are common. Although core genome identification appears to be obvious among very closely related genomes, it becomes more difficult when more distantly related genomes are compared. Here, we consider the core structure as a set of sufficiently long segments in which gene orders are conserved so that they are likely to have been inherited mainly through vertical transfer, and developed a method for identifying the core structure by finding the order of pre-identified orthologous groups (OGs that maximally retains the conserved gene orders. Results The method was applied to genome comparisons of two well-characterized families, Bacillaceae and Enterobacteriaceae, and identified their core structures comprising 1438 and 2125 OGs, respectively. The core sets contained most of the essential genes and their related genes, which were primarily included in the intersection of the two core sets comprising around 700 OGs. The definition of the genomic core based on gene order conservation was demonstrated to be more robust than the simpler approach based only on gene conservation. We also investigated the core structures in terms of G+C content homogeneity and phylogenetic congruence, and found that the core genes primarily exhibited the expected characteristic, i.e., being indigenous and sharing the same history, more than the non-core genes. Conclusion The results demonstrate that our strategy of genome alignment based on gene order conservation can provide an effective approach to identify the genomic core among moderately related microbial genomes.

  6. Genome cartography: charting the apicomplexan genome.

    Science.gov (United States)

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology. Copyright © 2011 Elsevier Ltd. All rights reserved.

  7. Large-scale inference of the point mutational spectrum in human segmental duplications

    Directory of Open Access Journals (Sweden)

    Rognes Torbjørn

    2009-01-01

    Full Text Available Abstract Background Recent segmental duplications are relatively large (≥ 1 kb genomic regions of high sequence identity (≥ 90%. They cover approximately 4–5% of the human genome and play important roles in gene evolution and genomic disease. The DNA sequence differences between copies of a segmental duplication represent the result of various mutational events over time, since any two duplication copies originated from the same ancestral DNA sequence. Based on this fact, we have developed a computational scheme for inference of point mutational events in human segmental duplications, which we collectively term duplication-inferred mutations (DIMs. We have characterized these nucleotide substitutions by comparing them with high-quality SNPs from dbSNP, both in terms of sequence context and frequency of substitution types. Results Overall, DIMs show a lower ratio of transitions relative to transversions than SNPs, although this ratio approaches that of SNPs when considering DIMs within most recent duplications. Our findings indicate that DIMs and SNPs in general are caused by similar mutational mechanisms, with some deviances at the CpG dinucleotide. Furthermore, we discover a large number of reference SNPs that coincide with computationally inferred DIMs. The latter reflects how sequence variation in duplicated sequences can be misinterpreted as ordinary allelic variation. Conclusion In summary, we show how DNA sequence analysis of segmental duplications can provide a genome-wide mutational spectrum that mirrors recent genome evolution. The inferred set of nucleotide substitutions represents a valuable complement to SNPs for the analysis of genetic variation and point mutagenesis.

  8. Identification and RNA segment assignment of six structural proteins of Scylla serrata reovirus.

    Science.gov (United States)

    Yuan, Yangyang; Fan, Dongyang; Zhang, Zhao; Yang, Jifang; Liu, Jingwen; Chen, Jigang

    2016-08-01

    Scylla serrata reovirus (SsRV) is one of the most prevalent viral pathogens of the mud crab (S. serrata). The virus represents an unassigned novel genus in the Reoviridae family, and contains 12 double-stranded RNA genomic segments. Previous analysis of virion proteins concluded that SsRV contains at least eight structural proteins, ranging from 25 to 160 kDa. Here, tandem time-of-flight mass spectrometry and Western blotting were used to re-identify the structural proteins. The results indicate that proteins encoded by SsRV segments S1, S3, S6, S9, S11, and S12 are structural proteins.

  9. Plant Genome Duplication Database.

    Science.gov (United States)

    Lee, Tae-Ho; Kim, Junah; Robertson, Jon S; Paterson, Andrew H

    2017-01-01

    Genome duplication, widespread in flowering plants, is a driving force in evolution. Genome alignments between/within genomes facilitate identification of homologous regions and individual genes to investigate evolutionary consequences of genome duplication. PGDD (the Plant Genome Duplication Database), a public web service database, provides intra- or interplant genome alignment information. At present, PGDD contains information for 47 plants whose genome sequences have been released. Here, we describe methods for identification and estimation of dates of genome duplication and speciation by functions of PGDD.The database is freely available at http://chibba.agtec.uga.edu/duplication/.

  10. Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ming SUN; Yuan-Ping TANG; Xiang-Zong MENG; Wen-Wen ZHANG; Shan LI; Zhi-Rui DENG; Zheng-Kai XU; Ren-Tao SONG

    2006-01-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)n type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  11. Pathogenesis of Focal Segmental Glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Beom Jin Lim

    2016-11-01

    Full Text Available Focal segmental glomerulosclerosis (FSGS is characterized by focal and segmental obliteration of glomerular capillary tufts with increased matrix. FSGS is classified as collapsing, tip, cellular, perihilar and not otherwise specified variants according to the location and character of the sclerotic lesion. Primary or idiopathic FSGS is considered to be related to podocyte injury, and the pathogenesis of podocyte injury has been actively investigated. Several circulating factors affecting podocyte permeability barrier have been proposed, but not proven to cause FSGS. FSGS may also be caused by genetic alterations. These genes are mainly those regulating slit diaphragm structure, actin cytoskeleton of podocytes, and foot process structure. The mode of inheritance and age of onset are different according to the gene involved. Recently, the role of parietal epithelial cells (PECs has been highlighted. Podocytes and PECs have common mesenchymal progenitors, therefore, PECs could be a source of podocyte repopulation after podocyte injury. Activated PECs migrate along adhesion to the glomerular tuft and may also contribute to the progression of sclerosis. Markers of activated PECs, including CD44, could be used to distinguish FSGS from minimal change disease. The pathogenesis of FSGS is very complex; however, understanding basic mechanisms of podocyte injury is important not only for basic research, but also for daily diagnostic pathology practice.

  12. Segmented holographic spectrum splitting concentrator

    Science.gov (United States)

    Ayala, Silvana P.; Vorndran, Shelby; Wu, Yuechen; Chrysler, Benjamin; Kostuk, Raymond K.

    2016-09-01

    This paper presents a segmented parabolic concentrator employing holographic spectral filters that provide focusing and spectral bandwidth separation capability to the system. Strips of low band gap silicon photovoltaic (PV) cells are formed into a parabolic surface as shown by Holman et. al. [1]. The surface of the PV segments is covered with holographic elements formed in dichromated gelatin. The holographic elements are designed to transmit longer wavelengths to silicon cells, and to reflect short wavelength light towards a secondary collector where high-bandgap PV cells are mounted. The system can be optimized for different combinations of diffuse and direct solar illumination conditions for particular geographical locations by controlling the concentration ratio and filtering properties of the holographic elements. In addition, the reflectivity of the back contact of the silicon cells is used to increase the optical path length and light trapping. This potentially allows the use of thin film silicon for the low bandgap PV cell material. The optical design combines the focusing properties of the parabolic concentrator and the holographic element to control the concentration ratio and uniformity of the spectral distribution at the high bandgap cell location. The presentation concludes with a comparison of different spectrum splitting holographic filter materials for this application.

  13. Comparison of genomic data via statistical distribution.

    Science.gov (United States)

    Amiri, Saeid; Dinov, Ivo D

    2016-10-21

    Sequence comparison has become an essential tool in bioinformatics, because highly homologous sequences usually imply significant functional or structural similarity. Traditional sequence analysis techniques are based on preprocessing and alignment, which facilitate measuring and quantitative characterization of genetic differences, variability and complexity. However, recent developments of next generation and whole genome sequencing technologies give rise to new challenges that are related to measuring similarity and capturing rearrangements of large segments contained in the genome. This work is devoted to illustrating different methods recently introduced for quantifying sequence distances and variability. Most of the alignment-free methods rely on counting words, which are small contiguous fragments of the genome. Our approach considers the locations of nucleotides in the sequences and relies more on appropriate statistical distributions. The results of this technique for comparing sequences, by extracting information and comparing matching fidelity and location regularization information, are very encouraging, specifically to classify mutation sequences.

  14. Transcriptional control in the segmentation gene network of Drosophila.

    Directory of Open Access Journals (Sweden)

    Mark D Schroeder

    2004-09-01

    Full Text Available The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross- regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a

  15. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparu

  16. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  17. A New Framework for Interactive Images Segmentation

    Directory of Open Access Journals (Sweden)

    MUHAMMAD ASHRAF

    2017-07-01

    Full Text Available Image segmentation has become a widely studied research problem in image processing. There exist different graph based solutions for interactive image segmentation but the domain of image segmentation still needs persistent improvements. The segmentation quality of existing techniques generally depends on the manual input provided in beginning, therefore, these algorithms may not produce quality segmentation with initial seed labels provided by a novice user. In this work we investigated the use of cellular automata in image segmentation and proposed a new algorithm that follows a cellular automaton in label propagation. It incorporates both the pixels? local and global information in the segmentation process. We introduced the novel global constraints in automata evolution rules; hence proposed scheme of automata evolution is more effective than the automata based earlier evolution schemes. Global constraints are also effective in deceasing the sensitivity towards small changes made in manual input; therefore proposed approach is less dependent on label seed marks. It can produce the quality segmentation with modest user efforts. Segmentation results indicate that the proposed algorithm performs better than the earlier segmentation techniques.

  18. Handwriting segmentation of unconstrained Oriya text

    Indian Academy of Sciences (India)

    N Tripathy; U Pal

    2006-12-01

    Segmentation of handwritten text into lines, words and characters is one of the important steps in the handwritten text recognition process. In this paper we propose a water reservoir concept-based scheme for segmentation of unconstrained Oriya handwritten text into individual characters. Here, at first, the text image is segmented into lines, and the lines are then segmented into individual words. For line segmentation, the document is divided into vertical stripes. Analysing the heights of the water reservoirs obtained from different components of the document, the width of a stripe is calculated. Stripe-wise horizontal histograms are then computed and the relationship of the peak–valley points of the histograms is used for line segmentation. Based on vertical projection profiles and structural features of Oriya characters, text lines are segmented into words. For character segmentation, at first, the isolated and connected (touching) characters in a word are detected. Using structural, topological and water reservoir concept-based features, characters of the word that touch are then segmented. From experiments we have observed that the proposed “touching character” segmentation module has 96·7% accuracy for two-character touching strings.

  19. FIST: a fast interactive segmentation technique

    Science.gov (United States)

    Padfield, Dirk; Bhotika, Rahul; Natanzon, Alexander

    2015-03-01

    Radiologists are required to read thousands of patient images every day, and any tools that can improve their workflow to help them make efficient and accurate measurements is of great value. Such an interactive tool must be intuitive to use, and we have found that users are accustomed to clicking on the contour of the object for segmentation and would like the final segmentation to pass through these points. The tool must also be fast to enable real-time interactive feedback. To meet these needs, we present a segmentation workflow that enables an intuitive method for fast interactive segmentation of 2D and 3D objects. Given simple user clicks on the contour of an object in one 2D view, the algorithm generates foreground and background seeds and computes foreground and background distributions that are used to segment the object in 2D. It then propagates the information to the two orthogonal planes in a 3D volume and segments all three 2D views. The automated segmentation is automatically updated as the user continues to add points around the contour, and the algorithm is re-run using the total set of points. Based on the segmented objects in these three views, the algorithm then computes a 3D segmentation of the object. This process requires only limited user interaction to segment complex shapes and significantly improves the workflow of the user.

  20. Anatomy-aware measurement of segmentation accuracy

    Science.gov (United States)

    Tizhoosh, H. R.; Othman, A. A.

    2016-03-01

    Quantifying the accuracy of segmentation and manual delineation of organs, tissue types and tumors in medical images is a necessary measurement that suffers from multiple problems. One major shortcoming of all accuracy measures is that they neglect the anatomical significance or relevance of different zones within a given segment. Hence, existing accuracy metrics measure the overlap of a given segment with a ground-truth without any anatomical discrimination inside the segment. For instance, if we understand the rectal wall or urethral sphincter as anatomical zones, then current accuracy measures ignore their significance when they are applied to assess the quality of the prostate gland segments. In this paper, we propose an anatomy-aware measurement scheme for segmentation accuracy of medical images. The idea is to create a "master gold" based on a consensus shape containing not just the outline of the segment but also the outlines of the internal zones if existent or relevant. To apply this new approach to accuracy measurement, we introduce the anatomy-aware extensions of both Dice coefficient and Jaccard index and investigate their effect using 500 synthetic prostate ultrasound images with 20 different segments for each image. We show that through anatomy-sensitive calculation of segmentation accuracy, namely by considering relevant anatomical zones, not only the measurement of individual users can change but also the ranking of users' segmentation skills may require reordering.

  1. RSRM Segment Train Derailment and Recovery

    Science.gov (United States)

    Taylor Jr., Robert H.; McConnaugghey, Paul K.; Beaman, David E.; Moore, Dennis R.; Reed, Harry

    2008-01-01

    On May 2, 2007, a freight train carrying segments of the space shuttle's solid rocket boosters derailed in Myrtlewood, Alabama, after a rail trestle collapsed. The train was carrying Reusable Solid Rocket Motors (RSRM) 98 center and forward segments (STS-120) and RSRM 99 aft segments (STS-122). Initially, it was not known if the segments had been seriously damaged. Four segments dropped approximately 10 feet when the trestle collapsed and one of those four rolled off the track onto its side. The exit cones and the other four segments, not yet on the trestle, remained on solid ground. ATK and NASA immediately dispatched an investigation and recovery team to determine the safety of the situation and eventually the usability of the segments and exit cones for flight. Instrumentation on each segment provided invaluable data to determine the acceleration loads imparted into each loaded segment and exit cone. This paper details the incident, recovery plan and the team work that created a success story that ended with the safe launch of STS120 using the four center segments and the launch of STS122 using the Aft exit cones assemblies.

  2. How evolution of genomes is reflected in exact DNA sequence match statistics.

    Science.gov (United States)

    Massip, Florian; Sheinman, Michael; Schbath, Sophie; Arndt, Peter F

    2015-02-01

    Genome evolution is shaped by a multitude of mutational processes, including point mutations, insertions, and deletions of DNA sequences, as well as segmental duplications. These mutational processes can leave distinctive qualitative marks in the statistical features of genomic DNA sequences. One such feature is the match length distribution (MLD) of exactly matching sequence segments within an individual genome or between the genomes of related species. These have been observed to exhibit characteristic power law decays in many species. Here, we show that simple dynamical models consisting solely of duplication and mutation processes can already explain the characteristic features of MLDs observed in genomic sequences. Surprisingly, we find that these features are largely insensitive to details of the underlying mutational processes and do not necessarily rely on the action of natural selection. Our results demonstrate how analyzing statistical features of DNA sequences can help us reveal and quantify the different mutational processes that underlie genome evolution.

  3. Promoter Prediction on a Genomic Scale—The Adh Experience

    Science.gov (United States)

    Ohler, Uwe

    2000-01-01

    We describe our statistical system for promoter recognition in genomic DNA with which we took part in the Genome Annotation Assessment Project (GASP1). We applied two versions of the system: the first uses a region-based approach toward transcription start site identification, namely, interpolated Markov chains; the second was a hybrid approach combining regions and signals within a stochastic segment model. We compare the results of both versions with each other and examine how well the application on a genomic scale compares with the results we previously obtained on smaller data sets. PMID:10779494

  4. CDIS: Circle Density Based Iris Segmentation

    Science.gov (United States)

    Gupta, Anand; Kumari, Anita; Kundu, Boris; Agarwal, Isha

    Biometrics is an automated approach of measuring and analysing physical and behavioural characteristics for identity verification. The stability of the Iris texture makes it a robust biometric tool for security and authentication purposes. Reliable Segmentation of Iris is a necessary precondition as an error at this stage will propagate into later stages and requires proper segmentation of non-ideal images having noises like eyelashes, etc. Iris Segmentation work has been done earlier but we feel it lacks in detecting iris in low contrast images, removal of specular reflections, eyelids and eyelashes. Hence, it motivates us to enhance the said parameters. Thus, we advocate a new approach CDIS for Iris segmentation along with new algorithms for removal of eyelashes, eyelids and specular reflections and pupil segmentation. The results obtained have been presented using GAR vs. FAR graphs at the end and have been compared with prior works related to segmentation of iris.

  5. Segmentation of Offline Handwritten Bengali Script

    CERN Document Server

    Basu, Subhadip; Kundu, Mahantapas; Nasipuri, Mita; Basu, Dipak K

    2012-01-01

    Character segmentation has long been one of the most critical areas of optical character recognition process. Through this operation, an image of a sequence of characters, which may be connected in some cases, is decomposed into sub-images of individual alphabetic symbols. In this paper, segmentation of cursive handwritten script of world's fourth popular language, Bengali, is considered. Unlike English script, Bengali handwritten characters and its components often encircle the main character, making the conventional segmentation methodologies inapplicable. Experimental results, using the proposed segmentation technique, on sample cursive handwritten data containing 218 ideal segmentation points show a success rate of 97.7%. Further feature-analysis on these segments may lead to actual recognition of handwritten cursive Bengali script.

  6. Multi-scale Modelling of Segmentation

    DEFF Research Database (Denmark)

    Hartmann, Martin; Lartillot, Olivier; Toiviainen, Petri

    2016-01-01

    While listening to music, people often unwittingly break down musical pieces into constituent chunks such as verses and choruses. Music segmentation studies have suggested that some consensus regarding boundary perception exists, despite individual differences. However, neither the effects...... of experimental task (i.e., real-time vs. annotated segmentation), nor of musicianship on boundary perception are clear. Our study assesses musicianship effects and differences between segmentation tasks. We conducted a real-time experiment to collect segmentations by musicians and nonmusicians from nine musical...... pieces. In a second experiment on non-real-time segmentation, musicians indicated boundaries and their strength for six examples. Kernel density estimation was used to develop multi-scale segmentation models. Contrary to previous research, no relationship was found between boundary strength and boundary...

  7. Evaluating the bases of supplier segmentation

    DEFF Research Database (Denmark)

    Day, Marc; Magnan, Gregory M.; Munkgaard Møller, Morten

    2010-01-01

    A taxonomy of segmentation bases is presented which builds a multi-disciplinary approach to the categorization of suppliers. Supplier segmentation, from a purchasing perspective, still appears to be in the early stages of providing a coherent strategic intent behind supplier assessment. Whilst fr...... segmentation covering supply market conditions, product/service characteristics, supplier characteristics, buyer characteristics, and buyer-supplier relational factors.......A taxonomy of segmentation bases is presented which builds a multi-disciplinary approach to the categorization of suppliers. Supplier segmentation, from a purchasing perspective, still appears to be in the early stages of providing a coherent strategic intent behind supplier assessment. Whilst...... opportunism. We augment existing approaches with reference to inter-organisational theory and the resource-based view to show different modes of inter-firm value creation that act as constituents of a strategic intent for segmentation. Our resulting taxonomy draws together a holistic view of supplier...

  8. Devnagari document segmentation using histogram approach

    CERN Document Server

    Dongre, Vikas J; 10.5121/ijcseit.2011.1305

    2011-01-01

    Document segmentation is one of the critical phases in machine recognition of any language. Correct segmentation of individual symbols decides the accuracy of character recognition technique. It is used to decompose image of a sequence of characters into sub images of individual symbols by segmenting lines and words. Devnagari is the most popular script in India. It is used for writing Hindi, Marathi, Sanskrit and Nepali languages. Moreover, Hindi is the third most popular language in the world. Devnagari documents consist of vowels, consonants and various modifiers. Hence proper segmentation of Devnagari word is challenging. A simple histogram based approach to segment Devnagari documents is proposed in this paper. Various challenges in segmentation of Devnagari script are also discussed.

  9. Charged line segments and ellipsoidal equipotentials

    CERN Document Server

    Curtright, T L; Chen, X; Haddad, M J; Karayev, S; Khadka, D B; Li, J

    2016-01-01

    This is a survey of the electrostatic potentials produced by charged straight-line segments, in various numbers of spatial dimensions, with comparisons between uniformly charged segments and those having non-uniform linear charge distributions that give rise to ellipsoidal equipotentials surrounding the segments. A uniform linear distribution of charge is compatible with ellipsoidal equipotentials only for three dimensions. In higher dimensions, the linear charge density giving rise to ellipsoidal equipotentials is counter-intuitive --- the charge distribution has a maximum at the center of the segment and vanishes at the ends of the segment. Only in two dimensions is the continuous charge distribution intuitive --- for that one case of ellipsoidal equipotentials, the charge is peaked at the ends of the segment and minimized at the center.

  10. Milling Stability Analysis Based on Chebyshev Segmentation

    Science.gov (United States)

    HUANG, Jianwei; LI, He; HAN, Ping; Wen, Bangchun

    2016-09-01

    Chebyshev segmentation method was used to discretize the time period contained in delay differential equation, then the Newton second-order difference quotient method was used to calculate the cutter motion vector at each time endpoint, and the Floquet theory was used to determine the stability of the milling system after getting the transfer matrix of milling system. Using the above methods, a two degree of freedom milling system stability issues were investigated, and system stability lobe diagrams were got. The results showed that the proposed methods have the following advantages. Firstly, with the same calculation accuracy, the points needed to represent the time period are less by the Chebyshev Segmentation than those of the average segmentation, and the computational efficiency of the Chebyshev Segmentation is higher. Secondly, if the time period is divided into the same parts, the stability lobe diagrams got by Chebyshev segmentation method are more accurate than those of the average segmentation.

  11. Segmentation of Ancient Telugu Text Documents

    Directory of Open Access Journals (Sweden)

    Srinivasa Rao A.V

    2012-07-01

    Full Text Available OCR of ancient document images remains a challenging task till date. Scanning process itself introduces deformation of document images. Cleaning process of these document images will result in information loss. Segmentation contributes an invariance process in OCR. Complex scripts, like derivatives of Brahmi, encounter many problems in the segmentation process. Segmentation of meaningful units, (instead of isolated patterns, revealed interesting trends. A segmentation technique for the ancient Telugu document image into meaningful units is proposed. The topological features of the meaningful units within the script line are adopted as a basis, while segmenting the text line. Horizontal profile pattern is convolved with Gaussian kernel. The statistical properties of meaningful units are explored by extensively analyzing the geometrical patterns of the meaningful unit. The efficiency of the proposed algorithm involving segmentation process is found to be 73.5% for the case of uncleaned document images.

  12. Birefringence analysis of segmented cladding fiber.

    Science.gov (United States)

    Kumar, Ajeet; Rastogi, Vipul; Agrawal, Arti; Rahman, B M A

    2012-05-20

    We present a full-vectorial modal analysis of a segmented cladding fiber (SCF). The analysis is based on the H-field vectorial finite element method (VFEM) employing polar mesh geometry. Using this method, we have analyzed the circular SCF and the elliptical SCF. We have found that the birefringence of the circular SCF is very small (1.0×10(-8)). Birefringence of a highly elliptical SCF can be altered to some extent by the number of segments and duty cycle of segmentation in the segmented cladding. However, the change is not profound. The analysis shows that the circular SCF possesses low birefringence and that the segmented cladding does not add any significant birefringence in an elliptical fiber. This result strongly indicates that small deviations in the segmented cladding parameters arising from fabrication process do not significantly affect the birefringence of the fiber.

  13. Discriminative parameter estimation for random walks segmentation.

    Science.gov (United States)

    Baudin, Pierre-Yves; Goodman, Danny; Kumrnar, Puneet; Azzabou, Noura; Carlier, Pierre G; Paragios, Nikos; Kumar, M Pawan

    2013-01-01

    The Random Walks (RW) algorithm is one of the most efficient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner. However, one of the main drawbacks of using the RW algorithm is that its parameters have to be hand-tuned. we propose a novel discriminative learning framework that estimates the parameters using a training dataset. The main challenge we face is that the training samples are not fully supervised. Specifically, they provide a hard segmentation of the images, instead of a probabilistic segmentation. We overcome this challenge by treating the optimal probabilistic segmentation that is compatible with the given hard segmentation as a latent variable. This allows us to employ the latent support vector machine formulation for parameter estimation. We show that our approach significantly outperforms the baseline methods on a challenging dataset consisting of real clinical 3D MRI volumes of skeletal muscles.

  14. Hierarchical image segmentation for learning object priors

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.; Li, Nan [TEMPLE UNIV.

    2010-11-10

    The proposed segmentation approach naturally combines experience based and image based information. The experience based information is obtained by training a classifier for each object class. For a given test image, the result of each classifier is represented as a probability map. The final segmentation is obtained with a hierarchial image segmentation algorithm that considers both the probability maps and the image features such as color and edge strength. We also utilize image region hierarchy to obtain not only local but also semi-global features as input to the classifiers. Moreover, to get robust probability maps, we take into account the region context information by averaging the probability maps over different levels of the hierarchical segmentation algorithm. The obtained segmentation results are superior to the state-of-the-art supervised image segmentation algorithms.

  15. POST-HOC SEGMENTATION USING MARKETING RESEARCH

    Directory of Open Access Journals (Sweden)

    CRISTINEL CONSTANTIN

    2012-10-01

    Full Text Available This paper is about an instrumental research conducted in order to compare the information given by two multivariate data analysis used fordividing a population in clusters. These methods are K-means cluster and TwoStep cluster, which are available in SPSS system. Such methods could be used in post-hoc market segmentations, which allow companies to find segments with specific behaviours or attitudes. The research scope is to find which of the two methods is better for market segmentation practice. The outcomes reveal that every method has strong points and weaknesses. These ones are related to the relevance of segments description and the statistic significance of the difference between segments. In this respect, the researchers should compare the results of the named analyses and choose the method which better discriminate between the market segments.

  16. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  17. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  18. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  19. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  20. Learning an Interactive Segmentation System

    CERN Document Server

    Nickisch, Hannes; Rother, Carsten

    2009-01-01

    Many successful applications of computer vision to image or video manipulation are interactive by nature. However, parameters of such systems are often trained neglecting the user. Traditionally, interactive systems have been treated in the same manner as their fully automatic counterparts. Their performance is evaluated by computing the accuracy of their solutions under some fixed set of user interactions. This paper proposes a new evaluation and learning method which brings the user in the loop. It is based on the use of an active robot user - a simulated model of a human user. We show how this approach can be used to evaluate and learn parameters of state-of-the-art interactive segmentation systems. We also show how simulated user models can be integrated into the popular max-margin method for parameter learning and propose an algorithm to solve the resulting optimisation problem.

  1. Community study suggests segmentation strategies.

    Science.gov (United States)

    Gagnard, A

    1989-01-01

    Results of a sample survey commissioned by a voluntary health organization in a major metropolitan area describes why individuals give their time and money to charitable organizations and what approaches are likely to result in such donations. Within demographic subgroups, the variables of age and income proved to be important factors with respect to why people gave and what appeals they prefer. The variables of gender and education were found to be of somewhat less importance. Findings were compared with a national Gallup study conducted in 1987. In an era of increasingly specialized marketing for all organizations, the findings offer voluntary and fund-raising organizations a basis for determining appropriate appeals for demographic segments in a community.

  2. Segment adaptive gradient angle interpolation.

    Science.gov (United States)

    Zwart, Christine M; Frakes, David H

    2013-08-01

    We introduce a new edge-directed interpolator based on locally defined, straight line approximations of image isophotes. Spatial derivatives of image intensity are used to describe the principal behavior of pixel-intersecting isophotes in terms of their slopes. The slopes are determined by inverting a tridiagonal matrix and are forced to vary linearly from pixel-to-pixel within segments. Image resizing is performed by interpolating along the approximated isophotes. The proposed method can accommodate arbitrary scaling factors, provides state-of-the-art results in terms of PSNR as well as other quantitative visual quality metrics, and has the advantage of reduced computational complexity that is directly proportional to the number of pixels.

  3. Toxic Anterior Segment Syndrome (TASS

    Directory of Open Access Journals (Sweden)

    Özlem Öner

    2011-12-01

    Full Text Available Toxic anterior segment syndrome (TASS is a sterile intraocular inflammation caused by noninfectious substances, resulting in extensive toxic damage to the intraocular tissues. Possible etiologic factors of TASS include surgical trauma, bacterial endotoxin, intraocular solutions with inappropriate pH and osmolality, preservatives, denatured ophthalmic viscosurgical devices (OVD, inadequate sterilization, cleaning and rinsing of surgical devices, intraocular lenses, polishing and sterilizing compounds which are related to intraocular lenses. The characteristic signs and symptoms such as blurred vision, corneal edema, hypopyon and nonreactive pupil usually occur 24 hours after the cataract surgery. The differential diagnosis of TASS from infectious endophthalmitis is important. The main treatment for TASS formation is prevention. TASS is a cataract surgery complication that is more commonly seen nowadays. In this article, the possible underlying causes as well as treatment and prevention methods of TASS are summarized. (Turk J Oph thal mol 2011; 41: 407-13

  4. An algorithm for segmenting range imagery

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, R.S.

    1997-03-01

    This report describes the technical accomplishments of the FY96 Cross Cutting and Advanced Technology (CC&AT) project at Los Alamos National Laboratory. The project focused on developing algorithms for segmenting range images. The image segmentation algorithm developed during the project is described here. In addition to segmenting range images, the algorithm can fuse multiple range images thereby providing true 3D scene models. The algorithm has been incorporated into the Rapid World Modelling System at Sandia National Laboratory.

  5. Communication with market segments - travel agencies' perspective

    OpenAIRE

    Lorena Bašan; Jasmina Dlačić; Željko Trezner

    2013-01-01

    Purpose – The purpose of this paper is to research the travel agencies’ communication with market segments. Communication with market segments takes into account marketing communication means as well as the implementation of different business orientations. Design – Special emphasis is placed on the use of different marketing communication means and their efficiency. Research also explores business orientation adaptation when approaching different market segments. Methodology – In explo...

  6. Distance measures for image segmentation evaluation

    OpenAIRE

    Monteiro, Fernando C.; Campilho, Aurélio C.

    2012-01-01

    In this paper we present a study of evaluation measures that enable the quantification of the quality of an image segmentation result. Despite significant advances in image segmentation techniques, evaluation of these techniques thus far has been largely subjective. Typically, the effectiveness of a new algorithm is demonstrated only by the presentation of a few segmented images and is otherwise left to subjective evaluation by the reader. Such an evaluation criterion can be useful for differ...

  7. Cluster Ensemble-based Image Segmentation

    OpenAIRE

    Xiaoru Wang; Junping Du; Shuzhe Wu; Xu Li; Fu Li

    2013-01-01

    Image segmentation is the foundation of computer vision applications. In this paper, we propose a new cluster ensemble-based image segmentation algorithm, which overcomes several problems of traditional methods. We make two main contributions in this paper. First, we introduce the cluster ensemble concept to fuse the segmentation results from different types of visual features effectively, which can deliver a better final result and achieve a much more stable performance for broad categories ...

  8. Efficient segmentation by sparse pixel classification

    DEFF Research Database (Denmark)

    Dam, Erik B; Loog, Marco

    2008-01-01

    Segmentation methods based on pixel classification are powerful but often slow. We introduce two general algorithms, based on sparse classification, for optimizing the computation while still obtaining accurate segmentations. The computational costs of the algorithms are derived......, and they are demonstrated on real 3-D magnetic resonance imaging and 2-D radiograph data. We show that each algorithm is optimal for specific tasks, and that both algorithms allow a speedup of one or more orders of magnitude on typical segmentation tasks....

  9. MRI Brain Tumor Segmentation Methods- A Review

    OpenAIRE

    Gursangeet, Kaur; Jyoti, Rani

    2016-01-01

    Medical image processing and its segmentation is an active and interesting area for  researchers. It has reached at the tremendous place in diagnosing tumors after the discovery of CT and MRI. MRI is an useful tool to detect the brain tumor and segmentation is performed to carry out the useful portion from an image. The purpose of this paper is to provide an overview of different image segmentation methods like watershed algorithm, morphological operations, neutrosophic sets, thresholding, K-...

  10. A unique case of segmental vasal atresia

    Science.gov (United States)

    Alalayet, Yasen Fayez; Alkasim, F; Shiba, N; Aldhuayan, I; Alhamaidi, S; Alghamdi, G; Aljobair, F; Shoura, J; Alkhlaif, R

    2014-01-01

    We report a case of a 2-year-old boy who presented with an empty left scrotum. Clinical examination revealed a left palpable undescended testis. During orchidopexy, segmental atresia of the vas deferens was found, and microsurgical repair was carried out. Segmental vasal atresia is an extremely rare condition and is infrequently diagnosed, especially in the pediatric age group. This is the first reported case of segmental vasal atresia without an association with cystic fibrosis. PMID:25419520

  11. Lifestyle market segmentation - efficiency and ethical issues

    OpenAIRE

    Pilstl, Michaela

    2010-01-01

    Lifestyle market segmentation can be very supportive for a successful marketing strategy of a company. However it is not clear whether lifestyle market segmentation is efficient and ethical or not. Several market segmentation concepts such as Cross-Cultural Consumer Characterization, VALS, PRIZM NE, Mosaic, ConneXions NE and GfK Roper Consumer Styles are analyzed in order to give an extensive overview of the offered concepts. The observation of efficiency issues in regards to market segmentat...

  12. Image Segmentation by Using Threshold Techniques

    CERN Document Server

    Al-amri, Salem Saleh; D., Khamitkar S

    2010-01-01

    This paper attempts to undertake the study of segmentation image techniques by using five threshold methods as Mean method, P-tile method, Histogram Dependent Technique (HDT), Edge Maximization Technique (EMT) and visual Technique and they are compared with one another so as to choose the best technique for threshold segmentation techniques image. These techniques applied on three satellite images to choose base guesses for threshold segmentation image.

  13. Military display market segment: helicopters

    Science.gov (United States)

    Desjardins, Daniel D.; Hopper, Darrel G.

    2004-09-01

    The military display market is analyzed in terms of one of its segments: helicopter displays. Parameters requiring special consideration, to include luminance ranges, contrast ratio, viewing angles, and chromaticity coordinates, are examined. Performance requirements for rotary-wing displays relative to several premier applications are summarized. Display sizes having aggregate defense applications of 5,000 units or greater and having DoD applications across 10 or more platforms, are tabulated. The issue of size commonality is addressed where distribution of active area sizes across helicopter platforms, individually, in groups of two through nine, and ten or greater, is illustrated. Rotary-wing displays are also analyzed by technology, where total quantities of such displays are broken out into CRT, LCD, AMLCD, EM, LED, Incandescent, Plasma and TFEL percentages. Custom, versus Rugged commercial, versus commercial off-the-shelf designs are contrasted. High and low information content designs are identified. Displays for several high-profile military helicopter programs are discussed, to include both technical specifications and program history. The military display market study is summarized with breakouts for the helicopter market segment. Our defense-wide study as of March 2004 has documented 1,015,494 direct view and virtual image displays distributed across 1,181 display sizes and 503 weapon systems. Helicopter displays account for 67,472 displays (just 6.6% of DoD total) and comprise 83 sizes (7.0% of total DoD) in 76 platforms (15.1% of total DoD). Some 47.6% of these rotary-wing applications involve low information content displays comprising just a few characters in one color; however, as per fixed-wing aircraft, the predominant instantiation involves higher information content units capable of showing changeable graphics, color and video.

  14. Bayesian segmentation of brainstem structures in MRI

    DEFF Research Database (Denmark)

    Iglesias, Juan Eugenio; Van Leemput, Koen; Bhatt, Priyanka

    2015-01-01

    In this paper we present a method to segment four brainstem structures (midbrain, pons, medulla oblongata and superior cerebellar peduncle) from 3D brain MRI scans. The segmentation method relies on a probabilistic atlas of the brainstem and its neighboring brain structures. To build the atlas, we...... the brainstem structures in novel scans. Thanks to the generative nature of the scheme, the segmentation method is robust to changes in MRI contrast or acquisition hardware. Using cross validation, we show that the algorithm can segment the structures in previously unseen T1 and FLAIR scans with great accuracy...

  15. Adaptive textural segmentation of medical images

    Science.gov (United States)

    Kuklinski, Walter S.; Frost, Gordon S.; MacLaughlin, Thomas

    1992-06-01

    A number of important problems in medical imaging can be described as segmentation problems. Previous fractal-based image segmentation algorithms have used either the local fractal dimension alone or the local fractal dimension and the corresponding image intensity as features for subsequent pattern recognition algorithms. An image segmentation algorithm that utilized the local fractal dimension, image intensity, and the correlation coefficient of the local fractal dimension regression analysis computation, to produce a three-dimension feature space that was partitioned to identify specific pixels of dental radiographs as being either bone, teeth, or a boundary between bone and teeth also has been reported. In this work we formulated the segmentation process as a configurational optimization problem and discuss the application of simulated annealing optimization methods to the solution of this specific optimization problem. The configurational optimization method allows information about both, the degree of correspondence between a candidate segment and an assumed textural model, and morphological information about the candidate segment to be used in the segmentation process. To apply this configurational optimization technique with a fractal textural model however, requires the estimation of the fractal dimension of an irregularly shaped candidate segment. The potential utility of a discrete Gerchberg-Papoulis bandlimited extrapolation algorithm to the estimation of the fractal dimension of an irregularly shaped candidate segment is also discussed.

  16. VIDEO SEGMENTATION USING A NOVEL LBP DESCRIPTOR

    Directory of Open Access Journals (Sweden)

    Zhongkun He

    2014-08-01

    Full Text Available Video segmentation is the basis for content-based video retrieval, object recognition, object tracking, and video compression. This paper proposes a kind of novel and easy spatial-temporal LBP coding method, using the spatial-temporal 2 × 2 × 2 neighborhood clique to encode the changes in a video. Based on the coding method, a scheme of video segmentation is developed. Compared to the traditional segmentation method, its distinguished advantage is that it does not need to construct the background model and is simple in computation. Experimental results indicate that this new algorithm can give satisfying segmentation results.

  17. A molecular view of onychophoran segmentation.

    Science.gov (United States)

    Janssen, Ralf

    2017-02-14

    This paper summarizes our current knowledge on the expression and assumed function of Drosophila and (other) arthropod segmentation gene orthologs in Onychophora, a closely related outgroup to Arthropoda. This includes orthologs of the so-called Drosophila segmentation gene cascade including the Hox genes, as well as other genetic factors and pathways involved in non-drosophilid arthropods. Open questions about and around the topic are addressed, such as the definition of segments in onychophorans, the unclear regulation of conserved expression patterns downstream of non-conserved factors, and the potential role of mesodermal patterning in onychophoran segmentation.

  18. Polarimetric Segmentation Using Wishart Test Statistic

    DEFF Research Database (Denmark)

    Skriver, Henning; Schou, Jesper; Nielsen, Allan Aasbjerg;

    2002-01-01

    A newly developed test statistic for equality of two complex covariance matrices following the complex Wishart distribution and an associated asymptotic probability for the test statistic has been used in a segmentation algorithm. The segmentation algorithm is based on the MUM (merge using moments......) approach, which is a merging algorithm for single channel SAR images. The polarimetric version described in this paper uses the above-mentioned test statistic for merging. The segmentation algorithm has been applied to polarimetric SAR data from the Danish dual-frequency, airborne polarimetric SAR, EMISAR....... The results show clearly an improved segmentation performance for the full polarimetric algorithm compared to single channel approaches....

  19. Review of segmentation process in consumer markets

    Directory of Open Access Journals (Sweden)

    Veronika Jadczaková

    2013-01-01

    Full Text Available Although there has been a considerable debate on market segmentation over five decades, attention was merely devoted to single stages of the segmentation process. In doing so, stages as segmentation base selection or segments profiling have been heavily covered in the extant literature, whereas stages as implementation of the marketing strategy or market definition were of a comparably lower interest. Capitalizing on this shortcoming, this paper strives to close the gap and provide each step of the segmentation process with equal treatment. Hence, the objective of this paper is two-fold. First, a snapshot of the segmentation process in a step-by-step fashion will be provided. Second, each step (where possible will be evaluated on chosen criteria by means of description, comparison, analysis and synthesis of 32 academic papers and 13 commercial typology systems. Ultimately, the segmentation stages will be discussed with empirical findings prevalent in the segmentation studies and last but not least suggestions calling for further investigation will be presented. This seven-step-framework may assist when segmenting in practice allowing for more confidential targeting which in turn might prepare grounds for creating of a differential advantage.

  20. Simultaneous Segmentation and Statistical Label Fusion.

    Science.gov (United States)

    Asman, Andrew J; Landmana, Bennett A

    2012-02-23

    Labeling or segmentation of structures of interest in medical imaging plays an essential role in both clinical and scientific understanding. Two of the common techniques to obtain these labels are through either fully automated segmentation or through multi-atlas based segmentation and label fusion. Fully automated techniques often result in highly accurate segmentations but lack the robustness to be viable in many cases. On the other hand, label fusion techniques are often extremely robust, but lack the accuracy of automated algorithms for specific classes of problems. Herein, we propose to perform simultaneous automated segmentation and statistical label fusion through the reformulation of a generative model to include a linkage structure that explicitly estimates the complex global relationships between labels and intensities. These relationships are inferred from the atlas labels and intensities and applied to the target using a non-parametric approach. The novelty of this approach lies in the combination of previously exclusive techniques and attempts to combine the accuracy benefits of automated segmentation with the robustness of a multi-atlas based approach. The accuracy benefits of this simultaneous approach are assessed using a multi-label multi- atlas whole-brain segmentation experiment and the segmentation of the highly variable thyroid on computed tomography images. The results demonstrate that this technique has major benefits for certain types of problems and has the potential to provide a paradigm shift in which the lines between statistical label fusion and automated segmentation are dramatically blurred.

  1. Probabilistic Segmentation of Folk Music Recordings

    Directory of Open Access Journals (Sweden)

    Ciril Bohak

    2016-01-01

    Full Text Available The paper presents a novel method for automatic segmentation of folk music field recordings. The method is based on a distance measure that uses dynamic time warping to cope with tempo variations and a dynamic programming approach to handle pitch drifting for finding similarities and estimating the length of repeating segment. A probabilistic framework based on HMM is used to find segment boundaries, searching for optimal match between the expected segment length, between-segment similarities, and likely locations of segment beginnings. Evaluation of several current state-of-the-art approaches for segmentation of commercial music is presented and their weaknesses when dealing with folk music are exposed, such as intolerance to pitch drift and variable tempo. The proposed method is evaluated and its performance analyzed on a collection of 206 folk songs of different ensemble types: solo, two- and three-voiced, choir, instrumental, and instrumental with singing. It outperforms current commercial music segmentation methods for noninstrumental music and is on a par with the best for instrumental recordings. The method is also comparable to a more specialized method for segmentation of solo singing folk music recordings.

  2. Study on segmented distribution for reliability evaluation

    Directory of Open Access Journals (Sweden)

    Huaiyuan Li

    2017-02-01

    Full Text Available In practice, the failure rate of most equipment exhibits different tendencies at different stages and even its failure rate curve behaves a multimodal trace during its life cycle. As a result, traditionally evaluating the reliability of equipment with a single model may lead to severer errors. However, if lifetime is divided into several different intervals according to the characteristics of its failure rate, piecewise fitting can more accurately approximate the failure rate of equipment. Therefore, in this paper, failure rate is regarded as a piecewise function, and two kinds of segmented distribution are put forward to evaluate reliability. In order to estimate parameters in the segmented reliability function, Bayesian estimation and maximum likelihood estimation (MLE of the segmented distribution are discussed in this paper. Since traditional information criterion is not suitable for the segmented distribution, an improved information criterion is proposed to test and evaluate the segmented reliability model in this paper. After a great deal of testing and verification, the segmented reliability model and its estimation methods presented in this paper are proven more efficient and accurate than the traditional non-segmented single model, especially when the change of the failure rate is time-phased or multimodal. The significant performance of the segmented reliability model in evaluating reliability of proximity sensors of leading-edge flap in civil aircraft indicates that the segmented distribution and its estimation method in this paper could be useful and accurate.

  3. DT-MRI segmentation using graph cuts

    Science.gov (United States)

    Weldeselassie, Yonas T.; Hamarneh, Ghassan

    2007-03-01

    An important problem in medical image analysis is the segmentation of anatomical regions of interest. Once regions of interest are segmented, one can extract shape, appearance, and structural features that can be analyzed for disease diagnosis or treatment evaluation. Diffusion tensor magnetic resonance imaging (DT-MRI) is a relatively new medical imaging modality that captures unique water diffusion properties and fiber orientation information of the imaged tissues. In this paper, we extend the interactive multidimensional graph cuts segmentation technique to operate on DT-MRI data by utilizing latest advances in tensor calculus and diffusion tensor dissimilarity metrics. The user interactively selects certain tensors as object ("obj") or background ("bkg") to provide hard constraints for the segmentation. Additional soft constraints incorporate information about both regional tissue diffusion as well as boundaries between tissues of different diffusion properties. Graph cuts are used to find globally optimal segmentation of the underlying 3D DT-MR image among all segmentations satisfying the constraints. We develop a graph structure from the underlying DT-MR image with the tensor voxels corresponding to the graph vertices and with graph edge weights computed using either Log-Euclidean or the J-divergence tensor dissimilarity metric. The topology of our segmentation is unrestricted and both obj and bkg segments may consist of several isolated parts. We test our method on synthetic DT data and apply it to real 2D and 3D MRI, providing segmentations of the corpus callosum in the brain and the ventricles of the heart.

  4. Wavelet-based technique for target segmentation

    Science.gov (United States)

    Sadjadi, Firooz A.

    1995-07-01

    Segmentation of targets embedded in clutter obtained by IR imaging sensors is one of the challenging problems in automatic target recognition (ATR). In this paper a new texture-based segmentation technique is presented that uses the statistics of 2D wavelet decomposition components of the lcoal sections of the image. A measure of statistical similarity is then used to segment the image and separate the target from the background. This technique is applied on a set of real sequential IR imagery and has shown to produce a high degree of segmentation accuracy across varying ranges.

  5. Interactive segmentation techniques algorithms and performance evaluation

    CERN Document Server

    He, Jia; Kuo, C-C Jay

    2013-01-01

    This book focuses on interactive segmentation techniques, which have been extensively studied in recent decades. Interactive segmentation emphasizes clear extraction of objects of interest, whose locations are roughly indicated by human interactions based on high level perception. This book will first introduce classic graph-cut segmentation algorithms and then discuss state-of-the-art techniques, including graph matching methods, region merging and label propagation, clustering methods, and segmentation methods based on edge detection. A comparative analysis of these methods will be provided

  6. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  7. A Unique 10 Segment Display for Bengali Numerals

    CERN Document Server

    Azad, Md Abul Kalam; Ahmad, Shabbir; Kamruzzaman, S M

    2010-01-01

    Segmented display is widely used for efficient display of alphanumeric characters. English numerals are displayed by 7 segment and 16 segment display. The segment size is uniform in this two display architecture. Display architecture using 8, 10, 11, 18 segments have been proposed for Bengali numerals 0...9 yet no display architecture is designed using segments of uniform size and uniform power consumption. In this paper we have proposed a uniform 10 segment architecture for Bengali numerals. This segment architecture uses segments of uniform size and no bent segment is used.

  8. Long-read sequence assembly of the gorilla genome

    Science.gov (United States)

    Gordon, David; Huddleston, John; Chaisson, Mark J. P.; Hill, Christopher M.; Kronenberg, Zev N.; Munson, Katherine M.; Malig, Maika; Raja, Archana; Fiddes, Ian; Hillier, LaDeana W.; Dunn, Christopher; Baker, Carl; Armstrong, Joel; Diekhans, Mark; Paten, Benedict; Shendure, Jay; Wilson, Richard K.; Haussler, David; Chin, Chen-Shan; Eichler, Evan E.

    2016-01-01

    Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome. PMID:27034376

  9. An overview on genome organization of marine organisms.

    Science.gov (United States)

    Costantini, Maria

    2015-12-01

    In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights.

  10. DHPC: a new tool to express genome structural features.

    Science.gov (United States)

    Deng, Xuegong; Deng, Xuemei; Rayner, Simon; Liu, Xiangdong; Zhang, Qingling; Yang, Yupu; Li, Ning

    2008-05-01

    The DHPC (DNA Hilbert-Peano curve) is a new tool for visualizing large-scale genome sequences by mapping sequences into a two-dimensional square. It utilizes the space-filling function of Hilbert-Peano mapping. By applying a Gauss smoothing technique and a user-defined color function, a large-scale genome sequence can be mapped into a two-dimensional color image. In the calculated DHPCs, many genome characteristics are revealed. In this article we introduce the method and show how DHPCs may be used to identify regions of different base composition. The power of the method is demonstrated by presenting multiple examples such as repeating sequences, degree of base bias, regions of homogeneity and their boundaries, and mark of annotated segments. We also present several genome curves generated by DHPC to demonstrate how DHPC can be used to find previously unidentified sequence features in these genomes.

  11. Genome-wide transcription analyses in rice using tiling microarrays

    DEFF Research Database (Denmark)

    Li, Lei; Wang, Xiangfeng; Stolc, Viktor;

    2006-01-01

    Sequencing and computational annotation revealed several features, including high gene numbers, unusual composition of the predicted genes and a large number of genes lacking homology to known genes, that distinguish the rice (Oryza sativa) genome from that of other fully sequenced model species....... We report here a full-genome transcription analysis of the indica rice subspecies using high-density oligonucleotide tiling microarrays. Our results provided expression data support for the existence of 35,970 (81.9%) annotated gene models and identified 5,464 unique transcribed intergenic regions...... activity between duplicated segments of the genome. Collectively, our results provide the first whole-genome transcription map useful for further understanding the rice genome. Udgivelsesdato: 2006-Jan...

  12. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  13. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  14. Between Two Fern Genomes

    OpenAIRE

    Sessa, Emily B.; Banks, Jo; Michael S Barker; Der, Joshua P; Duffy, Aaron M; Graham, Sean W.; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D; Kathleen M. Pryer; Rothfels, Carl J.; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M.

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense divers...

  15. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  16. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  17. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  18. Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation.

    Science.gov (United States)

    Chiu, Stephanie J; Li, Xiao T; Nicholas, Peter; Toth, Cynthia A; Izatt, Joseph A; Farsiu, Sina

    2010-08-30

    Segmentation of anatomical and pathological structures in ophthalmic images is crucial for the diagnosis and study of ocular diseases. However, manual segmentation is often a time-consuming and subjective process. This paper presents an automatic approach for segmenting retinal layers in Spectral Domain Optical Coherence Tomography images using graph theory and dynamic programming. Results show that this method accurately segments eight retinal layer boundaries in normal adult eyes more closely to an expert grader as compared to a second expert grader.

  19. Market Segmentation in Business Technology Base: The Case of Segmentation of Sparkling

    OpenAIRE

    Valéria Riscarolli; Universidade Nove de Julho - UNINOVE; Sandra Regina Silva dos Santos Souza; Universidade Nove de Julho - UNINOVE; Leonel Cezar Rodrigues; Universidade Nove de Julho - UNINOVE; Fabrícia Durieux Zucco; FURB e UNIVALI

    2014-01-01

    A common market segmentation premise for products and services rules consumer behavior as the segmentation center piece. Would this be the logic for segmentation used by small technology based companies? In this article we target at determining the principles of market segmentation used by a vitiwinery company, as research object. This company is recognized by its products excellence, either in domestic as well as in the foreign market, among 13 distinct countries. The research method used is...

  20. Automatic pelvis segmentation from x-ray images of a mouse model

    Science.gov (United States)

    Al Okashi, Omar M.; Du, Hongbo; Al-Assam, Hisham

    2017-05-01

    The automatic detection and quantification of skeletal structures has a variety of different applications for biological research. Accurate segmentation of the pelvis from X-ray images of mice in a high-throughput project such as the Mouse Genomes Project not only saves time and cost but also helps achieving an unbiased quantitative analysis within the phenotyping pipeline. This paper proposes an automatic solution for pelvis segmentation based on structural and orientation properties of the pelvis in X-ray images. The solution consists of three stages including pre-processing image to extract pelvis area, initial pelvis mask preparation and final pelvis segmentation. Experimental results on a set of 100 X-ray images showed consistent performance of the algorithm. The automated solution overcomes the weaknesses of a manual annotation procedure where intra- and inter-observer variations cannot be avoided.