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Sample records for hybrid mapping revealed

  1. Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions.

    Science.gov (United States)

    Turner, Leslie M; Harr, Bettina

    2014-12-09

    Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone between M. musculus musculus and M. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.

  2. Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea).

    Science.gov (United States)

    Xiao, Zhiliang; Hu, Yang; Zhang, Xiaoli; Xue, Yuqian; Fang, Zhiyuan; Yang, Limei; Zhang, Yangyong; Liu, Yumei; Li, Zhansheng; Liu, Xing; Liu, Zezhou; Lv, Honghao; Zhuang, Mu

    2017-06-05

    Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage ( Brassica oleracea ) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2 , respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1 , seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380 ) were found, whereas in the region of BoHL2 , two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810 ) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.

  3. Zebrafish syntenic relationship to human/mouse genomes revealed by radiation hybrid mapping

    International Nuclear Information System (INIS)

    Samonte, Irene E.

    2007-01-01

    Zebrafish (Danio rerio) is an excellent model system for vertebrate developmental analysis and a new model for human disorders. In this study, however, zebrafish was used to determine its syntenic relationship to human/mouse genomes using the zebrafish-hamster radiation hybrid panel. The focus was on genes residing on chromosomes 6 and 17 of human and mouse, respectively, and some other genes of either immunologic or evolutionary importance. Gene sequences of interest and zebrafish expressed sequence tags deposited in the GenBank were used in identifying zebrafish homologs. Polymerase chain reaction (PCR) amplification, cloning and subcloning, sequencing, and phylogenetic analysis were done to confirm the homology of the candidate genes in zebrafish. The promising markers were then tested in the 94 zebrafish-hamster radiation hybrid panel cell lines and submitted for logarithm of the odds (LOD) score analysis to position genes on the zebrafish map. A total of 19 loci were successfully mapped to zebrafish linkage groups 1, 14, 15, 19, and 20. Four of these loci were positioned in linkage group 20, whereas, 3 more loci were added in linkage group 19, thus increasing to 34 loci the number of human genes syntenic to the group. With the sequencing of the zebrafish genome, about 20 more MHC genes were reported linked on the same group. (Author)

  4. Radiation hybrid mapping of human chromosome 18

    International Nuclear Information System (INIS)

    Francke, U.; Moon, A.J.; Chang, E.; Foellmer, B.; Strauss, B.; Haschke, A.; Chihlin Hsieh; Geigl, E.M.; Welch, S.

    1990-01-01

    The authors have generated a Chinese hamster V79/380-6 HPRT minus x human leukocyte hybrid cell line (18/V79) with chromosome 18 as the only human chromosome that is retained at high frequency without specific selection. Hybrid cells were selected in HAT medium, and 164 individual colonies were isolated. Of 110 colonies screened for human DNA by PCR amplification using a primer specific for human Alu repeats 67 (61%) were positive. These were expanded in culture for large-scale DNA preparations. Retesting expanded clones by PCR with Alu and LINE primers has revealed unique patterns of amplification products. In situ hybridization of biotin labelled total human DNA to metaphase spreads from various hybrids revealed the presence of one or more human DNA fragments integrated in hamster chromosomes. The authors have generated a resource that should allow the construction of a radiation map, to be compared with the YAC contig map also under construction in their laboratory

  5. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet.

    Directory of Open Access Journals (Sweden)

    Sirjan Sapkota

    Full Text Available Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae. The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass is the apospory-specific genomic region (ASGR. Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH and varied in both karyotype and position of the ASGR on the ASGR-carrier chromosome among other apomictic Cenchrus/Pennisetum species. Using in silico transcript mapping and verification of physical positions of some of the transcripts via FISH, we discovered that the ASGR-carrier chromosome from P. squamulatum is collinear with chromosome 2 of foxtail millet and sorghum outside of the ASGR. The in silico ordering of the ASGR-carrier chromosome markers, previously unmapped in P. squamulatum, allowed for the identification of a backcross line with structural changes to the P. squamulatum ASGR-carrier chromosome derived from gamma irradiated pollen.

  6. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet.

    Science.gov (United States)

    Sapkota, Sirjan; Conner, Joann A; Hanna, Wayne W; Simon, Bindu; Fengler, Kevin; Deschamps, Stéphane; Cigan, Mark; Ozias-Akins, Peggy

    2016-01-01

    Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) and varied in both karyotype and position of the ASGR on the ASGR-carrier chromosome among other apomictic Cenchrus/Pennisetum species. Using in silico transcript mapping and verification of physical positions of some of the transcripts via FISH, we discovered that the ASGR-carrier chromosome from P. squamulatum is collinear with chromosome 2 of foxtail millet and sorghum outside of the ASGR. The in silico ordering of the ASGR-carrier chromosome markers, previously unmapped in P. squamulatum, allowed for the identification of a backcross line with structural changes to the P. squamulatum ASGR-carrier chromosome derived from gamma irradiated pollen.

  7. In Silico and Fluorescence In Situ Hybridization Mapping Reveals Collinearity between the Pennisetum squamulatum Apomixis Carrier-Chromosome and Chromosome 2 of Sorghum and Foxtail Millet

    OpenAIRE

    Sapkota, Sirjan; Conner, Joann A.; Hanna, Wayne W.; Simon, Bindu; Fengler, Kevin; Deschamps, St?phane; Cigan, Mark; Ozias-Akins, Peggy

    2016-01-01

    Apomixis, or clonal propagation through seed, is a trait identified within multiple species of the grass family (Poaceae). The genetic locus controlling apomixis in Pennisetum squamulatum (syn Cenchrus squamulatus) and Cenchrus ciliaris (syn Pennisetum ciliare, buffelgrass) is the apospory-specific genomic region (ASGR). Previously, the ASGR was shown to be highly conserved but inverted in marker order between P. squamulatum and C. ciliaris based on fluorescence in situ hybridization (FISH) a...

  8. Using a hybrid methodology of dasyametric mapping and data ...

    African Journals Online (AJOL)

    Using a hybrid methodology of dasyametric mapping and data interpolation techniques ... AFRICAN JOURNALS ONLINE (AJOL) · Journals · Advanced Search ... the value and accuracy of the developed methodology is that of the 2011 census ...

  9. Practical indoor mobile robot navigation using hybrid maps

    DEFF Research Database (Denmark)

    Özkil, Ali Gürcan; Fan, Zhun; Xiao, Jizhong

    2011-01-01

    This paper presents a practical navigation scheme for indoor mobile robots using hybrid maps. The method makes use of metric maps for local navigation and a topological map for global path planning. Metric maps are generated as 2D occupancy grids by a range sensor to represent local information...... about partial areas. The global topological map is used to indicate the connectivity of the 'places-of-interests' in the environment and the interconnectivity of the local maps. Visual tags on the ceiling to be detected by the robot provide valuable information and contribute to reliable localization...... robot and evaluated in a hospital environment....

  10. Histogram analysis reveals a better delineation of tumor volume from background in 18F-FET PET compared to CBV maps in a hybrid PET–MR studie in gliomas

    International Nuclear Information System (INIS)

    Filss, Christian P.; Stoffels, Gabriele; Galldiks, Norbert; Sabel, Michael; Wittsack, Hans J.; Coenen, Heinz H.; Shah, Nadim J.; Herzog, Hans

    2014-01-01

    Anatomical imaging with magnetic resonance imaging (MRI) is currently the method of first choice for diagnostic investigation of glial tumors. However, different MR sequences may over- or underestimate tumor size and thus it may not be possible to delineate tumor from adjacent brain. In order to compensate this confinement additonal MR sequences like perfusion weighted MRI (PWI) with regional cerebral blood volume (rCBV) or positron emission tomography (PET) with aminoacids are used to gain further information. Recent studies suggest that both of theses image modalities provide similar diagnostic information. For comparison tumor to brain ratios (TBR) with mean and maximum values are frequently used but results from different studies can often not be checked against each other. Furthermore, especially the maximum TBR in rCBV is at risk to be falsified by artifacts (e.g. blood vessels). These confinements are reduced by the use of histograms since all information of the VOIs are equally displayed. In this study we measured and compared the intersection of tumor and reference tissue histograms in 18 F-FET PET and rCBV maps in glioma patients. Methods: Twenty-seven glioma patients with contrast enhancing lesion on T1-weighted MR images were investigated using static 18 F-FET PET and rCBV in MRI using a PET–MR hybrid scanner. In all patients diagnosis was confirmed histologically (7 grade II gliomas, 6 grade III gliomas and 14 grade IV gliomas). We generated a set of tumor and reference tissue Volumes-of-Interest (VOIs) based on T1 weighted images in MRI with the tumor VOI defined by contrast enhancement and transferred these VOIs to the corresponding 18 F-FET PET scans and rCBV maps. From these VOIs we generated tumor and reference tissue histograms with a unity of one for each curve integral and measured the proportion of the area under the tumor curve that falls into the reference curve for 18 F-FET PET and rCBV maps for each patient. Results: The mean proportion

  11. Submicroscopic deletions at the WAGR locus, revealed by nonradioactive in situ hybridization.

    OpenAIRE

    Fantes, J A; Bickmore, W A; Fletcher, J M; Ballesta, F; Hanson, I M; van Heyningen, V

    1992-01-01

    Fluorescence in situ hybridization (FISH) with biotin-labeled probes mapping to 11p13 has been used for the molecular analysis of deletions of the WAGR (Wilms tumor, aniridia, genitourinary abnormalities, and mental retardation) locus. We have detected a submicroscopic 11p13 deletion in a child with inherited aniridia who subsequently presented with Wilms tumor in a horseshoe kidney, only revealed at surgery. The mother, who has aniridia, was also found to carry a deletion including both the ...

  12. Convergence of Hybrid Space Mapping Algorithms

    DEFF Research Database (Denmark)

    Madsen, Kaj; Søndergaard, Jacob

    2004-01-01

    may be poor, or the method may even fail to converge to a stationary point. We consider a convex combination of the space mapping technique with a classical optimization technique. The function to be optimized has the form \\$H \\$\\backslash\\$circ f\\$ where \\$H: \\$\\backslash\\$dR\\^m \\$\\backslash......\\$mapsto \\$\\backslash\\$dR\\$ is convex and \\$f: \\$\\backslash\\$dR\\^n \\$\\backslash\\$mapsto \\$\\backslash\\$dR\\^m\\$ is smooth. Experience indicates that the combined method maintains the initial efficiency of the space mapping technique. We prove that the global convergence property of the classical technique is also...

  13. Hybrid Message-Embedded Cipher Using Logistic Map

    OpenAIRE

    Mishra, Mina; Mankar, V. H.

    2012-01-01

    The proposed hybrid message embedded scheme consists of hill cipher combined with message embedded chaotic scheme. Message-embedded scheme using non-linear feedback shift register as non-linear function and 1-D logistic map as chaotic map is modified, analyzed and tested for avalanche property and strength against known plaintext attack and brute-force attack. Parameter of logistic map acts as a secret key. As we know that the minimum key space to resist brute-force attack is 2100, and it is ...

  14. Dark matter maps reveal cosmic scaffolding

    Energy Technology Data Exchange (ETDEWEB)

    Massey, R; Rhodes, J; Ellis, R; Scoville, N; Capak, P [CALTECH, Pasadena, CA 91125 (United States); Rhodes, J [CALTECH, Jet Prop Lab, Pasadena, CA 91109 (United States); Leauthaud, A; Kneib, J P [Lab Astrophys Marseille, F-13376 Marseille, (France); Finoguenov, A [Max Planck Inst Extraterr Phys, D-85748 Garching, (Germany); Bacon, D; Taylor, A [Inst Astron, Edinburgh EH9 3HJ, Midlothian, (United Kingdom); Aussel, H; Refregier, A [CNRS, CEA, Unite Mixte Rech, AIM, F-91191 Gif Sur Yvette, (France); Koekemoer, A; Mobasher, B [Univ Paris 07, CE Saclay, UMR 7158, F-91191 Gif Sur Yvette, (France); McCracken, H [Space Telescope Sci Inst, Baltimore, MD 21218 (United States); Pires, S; Starck, J L [Univ Paris 06, Inst Astrophys Paris, F-75014 Paris, (France); Pires, S [Ctr Etud Saclay, CEA, DSM, DAPNIA, SEDI, F-91191 Gif Sur Yvette, (France); Sasaki, S; Taniguchi, Y [Ehime Univ, Dept Phys, Matsuyama, Ehime 7908577, (Japan); Taylor, J [Univ Waterloo, Dept Phys and Astron, Waterloo, ON N2L 3G1, (Canada)

    2007-07-01

    Ordinary baryonic particles (such as protons and neutrons) account for only one-sixth of the total matter in the Universe. The remainder is a mysterious 'dark matter' component, which does not interact via electromagnetism and thus neither emits nor reflects light. As dark matter cannot be seen directly using traditional observations, very little is currently known about its properties. It does interact via gravity, and is most effectively probed through gravitational lensing: the deflection of light from distant galaxies by the gravitational attraction of foreground mass concentrations. This is a purely geometrical effect that is free of astrophysical assumptions and sensitive to all matter - whether baryonic or dark. Here we show high-fidelity maps of the large-scale distribution of dark matter, resolved in both angle and depth. We find a loose network of filaments, growing over time, which intersect in massive structures at the locations of clusters of galaxies. Our results are consistent with predictions of gravitationally induced structure formation, in which the initial, smooth distribution of dark matter collapses into filaments then into clusters, forming a gravitational scaffold into which gas can accumulate, and stars can be built. (authors)

  15. Dark matter maps reveal cosmic scaffolding

    International Nuclear Information System (INIS)

    Massey, R.; Rhodes, J.; Ellis, R.; Scoville, N.; Capak, P.; Rhodes, J.; Leauthaud, A.; Kneib, J.P.; Finoguenov, A.; Bacon, D.; Taylor, A.; Aussel, H.; Refregier, A.; Koekemoer, A.; Mobasher, B.; McCracken, H.; Pires, S.; Starck, J.L.; Pires, S.; Sasaki, S.; Taniguchi, Y.; Taylor, J.

    2007-01-01

    Ordinary baryonic particles (such as protons and neutrons) account for only one-sixth of the total matter in the Universe. The remainder is a mysterious 'dark matter' component, which does not interact via electromagnetism and thus neither emits nor reflects light. As dark matter cannot be seen directly using traditional observations, very little is currently known about its properties. It does interact via gravity, and is most effectively probed through gravitational lensing: the deflection of light from distant galaxies by the gravitational attraction of foreground mass concentrations. This is a purely geometrical effect that is free of astrophysical assumptions and sensitive to all matter - whether baryonic or dark. Here we show high-fidelity maps of the large-scale distribution of dark matter, resolved in both angle and depth. We find a loose network of filaments, growing over time, which intersect in massive structures at the locations of clusters of galaxies. Our results are consistent with predictions of gravitationally induced structure formation, in which the initial, smooth distribution of dark matter collapses into filaments then into clusters, forming a gravitational scaffold into which gas can accumulate, and stars can be built. (authors)

  16. Dark matter maps reveal cosmic scaffolding.

    Science.gov (United States)

    Massey, Richard; Rhodes, Jason; Ellis, Richard; Scoville, Nick; Leauthaud, Alexie; Finoguenov, Alexis; Capak, Peter; Bacon, David; Aussel, Hervé; Kneib, Jean-Paul; Koekemoer, Anton; McCracken, Henry; Mobasher, Bahram; Pires, Sandrine; Refregier, Alexandre; Sasaki, Shunji; Starck, Jean-Luc; Taniguchi, Yoshi; Taylor, Andy; Taylor, James

    2007-01-18

    Ordinary baryonic particles (such as protons and neutrons) account for only one-sixth of the total matter in the Universe. The remainder is a mysterious 'dark matter' component, which does not interact via electromagnetism and thus neither emits nor reflects light. As dark matter cannot be seen directly using traditional observations, very little is currently known about its properties. It does interact via gravity, and is most effectively probed through gravitational lensing: the deflection of light from distant galaxies by the gravitational attraction of foreground mass concentrations. This is a purely geometrical effect that is free of astrophysical assumptions and sensitive to all matter--whether baryonic or dark. Here we show high-fidelity maps of the large-scale distribution of dark matter, resolved in both angle and depth. We find a loose network of filaments, growing over time, which intersect in massive structures at the locations of clusters of galaxies. Our results are consistent with predictions of gravitationally induced structure formation, in which the initial, smooth distribution of dark matter collapses into filaments then into clusters, forming a gravitational scaffold into which gas can accumulate, and stars can be built.

  17. Human cDNA mapping using fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

    Genetic mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach generated 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  18. High resolution hybrid optical and acoustic sea floor maps (Invited)

    Science.gov (United States)

    Roman, C.; Inglis, G.

    2013-12-01

    This abstract presents a method for creating hybrid optical and acoustic sea floor reconstructions at centimeter scale grid resolutions with robotic vehicles. Multibeam sonar and stereo vision are two common sensing modalities with complementary strengths that are well suited for data fusion. We have recently developed an automated two stage pipeline to create such maps. The steps can be broken down as navigation refinement and map construction. During navigation refinement a graph-based optimization algorithm is used to align 3D point clouds created with both the multibeam sonar and stereo cameras. The process combats the typical growth in navigation error that has a detrimental affect on map fidelity and typically introduces artifacts at small grid sizes. During this process we are able to automatically register local point clouds created by each sensor to themselves and to each other where they overlap in a survey pattern. The process also estimates the sensor offsets, such as heading, pitch and roll, that describe how each sensor is mounted to the vehicle. The end results of the navigation step is a refined vehicle trajectory that ensures the points clouds from each sensor are consistently aligned, and the individual sensor offsets. In the mapping step, grid cells in the map are selectively populated by choosing data points from each sensor in an automated manner. The selection process is designed to pick points that preserve the best characteristics of each sensor and honor some specific map quality criteria to reduce outliers and ghosting. In general, the algorithm selects dense 3D stereo points in areas of high texture and point density. In areas where the stereo vision is poor, such as in a scene with low contrast or texture, multibeam sonar points are inserted in the map. This process is automated and results in a hybrid map populated with data from both sensors. Additional cross modality checks are made to reject outliers in a robust manner. The final

  19. A Hybrid Vision-Map Method for Urban Road Detection

    Directory of Open Access Journals (Sweden)

    Carlos Fernández

    2017-01-01

    Full Text Available A hybrid vision-map system is presented to solve the road detection problem in urban scenarios. The standardized use of machine learning techniques in classification problems has been merged with digital navigation map information to increase system robustness. The objective of this paper is to create a new environment perception method to detect the road in urban environments, fusing stereo vision with digital maps by detecting road appearance and road limits such as lane markings or curbs. Deep learning approaches make the system hard-coupled to the training set. Even though our approach is based on machine learning techniques, the features are calculated from different sources (GPS, map, curbs, etc., making our system less dependent on the training set.

  20. Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia.

    Science.gov (United States)

    Lin, Grace; Wang, Le; Ngoh, Si Te; Ji, Lianghui; Orbán, Laszlo; Yue, Gen Hua

    2018-02-01

    Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F 2 family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F 2 hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8-8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.

  1. Hybridity, Reflexivity and Mapping: A Collaborative Ethnography of Postcolonial Gameplay

    Directory of Open Access Journals (Sweden)

    Sybille Lammes

    2018-04-01

    Full Text Available To date, game studies has largely undertheorized the co-production of postcolonial stories, exploration, and mapping in games. Furthermore, as has been noted before (Carr, 2006, the work that has been done on postcolonialism and play so far often leaves the player out of the equation, even sometimes as a theoretical construct. Yet player experience is crucial to understanding such games, as narratives are not only built on the ‘master’ level of game mechanics, but also through the personal stories players processually (Ash, 2009; Thrift, 2008 develop through their journey of touring and mapping, thereby developing spatial stories (De Certeau, 1984; Jenkins, 2004; Lammes, 2009 that may present us with conflicting spatio-temporal accounts. Through a comparative and collaborative auto-ethnographic analysis of 'Civilization VI' (Sid Meier, 2016 – a turn-based strategy game – we want to push this discussion further and improve our theoretical understanding and analytical purchase of the triad relation between narrative and postcolonialism in games, thereby contributing to the field of postcolonial theory and game studies. Drawing on postcolonial geography, science and technology studies (STS, non-representational theory and game studies, we argue that games, through their playful, explorative and emergent qualities, are a powerful means of rethinking and reimagining colonial (histories in this postcolonial era (Lammes, 2009, 2010 including issues of spatio-temporality, cartography and the hybrid relation between women and machines.

  2. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  3. A scalable hybrid multi-robot SLAM method for highly detailed maps

    NARCIS (Netherlands)

    Pfingsthorn, M.; Slamet, B.; Visser, A.

    2008-01-01

    Recent successful SLAM methods employ hybrid map representations combining the strengths of topological maps and occupancy grids. Such representations often facilitate multi-agent mapping. In this paper, a successful SLAM method is presented, which is inspired by the manifold data structure by

  4. Reliable Radiation Hybrid Maps: An Efficient Scalable Clustering-based Approach

    Science.gov (United States)

    The process of mapping markers from radiation hybrid mapping (RHM) experiments is equivalent to the traveling salesman problem and, thereby, has combinatorial complexity. As an additional problem, experiments typically result in some unreliable markers that reduce the overall quality of the map. We ...

  5. Intersubject information mapping: revealing canonical representations of complex natural stimuli

    Directory of Open Access Journals (Sweden)

    Nikolaus Kriegeskorte

    2015-03-01

    Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

  6. Distributed neural system for emotional intelligence revealed by lesion mapping.

    Science.gov (United States)

    Barbey, Aron K; Colom, Roberto; Grafman, Jordan

    2014-03-01

    Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease.

  7. Distributed neural system for emotional intelligence revealed by lesion mapping

    Science.gov (United States)

    Colom, Roberto; Grafman, Jordan

    2014-01-01

    Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease. PMID:23171618

  8. Architecture of cognitive flexibility revealed by lesion mapping

    Science.gov (United States)

    Barbey, Aron K.; Colom, Roberto; Grafman, Jordan

    2013-01-01

    Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism–Extraversion–Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R2 = 0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

  9. Phylogenetic tests of a Cercopithecus monkey hybrid reveal X ...

    African Journals Online (AJOL)

    A captive Cercopithecus nictitans × C. cephus male was examined at loci on the X- and Y-chromosomes as a test of previously described phylogenetic methods for identifying hybrid Cercopithecus monkeys. The results confirm the reliability of such assays, indicating that they can be of immediate utility for studies of wild ...

  10. Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster.

    Science.gov (United States)

    He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

    2012-12-01

    Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes ("H-probes") for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin.

  11. Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

    Science.gov (United States)

    He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

    2012-01-01

    Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230

  12. Construction of radiation-reduced hybrids and their use in mapping of microclones from chromosome 10p11.2-q11.2

    International Nuclear Information System (INIS)

    Fujita, Shoichi; Shin, Eisei; Nakamura, Tsutomu; Kurahashi, Hiroki; Mori, Takesada; Takai, Shin-ichiro; Nishisho, Isamu; Kaneda, Yasufumi; Tanaka, Kiyoji.

    1993-01-01

    Radiation-reduced hybrids for mapping of DNA markers in the pericentromeric region of chromosome 10 were developed. A Chinese hamster/human somatic cell hybrid (762-8A) carrying chromosomes 10 and Y as the only human material were exposed to 40,000 rads of irradiation and then rescued by fusion with non-irradiated recipient Chinese hamster cells (GM459). Southern hybridization analyses revealed that 10 of 128 HAT-resistant clones contained human chromosomal fragments corresponding to at least one marker locus between FNRB (10p11.2) and RBP3 (10q11.2). These hybrids were then used to map microdissection clones previously isolated and roughly mapped to this chromosomal region by fluorescence in situ hybridization (FISH). Two of the six microclones studies could be mapped to the proximity of the D10S102 locus. These radiation hybrids are useful for the construction of refined genetic maps of the pericentromeric region of chromosome 10. (author) 50 refs

  13. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A

    Czech Academy of Sciences Publication Activity Database

    Balcárková, Barbora; Frenkel, Z.; Škopová, Monika; Abrouk, Michael; Kumar, A.; Chao, S.; Kianian, S. F.; Akhunov, E.; Korol, A.; Doležel, Jaroslav; Valárik, Miroslav

    2017-01-01

    Roč. 7, JAN 10 (2017), č. článku 2063. ISSN 1664-462X R&D Projects: GA MŠk(CZ) LO1204; GA ČR(CZ) GA14-07164S Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * bread wheat * high-density * agronomic traits * tetraploid wheat * hexaploid wheat * polyploid wheat * genetic maps * genomes * recombination * endosperm radiation hybrid panel * radiation hybrid map * wheat chromosome 4A * chromosome deletion bin map * Triticum aestivum * SNP iSelect array Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 4.298, year: 2016

  14. Construction of a map of chromosome 16 by using radiation hybrids

    International Nuclear Information System (INIS)

    Ceccherini, I.; Romeo, G.; Lawrence, S.; Morton, N.E.; Breuning, M.H.; Harris, P.C.; Himmelbauer, H.; Frischauf, A.M.; Sutherland, G.R.; Germino, G.G.; Reeders, S.T.

    1992-01-01

    A human-hamster cell hybrid carrying a single copy of chromosome 16 as the only human genetic material was irradiated with a single dose of γ-rays and then fused with a thymidine kinase-deficient hamster cell line (RJKM) to generate radiation hybrids retaining unselected fragments of this human chromosome. In two experiments, 223 hybrids were isolated in hypoxanthine/aminopterine/thymidine (HAT) medium and screened with 38 DNA probes, corresponding to anonymous DNA or gene sequences localized on chromosome 16. The most likely order and location of the 38 DNA sequences were established by multiple pairwise analysis and scaled to estimate physical distance in megabases. The order and the distances thus obtained are mostly consistent with available data on genetic and physical mapping of these markers, illustrating the usefulness of radiation hybrids for mapping

  15. Asymptotically stable phase synchronization revealed by autoregressive circle maps

    Science.gov (United States)

    Drepper, F. R.

    2000-11-01

    A specially designed of nonlinear time series analysis is introduced based on phases, which are defined as polar angles in spaces spanned by a finite number of delayed coordinates. A canonical choice of the polar axis and a related implicit estimation scheme for the potentially underlying autoregressive circle map (next phase map) guarantee the invertibility of reconstructed phase space trajectories to the original coordinates. The resulting Fourier approximated, invertibility enforcing phase space map allows us to detect conditional asymptotic stability of coupled phases. This comparatively general synchronization criterion unites two existing generalizations of the old concept and can successfully be applied, e.g., to phases obtained from electrocardiogram and airflow recordings characterizing cardiorespiratory interaction.

  16. Fine mapping of dominant X-linked incompatibility alleles in Drosophila hybrids.

    Science.gov (United States)

    Matute, Daniel R; Gavin-Smyth, Jackie

    2014-04-01

    Sex chromosomes have a large effect on reproductive isolation and play an important role in hybrid inviability. In Drosophila hybrids, X-linked genes have pronounced deleterious effects on fitness in male hybrids, which have only one X chromosome. Several studies have succeeded at locating and identifying recessive X-linked alleles involved in hybrid inviability. Nonetheless, the density of dominant X-linked alleles involved in interspecific hybrid viability remains largely unknown. In this report, we study the effects of a panel of small fragments of the D. melanogaster X-chromosome carried on the D. melanogaster Y-chromosome in three kinds of hybrid males: D. melanogaster/D. santomea, D. melanogaster/D. simulans and D. melanogaster/D. mauritiana. D. santomea and D. melanogaster diverged over 10 million years ago, while D. simulans (and D. mauritiana) diverged from D. melanogaster over 3 million years ago. We find that the X-chromosome from D. melanogaster carries dominant alleles that are lethal in mel/san, mel/sim, and mel/mau hybrids, and more of these alleles are revealed in the most divergent cross. We then compare these effects on hybrid viability with two D. melanogaster intraspecific crosses. Unlike the interspecific crosses, we found no X-linked alleles that cause lethality in intraspecific crosses. Our results reveal the existence of dominant alleles on the X-chromosome of D. melanogaster which cause lethality in three different interspecific hybrids. These alleles only cause inviability in hybrid males, yet have little effect in hybrid females. This suggests that X-linked elements that cause hybrid inviability in males might not do so in hybrid females due to differing sex chromosome interactions.

  17. Strong Convergence of Hybrid Algorithm for Asymptotically Nonexpansive Mappings in Hilbert Spaces

    Directory of Open Access Journals (Sweden)

    Juguo Su

    2012-01-01

    Full Text Available The hybrid algorithms for constructing fixed points of nonlinear mappings have been studied extensively in recent years. The advantage of this methods is that one can prove strong convergence theorems while the traditional iteration methods just have weak convergence. In this paper, we propose two types of hybrid algorithm to find a common fixed point of a finite family of asymptotically nonexpansive mappings in Hilbert spaces. One is cyclic Mann's iteration scheme, and the other is cyclic Halpern's iteration scheme. We prove the strong convergence theorems for both iteration schemes.

  18. Hybrid Map-Based Navigation Method for Unmanned Ground Vehicle in Urban Scenario

    Directory of Open Access Journals (Sweden)

    Huiyan Chen

    2013-07-01

    Full Text Available To reduce the data size of metric map and map matching computational cost in unmanned ground vehicle self-driving navigation in urban scenarios, a metric-topological hybrid map navigation system is proposed in this paper. According to the different positioning accuracy requirements, urban areas are divided into strong constraint (SC areas, such as roads with lanes, and loose constraint (LC areas, such as intersections and open areas. As direction of the self-driving vehicle is provided by traffic lanes and global waypoints in the road network, a simple topological map is fit for the navigation in the SC areas. While in the LC areas, the navigation of the self-driving vehicle mainly relies on the positioning information. Simultaneous localization and mapping technology is used to provide a detailed metric map in the LC areas, and a window constraint Markov localization algorithm is introduced to achieve accurate position using laser scanner. Furthermore, the real-time performance of the Markov algorithm is enhanced by using a constraint window to restrict the size of the state space. By registering the metric maps into the road network, a hybrid map of the urban scenario can be constructed. Real unmanned vehicle mapping and navigation tests demonstrated the capabilities of the proposed method.

  19. Genomic constitution of Festuca x Lolium hybrids revealed by the DArTFest array

    Czech Academy of Sciences Publication Activity Database

    Kopecký, David; Bartoš, Jan; Christelová, Pavla; Černoch, V.; Kilian, A.; Doležel, Jaroslav

    2011-01-01

    Roč. 122, č. 2 (2011), s. 355-363 ISSN 0040-5752 R&D Projects: GA MZe QH71267; GA ČR GP521/07/P479 Institutional research plan: CEZ:AV0Z50380511 Keywords : IN-SITU HYBRIDIZATION * GENETIC-LINKAGE MAP * PRATENSIS HUDS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.297, year: 2011

  20. Strong Convergence of Monotone Hybrid Method for Maximal Monotone Operators and Hemirelatively Nonexpansive Mappings

    Directory of Open Access Journals (Sweden)

    Chakkrid Klin-eam

    2009-01-01

    Full Text Available We prove strong convergence theorems for finding a common element of the zero point set of a maximal monotone operator and the fixed point set of a hemirelatively nonexpansive mapping in a Banach space by using monotone hybrid iteration method. By using these results, we obtain new convergence results for resolvents of maximal monotone operators and hemirelatively nonexpansive mappings in a Banach space.

  1. The chromosomal constitution of fish hybrid lineage revealed by 5S rDNA FISH.

    Science.gov (United States)

    Zhang, Chun; Ye, Lihai; Chen, Yiyi; Xiao, Jun; Wu, Yanhong; Tao, Min; Xiao, Yamei; Liu, Shaojun

    2015-12-03

    The establishment of the bisexual fertile fish hybrid lineage including the allodiploid and allotetraploid hybrids, from interspecific hybridization of red crucian carp (Carassius auratus red var. 2n = 100, 2n = AA) (♀) × common carp (Cyprinus carpio L. 2n = 100, 2n = BB) (♂), provided a good platform to investigate genetic relationship between the parents and their hybrid progenies. The chromosomal inheritance of diploid and allotetraploid hybrid progenies in successive generations, was studied by applying 5S rDNA fluorescence in situ hybridization. Signals of 5S rDNA distinguished the chromosomal constitution of common carp (B-genome) from red crucian carp (A-genome), in which two strong signals were observed on the first submetacentric chromosome, while no major signal was found in common carp. After fish hybridization, one strong signal of 5S rDNA was detected in the same locus on the chromosome of diploid hybrids. As expected, two strong signals were observed in 4nF3 tetraploid hybrids offspring and it is worth mentioning that two strong signals were detected in a separating bivalent of a primary spermatocyte in 4nF3. Furthermore, the mitosis of heterozygous chromosomes was shown normal and stable with blastular tissue histological studies. We revealed that 5S rDNA signal can be applied to discern A-genome from B-genome, and that 5S rDNA bearing chromosomes can be stably passed down in successive generations. Our work provided a significant method in fish breeding and this is important for studies in fish evolutionary biology.

  2. Comparative mapping reveals similar linkage of functional genes to ...

    Indian Academy of Sciences (India)

    genes between O. sativa and B. napus may have consistent function and control similar traits, which may be ..... acea chromosomes reveals islands of conserved organization. ... 1998 Conserved structure and function of the Arabidopsis flow-.

  3. A hierarchical approach of hybrid image classification for land use and land cover mapping

    Directory of Open Access Journals (Sweden)

    Rahdari Vahid

    2018-01-01

    Full Text Available Remote sensing data analysis can provide thematic maps describing land-use and land-cover (LULC in a short period. Using proper image classification method in an area, is important to overcome the possible limitations of satellite imageries for producing land-use and land-cover maps. In the present study, a hierarchical hybrid image classification method was used to produce LULC maps using Landsat Thematic mapper TM for the year of 1998 and operational land imager OLI for the year of 2016. Images were classified using the proposed hybrid image classification method, vegetation cover crown percentage map from normalized difference vegetation index, Fisher supervised classification and object-based image classification methods. Accuracy assessment results showed that the hybrid classification method produced maps with total accuracy up to 84 percent with kappa statistic value 0.81. Results of this study showed that the proposed classification method worked better with OLI sensor than with TM. Although OLI has a higher radiometric resolution than TM, the produced LULC map using TM is almost accurate like OLI, which is because of LULC definitions and image classification methods used.

  4. Empirical evaluation of a practical indoor mobile robot navigation method using hybrid maps

    DEFF Research Database (Denmark)

    Özkil, Ali Gürcan; Fan, Zhun; Xiao, Jizhong

    2010-01-01

    This video presents a practical navigation scheme for indoor mobile robots using hybrid maps. The method makes use of metric maps for local navigation and a topological map for global path planning. Metric maps are generated as occupancy grids by a laser range finder to represent local information...... about partial areas. The global topological map is used to indicate the connectivity of the ‘places-of-interests’ in the environment and the interconnectivity of the local maps. Visual tags on the ceiling to be detected by the robot provide valuable information and contribute to reliable localization...... that the method is implemented successfully on physical robot in a hospital environment, which provides a practical solution for indoor navigation....

  5. Genetic characterization and fine mapping of S25, a hybrid male sterility gene, on rice chromosome 12.

    Science.gov (United States)

    Kubo, Takahiko; Yoshimura, Atsushi; Kurata, Nori

    2018-02-10

    Hybrid male sterility genes are important factors in creating postzygotic reproductive isolation barriers in plants. One such gene, S25, is known to cause severe transmission ratio distortion in inter-subspecific progeny of cultivated rice Oryza sativa ssp. indica and japonica. To further characterize the S25 gene, we fine-mapped and genetically characterized the S25 gene using near-isogenic lines with reciprocal genetic backgrounds. We mapped the S25 locus within the 0.67-1.02 Mb region on rice chromosome 12. Further genetic analyses revealed that S25 substantially reduced male fertility in the japonica background, but not in the indica background. In first-generation hybrid progeny, S25 had a milder effect than it had in the japonica background. These results suggest that the expression of S25 is epistatically regulated by at least one partially dominant gene present in the indica genome. This finding supports our previous studies showing that hybrid male sterility due to pollen killer genes results from epistatic interaction with other genes that are hidden in the genetic background.

  6. Optimization of Antennas using a Hybrid Genetic-Algorithm Space-Mapping Algorithm

    DEFF Research Database (Denmark)

    Pantoja, M.F.; Bretones, A.R.; Meincke, Peter

    2006-01-01

    A hybrid global-local optimization technique for the design of antennas is presented. It consists of the subsequent application of a Genetic Algorithm (GA) that employs coarse models in the simulations and a space mapping (SM) that refines the solution found in the previous stage. The technique...

  7. A Hybrid Genetic-Algorithm Space-Mapping Tool for the Optimization of Antennas

    DEFF Research Database (Denmark)

    Pantoja, Mario Fernández; Meincke, Peter; Bretones, Amelia Rubio

    2007-01-01

    A hybrid global-local optimization technique for the design of antennas is presented. It consists of the subsequent application of a genetic algorithm (GA) that employs coarse models in the simulations and a space mapping (SM) that refines the solution found in the previous stage. The technique...

  8. Energy Management Strategies based on efficiency map for Fuel Cell Hybrid Vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Feroldi, Diego; Serra, Maria; Riera, Jordi [Institut de Robotica i Informatica Industrial (CSIC-UPC), C. Llorens i Artigas 4, 08028 Barcelona (Spain)

    2009-05-15

    The addition of a fast auxiliary power source like a supercapacitor bank in fuel cell-based vehicles has a great potential because permits a significant reduction of the hydrogen consumption and an improvement of the vehicle efficiency. The Energy Management Strategies, commanding the power split between the power sources in the hybrid arrangement to fulfil the power requirement, perform a fundamental role to achieve this objective. In this work, three strategies based on the knowledge of the fuel cell efficiency map are proposed. These strategies are attractive due to the relative simplicity of the real time implementation and the good performance. The strategies are tested both in a simulation environment and in an experimental setup using a 1.2-kW PEM fuel cell. The results, in terms of hydrogen consumption, are compared with an optimal case, which is assessed trough an advantageous technique also introduced in this work and with a pure fuel cell vehicle as well. This comparative reveals high efficiency and good performance, allowing to save up to 26% of hydrogen in urban scenarios. (author)

  9. Use of a human chromosome 11 radiation hybrid panel to map markers at 11q13

    International Nuclear Information System (INIS)

    Withers, D.; Richard, C. III; Meeker, T.C.; Maurer, S.; Evans, G.; Myers, R.M.; Cox, D.R.

    1990-01-01

    A human/hamster hybrid cell line containing human chromosome 11 was X-irradiated and 102-independent derivative lines were recovered. These 'radiation hybrids' contain random fragments of human chromosome 11. This radiation hybrid panel was used to score the retention of markers at band 11q13. Statistical analysis of marker co-retention patterns in the radiation hybrid panel permits a preliminary ordering and mapping of the markers used. The best order for six scored markers is: proximal - CD5 - CD20 - PGA - HST - BCL1 - SEA - distal. Additional markers are currently being scored. The six 11q13 markers above are spread over approximately 10-12 mB of DNA. The mapping data has implications for the identification of the bcl-1 gene. bcl-1 is the site of chromosome breakage in translocations associated with B lymphocytic malignancy. bcl-1 markers map at least 4 Mb away from any of four genes previously hypothesized to be activated by such translocations, thereby making them unlikely candidates for activation

  10. Toward accountable land use mapping: Using geocomputation to improve classification accuracy and reveal uncertainty

    NARCIS (Netherlands)

    Beekhuizen, J.; Clarke, K.C.

    2010-01-01

    The classification of satellite imagery into land use/cover maps is a major challenge in the field of remote sensing. This research aimed at improving the classification accuracy while also revealing uncertain areas by employing a geocomputational approach. We computed numerous land use maps by

  11. An Odometry-free Approach for Simultaneous Localization and Online Hybrid Map Building

    Directory of Open Access Journals (Sweden)

    Wei Hong Chin

    2016-11-01

    Full Text Available In this paper, a new approach is proposed for mobile robot localization and hybrid map building simultaneously without using any odometry hardware system. The proposed method termed as Genetic Bayesian ARAM which comprises two main components: 1 Steady state genetic algorithm (SSGA for self-localization and occupancy grid map building; 2 Bayesian Adaptive Resonance Associative Memory (ARAM for online topological map building. The model of the explored environment is formed as a hybrid representation, both topological and grid-based, and it is incrementally constructed during the exploration process. During occupancy map building, robot estimated self-position is updated by SSGA. At the same time, robot estimated self position is transmit to Bayesian ARAM for topological map building and localization. The effectiveness of our proposed approach is validated by a number of standardized benchmark datasets and real experimental results carried on mobile robot. Benchmark datasets are used to verify the proposed method capable of generating topological map in different environment conditions. Real robot experiment is to verify the proposed method can be implemented in real world.

  12. Thermal Analysis and Microhardness Mapping in Hybrid Laser Welds in a Structural Steel

    Science.gov (United States)

    2003-01-01

    conditions. Via the keyhole the laser beam brings about easier ignition of the arc, stabilization of the arc welding process, and penetration of the...with respect to the conventional GMAW or GTAW processes without the need for very close fit-up. This paper will compare an autogenous laser weld to a...UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP017864 TITLE: Thermal Analysis and Microhardness Mapping in Hybrid Laser

  13. Fuzzy Shannon Entropy: A Hybrid GIS-Based Landslide Susceptibility Mapping Method

    Directory of Open Access Journals (Sweden)

    Majid Shadman Roodposhti

    2016-09-01

    Full Text Available Assessing Landslide Susceptibility Mapping (LSM contributes to reducing the risk of living with landslides. Handling the vagueness associated with LSM is a challenging task. Here we show the application of hybrid GIS-based LSM. The hybrid approach embraces fuzzy membership functions (FMFs in combination with Shannon entropy, a well-known information theory-based method. Nine landslide-related criteria, along with an inventory of landslides containing 108 recent and historic landslide points, are used to prepare a susceptibility map. A random split into training (≈70% and testing (≈30% samples are used for training and validation of the LSM model. The study area—Izeh—is located in the Khuzestan province of Iran, a highly susceptible landslide zone. The performance of the hybrid method is evaluated using receiver operating characteristics (ROC curves in combination with area under the curve (AUC. The performance of the proposed hybrid method with AUC of 0.934 is superior to multi-criteria evaluation approaches using a subjective scheme in this research in comparison with a previous study using the same dataset through extended fuzzy multi-criteria evaluation with AUC value of 0.894, and was built on the basis of decision makers’ evaluation in the same study area.

  14. A gene-based radiation hybrid map of the gilthead sea bream Sparus aurata refines and exploits conserved synteny with Tetraodon nigroviridis

    Directory of Open Access Journals (Sweden)

    Tsalavouta Matina

    2007-02-01

    Full Text Available Abstract Background Comparative teleost studies are of great interest since they are important in aquaculture and in evolutionary issues. Comparing genomes of fully sequenced model fish species with those of farmed fish species through comparative mapping offers shortcuts for quantitative trait loci (QTL detections and for studying genome evolution through the identification of regions of conserved synteny in teleosts. Here a comparative mapping study is presented by radiation hybrid (RH mapping genes of the gilthead sea bream Sparus aurata, a non-model teleost fish of commercial and evolutionary interest, as it represents the worldwide distributed species-rich family of Sparidae. Results An additional 74 microsatellite markers and 428 gene-based markers appropriate for comparative mapping studies were mapped on the existing RH map of Sparus aurata. The anchoring of the RH map to the genetic linkage map resulted in 24 groups matching the karyotype of Sparus aurata. Homologous sequences to Tetraodon were identified for 301 of the gene-based markers positioned on the RH map of Sparus aurata. Comparison between Sparus aurata RH groups and Tetraodon chromosomes (karyotype of Tetraodon consists of 21 chromosomes in this study reveals an unambiguous one-to-one relationship suggesting that three Tetraodon chromosomes correspond to six Sparus aurata radiation hybrid groups. The exploitation of this conserved synteny relationship is furthermore demonstrated by in silico mapping of gilthead sea bream expressed sequence tags (EST that give a significant similarity hit to Tetraodon. Conclusion The addition of primarily gene-based markers increased substantially the density of the existing RH map and facilitated comparative analysis. The anchoring of this gene-based radiation hybrid map to the genome maps of model species broadened the pool of candidate genes that mainly control growth, disease resistance, sex determination and reversal, reproduction as well

  15. Radiation hybrid mapping of genes in the lithium-sensitive wnt signaling pathway.

    Science.gov (United States)

    Rhoads, A R; Karkera, J D; Detera-Wadleigh, S D

    1999-09-01

    Lithium, an effective drug in the treatment of bipolar disorder, has been proposed to disrupt the Wnt signaling pathway. To facilitate analysis of the possible involvement of elements of the Wnt pathway in human bipolar disorder, a high resolution radiation hybrid mapping (RHM) of these genes was performed. A fine physical location has been obtained for Wnt 7A, frizzled 3, 4 and 5, dishevelled 1, 2 and 3, GSK3beta, axin, alpha-catenin, the Armadillo repeat-containing genes (delta-catenin and ARVCF), and a frizzled-like protein (frpHE) using the Stanford Human Genome Center (SHGC) G3 panel. Most of these genes were previously mapped by fluorescence in situ hybridization (FISH). Frizzled 4, axin and frpHE did not have a previous chromosomal assignment and were linked by RHM to chromosome markers, SHGC-35131 at 11q22.1, NIB1488 at 16p13.3 and D7S2919 at 7p15.2, respectively. Interestingly, some of these genes were found to map within potential regions underlying susceptibility to bipolar disorder and schizophrenia as well as disorders of neurodevelopmental origin. This alternative approach of establishing the precise location of selected genetic components of a candidate pathway and determining if they map within previously defined susceptibility loci should help to identify plausible candidate genes that warrant further analysis through association and mutational scanning.

  16. Hybrid geomorphological maps as the basis for assessing geoconservation potential in Lech, Vorarlberg (Austria)

    Science.gov (United States)

    Seijmonsbergen, Harry; de Jong, Mat; Anders, Niels; de Graaff, Leo; Cammeraat, Erik

    2013-04-01

    Geoconservation potential is, in our approach, closely linked to the spatial distribution of geomorphological sites and thus, geomorphological inventories. Detailed geomorphological maps are translated, using a standardized workflow, into polygonal maps showing the potential geoconservation value of landforms. A new development is to semi-automatically extract in a GIS geomorphological information from high resolution topographical data, such as LiDAR, and combine this with conventional data types (e.g. airphotos, geological maps) into geomorphological maps. Such hybrid digital geomorphological maps are also easily translated into digital information layers which show the geoconservation potential in an area. We present a protocol for digital geomorphological mapping illustrated with an example for the municipality of Lech in Vorarlberg (Austria). The protocol consists of 5 steps: 1. data preparation, 2. generating training and validation samples, 3. parameterization, 4. feature extraction, and 5. assessing classification accuracy. The resulting semi-automated digital geomorphological map is then further validated, in two ways. Firstly, the map is manually checked with the help of a series of digital datasets (e.g. airphotos) in a digital 3D environment, such as ArcScene. The second validation is field visit, which preferably occurs in parallel to the digital evaluation, so that updates are quickly achieved. The final digital and coded geomorphological information layer is converted into a potential geoconservation map by weighting and ranking the landforms based on four criteria: scientific relevance, frequency of occurrence, disturbance, and environmental vulnerability. The criteria with predefined scores for the various landform types are stored in a separate GIS attribute table, which is joined to the attribute table of the hybrid geomorphological information layer in an automated procedure. The results of the assessment can be displayed as the potential

  17. Patterns of hybrid loss of imprinting reveal tissue- and cluster-specific regulation.

    Directory of Open Access Journals (Sweden)

    Christopher D Wiley

    Full Text Available Crosses between natural populations of two species of deer mice, Peromyscus maniculatus (BW, and P. polionotus (PO, produce parent-of-origin effects on growth and development. BW females mated to PO males (bwxpo produce growth-retarded but otherwise healthy offspring. In contrast, PO females mated to BW males (POxBW produce overgrown and severely defective offspring. The hybrid phenotypes are pronounced in the placenta and include POxBW conceptuses which lack embryonic structures. Evidence to date links variation in control of genomic imprinting with the hybrid defects, particularly in the POxBW offspring. Establishment of genomic imprinting is typically mediated by gametic DNA methylation at sites known as gDMRs. However, imprinted gene clusters vary in their regulation by gDMR sequences.Here we further assess imprinted gene expression and DNA methylation at different cluster types in order to discern patterns. These data reveal POxBW misexpression at the Kcnq1ot1 and Peg3 clusters, both of which lose ICR methylation in placental tissues. In contrast, some embryonic transcripts (Peg10, Kcnq1ot1 reactivated the silenced allele with little or no loss of DNA methylation. Hybrid brains also display different patterns of imprinting perturbations. Several cluster pairs thought to use analogous regulatory mechanisms are differentially affected in the hybrids.These data reinforce the hypothesis that placental and somatic gene regulation differs significantly, as does that between imprinted gene clusters and between species. That such epigenetic regulatory variation exists in recently diverged species suggests a role in reproductive isolation, and that this variation is likely to be adaptive.

  18. A Filtering Method to Reveal Crystalline Patterns from Atom Probe Microscopy Desorption Maps

    Science.gov (United States)

    2016-03-26

    reveal crystalline patterns from atom probe microscopy desorption maps Lan Yao Department of Materials Science and Engineering, University of Michigan, Ann...reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. Themethod filters atoms based on the time difference...between their evaporation and the evaporation of the previous atom . Since this time difference correlates with the location and the local structure of

  19. Computation of the Lyapunov exponents in the compass-gait model under OGY control via a hybrid Poincaré map

    International Nuclear Information System (INIS)

    Gritli, Hassène; Belghith, Safya

    2015-01-01

    Highlights: • A numerical calculation method of the Lyapunov exponents in the compass-gait model under OGY control is proposed. • A new linearization method of the impulsive hybrid dynamics around a one-periodic hybrid limit cycle is achieved. • We develop a simple analytical expression of a controlled hybrid Poincaré map. • A dimension reduction of the hybrid Poincaré map is realized. • We describe the numerical computation procedure of the Lyapunov exponents via the designed hybrid Poincaré map. - Abstract: This paper aims at providing a numerical calculation method of the spectrum of Lyapunov exponents in a four-dimensional impulsive hybrid nonlinear dynamics of a passive compass-gait model under the OGY control approach by means of a controlled hybrid Poincaré map. We present a four-dimensional simplified analytical expression of such hybrid map obtained by linearizing the uncontrolled impulsive hybrid nonlinear dynamics around a desired one-periodic passive hybrid limit cycle. In order to compute the spectrum of Lyapunov exponents, a dimension reduction of the controlled hybrid Poincaré map is realized. The numerical calculation of the spectrum of Lyapunov exponents using the reduced-dimension controlled hybrid Poincaré map is given in detail. In order to show the effectiveness of the developed method, the spectrum of Lyapunov exponents is calculated as the slope (bifurcation) parameter varies and hence used to predict the walking dynamics behavior of the compass-gait model under the OGY control.

  20. Hybrid image classification technique for land-cover mapping in the Arctic tundra, North Slope, Alaska

    Science.gov (United States)

    Chaudhuri, Debasish

    Remotely sensed image classification techniques are very useful to understand vegetation patterns and species combination in the vast and mostly inaccessible arctic region. Previous researches that were done for mapping of land cover and vegetation in the remote areas of northern Alaska have considerably low accuracies compared to other biomes. The unique arctic tundra environment with short growing season length, cloud cover, low sun angles, snow and ice cover hinders the effectiveness of remote sensing studies. The majority of image classification research done in this area as reported in the literature used traditional unsupervised clustering technique with Landsat MSS data. It was also emphasized by previous researchers that SPOT/HRV-XS data lacked the spectral resolution to identify the small arctic tundra vegetation parcels. Thus, there is a motivation and research need to apply a new classification technique to develop an updated, detailed and accurate vegetation map at a higher spatial resolution i.e. SPOT-5 data. Traditional classification techniques in remotely sensed image interpretation are based on spectral reflectance values with an assumption of the training data being normally distributed. Hence it is difficult to add ancillary data in classification procedures to improve accuracy. The purpose of this dissertation was to develop a hybrid image classification approach that effectively integrates ancillary information into the classification process and combines ISODATA clustering, rule-based classifier and the Multilayer Perceptron (MLP) classifier which uses artificial neural network (ANN). The main goal was to find out the best possible combination or sequence of classifiers for typically classifying tundra type vegetation that yields higher accuracy than the existing classified vegetation map from SPOT data. Unsupervised ISODATA clustering and rule-based classification techniques were combined to produce an intermediate classified map which was

  1. Characterization of a panel of somatic cell hybrids for regional mapping of the mouse X chromosome

    International Nuclear Information System (INIS)

    Avner, P.; Arnaud, D.; Amar, L.; Cambrou, J.; Winking, H.; Russell, L.B.

    1987-01-01

    A panel of five hybrid cell lines containing mouse X chromosomes with various deletions has been obtained by fusing splenocytes from male mice carrying one of a series of reciprocal X-autosome translocations with the azaguanine-resistant Chinese hamster cell line CH3g. These hybrids have been extensively characterized by using the allozymes hypoxanthine/guanine phosphoribosyltransferase (encoded by the Hprt locus) and α-galactosidase (Ags) and a series of 11 X-chromosome-specific DNA probes whose localization had been previously established by linkage studies. Such studies have established the genetic breakpoints of the T(X;12)13R1 and T(X;2)14R1 X-autosome translocations on the X chromosome and provided additional information as to the X-chromosome genetic breakpoints of the T(X;16)16H, T(X;4)7R1, and T(X;7)6R1 translocations. The data establish clearly that both the T(X;7)5RI and T(X;12)13R1 X-chromosome breakpoints are proximal to Hprt, the breakpoint of the former being more centromeric, lying as it does in the 9-centimorgan interval between the ornithine transcarbamoylase (Otc) and DXPas7 (M2C) loci. These five hybrid cell lines provide, with the previously characterized EBS4 hybrid cell line, a nested series of seven mapping intervals distributed along the length of the mouse X chromosome. Their characterization not only allows further correlation of the genetic and cytological X-chromosome maps but also should permit the rapid identification of DNA probes specific for particular regions of the mouse X chromosome

  2. Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

    Directory of Open Access Journals (Sweden)

    Heidi G. Parker

    2017-04-01

    Full Text Available There are nearly 400 modern domestic dog breeds with a unique histories and genetic profiles. To track the genetic signatures of breed development, we have assembled the most diverse dataset of dog breeds, reflecting their extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses, we uncover geographic patterns of development and independent origins of common traits. Our analyses reveal the hybrid history of breeds and elucidate the effects of immigration, revealing for the first time a suggestion of New World dog within some modern breeds. Finally, we used cladistics and haplotype sharing to show that some common traits have arisen more than once in the history of the dog. These analyses characterize the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds, and, by inference, transfer of trait and disease alleles among dog breeds.

  3. Transmission electron microscopic method for gene mapping on polytene chromosomes by in situ hybridization

    OpenAIRE

    Wu, Madeline; Davidson, Norman

    1981-01-01

    A transmission electron microscope method for gene mapping by in situ hybridization to Drosophila polytene chromosomes has been developed. As electron-opaque labels, we use colloidal gold spheres having a diameter of 25 nm. The spheres are coated with a layer of protein to which Escherichia coli single-stranded DNA is photochemically crosslinked. Poly(dT) tails are added to the 3' OH ends of these DNA strands, and poly(dA) tails are added to the 3' OH ends of a fragmented cloned Drosophila DN...

  4. Mapping Strategies and Sound Engine Design for an Augmented Hybrid Piano

    DEFF Research Database (Denmark)

    Dahlstedt, Palle

    2015-01-01

    Based on a combination of novel mapping techniques and carefully designed sound engines, I present an augmented hybrid piano specifically designed for improvisation. The mapping technique, originally developed for other control interfaces but here adapted to the piano keyboard, is based...... on a dynamic vectorization of control parameters, allowing both wild sonic exploration and minute intimate expression. The original piano sound is used as the sole sound source, subjected to processing techniques such as virtual resonance strings, dynamic buffer shuffling, and acoustic and virtual feedback....... Thanks to speaker and microphone placement, the acoustic and processed sounds interact in both directions and blend into one new instrument. This also allows for unorthodox playing (knocking, plucking, shouting). Processing parameters are controlled from the keyboard playing alone, allowing intuitive...

  5. Radiation hybrid mapping as one of the main methods of the creation of high resolution maps of human and animal genomes

    International Nuclear Information System (INIS)

    Sulimova, G.E.; Kompanijtsev, A.A.; Mojsyak, E.V.; Rakhmanaliev, Eh.R.; Klimov, E.A.; Udina, I.G.; Zakharov, I.A.

    2000-01-01

    Radiation hybrid mapping (RH mapping) is considered as one of the main method of constructing physical maps of mammalian genomes. In introduction, theoretical prerequisites of developing of the RH mapping and statistical methods of data analysis are discussed. Comparative characteristics of universal commercial panels of the radiation hybrid somatic cells (RH panels) are shown. In experimental part of the work, RH mapping is used to localize nucleotide sequences adjacent to Not I sites of human chromosome 3 with the aim to integrate contig map of Nor I clones to comprehensive maps of human genome. Five nucleotide sequences adjacent to the sites of integration of papilloma virus in human genome and expressed in the cells of cervical cancer involved localized. It is demonstrated that the region 13q14.3-q21.1 was enriched with nucleotide sequences involved in the processes of carcinogenesis. RH mapping can be considered as one of the most perspective applications of modern radiation biology in the field of molecular genetics, that is, in constructing physical maps of mammalian genomes with high resolution level [ru

  6. Polarization-dependent Imaging Contrast (PIC) mapping reveals nanocrystal orientation patterns in carbonate biominerals

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Pupa U.P.A., E-mail: pupa@physics.wisc.edu [University of Wisconsin-Madison, Departments of Physics and Chemistry, Madison, WI 53706 (United States)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer Nanocrystal orientation shown by Polarization-dependent Imaging Contrast (PIC) maps. Black-Right-Pointing-Pointer PIC-mapping of carbonate biominerals reveals their ultrastructure at the nanoscale. Black-Right-Pointing-Pointer The formation mechanisms of biominerals is discovered by PIC-mapping using PEEM. -- Abstract: Carbonate biominerals are one of the most interesting systems a physicist can study. They play a major role in the CO{sub 2} cycle, they master templation, self-assembly, nanofabrication, phase transitions, space filling, crystal nucleation and growth mechanisms. A new imaging modality was introduced in the last 5 years that enables direct observation of the orientation of carbonate single crystals, at the nano- and micro-scale. This is Polarization-dependent Imaging Contrast (PIC) mapping, which is based on X-ray linear dichroism, and uses PhotoElectron Emission spectroMicroscopy (PEEM). Here we present PIC-mapping results from biominerals, including the nacre and prismatic layers of mollusk shells, and sea urchin teeth. We describe various PIC-mapping approaches, and show that these lead to fundamental discoveries on the formation mechanisms of biominerals.

  7. QTL mapping of combining ability and heterosis of agronomic traits in rice backcross recombinant inbred lines and hybrid crosses.

    Directory of Open Access Journals (Sweden)

    Zhen Qu

    Full Text Available BACKGROUND: Combining ability effects are very effective genetic parameters in deciding the next phase of breeding programs. Although some breeding strategies on the basis of evaluating combining ability have been utilized extensively in hybrid breeding, little is known about the genetic basis of combining ability. Combining ability is a complex trait that is controlled by polygenes. With the advent and development of molecular markers, it is feasible to evaluate the genetic bases of combining ability and heterosis of elite rice hybrids through QTL analysis. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, we first developed a QTL-mapping method for dissecting combining ability and heterosis of agronomic traits. With three testcross populations and a BCRIL population in rice, biometric and QTL analyses were conducted for ten agronomic traits. The significance of general combining ability and special combining ability for most of the traits indicated the importance of both additive and non-additive effects on expression levels. A large number of additive effect QTLs associated with performance per se of BCRIL and general combining ability, and dominant effect QTLs associated with special combining ability and heterosis were identified for the ten traits. CONCLUSIONS/SIGNIFICANCE: The combining ability of agronomic traits could be analyzed by the QTL mapping method. The characteristics revealed by the QTLs for combining ability of agronomic traits were similar with those by multitudinous QTLs for agronomic traits with performance per se of BCRIL. Several QTLs (1-6 in this study were identified for each trait for combining ability. It demonstrated that some of the QTLs were pleiotropic or linked tightly with each other. The identification of QTLs responsible for combining ability and heterosis in the present study provides valuable information for dissecting genetic basis of combining ability.

  8. Hybrid Semantic Analysis for Mapping Adverse Drug Reaction Mentions in Tweets to Medical Terminology.

    Science.gov (United States)

    Emadzadeh, Ehsan; Sarker, Abeed; Nikfarjam, Azadeh; Gonzalez, Graciela

    2017-01-01

    Social networks, such as Twitter, have become important sources for active monitoring of user-reported adverse drug reactions (ADRs). Automatic extraction of ADR information can be crucial for healthcare providers, drug manufacturers, and consumers. However, because of the non-standard nature of social media language, automatically extracted ADR mentions need to be mapped to standard forms before they can be used by operational pharmacovigilance systems. We propose a modular natural language processing pipeline for mapping (normalizing) colloquial mentions of ADRs to their corresponding standardized identifiers. We seek to accomplish this task and enable customization of the pipeline so that distinct unlabeled free text resources can be incorporated to use the system for other normalization tasks. Our approach, which we call Hybrid Semantic Analysis (HSA), sequentially employs rule-based and semantic matching algorithms for mapping user-generated mentions to concept IDs in the Unified Medical Language System vocabulary. The semantic matching component of HSA is adaptive in nature and uses a regression model to combine various measures of semantic relatedness and resources to optimize normalization performance on the selected data source. On a publicly available corpus, our normalization method achieves 0.502 recall and 0.823 precision (F-measure: 0.624). Our proposed method outperforms a baseline based on latent semantic analysis and another that uses MetaMap.

  9. Comparative Genomic Hybridization of Human Malignant Gliomas Reveals Multiple Amplification Sites and Nonrandom Chromosomal Gains and Losses

    Science.gov (United States)

    Schròck, Evelin; Thiel, Gundula; Lozanova, Tanka; du Manoir, Stanislas; Meffert, Marie-Christine; Jauch, Anna; Speicher, Michael R.; Nürnberg, Peter; Vogel, Siegfried; Janisch, Werner; Donis-Keller, Helen; Ried, Thomas; Witkowski, Regine; Cremer, Thomas

    1994-01-01

    Nine human malignant gliomas (2 astrocytomas grade III and 7 glioblastomas) were analyzed using comparative genomic hybridization (CGH). In addition to the amplification of the EGFR gene at 7p12 in 4 of 9 cases, six new amplification sites were mapped to 1q32, 4q12, 7q21.1, 7q21.2-3, 12p, and 22q12. Nonrandom chromosomal gains and losses were identified with overrepresentation of chromosome 7 and underrepresentation of chromosome 10 as the most frequent events (1 of 2 astrocytomas, 7 of 7 glioblastomas). Gain of a part or the whole chromosome 19 and losses of chromosome bands 9pter-23 and 22q13 were detected each in five cases. Loss of chromosome band 17p13 and gain of chromosome 20 were revealed each in three cases. The validity of the CGH data was confirmed using interphase cytogenetics with YAC clones, chromosome painting in tumor metaphase spreads, and DNA fingerprinting. A comparison of CGH data with the results of chromosome banding analyses indicates that metaphase spreads accessible in primary tumor cell cultures may not represent the clones predominant in the tumor tissue ImagesFigure 1Figure 4Figure 6 PMID:8203461

  10. A screen for F1 hybrid male rescue reveals no major-effect hybrid lethality loci in the Drosophila melanogaster autosomal genome.

    Science.gov (United States)

    Cuykendall, Tawny N; Satyaki, P; Ji, Shuqing; Clay, Derek M; Edelman, Nathaniel B; Kimchy, Alexandra; Li, Ling-Hei; Nuzzo, Erin A; Parekh, Neil; Park, Suna; Barbash, Daniel A

    2014-10-27

    Hybrid sons between Drosophila melanogaster females and D. simulans males die as 3rd instar larvae. Two genes, D. melanogaster Hybrid male rescue (Hmr) on the X chromosome, and D. simulans Lethal hybrid rescue (Lhr) on chromosome II, interact to cause this lethality. Loss-of-function mutations in either gene suppress lethality, but several pieces of evidence suggest that additional factors are required for hybrid lethality. Here we screen the D. melanogaster autosomal genome by using the Bloomington Stock Center Deficiency kit to search for additional regions that can rescue hybrid male lethality. Our screen is designed to identify putative hybrid incompatibility (HI) genes similar to Hmr and Lhr which, when removed, are dominant suppressors of lethality. After screening 89% of the autosomal genome, we found no regions that rescue males to the adult stage. We did, however, identify several regions that rescue up to 13% of males to the pharate adult stage. This weak rescue suggests the presence of multiple minor-effect HI loci, but we were unable to map these loci to high resolution, presumably because weak rescue can be masked by genetic background effects. We attempted to test one candidate, the dosage compensation gene male specific lethal-3 (msl-3), by using RNA interference with short hairpin microRNA constructs targeted specifically against D. simulans msl-3 but failed to achieve knockdown, in part due to off-target effects. We conclude that the D. melanogaster autosomal genome likely does not contain additional major-effect HI loci. We also show that Hmr is insufficient to fully account for the lethality associated with the D. melanogaster X chromosome, suggesting that additional X-linked genes contribute to hybrid lethality. Copyright © 2014 Cuykendall et al.

  11. Mapping the electrostatic potential of Au nanoparticles using hybrid electron holography

    Energy Technology Data Exchange (ETDEWEB)

    Ozsoy-Keskinbora, Cigdem, E-mail: c.ozsoy@fkf.mpg.de [Stuttgart Center for Electron Microscopy, Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Boothroyd, Chris B.; Dunin-Borkowski, Rafal E. [Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich (Germany); Aken, Peter A. van [Stuttgart Center for Electron Microscopy, Max Planck Institute for Solid State Research, Heisenbergstr. 1, 70569 Stuttgart (Germany); Koch, Christoph T. [Structure Research & Electron Microscopy group, Department of Physics, Humboldt University of Berlin, Newtonstraße 15, 12489 Berlin (Germany)

    2016-06-15

    Electron holography is a powerful technique for characterizing electrostatic potentials, charge distributions, electric and magnetic fields, strain distributions and semiconductor dopant distributions with sub-nm spatial resolution. Mapping internal electrostatic and magnetic fields within nanoparticles and other low-dimensional materials by TEM requires both high spatial resolution and high phase sensitivity. Carrying out such an analysis fully quantitatively is even more challenging, since artefacts such as dynamical electron scattering may strongly affect the measurement. In-line electron holography, one of the variants of electron holography, features high phase sensitivity at high spatial frequencies, but suffers from inefficient phase recovery at low spatial frequencies. Off-axis electron holography, in contrast, can recover low spatial frequency phase information much more reliably, but is less effective in retrieving phase information at high spatial frequencies when compared to in-line holography. We investigate gold nanoparticles using hybrid electron holography at both atomic-resolution and intermediate magnification. Hybrid electron holography is a novel technique that synergistically combines off-axis and in-line electron holography, allowing the measurement of the complex wave function describing the scattered electrons with excellent signal-to-noise properties at both high and low spatial frequencies. The effect of dynamical electron scattering is minimized by beam tilt averaging. - Highlights: • Hybrid electron holography approach applied to Au nanoparticles. • Proof of principle of atomic resolution hybrid electron holography experiment demonstrated. • Dynamical scattering artifacts decrease by varying the illumination direction. • The effect of the number of iterations and noise on the low spatial frequencies in the phase are discussed.

  12. Mapping the electrostatic potential of Au nanoparticles using hybrid electron holography

    International Nuclear Information System (INIS)

    Ozsoy-Keskinbora, Cigdem; Boothroyd, Chris B.; Dunin-Borkowski, Rafal E.; Aken, Peter A. van; Koch, Christoph T.

    2016-01-01

    Electron holography is a powerful technique for characterizing electrostatic potentials, charge distributions, electric and magnetic fields, strain distributions and semiconductor dopant distributions with sub-nm spatial resolution. Mapping internal electrostatic and magnetic fields within nanoparticles and other low-dimensional materials by TEM requires both high spatial resolution and high phase sensitivity. Carrying out such an analysis fully quantitatively is even more challenging, since artefacts such as dynamical electron scattering may strongly affect the measurement. In-line electron holography, one of the variants of electron holography, features high phase sensitivity at high spatial frequencies, but suffers from inefficient phase recovery at low spatial frequencies. Off-axis electron holography, in contrast, can recover low spatial frequency phase information much more reliably, but is less effective in retrieving phase information at high spatial frequencies when compared to in-line holography. We investigate gold nanoparticles using hybrid electron holography at both atomic-resolution and intermediate magnification. Hybrid electron holography is a novel technique that synergistically combines off-axis and in-line electron holography, allowing the measurement of the complex wave function describing the scattered electrons with excellent signal-to-noise properties at both high and low spatial frequencies. The effect of dynamical electron scattering is minimized by beam tilt averaging. - Highlights: • Hybrid electron holography approach applied to Au nanoparticles. • Proof of principle of atomic resolution hybrid electron holography experiment demonstrated. • Dynamical scattering artifacts decrease by varying the illumination direction. • The effect of the number of iterations and noise on the low spatial frequencies in the phase are discussed.

  13. Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana.

    Science.gov (United States)

    Plötner, Björn; Nurmi, Markus; Fischer, Axel; Watanabe, Mutsumi; Schneeberger, Korbinian; Holm, Svante; Vaid, Neha; Schöttler, Mark Aurel; Walther, Dirk; Hoefgen, Rainer; Weigel, Detlef; Laitinen, Roosa A E

    2017-07-01

    Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F 2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  14. Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes"

    Directory of Open Access Journals (Sweden)

    Lemos Bernardo

    2010-12-01

    Full Text Available Abstract Background Hybrid male sterility (HMS is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Results Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. Conclusions The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

  15. Fine mapping of S37, a locus responsible for pollen and embryo sac sterility in hybrids between Oryza sativa L. and O. glaberrima Steud.

    Science.gov (United States)

    Shen, Yumin; Zhao, Zhigang; Ma, Hongyang; Bian, Xiaofeng; Yu, Yang; Yu, Xiaowen; Chen, Haiyuan; Liu, Linglong; Zhang, Wenwei; Jiang, Ling; Zhou, Jiawu; Tao, Dayun; Wan, Jianmin

    2015-11-01

    Hybrid sterility locus S37 between Oryza glaberrima and Oryza sativa results in both pollen and embryo sac sterility. Interspecific crossing between African cultivated rice Oryza glaberrima and Oryza sativa cultivars is hindered by hybrid sterility. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL)-S37 using Dianjingyou1 (DJY1) as the recipient parent and an African cultivated rice variety as the donor parent. Empty pollen and embryo sac sterility were observed in F1 hybrids between DJY1 and NIL-S37. Cytological analyses showed that pollen abortion in the F1 hybrids occurred at the late binucleate stage due to a failure of starch accumulation in pollen grains. In addition, partial abortion of the embryo sac in the F1 hybrid was observed during function megaspore developing into mature embryo sac. Molecular analysis revealed that the semi-sterility was largely caused by the abortion of male and female gametophytes carrying the S37 allele from DJY1. A population of 25,600 plants derived from the hybrid DJY1/NIL-S37 was developed to fine map S37. Based on the physical location of molecular markers, S37 locus was finally delimited to a region of 205 kb on the short arm of chromosome 1 in terms of reference sequences of cv. Nipponbare. Interestingly, an about 97-kb DNA segment was deleted in the NIL-S37 based on BAC clone information of O. glaberrima. Fifty-four open reading frames (ORF) were predicted in this 205-kb region of DJY1, whereas only 31 ORFs were in that of NIL-S37. These results are valuable for cloning of S37 gene and further breaking reproductive isolation between Oryza glaberrima and Oryza sativa cultivars, as well as marker-assisted transferring of the corresponding neutral allele in rice breeding programs.

  16. Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes".

    Science.gov (United States)

    Araripe, Luciana O; Montenegro, Horácio; Lemos, Bernardo; Hartl, Daniel L

    2010-12-14

    Hybrid male sterility (HMS) is a usual outcome of hybridization between closely related animal species. It arises because interactions between alleles that are functional within one species may be disrupted in hybrids. The identification of genes leading to hybrid sterility is of great interest for understanding the evolutionary process of speciation. In the current work we used marked P-element insertions as dominant markers to efficiently locate one genetic factor causing a severe reduction in fertility in hybrid males of Drosophila simulans and D. mauritiana. Our mapping effort identified a region of 9 kb on chromosome 3, containing three complete and one partial coding sequences. Within this region, two annotated genes are suggested as candidates for the HMS factor, based on the comparative molecular characterization and public-source information. Gene Taf1 is partially contained in the region, but yet shows high polymorphism with four fixed non-synonymous substitutions between the two species. Its molecular functions involve sequence-specific DNA binding and transcription factor activity. Gene agt is a small, intronless gene, whose molecular function is annotated as methylated-DNA-protein-cysteine S-methyltransferase activity. High polymorphism and one fixed non-synonymous substitution suggest this is a fast evolving gene. The gene trees of both genes perfectly separate D. simulans and D. mauritiana into monophyletic groups. Analysis of gene expression using microarray revealed trends that were similar to those previously found in comparisons between whole-genome hybrids and parental species. The identification following confirmation of the HMS candidate gene will add another case study leading to understanding the evolutionary process of hybrid incompatibility.

  17. Genetic and radiation hybrid mapping of the hyperekplexia region on chromosome 5q

    Energy Technology Data Exchange (ETDEWEB)

    Ryan, S.G.; O' Connell, P. (Univ. of Texas Health Science Center, San Antonio (United States)); Dixon, M.J. (Univ. of Manchester (United Kingdom)); Nigro, M.A. (Wayne State Univ., Detroit, MI (United States)); Kelts, K.A. (Black Hills Neurology, Rapid City, SD (United States)); Markand, O.N. (Indiana Univ., Indianopolis (United States)); Shiang, R.; Wasmuth, J.J. (Univ. of California, Irvine (United States)); Terry, J.C.

    1992-12-01

    Hyperekplexia, or startle disease (STHE), is an autosomal dominant neurologic disorder characterized by muscular rigidity of central nervous system origin, particularly in the neonatal period, and by an exaggerated startle response to sudden, unexpected acoustic or tactile stimuli. STHE responds dramatically to the benzodiazepine drug clonazepam, which acts at gamma-aminobutyric acid type A (GABA-A) receptors. The STHE locus (STHE) was recently assigned to chromosome 5q, on the basis of tight linkage to the colony-stimulating factor 1-receptor (CSF1-R) locus in a single large family. The authors performed linkage analysis in the original and three additional STHE pedigrees with eight chromosome 5q microsatellite markers and placed several of the most closely linked markers on an existing radiation hybrid (RH) map of the region. The results provide strong evidence for genetic locus homogeneity and assign STHE to a 5.9-cM interval defined by CSF1-R and D5S379, which are separated by an RH map distance of 74 centirays (roughly 2.2-3.7 Mb). Two polymorphic markers (D5S119 and D5S209) lie within this region, but they could not be ordered with respect to STHE. RH mapping eliminated the candidate genes GABRA1 and GABRG2, which encode GABA-A receptor components, by showing that they are telomeric to the target region. 45 refs., 4 figs., 4 tabs.

  18. Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes.

    Science.gov (United States)

    Zhang, Qi-Peng; Hu, Wen-Fang; Zhou, Ting-Ting; Kong, Shen-Shen; Liu, Zhi-Fang; Zheng, Rong-Quan

    2018-01-01

    Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa . In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa , evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini . Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini . By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa , and a cryptic species may also exist in Q. boulengeri . However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri . Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa .

  19. A high resolution radiation hybrid map of bovine chromosome 14 identifies scaffold rearrangement in the latest bovine assembly

    Directory of Open Access Journals (Sweden)

    Wang Zhiquan

    2007-07-01

    Full Text Available Abstract Background Radiation hybrid (RH maps are considered to be a tool of choice for fine mapping closely linked loci, considering that the resolution of linkage maps is determined by the number of informative meiosis and recombination events which may require very large mapping populations. Accurately defining the marker order on chromosomes is crucial for correct identification of quantitative trait loci (QTL, haplotype map construction and refinement of candidate gene searches. Results A 12 k Radiation hybrid map of bovine chromosome 14 was constructed using 843 single nucleotide polymorphism markers. The resulting map was aligned with the latest version of the bovine assembly (Btau_3.1 as well as other previously published RH maps. The resulting map identified distinct regions on Bovine chromosome 14 where discrepancies between this RH map and the bovine assembly occur. A major region of discrepancy was found near the centromere involving the arrangement and order of the scaffolds from the assembly. The map further confirms previously published conserved synteny blocks with human chromosome 8. As well, it identifies an extra breakpoint and conserved synteny block previously undetected due to lower marker density. This conserved synteny block is in a region where markers between the RH map presented here and the latest sequence assembly are in very good agreement. Conclusion The increase of publicly available markers shifts the rate limiting step from marker discovery to the correct identification of their order for further use by the research community. This high resolution map of bovine chromosome 14 will facilitate identification of regions in the sequence assembly where additional information is required to resolve marker ordering.

  20. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Science.gov (United States)

    Santos, Jansen Rodrigo Pereira; Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

    2018-01-01

    Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  1. QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

    Directory of Open Access Journals (Sweden)

    Jansen Rodrigo Pereira Santos

    Full Text Available Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN. Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

  2. The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Min, Xiaoshan; Akella, Radha; He, Haixia; Humphreys, John M.; Tsutakawa, Susan E.; Lee, Seung-Jae; Tainer, John A.; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-07-13

    MAP2Ks are dual-specificity protein kinases functioning at the center of three-tiered MAP kinase modules. The structure of the kinase domain of the MAP2K MEK6 with phosphorylation site mimetic aspartic acid mutations (MEK6/{Delta}N/DD) has been solved at 2.3 {angstrom} resolution. The structure reveals an autoinhibited elongated ellipsoidal dimer. The enzyme adopts an inactive conformation, based upon structural queues, despite the phosphomimetic mutations. Gel filtration and small-angle X-ray scattering analysis confirm that the crystallographically observed ellipsoidal dimer is a feature of MEK6/{Delta}N/DD and full-length unphosphorylated wild-type MEK6 in solution. The interface includes the phosphate binding ribbon of each subunit, part of the activation loop, and a rare 'arginine stack' between symmetry-related arginine residues in the N-terminal lobe. The autoinhibited structure likely confers specificity on active MAP2Ks. The dimer may also serve the function in unphosphorylated MEK6 of preventing activation loop phosphorylation by inappropriate kinases.

  3. Final report: Mapping Interactions in Hybrid Systems with Active Scanning Probes

    Energy Technology Data Exchange (ETDEWEB)

    Berezovsky, Jesse [Case Western Reserve Univ., Cleveland, OH (United States)

    2017-09-29

    This project aimed to study and map interactions between components of hybrid nanodevices using a novel scanning probe approach. To enable this work, we initially constructed a flexible experimental apparatus allowing for simultaneous scanning probe and confocal optical microscopy measurements. This setup was first used for all-optical measurements of nanostructures, with the focus then shifting to hybrid devices in which single coherent electron spins are coupled to micron-scale ferromagnetic elements, which may prove useful for addressing single spins, enhanced sensing, or spin-wave-mediated coupling of spins for quantum information applications. A significant breakthrough was the realization that it is not necessary to fabricate a magnetic structure on a scanning probe – instead a ferromagnetic vortex core can act as an integrated, solid state, scanning probe. The core of the vortex produces a very strong, localized fringe field which can be used analogously to an MFM tip. Unlike a traditional MFM tip, however, the vortex core is scanned within an integrated device (eliminating drift), and can be moved on vastly faster timescales. This approach allows the detailed investigation of interactions between single spins and complex driven ferromagnetic dynamics.

  4. 'Hybrid' multiple mapping conditioning on passive and reactive scalars

    Energy Technology Data Exchange (ETDEWEB)

    Cleary, M.J.; Kronenburg, A. [Department of Mechanical Engineering, Imperial College London, London SW7 2AZ (United Kingdom)

    2007-12-15

    A two-dimensional, hybridized multiple mapping conditioning (MMC) model is used to model local extinction and reignition phenomena in homogeneous, isotropic decaying turbulence. The equations are solved in a prescribed, jointly Gaussian reference space with stochastic reference variables emulating the fluctuations of the mixture fraction and normalized sensible enthalpy conditioning variables. In ''pure'' MMC the joint PDF of the conditioning scalars is a solved quantity. Here we use a hybrid method where the time evolution of the marginal PDF for mixture fraction is solved and a presumed {beta}-PDF is used for the conditional distribution of the normalized sensible enthalpy. Model results are compared with DNS in three flame cases with varying levels of local extinction, up to global extinction. Results for principal chemical species are in very good agreement with DNS and those for intermediate species are also satisfactory. The doubly conditioned MMC yields results which are considerably more accurate than those by modeling with conditioning on mixture fraction alone. A transformation of the Gaussian reference space casts the MMC model in the same form as conditional moment closure (CMC). The great advantage is that the MMC model contains the doubly conditioned scalar dissipation terms in closed form and these are generally found to be in good agreement with the DNS data. (author)

  5. Reconstruction of in-plane strain maps using hybrid dense sensor network composed of sensing skin

    International Nuclear Information System (INIS)

    Downey, Austin; Laflamme, Simon; Ubertini, Filippo

    2016-01-01

    The authors have recently developed a soft-elastomeric capacitive (SEC)-based thin film sensor for monitoring strain on mesosurfaces. Arranged in a network configuration, the sensing system is analogous to a biological skin, where local strain can be monitored over a global area. Under plane stress conditions, the sensor output contains the additive measurement of the two principal strain components over the monitored surface. In applications where the evaluation of strain maps is useful, in structural health monitoring for instance, such signal must be decomposed into linear strain components along orthogonal directions. Previous work has led to an algorithm that enabled such decomposition by leveraging a dense sensor network configuration with the addition of assumed boundary conditions. Here, we significantly improve the algorithm’s accuracy by leveraging mature off-the-shelf solutions to create a hybrid dense sensor network (HDSN) to improve on the boundary condition assumptions. The system’s boundary conditions are enforced using unidirectional RSGs and assumed virtual sensors. Results from an extensive experimental investigation demonstrate the good performance of the proposed algorithm and its robustness with respect to sensors’ layout. Overall, the proposed algorithm is seen to effectively leverage the advantages of a hybrid dense network for application of the thin film sensor to reconstruct surface strain fields over large surfaces. (paper)

  6. Mapping the electrostatic potential of Au nanoparticles using hybrid electron holography.

    Science.gov (United States)

    Ozsoy-Keskinbora, Cigdem; Boothroyd, Chris B; Dunin-Borkowski, Rafal E; van Aken, Peter A; Koch, Christoph T

    2016-06-01

    Electron holography is a powerful technique for characterizing electrostatic potentials, charge distributions, electric and magnetic fields, strain distributions and semiconductor dopant distributions with sub-nm spatial resolution. Mapping internal electrostatic and magnetic fields within nanoparticles and other low-dimensional materials by TEM requires both high spatial resolution and high phase sensitivity. Carrying out such an analysis fully quantitatively is even more challenging, since artefacts such as dynamical electron scattering may strongly affect the measurement. In-line electron holography, one of the variants of electron holography, features high phase sensitivity at high spatial frequencies, but suffers from inefficient phase recovery at low spatial frequencies. Off-axis electron holography, in contrast, can recover low spatial frequency phase information much more reliably, but is less effective in retrieving phase information at high spatial frequencies when compared to in-line holography. We investigate gold nanoparticles using hybrid electron holography at both atomic-resolution and intermediate magnification. Hybrid electron holography is a novel technique that synergistically combines off-axis and in-line electron holography, allowing the measurement of the complex wave function describing the scattered electrons with excellent signal-to-noise properties at both high and low spatial frequencies. The effect of dynamical electron scattering is minimized by beam tilt averaging. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft

    DEFF Research Database (Denmark)

    Kandra, L.; Abou Hachem, Maher; Gyemant, G.

    2006-01-01

    Subsite affinity maps of long substrate binding clefts in barley alpha-amylases, obtained using a series of maltooligosaccharides of degree of polymerization of 3-12, revealed unfavorable binding energies at the internal subsites -3 and -5 and at subsites -8 and +3/+4 defining these subsites...... as binding barriers. Barley a-amylase I mutants Y105A and T212Y at subsite -6 and +4 resulted in release or anchoring of bound substrate, thus modifying the affinities of other high-affinity subsites (-2 and +2) and barriers. The double mutant Y105A-T212Y displayed a hybrid subsite affinity profile......, converting barriers to binding areas. These findings highlight the dynamic binding energy distribution and the versatility of long maltooligosaccharide derivatives in mapping extended binding clefts in a-amylases....

  8. Unified Common Fixed Point Theorems for a Hybrid Pair of Mappings via an Implicit Relation Involving Altering Distance Function

    Directory of Open Access Journals (Sweden)

    Sunny Chauhan

    2014-01-01

    implicit relation, we prove a new coincidence and common fixed point theorem for a hybrid pair of occasionally coincidentally idempotent mappings in a metric space employing the common limit range property. Our main result improves and generalizes a host of previously known results. We also utilize suitable illustrative examples to substantiate the realized improvements in our results.

  9. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

    Directory of Open Access Journals (Sweden)

    Ashley S. Chaffin

    2016-07-01

    Full Text Available Hexaploid oat ( L., 2 = 6 = 42 is a member of the Poaceae family and has a large genome (∼12.5 Gb containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP array and genotyping-by-sequencing (GBS were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L. reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.

  10. Genomic markers reveal introgressive hybridization in the Indo-West Pacific mangroves: a case study.

    Directory of Open Access Journals (Sweden)

    Mei Sun

    2011-05-01

    Full Text Available Biodiversity of mangrove ecosystems is difficult to assess, at least partly due to lack of genetic verification of morphology-based documentation of species. Natural hybridization, on the one hand, plays an important role in evolution as a source of novel gene combinations and a mechanism of speciation. However, on the other hand, recurrent introgression allows gene flow between species and could reverse the process of genetic differentiation among populations required for speciation. To understand the dynamic evolutionary consequences of hybridization, this study examines genomic structure of hybrids and parental species at the population level. In the Indo-West Pacific, Bruguiera is one of the dominant mangrove genera and species ranges overlap extensively with one another. Morphological intermediates between sympatric Bruguiera gymnorrhiza and Bruguiera sexangula have been reported as a variety of B. sexangula or a new hybrid species, B. × rhynchopetala. However, the direction of hybridization and extent of introgression are unclear. A large number of species-specific inter-simple sequence repeat (ISSR markers were found in B. gymnorrhiza and B. sexangula, and the additive ISSR profiling of B. × rhynchopetala ascertained its hybrid status and identified its parental origin. The varying degree of scatterness among hybrid individuals in Principal Coordinate Analysis and results from NewHybrids analysis indicate that B. × rhynchopetala comprises different generations of introgressants in addition to F(1s. High genetic relatedness between B. × rhynchopetala and B. gymnorrhiza based on nuclear and chloroplast sequences suggests preferential hybrid backcrosses to B. gymnorrhiza. We conclude that B. × rhynchopetala has not evolved into an incipient hybrid species, and its persistence can be explained by recurrent hybridization and introgression. Genomic data provide insights into the hybridization dynamics of mangrove plants. Such information

  11. Construction of a restriction map and gene map of the lettuce chloroplast small single-copy region using Southern cross-hybridization.

    Science.gov (United States)

    Mitchelson, K R

    1996-01-01

    The small single-copy region (SSCR) of the chloroplast genome of many higher plants typically contain ndh genes encoding proteins that share homology with subunits of the respiratory-chain reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase complex of mitochondria. A map of the lettuce chloroplast SSCR has been determined by Southern cross-hybridization, taking advantage of the high degree of homology between a tobacco small single-copy fragment and a corresponding lettuce chloroplast fragment. The gene order of the SSCR of lettuce and tobacco chloroplasts is similar. The cross-hybridization method can rapidly create a primary gene map of unknown chloroplast fragments, thus providing detailed information of the localization and arrangement of genes and conserved open reading frame regions.

  12. The Brain–to–Pancreatic Islet Neuronal Map Reveals Differential Glucose Regulation From Distinct Hypothalamic Regions

    Science.gov (United States)

    Rosario, Wilfredo; Singh, Inderroop; Wautlet, Arnaud; Patterson, Christa; Flak, Jonathan; Becker, Thomas C.; Ali, Almas; Tamarina, Natalia; Philipson, Louis H.; Enquist, Lynn W.; Myers, Martin G.

    2016-01-01

    The brain influences glucose homeostasis, partly by supplemental control over insulin and glucagon secretion. Without this central regulation, diabetes and its complications can ensue. Yet, the neuronal network linking to pancreatic islets has never been fully mapped. Here, we refine this map using pseudorabies virus (PRV) retrograde tracing, indicating that the pancreatic islets are innervated by efferent circuits that emanate from the hypothalamus. We found that the hypothalamic arcuate nucleus (ARC), ventromedial nucleus (VMN), and lateral hypothalamic area (LHA) significantly overlap PRV and the physiological glucose-sensing enzyme glucokinase. Then, experimentally lowering glucose sensing, specifically in the ARC, resulted in glucose intolerance due to deficient insulin secretion and no significant effect in the VMN, but in the LHA it resulted in a lowering of the glucose threshold that improved glucose tolerance and/or improved insulin sensitivity, with an exaggerated counter-regulatory response for glucagon secretion. No significant effect on insulin sensitivity or metabolic homeostasis was noted. Thus, these data reveal novel direct neuronal effects on pancreatic islets and also render a functional validation of the brain-to-islet neuronal map. They also demonstrate that distinct regions of the hypothalamus differentially control insulin and glucagon secretion, potentially in partnership to help maintain glucose homeostasis and guard against hypoglycemia. PMID:27207534

  13. The Brain-to-Pancreatic Islet Neuronal Map Reveals Differential Glucose Regulation From Distinct Hypothalamic Regions.

    Science.gov (United States)

    Rosario, Wilfredo; Singh, Inderroop; Wautlet, Arnaud; Patterson, Christa; Flak, Jonathan; Becker, Thomas C; Ali, Almas; Tamarina, Natalia; Philipson, Louis H; Enquist, Lynn W; Myers, Martin G; Rhodes, Christopher J

    2016-09-01

    The brain influences glucose homeostasis, partly by supplemental control over insulin and glucagon secretion. Without this central regulation, diabetes and its complications can ensue. Yet, the neuronal network linking to pancreatic islets has never been fully mapped. Here, we refine this map using pseudorabies virus (PRV) retrograde tracing, indicating that the pancreatic islets are innervated by efferent circuits that emanate from the hypothalamus. We found that the hypothalamic arcuate nucleus (ARC), ventromedial nucleus (VMN), and lateral hypothalamic area (LHA) significantly overlap PRV and the physiological glucose-sensing enzyme glucokinase. Then, experimentally lowering glucose sensing, specifically in the ARC, resulted in glucose intolerance due to deficient insulin secretion and no significant effect in the VMN, but in the LHA it resulted in a lowering of the glucose threshold that improved glucose tolerance and/or improved insulin sensitivity, with an exaggerated counter-regulatory response for glucagon secretion. No significant effect on insulin sensitivity or metabolic homeostasis was noted. Thus, these data reveal novel direct neuronal effects on pancreatic islets and also render a functional validation of the brain-to-islet neuronal map. They also demonstrate that distinct regions of the hypothalamus differentially control insulin and glucagon secretion, potentially in partnership to help maintain glucose homeostasis and guard against hypoglycemia. © 2016 by the American Diabetes Association.

  14. Human cDNA mapping using fluorescence in situ hybridization. Progress report, April 1, 1992--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-03-04

    Genetic mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach generated 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  15. Plastid DNA analysis reveals cryptic hybridization in invasive dalmatian toadflax populations

    Science.gov (United States)

    Andrew Boswell; Sharlene E. Sing; Sarah M. Ward

    2016-01-01

    Gene flow between Dalmatian toadflax (DT) and yellow toadflax (YT), both aggressive invaders throughout the Intermountain West, is creating hybrid populations potentially more invasive than either parent species. To determine the direction of gene flow in these hybrid populations, species-diagnostic cytoplasmic markers were developed. Markers were based on...

  16. Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility.

    Science.gov (United States)

    Mořkovský, Libor; Janoušek, Václav; Reif, Jiří; Rídl, Jakub; Pačes, Jan; Choleva, Lukáš; Janko, Karel; Nachman, Michael W; Reifová, Radka

    2018-02-01

    Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (F ST ) and of high divergence (D xy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females. © 2018 John Wiley & Sons Ltd.

  17. Charactering the ZFAND3 gene mapped in the sex-determining locus in hybrid tilapia (Oreochromis spp.)

    Science.gov (United States)

    Ma, Keyi; Liao, Minghui; Liu, Feng; Ye, Baoqing; Sun, Fei; Yue, Gen Hua

    2016-01-01

    Zinc finger AN1-type domain 3 (ZFAND3) is essential for spermatogenesis in mice. However, its function in teleosts remains unclear. In this study, we characterized the ZFAND3 gene (termed as OsZFAND3) in an important food fish, tilapia. The OsZFAND3 cDNA sequence is 1,050 bp in length, containing an ORF of 615 bp, which encodes a putative peptide of 204 amino acid residues. Quantitative real-time PCR revealed that the OsZFAND3 transcripts were exclusively expressed in the testis and ovary. In situ hybridization showed that the high expression of OsZFAND3 transcripts was predominantly localized in the spermatocyte and spermatid. These results suggest that OsZFAND3 is involved in male germ cell maturation. Three single nucleotide polymorphisms (SNPs) were detected in the introns of OsZFAND3. The OsZFAND3 gene was mapped in the sex-determining locus on linkage group 1 (LG1). The three SNPs in the OsZFAND3 gene were strictly associated with sex phenotype, suggesting that the OsZFAND3 gene is tightly linked to the sex-determining locus. Our study provides new insights into the functions of the OsZFAND3 gene in tilapia and a foundation for further detailed analysis of the OsZFAND3 gene in sex determination and differentiation. PMID:27137111

  18. Association mapping in sunflower (Helianthus annuus L.) reveals independent control of apical vs. basal branching.

    Science.gov (United States)

    Nambeesan, Savithri U; Mandel, Jennifer R; Bowers, John E; Marek, Laura F; Ebert, Daniel; Corbi, Jonathan; Rieseberg, Loren H; Knapp, Steven J; Burke, John M

    2015-03-11

    Shoot branching is an important determinant of plant architecture and influences various aspects of growth and development. Selection on branching has also played an important role in the domestication of crop plants, including sunflower (Helianthus annuus L.). Here, we describe an investigation of the genetic basis of variation in branching in sunflower via association mapping in a diverse collection of cultivated sunflower lines. Detailed phenotypic analyses revealed extensive variation in the extent and type of branching within the focal population. After correcting for population structure and kinship, association analyses were performed using a genome-wide collection of SNPs to identify genomic regions that influence a variety of branching-related traits. This work resulted in the identification of multiple previously unidentified genomic regions that contribute to variation in branching. Genomic regions that were associated with apical and mid-apical branching were generally distinct from those associated with basal and mid-basal branching. Homologs of known branching genes from other study systems (i.e., Arabidopsis, rice, pea, and petunia) were also identified from the draft assembly of the sunflower genome and their map positions were compared to those of associations identified herein. Numerous candidate branching genes were found to map in close proximity to significant branching associations. In sunflower, variation in branching is genetically complex and overall branching patterns (i.e., apical vs. basal) were found to be influenced by distinct genomic regions. Moreover, numerous candidate branching genes mapped in close proximity to significant branching associations. Although the sunflower genome exhibits localized islands of elevated linkage disequilibrium (LD), these non-random associations are known to decay rapidly elsewhere. The subset of candidate genes that co-localized with significant associations in regions of low LD represents the most

  19. Longitudinal fluorescence in situ hybridization reveals cytogenetic evolution in myeloma relapsing after autologous transplantation

    Science.gov (United States)

    Merz, Maximilian; Jauch, Anna; Hielscher, Thomas; Mai, Elias K.; Seckinger, Anja; Hose, Dirk; Bertsch, Uta; Neben, Kai; Raab, Marc S.; Salwender, Hans; Blau, Igor W.; Lindemann, Hans-Walter; Schmidt-Wolf, Ingo; Scheid, Christof; Haenel, Mathias; Weisel, Katja; Goldschmidt, Hartmut; Hillengass, Jens

    2017-01-01

    To investigate cytogenetic evolution after upfront autologous stem cell transplantation for newly diagnosed myeloma we retrospectively analyzed fluorescence in situ hybridization results of 128 patients with paired bone marrow samples from the time of primary diagnosis and at relapse. High-risk cytogenetic abnormalities (deletion 17p and/or gain 1q21) occurred more frequently after relapse (odds ratio: 6.33; 95% confidence interval: 1.86–33.42; P<0.001). No significant changes were observed for defined IGH translocations [t(4;14); t(11;14); t(14;16)] or hyperdiploid karyotypes between primary diagnosis and relapse. IGH translocations with unknown partners occurred more frequently at relapse. New deletion 17p and/or gain 1q21 were associated with cytogenetic heterogeneity, since some de novo lesions with different copy numbers were present only in subclones. No distinct baseline characteristics were associated with the occurrence of new high-risk cytogenetic abnormalities after progression. Patients who relapsed after novel agent-based induction therapy had an increased risk of developing high-risk aberrations (odds ratio 10.82; 95% confidence interval: 1.65–127.66; P=0.03) compared to those who were treated with conventional chemotherapy. Survival analysis revealed dismal outcomes regardless of whether high-risk aberrations were present at baseline (hazard ratio, 3.53; 95% confidence interval: 1.53–8.14; P=0.003) or developed at relapse only (hazard ratio, 3.06; 95% confidence interval: 1.09–8.59; P=0.03). Our results demonstrate cytogenetic evolution towards high-risk disease after autologous transplantation and underline the importance of repeated genetic testing in relapsed myeloma (EudraCT number of the HD4 trial: 2004-000944-26). PMID:28495913

  20. Logarithmic r-θ mapping for hybrid optical neural network filter for multiple objects recognition within cluttered scenes

    Science.gov (United States)

    Kypraios, Ioannis; Young, Rupert C. D.; Chatwin, Chris R.; Birch, Phil M.

    2009-04-01

    θThe window unit in the design of the complex logarithmic r-θ mapping for hybrid optical neural network filter can allow multiple objects of the same class to be detected within the input image. Additionally, the architecture of the neural network unit of the complex logarithmic r-θ mapping for hybrid optical neural network filter becomes attractive for accommodating the recognition of multiple objects of different classes within the input image by modifying the output layer of the unit. We test the overall filter for multiple objects of the same and of different classes' recognition within cluttered input images and video sequences of cluttered scenes. Logarithmic r-θ mapping for hybrid optical neural network filter is shown to exhibit with a single pass over the input data simultaneously in-plane rotation, out-of-plane rotation, scale, log r-θ map translation and shift invariance, and good clutter tolerance by recognizing correctly the different objects within the cluttered scenes. We record in our results additional extracted information from the cluttered scenes about the objects' relative position, scale and in-plane rotation.

  1. Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus revealed by analyses of multiple mitochondrial and nuclear DNA loci

    Directory of Open Access Journals (Sweden)

    Wu Shi-Fang

    2011-07-01

    Full Text Available Abstract Background Interspecific hybridization may lead to the introgression of genes and genomes across species barriers and contribute to a reticulate evolutionary pattern and thus taxonomic uncertainties. Since several previous studies have demonstrated that introgressive hybridization has occurred among some species within Lepus, therefore it is possible that introgressive hybridization events also occur among Chinese Lepus species and contribute to the current taxonomic confusion. Results Data from four mtDNA genes, from 116 individuals, and one nuclear gene, from 119 individuals, provides the first evidence of frequent introgression events via historical and recent interspecific hybridizations among six Chinese Lepus species. Remarkably, the mtDNA of L. mandshuricus was completely replaced by mtDNA from L. timidus and L. sinensis. Analysis of the nuclear DNA sequence revealed a high proportion of heterozygous genotypes containing alleles from two divergent clades and that several haplotypes were shared among species, suggesting repeated and recent introgression. Furthermore, results from the present analyses suggest that Chinese hares belong to eight species. Conclusion This study provides a framework for understanding the patterns of speciation and the taxonomy of this clade. The existence of morphological intermediates and atypical mitochondrial gene genealogies resulting from frequent hybridization events likely contribute to the current taxonomic confusion of Chinese hares. The present study also demonstrated that nuclear gene sequence could offer a powerful complementary data set with mtDNA in tracing a complete evolutionary history of recently diverged species.

  2. Molecular data reveal complex hybridization and a cryptic species of neotropical wild cat.

    Science.gov (United States)

    Trigo, Tatiane C; Schneider, Alexsandra; de Oliveira, Tadeu G; Lehugeur, Livia M; Silveira, Leandro; Freitas, Thales R O; Eizirik, Eduardo

    2013-12-16

    Hybridization among animal species has recently become more recognized as an important phenomenon, especially in the context of recent radiations. Here we show that complex hybridization has led to contrasting patterns of genomic composition among closely related species of the Neotropical cat genus Leopardus. We show strong evidence of ancient hybridization and introgression between the pampas cat (L. colocolo) and northeastern populations of tigrina (L. tigrinus), leading to remarkable cytonuclear discordance in the latter. In contrast, southern tigrina populations show recent and continuing hybridization with Geoffroy's cat (L. geoffroyi), leading to extreme levels of interspecific admixture at their contact zone. Finally, we demonstrate that two seemingly continuous Brazilian tigrina populations show no evidence of ongoing gene flow between them, leading us to support their formal recognition as distinct species, namely L. tigrinus in the northeast and L. guttulus in the south. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Relativistic Fermi-Ulam map: Application to WEGA stellarator lower hybrid power operation

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, V.; Seidl, J.; Krlín, L.; Pánek, R.; Preinhaelter, J.; Urban, J. [Institute of Plasma Physics AS CR, v.v.i., Prague (Czech Republic); Laqua, H. P. [Max-Planck-Institute for Plasma Physics, Wendelsteinstr. 1, 17491 Greifswald (Germany)

    2014-06-15

    Analytical and numerical support is here provided in support of the explanation [Laqua et al., Plasma Phys. Controlled Fusion 56, 075022 (2014)] for the observation of ∼MeV electrons during Lower Hybrid (LH) operation in EC pre-heated plasma at the WEGA stellarator [Otte et al., Nukleonika, 57, 171 (2012)]. In the quoted experiments, LH power from the WEGA TE{sub 11} circular waveguide, 9 cm diameter, un-phased, 2.45 GHz antenna, is radiated into a B ≅ 0.5 T, n{sup ¯}{sub e} ≅ 5 × 10{sup 17} 1/m{sup 3} plasma at T{sub e} ≅ 10 eV bulk temperature with an EC-generated 50 keV population of electrons. In response, the fast electrons travel around flux or drift surfaces essentially without collisions, repeatedly interacting with the rf field close to the antenna mouth, and gaining energy in the process. Our WEGA antenna calculations indicate a predominantly standing electric field pattern at the antenna mouth. From a simple approximation of the corresponding Hamiltonian equations of motion, we derive here a relativistic generalization of the simplified area-preserving Fermi-Ulam (F-U) map [M. A. Lieberman and A. J. Lichtenberg, Phys. Rev. A 5, 1852 (1972), Lichtenberg et al., Physica D 1, 291 (1980)], allowing phase-space global stochasticity analysis. At typical WEGA plasma and antenna conditions, and with correlated phases between electron–antenna electric field interaction events, the F-U map and supporting numerical simulations predict an absolute energy barrier in the range of 300 keV. In contrast, with random phases intervening between interaction events, the electron energy can reach ∼MeV values, compatible with the measurements on WEGA [Laqua et al., Plasma Phys. Controlled Fusion 56, 075022 (2014)].

  4. Natural hybridization between Phlomis lycia D. Don x P. bourgaei Boiss., (Lamiaceae) revealed by RAPD markers.

    Science.gov (United States)

    Yüzbaşioğlu, Ertuğrul; Dadandi, Mehmet Yaşar; Ozcan, Sebahattin

    2008-05-01

    Randomly Amplified Polymorphic DNA markers (RAPD) were used to assess the hybrid identity of individuals sampled as Phlomis x termessi Davis. Out of 95 primers screened, 11 primers produced reproducible amplification patterns used for discrimination of P. x termessi and their parents. Eleven primers produced 81 bands. Forty two percent of the RAPD bands existed in parents. Of the 54 bands found in P. lycia, 19 were found only in this species and 7 of these were monomorphic. Similarly, of 57 RAPD bands observed in P. bourgaei, 18 were found only in P. bourgaei and 6 of these were monomorphic. Among hybrid individuals, 35 of the 73 markers were monomorphic. Fifteen of these existed in individual parents showing that parents were homozygous for these markers. Of the 35 monomorphic bands observed among hybrid individuals, 5 were present in the samples of one of the parents and completely absent from the samples of the other; therefore, additive inheritance is indicated. Of the 5 additive bands, 1 was inherited from P. bourgaei and 4 were inherited from P. lycia. Among 38 polymorhic markers observed in hybrid individuals, 9 were new and hybrid-specific. Pollen fertility was also investigated. Mean pollen fertility for P. lycia and P. bourgaei was 93% and 97% respectively. However, mean pollen fertility for hybrids was 65% (+/-10.5).

  5. Differential stress response of Saccharomyces hybrids revealed by monitoring Hsp104 aggregation and disaggregation.

    Science.gov (United States)

    Kempf, Claudia; Lengeler, Klaus; Wendland, Jürgen

    2017-07-01

    Proteotoxic stress may occur upon exposure of yeast cells to different stress conditions. The induction of stress response mechanisms is important for cells to adapt to changes in the environment and ensure survival. For example, during exposure to elevated temperatures the expression of heat shock proteins such as Hsp104 is induced in yeast. Hsp104 extracts misfolded proteins from aggregates to promote their refolding. We used an Hsp104-GFP reporter to analyze the stress profiles of Saccharomyces species hybrids. To this end a haploid S. cerevisiae strain, harboring a chromosomal HSP104-GFP under control of its endogenous promoter, was mated with stable haploids of S. bayanus, S. cariocanus, S. kudriavzevii, S. mikatae, S. paradoxus and S. uvarum. Stress response behaviors in these hybrids were followed over time by monitoring the appearance and dissolution of Hsp104-GFP foci upon heat shock. General stress tolerance of these hybrids was related to the growth rate detected during exposure to e.g. ethanol and oxidizing agents. We observed that hybrids were generally more resistant to high temperature and ethanol stress compared to their parental strains. Amongst the hybrids differential responses regarding the appearance of Hsp104-foci and the time required for dissolving these aggregates were observed. The S. cerevisiae/S. paradoxus hybrid, combining the two most closely related strains, performed best under these conditions. Copyright © 2017 Elsevier GmbH. All rights reserved.

  6. Comparison of Data Fusion Methods Using Crowdsourced Data in Creating a Hybrid Forest Cover Map

    Directory of Open Access Journals (Sweden)

    Myroslava Lesiv

    2016-03-01

    Full Text Available Data fusion represents a powerful way of integrating individual sources of information to produce a better output than could be achieved by any of the individual sources on their own. This paper focuses on the data fusion of different land cover products derived from remote sensing. In the past, many different methods have been applied, without regard to their relative merit. In this study, we compared some of the most commonly-used methods to develop a hybrid forest cover map by combining available land cover/forest products and crowdsourced data on forest cover obtained through the Geo-Wiki project. The methods include: nearest neighbour, naive Bayes, logistic regression and geographically-weighted logistic regression (GWR, as well as classification and regression trees (CART. We ran the comparison experiments using two data types: presence/absence of forest in a grid cell; percentage of forest cover in a grid cell. In general, there was little difference between the methods. However, GWR was found to perform better than the other tested methods in areas with high disagreement between the inputs.

  7. SiSeRHMap v1.0: a simulator for mapped seismic response using a hybrid model

    Science.gov (United States)

    Grelle, Gerardo; Bonito, Laura; Lampasi, Alessandro; Revellino, Paola; Guerriero, Luigi; Sappa, Giuseppe; Guadagno, Francesco Maria

    2016-04-01

    The SiSeRHMap (simulator for mapped seismic response using a hybrid model) is a computerized methodology capable of elaborating prediction maps of seismic response in terms of acceleration spectra. It was realized on the basis of a hybrid model which combines different approaches and models in a new and non-conventional way. These approaches and models are organized in a code architecture composed of five interdependent modules. A GIS (geographic information system) cubic model (GCM), which is a layered computational structure based on the concept of lithodynamic units and zones, aims at reproducing a parameterized layered subsoil model. A meta-modelling process confers a hybrid nature to the methodology. In this process, the one-dimensional (1-D) linear equivalent analysis produces acceleration response spectra for a specified number of site profiles using one or more input motions. The shear wave velocity-thickness profiles, defined as trainers, are randomly selected in each zone. Subsequently, a numerical adaptive simulation model (Emul-spectra) is optimized on the above trainer acceleration response spectra by means of a dedicated evolutionary algorithm (EA) and the Levenberg-Marquardt algorithm (LMA) as the final optimizer. In the final step, the GCM maps executor module produces a serial map set of a stratigraphic seismic response at different periods, grid solving the calibrated Emul-spectra model. In addition, the spectra topographic amplification is also computed by means of a 3-D validated numerical prediction model. This model is built to match the results of the numerical simulations related to isolate reliefs using GIS morphometric data. In this way, different sets of seismic response maps are developed on which maps of design acceleration response spectra are also defined by means of an enveloping technique.

  8. GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Johanna A Bac-Molenaar

    Full Text Available Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature.

  9. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth.

    Science.gov (United States)

    Zhang, Xuehai; Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Xiong, Lizhong; Yang, Wanneng; Yan, Jianbing

    2017-03-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize ( Zea mays ) recombinant inbred line population ( n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. © 2017 American Society of Plant Biologists. All Rights Reserved.

  10. Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

    Science.gov (United States)

    Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

    2011-01-01

    As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

  11. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways.

    Directory of Open Access Journals (Sweden)

    Mohan Babu

    2011-11-01

    Full Text Available As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium and prototrophic (minimal medium culture conditions. The differential patterns of genetic interactions detected among > 235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens and an important target.

  12. THREE-DIMENSIONAL DUST MAPPING REVEALS THAT ORION FORMS PART OF A LARGE RING OF DUST

    International Nuclear Information System (INIS)

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F.; Green, G.; Finkbeiner, D. P.; Burgett, W. S.; Chambers, K. C.; Kaiser, N.; Morgan, J. S.; Tonry, J. L.; Wainscoat, R. J.; Waters, C.; Draper, P. W.; Metcalfe, N.; Price, P. A.

    2015-01-01

    The Orion Molecular Complex is the nearest site of ongoing high-mass star formation, making it one of the most extensively studied molecular complexes in the Galaxy. We have developed a new technique for mapping the three-dimensional distribution of dust in the Galaxy using Pan-STARRS1 photometry. We isolate the dust at the distance to Orion using this technique, revealing a large (100 pc, 14° diameter), previously unrecognized ring of dust, which we term the ''Orion dust ring''. The ring includes Orion A and B, and is not coincident with current Hα features. The circular morphology suggests formation as an ancient bubble in the interstellar medium, though we have not been able to conclusively identify the source of the bubble. This hint at the history of Orion may have important consequences for models of high-mass star formation and triggered star formation

  13. Monotone Hybrid Projection Algorithms for an Infinitely Countable Family of Lipschitz Generalized Asymptotically Quasi-Nonexpansive Mappings

    Directory of Open Access Journals (Sweden)

    Watcharaporn Cholamjiak

    2009-01-01

    Full Text Available We prove a weak convergence theorem of the modified Mann iteration process for a uniformly Lipschitzian and generalized asymptotically quasi-nonexpansive mapping in a uniformly convex Banach space. We also introduce two kinds of new monotone hybrid methods and obtain strong convergence theorems for an infinitely countable family of uniformly Lipschitzian and generalized asymptotically quasi-nonexpansive mappings in a Hilbert space. The results improve and extend the corresponding ones announced by Kim and Xu (2006 and Nakajo and Takahashi (2003.

  14. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization

    Directory of Open Access Journals (Sweden)

    Gonser Rusty A

    2011-06-01

    Full Text Available Abstract Background The genomics era has produced an arsenal of resources from sequenced organisms allowing researchers to target species that do not have comparable mapping and sequence information. These new "non-model" organisms offer unique opportunities to examine environmental effects on genomic patterns and processes. Here we use comparative mapping as a first step in characterizing the genome organization of a novel animal model, the white-throated sparrow (Zonotrichia albicollis, which occurs as white or tan morphs that exhibit alternative behaviors and physiology. Morph is determined by the presence or absence of a complex chromosomal rearrangement. This species is an ideal model for behavioral genomics because the association between genotype and phenotype is absolute, making it possible to identify the genomic bases of phenotypic variation. Findings We initiated a genomic study in this species by characterizing the white-throated sparrow BAC library via filter hybridization with overgo probes designed for the chicken, turkey, and zebra finch. Cross-species hybridization resulted in 640 positive sparrow BACs assigned to 77 chicken loci across almost all macro-and microchromosomes, with a focus on the chromosomes associated with morph. Out of 216 overgos, 36% of the probes hybridized successfully, with an average number of 3.0 positive sparrow BACs per overgo. Conclusions These data will be utilized for determining chromosomal architecture and for fine-scale mapping of candidate genes associated with phenotypic differences. Our research confirms the utility of interspecies hybridization for developing comparative maps in other non-model organisms.

  15. A radiation hybrid map of chromosome 1D reveals synteny conservation at a wheat speciation locus

    Czech Academy of Sciences Publication Activity Database

    de Jimenez, M.K.M.; Bassi, F.M.; Ghavami, F.; Simons, K.; Šimková, Hana; Doležel, Jaroslav; Seth, K.; Kianian, S.F.

    2013-01-01

    Roč. 13, č. 1 (2013), s. 19-32 ISSN 1438-793X Institutional research plan: CEZ:AV0Z50380511 Keywords : Species cytoplasm specific * Wheat Zapper * Synteny Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.691, year: 2013

  16. Nuclear and mitochondrial DNA analysis reveals that hybridization between Fasciola hepatica and Fasciola gigantica occurred in China.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Peng, Mao; Hayashi, Kei; Shoriki, Takuya; Mohanta, Uday Kumar; Shibahara, Toshiyuki; Itagaki, Tadashi

    2017-02-01

    The well-known pathogens of fasciolosis, Fasciola hepatica (Fh) and Fasciola Gigantica (Fg), possess abundant mature sperms in their seminal vesicles, and thus, they reproduce bisexually. On the other hand, aspermic Fasciola flukes reported from Asian countries, which have no sperm in their seminal vesicles, probably reproduce parthenogenetically. The aim of this study was to reveal the origin of aspermic Fasciola flukes. The nuclear single copy markers, phosphoenolpyruvate carboxykinase and DNA polymerase delta, were employed for analysis of Fasciola species from China. The hybrid origin of aspermic Fasciola flukes was strongly suggested by the presence of the Fh/Fg type, which includes DNA fragments of both F. hepatica and F. gigantica. China can be regarded as the cradle of the interspecific hybridization because F. hepatica and F. gigantica were detected in the northern and southern parts of China, respectively, and hybrids flukes were distributed between the habitats of the two species. The Chinese origin was supported by the fact that a larger number of mitochondrial NADH dehydrogenase subunit 1 (nad1) haplotypes was detected in Chinese aspermic Fasciola populations than in aspermic populations from the neighbouring countries. Hereafter, 'aspermic' Fasciola flukes should be termed as 'hybrid' Fasciola flukes.

  17. Diverse mechanisms of plant resistance to cauliflower mosaic virus revealed by leaf skeleton hybridization.

    Science.gov (United States)

    Melcher, U; Brannan, C M; Gardner, C O; Essenberg, R C

    1992-01-01

    Plants not hosts for cauliflower mosaic virus (CaMV) may prevent systemic CaMV infection by interfering with dissemination of infection through the plant or by preventing viral replication and maturation. Leaf skeleton hybridization allows distinction between these two barriers. The technique assesses the spatial distribution of CaMV in an inoculated leaf by hybridization of a skeleton of the leaf with a CaMV DNA probe. Leaves or leaflets of soybean, cucumber, peanut, tomato, lettuce, spinach, pepper, onion, wheat, maize and barley, inoculated with CaMV DNA or CaMV virions were processed for leaf skeleton hybridization either immediately after inoculation or two weeks thereafter. Autoradiographic images of soybean and cucumber skeletons had many dark spots suggesting that CaMV DNA replication and local spread had occurred. Images of onion leaf skeletons prepared two weeks after inoculation with CaMV DNA had fewer spots. To test whether these spots resulted from CaMV replication, DNA was extracted from inoculated onion leaves and analyzed by electrophoresis, blotting and hybridization. Molecules recovered two weeks after inoculation resembled those inoculated, indicating absence of replication. For the other species, we found no evidence of local spread of CaMV infections. Thus, many plant species resist systemic CaMV infection by preventing replication or local spread of CaMV, while others solely prevent systemic movement of infection.

  18. Ultrafast optical snapshots of hybrid perovskites reveal the origin of multiband electronic transitions

    Science.gov (United States)

    Appavoo, Kannatassen; Nie, Wanyi; Blancon, Jean-Christophe; Even, Jacky; Mohite, Aditya D.; Sfeir, Matthew Y.

    2017-11-01

    Connecting the complex electronic excitations of hybrid perovskites to their intricate organic-inorganic lattice structure has critical implications for energy conversion and optoelectronic technologies. Here we detail the multiband, multivalley electronic structure of a halide hybrid perovskite by measuring the absorption transients of a millimeter-scale-grain thin film as it undergoes a thermally controlled reversible tetragonal-to-orthogonal phase transition. Probing nearly single grains of this hybrid perovskite, we observe an unreported energy splitting (degeneracy lifting) of the high-energy 2.6 eV band in the tetragonal phase that further splits as the rotational degrees of freedom of the disordered C H3N H3 + molecules are reduced when the sample is cooled. This energy splitting drastically increases during an extended phase-transition coexistence region that persists from 160 to 120 K, becoming more pronounced in the orthorhombic phase. By tracking the temperature-dependent optical transition energies and using symmetry analysis that describes the evolution of electronic states from the tetragonal phase to the orthorhombic phase, we assign this energy splitting to the nearly degenerate transitions in the tetragonal phase from both the R - and M -point-derived states. Importantly, these assignments explain how momentum conservation effects lead to long hot-carrier lifetimes in the room-temperature tetragonal phase, with faster hot-carrier relaxation when the hybrid perovskite structurally transitions to the orthorhombic phase due to enhanced scattering at the Γ point.

  19. A hybrid CPU-GPU accelerated framework for fast mapping of high-resolution human brain connectome.

    Directory of Open Access Journals (Sweden)

    Yu Wang

    Full Text Available Recently, a combination of non-invasive neuroimaging techniques and graph theoretical approaches has provided a unique opportunity for understanding the patterns of the structural and functional connectivity of the human brain (referred to as the human brain connectome. Currently, there is a very large amount of brain imaging data that have been collected, and there are very high requirements for the computational capabilities that are used in high-resolution connectome research. In this paper, we propose a hybrid CPU-GPU framework to accelerate the computation of the human brain connectome. We applied this framework to a publicly available resting-state functional MRI dataset from 197 participants. For each subject, we first computed Pearson's Correlation coefficient between any pairs of the time series of gray-matter voxels, and then we constructed unweighted undirected brain networks with 58 k nodes and a sparsity range from 0.02% to 0.17%. Next, graphic properties of the functional brain networks were quantified, analyzed and compared with those of 15 corresponding random networks. With our proposed accelerating framework, the above process for each network cost 80∼150 minutes, depending on the network sparsity. Further analyses revealed that high-resolution functional brain networks have efficient small-world properties, significant modular structure, a power law degree distribution and highly connected nodes in the medial frontal and parietal cortical regions. These results are largely compatible with previous human brain network studies. Taken together, our proposed framework can substantially enhance the applicability and efficacy of high-resolution (voxel-based brain network analysis, and have the potential to accelerate the mapping of the human brain connectome in normal and disease states.

  20. Time-resolved pH/pO2 mapping with luminescent hybrid sensors.

    Science.gov (United States)

    Schröder, Claudia R; Polerecky, Lubos; Klimant, Ingo

    2007-01-01

    A method for simultaneous and referenced 2D mapping of pH and pO2 is described. The experimental setup combines a fast gateable CCD camera as detector, a LED as excitation light source and a single-layer sensor membrane as optical transducer. The planar optode comprises a lipophilic fluorescein derivative (lifetime approximately 5 ns) and platinum(II) mesotetrakis(pentafluorophenyl)porphyrin (approximately 70 micros in the absence of a quencher) immobilized in a hydrogel matrix. Depending on the fluorescent pH indicator, a pH transition in the physiological range (pH 6-pH 8) or in the near-basic region (pH 7-pH 9) can be achieved. The measuring scheme involves the time-resolved acquisition of images in three windows during a series of square-shaped excitation pulses. A method allowing the calculation of both parameters from these three images is presented. The pH/pO2 hybrid sensor incorporating the pH indicator 2',7'-dihexyl-5(6)-N-octadecyl-carboxamidofluorescein was characterized in detail. The pH and pO2 were determined with a maximum deviation of 0.03 pH unit and 6.5 hPa pO2, respectively, within the range of pH 7.6-pH 8.7 and 0-200 hPa pO2 in test measurements. The ionic strength (IS) cross-sensitivity was found to be relatively small (pH/IS pO2/IS pO2 images obtained in natural marine sediment are presented.

  1. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.

    Directory of Open Access Journals (Sweden)

    Rebekah E Oliver

    Full Text Available A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42 has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.

  2. Microsatellite organization in the grasshopper Abracris flavolineata (Orthoptera: Acrididae revealed by FISH mapping: remarkable spreading in the A and B chromosomes.

    Directory of Open Access Journals (Sweden)

    Diogo Milani

    Full Text Available With the aim of acquiring deeper knowledge about repetitive DNAs chromosomal organization in grasshoppers, we used fluorescent in situ hybridization (FISH to map the distribution of 16 microsatellite repeats, including mono-, di-, tri- and tetra-nucleotides, in the chromosomes of the species Abracris flavolineata (Acrididae, which harbors B chromosome. FISH revealed two main patterns: (i exclusively scattered signals, and (ii scattered and specific signals, forming evident blocks. The enrichment was observed in both euchromatic and heterochromatic areas and only the motif (C30 was absent in heterochromatin. The A and B chromosomes were enriched with all the elements that were mapped, being observed in the B chromosome more distinctive blocks for (GA15 and (GAG10. For A complement distinctive blocks were noticed for (A30, (CA15, (CG15, (GA15, (CAC10, (CAA10, (CGG10, (GAA10, (GAC10 and (GATA8. These results revealed an intense spreading of microsatellites in the A. flavolineata genome that was independent of the A+T or G+C enrichment in the repeats. The data indicate that the microsatellites compose the B chromosome and could be involved in the evolution of this element in this species, although no specific relationship with any A chromosome was observed to discuss about its origin. The systematic analysis presented here contributes to the knowledge of repetitive DNA chromosomal organization among grasshoppers including the B chromosomes.

  3. Astronomer's new guide to the galaxy: largest map of cold dust revealed

    Science.gov (United States)

    2009-07-01

    -wave camera on the ESO-operated APEX telescope. APEX is located at an altitude of 5100 m on the arid plateau of Chajnantor in the Chilean Andes -- a site that allows optimal viewing in the submillimetre range. The Universe is relatively unexplored at submillimetre wavelengths, as extremely dry atmospheric conditions and advanced detector technology are required for such observations. The interstellar medium -- the material between the stars -- is composed of gas and grains of cosmic dust, rather like fine sand or soot. However, the gas is mostly hydrogen and relatively difficult to detect, so astronomers often search for these dense regions by looking for the faint heat glow of the cosmic dust grains. Submillimetre light allows astronomers to see these dust clouds shining, even though they obscure our view of the Universe at visible light wavelengths. Accordingly, the ATLASGAL map includes the denser central regions of our galaxy, in the direction of the constellation of Sagittarius -- home to a supermassive black hole (ESO 46/08) -- that are otherwise hidden behind a dark shroud of dust clouds. The newly released map also reveals thousands of dense dust clumps, many never seen before, which mark the future birthplaces of massive stars. The clumps are typically a couple of light-years in size, and have masses of between ten and a few thousand times the mass of our Sun. In addition, ATLASGAL has captured images of beautiful filamentary structures and bubbles in the interstellar medium, blown by supernovae and the winds of bright stars. Some striking highlights of the map include the centre of the Milky Way, the nearby massive and dense cloud of molecular gas called Sagittarius B2, and a bubble of expanding gas called RCW120, where the interstellar medium around the bubble is collapsing and forming new stars (see ESO 40/08). "It's exciting to get our first look at ATLASGAL, and we will be increasing the size of the map over the next year to cover all of the galactic plane

  4. Genetic dissection of hybrid incompatibilities between Drosophila simulans and D. mauritiana. II. Mapping hybrid male sterility loci on the third chromosome.

    Science.gov (United States)

    Tao, Yun; Zeng, Zhao-Bang; Li, Jian; Hartl, Daniel L; Laurie, Cathy C

    2003-08-01

    Hybrid male sterility (HMS) is a rapidly evolving mechanism of reproductive isolation in Drosophila. Here we report a genetic analysis of HMS in third-chromosome segments of Drosophila mauritiana that were introgressed into a D. simulans background. Qualitative genetic mapping was used to localize 10 loci on 3R and a quantitative trait locus (QTL) procedure (multiple-interval mapping) was used to identify 19 loci on the entire chromosome. These genetic incompatibilities often show dominance and complex patterns of epistasis. Most of the HMS loci have relatively small effects and generally at least two or three of them are required to produce complete sterility. Only one small region of the third chromosome of D. mauritiana by itself causes a high level of infertility when introgressed into D. simulans. By comparison with previous studies of the X chromosome, we infer that HMS loci are only approximately 40% as dense on this autosome as they are on the X chromosome. These results are consistent with the gradual evolution of hybrid incompatibilities as a by-product of genetic divergence in allopatric populations.

  5. New Hypervariable SSR Markers for Diversity Analysis, Hybrid Purity Testing and Trait Mapping in Pigeonpea [Cajanus cajan (L.) Millspaugh].

    Science.gov (United States)

    Bohra, Abhishek; Jha, Rintu; Pandey, Gaurav; Patil, Prakash G; Saxena, Rachit K; Singh, Indra P; Singh, D; Mishra, R K; Mishra, Ankita; Singh, F; Varshney, Rajeev K; Singh, N P

    2017-01-01

    Draft genome sequence in pigeonpea offers unprecedented opportunities for genomics assisted crop improvement via enabling access to genome-wide genetic markers. In the present study, 421 hypervariable simple sequence repeat (SSR) markers from the pigeonpea genome were screened on a panel of eight pigeonpea genotypes yielding marker validation and polymorphism percentages of 95.24 and 54.11%, respectively. The SSR marker assay uncovered a total of 570 alleles with three as an average number of alleles per marker. Similarly, the mean values for gene diversity and PIC were 0.44 and 0.37, respectively. The number of polymorphic markers ranged from 39 to 89 for different parental combinations. Further, 60 of these SSRs were assayed on 94 genotypes, and model based clustering using STRUCTURE resulted in the identification of the two subpopulations ( K = 2). This remained in close agreement with the clustering patterns inferred from genetic distance (GD)-based approaches i.e., dendrogram, factorial and principal coordinate analysis (PCoA). The AMOVA accounted majority of the genetic variation within groups (89%) in comparison to the variation existing between the groups (11%). A subset of these markers was implicated for hybrid purity testing. We also demonstrated utility of these SSR markers in trait mapping through association and bi-parental linkage analyses. The general linear (GLM) and mixed linear (MLM) models both detected a single SSR marker (CcGM03681) with R 2 = 16.4 as associated with the resistance to Fusarium wilt variant 2. Similarly, by using SSR data in a segregating backcross population, the corresponding restorer-of-fertility ( Rf ) locus was putatively mapped at 39 cM with the marker CcGM08896. However, The marker-trait associations (MTAs) detected here represent a very preliminary type and hence demand deeper investigations for conclusive evidence. Given their ability to reveal polymorphism in simple agarose gels, the hypervariable SSRs are valuable

  6. Human cDNA mapping using fluorescence in situ hybridization. Progress report, April 1--December 31, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1993-12-31

    The ultimate goal of this proposal is to create a cDNA map of the human genome. Mapping is approached using the techniques of high resolution fluorescence in situ hybridization (FISH). This technology and the results of its application are designed to rapidly generate whole genome as tool box of expressed sequence to speed the identification of human disease genes. The results of this study are intended to dovetail with and to link the results of existing technologies for creating backbone YAC and genetic maps. In the first eight months, this approach will generate 60--80% of the expressed sequence map, the remainder expected to be derived through more long-term, labor-intensive, regional chromosomal gene searches or sequencing. The laboratory has made significant progress in the set-up phase, in mapping fetal and adult brain and other cDNAs, in testing a model system for directly linking genetic and physical maps using FISH with small fragments, in setting up a database, and in establishing the validity and throughput of the system.

  7. A genome-wide map of hyper-edited RNA reveals numerous new sites

    Science.gov (United States)

    Porath, Hagit T.; Carmi, Shai; Levanon, Erez Y.

    2014-01-01

    Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive (‘hyper’) editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

  8. Metabolic connectivity mapping reveals effective connectivity in the resting human brain.

    Science.gov (United States)

    Riedl, Valentin; Utz, Lukas; Castrillón, Gabriel; Grimmer, Timo; Rauschecker, Josef P; Ploner, Markus; Friston, Karl J; Drzezga, Alexander; Sorg, Christian

    2016-01-12

    Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabolic connectivity mapping (MCM), that integrates undirected functional connectivity (FC) with local energy metabolism from fMRI and positron emission tomography (PET) data acquired simultaneously. This method is based on the concept that most energy required for neuronal communication is consumed postsynaptically, i.e., at the target neurons. We investigated MCM and possible changes in EC within the physiological range using "eyes open" versus "eyes closed" conditions in healthy subjects. Independent of condition, MCM reliably detected stable and bidirectional communication between early and higher visual regions. Moreover, we found stable top-down signaling from a frontoparietal network including frontal eye fields. In contrast, we found additional top-down signaling from all major clusters of the salience network to early visual cortex only in the eyes open condition. MCM revealed consistent bidirectional and unidirectional signaling across the entire cortex, along with prominent changes in network interactions across two simple brain states. We propose MCM as a novel approach for inferring EC from neuronal energy metabolism that is ideally suited to study signaling hierarchies in the brain and their defects in brain disorders.

  9. Purification of reversibly oxidized proteins (PROP reveals a redox switch controlling p38 MAP kinase activity.

    Directory of Open Access Journals (Sweden)

    Dennis J Templeton

    2010-11-01

    Full Text Available Oxidation of cysteine residues of proteins is emerging as an important means of regulation of signal transduction, particularly of protein kinase function. Tools to detect and quantify cysteine oxidation of proteins have been a limiting factor in understanding the role of cysteine oxidation in signal transduction. As an example, the p38 MAP kinase is activated by several stress-related stimuli that are often accompanied by in vitro generation of hydrogen peroxide. We noted that hydrogen peroxide inhibited p38 activity despite paradoxically increasing the activating phosphorylation of p38. To address the possibility that cysteine oxidation may provide a negative regulatory effect on p38 activity, we developed a biochemical assay to detect reversible cysteine oxidation in intact cells. This procedure, PROP, demonstrated in vivo oxidation of p38 in response to hydrogen peroxide and also to the natural inflammatory lipid prostaglandin J2. Mutagenesis of the potential target cysteines showed that oxidation occurred preferentially on residues near the surface of the p38 molecule. Cysteine oxidation thus controls a functional redox switch regulating the intensity or duration of p38 activity that would not be revealed by immunodetection of phosphoprotein commonly interpreted as reflective of p38 activity.

  10. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

    Directory of Open Access Journals (Sweden)

    Eileen eLuders

    2013-07-01

    Full Text Available Scientific studies addressing anatomical variations in meditators’ brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM. To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls, where meditators have been practicing close to twenty years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentate, entorhinal cortex, subiculum as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri- hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators – perhaps due to an attenuated release of stress hormones and decreased neurotoxicity.

  11. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

    Science.gov (United States)

    Luders, Eileen; Kurth, Florian; Toga, Arthur W.; Narr, Katherine L.; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators—perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  12. A picture on the wall: innovative mapping reveals cold-water coral refuge in submarine canyon.

    Directory of Open Access Journals (Sweden)

    Veerle A I Huvenne

    Full Text Available Cold-water corals are azooxanthellate species found throughout the ocean at water depths down to 5000 m. They occur in patches, reefs or large mound structures up to 380 m high, and as ecosystem engineers create important habitats for a diverse fauna. However, the majority of these habitats are now within reach of deep-sea bottom trawling. Many have been severely damaged or are under threat, despite recent protection initiatives. Here we present a cold-water coral habitat type that so far has been overlooked--quite literally--and that has received minimal impact from human activities. Vertical and overhanging cliffs in deep-sea canyons, revealed using an innovative approach to marine habitat mapping, are shown to provide the perfect substratum for extensive cold-water coral-based communities. Typical canyon-related processes, including locally enhanced internal tides and focussed downslope organic carbon transport, provide favourable environmental conditions (current regime, food input to sustain the communities, even outside the optimal depth and density envelopes reported elsewhere in the NE Atlantic. Our findings show that deep-sea canyons can form natural refuges for faunal communities sensitive to anthropogenic disturbance, and have the potential to fulfil the crucial role of larval sources for the recolonisation of damaged sites elsewhere on the margin.

  13. Comparative Genomic Hybridization (CGH) reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis).

    Science.gov (United States)

    Baker, Richard H; Wilkinson, Gerald S

    2010-09-16

    Chromosomal location has a significant effect on the evolutionary dynamics of genes involved in sexual dimorphism, impacting both the pattern of sex-specific gene expression and the rate of duplication and protein evolution for these genes. For nearly all non-model organisms, however, knowledge of chromosomal gene content is minimal and difficult to obtain on a genomic scale. In this study, we utilized Comparative Genomic Hybridization (CGH), using probes designed from EST sequence, to identify genes located on the X chromosome of four species in the stalk-eyed fly genus Teleopsis. Analysis of log(2) ratio values of female-to-male hybridization intensities from the CGH microarrays for over 3,400 genes reveals a strongly bimodal distribution that clearly differentiates autosomal from X-linked genes for all four species. Genotyping of 33 and linkage mapping of 28 of these genes in Teleopsis dalmanni indicate the CGH results correctly identified chromosomal location in all cases. Syntenic comparison with Drosophila indicates that 90% of the X-linked genes in Teleopsis are homologous to genes located on chromosome 2L in Drosophila melanogaster, suggesting the formation of a nearly complete neo-X chromosome from Muller element B in the dipteran lineage leading to Teleopsis. Analysis of gene movement both relative to Drosophila and within Teleopsis indicates that gene movement is significantly associated with 1) rates of protein evolution, 2) the pattern of gene duplication, and 3) the evolution of eyespan sexual dimorphism. Overall, this study reveals that diopsids are a critical group for understanding the evolution of sex chromosomes within Diptera. In addition, we demonstrate that CGH is a useful technique for identifying chromosomal sex-linkage and should be applicable to other organisms with EST or partial genomic information.

  14. Comparative Genomic Hybridization (CGH reveals a neo-X chromosome and biased gene movement in stalk-eyed flies (genus Teleopsis.

    Directory of Open Access Journals (Sweden)

    Richard H Baker

    2010-09-01

    Full Text Available Chromosomal location has a significant effect on the evolutionary dynamics of genes involved in sexual dimorphism, impacting both the pattern of sex-specific gene expression and the rate of duplication and protein evolution for these genes. For nearly all non-model organisms, however, knowledge of chromosomal gene content is minimal and difficult to obtain on a genomic scale. In this study, we utilized Comparative Genomic Hybridization (CGH, using probes designed from EST sequence, to identify genes located on the X chromosome of four species in the stalk-eyed fly genus Teleopsis. Analysis of log(2 ratio values of female-to-male hybridization intensities from the CGH microarrays for over 3,400 genes reveals a strongly bimodal distribution that clearly differentiates autosomal from X-linked genes for all four species. Genotyping of 33 and linkage mapping of 28 of these genes in Teleopsis dalmanni indicate the CGH results correctly identified chromosomal location in all cases. Syntenic comparison with Drosophila indicates that 90% of the X-linked genes in Teleopsis are homologous to genes located on chromosome 2L in Drosophila melanogaster, suggesting the formation of a nearly complete neo-X chromosome from Muller element B in the dipteran lineage leading to Teleopsis. Analysis of gene movement both relative to Drosophila and within Teleopsis indicates that gene movement is significantly associated with 1 rates of protein evolution, 2 the pattern of gene duplication, and 3 the evolution of eyespan sexual dimorphism. Overall, this study reveals that diopsids are a critical group for understanding the evolution of sex chromosomes within Diptera. In addition, we demonstrate that CGH is a useful technique for identifying chromosomal sex-linkage and should be applicable to other organisms with EST or partial genomic information.

  15. Genetics of hybrid male sterility between drosophila sibling species: a complex web of epistasis is revealed in interspecific studies.

    Science.gov (United States)

    Palopoli, M F; Wu, C I

    1994-10-01

    To study the genetic differences responsible for the sterility of their male hybrids, we introgressed small segments of an X chromosome from Drosophila simulans into a pure Drosophila mauritiana genetic background, then assessed the fertility of males carrying heterospecific introgressions of varying size. Although this analysis examined less than 20% of the X chromosome (roughly 5% of the euchromatic portion of the D. simulans genome), and the segments were introgressed in only one direction, a minimum of four factors that contribute to hybrid male sterility were revealed. At least two of the factors exhibited strong epistasis: males carrying either factor alone were consistently fertile, whereas males carrying both factors together were always sterile. Distinct spermatogenic phenotypes were observed for sterile introgressions of different lengths, and it appeared that an interaction between introgressed segments also influenced the stage of spermatogenic defect. Males with one category of introgression often produced large quantities of motile sperm and were observed copulating, but never inseminated females. Evidently these two species have diverged at a large number of loci which have varied effects on hybrid male fertility. By extrapolation, we estimate that there are at least 40 such loci on the X chromosome alone. Because these species exhibit little DNA-sequence divergence at arbitrarily chosen loci, it seems unlikely that the extensive functional divergence observed could be due mainly to random genetic drift. Significant epistasis between conspecific genes appears to be a common component of hybrid sterility between recently diverged species of Drosophila. The linkage relationships of interacting factors could shed light on the role played by epistatic selection in the dynamics of the allele substitutions responsible for reproductive barriers between species.

  16. Walking dynamics of the passive compass-gait model under OGY-based state-feedback control: Analysis of local bifurcations via the hybrid Poincaré map

    International Nuclear Information System (INIS)

    Gritli, Hassène; Belghith, Safya

    2017-01-01

    Highlights: • We study the passive walking dynamics of the compass-gait model under OGY-based state-feedback control. • We analyze local bifurcations via a hybrid Poincaré map. • We show exhibition of the super(sub)-critical flip bifurcation, the saddle-node(saddle) bifurcation and a saddle-flip bifurcation. • An analysis via a two-parameter bifurcation diagram is presented. • Some new hidden attractors in the controlled passive walking dynamics are displayed. - Abstract: In our previous work, we have analyzed the passive dynamic walking of the compass-gait biped model under the OGY-based state-feedback control using the impulsive hybrid nonlinear dynamics. Such study was carried out through bifurcation diagrams. It was shown that the controlled bipedal gait exhibits attractive nonlinear phenomena such as the cyclic-fold (saddle-node) bifurcation, the period-doubling (flip) bifurcation and chaos. Moreover, we revealed that, using the controlled continuous-time dynamics, we encountered a problem in finding, identifying and hence following branches of (un)stable solutions in order to characterize local bifurcations. The present paper solves such problem and then provides a further investigation of the controlled bipedal walking dynamics using the developed analytical expression of the controlled hybrid Poincaré map. Thus, we show that analysis via such Poincaré map allows to follow branches of both stable and unstable fixed points in bifurcation diagrams and hence to explore the complete dynamics of the controlled compass-gait biped model. We demonstrate the generation, other than the conventional local bifurcations in bipedal walking, i.e. the flip bifurcation and the saddle-node bifurcation, of a saddle-saddle bifurcation, a subcritical flip bifurcation and a new type of a local bifurcation, the saddle-flip bifurcation. In addition, to further understand the occurrence of the local bifurcations, we present an analysis with a two-parameter bifurcation

  17. Quantification of intensive hybrid coastal reclamation for revealing its impacts on macrozoobenthos

    International Nuclear Information System (INIS)

    Yan, Jiaguo; Cui, Baoshan; Zheng, Jingjing; Xie, Tian; Wang, Qing; Li, Shanze

    2015-01-01

    Managing and identifying the sources of anthropogenic stress in coastal wetlands requires an in-depth understanding of relationships between species diversity and human activities. Empirical and experimental studies provide clear evidence that coastal reclamation can have profound impacts on marine organisms, but the focus of such studies is generally on comparative or laboratory research. We developed a compound intensity index (reclamation intensity index, RI) on hybrid coastal reclamation, to quantify the impacts of reclamation on coastal ecosystems. We also made use of mean annual absolute changes to a number of biotic variables (biodiversity, species richness, biomass of total macrozoobenthos, and species richness and biomass of Polychaeta, Mollusca, Crustacea, and Echinodermata) to determine Hedges’d index, which is a measure of the potential effects of coastal reclamation. Our results showed that there was significant difference of coastal reclamation intensity between Yellow Sea, East China Sea and South China Sea, the biological changes in effect sizes of the three regions differed greatly over time. Our modelling analyses showed that hybrid coastal reclamation generally had significant negative impacts on species diversity and biomass of macrozoobenthos. These relationships varied among different taxonomic groups and included both linear and nonlinear relationships. The results indicated that a high-intensity of coastal reclamation contributed to a pronounced decline in species diversity and biomass, while lower-intensity reclamation, or reclamation within certain thresholds, resulted in a small increase in species diversity and biomass. These results have important implications for biodiversity conservation and the ecological restoration of coastal wetlands in face of the intensive reclamation activities. (letter)

  18. Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

    Science.gov (United States)

    Gosselin, Thierry; Normandeau, Eric; Lamothe, Manuel; Isabel, Nathalie; Audet, Céline; Bernatchez, Louis

    2016-01-01

    Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects of WGD as the ancestral salmonid underwent WGD relatively recently, ∼65 Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosome arm fusions and fissions. Assembly of large, outbred eukaryotic genomes can be difficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here, we generate a high-density linkage map (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid high-density linkage maps, including six species of Oncorhynchus, and one species for each of Salmo, Coregonus, and the nonduplicated sister group for the salmonids, Northern Pike Esox lucius for identifying post-duplicated homeologs. To facilitate this process, we developed MapComp to identify identical and proximate (i.e. nearby) markers between linkage maps using a reference genome of a related species as an intermediate, increasing the number of comparable markers between linkage maps by 5-fold. This enabled a characterization of the most likely history of retained chromosomal rearrangements post-WGD, and several conserved chromosomal inversions. Analyses of RADseq-based linkage maps from other taxa will also benefit from MapComp, available at: https://github.com/enormandeau/mapcomp/ PMID:28173098

  19. Issues of tsunami hazard maps revealed by the 2011 Tohoku tsunami

    Science.gov (United States)

    Sugimoto, M.

    2013-12-01

    Tsunami scientists are imposed responsibilities of selection for people's tsunami evacuation place after the 2011 Tohoku Tsunami in Japan. A lot of matured people died out of tsunami hazard zone based on tsunami hazard map though students made a miracle by evacuation on their own judgment in Kamaishi city. Tsunami hazard maps were based on numerical model smaller than actual magnitude 9. How can we bridge the gap between hazard map and future disasters? We have to discuss about using tsunami numerical model better enough to contribute tsunami hazard map. How do we have to improve tsunami hazard map? Tsunami hazard map should be revised included possibility of upthrust or downthrust after earthquakes and social information. Ground sank 1.14m below sea level in Ayukawa town, Tohoku. Ministry of Land, Infrastructure, Transport and Tourism's research shows around 10% people know about tsunami hazard map in Japan. However, people know about their evacuation places (buildings) through experienced drills once a year even though most people did not know about tsunami hazard map. We need wider spread of tsunami hazard with contingency of science (See the botom disaster handbook material's URL). California Emergency Management Agency (CEMA) team practically shows one good practice and solution to me. I followed their field trip in Catalina Island, California in Sep 2011. A team members are multidisciplinary specialists: A geologist, a GIS specialist, oceanographers in USC (tsunami numerical modeler) and a private company, a local policeman, a disaster manager, a local authority and so on. They check field based on their own specialties. They conduct an on-the-spot inspection of ambiguous locations between tsunami numerical model and real field conditions today. The data always become older. They pay attention not only to topographical conditions but also to social conditions: vulnerable people, elementary schools and so on. It takes a long time to check such field

  20. Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

    Science.gov (United States)

    Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

  1. Constant-scale natural boundary mapping to reveal global and cosmic processes

    CERN Document Server

    Clark, Pamela Elizabeth

    2013-01-01

    Whereas conventional maps can be expressed as outward-expanding formulae with well-defined central features and relatively poorly defined edges, Constant Scale Natural Boundary (CSNB) maps have well-defined boundaries that result from natural processes and thus allow spatial and dynamic relationships to be observed in a new way useful to understanding these processes. CSNB mapping presents a new approach to visualization that produces maps markedly different from those produced by conventional cartographic methods. In this approach, any body can be represented by a 3D coordinate system. For a regular body, with its surface relatively smooth on the scale of its size, locations of features can be represented by definite geographic grid (latitude and longitude) and elevation, or deviation from the triaxial ellipsoid defined surface. A continuous surface on this body can be segmented, its distinctive regional terranes enclosed, and their inter-relationships defined, by using selected morphologically identifiable ...

  2. Production, Marketing and Value Chain Mapping of 'Srijana' Tomato Hybrid Seed in Nepal

    Directory of Open Access Journals (Sweden)

    Dinesh Babu Thapa Magar

    2016-12-01

    Full Text Available A tomato variety known as ‘Srijana’ developed by Nepal Agricultural Research Council (NARC has been substantially popular among Nepalese farmers and entrepreneurs. To understand the seed value chain of the Srijana hybrid tomato, a survey was conducted in 2014/15 with public research and extension institutions, private seed companies/firms, non-governmental organization and community group including individual farmers, involved in Srijana tomato seed production. The survey covered random selection of 30 agro-vets and 30 farmers in Kathmandu valley, Kavre, Nuwakot, Dolakha and Kaski districts, Nepal where production of Srijana tomato seed is mostly concentrated. A focus group discussion was also conducted with commercial tomato farmers in each of the study districts. The study showed a total production of 293 kg Srijana seed having a value of around 47 million Nepalese Rupees (US $ 470 thousands in year 2013/14. Private sector was the dominant actor sharing about 85% of the total Srijana seed production followed by non-governmental organization (10%, farmers group (3% and governmental station/farm/centers (2%, respectively. Out of the total Srijana seed produced, about 95% was consumed in domestic market while 5% was exported to India. The study revealed increasing trend of production, supply and price of Srijana tomato seed. About 0.3 million NRs (US $ 3,000 profit was estimated through the production of Srijana tomato seed in 0.05 hectares (500 m2 of land. Agro-vets (private sector seed dealers were the major actors for supplying the seed from the producers to farms and received a higher profit margins. The farmers producing and selling the seed in technical assistance of public agencies received higher producer`s share (66.6% than farmers producing and selling seed through own group (60%, technical assistance of non-governmental organization (53.3%, and in contract with private seed companies (26.7%. Majority of commercial tomato farmers

  3. OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences.

    Science.gov (United States)

    Croce, Olivier; Chevenet, François; Christen, Richard

    2008-07-01

    The efficiency of molecular methods involving DNA/DNA hybridizations depends on the accurate prediction of the melting temperature (T(m)) of the duplex. Many softwares are available for T(m) calculations, but difficulties arise when one wishes to check if a given oligomer (PCR primer or probe) hybridizes well or not on more than a single sequence. Moreover, the presence of mismatches within the duplex is not sufficient to estimate specificity as it does not always significantly decrease the T(m). OHM (OligoHeatMap) is an online tool able to provide estimates of T(m) for a set of oligomers and a set of aligned sequences, not only as text files of complete results but also in a graphical way: T(m) values are translated into colors and displayed as a heat map image, either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree. OHM is freely available at http://bioinfo.unice.fr/ohm/, with links to the full source code and online help.

  4. Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

    Science.gov (United States)

    Ishida, Yasuko; Cui, Pin; Vielgrader, Hanna; Helgen, Kristofer M.; Roca, Alfred L.; Greenwood, Alex D.

    2014-01-01

    The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin. PMID:24752422

  5. Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.

    Directory of Open Access Journals (Sweden)

    Kyriakos Tsangaras

    Full Text Available The koala retrovirus (KoRV is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.

  6. Fluorescence In Situ Hybridization (FISH-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris and Relatives

    Directory of Open Access Journals (Sweden)

    Aiko Iwata-Otsubo

    2016-04-01

    Full Text Available Fluorescence in situ hybridization (FISH-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.

  7. Managing hybrid marketing systems.

    Science.gov (United States)

    Moriarty, R T; Moran, U

    1990-01-01

    As competition increases and costs become critical, companies that once went to market only one way are adding new channels and using new methods - creating hybrid marketing systems. These hybrid marketing systems hold the promise of greater coverage and reduced costs. But they are also hard to manage; they inevitably raise questions of conflict and control: conflict because marketing units compete for customers; control because new indirect channels are less subject to management authority. Hard as they are to manage, however, hybrid marketing systems promise to become the dominant design, replacing the "purebred" channel strategy in all kinds of businesses. The trick to managing the hybrid is to analyze tasks and channels within and across a marketing system. A map - the hybrid grid - can help managers make sense of their hybrid system. What the chart reveals is that channels are not the basic building blocks of a marketing system; marketing tasks are. The hybrid grid forces managers to consider various combinations of channels and tasks that will optimize both cost and coverage. Managing conflict is also an important element of a successful hybrid system. Managers should first acknowledge the inevitability of conflict. Then they should move to bound it by creating guidelines that spell out which customers to serve through which methods. Finally, a marketing and sales productivity (MSP) system, consisting of a central marketing database, can act as the central nervous system of a hybrid marketing system, helping managers create customized channels and service for specific customer segments.

  8. Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition.

    Directory of Open Access Journals (Sweden)

    Jianhua Fan

    Full Text Available Microalgae have been extensively investigated and exploited because of their competitive nutritive bioproducts and biofuel production ability. Chlorella are green algae that can grow well heterotrophically and photoautotrophically. Previous studies proved that shifting from heterotrophy to photoautotrophy in light-induced environments causes photooxidative damage as well as distinct physiologic features that lead to dynamic changes in Chlorella intracellular components, which have great potential in algal health food and biofuel production. However, the molecular mechanisms underlying the trophic transition remain unclear.In this study, suppression subtractive hybridization strategy was employed to screen and characterize genes that are differentially expressed in response to the light-induced shift from heterotrophy to photoautotrophy. Expressed sequence tags (ESTs were obtained from 770 and 803 randomly selected clones among the forward and reverse libraries, respectively. Sequence analysis identified 544 unique genes in the two libraries. The functional annotation of the assembled unigenes demonstrated that 164 (63.1% from the forward library and 62 (21.8% from the reverse showed significant similarities with the sequences in the NCBI non-redundant database. The time-course expression patterns of 38 selected differentially expressed genes further confirmed their responsiveness to a diverse trophic status. The majority of the genes enriched in the subtracted libraries were associated with energy metabolism, amino acid metabolism, protein synthesis, carbohydrate metabolism, and stress defense.The data presented here offer the first insights into the molecular foundation underlying the diverse microalgal trophic niche. In addition, the results can be used as a reference for unraveling candidate genes associated with the transition of Chlorella from heterotrophy to photoautotrophy, which holds great potential for further improving its lipid and

  9. The Use of Mapping in Child Welfare Investigations: A Strength-Based Hybrid Intervention

    Science.gov (United States)

    Lwin, Kristen; Versanov, Avi; Cheung, Connie; Goodman, Deborah; Andrews, Nancy

    2014-01-01

    To enhance strengths-based service, a large urban child welfare agency in Ontario, Canada implemented part of the Signs of Safety (SOS) model in 2010. SOS was created to engage families involved with the child welfare system, and is rooted in the beliefs of collaboration, strengths-based practice, and safety. The hybrid of the full SOS model…

  10. A new hybrid nonlinear congruential number generator based on higher functional power of logistic maps

    International Nuclear Information System (INIS)

    Cecen, Songul; Demirer, R. Murat; Bayrak, Coskun

    2009-01-01

    We propose a nonlinear congruential pseudorandom number generator consisting of summation of higher order composition of random logistic maps under certain congruential mappings. We change both bifurcation parameters of logistic maps in the interval of U=[3.5599,4) and coefficients of the polynomials in each higher order composition of terms up to degree d. This helped us to obtain a perfect random decorrelated generator which is infinite and aperiodic. It is observed from the simulation results that our new PRNG has good uniformity and power spectrum properties with very flat white noise characteristics. The results are interesting, new and may have applications in cryptography and in Monte Carlo simulations.

  11. Parametric mapping using spectral analysis for 11C-PBR28 PET reveals neuroinflammation in mild cognitive impairment subjects.

    Science.gov (United States)

    Fan, Zhen; Dani, Melanie; Femminella, Grazia D; Wood, Melanie; Calsolaro, Valeria; Veronese, Mattia; Turkheimer, Federico; Gentleman, Steve; Brooks, David J; Hinz, Rainer; Edison, Paul

    2018-07-01

    Neuroinflammation and microglial activation play an important role in amnestic mild cognitive impairment (MCI) and Alzheimer's disease. In this study, we investigated the spatial distribution of neuroinflammation in MCI subjects, using spectral analysis (SA) to generate parametric maps and quantify 11 C-PBR28 PET, and compared these with compartmental and other kinetic models of quantification. Thirteen MCI and nine healthy controls were enrolled in this study. Subjects underwent 11 C-PBR28 PET scans with arterial cannulation. Spectral analysis with an arterial plasma input function was used to generate 11 C-PBR28 parametric maps. These maps were then compared with regional 11 C-PBR28 V T (volume of distribution) using a two-tissue compartment model and Logan graphic analysis. Amyloid load was also assessed with 18 F-Flutemetamol PET. With SA, three component peaks were identified in addition to blood volume. The 11 C-PBR28 impulse response function (IRF) at 90 min produced the lowest coefficient of variation. Single-subject analysis using this IRF demonstrated microglial activation in five out of seven amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake revealed a group-wise significant increase in neuroinflammation in amyloid-positive MCI subjects versus HC in multiple cortical association areas, and particularly in the temporal lobe. Interestingly, compartmental analysis detected group-wise increase in 11 C-PBR28 binding in the thalamus of amyloid-positive MCI subjects, while Logan parametric maps did not perform well. This study demonstrates for the first time that spectral analysis can be used to generate parametric maps of 11 C-PBR28 uptake, and is able to detect microglial activation in amyloid-positive MCI subjects. IRF parametric maps of 11 C-PBR28 uptake allow voxel-wise single-subject analysis and could be used to evaluate microglial activation in individual subjects.

  12. Updating rDNA restriction enzyme maps of Tetrahymena reveals four new intron-containing species

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Simon, E M; Engberg, J

    1985-01-01

    an intron in the 26s rRNA coding region. The evolutionary relationship among the species of the T. pyriformis complex was examined on the basis of the rDNA maps with emphasis on similarities between two of the new species and the widely studied T. thermophila and T. pigmentosa. Examination of a large number...

  13. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

    DEFF Research Database (Denmark)

    Mckinney, G. J.; Seeb, L. W.; Larson, W. A.

    2016-01-01

    Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged...

  14. Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan.

    Directory of Open Access Journals (Sweden)

    Maleeha Maria

    Full Text Available Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD.We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA, retinitis pigmentosa (RP, congenital stationary night blindness (CSNB, or cone dystrophy (CD. We employed genome-wide single nucleotide polymorphism (SNP array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families.Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1.Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.

  15. Mapping resistance to powdery mildew in barley reveals a large-effect nonhost resistance QTL.

    Science.gov (United States)

    Romero, Cynara C T; Vermeulen, Jasper P; Vels, Anton; Himmelbach, Axel; Mascher, Martin; Niks, Rients E

    2018-05-01

    Resistance factors against non-adapted powdery mildews were mapped in barley. Some QTLs seem effective only to non-adapted mildews, while others also play a role in defense against the adapted form. The durability and effectiveness of nonhost resistance suggests promising practical applications for crop breeding, relying upon elucidation of key aspects of this type of resistance. We investigated which genetic factors determine the nonhost status of barley (Hordeum vulgare L.) to powdery mildews (Blumeria graminis). We set out to verify whether genes involved in nonhost resistance have a wide effectiveness spectrum, and whether nonhost resistance genes confer resistance to the barley adapted powdery mildew. Two barley lines, SusBgt SC and SusBgt DC , with some susceptibility to the wheat powdery mildew B. graminis f.sp. tritici (Bgt) were crossed with cv Vada to generate two mapping populations. Each population was assessed for level of infection against four B. graminis ff.spp, and QTL mapping analyses were performed. Our results demonstrate polygenic inheritance for nonhost resistance, with some QTLs effective only to non-adapted mildews, while others play a role against adapted and non-adapted forms. Histology analyses of nonhost interaction show that most penetration attempts are stopped in association with papillae, and also suggest independent layers of defence at haustorium establishment and conidiophore formation. Nonhost resistance of barley to powdery mildew relies mostly on non-hypersensitive mechanisms. A large-effect nonhost resistance QTL mapped to a 1.4 cM interval is suitable for map-based cloning.

  16. On Strong Convergence by the Hybrid Method for Equilibrium and Fixed Point Problems for an Inifnite Family of Asymptotically Nonexpansive Mappings

    Directory of Open Access Journals (Sweden)

    Cai Gang

    2009-01-01

    Full Text Available We introduce two modifications of the Mann iteration, by using the hybrid methods, for equilibrium and fixed point problems for an infinite family of asymptotically nonexpansive mappings in a Hilbert space. Then, we prove that such two sequences converge strongly to a common element of the set of solutions of an equilibrium problem and the set of common fixed points of an infinite family of asymptotically nonexpansive mappings. Our results improve and extend the results announced by many others.

  17. Mapping organelle motion reveals a vesicular conveyor belt spatially replenishing secretory vesicles in stimulated chromaffin cells.

    Science.gov (United States)

    Maucort, Guillaume; Kasula, Ravikiran; Papadopulos, Andreas; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Meunier, Frederic A

    2014-01-01

    How neurosecretory cells spatially adjust their secretory vesicle pools to replenish those that have fused and released their hormonal content is currently unknown. Here we designed a novel set of image analyses to map the probability of tracked organelles undergoing a specific type of movement (free, caged or directed). We then applied our analysis to time-lapse z-stack confocal imaging of secretory vesicles from bovine Chromaffin cells to map the global changes in vesicle motion and directionality occurring upon secretagogue stimulation. We report a defined region abutting the cortical actin network that actively transports secretory vesicles and is dissipated by actin and microtubule depolymerizing drugs. The directionality of this "conveyor belt" towards the cell surface is activated by stimulation. Actin and microtubule networks therefore cooperatively probe the microenvironment to transport secretory vesicles to the periphery, providing a mechanism whereby cells globally adjust their vesicle pools in response to secretagogue stimulation.

  18. Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

    Science.gov (United States)

    Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

    2015-10-19

    DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

  19. A Novel 1D Hybrid Chaotic Map-Based Image Compression and Encryption Using Compressed Sensing and Fibonacci-Lucas Transform

    Directory of Open Access Journals (Sweden)

    Tongfeng Zhang

    2016-01-01

    Full Text Available A one-dimensional (1D hybrid chaotic system is constructed by three different 1D chaotic maps in parallel-then-cascade fashion. The proposed chaotic map has larger key space and exhibits better uniform distribution property in some parametric range compared with existing 1D chaotic map. Meanwhile, with the combination of compressive sensing (CS and Fibonacci-Lucas transform (FLT, a novel image compression and encryption scheme is proposed with the advantages of the 1D hybrid chaotic map. The whole encryption procedure includes compression by compressed sensing (CS, scrambling with FLT, and diffusion after linear scaling. Bernoulli measurement matrix in CS is generated by the proposed 1D hybrid chaotic map due to its excellent uniform distribution. To enhance the security and complexity, transform kernel of FLT varies in each permutation round according to the generated chaotic sequences. Further, the key streams used in the diffusion process depend on the chaotic map as well as plain image, which could resist chosen plaintext attack (CPA. Experimental results and security analyses demonstrate the validity of our scheme in terms of high security and robustness against noise attack and cropping attack.

  20. Saliency U-Net: A regional saliency map-driven hybrid deep learning network for anomaly segmentation

    Science.gov (United States)

    Karargyros, Alex; Syeda-Mahmood, Tanveer

    2018-02-01

    Deep learning networks are gaining popularity in many medical image analysis tasks due to their generalized ability to automatically extract relevant features from raw images. However, this can make the learning problem unnecessarily harder requiring network architectures of high complexity. In case of anomaly detection, in particular, there is often sufficient regional difference between the anomaly and the surrounding parenchyma that could be easily highlighted through bottom-up saliency operators. In this paper we propose a new hybrid deep learning network using a combination of raw image and such regional maps to more accurately learn the anomalies using simpler network architectures. Specifically, we modify a deep learning network called U-Net using both the raw and pre-segmented images as input to produce joint encoding (contraction) and expansion paths (decoding) in the U-Net. We present results of successfully delineating subdural and epidural hematomas in brain CT imaging and liver hemangioma in abdominal CT images using such network.

  1. Patterns of Limnohabitans Microdiversity across a Large Set of Freshwater Habitats as Revealed by Reverse Line Blot Hybridization

    Science.gov (United States)

    Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, Martin W.

    2013-01-01

    Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria

  2. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by Reverse Line Blot Hybridization.

    Directory of Open Access Journals (Sweden)

    Jan Jezbera

    Full Text Available Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S-23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of

  3. Distribution of 45S rDNA in Modern Rose Cultivars (Rosa hybrida), Rosa rugosa, and Their Interspecific Hybrids Revealed by Fluorescence in situ Hybridization.

    Science.gov (United States)

    Ding, Xiao-Liu; Xu, Ting-Liang; Wang, Jing; Luo, Le; Yu, Chao; Dong, Gui-Min; Pan, Hui-Tang; Zhang, Qi-Xiang

    2016-01-01

    To elucidate the evolutionary dynamics of the location and number of rDNA loci in the process of polyploidization in the genus Rosa, we examined 45S rDNA sites in the chromosomes of 6 modern rose cultivars (R. hybrida), 5 R. rugosa cultivars, and 20 hybrid progenies by fluorescence in situ hybridization. Variation in the number of rDNA sites in parents and their interspecific hybrids was detected. As expected, 4 rDNA sites were observed in the genomes of 4 modern rose cultivars, while 3 hybridization sites were observed in the 2 others. Two expected rDNA sites were found in 2 R. rugosa cultivars, while in the other 3 R. rugosa cultivars 4 sites were present. Among the 20 R. hybrida × R. rugosa offspring, 13 carried the expected number of rDNA sites, and 1 had 6 hybridization sites, which exceeded the expected number by far. The other 6 offspring had either 2 or 3 hybridization sites, which was less than expected. Differences in the number of rDNA loci were observed in interspecific offspring, indicating that rDNA loci exhibit instability after distant hybridization events. Abnormal chromosome pairing may be the main factor explaining the variation in rDNA sites during polyploidization. © 2016 S. Karger AG, Basel.

  4. Complete physical mapping of IL6 reveals a new marker associated with chronic periodontitis.

    Science.gov (United States)

    Farhat, S B; de Souza, C M; Braosi, A P R; Kim, S H; Tramontina, V A; Papalexiou, V; Olandoski, M; Mira, M T; Luczyszyn, S M; Trevilatto, P C

    2017-04-01

    Interleukin-6 (IL-6) is a powerful stimulator of osteoclast differentiation and bone resorption. Production of IL-6 is modulated by polymorphisms, and higher levels of this cytokine are found locally in patients with chronic periodontitis. In this study we performed a modern approach - Complete physical mapping of the IL6 gene - to identify the polymorphisms associated with chronic periodontitis in a southern Brazilian population sample. One-hundred and nine individuals of both genders (mean age: 41.5 ± 8.5 years) were divided into a study group (56 participants with periodontitis) and a control group (53 individuals without periodontitis). After collection and purification of DNA, nine tag single nucleotide polymorphisms (SNPs; rs1524107, rs2069835, rs2069837, rs2069838, rs2069840, rs2069842, rs2069843, rs2069845 and rs2069849) covering the entire gene were selected according to the information available on the International HapMap Project website and evaluated using real-time PCR. Differences in the distribution of the following parameters were statistically significant between study and control groups: number of teeth (p = 0.030); probing depth (p chronic periodontitis in a Brazilian population in the presence of clinical variables, such as visible plaque, dentist visit frequency and dental floss use, and was suggested for the first time as a marker of susceptibility to chronic periodontitis. Complete physical mapping of IL6 (using tag SNPs) was carried out for the first time, unveiling allele G of polymorphism rs2069837 (located in the second intron of IL6) as a suggestive marker of protection against chronic periodontitis in a Brazilian population. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  5. SPATIAL VARIATIONS OF PAH PROPERTIES IN M17SW REVEALED BY SPITZER /IRS SPECTRAL MAPPING

    Energy Technology Data Exchange (ETDEWEB)

    Yamagishi, M. [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Chuo-ku, Sagamihara 252-5210 (Japan); Kaneda, H.; Ishihara, D.; Oyabu, S.; Suzuki, T.; Nishimura, A.; Kohno, M. [Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan); Onaka, T.; Ohashi, S. [Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Nagayama, T.; Matsuo, M. [Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima 890-0065 (Japan); Umemoto, T.; Minamidani, T.; Fujita, S. [Nobeyama Radio Observatory, National Astronomical Observatory of Japan (NAOJ), National Institutes of Natural Sciences (NINS), 462-2, Nobeyama, Minamimaki, Minamisaku, Nagano 384-1305 (Japan); Tsuda, Y., E-mail: yamagish@ir.isas.jaxa.jp [Graduate School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino, Tokyo 191-0042 (Japan)

    2016-12-20

    We present Spitzer /IRS mid-infrared spectral maps of the Galactic star-forming region M17 as well as IRSF/SIRIUS Br γ and Nobeyama 45 m/FOREST {sup 13}CO ( J = 1–0) maps. The spectra show prominent features due to polycyclic aromatic hydrocarbons (PAHs) at wavelengths of 6.2, 7.7, 8.6, 11.3, 12.0, 12.7, 13.5, and 14.2  μ m. We find that the PAH emission features are bright in the region between the H ii region traced by Br γ and the molecular cloud traced by {sup 13}CO, supporting that the PAH emission originates mostly from photo-dissociation regions. Based on the spatially resolved Spitzer /IRS maps, we examine spatial variations of the PAH properties in detail. As a result, we find that the interband ratio of PAH 7.7  μ m/PAH 11.3  μ m varies locally near M17SW, but rather independently of the distance from the OB stars in M17, suggesting that the degree of PAH ionization is mainly controlled by local conditions rather than the global UV environments determined by the OB stars in M17. We also find that the interband ratios of the PAH 12.0  μ m, 12.7  μ m, 13.5  μ m, and 14.2  μ m features to the PAH 11.3  μ m feature are high near the M17 center, which suggests structural changes of PAHs through processing due to intense UV radiation, producing abundant edgy irregular PAHs near the M17 center.

  6. Unfolding Leonardo DA Vinci's Globe (ad 1504) to Reveal its Historical World Map

    Science.gov (United States)

    Verhoeven, G. J.; Missinne, S. J.

    2017-08-01

    This paper reports in detail on the image-based modelling and unwrapping approach used to create a two-dimensional projected map of an astonishing ostrich egg globe from AD 1504. This miniature egg globe is not only the oldest extant engraved globe, but it is also the oldest post-Columbian globe of the world and the first ever to depict Newfoundland and many other territories. The intention of digitally recording the surface geometry and colour of this unique artefact was to portray the original layout of the world map used by the Florentine Renaissance artist to make this globe. In addition, it was expected to substantiate iconographical details, which are hard to study at its scale of 1:80,000,000. The ostrich egg globe is the prototype of the Lenox Globe kept at the New York Public Library. The latter is very beneficial to examine how the egg globe looked like before being glued together at its equator. On the other hand, unfolding the map engraved in the ostrich egg halves enables a more detailed study of the remarkable details visible on both globes, since the engravings on the quasi-white egg surface are much easier to discern than those of the highly reflective red copper Lenox Globe. Finally, a detailed study of the unwrapped 3D surface is essential to learn more about the world vision of its creator and the incredible efforts that went into making this globe. Thanks to some particular pictographic details as well as the way in which the engravings are applied (by a left-handed person), the globe artist can be identified as Leonardo da Vinci.

  7. UNFOLDING LEONARDO DA VINCI’S GLOBE (AD 1504 TO REVEAL ITS HISTORICAL WORLD MAP

    Directory of Open Access Journals (Sweden)

    G. J. Verhoeven

    2017-08-01

    Full Text Available This paper reports in detail on the image-based modelling and unwrapping approach used to create a two-dimensional projected map of an astonishing ostrich egg globe from AD 1504. This miniature egg globe is not only the oldest extant engraved globe, but it is also the oldest post-Columbian globe of the world and the first ever to depict Newfoundland and many other territories. The intention of digitally recording the surface geometry and colour of this unique artefact was to portray the original layout of the world map used by the Florentine Renaissance artist to make this globe. In addition, it was expected to substantiate iconographical details, which are hard to study at its scale of 1:80,000,000. The ostrich egg globe is the prototype of the Lenox Globe kept at the New York Public Library. The latter is very beneficial to examine how the egg globe looked like before being glued together at its equator. On the other hand, unfolding the map engraved in the ostrich egg halves enables a more detailed study of the remarkable details visible on both globes, since the engravings on the quasi-white egg surface are much easier to discern than those of the highly reflective red copper Lenox Globe. Finally, a detailed study of the unwrapped 3D surface is essential to learn more about the world vision of its creator and the incredible efforts that went into making this globe. Thanks to some particular pictographic details as well as the way in which the engravings are applied (by a left-handed person, the globe artist can be identified as Leonardo da Vinci.

  8. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng

    2012-08-10

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Direct structural mapping of organic field-effect transistors reveals bottlenecks to carrier transport

    KAUST Repository

    Li, Ruipeng; Ward, Jeremy W.; Smilgies, Detlef Matthias; Payne, Marcia M.; Anthony, John Edward; Jurchescu, Oana D.; Amassian, Aram

    2012-01-01

    X-ray microbeam scattering is used to map the microstructure of the organic semiconductor along the channel length of solution-processed bottom-contact OFET devices. Contact-induced nucleation is known to influence the crystallization behavior within the channel. We find that microstructural inhomogeneities in the center of the channel act as a bottleneck to charge transport. This problem can be overcome by controlling crystallization of the preferable texture, thus favoring more efficient charge transport throughout the channel. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

    DEFF Research Database (Denmark)

    Kieffer-Kwon, Kyong-Rim; Tang, Zhonghui; Mathe, Ewy

    2013-01-01

    IA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which...... associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during...

  11. Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

    Directory of Open Access Journals (Sweden)

    McGuire Patrick E

    2010-12-01

    Full Text Available Abstract Background A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. Results Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. Conclusions In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large

  12. Assignment of the gene for human tetranectin (TNA) to chromosome 3p22-->p21.3 by somatic cell hybrid mapping

    DEFF Research Database (Denmark)

    Durkin, M E; Naylor, S L; Albrechtsen, R

    1997-01-01

    Tetranectin is a plasminogen-binding protein that is induced during the mineralization phase of osteogenesis. By screening a human chromosome 3 somatic cell hybrid mapping panel, we have localized the human tetranectin gene (TNA) to 3p22-->p21.3, which is distinct from the loci of two human...

  13. High-Throughput Phenotyping and QTL Mapping Reveals the Genetic Architecture of Maize Plant Growth1[OPEN

    Science.gov (United States)

    Huang, Chenglong; Wu, Di; Qiao, Feng; Li, Wenqiang; Duan, Lingfeng; Wang, Ke; Xiao, Yingjie; Chen, Guoxing; Liu, Qian; Yang, Wanneng

    2017-01-01

    With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction. PMID:28153923

  14. Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch

    Directory of Open Access Journals (Sweden)

    Cristian Araneda

    2012-01-01

    Full Text Available Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss, various quantitative trait loci (QTL that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch. The four loci were identified in females from two populations (early and late spawners produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC that were strongly associated with spawning time in coho salmon (p < 0.0002 were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10 with a suggestive association (p = 0.00035 mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map.

  15. An updated stress map of the continental United States reveals heterogeneous intraplate stress

    Science.gov (United States)

    Levandowski, Will; Herrmann, Robert B.; Briggs, Rich; Boyd, Oliver; Gold, Ryan

    2018-06-01

    Knowledge of the state of stress in Earth's crust is key to understanding the forces and processes responsible for earthquakes. Historically, low rates of natural seismicity in the central and eastern United States have complicated efforts to understand intraplate stress, but recent improvements in seismic networks and the spread of human-induced seismicity have greatly improved data coverage. Here, we compile a nationwide stress map based on formal inversions of focal mechanisms that challenges the idea that deformation in continental interiors is driven primarily by broad, uniform stress fields derived from distant plate boundaries. Despite plate-boundary compression, extension dominates roughly half of the continent, and second-order forces related to lithospheric structure appear to control extension directions. We also show that the states of stress in several active eastern United States seismic zones differ significantly from those of surrounding areas and that these anomalies cannot be explained by transient processes, suggesting that earthquakes are focused by persistent, locally derived sources of stress. Such spatially variable intraplate stress appears to justify the current, spatially variable estimates of seismic hazard. Future work to quantify sources of stress, stressing-rate magnitudes and their relationship with strain and earthquake rates could allow prospective mapping of intraplate hazard.

  16. Application of dissociation curve analysis to radiation hybrid panel marker scoring: generation of a map of river buffalo (B. bubalis chromosome 20

    Directory of Open Access Journals (Sweden)

    Schäffer Alejandro A

    2008-11-01

    Full Text Available Abstract Background Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequencing, mapping tools such as radiation hybrid DNA panels remain useful aids for sequence assembly, focused resequencing efforts, and for building physical maps of species that have not yet been sequenced. For placement of specific, individual genes or markers on a map, low-throughput methods remain commonplace. Typically, PCR amplification of DNA from each panel cell line is followed by gel electrophoresis and scoring of each clone for the presence or absence of PCR product. To improve sensitivity and efficiency of radiation hybrid panel analysis in comparison to gel-based methods, we adapted fluorescence-based real-time PCR and dissociation curve analysis for use as a novel scoring method. Results As proof of principle for this dissociation curve method, we generated new maps of river buffalo (Bubalus bubalis chromosome 20 by both dissociation curve analysis and conventional marker scoring. We also obtained sequence data to augment dissociation curve results. Few genes have been previously mapped to buffalo chromosome 20, and sequence detail is limited, so 65 markers were screened from the orthologous chromosome of domestic cattle. Thirty bovine markers (46% were suitable as cross-species markers for dissociation curve analysis in the buffalo radiation hybrid panel under a standard protocol, compared to 25 markers suitable for conventional typing. Computational analysis placed 27 markers on a chromosome map generated by the new method, while the gel-based approach produced only 20 mapped markers. Among 19 markers common to both maps, the marker order on the map was maintained perfectly. Conclusion Dissociation curve

  17. Neurog1 Genetic Inducible Fate Mapping (GIFM) Reveals the Existence of Complex Spatiotemporal Cyto-Architectures in the Developing Cerebellum.

    Science.gov (United States)

    Obana, Edwin A; Lundell, Travis G; Yi, Kevin J; Radomski, Kryslaine L; Zhou, Qiong; Doughty, Martin L

    2015-06-01

    Neurog1 is a pro-neural basic helix-loop-helix (bHLH) transcription factor expressed in progenitor cells located in the ventricular zone and subsequently the presumptive white matter tracts of the developing mouse cerebellum. We used genetic inducible fate mapping (GIFM) with a transgenic Neurog1-CreER allele to characterize the contributions of Neurog1 lineages to cerebellar circuit formation in mice. GIFM reveals Neurog1-expressing progenitors are fate-mapped to become Purkinje cells and all GABAergic interneuron cell types of the cerebellar cortex but not glia. The spatiotemporal sequence of GIFM is unique to each neuronal cell type. GIFM on embryonic days (E) 10.5 to E12.5 labels Purkinje cells with different medial-lateral settling patterns depending on the day of tamoxifen delivery. GIFM on E11.5 to P7 labels interneurons and the timing of tamoxifen administration correlates with the final inside-to-outside resting position of GABAergic interneurons in the cerebellar cortex. Proliferative status and long-term BrdU retention of GIFM lineages reveals Purkinje cells express Neurog1 around the time they become post-mitotic. In contrast, GIFM labels mitotic and post-mitotic interneurons. Neurog1-CreER GIFM reveals a correlation between the timing of Neurog1 expression and the spatial organization of GABAergic neurons in the cerebellar cortex with possible implications for cerebellar circuit assembly.

  18. Map-Based Power-Split Strategy Design with Predictive Performance Optimization for Parallel Hybrid Electric Vehicles

    Directory of Open Access Journals (Sweden)

    Jixiang Fan

    2015-09-01

    Full Text Available In this paper, a map-based optimal energy management strategy is proposed to improve the consumption economy of a plug-in parallel hybrid electric vehicle. In the design of the maps, which provide both the torque split between engine and motor and the gear shift, not only the current vehicle speed and power demand, but also the optimality based on the predicted trajectory of vehicle dynamics are considered. To seek the optimality, the equivalent consumption, which trades off the fuel and electricity usages, is chosen as the cost function. Moreover, in order to decrease the model errors in the process of optimization conducted in the discrete time domain, the variational integrator is employed to calculate the evolution of the vehicle dynamics. To evaluate the proposed energy management strategy, the simulation results performed on a professional GT-Suit simulator are demonstrated and the comparison to a real-time optimization method is also given to show the advantage of the proposed off-line optimization approach.

  19. Intraoperative mapping during repeat awake craniotomy reveals the functional plasticity of adult cortex.

    Science.gov (United States)

    Southwell, Derek G; Hervey-Jumper, Shawn L; Perry, David W; Berger, Mitchel S

    2016-05-01

    OBJECT To avoid iatrogenic injury during the removal of intrinsic cerebral neoplasms such as gliomas, direct electrical stimulation (DES) is used to identify cortical and subcortical white matter pathways critical for language, motor, and sensory function. When a patient undergoes more than 1 brain tumor resection as in the case of tumor recurrence, the use of DES provides an unusual opportunity to examine brain plasticity in the setting of neurological disease. METHODS The authors examined 561 consecutive cases in which patients underwent DES mapping during surgery forglioma resection. "Positive" and "negative" sites-discrete cortical regions where electrical stimulation did (positive) or did not (negative) produce transient sensory, motor, or language disturbance-were identified prior to tumor resection and documented by intraoperative photography for categorization into functional maps. In this group of 561 patients, 18 were identified who underwent repeat surgery in which 1 or more stimulation sites overlapped with those tested during the initial surgery. The authors compared intraoperative sensory, motor, or language mapping results between initial and repeat surgeries, and evaluated the clinical outcomes for these patients. RESULTS A total of 117 sites were tested for sensory (7 sites, 6.0%), motor (9 sites, 7.7%), or language (101 sites, 86.3%) function during both initial and repeat surgeries. The mean interval between surgical procedures was 4.1 years. During initial surgeries, 95 (81.2%) of 117 sites were found to be negative and 22 (18.8%) of 117 sites were found to be positive. During repeat surgeries, 103 (88.0%) of 117 sites were negative and 14 (12.0%) of 117 were positive. Of the 95 sites that were negative at the initial surgery, 94 (98.9%) were also negative at the repeat surgery, while 1 (1.1%) site was found to be positive. Of the 22 sites that were initially positive, 13 (59.1%) remained positive at repeat surgery, while 9 (40.9%) had become

  20. Mapping differentiation under mixed culture conditions reveals a tunable continuum of T cell fates.

    Directory of Open Access Journals (Sweden)

    Yaron E Antebi

    2013-07-01

    Full Text Available Cell differentiation is typically directed by external signals that drive opposing regulatory pathways. Studying differentiation under polarizing conditions, with only one input signal provided, is limited in its ability to resolve the logic of interactions between opposing pathways. Dissection of this logic can be facilitated by mapping the system's response to mixtures of input signals, which are expected to occur in vivo, where cells are simultaneously exposed to various signals with potentially opposing effects. Here, we systematically map the response of naïve T cells to mixtures of signals driving differentiation into the Th1 and Th2 lineages. We characterize cell state at the single cell level by measuring levels of the two lineage-specific transcription factors (T-bet and GATA3 and two lineage characteristic cytokines (IFN-γ and IL-4 that are driven by these transcription regulators. We find a continuum of mixed phenotypes in which individual cells co-express the two lineage-specific master regulators at levels that gradually depend on levels of the two input signals. Using mathematical modeling we show that such tunable mixed phenotype arises if autoregulatory positive feedback loops in the gene network regulating this process are gradual and dominant over cross-pathway inhibition. We also find that expression of the lineage-specific cytokines follows two independent stochastic processes that are biased by expression levels of the master regulators. Thus, cytokine expression is highly heterogeneous under mixed conditions, with subpopulations of cells expressing only IFN-γ, only IL-4, both cytokines, or neither. The fraction of cells in each of these subpopulations changes gradually with input conditions, reproducing the continuous internal state at the cell population level. These results suggest a differentiation scheme in which cells reflect uncertainty through a continuously tuneable mixed phenotype combined with a biased

  1. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Cordero

    2015-11-01

    Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

  2. High-resolution mapping reveals links of HP1 with active and inactive chromatin components.

    Directory of Open Access Journals (Sweden)

    Elzo de Wit

    2007-03-01

    Full Text Available Heterochromatin protein 1 (HP1 is commonly seen as a key factor of repressive heterochromatin, even though a few genes are known to require HP1-chromatin for their expression. To obtain insight into the targeting of HP1 and its interplay with other chromatin components, we have mapped HP1-binding sites on Chromosomes 2 and 4 in Drosophila Kc cells using high-density oligonucleotide arrays and the DNA adenine methyltransferase identification (DamID technique. The resulting high-resolution maps show that HP1 forms large domains in pericentric regions, but is targeted to single genes on chromosome arms. Intriguingly, HP1 shows a striking preference for exon-dense genes on chromosome arms. Furthermore, HP1 binds along entire transcription units, except for 5' regions. Comparison with expression data shows that most of these genes are actively transcribed. HP1 target genes are also marked by the histone variant H3.3 and dimethylated histone 3 lysine 4 (H3K4me2, which are both typical of active chromatin. Interestingly, H3.3 deposition, which is usually observed along entire transcription units, is limited to the 5' ends of HP1-bound genes. Thus, H3.3 and HP1 are mutually exclusive marks on active chromatin. Additionally, we observed that HP1-chromatin and Polycomb-chromatin are nonoverlapping, but often closely juxtaposed, suggesting an interplay between both types of chromatin. These results demonstrate that HP1-chromatin is transcriptionally active and has extensive links with several other chromatin components.

  3. A high-resolution whole genome radiation hybrid map of human chromosome 17q22-q25.3 across the genes for GH and TK

    Energy Technology Data Exchange (ETDEWEB)

    Foster, J.W.; Schafer, A.J.; Critcher, R. [Univ. of Cambridge (United Kingdom)] [and others

    1996-04-15

    We have constructed a whole genome radiation hybrid (WG-RH) map across a region of human chromosome 17q, from growth hormone (GH) to thymidine kinase (TK). A panel of 128 WG-RH hybrid cell lines generated by X-irradiation and fusion has been tested for the retention of 39 sequence-tagged site (STS) markers by the polymerase chain reaction. This genome mapping technique has allowed the integration of existing VNTR and microsatellite markers with additional new markers and existing STS markers previously mapped to this region by other means. The WG-RH map includes eight expressed sequence tag (EST) and three anonymous markers developed for this study, together with 23 anonymous microsatellites and five existing ESTs. Analysis of these data resulted in a high-density comprehensive map across this region of the genome. A subset of these markers has been used to produce a framework map consisting of 20 loci ordered with odds greater than 1000:1. The markers are of sufficient density to build a YAC contig across this region based on marker content. We have developed sequence tags for both ends of a 2.1-Mb YAC and mapped these using the WG-RH panel, allowing a direct comparison of cRay{sub 6000} to physical distance. 31 refs., 3 figs., 2 tabs.

  4. A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.

    Science.gov (United States)

    Quilodrán, Claudio S; Currat, Mathias; Montoya-Burgos, Juan I

    2014-01-01

    Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as "distant hybridization," the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.

  5. A General Model of Distant Hybridization Reveals the Conditions for Extinction in Atlantic Salmon and Brown Trout

    Science.gov (United States)

    Quilodrán, Claudio S.; Currat, Mathias; Montoya-Burgos, Juan I.

    2014-01-01

    Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as “distant hybridization,” the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action. PMID:25003336

  6. A general model of distant hybridization reveals the conditions for extinction in Atlantic salmon and brown trout.

    Directory of Open Access Journals (Sweden)

    Claudio S Quilodrán

    Full Text Available Interspecific hybridization is common in nature but can be increased in frequency or even originated by human actions, such as species introduction or habitat modification, which may threaten species persistence. When hybridization occurs between distantly related species, referred to as "distant hybridization," the resulting hybrids are generally infertile or fertile but do not undergo chromosomal recombination during gametogenesis. Here, we present a model describing this frequent but poorly studied interspecific hybridization to assess its consequences on parental species and to anticipate the conditions under which they can reach extinction. Our general model fully incorporates three important processes: density-dependent competition, dominance/recessivity inheritance of traits and assortative mating. We demonstrate its use and flexibility by assessing population extinction risk between Atlantic salmon and brown trout in Norway, whose interbreeding has recently increased due to farmed fish releases into the wild. We identified the set of conditions under which hybridization may threaten salmonid species. Thanks to the flexibility of our model, we evaluated the effect of an additional risk factor, a parasitic disease, and showed that the cumulative effects dramatically increase the extinction risk. The consequences of distant hybridization are not genetically, but demographically mediated. Our general model is useful to better comprehend the evolution of such hybrid systems and we demonstrated its importance in the field of conservation biology to set up management recommendations when this increasingly frequent type of hybridization is in action.

  7. Comprehensive Analysis of ETS Family Members in Melanoma by Fluorescence In Situ Hybridization Reveals Recurrent ETV1 Amplification

    Science.gov (United States)

    Mehra, Rohit; Dhanasekaran, Saravana M; Palanisamy, Nallasivam; Vats, Pankaj; Cao, Xuhong; Kim, Jung H; Kim, David SL; Johnson, Timothy; Fullen, Douglas R; Chinnaiyan, Arul M

    2013-01-01

    E26 transformation-specific (ETS) transcription factors are known to be involved in gene aberrations in various malignancies including prostate cancer; however, their role in melanoma oncogenesis has yet to be fully explored. We have completed a comprehensive fluorescence in situ hybridization (FISH)-based screen for all 27 members of the ETS transcription factor family on two melanoma tissue microarrays, representing 223 melanomas, 10 nevi, and 5 normal skin tissues. None of the melanoma cases demonstrated ETS fusions; however, 6 of 114 (5.3%) melanomas were amplified for ETV1 using a break-apart FISH probe. For the six positive cases, locus-controlled FISH probes revealed that two of six cases were amplified for the ETV1 region, whereas four cases showed copy gains of the entire chromosome 7. The remaining 26 ETS family members showed no chromosomal aberrations by FISH. Quantitative polymerase chain reaction showed an average 3.4-fold (P value = .00218) increased expression of ETV1 in melanomas, including the FISH ETV1-amplified cases, when compared to other malignancies (prostate, breast, and bladder carcinomas). These data suggest that a subset of melanomas overexpresses ETV1 and amplification of ETV1 may be one mechanism for achieving high gene expression. PMID:23908683

  8. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    Science.gov (United States)

    Aksoy, B.; Rehman, A.; Bayraktar, H.; Alaca, B. E.

    2017-04-01

    overcome this challenge and provides a displacement measurement resolution of 116 nm and a strain resolution of 0.04% over a gage length of 300 µm. Similarly, the ability to capture inhomogeneities is demonstrated by mapping strain around a thru-hole. The robustness of the technique is also evaluated, where no appreciable change in strain measurement is observed despite the significant variations imposed on the measurement mesh. The proposed approach introduces critical improvements for the determination of displacement and strain gradients in elastomers regarding the real-time nature of strain mapping with a microscale spatial resolution.

  9. High-resolution spatiotemporal strain mapping reveals non-uniform deformation in micropatterned elastomers

    International Nuclear Information System (INIS)

    Aksoy, B; Alaca, B E; Rehman, A; Bayraktar, H

    2017-01-01

    overcome this challenge and provides a displacement measurement resolution of 116 nm and a strain resolution of 0.04% over a gage length of 300 µ m. Similarly, the ability to capture inhomogeneities is demonstrated by mapping strain around a thru-hole. The robustness of the technique is also evaluated, where no appreciable change in strain measurement is observed despite the significant variations imposed on the measurement mesh. The proposed approach introduces critical improvements for the determination of displacement and strain gradients in elastomers regarding the real-time nature of strain mapping with a microscale spatial resolution. (paper)

  10. Epitope mapping of the major allergen from Atlantic cod in Spanish population reveals different IgE-binding patterns.

    Science.gov (United States)

    Perez-Gordo, Marina; Pastor-Vargas, Carlos; Lin, Jing; Bardina, Ludmilla; Cases, Barbara; Ibáñez, Maria Dolores; Vivanco, Fernando; Cuesta-Herranz, Javier; Sampson, Hugh A

    2013-07-01

    IgE-epitope mapping of allergens reveal important information about antigen components involved in allergic reactions. The peptide-based microarray immunoassay has been used to map epitopes of some food allergens. We developed a peptide microarray immunoassay to map allergenic epitopes in parvalbumin from Atlantic cod (Gad m 1), the most consumed cod species in Spain. Sera from 13 fish-allergic patients with specific IgE to cod parvalbumin were used. A library of overlapping peptides was synthesized, representing the primary sequence of Gad m 1. Peptides were used to analyze allergen-specific IgE antibodies in patient sera. 100% of the patients recognized one antigenic region of 15 amino acids in length in Gad m 1. This region only partially correlated with one of the three antigenic determinants of Gad c 1 (Allergen M), parvalbumin from Baltic cod (Gadus callarias). In the 3D model of the protein, this region was located on the surface of the protein. We have identified a relevant antigenic region in Gad m 1. This epitope could be considered as a severity marker and provides additional information to improve fish allergy diagnosis and the design of safe immunotherapeutic tools. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. A Hybrid Color Mapping Approach to Fusing MODIS and Landsat Images for Forward Prediction

    OpenAIRE

    Chiman Kwan; Bence Budavari; Feng Gao; Xiaolin Zhu

    2018-01-01

    We present a new, simple, and efficient approach to fusing MODIS and Landsat images. It is well known that MODIS images have high temporal resolution and low spatial resolution, whereas Landsat images are just the opposite. Similar to earlier approaches, our goal is to fuse MODIS and Landsat images to yield high spatial and high temporal resolution images. Our approach consists of two steps. First, a mapping is established between two MODIS images, where one is at an earlier time, t1, and the...

  12. Quantitative Susceptibility Mapping Reveals an Association between Brain Iron Load and Depression Severity

    Directory of Open Access Journals (Sweden)

    Shun Yao

    2017-08-01

    Full Text Available Previous studies have detected abnormal serum ferritin levels in patients with depression; however, the results have been inconsistent. This study used quantitative susceptibility mapping (QSM for the first time to examine brain iron concentration in depressed patients and evaluated whether it is related to severity. We included three groups of age- and gender-matched participants: 30 patients with mild-moderate depression (MD, 14 patients with major depression disorder (MDD and 20 control subjects. All participants underwent MR scans with a 3D gradient-echo sequence reconstructing for QSM and performed the 17-item Hamilton Depression Rating Scale (HDRS test. In MDD, the susceptibility value in the bilateral putamen was significantly increased compared with MD or control subjects. In addition, a significant difference was also observed in the left thalamus in MDD patients compared with controls. However, the susceptibility values did not differ between MD patients and controls. The susceptibility values positively correlated with the severity of depression as indicated by the HDRS scores. Our results provide evidence that brain iron deposition may be associated with depression and may even be a biomarker for investigating the pathophysiological mechanism of depression.

  13. Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism.

    Science.gov (United States)

    Kim, Yongsoo; Yang, Guangyu Robert; Pradhan, Kith; Venkataraju, Kannan Umadevi; Bota, Mihail; García Del Molino, Luis Carlos; Fitzgerald, Greg; Ram, Keerthi; He, Miao; Levine, Jesse Maurica; Mitra, Partha; Huang, Z Josh; Wang, Xiao-Jing; Osten, Pavel

    2017-10-05

    The stereotyped features of neuronal circuits are those most likely to explain the remarkable capacity of the brain to process information and govern behaviors, yet it has not been possible to comprehensively quantify neuronal distributions across animals or genders due to the size and complexity of the mammalian brain. Here we apply our quantitative brain-wide (qBrain) mapping platform to document the stereotyped distributions of mainly inhibitory cell types. We discover an unexpected cortical organizing principle: sensory-motor areas are dominated by output-modulating parvalbumin-positive interneurons, whereas association, including frontal, areas are dominated by input-modulating somatostatin-positive interneurons. Furthermore, we identify local cell type distributions with more cells in the female brain in 10 out of 11 sexually dimorphic subcortical areas, in contrast to the overall larger brains in males. The qBrain resource can be further mined to link stereotyped aspects of neuronal distributions to known and unknown functions of diverse brain regions. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Genetic diversity of sea-island cotton (Gossypium barbadense) revealed by mapped SSRs.

    Science.gov (United States)

    Wang, X Q; Feng, C H; Lin, Z X; Zhang, X L

    2011-12-08

    In order to evaluate the genetic diversity of sea-island cotton (Gossypium barbadense), 237 commonly mapped SSR markers covering the cotton genome were used to genotype 56 sea-island cotton accessions. A total of 218 polymorphic primer pairs (91.98%) amplified 361 loci, with a mean of 1.66 loci. Polymorphism information content values of the SSR primers ranged from 0.035 to 0.862, with a mean of 0.320. The highest mean polymorphism information content value for the SSR motifs was from a compound motif (0.402), and for the chromosomes it was Chr10 (0.589); the highest ratio of polymorphic primers in Xinjiang accessions was from Chr21 (83.33%). Genetic diversity was high in Xinjiang accessions. AMOVA showed that variation was 8 and 92% among populations and within populations, respectively. The 56 sea-island accessions were divided into three groups in the UPGMA dendrogram: Xinhai5 was in the first group; accessions from Xinjiang, except the five main ones, were in the second group, and the other 34 accessions were in the third group. Accessions from the former Soviet Union and Xinjiang main accessions were closely related. Both PCA and UPGMA confirmed that Xinhai5 was distinct from the other accessions, and accessions from Xinjiang were in an independent group. Given the differences between principal components analysis and UPGMA results, it is necessary to combine molecular markers and pedigree information so that genetic diversity can be objectively analyzed.

  15. Mapping the heavens the radical scientific ideas that reveal the cosmos

    CERN Document Server

    Natarajan, Priyamvada

    2016-01-01

    This book provides a tour of the greatest hits of cosmological discoveries the ideas that reshaped our universe over the past century. The cosmos, once understood as a stagnant place, filled with the ordinary, is now a universe that is expanding at an accelerating pace, propelled by dark energy and structured by dark matter. Priyamvada Natarajan, our guide to these ideas, is someone at the forefront of the research an astrophysicist who literally creates maps of invisible matter in the universe. She not only explains for a wide audience the science behind these essential ideas but also provides an understanding of how radical scientific theories gain acceptance. The formation and growth of black holes, dark matter halos, the accelerating expansion of the universe, the echo of the big bang, the discovery of exoplanets, and the possibility of other universes these are some of the puzzling cosmological topics of the early twenty-first century. Natarajan discusses why the acceptance of new ideas about the univer...

  16. An integrative architecture for general intelligence and executive function revealed by lesion mapping

    Science.gov (United States)

    Colom, Roberto; Solomon, Jeffrey; Krueger, Frank; Forbes, Chad; Grafman, Jordan

    2012-01-01

    Although cognitive neuroscience has made remarkable progress in understanding the involvement of the prefrontal cortex in executive control, the broader functional networks that support high-level cognition and give rise to general intelligence remain to be well characterized. Here, we investigated the neural substrates of the general factor of intelligence (g) and executive function in 182 patients with focal brain damage using voxel-based lesion–symptom mapping. The Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System were used to derive measures of g and executive function, respectively. Impaired performance on these measures was associated with damage to a distributed network of left lateralized brain areas, including regions of frontal and parietal cortex and white matter association tracts, which bind these areas into a coordinated system. The observed findings support an integrative framework for understanding the architecture of general intelligence and executive function, supporting their reliance upon a shared fronto-parietal network for the integration and control of cognitive representations and making specific recommendations for the application of the Wechsler Adult Intelligence Scale and Delis–Kaplan Executive Function System to the study of high-level cognition in health and disease. PMID:22396393

  17. Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

    Science.gov (United States)

    Mao, Peng; Brown, Alexander J; Malc, Ewa P; Mieczkowski, Piotr A; Smerdon, Michael J; Roberts, Steven A; Wyrick, John J

    2017-10-01

    DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers. © 2017 Mao et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Proposed hybrid-classifier ensemble algorithm to map snow cover area

    Science.gov (United States)

    Nijhawan, Rahul; Raman, Balasubramanian; Das, Josodhir

    2018-01-01

    Metaclassification ensemble approach is known to improve the prediction performance of snow-covered area. The methodology adopted in this case is based on neural network along with four state-of-art machine learning algorithms: support vector machine, artificial neural networks, spectral angle mapper, K-mean clustering, and a snow index: normalized difference snow index. An AdaBoost ensemble algorithm related to decision tree for snow-cover mapping is also proposed. According to available literature, these methods have been rarely used for snow-cover mapping. Employing the above techniques, a study was conducted for Raktavarn and Chaturangi Bamak glaciers, Uttarakhand, Himalaya using multispectral Landsat 7 ETM+ (enhanced thematic mapper) image. The study also compares the results with those obtained from statistical combination methods (majority rule and belief functions) and accuracies of individual classifiers. Accuracy assessment is performed by computing the quantity and allocation disagreement, analyzing statistic measures (accuracy, precision, specificity, AUC, and sensitivity) and receiver operating characteristic curves. A total of 225 combinations of parameters for individual classifiers were trained and tested on the dataset and results were compared with the proposed approach. It was observed that the proposed methodology produced the highest classification accuracy (95.21%), close to (94.01%) that was produced by the proposed AdaBoost ensemble algorithm. From the sets of observations, it was concluded that the ensemble of classifiers produced better results compared to individual classifiers.

  19. Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum).

    Science.gov (United States)

    Wen, Tianwang; Wu, Mi; Shen, Chao; Gao, Bin; Zhu, De; Zhang, Xianlong; You, Chunyuan; Lin, Zhongxu

    2018-02-24

    Brown fibre cotton is an environmental-friendly resource that plays a key role in the textile industry. However, the fibre quality and yield of natural brown cotton are poor, and fundamental research on brown cotton is relatively scarce. To understand the genetic basis of brown fibre cotton, we constructed linkage and association populations to systematically examine brown fibre accessions. We fine-mapped the brown fibre region, Lc 1 , and dissected it into 2 loci, qBF-A07-1 and qBF-A07-2. The qBF-A07-1 locus mediates the initiation of brown fibre production, whereas the shade of the brown fibre is affected by the interaction between qBF-A07-1 and qBF-A07-2. Gh_A07G2341 and Gh_A07G0100 were identified as candidate genes for qBF-A07-1 and qBF-A07-2, respectively. Haploid analysis of the signals significantly associated with these two loci showed that most tetraploid modern brown cotton accessions exhibit the introgression signature of Gossypium barbadense. We identified 10 quantitative trait loci (QTLs) for fibre yield and 19 QTLs for fibre quality through a genome-wide association study (GWAS) and found that qBF-A07-2 negatively affects fibre yield and quality through an epistatic interaction with qBF-A07-1. This study sheds light on the genetics of fibre colour and lint-related traits in brown fibre cotton, which will guide the elite cultivars breeding of brown fibre cotton. © 2018 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  20. A Fate Map of the Murine Pancreas Buds Reveals a Multipotent Ventral Foregut Organ Progenitor

    Science.gov (United States)

    Angelo, Jesse R.; Guerrero-Zayas, Mara-Isel; Tremblay, Kimberly D.

    2012-01-01

    The definitive endoderm is the embryonic germ layer that gives rise to the budding endodermal organs including the thyroid, lung, liver and pancreas as well as the remainder of the gut tube. DiI fate mapping and whole embryo culture were used to determine the endodermal origin of the 9.5 days post coitum (dpc) dorsal and ventral pancreas buds. Our results demonstrate that the progenitors of each bud occupy distinct endodermal territories. Dorsal bud progenitors are located in the medial endoderm overlying somites 2–4 between the 2 and 11 somite stage (SS). The endoderm forming the ventral pancreas bud is found in 2 distinct regions. One territory originates from the left and right lateral endoderm caudal to the anterior intestinal portal by the 6 SS and the second domain is derived from the ventral midline of the endoderm lip (VMEL). Unlike the laterally located ventral foregut progenitors, the VMEL population harbors a multipotent progenitor that contributes to the thyroid bud, the rostral cap of the liver bud, ventral midline of the liver bud and the midline of the ventral pancreas bud in a temporally restricted manner. This data suggests that the midline of the 9.5 dpc thyroid, liver and ventral pancreas buds originates from the same progenitor population, demonstrating a developmental link between all three ventral foregut buds. Taken together, these data define the location of the dorsal and ventral pancreas progenitors in the prespecified endodermal sheet and should lead to insights into the inductive events required for pancreas specification. PMID:22815796

  1. Heterotic trait locus (HTL) mapping identifies intra-locus interactions that underlie reproductive hybrid vigor in Sorghum bicolor.

    Science.gov (United States)

    Ben-Israel, Imri; Kilian, Benjamin; Nida, Habte; Fridman, Eyal

    2012-01-01

    Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL) mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested) with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1) in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis.

  2. Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior.

    Science.gov (United States)

    Portugues, Ruben; Feierstein, Claudia E; Engert, Florian; Orger, Michael B

    2014-03-19

    Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate but ordered pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments systematically reveal the functional architecture of neural circuits underlying a sensorimotor behavior in a vertebrate brain. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Revealing the cerebral regions and networks mediating vulnerability to depression: oxidative metabolism mapping of rat brain.

    Science.gov (United States)

    Harro, Jaanus; Kanarik, Margus; Kaart, Tanel; Matrov, Denis; Kõiv, Kadri; Mällo, Tanel; Del Río, Joaquin; Tordera, Rosa M; Ramirez, Maria J

    2014-07-01

    The large variety of available animal models has revealed much on the neurobiology of depression, but each model appears as specific to a significant extent, and distinction between stress response, pathogenesis of depression and underlying vulnerability is difficult to make. Evidence from epidemiological studies suggests that depression occurs in biologically predisposed subjects under impact of adverse life events. We applied the diathesis-stress concept to reveal brain regions and functional networks that mediate vulnerability to depression and response to chronic stress by collapsing data on cerebral long term neuronal activity as measured by cytochrome c oxidase histochemistry in distinct animal models. Rats were rendered vulnerable to depression either by partial serotonergic lesion or by maternal deprivation, or selected for a vulnerable phenotype (low positive affect, low novelty-related activity or high hedonic response). Environmental adversity was brought about by applying chronic variable stress or chronic social defeat. Several brain regions, most significantly median raphe, habenula, retrosplenial cortex and reticular thalamus, were universally implicated in long-term metabolic stress response, vulnerability to depression, or both. Vulnerability was associated with higher oxidative metabolism levels as compared to resilience to chronic stress. Chronic stress, in contrast, had three distinct patterns of effect on oxidative metabolism in vulnerable vs. resilient animals. In general, associations between regional activities in several brain circuits were strongest in vulnerable animals, and chronic stress disrupted this interrelatedness. These findings highlight networks that underlie resilience to stress, and the distinct response to stress that occurs in vulnerable subjects. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

    Science.gov (United States)

    Stukenbrock, Eva H; Dutheil, Julien Y

    2018-03-01

    Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

  5. Strong Convergence for Hybrid Implicit S-Iteration Scheme of Nonexpansive and Strongly Pseudocontractive Mappings

    Directory of Open Access Journals (Sweden)

    Shin Min Kang

    2014-01-01

    Full Text Available Let K be a nonempty closed convex subset of a real Banach space E, let S:K→K be nonexpansive, and let  T:K→K be Lipschitz strongly pseudocontractive mappings such that p∈FS∩FT=x∈K:Sx=Tx=x and x-Sy≤Sx-Sy and x-Ty≤Tx-Ty for all x, y∈K. Let βn be a sequence in 0, 1 satisfying (i ∑n=1∞βn=∞; (ii limn→∞⁡βn=0. For arbitrary x0∈K, let xn be a sequence iteratively defined by xn=Syn, yn=1-βnxn-1+βnTxn, n≥1. Then the sequence xn converges strongly to a common fixed point p of S and T.

  6. Imaging Plasmon Hybridization of Fano Resonances via Hot-Electron-Mediated Absorption Mapping.

    Science.gov (United States)

    Simoncelli, Sabrina; Li, Yi; Cortés, Emiliano; Maier, Stefan A

    2018-05-04

    The inhibition of radiative losses in dark plasmon modes allows storing electromagnetic energy more efficiently than in far-field excitable bright-plasmon modes. As such, processes benefiting from the enhanced absorption of light in plasmonic materials could also take profit of dark plasmon modes to boost and control nanoscale energy collection, storage, and transfer. We experimentally probe this process by imaging with nanoscale precision the hot-electron driven desorption of thiolated molecules from the surface of gold Fano nanostructures, investigating the effect of wavelength and polarization of the incident light. Spatially resolved absorption maps allow us to show the contribution of each element of the nanoantenna in the hot-electron driven process and their interplay in exciting a dark plasmon mode. Plasmon-mode engineering allows control of nanoscale reactivity and offers a route to further enhance and manipulate hot-electron driven chemical reactions and energy-conversion and transfer at the nanoscale.

  7. A first glimpse of wild lupin karyotype variation as revealed by comparative cytogenetic mapping

    Directory of Open Access Journals (Sweden)

    Karolina Susek

    2016-07-01

    Full Text Available Insight into plant genomes at the cytomolecular level provides useful information about their karyotype structure, enabling inferences about taxonomic relationships and evolutionary origins. The Old World lupins demonstrate a high level of genomic diversification involving variation in chromosome numbers (2n=32-52, basic chromosome numbers (x=5-7, 9, 13 and in nuclear genome size (2C DNA=0.97-2.68 pg. Lupins comprise both crop and wild species and provide an intriguing system to study karyotype evolution.In order to investigate lupin chromosome structure, heterologous FISH was used. Sixteen BACs that had been generated as chromosome markers for the reference species, Lupinus angustifolius, were used to identify chromosomes in the wild species and explore karyotype variation. While all ‘single-locus’ in L. angustifolius, in the wild lupins these clones proved to be ‘single-locus’, ‘single-locus’ with additional signals, ‘repetitive’ or had no detectable BAC-FISH signal. The diverse distribution of the clones in the targeted genomes suggests a complex evolution history, which possibly involved multiple chromosomal changes such as fusions/fissions and repetitive sequence amplification. Twelve BACs were sequenced and we found numerous transposable elements including DNA transposons as well as LTR and non-LTR retrotransposons with varying quantity and composition among the different lupin species. However, at this preliminary stage, no correlation was observed between the pattern of BAC-FISH signals and the repeat content in particular BACs. Here, we describe the first BAC-based chromosome-specific markers for the wild species: L. cosentinii, L. cryptanthus, L. pilosus, L. micranthus and one New World lupin, L. multiflorus. These BACs could constitute the basis for an assignment of the chromosomal and genetic maps of other lupins, e.g. L. albus and L. luteus. Moreover, we identified karyotype variation that helps illustrate the

  8. Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.

    Directory of Open Access Journals (Sweden)

    Frank P Diekstra

    Full Text Available Amyotrophic lateral sclerosis (ALS is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls. These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls. Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27 × 10(-51 withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible

  9. Mapping of coma anisotropies to plasma structures of weak comets: a 3-D hybrid simulation study

    Directory of Open Access Journals (Sweden)

    N. Gortsas

    2009-04-01

    Full Text Available The effects of coma anisotropies on the plasma environment of comets have been studied by means of a 3-D hybrid model which treats electrons as a massless, charge-neutralizing fluid, whereas ion dynamics are covered by a kinetic approach. From Earth-based observations as well as from in-situ spacecraft measurements the shape of the coma of many comets is ascertained to be anisotropic. However, most plasma simulation studies deploy a spherically symmetric activity pattern. In this paper anisotropy is studied by considering three different coma shape models. The first model is derived from the Haser model and is characterised by spherically symmetry. This reference model is then compared with two different neutral gas shape models: the dayside restricted model with no nightside activity and a cone shaped model with opening angle of π/2. In all models the integrated surface activity is kept constant. The simulations have been done for the Rosetta target comet 67P/Churyumov-Gerasimenko for two heliocentric distances, 1.30 AU and 3.25 AU. It is found that shock formation processes are modified as a result of increasing spatial confinement. Characteristic plasma structures of comets such as the bow shock, magnetic barrier region and the ion composition boundary exhibit a shift towards the sun. In addition, the cone shaped model leads to a strong increase of the mass-loaded region which in turn leads to a smooth deceleration of the solar wind flow and an increasing degree of mixture between the solar wind and cometary ion species. This creates an additional transport channel of the magnetic field from the magnetic barrier region away which in turn leads to a broadening of this region. In addition, it leads to an ion composition boundary which is only gradually developed.

  10. Suppression subtractive hybridization profiles of radial growth phase and metastatic melanoma cell lines reveal novel potential targets

    International Nuclear Information System (INIS)

    Sousa, Josane F; Espreafico, Enilza M

    2008-01-01

    Melanoma progression occurs through three major stages: radial growth phase (RGP), confined to the epidermis; vertical growth phase (VGP), when the tumor has invaded into the dermis; and metastasis. In this work, we used suppression subtractive hybridization (SSH) to investigate the molecular signature of melanoma progression, by comparing a group of metastatic cell lines with an RGP-like cell line showing characteristics of early neoplastic lesions including expression of the metastasis suppressor KISS1, lack of αvβ3-integrin and low levels of RHOC. Two subtracted cDNA collections were obtained, one (RGP library) by subtracting the RGP cell line (WM1552C) cDNA from a cDNA pool from four metastatic cell lines (WM9, WM852, 1205Lu and WM1617), and the other (Met library) by the reverse subtraction. Clones were sequenced and annotated, and expression validation was done by Northern blot and RT-PCR. Gene Ontology annotation and searches in large-scale melanoma expression studies were done for the genes identified. We identified 367 clones from the RGP library and 386 from the Met library, of which 351 and 368, respectively, match human mRNA sequences, representing 288 and 217 annotated genes. We confirmed the differential expression of all genes selected for validation. In the Met library, we found an enrichment of genes in the growth factors/receptor, adhesion and motility categories whereas in the RGP library, enriched categories were nucleotide biosynthesis, DNA packing/repair, and macromolecular/vesicular trafficking. Interestingly, 19% of the genes from the RGP library map to chromosome 1 against 4% of the ones from Met library. This study identifies two populations of genes differentially expressed between melanoma cell lines from two tumor stages and suggests that these sets of genes represent profiles of less aggressive versus metastatic melanomas. A search for expression profiles of melanoma in available expression study databases allowed us to point to a

  11. Combining stated and revealed choice research to simulate the neighbor effect: The case of hybrid-electric vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Axsen, Jonn [Institute of Transportation Studies, Univ. of California at Davis, 2028 Academic Surge, One Shields Avenue, Davis, CA 95616 (United States); Mountain, Dean C. [DeGroote School of Business, McMaster Univ., 1280 Main Street West, Hamilton, ON L8S 4M4 (Canada); Jaccard, Mark [School of Resource and Environmental Management, Simon Fraser Univ., 8888 Univ. Drive, Burnaby, BC V5A 1S6 (Canada)

    2009-08-15

    According to intuition and theories of diffusion, consumer preferences develop along with technological change. However, most economic models designed for policy simulation unrealistically assume static preferences. To improve the behavioral realism of an energy-economy policy model, this study investigates the ''neighbor effect'', where a new technology becomes more desirable as its adoption becomes more widespread in the market. We measure this effect as a change in aggregated willingness to pay under different levels of technology penetration. Focusing on hybrid-electric vehicles (HEVs), an online survey experiment collected stated preference (SP) data from 535 Canadian and 408 Californian vehicle owners under different hypothetical market conditions. Revealed preference (RP) data was collected from the same respondents by eliciting the year, make and model of recent vehicle purchases from regions with different degrees of HEV popularity: Canada with 0.17% new market share, and California with 3.0% new market share. We compare choice models estimated from RP data only with three joint SP-RP estimation techniques, each assigning a different weight to the influence of SP and RP data in coefficient estimates. Statistically, models allowing more RP influence outperform SP influenced models. However, results suggest that because the RP data in this study is afflicted by multicollinearity, techniques that allow more SP influence in the beta estimates while maintaining RP data for calibrating vehicle class constraints produce more realistic estimates of willingness to pay. Furthermore, SP influenced coefficient estimates also translate to more realistic behavioral parameters for CIMS, allowing more sensitivity to policy simulations. (author)

  12. Combining stated and revealed choice research to simulate the neighbor effect: The case of hybrid-electric vehicles

    International Nuclear Information System (INIS)

    Axsen, Jonn; Mountain, Dean C.; Jaccard, Mark

    2009-01-01

    According to intuition and theories of diffusion, consumer preferences develop along with technological change. However, most economic models designed for policy simulation unrealistically assume static preferences. To improve the behavioral realism of an energy-economy policy model, this study investigates the ''neighbor effect'', where a new technology becomes more desirable as its adoption becomes more widespread in the market. We measure this effect as a change in aggregated willingness to pay under different levels of technology penetration. Focusing on hybrid-electric vehicles (HEVs), an online survey experiment collected stated preference (SP) data from 535 Canadian and 408 Californian vehicle owners under different hypothetical market conditions. Revealed preference (RP) data was collected from the same respondents by eliciting the year, make and model of recent vehicle purchases from regions with different degrees of HEV popularity: Canada with 0.17% new market share, and California with 3.0% new market share. We compare choice models estimated from RP data only with three joint SP-RP estimation techniques, each assigning a different weight to the influence of SP and RP data in coefficient estimates. Statistically, models allowing more RP influence outperform SP influenced models. However, results suggest that because the RP data in this study is afflicted by multicollinearity, techniques that allow more SP influence in the beta estimates while maintaining RP data for calibrating vehicle class constraints produce more realistic estimates of willingness to pay. Furthermore, SP influenced coefficient estimates also translate to more realistic behavioral parameters for CIMS, allowing more sensitivity to policy simulations. (author)

  13. Mapping evaporative water loss in desert passerines reveals an expanding threat of lethal dehydration.

    Science.gov (United States)

    Albright, Thomas P; Mutiibwa, Denis; Gerson, Alexander R; Smith, Eric Krabbe; Talbot, William A; O'Neill, Jacqueline J; McKechnie, Andrew E; Wolf, Blair O

    2017-02-28

    Extreme high environmental temperatures produce a variety of consequences for wildlife, including mass die-offs. Heat waves are increasing in frequency, intensity, and extent, and are projected to increase further under climate change. However, the spatial and temporal dynamics of die-off risk are poorly understood. Here, we examine the effects of heat waves on evaporative water loss (EWL) and survival in five desert passerine birds across the southwestern United States using a combination of physiological data, mechanistically informed models, and hourly geospatial temperature data. We ask how rates of EWL vary with temperature across species; how frequently, over what areas, and how rapidly lethal dehydration occurs; how EWL and die-off risk vary with body mass; and how die-off risk is affected by climate warming. We find that smaller-bodied passerines are subject to higher rates of mass-specific EWL than larger-bodied counterparts and thus encounter potentially lethal conditions much more frequently, over shorter daily intervals, and over larger geographic areas. Warming by 4 °C greatly expands the extent, frequency, and intensity of dehydration risk, and introduces new threats for larger passerine birds, particularly those with limited geographic ranges. Our models reveal that increasing air temperatures and heat wave occurrence will potentially have important impacts on the water balance, daily activity, and geographic distribution of arid-zone birds. Impacts may be exacerbated by chronic effects and interactions with other environmental changes. This work underscores the importance of acute risks of high temperatures, particularly for small-bodied species, and suggests conservation of thermal refugia and water sources.

  14. Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation.

    Science.gov (United States)

    Löffler, Markus W; Kowalewski, Daniel J; Backert, Linus; Bernhardt, Jörg; Adam, Patrick; Schuster, Heiko; Dengler, Florian; Backes, Daniel; Kopp, Hans-Georg; Beckert, Stefan; Wagner, Silvia; Königsrainer, Ingmar; Kohlbacher, Oliver; Kanz, Lothar; Königsrainer, Alfred; Rammensee, Hans-Georg; Stevanovic, Stefan; Haen, Sebastian P

    2018-05-22

    Immune cell infiltrates have proven highly relevant for colorectal carcinoma (CRC) prognosis, making CRC a promising candidate for immunotherapy. Since tumors interact with the immune system via HLA-presented peptide ligands, exact knowledge of the peptidome constitution is fundamental for understanding this relationship. Here we comprehensively describe the naturally presented HLA-ligandome of CRC and corresponding non-malignant colon (NMC) tissue. Mass spectrometry identified 35,367 and 28,132 HLA-class I ligands on CRC and NMC, attributable to 7,684 and 6,312 distinct source proteins, respectively. Cancer-exclusive peptides were assessed on source protein level using Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein analysis through evolutionary relationships (PANTHER), revealing pathognomonic CRC-associated pathways including Wnt, TGF-β, PI3K, p53, and RTK-RAS. Relative quantitation of peptide presentation on paired CRC and NMC tissue further identified source proteins from cancer- and infection-associated pathways to be over-represented merely within the CRC ligandome. From the pool of tumor-exclusive peptides, a selected HLA-ligand subset was assessed for immunogenicity, with the majority exhibiting an existing T cell repertoire. Overall, these data show that the HLA-ligandome reflects cancer-associated pathways implicated in CRC oncogenesis, suggesting that alterations in tumor cell metabolism could result in cancer-specific, albeit not mutation-derived tumor-antigens. Hence, a defined pool of unique tumor peptides, attributable to complex cellular alterations that are exclusive to malignant cells might comprise promising candidates for immunotherapeutic applications. Copyright ©2018, American Association for Cancer Research.

  15. Brain-to-brain hyperclassification reveals action-specific motor mapping of observed actions in humans.

    Science.gov (United States)

    Smirnov, Dmitry; Lachat, Fanny; Peltola, Tomi; Lahnakoski, Juha M; Koistinen, Olli-Pekka; Glerean, Enrico; Vehtari, Aki; Hari, Riitta; Sams, Mikko; Nummenmaa, Lauri

    2017-01-01

    Seeing an action may activate the corresponding action motor code in the observer. It remains unresolved whether seeing and performing an action activates similar action-specific motor codes in the observer and the actor. We used novel hyperclassification approach to reveal shared brain activation signatures of action execution and observation in interacting human subjects. In the first experiment, two "actors" performed four types of hand actions while their haemodynamic brain activations were measured with 3-T functional magnetic resonance imaging (fMRI). The actions were videotaped and shown to 15 "observers" during a second fMRI experiment. Eleven observers saw the videos of one actor, and the remaining four observers saw the videos of the other actor. In a control fMRI experiment, one of the actors performed actions with closed eyes, and five new observers viewed these actions. Bayesian canonical correlation analysis was applied to functionally realign observers' and actors' fMRI data. Hyperclassification of the seen actions was performed with Bayesian logistic regression trained on actors' data and tested with observers' data. Without the functional realignment, between-subjects accuracy was at chance level. With the realignment, the accuracy increased on average by 15 percentage points, exceeding both the chance level and the accuracy without functional realignment. The highest accuracies were observed in occipital, parietal and premotor cortices. Hyperclassification exceeded chance level also when the actor did not see her own actions. We conclude that the functional brain activation signatures underlying action execution and observation are partly shared, yet these activation signatures may be anatomically misaligned across individuals.

  16. Epitope mapping for monoclonal antibody reveals the activation mechanism for αVβ3 integrin.

    Directory of Open Access Journals (Sweden)

    Tetsuji Kamata

    Full Text Available Epitopes for a panel of anti-αVβ3 monoclonal antibodies (mAbs were investigated to explore the activation mechanism of αVβ3 integrin. Experiments utilizing αV/αIIb domain-swapping chimeras revealed that among the nine mAbs tested, five recognized the ligand-binding β-propeller domain and four recognized the thigh domain, which is the upper leg of the αV chain. Interestingly, the four mAbs included function-blocking as well as non-functional mAbs, although they bound at a distance from the ligand-binding site. The epitopes for these four mAbs were further determined using human-to-mouse αV chimeras. Among the four, P3G8 recognized an amino acid residue, Ser-528, located on the side of the thigh domain, while AMF-7, M9, and P2W7 all recognized a common epitope, Ser-462, that was located close to the α-genu, where integrin makes a sharp bend in the crystal structure. Fibrinogen binding studies for cells expressing wild-type αVβ3 confirmed that AMF-7, M9, and P2W7 were inhibitory, while P3G8 was non-functional. However, these mAbs were all unable to block binding when αVβ3 was constrained in its extended conformation. These results suggest that AMF-7, M9, and P2W7 block ligand binding allosterically by stabilizing the angle of the bend in the bent conformation. Thus, a switchblade-like movement of the integrin leg is indispensable for the affinity regulation of αVβ3 integrin.

  17. Decreasing Data Analytics Time: Hybrid Architecture MapReduce-Massive Parallel Processing for a Smart Grid

    Directory of Open Access Journals (Sweden)

    Abdeslam Mehenni

    2017-03-01

    Full Text Available As our populations grow in a world of limited resources enterprise seek ways to lighten our load on the planet. The idea of modifying consumer behavior appears as a foundation for smart grids. Enterprise demonstrates the value available from deep analysis of electricity consummation histories, consumers’ messages, and outage alerts, etc. Enterprise mines massive structured and unstructured data. In a nutshell, smart grids result in a flood of data that needs to be analyzed, for better adjust to demand and give customers more ability to delve into their power consumption. Simply put, smart grids will increasingly have a flexible data warehouse attached to them. The key driver for the adoption of data management strategies is clearly the need to handle and analyze the large amounts of information utilities are now faced with. New approaches to data integration are nauseating moment; Hadoop is in fact now being used by the utility to help manage the huge growth in data whilst maintaining coherence of the Data Warehouse. In this paper we define a new Meter Data Management System Architecture repository that differ with three leaders MDMS, where we use MapReduce programming model for ETL and Parallel DBMS in Query statements(Massive Parallel Processing MPP.

  18. CGI: Java software for mapping and visualizing data from array-based comparative genomic hybridization and expression profiling.

    Science.gov (United States)

    Gu, Joyce Xiuweu-Xu; Wei, Michael Yang; Rao, Pulivarthi H; Lau, Ching C; Behl, Sanjiv; Man, Tsz-Kwong

    2007-10-06

    With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator) that matches the BAC clones from array-based comparative genomic hybridization (aCGH) to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specific BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  19. CGI: Java Software for Mapping and Visualizing Data from Array-based Comparative Genomic Hybridization and Expression Profiling

    Directory of Open Access Journals (Sweden)

    Joyce Xiuweu-Xu Gu

    2007-01-01

    Full Text Available With the increasing application of various genomic technologies in biomedical research, there is a need to integrate these data to correlate candidate genes/regions that are identified by different genomic platforms. Although there are tools that can analyze data from individual platforms, essential software for integration of genomic data is still lacking. Here, we present a novel Java-based program called CGI (Cytogenetics-Genomics Integrator that matches the BAC clones from array-based comparative genomic hybridization (aCGH to genes from RNA expression profiling datasets. The matching is computed via a fast, backend MySQL database containing UCSC Genome Browser annotations. This program also provides an easy-to-use graphical user interface for visualizing and summarizing the correlation of DNA copy number changes and RNA expression patterns from a set of experiments. In addition, CGI uses a Java applet to display the copy number values of a specifi c BAC clone in aCGH experiments side by side with the expression levels of genes that are mapped back to that BAC clone from the microarray experiments. The CGI program is built on top of extensible, reusable graphic components specifically designed for biologists. It is cross-platform compatible and the source code is freely available under the General Public License.

  20. Fluorescence in situ hybridization karyotyping reveals the presence of two distinct genomes in the taxon Aegilops tauschii

    OpenAIRE

    Zhao, Laibin; Ning, Shunzong; Yi, Yingjin; Zhang, Lianquan; Yuan, Zhongwei; Wang, Jirui; Zheng, Youliang; Hao, Ming; Liu, Dengcai

    2018-01-01

    Background Aegilops tauschii is the donor of the bread wheat D genome. Based on spike morphology, the taxon has conventionally been subdivided into ssp. tauschii and ssp. strangulata. The present study was intended to address the poor match between this whole plant morphology-based subdivision and genetic relationships inferred from genotyping by fluorescence in situ hybridization karyotyping a set of 31 Ae. tauschii accessions. Results The distribution of sites hybridizing to the two probes ...

  1. In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins.

    Science.gov (United States)

    Fang, Pan; Wang, Xin-Jian; Xue, Yu; Liu, Ming-Qi; Zeng, Wen-Feng; Zhang, Yang; Zhang, Lei; Gao, Xing; Yan, Guo-Quan; Yao, Jun; Shen, Hua-Li; Yang, Peng-Yuan

    2016-06-21

    N-glycosylation is one of the most prominent and abundant posttranslational modifications of proteins. It is estimated that over 50% of mammalian proteins undergo glycosylation. However, the analysis of N-glycoproteins has been limited by the available analytical technology. In this study, we comprehensively mapped the N-glycosylation sites in the mouse brain proteome by combining complementary methods, which included seven protease treatments, four enrichment techniques and two fractionation strategies. Altogether, 13492 N-glycopeptides containing 8386 N-glycosylation sites on 3982 proteins were identified. After evaluating the performance of the above methods, we proposed a simple and efficient workflow for large-scale N-glycosylation site mapping. The optimized workflow yielded 80% of the initially identified N-glycosylation sites with considerably less effort. Analysis of the identified N-glycoproteins revealed that many of the mouse brain proteins are N-glycosylated, including those proteins in critical pathways for nervous system development and neurological disease. Additionally, several important biomarkers of various diseases were found to be N-glycosylated. These data confirm that N-glycosylation is important in both physiological and pathological processes in the brain, and provide useful details about numerous N-glycosylation sites in brain proteins.

  2. Mapping of rDNA on the chromosomes of Eleusine species by fluorescence in situ hybridization.

    Science.gov (United States)

    Bisht, M S; Mukai, Y

    2000-12-01

    Mapping of rDNA sites on the chromosomes of four diploid and two tetraploid species of Eleusine has provided valuable information on genome relationship between the species. Presence of 18S-5.8S-26S rDNA on the largest pair of the chromosomes, location of 5S rDNA at four sites on two pairs of chromosomes and presence of 18S-5.8S-26S and 5S rDNA at same location on one pair of chromosomes have clearly differentiated E. multiflora from rest of the species of Eleusine. The two tetraploid species, E. coracana and E. africana have the same number of 18S-5.8S-26S and 5S rDNA sites and located at similar position on the chromosomes. Diploid species, E. indica, E. floccifolia and E. tristachya have the same 18S-5.8S-26S sites and location on the chromosomes which also resembled with the two pairs of 18S-5.8S-26S rDNA locations in tetraploid species, E. coracana and E. africana. The 5S rDNA sites on chromosomes of E. indica and E. floccifolia were also comparable to the 5S rDNA sites of E. africana and E. coracana. The similarity of the rDNA sites and their location on chromosomes in the three diploid and two polyploid species also supports the view that genome donors to tetraploid species may be from these diploid species.

  3. Sixty-five radiation hybrids for the short arm of human chromosome 6: their value as a mapping panel and as a source for rapid isolation of new probes using repeat element-mediated PCR

    International Nuclear Information System (INIS)

    Zoghbi, H.Y.; McCall, A.E.; LeBorgne-Demarquoy, F.

    1991-01-01

    We have used an irradiation and fusion procedure to generate somatic cell hybrids that retain fragments of the short arm of human chromosome 6 (6p). To identify hybrids retaining human material, we performed repeat element-mediated PCR on crude lysates of cells from individual clones. Sixty-five hybrids were shown to contain human material and fifty of those contained one or more 6p-specific probes. Detailed characterization of these hybrids identified a subset that divides 6p into ten mapping intervals. Using repeat element-mediated PCR, we were able to isolate and map 61 new DNA fragments from specific regions of 6p. Fifteen of these fragments were used to screen for restriction fragment length polymorphisms (RFLPs), and nine identified RFLPs with one or more enzymes. The radiation hybrids described in this study provide a valuable resource for high-resolution mapping of 6p and for the rapid isolation of region-specific markers

  4. Morphometric differences in planum temporale in schizophrenia and bipolar disorder revealed by statistical analysis of Labeled Cortical Depth Maps

    Directory of Open Access Journals (Sweden)

    J Tilak eRatnanather

    2014-08-01

    Full Text Available Differences in cortical thickness in the lateral temporal lobe, including the planum temporale (PT, have been reported in MRI studies of schizophrenia (SCZ and bipolar disorder (BPD patients. Most of these studies have used a single-valued global or local measure for thickness. However, additional and complementary information can be obtained by generating Labelled Cortical Depth Maps (LCDMs, which are distances of labeled gray matter voxels from the nearest point on the gray/white matter (inner cortical surface. Statistical analyses of pooled and censored LCDM distances reveal subtle differences in PT between SCZ and BPD groups from data generated by Ratnanather et al. (Schizophrenia Research, http://dx.doi.org/10.1016/j.schres.2013.08.014. These results confirm that the left PT (LPT is more sensitive than the right PT in distinguishing between SCZ, BPD and healthy controls. Also confirmed is a strong gender effect, with a thicker PT seen in males than in females. The differences between groups at smaller distances in the LPT revealed by pooled and censored LCDM analysis suggest that SCZ and BPD have different effects on the cortical mantle close to the gray/white matter surface. This is consistent with reported subtle changes in the cortical mantle observed in postmortem studies.

  5. Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses.

    Directory of Open Access Journals (Sweden)

    Hadar Israeli

    2017-04-01

    Full Text Available Cell entry of many enveloped viruses occurs by engagement with cellular receptors, followed by internalization into endocytic compartments and pH-induced membrane fusion. A previously unnoticed step of receptor switching was found to be critical during cell entry of two devastating human pathogens: Ebola and Lassa viruses. Our recent studies revealed the functional role of receptor switching to LAMP1 for triggering membrane fusion by Lassa virus and showed the involvement of conserved histidines in this switching, suggesting that other viruses from this family may also switch to LAMP1. However, when we investigated viruses that are genetically close to Lassa virus, we discovered that they cannot bind LAMP1. A crystal structure of the receptor-binding module from Morogoro virus revealed structural differences that allowed mapping of the LAMP1 binding site to a unique set of Lassa residues not shared by other viruses in its family, illustrating a key difference in the cell-entry mechanism of Lassa virus that may contribute to its pathogenicity.

  6. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin

    Science.gov (United States)

    Lowrey, Liam; Woodhams, Douglas C.; Tacchi, Luca

    2015-01-01

    The mucosal surfaces of wild and farmed aquatic vertebrates face the threat of many aquatic pathogens, including fungi. These surfaces are colonized by diverse symbiotic bacterial communities that may contribute to fight infection. Whereas the gut microbiome of teleosts has been extensively studied using pyrosequencing, this tool has rarely been employed to study the compositions of the bacterial communities present on other teleost mucosal surfaces. Here we provide a topographical map of the mucosal microbiome of an aquatic vertebrate, the rainbow trout (Oncorhynchus mykiss). Using 16S rRNA pyrosequencing, we revealed novel bacterial diversity at each of the five body sites sampled and showed that body site is a strong predictor of community composition. The skin exhibited the highest diversity, followed by the olfactory organ, gills, and gut. Flectobacillus was highly represented within skin and gill communities. Principal coordinate analysis and plots revealed clustering of external sites apart from internal sites. A highly diverse community was present within the epithelium, as demonstrated by confocal microscopy and pyrosequencing. Using in vitro assays, we demonstrated that two Arthrobacter sp. skin isolates, a Psychrobacter sp. strain, and a combined skin aerobic bacterial sample inhibit the growth of Saprolegnia australis and Mucor hiemalis, two important aquatic fungal pathogens. These results underscore the importance of symbiotic bacterial communities of fish and their potential role for the control of aquatic fungal diseases. PMID:26209676

  7. Assessment of fusion facility dose rate map using mesh adaptivity enhancements of hybrid Monte Carlo/deterministic techniques

    International Nuclear Information System (INIS)

    Ibrahim, Ahmad M.; Wilson, Paul P.; Sawan, Mohamed E.; Mosher, Scott W.; Peplow, Douglas E.; Grove, Robert E.

    2014-01-01

    Highlights: •Calculate the prompt dose rate everywhere throughout the entire fusion energy facility. •Utilize FW-CADIS to accurately perform difficult neutronics calculations for fusion energy systems. •Develop three mesh adaptivity algorithms to enhance FW-CADIS efficiency in fusion-neutronics calculations. -- Abstract: Three mesh adaptivity algorithms were developed to facilitate and expedite the use of the CADIS and FW-CADIS hybrid Monte Carlo/deterministic techniques in accurate full-scale neutronics simulations of fusion energy systems with immense sizes and complicated geometries. First, a macromaterial approach enhances the fidelity of the deterministic models without changing the mesh. Second, a deterministic mesh refinement algorithm generates meshes that capture as much geometric detail as possible without exceeding a specified maximum number of mesh elements. Finally, a weight window coarsening algorithm decouples the weight window mesh and energy bins from the mesh and energy group structure of the deterministic calculations in order to remove the memory constraint of the weight window map from the deterministic mesh resolution. The three algorithms were used to enhance an FW-CADIS calculation of the prompt dose rate throughout the ITER experimental facility and resulted in a 23.3% increase in the number of mesh tally elements in which the dose rates were calculated in a 10-day Monte Carlo calculation. Additionally, because of the significant increase in the efficiency of FW-CADIS simulations, the three algorithms enabled this difficult calculation to be accurately solved on a regular computer cluster, eliminating the need for a world-class super computer

  8. Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.).

    Science.gov (United States)

    Dou, Junling; Zhao, Shengjie; Lu, Xuqiang; He, Nan; Zhang, Lei; Ali, Aslam; Kuang, Hanhui; Liu, Wenge

    2018-04-01

    A 159 bp deletion in ClFS1 gene encoding IQD protein is responsible for fruit shape in watermelon. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is known for its rich diversity in fruit size and shape. Fruit shape has been one of the major objectives of watermelon breeding. However, the candidate genes and the underlying genetic mechanism for such an important trait in watermelon are unknown. In this study, we identified a locus on chromosome 3 of watermelon genome controlling fruit shape. Segregation analysis in F 2 and BC 1 populations derived from a cross between two inbred lines "Duan125" (elongate fruit) and "Zhengzhouzigua" (spherical fruit) suggests that fruit shape of watermelon is controlled by a single locus and elongate fruit (OO) is incompletely dominant to spherical fruit (oo) with the heterozygote (Oo) being oval fruit. GWAS profiles among 315 accessions identified a major locus designated on watermelon chromosome 3, which was confirmed by BSA-seq mapping in the F 2 population. The candidate gene was mapped to a region 46 kb on chromosome 3. There were only four genes present in the corresponding region in the reference genome. Four candidate genes were sequenced in this region, revealing that the CDS of Cla011257 had a 159 bp deletion which resulted in the omission of 53 amino acids in elongate watermelon. An indel marker was derived from the 159 bp deletion to test the F 2 population and 105 watermelon accessions. The results showed that Cla011257 cosegregated with watermelon fruit shape. In addition, the Cla011257 expression was the highest at ovary formation stage. The predicted protein of the Cla011257 gene fitted in IQD protein family which was reported to have association with cell arrays and Ca 2+ -CaM signaling modules. Clear understanding of the genes facilitating the fruit shape along with marker association selection will be an effective way to develop new cultivars.

  9. Awake craniotomy for cortical language mapping and resection of an arteriovenous malformation adjacent to eloquent areas under general anesthesia — A hybrid approach

    Directory of Open Access Journals (Sweden)

    Pree Nimmannitya

    2015-12-01

    Full Text Available Surgery of arteriovenous malformation (AVM is sometimes challenging and carries a high risk of morbidity, especially when the AVM is located in an eloquent area of the brain. Unlike gliomas, awake craniotomy has not been widely used for resection of AVM. The authors present a case of an AVM in the left frontal lobe which was successfully removed with the aid of awake craniotomy with cortical language mapping. In conclusion, awake craniotomy for functional cortical mapping is beneficial for AVM resection, especially when the lesion is located in or adjacent to eloquent areas of the brain. A hybrid approach with functional mapping in the awake condition and AVM resection under general anesthesia may be useful in selected cases. Furthermore, en bloc resection with the nidus embedded in the brain parenchyma may be a useful means of removal to reduce operation time and intraoperative blood loss if there is no apparent functional cortex surrounding the AVM, as in the present case.

  10. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by reverse line blot hybridization

    Czech Academy of Sciences Publication Activity Database

    Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, M.W.

    2013-01-01

    Roč. 8, č. 3 (2013), e58527 E-ISSN 1932-6203 R&D Projects: GA ČR(CZ) GAP504/10/0566; GA ČR(CZ) GEEEF/10/E011 Institutional support: RVO:60077344 Keywords : Limnohabitans * microdiversity * habitats * hybridization Subject RIV: DA - Hydrology ; Limnology Impact factor: 3.534, year: 2013

  11. Deep sequencing of amplicons reveals widespread intraspecific hybridization and multiple origins of polyploidy in big sagebrush (Artemisia tridentata, Asteraceae)

    Science.gov (United States)

    Bryce A. Richardson; Justin T. Page; Prabin Bajgain; Stewart C. Sanderson; Joshua A. Udall

    2012-01-01

    Premise of the study: Hybridization has played an important role in the evolution and ecological adaptation of diploid and polyploid plants. Artemisia tridentata (Asteraceae) tetraploids are extremely widespread and of great ecological importance. These tetraploids are often taxonomically identified as A. tridentata subsp. wyomingensis or as autotetraploids of diploid...

  12. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato

    OpenAIRE

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-01-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene...

  13. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids.

    Science.gov (United States)

    Wang, Zhicheng; Cui, Jun; Song, Jian; Wang, Haoze; Gao, Kailun; Qiu, Xuemei; Gou, Meng; Li, Xin; Hu, Ziwen; Wang, Xiuli; Chang, Yaqing

    2018-04-01

    Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.

  14. Construction of a river buffalo (Bubalus bubalis whole-genome radiation hybrid panel and preliminary RH mapping of chromosomes 3 and 10

    Directory of Open Access Journals (Sweden)

    J.E. Womack

    2010-02-01

    Full Text Available The buffalo (Bubalus bubalis not only is a useful source of milk, it also provides meat and works as a natural source of labor and biogas. To establish a project for buffalo genome mapping a 5,000-rad whole genome radiation hybrid panel was constructed for river buffalo and used to build preliminary RH maps from two chromosomes (BBU 3 and BBU10. The preliminary maps contain 66 markers, including coding genes, cattle ESTs and microsatellite loci. The RH maps presented here are the starting point for mapping additional loci, in particular, genes and expressed sequence tags that will allow detailed comparative maps between buffalo, cattle and other species to be constructed. A large quantity of DNA has been prepared from the cell lines forming the RH panel reported here and will be made publicly available to the international community both for the study of chromosome evolution and for the improvement of traits important to the role of buffalo in animal agriculture.

  15. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes.

    Science.gov (United States)

    Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

    2015-10-16

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

  16. On-target labeling of intracellular metabolites combined with chemical mapping of individual hyphae revealing cytoplasmic relocation of isotopologues.

    Science.gov (United States)

    Hu, Jie-Bi; Chen, Yu-Chie; Urban, Pawel L

    2012-06-05

    A microscale analytical platform integrating microbial cell culture, isotopic labeling, along with visual and mass spectrometric imaging with single-cell resolution has been developed and applied in the monitoring of cellular metabolism in fungal mycelium. The method implements open chips with a two-dimensional surface pattern composed of hydrophobic and hydrophilic zones. Two hydrophilic islands are used as medium reservoirs, while the hydrophobic area constitutes the support for the growing aerial hyphae, which do not have direct contact with the medium. The first island, containing (12)C(6)-glucose medium, was initially inoculated with the mycelium (Neurospora crassa), and following the initial incubation period, the hyphae progressed toward the second medium island, containing an isotopically labeled substrate ((13)C(6)-glucose). The (13)C atoms were gradually incorporated into cellular metabolites, which was revealed by MALDI-MS. The fate of the chitin-biosynthesis precursor, uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), was monitored by recording mass spectra with characteristic isotopic patterns, which indicated the presence of various (12)C/(13)C isotopologues. The method enabled mapping the (13)C-labeled UDP-GlcNAc in fungal mycelium and recording its redistribution in hyphae, directly on the chip.

  17. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finely, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Sotrey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  18. Revealing the distinct habitat ranges and hybrid zone of genetic sub-populations within Pseudo-nitzschia pungens (Bacillariophyceae) in the West Pacific area.

    Science.gov (United States)

    Kim, Jin Ho; Wang, Pengbin; Park, Bum Soo; Kim, Joo-Hwan; Patidar, Shailesh Kumar; Han, Myung-Soo

    2018-03-01

    Genetic sub-populations (clades) of cosmopolitan marine diatom Pseudo-nitzschia pungens might have distinct habitats, and their hybrid zone is suspected in higher latitude area of the West Pacific area, however, it is still unrevealed because of technical difficulties and lack of evidences in natural environments. The aim of this study is to investigate the habitat characteristics of each clade of P. pungens on geographical distribution with the habitat temperature ranges of each clade and to reveal their hybrid zone in the West Pacific area. We employed the 137 number of nucleotide sequences of P. pungens and its sampling data (spatial and temporal scale) originated from the West Pacific area, and used field application of qPCR assay for intra-specific level of P. pungens. Only two genotypes, clade I and III, were identified in the West Pacific area. Clade I was distributed from 39 to 32.3°N, and clade III were from 1.4 to 34.4°N. The estimated habitat temperature for the clade I and clade III ranges were 8.1-26.9 °C and 24.2-31.2 °C, respectively. The latitudinal distributions and temperature ranges of each clade were significantly different. The qPCR assay employed, and results suggested that the hybrid zone for clade I and III has been observed in the southern Korean coasts, and clade III might be introduced from the Southern Pacific area. The cell abundances of clade III were strongly related with the higher seawater temperature and warm current force. This study has defined distinct habitat characteristics of genetically different sub-populations of P. pungens, and revealed its hybrid zone in natural environment for the first time. We also provided strong evidences about dispersion of the population of clade III to higher latitude in the West Pacific area. Copyright © 2018. Published by Elsevier B.V.

  19. Distribution and ecological preferences of the freshwater lineage LimA (genus Limnohabitans) revealed by a new double hybridization approach

    Czech Academy of Sciences Publication Activity Database

    Shabarova, Tatiana; Kasalický, Vojtěch; Šimek, Karel; Nedoma, Jiří; Znachor, Petr; Posch, T.; Pernthaler, J.; Salcher, Michaela M.

    2017-01-01

    Roč. 19, č. 3 (2017), s. 1296-1309 ISSN 1462-2912 R&D Projects: GA ČR(CZ) GA13-00243S; GA ČR GA15-12197S; GA ČR GA15-09721S Institutional support: RVO:60077344 Keywords : dissolved organic-matter * in-situ hybridization * bacterial community composition * polynucleobacter-necessarius Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 5.395, year: 2016

  20. Comparative mapping of DNA probes derived from the V{sub k} immunoglobulin gene regions on human and great ape chromosomes by fluorescence in situ hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, N.; Wienberg, J.; Ermert, K. [Universitaet Muenchen (Germany)] [and others

    1995-03-01

    Fluorescence in situ hybridization (FISH) of cosmid clones of human V{sub K} gene regions to human and primate chromosomes contributed to the dating of chromosome reorganizations in evolution. A clone from the K locus at 2p11-p12 (cos 106) hybridized to the assumed homologous chromosome bands in the chimpanzees Pan troglodytes (PTR) and P. paniscus (PPA), the Gorilla gorilla (GGO), and the orangutan Pongo Pygmaeus (PPY). Human and both chimpanzees differed from gorilla and orangutan by the mapping of cos 170, a clone derived from chromosome 2cen-q11.2; the transposition of this orphon to the other side of the centromere can, therefore, be dated after the human/chimpanzee and gorilla divergence. Hybridization to homologous bands was also found with a cosmid clone containing a V{sub K}I orphon located on chromosome 1 (cos 115, main signal at 1q31-q32), although the probe is not fully unique. Also, a clone derived from the orphon V{sub K} region on chromosome 22q11 (cos 121) hybridized to the homologous bands in the great apes. This indicates that the orphons on human chromosomes 1 and 22 had been translocated early in primate evolution. 18 refs., 2 figs.

  1. The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells

    Directory of Open Access Journals (Sweden)

    Andrew Parker

    2015-12-01

    Full Text Available Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182 in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss.

  2. A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

    Directory of Open Access Journals (Sweden)

    Yuan Yuan Shi

    Full Text Available BACKGROUND: The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. RESULTS: F2 workers (N = 103 were genotyped for 126,990 single nucleotide polymorphisms (SNPs. After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM with the largest linkage group (180 loci measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. CONCLUSION: We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

  3. A Dense Brown Trout (Salmo trutta) Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Science.gov (United States)

    Leitwein, Maeva; Guinand, Bruno; Pouzadoux, Juliette; Desmarais, Erick; Berrebi, Patrick; Gagnaire, Pierre-Alexandre

    2017-01-01

    High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta), a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π) was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout. PMID:28235829

  4. A Dense Brown Trout (Salmo trutta Linkage Map Reveals Recent Chromosomal Rearrangements in the Salmo Genus and the Impact of Selection on Linked Neutral Diversity

    Directory of Open Access Journals (Sweden)

    Maeva Leitwein

    2017-04-01

    Full Text Available High-density linkage maps are valuable tools for conservation and eco-evolutionary issues. In salmonids, a complex rediploidization process consecutive to an ancient whole genome duplication event makes linkage maps of prime importance for investigating the evolutionary history of chromosome rearrangements. Here, we developed a high-density consensus linkage map for the brown trout (Salmo trutta, a socioeconomically important species heavily impacted by human activities. A total of 3977 ddRAD markers were mapped and ordered in 40 linkage groups using sex- and lineage-averaged recombination distances obtained from two family crosses. Performing map comparison between S. trutta and its sister species, S. salar, revealed extensive chromosomal rearrangements. Strikingly, all of the fusion and fission events that occurred after the S. salar/S. trutta speciation happened in the Atlantic salmon branch, whereas the brown trout remained closer to the ancestral chromosome structure. Using the strongly conserved synteny within chromosome arms, we aligned the brown trout linkage map to the Atlantic salmon genome sequence to estimate the local recombination rate in S. trutta at 3721 loci. A significant positive correlation between recombination rate and within-population nucleotide diversity (π was found, indicating that selection constrains variation at linked neutral sites in brown trout. This new high-density linkage map provides a useful genomic resource for future aquaculture, conservation, and eco-evolutionary studies in brown trout.

  5. Sequence-Based Mapping and Genome Editing Reveal Mutations in Stickleback Hps5 Cause Oculocutaneous Albinism and the casper Phenotype

    Directory of Open Access Journals (Sweden)

    James C. Hart

    2017-09-01

    Full Text Available Here, we present and characterize the spontaneous X-linked recessive mutation casper, which causes oculocutaneous albinism in threespine sticklebacks (Gasterosteus aculeatus. In humans, Hermansky-Pudlak syndrome results in pigmentation defects due to disrupted formation of the melanin-containing lysosomal-related organelle (LRO, the melanosome. casper mutants display not only reduced pigmentation of melanosomes in melanophores, but also reductions in the iridescent silver color from iridophores, while the yellow pigmentation from xanthophores appears unaffected. We mapped casper using high-throughput sequencing of genomic DNA from bulked casper mutants to a region of the stickleback X chromosome (chromosome 19 near the stickleback ortholog of Hermansky-Pudlak syndrome 5 (Hps5. casper mutants have an insertion of a single nucleotide in the sixth exon of Hps5, predicted to generate an early frameshift. Genome editing using CRISPR/Cas9 induced lesions in Hps5 and phenocopied the casper mutation. Injecting single or paired Hps5 guide RNAs revealed higher incidences of genomic deletions from paired guide RNAs compared to single gRNAs. Stickleback Hps5 provides a genetic system where a hemizygous locus in XY males and a diploid locus in XX females can be used to generate an easily scored visible phenotype, facilitating quantitative studies of different genome editing approaches. Lastly, we show the ability to better visualize patterns of fluorescent transgenic reporters in Hps5 mutant fish. Thus, Hps5 mutations present an opportunity to study pigmented LROs in the emerging stickleback model system, as well as a tool to aid in assaying genome editing and visualizing enhancer activity in transgenic fish.

  6. Raman chemical mapping reveals site of action of HIV protease inhibitors in HPV16 E6 expressing cervical carcinoma cells.

    Science.gov (United States)

    Kim, Dong-Hyun; Jarvis, Roger M; Allwood, J William; Batman, Gavin; Moore, Rowan E; Marsden-Edwards, Emma; Hampson, Lynne; Hampson, Ian N; Goodacre, Royston

    2010-12-01

    It has been shown that the HIV protease inhibitors indinavir and lopinavir may have activity against the human papilloma virus (HPV) type 16 inhibiting HPV E6-mediated proteasomal degradation of p53 in cultured cervical carcinoma cells. However, their mode and site of action is unknown. HPV-negative C33A cervical carcinoma cells and the same cells stably transfected with E6 (C33AE6) were exposed to indinavir and lopinavir at concentrations of 1 mM and 30 μM, respectively. The intracellular distribution of metabolites and metabolic changes induced by these treatments were investigated by Raman microspectroscopic imaging combined with the analysis of cell fractionation products by liquid chromatography-mass spectrometry (LC-MS). A uniform cellular distribution of proteins was found in drug-treated cells irrespective of cell type. Indinavir was observed to co-localise with nucleic acid in the nucleus, but only in E6 expressing cells. Principal components analysis (PCA) score maps generated on the full Raman hypercube and the corresponding PCA loadings plots revealed that the majority of metabolic variations influenced by the drug exposure within the cells were associated with changes in nucleic acids. Analysis of cell fractionation products by LC-MS confirmed that the level of indinavir in nuclear extracts was approximately eight-fold greater than in the cytoplasm. These data demonstrate that indinavir undergoes enhanced nuclear accumulation in E6-expressing cells, which suggests that this is the most likely site of action for this compound against HPV.

  7. Pressure pain sensitivity topographical maps reveal bilateral hyperalgesia of the hands in patients with unilateral carpal tunnel syndrome.

    Science.gov (United States)

    Fernández-de-Las-Peñas, César; Madeleine, Pascal; Martínez-Perez, Almudena; Arendt-Nielsen, Lars; Jiménez-García, Rodrigo; Pareja, Juan A

    2010-08-01

    To assess topographical pressure pain sensitivity maps of the hand in patients with unilateral carpal tunnel syndrome (CTS) as compared with healthy subjects. A total of 20 women with CTS (ages 32-52 years) and 20 healthy matched women (ages 32-51 years) were recruited. Pressure pain thresholds (PPTs) were measured bilaterally over 30 locations of the palm of each hand by an assessor blinded to the subjects' conditions. Patients showed lower PPTs in both hands in all of the measurement points as compared with controls (P < 0.001 for all). PPTs were lower in those points over the proximal phalanx of the fingers and the thenar eminency as compared with those points located over the distal phalanx of the fingers (P < 0.001). CTS patients showed lower PPT levels in dermatomes C6, C7, and C8 when compared with healthy controls (P < 0.001 for all), but without differences between dermatomes (P = 0.4). PPT was negatively correlated with both hand pain intensity and duration of symptoms (P < 0.001 for all). Our findings revealed bilateral generalized pressure pain hyperalgesia in unilateral CTS because lower PPT levels were found in all of the points. The pressure pain hyperalgesia was not uniformly distributed since PPTs were lower in points over the proximal phalanx of the fingers and the thenar eminency as compared with those points located over the distal phalanx of the fingers. The decrease in PPT levels was associated with the intensity and the duration of the pain symptoms, supporting a role of both peripheral and central sensitization mechanisms in this pain condition.

  8. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

    Directory of Open Access Journals (Sweden)

    Kouji Satoh

    Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

  9. Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

    Directory of Open Access Journals (Sweden)

    Sharat K. Pradhan

    2017-04-01

    Full Text Available Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

  10. Mapping the transcription start points of the Staphylococcus aureus eap, emp, and vwb promoters reveals a conserved octanucleotide sequence that is essential for expression of these genes.

    Science.gov (United States)

    Harraghy, Niamh; Homerova, Dagmar; Herrmann, Mathias; Kormanec, Jan

    2008-01-01

    Mapping the transcription start points of the eap, emp, and vwb promoters revealed a conserved octanucleotide sequence (COS). Deleting this sequence abolished the expression of eap, emp, and vwb. However, electrophoretic mobility shift assays gave no evidence that this sequence was a binding site for SarA or SaeR, known regulators of eap and emp.

  11. High resolution linkage maps of the model organism Petunia reveal substantial synteny decay with the related genome of tomato.

    Science.gov (United States)

    Bossolini, Eligio; Klahre, Ulrich; Brandenburg, Anna; Reinhardt, Didier; Kuhlemeier, Cris

    2011-04-01

    Two linkage maps were constructed for the model plant Petunia. Mapping populations were obtained by crossing the wild species Petunia axillaris subsp. axillaris with Petunia inflata, and Petunia axillaris subsp. parodii with Petunia exserta. Both maps cover the seven chromosomes of Petunia, and span 970 centimorgans (cM) and 700 cM of the genomes, respectively. In total, 207 markers were mapped. Of these, 28 are multilocus amplified fragment length polymorphism (AFLP) markers and 179 are gene-derived markers. For the first time we report on the development and mapping of 83 Petunia microsatellites. The two maps retain the same marker order, but display significant differences of recombination frequencies at orthologous mapping intervals. A complex pattern of genomic rearrangements was detected with the related genome of tomato (Solanum lycopersicum), indicating that synteny between Petunia and other Solanaceae crops has been considerably disrupted. The newly developed markers will facilitate the genetic characterization of mutants and ecological studies on genetic diversity and speciation within the genus Petunia. The maps will provide a powerful tool to link genetic and genomic information and will be useful to support sequence assembly of the Petunia genome.

  12. Genomic networks of hybrid sterility.

    Directory of Open Access Journals (Sweden)

    Leslie M Turner

    2014-02-01

    Full Text Available Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities". The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL. Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is

  13. Genomic networks of hybrid sterility.

    Science.gov (United States)

    Turner, Leslie M; White, Michael A; Tautz, Diethard; Payseur, Bret A

    2014-02-01

    Hybrid dysfunction, a common feature of reproductive barriers between species, is often caused by negative epistasis between loci ("Dobzhansky-Muller incompatibilities"). The nature and complexity of hybrid incompatibilities remain poorly understood because identifying interacting loci that affect complex phenotypes is difficult. With subspecies in the early stages of speciation, an array of genetic tools, and detailed knowledge of reproductive biology, house mice (Mus musculus) provide a model system for dissecting hybrid incompatibilities. Male hybrids between M. musculus subspecies often show reduced fertility. Previous studies identified loci and several X chromosome-autosome interactions that contribute to sterility. To characterize the genetic basis of hybrid sterility in detail, we used a systems genetics approach, integrating mapping of gene expression traits with sterility phenotypes and QTL. We measured genome-wide testis expression in 305 male F2s from a cross between wild-derived inbred strains of M. musculus musculus and M. m. domesticus. We identified several thousand cis- and trans-acting QTL contributing to expression variation (eQTL). Many trans eQTL cluster into eleven 'hotspots,' seven of which co-localize with QTL for sterility phenotypes identified in the cross. The number and clustering of trans eQTL-but not cis eQTL-were substantially lower when mapping was restricted to a 'fertile' subset of mice, providing evidence that trans eQTL hotspots are related to sterility. Functional annotation of transcripts with eQTL provides insights into the biological processes disrupted by sterility loci and guides prioritization of candidate genes. Using a conditional mapping approach, we identified eQTL dependent on interactions between loci, revealing a complex system of epistasis. Our results illuminate established patterns, including the role of the X chromosome in hybrid sterility. The integrated mapping approach we employed is applicable in a broad

  14. Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping.

    Science.gov (United States)

    Jessup, R W; Burson, B L; Burow, O; Wang, Y W; Chang, C; Li, Z; Paterson, A H; Hussey, M A

    2003-04-01

    Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

  15. Graph Structure-Based Simultaneous Localization and Mapping Using a Hybrid Method of 2D Laser Scan and Monocular Camera Image in Environments with Laser Scan Ambiguity

    Directory of Open Access Journals (Sweden)

    Taekjun Oh

    2015-07-01

    Full Text Available Localization is an essential issue for robot navigation, allowing the robot to perform tasks autonomously. However, in environments with laser scan ambiguity, such as long corridors, the conventional SLAM (simultaneous localization and mapping algorithms exploiting a laser scanner may not estimate the robot pose robustly. To resolve this problem, we propose a novel localization approach based on a hybrid method incorporating a 2D laser scanner and a monocular camera in the framework of a graph structure-based SLAM. 3D coordinates of image feature points are acquired through the hybrid method, with the assumption that the wall is normal to the ground and vertically flat. However, this assumption can be relieved, because the subsequent feature matching process rejects the outliers on an inclined or non-flat wall. Through graph optimization with constraints generated by the hybrid method, the final robot pose is estimated. To verify the effectiveness of the proposed method, real experiments were conducted in an indoor environment with a long corridor. The experimental results were compared with those of the conventional GMappingapproach. The results demonstrate that it is possible to localize the robot in environments with laser scan ambiguity in real time, and the performance of the proposed method is superior to that of the conventional approach.

  16. Detection of Anomalous Noise Events on Low-Capacity Acoustic Nodes for Dynamic Road Traffic Noise Mapping within an Hybrid WASN

    Directory of Open Access Journals (Sweden)

    Rosa Ma Alsina-Pagès

    2018-04-01

    Full Text Available One of the main aspects affecting the quality of life of people living in urban and suburban areas is the continuous exposure to high road traffic noise (RTN levels. Nowadays, thanks to Wireless Acoustic Sensor Networks (WASN noise in Smart Cities has started to be automatically mapped. To obtain a reliable picture of the RTN, those anomalous noise events (ANE unrelated to road traffic (sirens, horns, people, etc. should be removed from the noise map computation by means of an Anomalous Noise Event Detector (ANED. In Hybrid WASNs, with master-slave architecture, ANED should be implemented in both high-capacity (Hi-Cap and low-capacity (Lo-Cap sensors, following the same principle to obtain consistent results. This work presents an ANED version to run in real-time on μ Controller-based Lo-Cap sensors of a hybrid WASN, discriminating RTN from ANE through their Mel-based spectral energy differences. The experiments, considering 9 h and 8 min of real-life acoustic data from both urban and suburban environments, show the feasibility of the proposal both in terms of computational load and in classification accuracy. Specifically, the ANED Lo-Cap requires around 1 6 of the computational load of the ANED Hi-Cap, while classification accuracies are slightly lower (around 10%. However, preliminary analyses show that these results could be improved in around 4% in the future by means of considering optimal frequency selection.

  17. Detection of Anomalous Noise Events on Low-Capacity Acoustic Nodes for Dynamic Road Traffic Noise Mapping within an Hybrid WASN.

    Science.gov (United States)

    Alsina-Pagès, Rosa Ma; Alías, Francesc; Socoró, Joan Claudi; Orga, Ferran

    2018-04-20

    One of the main aspects affecting the quality of life of people living in urban and suburban areas is the continuous exposure to high road traffic noise (RTN) levels. Nowadays, thanks to Wireless Acoustic Sensor Networks (WASN) noise in Smart Cities has started to be automatically mapped. To obtain a reliable picture of the RTN, those anomalous noise events (ANE) unrelated to road traffic (sirens, horns, people, etc.) should be removed from the noise map computation by means of an Anomalous Noise Event Detector (ANED). In Hybrid WASNs, with master-slave architecture, ANED should be implemented in both high-capacity (Hi-Cap) and low-capacity (Lo-Cap) sensors, following the same principle to obtain consistent results. This work presents an ANED version to run in real-time on μ Controller-based Lo-Cap sensors of a hybrid WASN, discriminating RTN from ANE through their Mel-based spectral energy differences. The experiments, considering 9 h and 8 min of real-life acoustic data from both urban and suburban environments, show the feasibility of the proposal both in terms of computational load and in classification accuracy. Specifically, the ANED Lo-Cap requires around 1 6 of the computational load of the ANED Hi-Cap, while classification accuracies are slightly lower (around 10%). However, preliminary analyses show that these results could be improved in around 4% in the future by means of considering optimal frequency selection.

  18. Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes.

    Directory of Open Access Journals (Sweden)

    Yunsheng Wang

    Full Text Available In this study, we identified and compared nucleotide-binding site (NBS domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China. Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.

  19. Human cDNA mapping using fluorescence in situ hybridization. Final progress report, April 1, 1994--July 31, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Korenberg, J.R.

    1997-12-31

    The ultimate goal of this research is to generate and apply novel technologies to speed completion and integration of the human genome map and sequence with biomedical problems. To do this, techniques were developed and genome-wide resources generated. This includes a genome-wide Mapped and Integrated BAC/PAC Resource that has been used for gene finding, map completion and anchoring, breakpoint definition and sequencing. In the last period of the grant, the Human Mapped BAC/PAC Resource was also applied to determine regions of human variation and to develop a novel paradigm of primate evolution through to humans. Further, in order to more rapidly evaluate animal models of human disease, a BAC Map of the mouse was generated in collaboration with the MTI Genome Center, Dr. Bruce Birren.

  20. The goya mouse mutant reveals distinct newly identified roles for MAP3K1 in the development and survival of cochlear sensory hair cells.

    Science.gov (United States)

    Parker, Andrew; Cross, Sally H; Jackson, Ian J; Hardisty-Hughes, Rachel; Morse, Susan; Nicholson, George; Coghill, Emma; Bowl, Michael R; Brown, Steve D M

    2015-12-01

    Mitogen-activated protein kinase, MAP3K1, plays an important role in a number of cellular processes, including epithelial migration during eye organogenesis. In addition, studies in keratinocytes indicate that MAP3K1 signalling through JNK is important for actin stress fibre formation and cell migration. However, MAP3K1 can also act independently of JNK in the regulation of cell proliferation and apoptosis. We have identified a mouse mutant, goya, which exhibits the eyes-open-at-birth and microphthalmia phenotypes. In addition, these mice also have hearing loss. The goya mice carry a splice site mutation in the Map3k1 gene. We show that goya and kinase-deficient Map3k1 homozygotes initially develop supernumerary cochlear outer hair cells (OHCs) that subsequently degenerate, and a progressive profound hearing loss is observed by 9 weeks of age. Heterozygote mice also develop supernumerary OHCs, but no cellular degeneration or hearing loss is observed. MAP3K1 is expressed in a number of inner-ear cell types, including outer and inner hair cells, stria vascularis and spiral ganglion. Investigation of targets downstream of MAP3K1 identified an increase in p38 phosphorylation (Thr180/Tyr182) in multiple cochlear tissues. We also show that the extra OHCs do not arise from aberrant control of proliferation via p27KIP1. The identification of the goya mutant reveals a signalling molecule involved with hair-cell development and survival. Mammalian hair cells do not have the ability to regenerate after damage, which can lead to irreversible sensorineural hearing loss. Given the observed goya phenotype, and the many diverse cellular processes that MAP3K1 is known to act upon, further investigation of this model might help to elaborate upon the mechanisms underlying sensory hair cell specification, and pathways important for their survival. In addition, MAP3K1 is revealed as a new candidate gene for human sensorineural hearing loss. © 2015. Published by The Company of

  1. A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq).

    Science.gov (United States)

    Recknagel, Hans; Elmer, Kathryn R; Meyer, Axel

    2013-01-01

    Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F(2) hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F(2) offspring, we calculated a genome-wide mutation rate of 6.6 × 10(-8) mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.

  2. Transcriptional profiles of hybrid Eucalyptus genotypes with contrasting lignin content reveal that monolignol biosynthesis-related genes regulate wood composition

    Directory of Open Access Journals (Sweden)

    Tomotaka eShinya

    2016-04-01

    Full Text Available Eucalyptus species constitutes the most widely planted hardwood trees in temperate and subtropical regions. In this study, we compared the transcript levels of genes involved in lignocellulose formation such as cellulose, hemicellulose and lignin biosynthesis in two selected three-year old hybrid Eucalyptus (Eucalyptus urophylla x E. grandis genotypes (AM063 and AM380 that have different lignin content. AM063 and AM380 had 20.2 and 35.5% of Klason lignin content and 59.0% and 48.2%, -cellulose contents, respectively. We investigated the correlation between wood properties and transcript levels of wood formation-related genes using RNA-seq with total RNAs extracted from developing xylem tissues at a breast height. Transcript levels of cell wall construction genes such as cellulose synthase (CesA and sucrose synthase (SUSY were almost the same in both genotypes. However, AM063 exhibited higher transcript levels of UDP-glucose pyrophosphorylase (UGP and xyloglucan endotransglucoxylase (XTH than those in AM380. Most monolignol biosynthesis- related isozyme genes showed higher transcript levels in AM380. These results indicate monolignol biosynthesis-related genes may regulate wood composition in Eucalyptus. Flavonoids contents were also observed at much higher levels in AM380 as a result of the elevated transcript levels of common phenylpropanoid pathway genes, phenylalanine ammonium lyase (PAL, cinnamate-4-hydroxylase (C4H and 4-coumarate-CoA ligase (4CL. Secondary plant cell wall formation is regulated by many transcription factors. We analyzed genes encoding NAC, WRKY, AP2/ERF and KNOX transcription factors and found higher transcript levels of these genes in AM380. We also observed increased transcription of some MYB and LIM domain transcription factors in AM380 compared to AM063. All these results show that genes related to monolignol biosynthesis may regulate the wood composition and help maintain the ratio of cellulose and lignin contents

  3. Physical mapping of the split hand/split foot (SHSF) locus on chromosome 7 reveals a relationship between SHSF and the syndromic ectrodactylies

    Energy Technology Data Exchange (ETDEWEB)

    Poorkaj, P.; Nunes, M.E.; Geshuri, D. [Univ. of Washington, Seattle, WA (United States)] [and others

    1994-09-01

    Split hand/split foot (also knows as ectrodactyly) is a human developmental malformation characterized by missing digits and claw-like extremities. An autosomal dominant form of this disorder has been mapped to 7q21.3-q22.1 on the basis of SHSF-associated chromosomal rearrangements: this locus has been designated SHFD1. We have constructed a physical map of the SHFD1 region that consists of contiguous yeast artificial chromosome clones and spans approximately 8 Mb. Somatic cell hybrid and fluorescent in situ hybridization analyses were used to define SHSF-associated chromosomal breakpoints in fourteen patients. A critical interval of about 1 Mb was established for SHFD1 by analysis of six patients with deletions. Translocation and inversion breakpoints in seven other patients were found to localize within a 500-700 kb interval within the critical region. Several candidate genes including DLX5 and DLX6 (members of the Drosophilia Distal-less homeobox-containing gene family) localize to this region. At least four of these genes are expressed in the developing mouse limb bud. Of particular interest is the observation that 8 of the 14 patients studied have syndromic ectrodactyly, which is characterized by the association of SHSF with a variety of other anomalies including cleft lip/palate, ectodermal dysplasia, and renal anomalies. Thus, these data implicate a single gene or cluster of genes at the SHFD1 locus in a wide range of developmental processes and serve to establish a molecular genetic relationship between simple SHSF and a broad group of human birth defects.

  4. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

    NARCIS (Netherlands)

    Zhang, Z.; Mao, L.; Chen, Junshi; Bu, F.; Li, G.; Sun, J.; Li, S.; Sun, H.; Jiao, C.; Blakely, R.; Pan, J.; Cai, R.; Luo, R.; Peer, Van de Y.; Jacobsen, E.; Fei, Z.; Huang, S.

    2015-01-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep

  5. The structure of pairwise correlation in mouse primary visual cortex reveals functional organization in the absence of an orientation map.

    Science.gov (United States)

    Denman, Daniel J; Contreras, Diego

    2014-10-01

    Neural responses to sensory stimuli are not independent. Pairwise correlation can reduce coding efficiency, occur independent of stimulus representation, or serve as an additional channel of information, depending on the timescale of correlation and the method of decoding. Any role for correlation depends on its magnitude and structure. In sensory areas with maps, like the orientation map in primary visual cortex (V1), correlation is strongly related to the underlying functional architecture, but it is unclear whether this correlation structure is an essential feature of the system or arises from the arrangement of cells in the map. We assessed the relationship between functional architecture and pairwise correlation by measuring both synchrony and correlated spike count variability in mouse V1, which lacks an orientation map. We observed significant pairwise synchrony, which was organized by distance and relative orientation preference between cells. We also observed nonzero correlated variability in both the anesthetized (0.16) and awake states (0.18). Our results indicate that the structure of pairwise correlation is maintained in the absence of an underlying anatomical organization and may be an organizing principle of the mammalian visual system preserved by nonrandom connectivity within local networks. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Fine Mapping of the Dominant Potyvirus Resistance Gene Pvr7 Reveals a Relationship with Pvr4 in Capsicum annuum.

    Science.gov (United States)

    Venkatesh, Jelli; An, Jeongtak; Kang, Won-Hee; Jahn, Molly; Kang, Byoung-Cheorl

    2018-01-01

    Pepper mottle virus (PepMoV) is the most common potyvirus infection of pepper plants and causes significant yield losses. The Pvr7 gene from Capsicum chinense PI159236 and the Pvr4 gene from C. annuum CM334 both have been reported to confer dominant resistance to PepMoV. The Pvr7 locus conferring resistance to PepMoV in C. annuum '9093' was previously mapped to chromosome 10. To develop a high-resolution map of the Pvr7 locus in 9093, we constructed an intraspecific F 2 mapping population consisting of 916 individuals by crossing PepMoV-resistant C. annuum '9093' and the PepMoV-susceptible C. annuum 'Jeju'. To delimit the Pvr7 target region, single-nucleotide polymorphism (SNP) markers derived from the Pvr4 region were used for genotyping the F 2 population. Molecular mapping delimited the Pvr7 locus to a physical interval of 258 kb, which was the same region as Pvr4 on chromosome 10. Three SNP markers derived from Pvr4 mapping perfectly cosegregated with PepMoV resistance. Sequencing analyses of the Pvr7 flanking markers and the Pvr4-specific gene indicated that Pvr7 and Pvr4 are the same gene. Resistance spectrum analysis of 9093 against pepper potyviruses showed that 9093 has a resistance spectrum similar to that of cultivar CM334. These combined results demonstrate that, unlike previously thought, the dominant PepMoV resistance in 9093 could be derived from C. annuum 'CM334', and that Pvr4 and Pvr7 should be considered as the same locus.

  7. A populational survey of 45S rDNA polymorphism in the Jefferson salamander Ambystoma jeffersonianum revealed by fluorescence in situ hybridization (FISH

    Directory of Open Access Journals (Sweden)

    Jinzhong FU

    2009-04-01

    Full Text Available The chromosomal localization of 45S ribosomal RNA genes in Ambystoma jeffersonianum was determined by fluorescence in situ hybridization with 18S rDNA fragment as a probe (FISH-rDNA. Our results revealed the presence of rDNA polymorphism among A.jeffersonianum populations in terms of number, location and FISH signal intensity on the chromosomes. Nine rDNA cytotypes were found in ten geographically isolated populations and most of them contained derivative rDNA sites. Our preliminary study provides strong indication of karyotypic diversification of A.jeffersonianum that is demonstrated by intraspecific variation of 45S rDNA cytotypes. rDNA cytotype polymorphism has been described in many other caudate amphibians. We predict that habitat isolation, low dispersal ability and decline of effective population size could facilitate the fixation and accumulation of variable rDNA cytotypes during their chromosome evolution.

  8. Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

    NARCIS (Netherlands)

    Glubb, Dylan M.; Maranian, Mel J.; Michailidou, Kyriaki; Pooley, Karen A.; Meyer, Kerstin B.; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A.; Hillman, Kristine M.; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L.; Southey, Melissa C.; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K.; Broeks, Annegien; Hogervorst, Frans B.; van der Schoot, C. Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A.; Ruebner, Matthias; Ekici, Arif B.; Beckmann, Matthias W.; Peto, Julian; Dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D. P.; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L.; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K.; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A.; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V.; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Wu, Anna H.; Tseng, Chiu-Chen; van den Berg, David; Stram, Daniel O.; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J.; Olson, Janet E.; Hallberg, Emily; Vachon, Celine; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M. Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L.; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A. E. M.; Seynaeve, Caroline; van Asperen, Christi J.; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W. M.; Collée, J. Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S.; Reed, Malcolm W. R.; Blot, William; Signorello, Lisa B.; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E.; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M. Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S.; Brown, Melissa A.; Ponder, Bruce A. J.; Chenevix-Trench, Georgia; Thompson, Deborah J.; Edwards, Stacey L.; Easton, Douglas F.; Dunning, Alison M.; French, Juliet D.

    2015-01-01

    Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and

  9. Fine-scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1

    NARCIS (Netherlands)

    D.M. Glubb (Dylan); M. Maranian (Melanie); K. Michailidou (Kyriaki); K.A. Pooley (Karen); K.B. Meyer (Kerstin); S. Kar (Siddhartha); A.F.C. Carlebur; M. O'Reilly (Marian); J.A. Betts (Joshua); K.M. Hillman (Kristine); S. Kaufmann (Susanne); J. Beesley (Jonathan); S. Canisius (Sander); J.L. Hopper (John); M.C. Southey (Melissa); H. Tsimiklis (Helen); C. Apicella (Carmel); M.K. Schmidt (Marjanka); A. Broeks (Annegien); F.B.L. Hogervorst (Frans); C.E. van der Schoot (Ellen); K.R. Muir (K.); A. Lophatananon (Artitaya); S. Stewart-Brown (Sarah); P. Siriwanarangsan (Pornthep); P.A. Fasching (Peter); M. Ruebner (Matthias); A.B. Ekici (Arif); M.W. Beckmann (Matthias); J. Peto (Julian); I. dos Santos Silva (Isabel); O. Fletcher (Olivia); N. Johnson (Nichola); P.D.P. Pharoah (Paul D.P.); M.K. Bolla (Manjeet); Q. Wang (Qing); J. Dennis (Joe); E.J. Sawyer (Elinor); I.P. Tomlinson (Ian); M. Kerin (Michael); N. Miller (Nicola); B. Burwinkel (Barbara); F. Marme (Federick); R. Yang (Rongxi); H. Surowy (Harald); P. Guénel (Pascal); T. Truong (Thérèse); F. Menegaux (Florence); M. Sanchez (Marie); S.E. Bojesen (Stig); B.G. Nordestgaard (Børge); S.F. Nielsen (Sune); H. Flyger (Henrik); A. González-Neira (Anna); J. Benítez (Javier); M.P. Zamora (Pilar); J.I. Arias Pérez (José Ignacio); H. Anton-Culver (Hoda); S.L. Neuhausen (Susan); H. Brenner (Hermann); A.K. Dieffenbach (Aida Karina); V. Arndt (Volker); C. Stegmaier (Christa); A. Meindl (Alfons); R.K. Schmutzler (Rita); H. Brauch (Hiltrud); Y.-D. Ko (Yon-Dschun); T. Brüning (Thomas); H. Nevanlinna (Heli); T.A. Muranen (Taru); K. Aittomäki (Kristiina); C. Blomqvist (Carl); K. Matsuo (Keitaro); H. Ito (Hidemi); H. Iwata (Hisato); H. Tanaka (Hideo); T. Dörk (Thilo); N.V. Bogdanova (Natalia); S. Helbig (Sonja); A. Lindblom (Annika); S. Margolin (Sara); A. Mannermaa (Arto); V. Kataja (Vesa); V-M. Kosma (Veli-Matti); J.M. Hartikainen (J.); A.H. Wu (Anna H.); C.-C. Tseng (Chiu-Chen); D. Van Den Berg (David); D.O. Stram (Daniel O.); D. Lambrechts (Diether); H. Zhao (Hui); C. Weltens (Caroline); E. van Limbergen (Erik); J. Chang-Claude (Jenny); D. Flesch-Janys (Dieter); A. Rudolph (Anja); P. Seibold (Petra); P. Radice (Paolo); P. Peterlongo (Paolo); M. Barile (Monica); F. Capra (Fabio); F.J. Couch (Fergus); J.E. Olson (Janet); B. Hallberg (Boubou); C. Vachon (Celine); G.G. Giles (Graham); R.L. Milne (Roger); C.A. McLean (Catriona Ann); C.A. Haiman (Christopher); B.E. Henderson (Brian); F.R. Schumacher (Fredrick); L. Le Marchand (Loic); J. Simard (Jacques); M.S. Goldberg (Mark); F. Labrèche (France); M. Dumont (Martine); S.-H. Teo (Soo-Hwang); C.H. Yip (Cheng Har); M.-H. See (Mee-Hoong); B.K. Cornes (Belinda); C-Y. Cheng (Ching-Yu); M.K. Ikram (Kamran); V. Kristensen (Vessela); W. Zheng (Wei); S.L. Halverson (Sandra L.); M. Shrubsole (Martha); J. Long (Jirong); R. Winqvist (Robert); K. Pykäs (Katri); A. Jukkola-Vuorinen (Arja); S. Kauppila (Saila); I.L. Andrulis (Irene); J.A. Knight (Julia); G. Glendon (Gord); S. Tchatchou (Sandrine); P. Devilee (Peter); R.A.E.M. Tollenaar (Rob); C.M. Seynaeve (Caroline); C.J. van Asperen (Christi); M. García-Closas (Montserrat); J.D. Figueroa (Jonine); S.J. Chanock (Stephen); J. Lissowska (Jolanta); K. Czene (Kamila); D. Klevebring (Daniel); H. Darabi (Hatef); M. Eriksson (Mikael); M.J. Hooning (Maartje); A. Hollestelle (Antoinette); J.W.M. Martens (John W. M.); J.M. Collée (Margriet); P. Hall (Per); J. Li (Jingmei); K. Humphreys (Keith); X.-O. Shu (Xiao-Ou); W. Lu (Wei); Y.-T. Gao (Yu-Tang); H. Cai (Hui); A. Cox (Angela); S.S. Cross (Simon); M.W.R. Reed (Malcolm); W.J. Blot (William); L.B. Signorello (Lisa B.); Q. Cai (Qiuyin); M. Shah (Mitul); M. Ghoussaini (Maya); D. Kang (Daehee); J.-Y. Choi (J.); S.K. Park (Sue); D-Y. Noh (Dong-Young); M. Hartman (Mikael); X. Miao; W.-Y. Lim (Wei-Yen); A. Tang (Anthony); U. Hamann (Ute); D. Torres (Diana); A. Jakubowska (Anna); J. Lubinski (Jan); K. Jaworska (Katarzyna); K. Durda (Katarzyna); S. Sangrajrang (Suleeporn); V. Gaborieau (Valerie); P. Brennan (Paul); J.D. McKay (James); C. Olswold (Curtis); S. Slager (Susan); A.E. Toland (Amanda); D. Yannoukakos (Drakoulis); C-Y. Shen (Chen-Yang); P.-E. Wu (Pei-Ei); J-C. Yu (Jyh-Cherng); M.-F. Hou (Ming-Feng); A.J. Swerdlow (Anthony ); A. Ashworth (Alan); N. Orr (Nick); M. Jones (Michael); G. Pita (Guillermo); M.R. Alonso (Rosario); N. Álvarez (Nuria); D. Herrero (Daniel); D.C. Tessier (Daniel C.); D. Vincent (Daniel); F. Bacot (Francois); C. Luccarini (Craig); C. Baynes (Caroline); S. Ahmed (Shahana); S. Healey (Sue); M. Brown (Melissa); B.A.J. Ponder (Bruce A.J.); G. Chenevix-Trench (Georgia); D. Thompson (Deborah); S.L. Edwards (Stacey); D.F. Easton (Douglas); A.M. Dunning (Alison); J.D. French (Juliet)

    2015-01-01

    textabstractGenome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer

  10. Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

    Science.gov (United States)

    Traverse, Charles C; Ochman, Howard

    2017-08-29

    Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola , which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. IMPORTANCE The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions-errors that potentially have more dire effects on protein function-is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions

  11. Feasibility of mapping low-multiplicity genes by in situ hybridization. [/sup 125/I and tritium tracers

    Energy Technology Data Exchange (ETDEWEB)

    Atwood, K C; Henderson, A S; Kacian, D; Eicher, E M

    1975-01-01

    The assignment of human hemoglobin loci to 2q and Bq was followed by objections based on the low specific activity of their /sup 3/H-mRNA, estimated as somewhere between 100 and 1000 dpm/..mu..g. With that preparation, the time required for one disintegration per molecule is between 80,000 and 8000 years. The consideration that globin loci may contain as many as 10 copies does not help. In view of these incontestably valid objections, it is instructive to compare the foregoing experiment with another in which the chromosomes were hybridized with cDNA copied from human reticulocyte mRNA by means of the reverse transcriptase from avian myeloblastosis virus. Our preparation had a specific activity of 1.4 x 10/sup 8/ dpm/..mu..g, requiring less than a month per disintegration per molecule. Despite the rather more favorable anticipated exposure time, successful localization was by no means expected. The use of cDNA precluded the enzymatic removal of background; the concentration of DNA applied to the slides, 0.03 ..mu..g/ml, was unfavorable for hybridization; and the copying reaction, primed with oligo-dT, probably attached stretches up to T/sub 20/ to the structural sequence, with the possibility that these might hybridize to uninteresting chromosomal regions. Results indicate that the original assignments of the human globin loci are correct.

  12. Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity.

    Science.gov (United States)

    King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

    2013-10-01

    Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring 'nontoxic' provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F₂ mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F₂ plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. © 2013 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  13. A hybrid model for mapping relative differences in belowground biomass and root: Shoot ratios using spectral reflectance, foliar N and plant biophysical data within coastal marsh

    Science.gov (United States)

    Jessica L. O'Connell,; Byrd, Kristin B.; Maggi Kelly,

    2015-01-01

    Broad-scale estimates of belowground biomass are needed to understand wetland resiliency and C and N cycling, but these estimates are difficult to obtain because root:shoot ratios vary considerably both within and between species. We used remotely-sensed estimates of two aboveground plant characteristics, aboveground biomass and % foliar N to explore biomass allocation in low diversity freshwater impounded peatlands (Sacramento-San Joaquin River Delta, CA, USA). We developed a hybrid modeling approach to relate remotely-sensed estimates of % foliar N (a surrogate for environmental N and plant available nutrients) and aboveground biomass to field-measured belowground biomass for species specific and mixed species models. We estimated up to 90% of variation in foliar N concentration using partial least squares (PLS) regression of full-spectrum field spectrometer reflectance data. Landsat 7 reflectance data explained up to 70% of % foliar N and 67% of aboveground biomass. Spectrally estimated foliar N or aboveground biomass had negative relationships with belowground biomass and root:shoot ratio in both Schoenoplectus acutus and Typha, consistent with a balanced growth model, which suggests plants only allocate growth belowground when additional nutrients are necessary to support shoot development. Hybrid models explained up to 76% of variation in belowground biomass and 86% of variation in root:shoot ratio. Our modeling approach provides a method for developing maps of spatial variation in wetland belowground biomass.

  14. Atrial fibrillation driven by micro-anatomic intramural re-entry revealed by simultaneous sub-epicardial and sub-endocardial optical mapping in explanted human hearts.

    Science.gov (United States)

    Hansen, Brian J; Zhao, Jichao; Csepe, Thomas A; Moore, Brandon T; Li, Ning; Jayne, Laura A; Kalyanasundaram, Anuradha; Lim, Praise; Bratasz, Anna; Powell, Kimerly A; Simonetti, Orlando P; Higgins, Robert S D; Kilic, Ahmet; Mohler, Peter J; Janssen, Paul M L; Weiss, Raul; Hummel, John D; Fedorov, Vadim V

    2015-09-14

    The complex architecture of the human atria may create physical substrates for sustained re-entry to drive atrial fibrillation (AF). The existence of sustained, anatomically defined AF drivers in humans has been challenged partly due to the lack of simultaneous endocardial-epicardial (Endo-Epi) mapping coupled with high-resolution 3D structural imaging. Coronary-perfused human right atria from explanted diseased hearts (n = 8, 43-72 years old) were optically mapped simultaneously by three high-resolution CMOS cameras (two aligned Endo-Epi views (330 µm2 resolution) and one panoramic view). 3D gadolinium-enhanced magnetic resonance imaging (GE-MRI, 80 µm3 resolution) revealed the atrial wall structure varied in thickness (1.0 ± 0.7-6.8 ± 2.4 mm), transmural fiber angle differences, and interstitial fibrosis causing transmural activation delay from 23 ± 11 to 43 ± 22 ms at increased pacing rates. Sustained AF (>90 min) was induced by burst pacing during pinacidil (30-100 µM) perfusion. Dual-sided sub-Endo-sub-Epi optical mapping revealed that AF was driven by spatially and temporally stable intramural re-entry with 107 ± 50 ms cycle length and transmural activation delay of 67 ± 31 ms. Intramural re-entrant drivers were captured primarily by sub-Endo mapping, while sub-Epi mapping visualized re-entry or 'breakthrough' patterns. Re-entrant drivers were anchored on 3D micro-anatomic tracks (15.4 ± 2.2 × 6.0 ± 2.3 mm2, 2.9 ± 0.9 mm depth) formed by atrial musculature characterized by increased transmural fiber angle differences and interstitial fibrosis. Targeted radiofrequency ablation of the tracks verified these re-entries as drivers of AF. Integrated 3D structural-functional mapping of diseased human right atria ex vivo revealed that the complex atrial microstructure caused significant differences between Endo vs. Epi activation during pacing and sustained AF driven by intramural re-entry anchored to fibrosis-insulated atrial bundles. Published on

  15. Mapping of tecto-lineaments and investigate their association with earthquakes in Egypt: a hybrid approach using remote sensing data

    Directory of Open Access Journals (Sweden)

    Samy Ismail Elmahdy

    2016-03-01

    Full Text Available This study integrates quantitative methods to detect surface and near-surface geological linear structures from digital elevation model. A set of altitude, slope and shaded relief maps was enhanced by applying Sobel filter with 10% threshold and percentile stretch to detect geological fractures and their displacements over regional scale. Topographic fabric grain algorithm, which classifies point lines into the ridge/valley and quantifies the degree to which all the ridges and valleys are aligned in the same direction, was used to auto-detect lineaments. About 1300 linear features were computed and their orientations were statistically analysed using rose diagrams. The enhanced morphometric maps successfully visualized fault zones and their displacements and detected the regional fault zones cutting across the entire Egypt. Their trends were found to be in the NE–SW, NNE–SSW, NW–SE, NNW–SSE, N–S, E–W and WNW–ESE directions. The results obtained using the integrated methods were compared with those in geological and seismic maps of Egypt and showed strong agreement in several places. This proposed method may be useful for mapping concealed geological structures, where geophysical surveying is difficult and geological information not available.

  16. Change point analysis of travel routes reveals novel insights into foraging strategies and cognitive maps of wild baboons.

    Science.gov (United States)

    Noser, Rahel; Byrne, Richard W

    2014-05-01

    Efficient space use is a critical challenge for animals relying on stationary resources. It is often difficult with purely observational methods to gain unambiguous insight into any ability of primates to manage and process spatial information. Investigating the visible signs of the decision processes underlying space use often leaves open important issues. We applied the change point test [Byrne et al. (2009). Anim Behav 77: 619-631], a statistical tool to objectively determine change points (CPs) in animal travel paths, to investigate to what degree directional changes in our study group's (Papio ursinus) dry season ranging were associated with important resources and prominent landmarks. One-third of directional changes were associated with fruit feeding, 1/3 with traveling, and 1/3 with dry matter feeding, travel feeding and with drinking. When directional changes were associated with traveling, the subsequent directional changes were likely to result in fruit feeding. Fruit feeding mostly occurred at the apex of the day journeys, while drinking, dry matter feeding, and travel feeding often occurred along straight travel segments. The majority of directional changes did not occur in clusters at distinctive locations, but at distances of more than 120 m apart from each other, many of them along prominent landmarks. We conclude that the CPs do not represent nodes or route bends of a network map. Rather, they represent (1) locations where the decision to turn back to their sleeping site was taken, and (2) locations next to important landmarks (changes of slope, car tracks) where slight adjustment of a movement direction was possible. We found no evidence for a Euclidean map and discuss our findings in the light of a network map representation of space. © 2013 Wiley Periodicals, Inc.

  17. Hybrid perovskite solar cells: In situ investigation of solution-processed PbI2 reveals metastable precursors and a pathway to producing porous thin films

    KAUST Repository

    Barrit, Dounya

    2017-04-17

    The successful and widely used two-step process of producing the hybrid organic-inorganic perovskite CH3NH3PbI3, consists of converting a solution deposited PbI2 film by reacting it with CH3NH3I. Here, we investigate the solidification of PbI2 films from a DMF solution by performing in situ grazing incidence wide angle X-ray scattering (GIWAXS) measurements. The measurements reveal an elaborate sol–gel process involving three PbI2⋅DMF solvate complexes—including disordered and ordered ones—prior to PbI2 formation. The ordered solvates appear to be metastable as they transform into the PbI2 phase in air within minutes without annealing. Morphological analysis of air-dried and annealed films reveals that the air-dried PbI2 is substantially more porous when the coating process produces one of the intermediate solvates, making this more suitable for subsequent conversion into the perovskite phase. The observation of metastable solvates on the pathway to PbI2 formation open up new opportunities for influencing the two-step conversion of metal halides into efficient light harvesting or emitting perovskite semiconductors.

  18. A genome-wide RNAi screen reveals MAP kinase phosphatases as key ERK pathway regulators during embryonic stem cell differentiation.

    Directory of Open Access Journals (Sweden)

    Shen-Hsi Yang

    Full Text Available Embryonic stem cells and induced pluripotent stem cells represent potentially important therapeutic agents in regenerative medicine. Complex interlinked transcriptional and signaling networks control the fate of these cells towards maintenance of pluripotency or differentiation. In this study we have focused on how mouse embryonic stem cells begin to differentiate and lose pluripotency and, in particular, the role that the ERK MAP kinase and GSK3 signaling pathways play in this process. Through a genome-wide siRNA screen we have identified more than 400 genes involved in loss of pluripotency and promoting the onset of differentiation. These genes were functionally associated with the ERK and/or GSK3 pathways, providing an important resource for studying the roles of these pathways in controlling escape from the pluripotent ground state. More detailed analysis identified MAP kinase phosphatases as a focal point of regulation and demonstrated an important role for these enzymes in controlling ERK activation kinetics and subsequently determining early embryonic stem cell fate decisions.

  19. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

    Science.gov (United States)

    Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

    2012-01-01

    A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

  20. Spatiotemporal maps reveal regional differences in the effects on gut motility for Lactobacillus reuteri and rhamnosus strains.

    Science.gov (United States)

    Wu, R Y; Pasyk, M; Wang, B; Forsythe, P; Bienenstock, J; Mao, Y-K; Sharma, P; Stanisz, A M; Kunze, W A

    2013-03-01

    Commensal bacteria such as probiotics that are neuroactive acutely affect the amplitudes of intestinal migrating motor complexes (MMCs). What is lacking for an improved understanding of these motility effects are region specific measurements of velocity and frequency. We have combined intraluminal pressure recordings with spatiotemporal diameter maps to analyze more completely effects of different strains of beneficial bacteria on motility. Intraluminal peak pressure (PPr) was measured and video recordings made of mouse ex vivo jejunum and colon segments before and after intraluminal applications of Lactobacillus rhamnosus (JB-1) or Lactobacillus reuteri (DSM 17938). Migrating motor complex frequency and velocity were calculated. JB-1 decreased jejunal frequencies by 56% and 34% in colon. Jejunal velocities increased 171%, but decreased 31% in colon. Jejunal PPr decreased by 55% and in colon by 21%. DSM 17938 increased jejunal frequencies 63% and in colon 75%; jejunal velocity decreased 57%, but increased in colon 146%; jejunal PPr was reduced 26% and 12% in colon. TRAM-34 decreased frequency by 71% and increased velocity 200% for jejunum, but increased frequency 46% and velocity 50% for colon; PPr was decreased 59% for jejunum and 39% for colon. The results show that probiotics and other beneficial bacteria have strain and region-specific actions on gut motility that can be successfully discriminated using spatiotemporal mapping of diameter changes. Effects are not necessarily the same in colon and jejunum. Further research is needed on the detailed effects of the strains on enteric neuron currents for each gut region. © 2013 Blackwell Publishing Ltd.

  1. Fine-scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1

    DEFF Research Database (Denmark)

    Glubb, Dylan M; Maranian, Mel J; Michailidou, Kyriaki

    2015-01-01

    evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10(-5)]) and five variants composing iCHAV3 (lead rs11949391; ER(+): OR = 0.90, 95% CI = 0.87-0.93, pcond = 1.4 × 10(-4)). Twenty-six percent......CHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3...

  2. Mapping of Saccharomyces cerevisiae metabolites in fermenting wheat straight-dough reveals succinic acid as pH-determining factor.

    Science.gov (United States)

    Jayaram, Vinay B; Cuyvers, Sven; Lagrain, Bert; Verstrepen, Kevin J; Delcour, Jan A; Courtin, Christophe M

    2013-01-15

    Fermenting yeast does not merely cause dough leavening, but also contributes to the bread aroma and might alter dough rheology. Here, the yeast carbon metabolism was mapped during bread straight-dough fermentation. The concentration of most metabolites changed quasi linearly as a function of fermentation time. Ethanol and carbon dioxide concentrations reached up to 60 mmol/100g flour. Interestingly, high levels of glycerol (up to 10 mmol/100g flour) and succinic acid (up to 1.6 mmol/100g flour) were produced during dough fermentation. Further tests showed that, contrary to current belief, the pH decrease in fermenting dough is primarily caused by the production of succinic acid by the yeast instead of carbon dioxide dissolution or bacterial organic acids. Together, our results provide a comprehensive overview of metabolite production during dough fermentation and yield insight into the importance of some of these metabolites for dough properties. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. Brain regions involved in voluntary movements as revealed by radioisotopic mapping of CBF or CMR-glucose changes

    DEFF Research Database (Denmark)

    Lassen, N A; Ingvar, D H

    1990-01-01

    Mapping of cortical and subcortical grey matter active during voluntary movements by means of measurements of local increases of CBF or CMR-Glucose is reviewed. Most of the studies concern observations in man during hand movements using the intracarotid Xenon-133 injection technique, an approach...... that only allows to image the cortex of the hemisphere on one side (the injected side) of the brain. The results show that simple static or repetitive movements mainly activate the contralateral primary hand area (MI and SI); complex preprogrammed or spontaneous purposeful movements the supplementary motor...... area SMA on both sides increase in CBF/CMR-glucose and even internally ("mentally") going through the trained movements, causes such changes; complex purposeful movements also activate the premotor cortex, a response that is bilateral with greatest response contralaterally. Studies in patients...

  4. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash

    Science.gov (United States)

    Holdsworth, William L.; LaPlant, Kyle E.; Bell, Duane C.; Jahn, Molly M.; Mazourek, Michael

    2016-01-01

    Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection. PMID:27936008

  5. Fine mapping of shattering locus Br2 reveals a putative chromosomal inversion polymorphism between the two lineages of Aegilops tauschii.

    Science.gov (United States)

    Zhang, Zhengzhi; Zhu, Huilan; Gill, Bikram S; Li, Wanlong

    2015-04-01

    This work laid the foundation for cloning of shattering gene Br2 and provided first line of evidence that two major Aegilops tauschii lineages are differentiated by an inversion polymorphism. Chromosome inversions often accompany population differentiation and capture local adaptation during speciation. Aegilops tauschii, the D-genome donor species of hexaploid wheat, consists of two genetically isolated lineages, L1 and L2, but little is known about the genetic mechanisms underlying the population differentiation in this diploid species. During fine mapping of the shattering gene Br2 using a large F2 population derived from a cross between TA1604 (an L1 accession) and AL8/78 (an L2 accession), we found contrasting patterns of crossover distribution in the Br2 interval and neighboring regions despite the high local gene synteny with Brachypodium distachyon and rice. Br2 was localized in a 0.08-cM interval, and 13 marker loci formed a block, where single-crossovers were completely suppressed, but double-crossovers were enriched with a recombination rate of ~11 cM/Mb. In contrast, in a neighboring region no double-crossover was recovered, but single-crossover rate reached 24 cM/Mb, which is much higher than the genome-wide average. This result suggests a putative inversion polymorphism between the parental lines in the Br2 region. Genotyping using the markers from the Br2 region divided a collection of 55 randomly sampled A. tauschii accessions into two major groups, and they are largely genetically isolated. The two groups correspond to the L1 and L2 lineages based on their geographic distribution patterns. This provides first evidence that inversions may underlie the evolution of A. tauschii lineages. The presence of inter-lineage inversions may complicate map-based cloning in A. tauschii and transfer of useful traits to wheat.

  6. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max reveals extensive chromosome rearrangements in the genus Glycine.

    Directory of Open Access Journals (Sweden)

    Sungyul Chang

    Full Text Available Soybean (Glycine max L. Mer., like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth. Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib. de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L. chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean

  7. Cultivar-Based Introgression Mapping Reveals Wild Species-Derived Pm-0, the Major Powdery Mildew Resistance Locus in Squash.

    Science.gov (United States)

    Holdsworth, William L; LaPlant, Kyle E; Bell, Duane C; Jahn, Molly M; Mazourek, Michael

    2016-01-01

    Powdery mildew is a major fungal disease on squash and pumpkin (Cucurbita spp.) in the US and throughout the world. Genetic resistance to the disease is not known to occur naturally within Cucurbita pepo and only infrequently in Cucurbita moschata, but has been achieved in both species through the introgression of a major resistance gene from the wild species Cucurbita okeechobeensis subsp. martinezii. At present, this gene, Pm-0, is used extensively in breeding, and is found in nearly all powdery mildew-resistant C. pepo and C. moschata commercial cultivars. In this study, we mapped C. okeechobeensis subsp. martinezii-derived single nucleotide polymorphism (SNP) alleles in a set of taxonomically and morphologically diverse and resistant C. pepo and C. moschata cultivars bred at Cornell University that, by common possession of Pm-0, form a shared-trait introgression panel. High marker density was achieved using genotyping-by-sequencing, which yielded over 50,000 de novo SNP markers in each of the three Cucurbita species genotyped. A single 516.4 kb wild-derived introgression was present in all of the resistant cultivars and absent in a diverse set of heirlooms that predated the Pm-0 introgression. The contribution of this interval to powdery mildew resistance was confirmed by association mapping in a C. pepo cultivar panel that included the Cornell lines, heirlooms, and 68 additional C. pepo cultivars and with an independent F2 population derived from C. okeechobeensis subsp. martinezii x C. moschata. The interval was refined to a final candidate interval of 76.4 kb and CAPS markers were developed inside this interval to facilitate marker-assisted selection.

  8. Autozygosity mapping of a large consanguineous Pakistani family reveals a novel non-syndromic autosomal recessive mental retardation locus on 11p15-tel

    DEFF Research Database (Denmark)

    Rehman, Shoaib ur; Baig, Shahid Mahmood; Eiberg, Hans

    2011-01-01

    done in all sampled individuals in the family. The nuclear central loop in the five generation family showed homozygosity for a 6-Mb telomeric region on 11p15, whereas all other linkage regions were excluded by calculation of logarithm of odds (LOD) for the SNP microarray data. A maximum LOD score of Z......Autosomal recessive inherited mental retardation is an extremely heterogeneous disease and accounts for approximately 25% of all non-syndromic mental retardation cases. Autozygosity mapping of a large consanguineous Pakistani family revealed a novel locus for non-syndromic autosomal recessive...

  9. Improved Culture Medium (TiKa) for Mycobacterium avium Subspecies Paratuberculosis (MAP) Matches qPCR Sensitivity and Reveals Significant Proportions of Non-viable MAP in Lymphoid Tissue of Vaccinated MAP Challenged Animals

    DEFF Research Database (Denmark)

    Bull, Tim J.; Munshil, Tulika; Melvang, Heidi Mikkelsen

    2017-01-01

    The quantitative detection of viable pathogen load is an important tool in determining the degree of infection in animals and contamination of foodstuffs. Current conventional culture methods are limited in their ability to determine these levels in Mycobacterium avium subspecies paratuberculosis......Ka culture equates well with qPCR and provides important evidence that accuracy in estimating viable MAP load using DNA tests alone may vary significantly between samples of mucosal and lymphatic origin....... (MAP) due to slow growth, clumping and low recoverability issues. The principle goal of this study was to evaluate a novel culturing process (TiKa) with unique ability to stimulate MAP growth from low sample loads and dilutions. We demonstrate it was able to stimulate a mean 29-fold increase...

  10. Family-based linkage and association mapping reveals novel genes affecting Plum pox virus infection in Arabidopsis thaliana.

    Science.gov (United States)

    Pagny, Gaëlle; Paulstephenraj, Pauline S; Poque, Sylvain; Sicard, Ophélie; Cosson, Patrick; Eyquard, Jean-Philippe; Caballero, Mélodie; Chague, Aurélie; Gourdon, Germain; Negrel, Lise; Candresse, Thierry; Mariette, Stéphanie; Decroocq, Véronique

    2012-11-01

    Sharka is a devastating viral disease caused by the Plum pox virus (PPV) in stone fruit trees and few sources of resistance are known in its natural hosts. Since any knowledge gained from Arabidopsis on plant virus susceptibility factors is likely to be transferable to crop species, Arabidopsis's natural variation was searched for host factors essential for PPV infection. To locate regions of the genome associated with susceptibility to PPV, linkage analysis was performed on six biparental populations as well as on multiparental lines. To refine quantitative trait locus (QTL) mapping, a genome-wide association analysis was carried out using 147 Arabidopsis accessions. Evidence was found for linkage on chromosomes 1, 3 and 5 with restriction of PPV long-distance movement. The most relevant signals occurred within a region at the bottom of chromosome 3, which comprises seven RTM3-like TRAF domain-containing genes. Since the resistance mechanism analyzed here is recessive and the rtm3 knockout mutant is susceptible to PPV infection, it suggests that other gene(s) present in the small identified region encompassing RTM3 are necessary for PPV long-distance movement. In consequence, we report here the occurrence of host factor(s) that are indispensable for virus long-distance movement. © 2012 INRA. New Phytologist © 2012 New Phytologist Trust.

  11. Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

    Energy Technology Data Exchange (ETDEWEB)

    Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak P.; Woodruff, Teresa K.; O' Halloran, Thomas V.

    2014-12-15

    Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes

  12. Granger causality mapping during joint actions reveals evidence for forward models that could overcome sensory-motor delays.

    Directory of Open Access Journals (Sweden)

    Idil Kokal

    Full Text Available Studies investigating joint actions have suggested a central role for the putative mirror neuron system (pMNS because of the close link between perception and action provided by these brain regions [1], [2], [3]. In contrast, our previous functional magnetic resonance imaging (fMRI experiment demonstrated that the BOLD response of the pMNS does not suggest that it directly integrates observed and executed actions during joint actions [4]. To test whether the pMNS might contribute indirectly to the integration process by sending information to brain areas responsible for this integration (integration network, here we used Granger causality mapping (GCM [5]. We explored the directional information flow between the anterior sites of the pMNS and previously identified integrative brain regions. We found that the left BA44 sent more information than it received to both the integration network (left thalamus, right middle occipital gyrus and cerebellum and more posterior nodes of the pMNS (BA2. Thus, during joint actions, two anatomically separate networks therefore seem effectively connected and the information flow is predominantly from anterior to posterior areas of the brain. These findings suggest that the pMNS is involved indirectly in joint actions by transforming observed and executed actions into a common code and is part of a generative model that could predict the future somatosensory and visual consequences of observed and executed actions in order to overcome otherwise inevitable neural delays.

  13. Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea Using QTL-seq Reveals Markers for Marker-Assisted Selection

    Directory of Open Access Journals (Sweden)

    Josh Clevenger

    2018-02-01

    Full Text Available Late leaf spot (LLS; Cercosporidium personatum is a major fungal disease of cultivated peanut (Arachis hypogaea. A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

  14. Fluorescence in situ hybridization mapping of six loci containing genes involved in the dioxin metabolism of domestic bovids.

    Science.gov (United States)

    Genualdo, Viviana; Spalenza, Veronica; Perucatti, Angela; Iannuzzi, Alessandra; Di Meo, Giulia Pia; Caputi-Jambrenghi, Annamaria; Vonghia, Gino; Rasero, Roberto; Nebbia, Carlo; Sacchi, Paola; Iannuzzi, Leopoldo

    2011-05-01

    Six loci containing genes involved in the dioxin metabolism (ARNT, AHR, CYP1A1, CYP1A2, CYP1B1 and AHRR) were assigned, for the first time, to cattle (Bos taurus, 2n = 60, BTA), river buffalo (Bubalus bubalis, 2n = 50, BBU), sheep (Ovis aries, 2n = 54, OAR) and goat (Capra hircus, 2n = 60, CHI) chromosomes by comparative FISH-mapping and R-banding using bovine BAC-clones. The following chromosome locations were found: ARNT to BTA3q21, BBU6q21, OAR1p21 and CHI3q21, AHR to BTA4q15, BBU8q15, OAR4q15 and CHI4q15; CYP1A1 and CYP1A2 to BTA21q17, BBU20q17, OAR18q17 and CHI21q17; CYP1B1 to BTA11q16, BBU12q22, OAR3p16 and CHI11q16, AHRR to BTA20q24, BBU19q24, OAR16q24 and CHI20q24. All loci were mapped at the same homoeologous chromosomes and chromosome bands of the four bovid species. Comparisons with corresponding human locations were also reported.

  15. Growth and mass wasting of volcanic centers in the northern South Sandwich arc, South Atlantic, revealed by new multibeam mapping

    OpenAIRE

    Leat, Philip T.; Tate, Alex J.; Tappin, David R.; Day, Simon J.; Owen, Matthew J.

    2010-01-01

    New multibeam (swath) bathymetric sonar data acquired using an EM120 system on the RRS James Clark Ross, supplemented by sub-bottom profiling, reveals the underwater morphology of a not, vert, similar 12,000 km2 area in the northern part of the mainly submarine South Sandwich volcanic arc. The new data extend between 55° 45′S and 57° 20′S and include Protector Shoal and the areas around Zavodovski, Visokoi and the Candlemas islands groups. Each of these areas is a discrete volcanic center. T...

  16. Mapping of PARK2 and PACRG overlapping regulatory region reveals LD structure and functional variants in association with leprosy in unrelated indian population groups.

    Science.gov (United States)

    Chopra, Rupali; Ali, Shafat; Srivastava, Amit K; Aggarwal, Shweta; Kumar, Bhupender; Manvati, Siddharth; Kalaiarasan, Ponnusamy; Jena, Mamta; Garg, Vijay K; Bhattacharya, Sambit N; Bamezai, Rameshwar N K

    2013-01-01

    Leprosy is a chronic infectious disease caused by Mycobacterium Leprae, where the host genetic background plays an important role toward the disease pathogenesis. Various studies have identified a number of human genes in association with leprosy or its clinical forms. However, non-replication of results has hinted at the heterogeneity among associations between different population groups, which could be due to differently evolved LD structures and differential frequencies of SNPs within the studied regions of the genome. A need for systematic and saturated mapping of the associated regions with the disease is warranted to unravel the observed heterogeneity in different populations. Mapping of the PARK2 and PACRG gene regulatory region with 96 SNPs, with a resolution of 1 SNP per 1 Kb for PARK2 gene regulatory region in a North Indian population, showed an involvement of 11 SNPs in determining the susceptibility towards leprosy. The association was replicated in a geographically distinct and unrelated population from Orissa in eastern India. In vitro reporter assays revealed that the two significantly associated SNPs, located 63.8 kb upstream of PARK2 gene and represented in a single BIN of 8 SNPs, influenced the gene expression. A comparison of BINs between Indian and Vietnamese populations revealed differences in the BIN structures, explaining the heterogeneity and also the reason for non-replication of the associated genomic region in different populations.

  17. High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

    Science.gov (United States)

    Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

    2012-08-01

    Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

  18. Mapping the human translation elongation factor eEF1H complex using the yeast two-hybrid system

    DEFF Research Database (Denmark)

    Mansilla, Francisco; Friis, Irene; Jadidi, Mandana

    2002-01-01

    In eukaryotes, the eukaryotic translation elongation factor eEF1A responsible for transporting amino-acylated tRNA to the ribosome forms a higher-order complex, eEF1H, with its guanine-nucleotide-exchange factor eEF1B. In metazoans, eEF1B consists of three subunits: eEF1B alpha, eEF1B eta and eEF1B...... of in vitro experiments have been proposed for the macromolecular organization of the eEF1H complex. However, these models differ in various aspects. This might be due to the difficulties of handling, particularly the eEF1B beta and eEF1B gamma subunits in vitro. Here, the human eEF1H complex is for the first...... gamma:eEF1B beta, where the last was observed using a three-hybrid approach. Surprisingly, eEF1A2 showed no or only little affinity for the guanine-nucleotide-exchange factors. Truncated versions of the subunits of eEF1B were used to orientate these subunits within the resulting model. The model unit...

  19. A simple genetic incompatibility causes hybrid male sterility in mimulus.

    Science.gov (United States)

    Sweigart, Andrea L; Fishman, Lila; Willis, John H

    2006-04-01

    Much evidence has shown that postzygotic reproductive isolation (hybrid inviability or sterility) evolves by the accumulation of interlocus incompatibilities between diverging populations. Although in theory only a single pair of incompatible loci is needed to isolate species, empirical work in Drosophila has revealed that hybrid fertility problems often are highly polygenic and complex. In this article we investigate the genetic basis of hybrid sterility between two closely related species of monkeyflower, Mimulus guttatus and M. nasutus. In striking contrast to Drosophila systems, we demonstrate that nearly complete hybrid male sterility in Mimulus results from a simple genetic incompatibility between a single pair of heterospecific loci. We have genetically mapped this sterility effect: the M. guttatus allele at the hybrid male sterility 1 (hms1) locus acts dominantly in combination with recessive M. nasutus alleles at the hybrid male sterility 2 (hms2) locus to cause nearly complete hybrid male sterility. In a preliminary screen to find additional small-effect male sterility factors, we identified one additional locus that also contributes to some of the variation in hybrid male fertility. Interestingly, hms1 and hms2 also cause a significant reduction in hybrid female fertility, suggesting that sex-specific hybrid defects might share a common genetic basis. This possibility is supported by our discovery that recombination is reduced dramatically in a cross involving a parent with the hms1-hms2 incompatibility.

  20. Comprehensive Binary Interaction Mapping of SH2 Domains via Fluorescence Polarization Reveals Novel Functional Diversification of ErbB Receptors

    Science.gov (United States)

    Ciaccio, Mark F.; Chuu, Chih-pin; Jones, Richard B.

    2012-01-01

    First-generation interaction maps of Src homology 2 (SH2) domains with receptor tyrosine kinase (RTK) phosphosites have previously been generated using protein microarray (PM) technologies. Here, we developed a large-scale fluorescence polarization (FP) methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB) domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry procedures. This

  1. Comprehensive binary interaction mapping of SH2 domains via fluorescence polarization reveals novel functional diversification of ErbB receptors.

    Directory of Open Access Journals (Sweden)

    Ronald J Hause

    Full Text Available First-generation interaction maps of Src homology 2 (SH2 domains with receptor tyrosine kinase (RTK phosphosites have previously been generated using protein microarray (PM technologies. Here, we developed a large-scale fluorescence polarization (FP methodology that was able to characterize interactions between SH2 domains and ErbB receptor phosphosites with higher fidelity and sensitivity than was previously achieved with PMs. We used the FP assay to query the interaction of synthetic phosphopeptides corresponding to 89 ErbB receptor intracellular tyrosine sites against 93 human SH2 domains and 2 phosphotyrosine binding (PTB domains. From 358,944 polarization measurements, the affinities for 1,405 unique biological interactions were determined, 83% of which are novel. In contrast to data from previous reports, our analyses suggested that ErbB2 was not more promiscuous than the other ErbB receptors. Our results showed that each receptor displays unique preferences in the affinity and location of recruited SH2 domains that may contribute to differences in downstream signaling potential. ErbB1 was enriched versus the other receptors for recruitment of domains from RAS GEFs whereas ErbB2 was enriched for recruitment of domains from tyrosine and phosphatidyl inositol phosphatases. ErbB3, the kinase inactive ErbB receptor family member, was predictably enriched for recruitment of domains from phosphatidyl inositol kinases and surprisingly, was enriched for recruitment of domains from tyrosine kinases, cytoskeletal regulatory proteins, and RHO GEFs but depleted for recruitment of domains from phosphatidyl inositol phosphatases. Many novel interactions were also observed with phosphopeptides corresponding to ErbB receptor tyrosines not previously reported to be phosphorylated by mass spectrometry, suggesting the existence of many biologically relevant RTK sites that may be phosphorylated but below the detection threshold of standard mass spectrometry

  2. Comparative transcriptome analysis reveals carbohydrate and lipid metabolism blocks in Brassica napus L. male sterility induced by the chemical hybridization agent monosulfuron ester sodium.

    Science.gov (United States)

    Li, Zhanjie; Cheng, Yufeng; Cui, Jianmin; Zhang, Peipei; Zhao, Huixian; Hu, Shengwu

    2015-03-17

    Chemical hybridization agents (CHAs) are often used to induce male sterility for the production of hybrid seeds. We previously discovered that monosulfuron ester sodium (MES), an acetolactate synthase (ALS) inhibitor of the herbicide sulfonylurea family, can induce rapeseed (Brassica napus L.) male sterility at approximately 1% concentration required for its herbicidal activity. To find some clues to the mechanism of MES inducing male sterility, the ultrastructural cytology observations, comparative transcriptome analysis, and physiological analysis on carbohydrate content were carried out in leaves and anthers at different developmental stages between the MES-treated and mock-treated rapeseed plants. Cytological analysis revealed that the plastid ultrastructure was abnormal in pollen mother cells and tapetal cells in male sterility anthers induced by MES treatment, with less material accumulation in it. However, starch granules were observed in chloroplastids of the epidermis cells in male sterility anthers. Comparative transcriptome analysis identified 1501 differentially expressed transcripts (DETs) in leaves and anthers at different developmental stages, most of these DETs being localized in plastid and mitochondrion. Transcripts involved in metabolism, especially in carbohydrate and lipid metabolism, and cellular transport were differentially expressed. Pathway visualization showed that the tightly regulated gene network for metabolism was reprogrammed to respond to MES treatment. The results of cytological observation and transcriptome analysis in the MES-treated rapeseed plants were mirrored by carbohydrate content analysis. MES treatment led to decrease in soluble sugars content in leaves and early stage buds, but increase in soluble sugars content and decrease in starch content in middle stage buds. Our integrative results suggested that carbohydrate and lipid metabolism were influenced by CHA-MES treatment during rapeseed anther development, which might

  3. Multiple sex-associated regions and a putative sex chromosome in zebrafish revealed by RAD mapping and population genomics.

    Directory of Open Access Journals (Sweden)

    Jennifer L Anderson

    Full Text Available Within vertebrates, major sex determining genes can differ among taxa and even within species. In zebrafish (Danio rerio, neither heteromorphic sex chromosomes nor single sex determination genes of large effect, like Sry in mammals, have yet been identified. Furthermore, environmental factors can influence zebrafish sex determination. Although progress has been made in understanding zebrafish gonad differentiation (e.g. the influence of germ cells on gonad fate, the primary genetic basis of zebrafish sex determination remains poorly understood. To identify genetic loci associated with sex, we analyzed F(2 offspring of reciprocal crosses between Oregon *AB and Nadia (NA wild-type zebrafish stocks. Genome-wide linkage analysis, using more than 5,000 sequence-based polymorphic restriction site associated (RAD-tag markers and population genomic analysis of more than 30,000 single nucleotide polymorphisms in our *ABxNA crosses revealed a sex-associated locus on the end of the long arm of chr-4 for both cross families, and an additional locus in the middle of chr-3 in one cross family. Additional sequencing showed that two SNPs in dmrt1 previously suggested to be functional candidates for sex determination in a cross of ABxIndia wild-type zebrafish, are not associated with sex in our AB fish. Our data show that sex determination in zebrafish is polygenic and that different genes may influence sex determination in different strains or that different genes become more important under different environmental conditions. The association of the end of chr-4 with sex is remarkable because, unique in the karyotype, this chromosome arm shares features with known sex chromosomes: it is highly heterochromatic, repetitive, late replicating, and has reduced recombination. Our results reveal that chr-4 has functional and structural properties expected of a sex chromosome.

  4. Travelling in time with networks: Revealing present day hybridization versus ancestral polymorphism between two species of brown algae, Fucus vesiculosus and F. spiralis

    Directory of Open Access Journals (Sweden)

    Pearson Gareth A

    2011-01-01

    Full Text Available Abstract Background Hybridization or divergence between sympatric sister species provides a natural laboratory to study speciation processes. The shared polymorphism in sister species may either be ancestral or derive from hybridization, and the accuracy of analytic methods used thus far to derive convincing evidence for the occurrence of present day hybridization is largely debated. Results Here we propose the application of network analysis to test for the occurrence of present day hybridization between the two species of brown algae Fucus spiralis and F. vesiculosus. Individual-centered networks were analyzed on the basis of microsatellite genotypes from North Africa to the Pacific American coast, through the North Atlantic. Two genetic distances integrating different time steps were used, the Rozenfeld (RD; based on alleles divergence and the Shared Allele (SAD; based on alleles identity distances. A diagnostic level of genotype divergence and clustering of individuals from each species was obtained through RD while screening for exchanges through putative hybridization was facilitated using SAD. Intermediate individuals linking both clusters on the RD network were those sampled at the limits of the sympatric zone in Northwest Iberia. Conclusion These results suggesting rare hybridization were confirmed by simulation of hybrids and F2 with directed backcrosses. Comparison with the Bayesian method STRUCTURE confirmed the usefulness of both approaches and emphasized the reliability of network analysis to unravel and study hybridization

  5. THE MULTI-PHASE COLD FOUNTAIN IN M82 REVEALED BY A WIDE, SENSITIVE MAP OF THE MOLECULAR INTERSTELLAR MEDIUM

    International Nuclear Information System (INIS)

    Leroy, Adam K.; Martini, Paul; Walter, Fabian; Roussel, Hélène; Sandstrom, Karin; Ott, Jürgen; Weiss, Axel; Bolatto, Alberto D.; Schuster, Karl; Dessauges-Zavadsky, Miroslava

    2015-01-01

    We present a wide area (≈8 × 8 kpc), sensitive map of CO (2–1) emission around the nearby starburst galaxy M82. Molecular gas extends far beyond the stellar disk, including emission associated with the well-known outflow as far as 3 kpc from M82's midplane. Kinematic signatures of the outflow are visible in both the CO and H i emission: both tracers show a minor axis velocity gradient and together they show double peaked profiles, consistent with a hot outflow bounded by a cone made of a mix of atomic and molecular gas. Combining our CO and H i data with observations of the dust continuum, we study the changing properties of the cold outflow as it leaves the disk. While H 2 dominates the ISM near the disk, the dominant phase of the cool medium changes as it leaves the galaxy and becomes mostly atomic after about a kpc. Several arguments suggest that regardless of phase, the mass in the cold outflow does not make it far from the disk; the mass flux through surfaces above the disk appears to decline with a projected scale length of ≈1–2 kpc. The cool material must also end up distributed over a much wider angle than the hot outflow based on the nearly circular isophotes of dust and CO at low intensity and the declining rotation velocities as a function of height from the plane. The minor axis of M82 appears so striking at many wavelengths because the interface between the hot wind cavity and the cool gas produces Hα, hot dust, polycyclic aromatic hydrocarbon emission, and scattered UV light. We also show the level at which a face-on version of M82 would be detectable as an outflow based on unresolved spectroscopy. Finally, we consider multiple constraints on the CO-to-H 2 conversion factor, which must change across the galaxy but appears to be only a factor of ≈2 lower than the Galactic value in the outflow

  6. THE MULTI-PHASE COLD FOUNTAIN IN M82 REVEALED BY A WIDE, SENSITIVE MAP OF THE MOLECULAR INTERSTELLAR MEDIUM

    Energy Technology Data Exchange (ETDEWEB)

    Leroy, Adam K.; Martini, Paul [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States); Walter, Fabian [Max Planck Institute für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); Roussel, Hélène [Institut d’Astrophysique de Paris, Sorbonne Universités, UPMC (Univ. Paris 06), CNRS (UMR 7095), F-75014 Paris (France); Sandstrom, Karin [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Ott, Jürgen [National Radio Astronomy Observatory, P.O. Box O, 1003 Lopezville Road, Socorro, NM 87801 (United States); Weiss, Axel [Max-Planck-Institut für Radioastronomie, Auf dem Hgel 69, D-53121 Bonn (Germany); Bolatto, Alberto D. [Department of Astronomy, University of Maryland, College Park, MD (United States); Schuster, Karl [IRAM, 300 rue de la Piscine, F-38406 St. Martin d’Hères (France); Dessauges-Zavadsky, Miroslava [Observatoire de Geneve, 1290 Sauverny (Switzerland)

    2015-12-01

    We present a wide area (≈8 × 8 kpc), sensitive map of CO (2–1) emission around the nearby starburst galaxy M82. Molecular gas extends far beyond the stellar disk, including emission associated with the well-known outflow as far as 3 kpc from M82's midplane. Kinematic signatures of the outflow are visible in both the CO and H i emission: both tracers show a minor axis velocity gradient and together they show double peaked profiles, consistent with a hot outflow bounded by a cone made of a mix of atomic and molecular gas. Combining our CO and H i data with observations of the dust continuum, we study the changing properties of the cold outflow as it leaves the disk. While H{sub 2} dominates the ISM near the disk, the dominant phase of the cool medium changes as it leaves the galaxy and becomes mostly atomic after about a kpc. Several arguments suggest that regardless of phase, the mass in the cold outflow does not make it far from the disk; the mass flux through surfaces above the disk appears to decline with a projected scale length of ≈1–2 kpc. The cool material must also end up distributed over a much wider angle than the hot outflow based on the nearly circular isophotes of dust and CO at low intensity and the declining rotation velocities as a function of height from the plane. The minor axis of M82 appears so striking at many wavelengths because the interface between the hot wind cavity and the cool gas produces Hα, hot dust, polycyclic aromatic hydrocarbon emission, and scattered UV light. We also show the level at which a face-on version of M82 would be detectable as an outflow based on unresolved spectroscopy. Finally, we consider multiple constraints on the CO-to-H{sub 2} conversion factor, which must change across the galaxy but appears to be only a factor of ≈2 lower than the Galactic value in the outflow.

  7. Loss of Mitogen-Activated Protein Kinase Kinase Kinase 4 (MAP3K4) Reveals a Requirement for MAPK Signalling in Mouse Sex Determination

    Science.gov (United States)

    Bogani, Debora; Siggers, Pam; Brixey, Rachel; Warr, Nick; Beddow, Sarah; Edwards, Jessica; Williams, Debbie; Wilhelm, Dagmar; Koopman, Peter; Flavell, Richard A.; Chi, Hongbo; Ostrer, Harry; Wells, Sara; Cheeseman, Michael; Greenfield, Andy

    2009-01-01

    Sex determination in mammals is controlled by the presence or absence of the Y-linked gene SRY. In the developing male (XY) gonad, sex-determining region of the Y (SRY) protein acts to up-regulate expression of the related gene, SOX9, a transcriptional regulator that in turn initiates a downstream pathway of testis development, whilst also suppressing ovary development. Despite the requirement for a number of transcription factors and secreted signalling molecules in sex determination, intracellular signalling components functioning in this process have not been defined. Here we report a role for the phylogenetically ancient mitogen-activated protein kinase (MAPK) signalling pathway in mouse sex determination. Using a forward genetic screen, we identified the recessive boygirl (byg) mutation. On the C57BL/6J background, embryos homozygous for byg exhibit consistent XY gonadal sex reversal. The byg mutation is an A to T transversion causing a premature stop codon in the gene encoding MAP3K4 (also known as MEKK4), a mitogen-activated protein kinase kinase kinase. Analysis of XY byg/byg gonads at 11.5 d post coitum reveals a growth deficit and a failure to support mesonephric cell migration, both early cellular processes normally associated with testis development. Expression analysis of mutant XY gonads at the same stage also reveals a dramatic reduction in Sox9 and, crucially, Sry at the transcript and protein levels. Moreover, we describe experiments showing the presence of activated MKK4, a direct target of MAP3K4, and activated p38 in the coelomic region of the XY gonad at 11.5 d post coitum, establishing a link between MAPK signalling in proliferating gonadal somatic cells and regulation of Sry expression. Finally, we provide evidence that haploinsufficiency for Map3k4 accounts for T-associated sex reversal (Tas). These data demonstrate that MAP3K4-dependent signalling events are required for normal expression of Sry during testis development, and create a novel

  8. Loss of mitogen-activated protein kinase kinase kinase 4 (MAP3K4 reveals a requirement for MAPK signalling in mouse sex determination.

    Directory of Open Access Journals (Sweden)

    Debora Bogani

    2009-09-01

    Full Text Available Sex determination in mammals is controlled by the presence or absence of the Y-linked gene SRY. In the developing male (XY gonad, sex-determining region of the Y (SRY protein acts to up-regulate expression of the related gene, SOX9, a transcriptional regulator that in turn initiates a downstream pathway of testis development, whilst also suppressing ovary development. Despite the requirement for a number of transcription factors and secreted signalling molecules in sex determination, intracellular signalling components functioning in this process have not been defined. Here we report a role for the phylogenetically ancient mitogen-activated protein kinase (MAPK signalling pathway in mouse sex determination. Using a forward genetic screen, we identified the recessive boygirl (byg mutation. On the C57BL/6J background, embryos homozygous for byg exhibit consistent XY gonadal sex reversal. The byg mutation is an A to T transversion causing a premature stop codon in the gene encoding MAP3K4 (also known as MEKK4, a mitogen-activated protein kinase kinase kinase. Analysis of XY byg/byg gonads at 11.5 d post coitum reveals a growth deficit and a failure to support mesonephric cell migration, both early cellular processes normally associated with testis development. Expression analysis of mutant XY gonads at the same stage also reveals a dramatic reduction in Sox9 and, crucially, Sry at the transcript and protein levels. Moreover, we describe experiments showing the presence of activated MKK4, a direct target of MAP3K4, and activated p38 in the coelomic region of the XY gonad at 11.5 d post coitum, establishing a link between MAPK signalling in proliferating gonadal somatic cells and regulation of Sry expression. Finally, we provide evidence that haploinsufficiency for Map3k4 accounts for T-associated sex reversal (Tas. These data demonstrate that MAP3K4-dependent signalling events are required for normal expression of Sry during testis development, and

  9. Single-Cell Transcriptomics and Fate Mapping of Ependymal Cells Reveals an Absence of Neural Stem Cell Function.

    Science.gov (United States)

    Shah, Prajay T; Stratton, Jo A; Stykel, Morgan Gail; Abbasi, Sepideh; Sharma, Sandeep; Mayr, Kyle A; Koblinger, Kathrin; Whelan, Patrick J; Biernaskie, Jeff

    2018-05-03

    Ependymal cells are multi-ciliated cells that form the brain's ventricular epithelium and a niche for neural stem cells (NSCs) in the ventricular-subventricular zone (V-SVZ). In addition, ependymal cells are suggested to be latent NSCs with a capacity to acquire neurogenic function. This remains highly controversial due to a lack of prospective in vivo labeling techniques that can effectively distinguish ependymal cells from neighboring V-SVZ NSCs. We describe a transgenic system that allows for targeted labeling of ependymal cells within the V-SVZ. Single-cell RNA-seq revealed that ependymal cells are enriched for cilia-related genes and share several stem-cell-associated genes with neural stem or progenitors. Under in vivo and in vitro neural-stem- or progenitor-stimulating environments, ependymal cells failed to demonstrate any suggestion of latent neural-stem-cell function. These findings suggest remarkable stability of ependymal cell function and provide fundamental insights into the molecular signature of the V-SVZ niche. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export.

    Science.gov (United States)

    Karijolich, John; Zhao, Yang; Alla, Ravi; Glaunsinger, Britt

    2017-06-02

    Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  11. Atypical category processing and hemispheric asymmetries in high-functioning children with autism: revealed through high-density EEG mapping.

    Science.gov (United States)

    Fiebelkorn, Ian C; Foxe, John J; McCourt, Mark E; Dumas, Kristina N; Molholm, Sophie

    2013-05-01

    Behavioral evidence for an impaired ability to group objects based on similar physical or semantic properties in autism spectrum disorders (ASD) has been mixed. Here, we recorded brain activity from high-functioning children with ASD as they completed a visual-target detection task. We then assessed the extent to which object-based selective attention automatically generalized from targets to non-target exemplars from the same well-known object class (e.g., dogs). Our results provide clear electrophysiological evidence that children with ASD (N=17, aged 8-13 years) process the similarity between targets (e.g., a specific dog) and same-category non-targets (SCNT) (e.g., another dog) to a lesser extent than do their typically developing (TD) peers (N=21). A closer examination of the data revealed striking hemispheric asymmetries that were specific to the ASD group. These findings align with mounting evidence in the autism literature of anatomic underconnectivity between the cerebral hemispheres. Years of research in individuals with TD have demonstrated that the left hemisphere (LH) is specialized toward processing local (or featural) stimulus properties and the right hemisphere (RH) toward processing global (or configural) stimulus properties. We therefore propose a model where a lack of communication between the hemispheres in ASD, combined with typical hemispheric specialization, is a root cause for impaired categorization and the oft-observed bias to process local over global stimulus properties. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Elastic Model Transitions: a Hybrid Approach Utilizing Quadratic Inequality Constrained Least Squares (LSQI) and Direct Shape Mapping (DSM)

    Science.gov (United States)

    Jurenko, Robert J.; Bush, T. Jason; Ottander, John A.

    2014-01-01

    A method for transitioning linear time invariant (LTI) models in time varying simulation is proposed that utilizes both quadratically constrained least squares (LSQI) and Direct Shape Mapping (DSM) algorithms to determine physical displacements. This approach is applicable to the simulation of the elastic behavior of launch vehicles and other structures that utilize multiple LTI finite element model (FEM) derived mode sets that are propagated throughout time. The time invariant nature of the elastic data for discrete segments of the launch vehicle trajectory presents a problem of how to properly transition between models while preserving motion across the transition. In addition, energy may vary between flex models when using a truncated mode set. The LSQI-DSM algorithm can accommodate significant changes in energy between FEM models and carries elastic motion across FEM model transitions. Compared with previous approaches, the LSQI-DSM algorithm shows improvements ranging from a significant reduction to a complete removal of transients across FEM model transitions as well as maintaining elastic motion from the prior state.

  13. Hybridization of two megacephalic map turtles (testudines: emydidae: Graptemys) in the Choctawhatchee River drainage of Alabama and Florida

    Science.gov (United States)

    Godwin, James; Lovich, Jeffrey E.; Ennen, Joshua R.; Kreiser, Brian R.; Folt, Brian; Lechowicz, Chris

    2014-01-01

    Map turtles of the genus Graptemys are highly aquatic and rarely undergo terrestrial movements, and limited dispersal among drainages has been hypothesized to drive drainage-specific endemism and high species richness of this group in the southeastern United States. Until recently, two members of the megacephalic “pulchra clade,” Graptemys barbouri andGraptemys ernsti, were presumed to be allopatric with a gap in both species' ranges in the Choctawhatchee River drainage. In this paper, we analyzed variation in morphology (head and shell patterns) and genetics (mitochondrial DNA and microsatellite loci) from G. barbouri, G. ernsti, and Graptemys sp. collected from the Choctawhatchee River drainage, and we document the syntopic occurrence of those species and back-crossed individuals of mixed ancestry in the Choctawhatchee River drainage. Our results provide a first counter-example to the pattern of drainage-specific endemism in megacephalic Graptemys. Geologic events associated with Pliocene and Pleistocene sea level fluctuations and the existence of paleo-river systems appear to have allowed the invasion of the Choctawhatchee system by these species, and the subsequent introgression likely predates any potential human-mediated introduction.

  14. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

    Science.gov (United States)

    Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

    2017-10-24

    Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

  15. MARCADORES RAPD PARA MAPEAMENTO GENÉTICO E SELEÇÃO DE HÍBRIDOS DE CITROS RAPD MARKERS TO GENETIC MAPPING AND SELECTION OF CITRUS HYBRIDS

    Directory of Open Access Journals (Sweden)

    ROBERTO PEDROSO DE OLIVEIRA

    2001-12-01

    Full Text Available Os marcadores moleculares apresentam várias aplicações no melhoramento de plantas, permitindo uma série de análises genéticas. Este trabalho foi realizado com o objetivo de estabelecer marcadores RAPD para serem utilizados em estudos de mapeamento genético e na seleção de híbridos entre tangerina-'Cravo' (Citrus reticulata Blanco e laranja-'Pêra' (C. sinensis (L. Osbeck. Extraiu-se DNA de folhas dos parentais e de seis híbridos F1. As reações de amplificação foram preparadas em 13 uL de solução, constituída por tampão 1x GIBCO BRL; soluções 1,54 mM de MgCl2 e 0,2 mM de cada dNTP; 15 ng de cada 'primer'; 1,5 unidade de 'Taq DNA Polymerase' e 15 ng de DNA genômico. As reações foram realizadas em termocicladores programados para 36 ciclos de 1 min a 92ºC, 1 min a 36ºC, 2 min a 72ºC e 10 min de extensão a 72ºC. Foram testados 'primers' decâmeros arbitrários dos 'kits' A, AB, AT, AV, B, C, D, E, G, H, M, N, P, Q, R e U da Operon, sendo selecionados 113 por apresentarem polimorfismo, com número de marcadores variando de 1 a 6 por 'primer'. Esses 'primers' amplificaram 201 (23,13% bandas polimórficas, aplicáveis no mapeamento genético e seleção de híbridos. A freqüência de 'primers' com 1; 2; 3; 4; 5 e 6 bandas polimórficas foi de 49,5%, 33,6%, 9,7%, 4,4%, 1,8% e 1,0%, respectivamente.Molecular markers have many applications in plant breeding, enabling some types of genetic analyses. The aim of this work was to establish RAPD markers to be used to genetic mapping studies and selection of hybrids between 'Cravo' tangerine (Citrus reticulata Blanco and 'Pêra' orange (C. sinensis (L. Osbeck. DNA of the parents and six hybrids F1 was isolated from the leaves. The amplification reactions were performed in volumes of 13 µL, composed by GIBCO BRL 1x buffer, 1,54 mM MgCl2, 0,2 mM of each dNTP, 15 ng of each primer, 1,5 unit of Taq DNA Polymerase and 15 ng of genomic DNA. These reactions were carried out in

  16. Evidence of Natural Hybridization and Introgression between Vasconcellea Species (Caricaceae) from Southern Ecuador Revealed by Chloroplast, Mitochondrial and Nuclear DNA Markers

    Science.gov (United States)

    VAN DROOGENBROECK, B.; KYNDT, T.; ROMEIJN-PEETERS, E.; VAN THUYNE, W.; GOETGHEBEUR, P.; ROMERO-MOTOCHI, J. P.; GHEYSEN, G.

    2006-01-01

    • Background and Aims Vasconcellea × heilbornii is believed to be of natural hybrid origin between V. cundinamarcensis and V. stipulata, and is often difficult to discriminate from V. stipulata on morphological grounds. The aim of this paper is to examine individuals of these three taxa and of individuals from the closely related species V. parviflora and V. weberbaueri, which all inhabit a hybrid zone in southern Ecuador. • Methods Molecular data from mitochondrial, chloroplast and nuclear DNA from 61 individuals were analysed. • Key Results Molecular analysis confirmed occasional contemporary hybridization between V. stipulata, V. cundinamarcensis and V. × heilbornii and suggested the possible involvement of V. weberbaueri in the origin of V. × heilbornii. In addition, the molecular data indicated unidirectional introgression of the V. cundinamarcensis nuclear genome into that of V. stipulata. Several of the individuals examined with morphology similar to that of V. stipulata had genetic traces of hybridization with V. cundinamarcensis, which only seems to act as pollen donor in interspecific hybridization events. Molecular analyses also strongly suggested that most of the V. × heilbornii individuals are not F1 hybrids but instead are progeny of repeated backcrosses with V. stipulata. • Conclusions The results of the present study point to the need for re-evaluation of natural populations of V. stipulata and V. × heilbornii. In general, this analysis demonstrates the complex patterns of genetic and morphological diversity found in natural plant hybrid zones. PMID:16500954

  17. 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.

  18. Transgenic Analysis of the Leishmania MAP Kinase MPK10 Reveals an Auto-inhibitory Mechanism Crucial for Stage-Regulated Activity and Parasite Viability

    DEFF Research Database (Denmark)

    Cayla, M.; Rachidi, N.; Leclercq, O.

    2014-01-01

    Protozoan pathogens of the genus Leishmania have evolved unique signaling mechanisms that can sense changes in the host environment and trigger adaptive stage differentiation essential for host cell infection. The signaling mechanisms underlying parasite development remain largely elusive even...... though Leishmania mitogen-activated protein kinases (MAPKs) have been linked previously to environmentally induced differentiation and virulence. Here, we unravel highly unusual regulatory mechanisms for Leishmania MAP kinase 10 (MPK10). Using a transgenic approach, we demonstrate that MPK10 is stage...... at position 395 that could be implicated in kinase regulation. Finally, we uncovered a feedback loop that limits MPK10 activity through dephosphorylation of the tyrosine residue of the TxY motif. Together our data reveal novel aspects of protein kinase regulation in Leishmania, and propose MPK10...

  19. VNTR internal structure mapping at the {alpha}-globin 3{prime}HVR locus reveals a hierachy of related lineages in oceania

    Energy Technology Data Exchange (ETDEWEB)

    Martinson, J.J.; Clegg, J.B.; Boyce, A.J. [Univ. of Oxford (United Kingdom)

    1994-09-01

    Analysis of the {alpha}-globin gene complex in Oceania has revealed many different rearrangements which remove one of the adult globin genes. Frequencies of these deletion chromosomes are elevated by malarial resistance conferred by the resulting {alpha}-thalassaemia. One particular deletion chromosome, designated -{alpha}{sup 3.7}III, is found at high levels in Melanesia and Polynesia: RFLP haplotype analysis shows that this deletion is always found on chromosomes bearing the IIIa haplotype and is likely to be the product of one single rearrangement event. A subset of the -{alpha}{sup 3.7}III chromosomes carries a more recent mutation which generates the haemoglobin variant HbJ{sup Tongariki}. We have characterized the allelic variation at the 3{prime}HVR VNTR locus located 6 kb from the globin genes in each of these groups of chromosomes. We have determined the internal structure of these alleles by RFLP mapping of PCR-amplified DNA: within each group, the allelic diversity results from the insertion and/or deletion of small {open_quotes}motifs{close_quotes} of up to 6 adjacent repeats. Mapping of 3{prime}HVR alleles associated with other haplotypes reveals that these are composed of repeat arrays that are substantially different to those derived from IIIa chromosomes, indicating that interchromosomal recombination between heterologous haplotypes does not account for any of the diversity seen to date. We have recently shown that allelic size variation at the two VNTR loci flanking the {alpha}-globin complex is very closely linked to the haplotypes known to be present at this locus. Here we show that, within a haplotype, VNTR alleles are very closely related to each other on the basis of internal structure and demonstrate that intrachromosomal mutation processes involving small numbers of tandem repeats are the main cause of variation at this locus.

  20. Revealing the synergetic effects in Ni nanoparticle-carbon nanotube hybrids by scanning transmission X-ray microscopy and their application in the hydrolysis of ammonia borane.

    Science.gov (United States)

    Zhao, Guanqi; Zhong, Jun; Wang, Jian; Sham, Tsun-Kong; Sun, Xuhui; Lee, Shuit-Tong

    2015-06-07

    The hybrids of carbon nanotubes (CNTs) and the supported Ni nanoparticles (NPs) have been studied by scanning transmission X-ray microscopy (STXM) and tested by the hydrolysis reaction of ammonia borane (AB, NH3BH3). Data clearly showed the existence of a strong interaction between Ni NPs and thin CNTs (C-O-Ni bonds), which favored the tunable (buffer) electronic structure of Ni NPs facilitating the catalytic process. The hydrolysis process of AB confirmed the hypothesis that the hybrids with a strong interfacial interaction would show superior catalytic performance, while the hybrids with a weak interfacial interaction show poor performance. Our results provide a wealth of detailed information regarding the electronic structure of the NP-CNT hybrids and provide guidance towards the rational design of high-performance catalysts for energy applications.

  1. Genomic Diversity of Burkholderia pseudomallei Clinical Isolates: Subtractive Hybridization Reveals a Burkholderia mallei-Specific Propage in B. pseudomallei 1026b

    National Research Council Canada - National Science Library

    DeShazer, David

    2004-01-01

    .... pseudomallei, 1026b and K96243. Numerous mobile genetic elements, including a temperate bacteriophage designated phi1026b, were identified among the 1026b-specific suppression subtractive hybridization products...

  2. IgV peptide mapping of native Ro60 autoantibody proteomes in primary Sjögren's syndrome reveals molecular markers of Ro/La diversification.

    Science.gov (United States)

    Wang, Jing J; Al Kindi, Mahmood A; Colella, Alex D; Dykes, Lukah; Jackson, Michael W; Chataway, Tim K; Reed, Joanne H; Gordon, Tom P

    2016-12-01

    We have used high-resolution mass spectrometry to sequence precipitating anti-Ro60 proteomes from sera of patients with primary Sjögren's syndrome and compare immunoglobulin variable-region (IgV) peptide signatures in Ro/La autoantibody subsets. Anti-Ro60 were purified by elution from native Ro60-coated ELISA plates and subjected to combined de novo amino acid sequencing and database matching. Monospecific anti-Ro60 Igs comprised dominant public and minor private sets of IgG1 kappa and lambda restricted heavy and light chains. Specific IgV amino acid substitutions stratified anti-Ro60 from anti-Ro60/La responses, providing a molecular fingerprint of Ro60/La determinant spreading and suggesting that different forms of Ro60 antigen drive these responses. Sequencing of linked anti-Ro52 proteomes from individual patients and comparison with their anti-Ro60 partners revealed sharing of a dominant IGHV3-23/IGKV3-20 paired clonotype but with divergent IgV mutational signatures. In summary, anti-Ro60 IgV peptide mapping provides insights into Ro/La autoantibody diversification and reveals serum-based molecular markers of humoral Ro60 autoimmunity. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population.

    Science.gov (United States)

    De Keyser, Ellen; Desmet, Laurence; Van Bockstaele, Erik; De Riek, Jan

    2013-06-24

    Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H. Currently in plant

  4. Genetic Mapping in Mice Reveals the Involvement of Pcdh9 in Long-Term Social and Object Recognition and Sensorimotor Development.

    Science.gov (United States)

    Bruining, Hilgo; Matsui, Asuka; Oguro-Ando, Asami; Kahn, René S; Van't Spijker, Heleen M; Akkermans, Guus; Stiedl, Oliver; van Engeland, Herman; Koopmans, Bastijn; van Lith, Hein A; Oppelaar, Hugo; Tieland, Liselotte; Nonkes, Lourens J; Yagi, Takeshi; Kaneko, Ryosuke; Burbach, J Peter H; Yamamoto, Nobuhiko; Kas, Martien J

    2015-10-01

    Quantitative genetic analysis of basic mouse behaviors is a powerful tool to identify novel genetic phenotypes contributing to neurobehavioral disorders. Here, we analyzed genetic contributions to single-trial, long-term social and nonsocial recognition and subsequently studied the functional impact of an identified candidate gene on behavioral development. Genetic mapping of single-trial social recognition was performed in chromosome substitution strains, a sophisticated tool for detecting quantitative trait loci (QTL) of complex traits. Follow-up occurred by generating and testing knockout (KO) mice of a selected QTL candidate gene. Functional characterization of these mice was performed through behavioral and neurological assessments across developmental stages and analyses of gene expression and brain morphology. Chromosome substitution strain 14 mapping studies revealed an overlapping QTL related to long-term social and object recognition harboring Pcdh9, a cell-adhesion gene previously associated with autism spectrum disorder. Specific long-term social and object recognition deficits were confirmed in homozygous (KO) Pcdh9-deficient mice, while heterozygous mice only showed long-term social recognition impairment. The recognition deficits in KO mice were not associated with alterations in perception, multi-trial discrimination learning, sociability, behavioral flexibility, or fear memory. Rather, KO mice showed additional impairments in sensorimotor development reflected by early touch-evoked biting, rotarod performance, and sensory gating deficits. This profile emerged with structural changes in deep layers of sensory cortices, where Pcdh9 is selectively expressed. This behavior-to-gene study implicates Pcdh9 in cognitive functions required for long-term social and nonsocial recognition. This role is supported by the involvement of Pcdh9 in sensory cortex development and sensorimotor phenotypes. Copyright © 2015 Society of Biological Psychiatry. Published

  5. Concept Mapping

    Science.gov (United States)

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  6. A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits

    Directory of Open Access Journals (Sweden)

    Laurent Pascal

    2006-03-01

    Full Text Available Abstract Background A number of different quantitative trait loci (QTL for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6. Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. Results Therefore, we constructed a high-resolution radiation hybrid (RH map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. Conclusion The gene-anchored high-resolution RH map (1 locus/300 kb for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and

  7. Rock-avalanche dynamics revealed by large-scale field mapping and seismic signals at a highly mobile avalanche in the West Salt Creek valley, western Colorado

    Science.gov (United States)

    Coe, Jeffrey A.; Baum, Rex L.; Allstadt, Kate E.; Kochevar, Bernard; Schmitt, Robert G.; Morgan, Matthew L.; White, Jonathan L.; Stratton, Benjamin T.; Hayashi, Timothy A.; Kean, Jason W.

    2016-01-01

    On 25 May 2014, a rain-on-snow–induced rock avalanche occurred in the West Salt Creek valley on the northern flank of Grand Mesa in western Colorado (United States). The avalanche mobilized from a preexisting rock slide in the Green River Formation and traveled 4.6 km down the confined valley, killing three people. The avalanche was rare for the contiguous United States because of its large size (54.5 Mm3) and high mobility (height/length = 0.14). To understand the avalanche failure sequence, mechanisms, and mobility, we conducted a forensic analysis using large-scale (1:1000) structural mapping and seismic data. We used high-resolution, unmanned aircraft system imagery as a base for field mapping, and analyzed seismic data from 22 broadband stations (distances earth and tracked these forces using curves in the avalanche path. Our results revealed that the rock avalanche was a cascade of landslide events, rather than a single massive failure. The sequence began with an early morning landslide/debris flow that started ∼10 h before the main avalanche. The main avalanche lasted ∼3.5 min and traveled at average velocities ranging from 15 to 36 m/s. For at least two hours after the avalanche ceased movement, a central, hummock-rich core continued to move slowly. Since 25 May 2014, numerous shallow landslides, rock slides, and rock falls have created new structures and modified avalanche topography. Mobility of the main avalanche and central core was likely enhanced by valley floor material that liquefied from undrained loading by the overriding avalanche. Although the base was likely at least partially liquefied, our mapping indicates that the overriding avalanche internally deformed predominantly by sliding along discrete shear surfaces in material that was nearly dry and had substantial frictional strength. These results indicate that the West Salt Creek avalanche, and probably other long-traveled avalanches, could be modeled as two layers: a thin, liquefied

  8. Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques.

    Directory of Open Access Journals (Sweden)

    Qiong Pan

    Full Text Available Complex chromosome rearrangements (CCRs, which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques.

  9. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers

    DEFF Research Database (Denmark)

    Gaasenbeek, Michelle; Howarth, Kimberley; Rowan, Andrew J

    2006-01-01

    Cancers with chromosomal instability (CIN) are held to be aneuploid/polyploid with multiple large-scale gains/deletions, but the processes underlying CIN are unclear and different types of CIN might exist. We investigated colorectal cancer cell lines using array-comparative genomic hybridization...

  10. Recent introgressive hybridization revealed by exclusive mtDNA transfer from Oreochromis leucostictus (Trewavas, 1933) to Oreochromis niloticus (Linnaeus, 1758) in Lake Baringo, Kenya

    OpenAIRE

    Nyingi, Dorothy W.; Agnèse, Jean-François

    2007-01-01

    Nuclear DNA and mtDNA polymorphisms were surveyed in various species of East African Oreochromis. In Lake Baringo, where only Oreochromis niloticus baringoensis is present, alien mtDNA haplotypes were observed, apparently the result of introgressive hybridization with Oreochromis leucostictus. This introgression is not accompanied by any substantial or recorded transfer of nuclear genes into O. n. baringoensis.

  11. Comparative genomic hybridization (CGH) analysis of stage 4 neuroblastoma reveals high frequency of 11q deletion in tumors lacking MYCN amplification

    NARCIS (Netherlands)

    Plantaz, D.; Vandesompele, J.; van Roy, N.; Lastowska, M.; Bown, N.; Combaret, V.; Favrot, M. C.; Delattre, O.; Michon, J.; Bénard, J.; Hartmann, O.; Nicholson, J. C.; Ross, F. M.; Brinkschmidt, C.; Laureys, G.; Caron, H.; Matthay, K. K.; Feuerstein, B. G.; Speleman, F.

    2001-01-01

    We have studied the occurrence and association of 11q deletions with other chromosomal imbalances in Stage 4 neuroblastomas. To this purpose we have performed comparative genomic hybridization (CGH) analysis on 50 Stage 4 neuroblastomas and these data were analyzed together with those from 33

  12. Molecular Mapping of D1, D2 and ms5 Revealed Linkage between the Cotyledon Color Locus D2 and the Male-Sterile Locus ms5 in Soybean

    Directory of Open Access Journals (Sweden)

    Alina Ott

    2013-07-01

    Full Text Available In soybean, genic male sterility can be utilized as a tool to develop hybrid seed. Several male-sterile, female-fertile mutants have been identified in soybean. The male-sterile, female-fertile ms5 mutant was selected after fast neutron irradiation. Male-sterility due to ms5 was associated with the “stay-green” cotyledon color mutation. The cotyledon color trait in soybean is controlled by two loci, D1 and D2. Association between cotyledon color and male-sterility can be instrumental in early phenotypic selection of sterility for hybrid seed production. The use of such selection methods saves time, money, and space, as fewer seeds need to be planted and screened for sterility. The objectives of this study were to compare anther development between male-fertile and male-sterile plants, to investigate the possible linkages among the Ms5, D1 and D2 loci, and to determine if any of the d1 or d2 mutations can be applied in hybrid seed production. The cytological analysis during anther development displayed optically clear, disintegrating microspores and enlarged, engorged pollen in the male-sterile, female-fertile ms5ms5 plants, a common characteristic of male-sterile mutants. The D1 locus was mapped to molecular linkage group (MLG D1a and was flanked by Satt408 and BARCSOYSSR_01_1622. The ms5 and D2 loci were mapped to MLG B1 with a genetic distance ~12.8 cM between them. These results suggest that use of the d2 mutant in the selection of male-sterile line may attenuate the cost hybrid seed production in soybean.

  13. In Situ Hybridization Method Reveals (Pro)renin Receptor Expressing Cells in the Pituitary Gland of Rats: Correlation with Anterior Pituitary Hormones.

    Science.gov (United States)

    Takahashi, Kazuhiro; Yatabe, Megumi; Fujiwara, Ken; Hirose, Takuo; Totsune, Kazuhito; Yashiro, Takashi

    2013-02-28

    Expression of (pro)renin receptor ((P)RR), a specific receptor for renin and prorenin, was studied in rat pituitary gland. In situ hybridization showed that cells expressing (P)RR mRNA were widely distributed in the anterior lobe and intermediate lobe of the pituitary gland. Double-staining using in situ hybridization for (P)RR mRNA and immunohistochemistry for the pituitary hormones showed that (P)RR mRNA was expressed in most of the GH cells and ACTH cells in the anterior lobe. (P)RR mRNA was also expressed in a few prolactin cells and TSH cells, but not in LH cells. The present study has shown for the first time the distribution of (P)RR mRNA expressing cells in the rat pituitary gland. These findings suggest that (P)RR plays physiological roles in the pituitary gland, such as the modulation of the pituitary hormone secretion.

  14. In Situ Hybridization Method Reveals (Pro)renin Receptor Expressing Cells in the Pituitary Gland of Rats: Correlation with Anterior Pituitary Hormones

    International Nuclear Information System (INIS)

    Takahashi, Kazuhiro; Yatabe, Megumi; Fujiwara, Ken; Hirose, Takuo; Totsune, Kazuhito; Yashiro, Takashi

    2013-01-01

    Expression of (pro)renin receptor ((P)RR), a specific receptor for renin and prorenin, was studied in rat pituitary gland. In situ hybridization showed that cells expressing (P)RR mRNA were widely distributed in the anterior lobe and intermediate lobe of the pituitary gland. Double-staining using in situ hybridization for (P)RR mRNA and immunohistochemistry for the pituitary hormones showed that (P)RR mRNA was expressed in most of the GH cells and ACTH cells in the anterior lobe. (P)RR mRNA was also expressed in a few prolactin cells and TSH cells, but not in LH cells. The present study has shown for the first time the distribution of (P)RR mRNA expressing cells in the rat pituitary gland. These findings suggest that (P)RR plays physiological roles in the pituitary gland, such as the modulation of the pituitary hormone secretion

  15. A combined RT-PCR and dot-blot hybridization method reveals the coexistence of SJNNV and RGNNV betanodavirus genotypes in wild meagre (Argyrosomus regius).

    Science.gov (United States)

    Lopez-Jimena, B; Cherif, N; Garcia-Rosado, E; Infante, C; Cano, I; Castro, D; Hammami, S; Borrego, J J; Alonso, M C

    2010-10-01

    To detect the possible coexistence of striped jack nervous necrosis virus (SJNNV) and red-spotted grouper nervous necrosis virus (RGNNV) genotypes in a single fish, a methodology based on the combination of PCR amplification and blot hybridization has been developed and applied in this study. The degenerate primers designed for the PCR procedure target the T4 region within the capsid gene, resulting in the amplification of both genotypes. The subsequent hybridization of these amplification products with two different specific digoxigenin-labelled probes resulted in the identification of both genotypes separately. The application of the RT-PCR protocol to analyse blood samples from asymptomatic wild meagre (Argyrosomus regius) specimens has shown a 46.87% of viral nervous necrosis virus carriers. The combination of RT-PCR and blot hybridization increases the detection rate up to 90.62%, and, in addition, it has shown the coexistence of both genotypes in 18 out of the 32 specimens analysed (56.25%). This study reports the coexistence of betanodaviruses belonging to two different genotypes (SJNNV and RGNNV) in wild fish specimens. This is the first report demonstrating the presence of SJNNV and RGNNV genotypes in the same specimen. This study also demonstrates a carrier state in this fish species for the first time. © 2010 The Authors. Journal compilation © 2010 The Society for Applied Microbiology.

  16. The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes

    Directory of Open Access Journals (Sweden)

    Claude Pasquier

    2017-07-01

    Full Text Available Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson–Crick duplex. The “triplex-forming oligonucleotide” (TFO can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the “triplex-forming oligonucleotide” in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster. These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

  17. Control over the Strength of Connections Between Modules: A Double Dissociation Between Stimulus Format and Task Revealed by Granger Causality Mapping in fMRI

    Directory of Open Access Journals (Sweden)

    Britt eAnderson

    2015-03-01

    Full Text Available Drawing on theoretical and computational work with the localist Dual Route reading model and results from behavioral studies, Besner, Moroz, and O'Malley (2011 proposed that the ability to perform tasks that require overriding stimulus-specific defaults (e.g., semantics when naming Arabic numerals, and phonology when evaluating the parity of number words necessitate the ability to modulate the strength of connections between cognitive modules for lexical representation, semantics, and phonology on a task- and stimulus-specific basis. We used fMRI to evaluate this account by assessing changes in functional connectivity while participants performed tasks that did and did not require such stimulus-task default overrides. The occipital region showing the greatest modulation of BOLD signal strength for the two stimulus types was used as the seed region for Granger Causality Mapping (GCM. Our GCM analysis revealed a region of rostromedial frontal cortex with a crossover interaction. When participants performed tasks that required overriding stimulus type defaults (i.e., parity judgments of number words and naming Arabic numerals functional connectivity between the occipital region and rostromedial frontal cortex was present. Statistically significant functional connectivity was absent when the tasks were the default for the stimulus type (i.e., parity judgments of Arabic numerals and reading number words. This frontal region (BA 10 has previously been shown to be involved in goal-directed behaviour and maintenance of a specific task-set. We conclude that overriding stimulus-task defaults requires a modulation of connection strengths between cognitive modules and that the override mechanism predicted from cognitive theory is instantiated by frontal modulation of neural activity of brain regions specialized for sensory processing.

  18. Homozygosity mapping reveals new nonsense mutation in the FAM161A gene causing autosomal recessive retinitis pigmentosa in a Palestinian family.

    Science.gov (United States)

    Zobor, Ditta; Balousha, Ghassan; Baumann, Britta; Wissinger, Bernd

    2014-01-01

    Retinitis pigmentosa (RP) is a heterogenous group of inherited retinal degenerations caused by mutations in at least 45 genes. Recently, the FAM161A gene was identified as the causative gene for RP28, an autosomal recessive form of RP. We performed a clinical and molecular genetic study of a consanguineous Palestinian family with two three siblings affected with retinitis pigmentosa. DNA samples were collected from the index patient, his father, his affected sister, and two non-affected brothers. DNA sample from the index was subjected to high resolution genome-wide SNP array. Assuming identity-by-descent in this consanguineous family we applied homozygosity mapping to identify disease causing genes. The index patient reported night blindness since the age of 20 years, followed by moderate disease progression with decrease of peripheral vision, the development of photophobia and later on reduced central vision. At the age of 40 his visual acuity was counting fingers (CF) for both eyes, color discrimination was not possible and his visual fields were severely constricted. Funduscopic examination revealed a typical appearance of advanced RP with optic disc pallor, narrowed retinal vessels, bone-spicule like pigmentary changes in the mid-periphery and atrophic changes in the macula. His younger affected brother (37 years) was reported with overall milder symptoms, while the youngest sister (21 years) reported problems only with night vision. Applying high-density SNP arrays we identified several homozygous genomic regions one of which included the recently identified FAM161A gene mutated in RP28-linked autosomal recessive RP. Sequencing analysis revealed the presence of a novel homozygous nonsense mutation, c.1003C>T/p.R335X in the index patient and the affected sister. We identified an RP28-linked RP family in the Palestinian population caused by a novel nonsense mutation in FAM161A. RP in this family shows a typical disease onset with moderate to rapid progression

  19. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    , a part of the brain that controls vital bodily functions, we employed locked nucleic acid (LNA) - fluorescent in situ hybridization (FISH). The expression pattern of the mature miRNAs miR-7a, miR-7b, miR-137 and miR-153 in mouse brain tissue sections was investigated. Whereas all studied miRNAs were......R-7a expression was particularly prominent in the subfornical organ, suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a was seen in mouse and rat hypothalamus. By combining LNA-FISH with immunohistochemistry...

  20. Revealing the properties of defects formed by CH3NH2 molecules in organic-inorganic hybrid perovskite MAPbBr3

    Science.gov (United States)

    Wang, Ji; Zhang, Ao; Yan, Jun; Li, Dan; Chen, Yunlin

    2017-03-01

    The properties of defects in organic-inorganic hybrid perovskite are widely studied from the first-principles calculation. However, the defects of methylamine (methylamine = CH3NH2), which would be easily formed during the preparation of the organic-inorganic hybrid perovskite, are rarely investigated. Thermodynamic properties as well as defect states of methylamine embedded MAPbX3 (MA = methyl-ammonium = CH3NH3, X = Br, I) are studied based on first-principles calculations of density functional theory. It was found that there is a shallow defect level near the highest occupied molecular orbital, which induced by the interstitial methylamine defect in MAPbBr3, will lead to an increase of photoluminescence. The calculation results showed that interstitial defect states of methylamine may move deeper due to the interaction between methylamine molecules and methyl-ammonium cations. It was also showed that the interstitial methylamine defect is stable at room temperature, and the defect can be removed easily by annealing.

  1. Hybrid PET/MR imaging: an algorithm to reduce metal artifacts from dental implants in Dixon-based attenuation map generation using a multiacquisition variable-resonance image combination sequence.

    Science.gov (United States)

    Burger, Irene A; Wurnig, Moritz C; Becker, Anton S; Kenkel, David; Delso, Gaspar; Veit-Haibach, Patrick; Boss, Andreas

    2015-01-01

    It was the aim of this study to implement an algorithm modifying Dixon-based MR imaging datasets for attenuation correction in hybrid PET/MR imaging with a multiacquisition variable resonance image combination (MAVRIC) sequence to reduce metal artifacts. After ethics approval, in 8 oncologic patients with dental implants data were acquired in a trimodality setup with PET/CT and MR imaging. The protocol included a whole-body 3-dimensional dual gradient-echo sequence (Dixon) used for MR imaging-based PET attenuation correction and a high-resolution MAVRIC sequence, applied in the oral area compromised by dental implants. An algorithm was implemented correcting the Dixon-based μ maps using the MAVRIC in areas of Dixon signal voids. The artifact size of the corrected μ maps was compared with the uncorrected MR imaging μ maps. The algorithm was robust in all patients. There was a significant reduction in mean artifact size of 70.5% between uncorrected and corrected μ maps from 697 ± 589 mm(2) to 202 ± 119 mm(2) (P = 0.016). The proposed algorithm could improve MR imaging-based attenuation correction in critical areas, when standard attenuation correction is hampered by metal artifacts, using a MAVRIC. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  2. BOLD Imaging in Awake Wild-Type and Mu-Opioid Receptor Knock-Out Mice Reveals On-Target Activation Maps in Response to Oxycodone

    Directory of Open Access Journals (Sweden)

    Kelsey Moore

    2016-11-01

    Full Text Available Blood oxygen level dependent (BOLD imaging in awake mice was used to identify differences in brain activity between wild-type, and Mu (µ opioid receptor knock-outs (MuKO in response to oxycodone (OXY. Using a segmented, annotated MRI mouse atlas and computational analysis, patterns of integrated positive and negative BOLD activity were identified across 122 brain areas. The pattern of positive BOLD showed enhanced activation across the brain in WT mice within 15 min of intraperitoneal administration of 2.5 mg of OXY. BOLD activation was detected in 72 regions out of 122, and was most prominent in areas of high µ opioid receptor density (thalamus, ventral tegmental area, substantia nigra, caudate putamen, basal amygdala and hypothalamus, and focus on pain circuits indicated strong activation in major pain processing centers (central amygdala, solitary tract, parabrachial area, insular cortex, gigantocellularis area, ventral thalamus primary sensory cortex and prelimbic cortex. Importantly, the OXY-induced positive BOLD was eliminated in MuKO mice in most regions, with few exceptions (some cerebellar nuclei, CA3 of the hippocampus, medial amygdala and preoptic areas. This result indicates that most effects of OXY on positive BOLD are mediated by the µ opioid receptor (on-target effects. OXY also caused an increase in negative BOLD in WT mice in few regions (16 out of 122 and, unlike the positive BOLD response the negative BOLD was only partially eliminated in the MuKO mice (cerebellum, and in some case intensified (hippocampus. Negative BOLD analysis therefore shows activation and deactivation events in the absence of the µ receptor for some areas where receptor expression is normally extremely low or absent (off-target effects. Together, our approach permits establishing opioid-induced BOLD activation maps in awake mice. In addition, comparison of WT and MuKO mutant mice reveals both on-target and off-target activation events, and set an OXY

  3. Global mapping of cell type-specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation.

    Directory of Open Access Journals (Sweden)

    Hironori Waki

    2011-10-01

    Full Text Available Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type-specific gene expression. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq. FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation, while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARγ and C/EBPα, the master regulators of adipocyte differentiation. Computational motif analyses of the adipocyte-specific FAIRE peaks revealed enrichment of a binding motif for nuclear family I (NFI transcription factors. Indeed, ChIP assay showed that NFI occupy the adipocyte-specific FAIRE peaks and/or the PPARγ binding sites near PPARγ, C/EBPα, and aP2 genes. Overexpression of NFIA in 3T3-L1 cells resulted in robust induction of these genes and lipid droplet formation without differentiation stimulus. Overexpression of dominant-negative NFIA or siRNA-mediated knockdown of NFIA or NFIB significantly suppressed both induction of genes and lipid accumulation during differentiation, suggesting a physiological function of these factors in the adipogenic program. Together, our

  4. High-resolution mapping reveals linkage between genes in common bean cultivar Ouro Negro conferring resistance to the rust, anthracnose, and angular leaf spot diseases.

    Science.gov (United States)

    Valentini, Giseli; Gonçalves-Vidigal, Maria Celeste; Hurtado-Gonzales, Oscar P; de Lima Castro, Sandra Aparecida; Cregan, Perry B; Song, Qijian; Pastor-Corrales, Marcial A

    2017-08-01

    Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 4 /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean. Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 4 /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F 2:3 families from the Rudá (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 4 /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 4 /Phg-3 cluster were closely linked. Genotyping the F 2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 4 /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 4 /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 4 /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 4 /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

  5. Hybrid incompatibilities in the parasitic wasp genus Nasonia: negative effects of hemizygosity and the identification of transmission ratio distortion loci.

    Science.gov (United States)

    Koevoets, T; Niehuis, O; van de Zande, L; Beukeboom, L W

    2012-03-01

    The occurrence of hybrid incompatibilities forms an important stage during the evolution of reproductive isolation. In early stages of speciation, males and females often respond differently to hybridization. Haldane's rule states that the heterogametic sex suffers more from hybridization than the homogametic sex. Although haplodiploid reproduction (haploid males, diploid females) does not involve sex chromosomes, sex-specific incompatibilities are predicted to be prevalent in haplodiploid species. Here, we evaluate the effect of sex/ploidy level on hybrid incompatibilities and locate genomic regions that cause increased mortality rates in hybrid males of the haplodiploid wasps Nasonia vitripennis and Nasonia longicornis. Our data show that diploid F(1) hybrid females suffer less from hybridization than haploid F(2) hybrid males. The latter not only suffer from an increased mortality rate, but also from behavioural and spermatogenic sterility. Genetic mapping in recombinant F(2) male hybrids revealed that the observed hybrid mortality is most likely due to a disruption of cytonuclear interactions. As these sex-specific hybrid incompatibilities follow predictions based on Haldane's rule, our data accentuate the need to broaden the view of Haldane's rule to include species with haplodiploid sex determination, consistent with Haldane's original definition.

  6. Admixture mapping in the Hispanic Community Health Study/Study of Latinos reveals regions of genetic associations with blood pressure traits.

    Directory of Open Access Journals (Sweden)

    Tamar Sofer

    Full Text Available Admixture mapping can be used to detect genetic association regions in admixed populations, such as Hispanics/Latinos, by estimating associations between local ancestry allele counts and the trait of interest. We performed admixture mapping of the blood pressure traits systolic and diastolic blood pressure (SBP, DBP, mean arterial pressure (MAP, and pulse pressure (PP, in a dataset of 12,116 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL. Hispanics/Latinos have three predominant ancestral populations (European, African, and Amerindian, for each of which we separately tested local ancestry intervals across the genome. We identified four regions that were significantly associated with a blood pressure trait at the genome-wide admixture mapping level. A 6p21.31 Amerindian ancestry association region has multiple known associations, but none explained the admixture mapping signal. We identified variants that completely explained this signal. One of these variants had p-values of 0.02 (MAP and 0.04 (SBP in replication testing in Pima Indians. A 11q13.4 Amerindian ancestry association region spans a variant that was previously reported (p-value = 0.001 in a targeted association study of Blood Pressure (BP traits and variants in the vitamin D pathway. There was no replication evidence supporting an association in the identified 17q25.3 Amerindian ancestry association region. For a region on 6p12.3, associated with African ancestry, we did not identify any candidate variants driving the association. It may be driven by rare variants. Whole genome sequence data may be necessary to fine map these association signals, which may contribute to disparities in BP traits between diverse populations.

  7. A Novel Audio Cryptosystem Using Chaotic Maps and DNA Encoding

    Directory of Open Access Journals (Sweden)

    S. J. Sheela

    2017-01-01

    Full Text Available Chaotic maps have good potential in security applications due to their inherent characteristics relevant to cryptography. This paper introduces a new audio cryptosystem based on chaotic maps, hybrid chaotic shift transform (HCST, and deoxyribonucleic acid (DNA encoding rules. The scheme uses chaotic maps such as two-dimensional modified Henon map (2D-MHM and standard map. The 2D-MHM which has sophisticated chaotic behavior for an extensive range of control parameters is used to perform HCST. DNA encoding technology is used as an auxiliary tool which enhances the security of the cryptosystem. The performance of the algorithm is evaluated for various speech signals using different encryption/decryption quality metrics. The simulation and comparison results show that the algorithm can achieve good encryption results and is able to resist several cryptographic attacks. The various types of analysis revealed that the algorithm is suitable for narrow band radio communication and real-time speech encryption applications.

  8. An extended anchored linkage map and virtual mapping for the american mink genome based on homology to human and dog

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Ansari, S.; Farid, A.

    2009-01-01

    hybridization (FISH) and/or by means of human/dog/mink comparative homology. The average interval between markers is 8.5 cM and the linkage groups collectively span 1340 cM. In addition, 217 and 275 mink microsatellites have been placed on human and dog genomes, respectively. In conjunction with the existing...... comparative human/dog/mink data, these assignments represent useful virtual maps for the American mink genome. Comparison of the current human/dog assembled sequential map with the existing Zoo-FISH-based human/dog/mink maps helped to refine the human/dog/mink comparative map. Furthermore, comparison...... of the human and dog genome assemblies revealed a number of large synteny blocks, some of which are corroborated by data from the mink linkage map....

  9. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes.

    Science.gov (United States)

    Weng, Yiqun; Colle, Marivi; Wang, Yuhui; Yang, Luming; Rubinstein, Mor; Sherman, Amir; Ophir, Ron; Grumet, Rebecca

    2015-09-01

    QTL analysis in multi-development stages with different QTL models identified 12 consensus QTLs underlying fruit elongation and radial growth presenting a dynamic view of genetic control of cucumber fruit development. Fruit size is an important quality trait in cucumber (Cucumis sativus L.) of different market classes. However, the genetic and molecular basis of fruit size variations in cucumber is not well understood. In this study, we conducted QTL mapping of fruit size in cucumber using F2, F2-derived F3 families and recombinant inbred lines (RILs) from a cross between two inbred lines Gy14 (North American picking cucumber) and 9930 (North China fresh market cucumber). Phenotypic data of fruit length and diameter were collected at three development stages (anthesis, immature and mature fruits) in six environments over 4 years. QTL analysis was performed with three QTL models including composite interval mapping (CIM), Bayesian interval mapping (BIM), and multiple QTL mapping (MQM). Twenty-nine consistent and distinct QTLs were detected for nine traits from multiple mapping populations and QTL models. Synthesis of information from available fruit size QTLs allowed establishment of 12 consensus QTLs underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Discussion was presented in the context of domestication and diversifying selection of fruit length and diameter, marker-assisted selection of fruit size, as well as identification of candidate genes for fruit size QTLs in cucumber.

  10. Mechanisms of Transmission Ratio Distortion at Hybrid Sterility Loci Within and Between Mimulus Species

    Directory of Open Access Journals (Sweden)

    Rachel E. Kerwin

    2017-11-01

    Full Text Available Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 (hms1 and hybrid male sterility 2 (hms2 in the closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. By performing reciprocal backcrosses with introgression lines (ILs, we find evidence for gametic expression of the hms1-hms2 incompatibility. Surprisingly, however, hybrid transmission ratios at hms1 do not reflect this incompatibility, suggesting that additional mechanisms counteract the effects of gametic sterility. Indeed, our backcross experiment shows hybrid transmission bias toward M. guttatus through both pollen and ovules, an effect that is particularly strong when hms2 is homozygous for M. nasutus alleles. In contrast, we find little evidence for hms1 transmission bias in crosses within M. guttatus, providing no indication of selfish evolution at this locus. Although we do not yet have sufficient genetic resolution to determine if hybrid sterility and transmission ratio distortion (TRD map to the same loci, our preliminary fine-mapping uncovers a genetically independent hybrid lethality system involving at least two loci linked to hms1. This fine-scale dissection of TRD at hms1 and hms2 provides insight into genomic differentiation between closely related Mimulus species and reveals multiple mechanisms of hybrid dysfunction.

  11. Mechanisms of Transmission Ratio Distortion at Hybrid Sterility Loci Within and Between Mimulus Species.

    Science.gov (United States)

    Kerwin, Rachel E; Sweigart, Andrea L

    2017-11-06

    Hybrid incompatibilities are a common correlate of genomic divergence and a potentially important contributor to reproductive isolation. However, we do not yet have a detailed understanding of how hybrid incompatibility loci function and evolve within their native species, or why they are dysfunctional in hybrids. Here, we explore these issues for a well-studied, two-locus hybrid incompatibility between hybrid male sterility 1 ( hms1 ) and hybrid male sterility 2 ( hms2 ) in the closely related yellow monkeyflower species Mimulus guttatus and M. nasutus By performing reciprocal backcrosses with introgression lines (ILs), we find evidence for gametic expression of the hms1-hms2 incompatibility. Surprisingly, however, hybrid transmission ratios at hms1 do not reflect this incompatibility, suggesting that additional mechanisms counteract the effects of gametic sterility. Indeed, our backcross experiment shows hybrid transmission bias toward M. guttatus through both pollen and ovules, an effect that is particularly strong when hms2 is homozygous for M. nasutus alleles. In contrast, we find little evidence for hms1 transmission bias in crosses within M. guttatus , providing no indication of selfish evolution at this locus. Although we do not yet have sufficient genetic resolution to determine if hybrid sterility and transmission ratio distortion (TRD) map to the same loci, our preliminary fine-mapping uncovers a genetically independent hybrid lethality system involving at least two loci linked to hms1 This fine-scale dissection of TRD at hms1 and hms2 provides insight into genomic differentiation between closely related Mimulus species and reveals multiple mechanisms of hybrid dysfunction. Copyright © 2017 Kerwin and Sweigart.

  12. In situ hybridization reveals that type I and III collagens are produced by pericytes in the anterior pituitary gland of rats.

    Science.gov (United States)

    Fujiwara, Ken; Jindatip, Depicha; Kikuchi, Motoshi; Yashiro, Takashi

    2010-12-01

    Type I and III collagens widely occur in the rat anterior pituitary gland and are the main components of the extracellular matrix (ECM). Although ECM components possibly play an important role in the function of the anterior pituitary gland, little is known about collagen-producing cells. Type I collagen is a heterotrimer of two α1(I) chains (the product of the col1a1 gene) and one α2(I) chain (the product of the col1a2 gene). Type III collagen is a homotrimer of α1(III) chains (the product of the col3a1 gene). We used in situ hybridization with digoxigenin-labeled cRNA probes to examine the expression of col1a1, col1a2, and col3a1 mRNAs in the pituitary gland of adult rats. mRNA expression for these collagen genes was clearly observed, and cells expressing col1a1, col1a2, and col3a1 mRNA were located around capillaries in the gland. We also investigated the possible double-staining of collagen mRNA and pituitary hormones, S-100 protein (a marker of folliculo-stellate cells), or desmin (a marker of pericytes). Col1a1 and col3a1 mRNA were identified in desmin-immunopositive cells. Thus, only pericytes produce type I and III collagens in the rat anterior pituitary gland.

  13. Angiofibroma of soft tissue with fibrohistiocytic features and intratumor genetic heterogeneity of NCOA2 gene rearrangement revealed by chromogenic in situ hybridization: a case report.

    Science.gov (United States)

    Fukuda, Yumiko; Motoi, Toru; Kato, Ikuma; Ikegami, Masachika; Funata, Nobuaki; Ohtomo, Rie; Horiguchi, Shinichiro; Goto, Takahiro; Hishima, Tsunekazu

    2014-05-01

    Angiofibroma of soft tissue is a recently described soft tissue tumor that is characterized by fibroblastic spindle tumor cells with arborizing capillary proliferation. Cytogenetically, it harbors a specific fusion gene involving the nuclear receptor coactivator 2 (NCOA2) gene. We report here additional new pathological and cytogenetic features. A soft tissue tumor in the left thigh of 73-year-old female was investigated. Microscopically, histiocytoid tumor cells were scattered in an edematous background with branching capillary proliferation. Immunohistochemically, we identified that the tumor cells were positive for histiocytic markers such as CD68 and CD163. Rearrangement of the NCOA2 gene was detected successfully by chromogenic in situ hybridization; however, abnormal signal patterns were observed in only a small subset of tumor cells. Unlike typical tumors with bland spindle cells, the present tumor needs to be distinguished from myxoid, dendritic and clear cell tumors. This case may suggest that angiofibroma of soft tissue is not in the center of the fibroblastic/myofibroblastic tumor group, but rather shows a fibrohistiocytic nature. We also found intratumor genetic heterogeneity, which is uncommon for a translocation-associated tumor. Therefore, careful evaluation is required to detect the gene rearrangement in this tumor entity. © 2014 The Authors. Pathology International © 2014 Japanese Society of Pathology and Wiley Publishing Asia Pty Ltd.

  14. Cytogenetics of Festulolium (Festuca x Lolium hybrids).

    Science.gov (United States)

    Kopecký, D; Lukaszewski, A J; Dolezel, J

    2008-01-01

    Grasses are the most important and widely cultivated crops. Among them, ryegrasses (Lolium spp.) and fescues (Festuca spp.) provide high quality fodder for livestock, are used for turf and amenity purposes, and play a fundamental role in environment protection. Species from the two genera display complementary agronomic characteristics and are often grown in mixtures. Breeding efforts to combine desired features in single entities culminated with the production of Festuca x Lolium hybrids. The so called Festuloliums enjoy a considerable commercial success with numerous cultivars registered all over the world. They are also very intriguing from a strictly cytogenetic point of view as the parental chromosomes recombine freely in hybrids. Until a decade ago this phenomenon was only known in general quantitative terms. The introduction of molecular cytogenetic tools such as FISH and GISH permitted detailed studies of intergeneric chromosome recombination and karyotyping of Festulolium cultivars. These tools were also invaluable in revealing the origin of polyploid fescues, and facilitated the development of chromosome substitution and introgression lines and physical mapping of traits of interest. Further progress in this area will require the development of a larger set of cytogenetic markers and high-resolution cytogenetic maps. It is expected that the Lolium-Festuca complex will continue providing opportunities for breeding superior grass cultivars and the complex will remain an attractive platform for fundamental research of the early steps of hybrid speciation and interaction of parental genomes, as well as the processes of chromosome pairing, elimination and recombination. 2008 S. Karger AG, Basel

  15. Hybrid perovskite solar cells: In situ investigation of solution-processed PbI2 reveals metastable precursors and a pathway to producing porous thin films

    KAUST Repository

    Barrit, Dounya; Sheikh, Arif D.; Munir, Rahim; Barbe, Jeremy; Li, Ruipeng; Smilgies, Detlef-M.; Amassian, Aram

    2017-01-01

    from a DMF solution by performing in situ grazing incidence wide angle X-ray scattering (GIWAXS) measurements. The measurements reveal an elaborate sol–gel process involving three PbI2⋅DMF solvate complexes—including disordered and ordered ones

  16. Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

    NARCIS (Netherlands)

    Dijk, van T.; Pagliarani, G.; Pikunova, A.; Noordijk, Y.; Yilmaz-Temel, H.; Meulenbroek, B.; Visser, R.G.F.; Weg, van de W.E.

    2014-01-01

    Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map

  17. A dense SNP-based linkage map for Atlantic salmon (Salmo salar reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns

    Directory of Open Access Journals (Sweden)

    Lien Sigbjørn

    2011-12-01

    Full Text Available Abstract Background The Atlantic salmon genome is in the process of returning to a diploid state after undergoing a whole genome duplication (WGD event between 25 and100 million years ago. Existing data on the proportion of paralogous sequence variants (PSVs, multisite variants (MSVs and other types of complex sequence variation suggest that the rediplodization phase is far from over. The aims of this study were to construct a high density linkage map for Atlantic salmon, to characterize the extent of rediploidization and to improve our understanding of genetic differences between sexes in this species. Results A linkage map for Atlantic salmon comprising 29 chromosomes and 5650 single nucleotide polymorphisms (SNPs was constructed using genotyping data from 3297 fish belonging to 143 families. Of these, 2696 SNPs were generated from ESTs or other gene associated sequences. Homeologous chromosomal regions were identified through the mapping of duplicated SNPs and through the investigation of syntenic relationships between Atlantic salmon and the reference genome sequence of the threespine stickleback (Gasterosteus aculeatus. The sex-specific linkage maps spanned a total of 2402.3 cM in females and 1746.2 cM in males, highlighting a difference in sex specific recombination rate (1.38:1 which is much lower than previously reported in Atlantic salmon. The sexes, however, displayed striking differences in the distribution of recombination sites within linkage groups, with males showing recombination strongly localized to telomeres. Conclusion The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization, aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence.

  18. Differential ontogenetic patterns of levocabastine-sensitive neurotensin NT2 receptors and of NT1 receptors in the rat brain revealed by in situ hybridization.

    Science.gov (United States)

    Lépée-Lorgeoux, I; Betancur, C; Rostène, W; Pélaprat, D

    1999-03-12

    The postnatal ontogeny of the levocabastine-sensitive neurotensin receptor (NT2) mRNA was studied by in situ hybridization in the rat brain and compared with the distribution of the levocabastine-insensitive NT1 receptor. NT2 receptor mRNA was absent at birth from all brain structures except the ependymal cell layer lining the ventricles. The development of NT2 receptor mRNA followed three ontogenetic patterns. The first pattern, involving the majority of the cerebral gray matter, was characterized by a continuous increase from postnatal day 5 (P5) to P30. The second one, involving regions rich in myelinated fibers such as the corpus callosum and lacunosum moleculare layer of the hippocampus, exhibited a pronounced increase between P5 and P10, peaked at P15 and was followed by a plateau or a slight decrease. The third pattern was observed in the ependymal cell layer lining the olfactory and lateral ventricles, where the high labeling already present at birth continued to increase during development. These different developmental patterns could reflect the variety of cells expressing NT2 receptor mRNA, including neurons, protoplasmic astrocytes in gray matter, fibrous astrocytes present in myelinated fibers tracts, and ependymal cells. In contrast, NT1 receptor mRNA, which seems to be associated only with neurons, was highly and transiently expressed during the perinatal period in the cerebral cortex, hippocampus and striatal neuroepithelium. Other regions, notably the ventral tegmental area and substantia nigra compacta, exhibited a gradual increase in NT1 receptor signal, reaching adult levels by P21. Both the differential localization and ontogenetic profiles of NT1 and NT2 receptor mRNAs suggest different involvement of these two receptors in brain functions and development. Copyright 1999 Elsevier Science B.V.

  19. Gravity Modes Reveal the Internal Rotation of a Post-mass-transfer Gamma Doradus/Delta Scuti Hybrid Pulsator in Kepler Eclipsing Binary KIC 9592855

    Science.gov (United States)

    Guo, Z.; Gies, D. R.; Matson, R. A.

    2017-12-01

    We report the discovery of a post-mass-transfer Gamma Doradus/Delta Scuti hybrid pulsator in the eclipsing binary KIC 9592855. This binary has a circular orbit, an orbital period of 1.2 days, and contains two stars of almost identical masses ({M}1=1.72 {M}⊙ ,{M}2=1.71 {M}⊙ ). However, the cooler secondary star is more evolved ({R}2=1.96 {R}⊙ ), while the hotter primary is still on the zero-age-main-sequence ({R}1=1.53 {R}⊙ ). Coeval models from single-star evolution cannot explain the observed masses and radii, and binary evolution with mass-transfer needs to be invoked. After subtracting the binary light curve, the Fourier spectrum shows low-order pressure-mode pulsations, and more dominantly, a cluster of low-frequency gravity modes at about 2 day-1. These g-modes are nearly equally spaced in period, and the period spacing pattern has a negative slope. We identify these g-modes as prograde dipole modes and find that they stem from the secondary star. The frequency range of unstable p-modes also agrees with that of the secondary. We derive the internal rotation rate of the convective core and the asymptotic period spacing from the observed g-modes. The resulting values suggest that the core and envelope rotate nearly uniformly, i.e., their rotation rates are both similar to the orbital frequency of this synchronized binary.

  20. Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes

    Directory of Open Access Journals (Sweden)

    María Arriba

    2017-01-01

    Full Text Available AIM: To investigate whether chromosomal instability (CIN is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability and CIMP (CpG island methylator phenotype in early-onset colorectal cancer (EOCRC. METHODS: Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis were analyzed by array comparative genomic hybridization (aCGH, in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs and the MSI/CIMP condition in EOCRC. RESULTS: Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B and four secondary clusters (A1, A2, B3, B4. The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC, which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS: Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.

  1. A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters (Crassostrea gigas × Crassostrea angulata Using Genotyping-by-Sequencing

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-05-01

    Full Text Available Oysters are among the most important species in global aquaculture. Crassostrea gigas, and its subspecies C. angulata, are the major cultured species. To determine the genetic basis of growth-related traits in oysters, we constructed a second-generation linkage map from 3367 single-nucleotide polymorphisms (SNPs based on genotyping-by-sequencing, genotyped from a C. gigas × C. angulata hybrid family. These 3367 SNPs were distributed on 1695 markers, which were assigned to 10 linkage groups. The genetic linkage map had a total length of 1084.3 cM, with an average of 0.8 cM between markers; it thus represents the densest genetic map constructed for oysters to date. Twenty-seven quantitative trait loci (QTL for five growth-related traits were detected. These QTL could explain 4.2–7.7% (mean = 5.4% of the phenotypic variation. In total, 50.8% of phenotypic variance for shell width, 7.7% for mass weight, and 34.1% for soft tissue weight were explained. The detected QTL were distributed among eight linkage groups, and more than half (16 were concentrated within narrow regions in their respective linkage groups. Thirty-eight annotated genes were identified within the QTL regions, two of which are key genes for carbohydrate metabolism. Other genes were found to participate in assembly and regulation of the actin cytoskeleton, signal transduction, and regulation of cell differentiation and development. The newly developed high-density genetic map, and the QTL and candidate genes identified provide a valuable genetic resource and a basis for marker-assisted selection for C. gigas and C. angulata.

  2. A putative hybrid swarm within Oonopsis foliosa (Asteraceae: Astereae)

    Science.gov (United States)

    Hughes, J.F.; Brown, G.K.

    2004-01-01

    Oo??nopsis foliosa var. foliosa and var. monocephala are endemic to short-grass steppe of southeastern Colorado and until recently were considered geographically disjunct. The only known qualitative feature separating these 2 varieties is floral head type; var. foliosa has radiate heads, whereas var. monocephala heads are discoid. Sympatry between these varieties is restricted to a small area in which a range of parental types and intermediate head morphologies is observed. We used distribution mapping, morphometric analyses, chromosome cytology, and pollen stainability to characterize the sympatric zone. Morphometrics confirms that the only discrete difference between var. foliosa and var. monocephala is radiate versus discoid heads, respectively. The outer florets of putative hybrid individuals ranged from conspicuously elongated yet radially symmetric disc-floret corollas, to elongated radially asymmetric bilabiate- or deeply cleft corollas, to stunted ray florets with appendages remnant of corolla lobes. Chromosome cytology of pollen mother cells from both putative parental varieties and a series of intermediate morphological types collected at the sympatric zone reveal evidence of translocation heterozygosity. Pollen stainability shows no significant differences in viability between the parental varieties and putative hybrids. The restricted distribution of putative hybrids to a narrow zone of sympatry between the parental types and the presence of meiotic chromosome-pairing anomalies in these intermediate plants are consistent with a hybrid origin. The high stainability of putative-hybrid pollen adds to a growing body of evidence that hybrids are not universally unfit.

  3. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758 reveals slow genome and chromosome evolution in the Apidae

    Directory of Open Access Journals (Sweden)

    Kube Michael

    2011-01-01

    Full Text Available Abstract Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.

  4. Recognition of ERK MAP kinase by PEA-15 reveals a common docking site within the death domain and death effector domain

    OpenAIRE

    Hill, Justine M.; Vaidyanathan, Hema; Ramos, Joe W.; Ginsberg, Mark H.; Werner, Milton H.

    2002-01-01

    PEA-15 is a multifunctional protein that modulates signaling pathways which control cell proliferation and cell death. In particular, PEA-15 regulates the actions of the ERK MAP kinase cascade by binding to ERK and altering its subcellular localization. The three-dimensional structure of PEA-15 has been determined using NMR spectroscopy and its interaction with ERK defined by characterization of mutants that modulate ERK function. PEA-15 is composed of an N-terminal death effector domain (DED...

  5. High-throughput sequencing of Campylobacter jejuni insertion mutant libraries reveals mapA as a fitness factor for chicken colonization.

    Science.gov (United States)

    Johnson, Jeremiah G; Livny, Jonathan; Dirita, Victor J

    2014-06-01

    Campylobacter jejuni is a leading cause of gastrointestinal infections worldwide, due primarily to its ability to asymptomatically colonize the gastrointestinal tracts of agriculturally relevant animals, including chickens. Infection often occurs following consumption of meat that was contaminated by C. jejuni during harvest. Because of this, much interest lies in understanding the mechanisms that allow C. jejuni to colonize the chicken gastrointestinal tract. To address this, we generated a C. jejuni transposon mutant library that is amenable to insertion sequencing and introduced this mutant pool into day-of-hatch chicks. Following deep sequencing of C. jejuni mutants in the cecal outputs, several novel factors required for efficient colonization of the chicken gastrointestinal tract were identified, including the predicted outer membrane protein MapA. A mutant strain lacking mapA was constructed and found to be significantly reduced for chicken colonization in both competitive infections and monoinfections. Further, we found that mapA is required for in vitro competition with wild-type C. jejuni but is dispensable for growth in monoculture.

  6. From hybrid swarms to swarms of hybrids

    Science.gov (United States)

    Stohlgren, Thomas J.; Szalanski, Allen L; Gaskin, John F.; Young, Nicholas E.; West, Amanda; Jarnevich, Catherine S.; Tripodi, Amber

    2014-01-01

    Science has shown that the introgression or hybridization of modern humans (Homo sapiens) with Neanderthals up to 40,000 YBP may have led to the swarm of modern humans on earth. However, there is little doubt that modern trade and transportation in support of the humans has continued to introduce additional species, genotypes, and hybrids to every country on the globe. We assessed the utility of species distributions modeling of genotypes to assess the risk of current and future invaders. We evaluated 93 locations of the genus Tamarix for which genetic data were available. Maxent models of habitat suitability showed that the hybrid, T. ramosissima x T. chinensis, was slightly greater than the parent taxa (AUCs > 0.83). General linear models of Africanized honey bees, a hybrid cross of Tanzanian Apis mellifera scutellata and a variety of European honey bee including A. m. ligustica, showed that the Africanized bees (AUC = 0.81) may be displacing European honey bees (AUC > 0.76) over large areas of the southwestern U.S. More important, Maxent modeling of sub-populations (A1 and A26 mitotypes based on mDNA) could be accurately modeled (AUC > 0.9), and they responded differently to environmental drivers. This suggests that rapid evolutionary change may be underway in the Africanized bees, allowing the bees to spread into new areas and extending their total range. Protecting native species and ecosystems may benefit from risk maps of harmful invasive species, hybrids, and genotypes.

  7. Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

    Czech Academy of Sciences Publication Activity Database

    Kumar, A.; Seetan, R.; Mergoum, M.; Tiwari, V.K.; Iqbal, M.; Wang, Y.; Al-Azzam, O.; Šimková, Hana; Luo, M.C.; Dvorak, J.; Gu, Y.Q.; Denton, A.; Kilian, A.; Lazo, G.R.; Kianian, S.F.

    2015-01-01

    Roč. 16, OCT 16 (2015), s. 800 ISSN 1471-2164 R&D Projects: GA ČR(CZ) GAP501/12/2554 Institutional support: RVO:61389030 Keywords : Aegilops tauschii * Deletion * Physical mapping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.867, year: 2015

  8. Genome-wide association mapping reveals a rich genetic architecture of stripe rust resistance loci in emmer wheat (Triticum turgidum ssp. dicoccum).

    Science.gov (United States)

    Liu, Weizhen; Maccaferri, Marco; Chen, Xianming; Laghetti, Gaetano; Pignone, Domenico; Pumphrey, Michael; Tuberosa, Roberto

    2017-11-01

    SNP-based genome scanning in worldwide domesticated emmer germplasm showed high genetic diversity, rapid linkage disequilibrium decay and 51 loci for stripe rust resistance, a large proportion of which were novel. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum), one of the oldest domesticated crops in the world, is a potentially rich reservoir of variation for improvement of resistance/tolerance to biotic and abiotic stresses in wheat. Resistance to stripe rust (Puccinia striiformis f. sp. tritici) in emmer wheat has been under-investigated. Here, we employed genome-wide association (GWAS) mapping with a mixed linear model to dissect effective stripe rust resistance loci in a worldwide collection of 176 cultivated emmer wheat accessions. Adult plants were tested in six environments and seedlings were evaluated with five races from the United States and one from Italy under greenhouse conditions. Five accessions were resistant across all experiments. The panel was genotyped with the wheat 90,000 Illumina iSelect single nucleotide polymorphism (SNP) array and 5106 polymorphic SNP markers with mapped positions were obtained. A high level of genetic diversity and fast linkage disequilibrium decay were observed. In total, we identified 14 loci associated with field resistance in multiple environments. Thirty-seven loci were significantly associated with all-stage (seedling) resistance and six of them were effective against multiple races. Of the 51 total loci, 29 were mapped distantly from previously reported stripe rust resistance genes or quantitative trait loci and represent newly discovered resistance loci. Our results suggest that GWAS is an effective method for characterizing genes in cultivated emmer wheat and confirm that emmer wheat is a rich source of stripe rust resistance loci that can be used for wheat improvement.

  9. The first human epitope map of the alphaviral E1 and E2 proteins reveals a new E2 epitope with significant virus neutralizing activity.

    Directory of Open Access Journals (Sweden)

    Ann R Hunt

    2010-07-01

    Full Text Available Venezuelan equine encephalitis virus (VEEV is responsible for VEE epidemics that occur in South and Central America and the U.S. The VEEV envelope contains two glycoproteins E1 (mediates cell membrane fusion and E2 (binds receptor and elicits virus neutralizing antibodies. Previously we constructed E1 and E2 epitope maps using murine monoclonal antibodies (mMAbs. Six E2 epitopes (E2(c,d,e,f,g,h bound VEEV-neutralizing antibody and mapped to amino acids (aa 182-207. Nothing is known about the human antibody repertoire to VEEV or epitopes that engage human virus-neutralizing antibodies. There is no specific treatment for VEE; however virus-neutralizing mMAbs are potent protective and therapeutic agents for mice challenged with VEEV by either peripheral or aerosol routes. Therefore, fully human MAbs (hMAbs with virus-neutralizing activity should be useful for prevention or clinical treatment of human VEE.We used phage-display to isolate VEEV-specific hFabs from human bone marrow donors. These hFabs were characterized by sequencing, specificity testing, VEEV subtype cross-reactivity using indirect ELISA, and in vitro virus neutralization capacity. One E2-specific neutralizing hFAb, F5n, was converted into IgG, and its binding site was identified using competitive ELISA with mMAbs and by preparing and sequencing antibody neutralization-escape variants.Using 11 VEEV-reactive hFabs we constructed the first human epitope map for the alphaviral surface proteins E1 and E2. We identified an important neutralization-associated epitope unique to the human immune response, E2 aa115-119. Using a 9 A resolution cryo-electron microscopy map of the Sindbis virus E2 protein, we showed the probable surface location of this human VEEV epitope.The VEEV-neutralizing capacity of the hMAb F5 nIgG is similar to that exhibited by the humanized mMAb Hy4 IgG. The Hy4 IgG has been shown to limit VEEV infection in mice both prophylactically and therapeutically. Administration

  10. Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents

    Directory of Open Access Journals (Sweden)

    Jennifer H Hou

    2014-09-01

    Full Text Available The cardiac action potential (AP and the consequent cytosolic Ca2+ transient are key indicators of cardiac function. Natural developmental processes, as well as many drugs and pathologies change the waveform, propagation, or variability (between cells or over time of these parameters. Here we apply a genetically encoded dual-function calcium and voltage reporter (CaViar to study the development of the zebrafish heart in vivo between 1.5 and 4 days post fertilization (dpf. We developed a high-sensitivity spinning disk confocal microscope and associated software for simultaneous three-dimensional optical mapping of voltage and calcium. We produced a transgenic zebrafish line expressing CaViar under control of the heart-specific cmlc2 promoter, and applied ion channel blockers at a series of developmental stages to map the maturation of the action potential in vivo. Early in development, the AP initiated via a calcium current through L-type calcium channels. Between 90 – 102 hours post fertilization (hpf, the ventricular AP switched to a sodium-driven upswing, while the atrial AP remained calcium driven. In the adult zebrafish heart, a sodium current drives the AP in both the atrium and ventricle. Simultaneous voltage and calcium imaging with genetically encoded reporters provides a new approach for monitoring cardiac development, and the effects of drugs on cardiac function.

  11. CdS nanorods/organic hybrid LED array and the piezo-phototronic effect of the device for pressure mapping.

    Science.gov (United States)

    Bao, Rongrong; Wang, Chunfeng; Dong, Lin; Shen, Changyu; Zhao, Kun; Pan, Caofeng

    2016-04-21

    As widely applied in light-emitting diodes and optical devices, CdS has attracted the attention of many researchers due to its nonlinear properties and piezo-electronic effect. Here, we demonstrate a LED array composed of PSS and CdS nanorods and research the piezo-photonic effect of the array device. The emission intensity of the device depends on the electron-hole recombination at the interface of the p-n junction which can be adjusted using the piezo-phototronic effect and can be used to map the pressure applied on the surface of the device with spatial resolution as high as 1.5 μm. A flexible LED device array has been prepared using a CdS nanorod array on a Au/Cr/kapton substrate. This device may be used in the field of strain mapping using its high pressure spatial-resolution and flexibility.

  12. Phenotypic characterization of Leishmania spp. causing cutaneous leishmaniasis in the lower Amazon region, western Pará state, Brazil, reveals a putative hybrid parasite, Leishmania (Viannia guyanensis × Leishmania (Viannia shawi shawi

    Directory of Open Access Journals (Sweden)

    Jennings Yara Lins

    2014-01-01

    Full Text Available We phenotypically characterized 43 leishmanial parasites from cutaneous leishmaniasis by isoenzyme electrophoresis and the indirect immunofluorescence antibody test (23 McAbs. Identifications revealed 11 (25.6% strains of Leishmania (V. braziliensis, 4 (9.3% of L. (V. shawi shawi, 7 (16.3% of L. (V. shawi santarensis, 6 (13.9% of L. (V. guyanensis and L. (V. lainsoni, 2 (4.7% of L. (L. amazonensis, and 7 (16.3% of a putative hybrid parasite, L. (V. guyanensis/L. (V. shawi shawi. McAbs detected three different serodemes of L. (V. braziliensis: I-7, II-1, and III-3 strains. Among the strains of L. (V. shawi we identified two populations: one (7 strains expressing the B19 epitope that was previously considered to be species-specific for L. (V. guyanensis. We have given this population sub-specific rank, naming it L. (V. s. santarensis. The other one (4 strains did not express the B19 epitope like the L. (V. shawi reference strain, which we now designate as L. (V. s. shawi. For the first time in the eastern Brazilian Amazon we register a putative hybrid parasite (7 strains, L. (V. guyanensis/L. (V. s. shawi, characterized by a new 6PGDH three-band profile at the level of L. (V. guyanensis. Its PGM profile, however, was very similar to that of L. (V. s. shawi. These results suggest that the lower Amazon region – western Pará state, Brazil, represents a biome where L. (V. guyanensis and L. (V. s. shawi exchange genetic information.

  13. Phenotypic characterization of Leishmania spp. causing cutaneous leishmaniasis in the lower Amazon region, western Pará state, Brazil, reveals a putative hybrid parasite, Leishmania (Viannia) guyanensis × Leishmania (Viannia) shawi shawi

    Science.gov (United States)

    Jennings, Yara Lins; de Souza, Adelson Alcimar Almeida; Ishikawa, Edna Aoba; Shaw, Jeffrey; Lainson, Ralph; Silveira, Fernando

    2014-01-01

    We phenotypically characterized 43 leishmanial parasites from cutaneous leishmaniasis by isoenzyme electrophoresis and the indirect immunofluorescence antibody test (23 McAbs). Identifications revealed 11 (25.6%) strains of Leishmania (V.) braziliensis, 4 (9.3%) of L. (V.) shawi shawi, 7 (16.3%) of L. (V.) shawi santarensis, 6 (13.9%) of L. (V.) guyanensis and L. (V.) lainsoni, 2 (4.7%) of L. (L.) amazonensis, and 7 (16.3%) of a putative hybrid parasite, L. (V.) guyanensis/L. (V.) shawi shawi. McAbs detected three different serodemes of L. (V.) braziliensis: I-7, II-1, and III-3 strains. Among the strains of L. (V.) shawi we identified two populations: one (7 strains) expressing the B19 epitope that was previously considered to be species-specific for L. (V.) guyanensis. We have given this population sub-specific rank, naming it L. (V.) s. santarensis. The other one (4 strains) did not express the B19 epitope like the L. (V.) shawi reference strain, which we now designate as L. (V.) s. shawi. For the first time in the eastern Brazilian Amazon we register a putative hybrid parasite (7 strains), L. (V.) guyanensis/L. (V.) s. shawi, characterized by a new 6PGDH three-band profile at the level of L. (V.) guyanensis. Its PGM profile, however, was very similar to that of L. (V.) s. shawi. These results suggest that the lower Amazon region – western Pará state, Brazil, represents a biome where L. (V.) guyanensis and L. (V.) s. shawi exchange genetic information. PMID:25083790

  14. Historical mapping reveals causes and temporal patterns of woodland contraction in Austur-Skaftafellssýsla from the 12th century AD to present

    Science.gov (United States)

    Sigurmundsson, Friðþór S.; Gísladóttir, Guðrún; Erlendsson, Egill; Þorbjarnarson, Höskuldur

    2016-04-01

    Land-cover changes in Iceland over the last millennium encompass birch (Betula pubescens) woodland depletion and extensive soil erosion. Yet few studies have focused on spatial change of birch woodland coverage in Iceland over centuries and why and how the woodland depletion took place. The main objectives of this study are: (1) to map the woodland distribution today in Austur-Skaftafellssýsla (3041 km2) in southern Iceland; (2) to map woodland holdings over a period of 900 years from eleventh. AD 1100 to the early 20th century; (3) explain the relative impacts of socio-economic and natural forces on woodland cover over this period. We use a combined approach of historical reconstruction from diverse written archives, GIS techniques and field work. The woodland in Austur-Skaftafellssýsla now covers 73.2 km2 (2.5% of the study area). The woodland holdings, 44 in total, are regularly listed in the church inventories from 1179 to 1570 and are owned by the church. In the first complete register for the district in 1641 the woodland holdings were 73, owned and used by 58 estates, and distributed across Austur-Skaftafellssýsla. All the main patches of woodland remain today, with the exception of four minor woodlands which were exhausted near the end of the 19th century. The woodland was used for firewood and charcoal making as well as grazing during the study period but, crucially, in most cases only one estate had authority over each holding, none were commons. The main driving force behind the development of woodlands was socio-economic, rather than natural, where the form of ownership was fundamental for the fate of the woodland. Harsh climate and volcanism were not directly responsible for woodland depletion. The latter half of the 19th century was the period of greatest woodland loss. This period coincides with considerable expansion in livestock numbers, especially sheep and associated all year around grazing, at a time when the Little Ice Age culminated in

  15. Mapping out Map Libraries

    Directory of Open Access Journals (Sweden)

    Ferjan Ormeling

    2008-09-01

    Full Text Available Discussing the requirements for map data quality, map users and their library/archives environment, the paper focuses on the metadata the user would need for a correct and efficient interpretation of the map data. For such a correct interpretation, knowledge of the rules and guidelines according to which the topographers/cartographers work (such as the kind of data categories to be collected, and the degree to which these rules and guidelines were indeed followed are essential. This is not only valid for the old maps stored in our libraries and archives, but perhaps even more so for the new digital files as the format in which we now have to access our geospatial data. As this would be too much to ask from map librarians/curators, some sort of web 2.0 environment is sought where comments about data quality, completeness and up-to-dateness from knowledgeable map users regarding the specific maps or map series studied can be collected and tagged to scanned versions of these maps on the web. In order not to be subject to the same disadvantages as Wikipedia, where the ‘communis opinio’ rather than scholarship, seems to be decisive, some checking by map curators of this tagged map use information would still be needed. Cooperation between map curators and the International Cartographic Association ( ICA map and spatial data use commission to this end is suggested.

  16. Fine-scale linkage mapping reveals a small set of candidate genes influencing honey bee grooming behavior in response to Varroa mites.

    Directory of Open Access Journals (Sweden)

    Miguel E Arechavaleta-Velasco

    Full Text Available Populations of honey bees in North America have been experiencing high annual colony mortality for 15-20 years. Many apicultural researchers believe that introduced parasites called Varroa mites (V. destructor are the most important factor in colony deaths. One important resistance mechanism that limits mite population growth in colonies is the ability of some lines of honey bees to groom mites from their bodies. To search for genes influencing this trait, we used an Illumina Bead Station genotyping array to determine the genotypes of several hundred worker bees at over a thousand single-nucleotide polymorphisms in a family that was apparently segregating for alleles influencing this behavior. Linkage analyses provided a genetic map with 1,313 markers anchored to genome sequence. Genotypes were analyzed for association with grooming behavior, measured as the time that individual bees took to initiate grooming after mites were placed on their thoraces. Quantitative-trait-locus interval mapping identified a single chromosomal region that was significant at the chromosome-wide level (p<0.05 on chromosome 5 with a LOD score of 2.72. The 95% confidence interval for quantitative trait locus location contained only 27 genes (honey bee official gene annotation set 2 including Atlastin, Ataxin and Neurexin-1 (AmNrx1, which have potential neurodevelopmental and behavioral effects. Atlastin and Ataxin homologs are associated with neurological diseases in humans. AmNrx1 codes for a presynaptic protein with many alternatively spliced isoforms. Neurexin-1 influences the growth, maintenance and maturation of synapses in the brain, as well as the type of receptors most prominent within synapses. Neurexin-1 has also been associated with autism spectrum disorder and schizophrenia in humans, and self-grooming behavior in mice.

  17. Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Thudi, Mahendar; Khan, Aamir W; Kumar, Vinay; Gaur, Pooran M; Katta, Krishnamohan; Garg, Vanika; Roorkiwal, Manish; Samineni, Srinivasan; Varshney, Rajeev K

    2016-01-27

    Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach. A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads, with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome. Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively. Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for

  18. Mapping glaucoma patients' 30-2 and 10-2 visual fields reveals clusters of test points damaged in the 10-2 grid that are not sampled in the sparse 30-2 grid.

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    Ryo Asaoka

    Full Text Available PURPOSE: To cluster test points in glaucoma patients' 30-2 and 10-2 visual field (VF (Humphrey Field Analyzer: HFA, Carl Zeiss Meditec, Dublin, CA in order to map the different regions damaged by the disease. METHOD: This retrospective study included 128 eyes from 128 patients. 142 total deviation (TD values (74 from the 30-2 VF and 68 from the 10-2 VF were clustered using the 'Hierarchical Ordered Partitioning And Collapsing Hybrid-Partitioning Around Medoids' algorithm. The stability of the identified clusters was evaluated using bootstrapping. RESULTS: 65 sectors were identified in total: 38 sectors were located outside the 10-2 VF whereas 29 sectors were located inside the 10-2 VF (two sectors overlap in both grids. The mapping of many sectors appeared to follow the distribution of retinal nerve fiber bundles. The results of bootstrapping suggested clusters were stable whether they were outside or inside the 10-2 VF. CONCLUSION: A considerable number of sectors were identified in the 10-2 VF area, despite the fact that clustering was carried out on all points in both the 30-2 VF and 10-2 VF simultaneously. These findings suggest that glaucomatous central VF deterioration cannot be picked up by the 30-2 test grid alone, because of poor spatial sampling; denser estimation of the central ten degrees, than offered by the 30-2 test grid alone, is needed. It may be beneficial to develop a new VF test grid that combines test points from 30-2 and 10-2 VFs--the results of this study could help to devise this test grid.

  19. Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (O. mykiss)

    Science.gov (United States)

    2013-01-01

    Background Introgressive hybridization is an important evolutionary process that can lead to the creation of novel genome structures and thus potentially new genetic variation for selection to act upon. On the other hand, hybridization with introduced species can threaten native species, such as cutthroat trout (Oncorhynchus clarkii) following the introduction of rainbow trout (O. mykiss). Neither the evolutionary consequences nor conservation implications of rainbow trout introgression in cutthroat trout is well understood. Therefore, we generated a genetic linkage map for rainbow-Yellowstone cutthroat trout (O. clarkii bouvieri) hybrids to evaluate genome processes that may help explain how introgression affects hybrid genome evolution. Results The hybrid map closely aligned with the rainbow trout map (a cutthroat trout map does not exist), sharing all but one linkage group. This linkage group (RYHyb20) represented a fusion between an acrocentric (Omy28) and a metacentric chromosome (Omy20) in rainbow trout. Additional mapping in Yellowstone cutthroat trout indicated the two rainbow trout homologues were fused in the Yellowstone genome. Variation in the number of hybrid linkage groups (28 or 29) likely depended on a Robertsonian rearrangement polymorphism within the rainbow trout stock. Comparison between the female-merged F1 map and a female consensus rainbow trout map revealed that introgression suppressed recombination across large genomic regions in 5 hybrid linkage groups. Two of these linkage groups (RYHyb20 and RYHyb25_29) contained confirmed chromosome rearrangements between rainbow and Yellowstone cutthroat trout indicating that rearrangements may suppress recombination. The frequency of allelic and genotypic segregation distortion varied among parents and families, suggesting few incompatibilities exist between rainbow and Yellowstone cutthroat trout genomes. Conclusions Chromosome rearrangements suppressed recombination in the hybrids. This result

  20. Subpixel mapping and test beam studies with a HV2FEI4v2 CMOS-Sensor-Hybrid Module for the ATLAS inner detector upgrade

    Science.gov (United States)

    Bisanz, T.; Große-Knetter, J.; Quadt, A.; Rieger, J.; Weingarten, J.

    2017-08-01

    The upgrade to the High Luminosity Large Hadron Collider will increase the instantaneous luminosity by more than a factor of 5, thus creating significant challenges to the tracking systems of all experiments. Recent advancement of active pixel detectors designed in CMOS processes provide attractive alternatives to the well-established hybrid design using passive sensors since they allow for smaller pixel sizes and cost effective production. This article presents studies of a high-voltage CMOS active pixel sensor designed for the ATLAS tracker upgrade. The sensor is glued to the read-out chip of the Insertable B-Layer, forming a capacitively coupled pixel detector. The pixel pitch of the device under test is 33× 125 μm2, while the pixels of the read-out chip have a pitch of 50× 250 μm2. Three pixels of the CMOS device are connected to one read-out pixel, the information of which of these subpixels is hit is encoded in the amplitude of the output signal (subpixel encoding). Test beam measurements are presented that demonstrate the usability of this subpixel encoding scheme.

  1. An integrated high-performance beam optics-nuclear processes framework with hybrid transfer map-Monte Carlo particle transport and optimization

    Energy Technology Data Exchange (ETDEWEB)

    Bandura, L., E-mail: bandura@msu.ed [Argonne National Laboratory, Argonne, IL 60439 (United States); Erdelyi, B. [Argonne National Laboratory, Argonne, IL 60439 (United States); Northern Illinois University, DeKalb, IL 60115 (United States); Nolen, J. [Argonne National Laboratory, Argonne, IL 60439 (United States)

    2010-12-01

    An integrated beam optics-nuclear processes framework is essential for accurate simulation of fragment separator beam dynamics. The code COSY INFINITY provides powerful differential algebraic methods for modeling and beam dynamics simulations in absence of beam-material interactions. However, these interactions are key for accurately simulating the dynamics of heavy ion fragmentation and fission. We have developed an extended version of the code that includes these interactions, and a set of new tools that allow efficient and accurate particle transport: by transfer map in vacuum and by Monte Carlo methods in materials. The new framework is presented, along with several examples from a preliminary layout of a fragment separator for a facility for rare isotope beams.

  2. An integrated high-performance beam optics-nuclear processes framework with hybrid transfer map-Monte Carlo particle transport and optimization

    International Nuclear Information System (INIS)

    Bandura, L.; Erdelyi, B.; Nolen, J.

    2010-01-01

    An integrated beam optics-nuclear processes framework is essential for accurate simulation of fragment separator beam dynamics. The code COSY INFINITY provides powerful differential algebraic methods for modeling and beam dynamics simulations in absence of beam-material interactions. However, these interactions are key for accurately simulating the dynamics of heavy ion fragmentation and fission. We have developed an extended version of the code that includes these interactions, and a set of new tools that allow efficient and accurate particle transport: by transfer map in vacuum and by Monte Carlo methods in materials. The new framework is presented, along with several examples from a preliminary layout of a fragment separator for a facility for rare isotope beams.

  3. QTL mapping of root traits in phosphorus-deficient soils reveals important genomic regions for improving NDVI and grain yield in barley.

    Science.gov (United States)

    Gong, Xue; McDonald, Glenn

    2017-09-01

    Major QTLs for root rhizosheath size are not correlated with grain yield or yield response to phosphorus. Important QTLs were found to improve phosphorus efficiency. Root traits are important for phosphorus (P) acquisition, but they are often difficult to characterize and their breeding values are seldom assessed under field conditions. This has shed doubts on using seedling-based criteria of root traits to select and breed for P efficiency. Eight root traits were assessed under controlled conditions in a barley doubled-haploid population in soils differing in P levels. The population was also phenotyped for grain yield, normalized difference vegetation index (NDVI), grain P uptake and P utilization efficiency at maturity (PutE GY ) under field conditions. Several quantitative traits loci (QTLs) from the root screening and the field trials were co-incident. QTLs for root rhizosheath size and root diameter explained the highest phenotypic variation in comparison to QTLs for other root traits. Shared QTLs were found between root diameter and grain yield, and total root length and PutE GY . A common major QTL for rhizosheath size and NDVI was mapped to the HvMATE gene marker on chromosome 4H. Collocations between major QTLs for NDVI and grain yield were detected on chromosomes 6H and 7H. When results from BIP and MET were combined, QTLs detected for grain yield were also those QTLs found for NDVI. QTLs qGY5H, qGY6H and qGY7Hb on 7H were robust QTLs in improving P efficiency. A selection of multiple loci may be needed to optimize the breeding outcomes due to the QTL x Environment interaction. We suggest that rhizosheath size alone is not a reliable trait to predict P efficiency or grain yield.

  4. Genetic mapping reveals a dominant awn-inhibiting gene related to differentiation of the variety anathera in the wild diploid wheat Aegilops tauschii.

    Science.gov (United States)

    Nishijima, Ryo; Ikeda, Tatsuya M; Takumi, Shigeo

    2018-02-01

    Aegilops tauschii, a wild wheat relative, is the D-genome donor of common wheat. Subspecies and varieties of Ae. tauschii are traditionally classified based on differences in their inflorescence architecture. However, the genetic information for their diversification has been quite limited in the wild wheat relatives. The variety anathera has no awn on the lemma, but the genetic basis for this diagnostic character is unknown. Wide variations in awn length traits at the top and middle spikes were found in the Ae. tauschii core collection, and the awn length at the middle spike was significantly smaller in the eastward-dispersed sublineage than in those in other sublineages. To clarify loci controlling the awnless phenotype of var. anathera, we measured awn length of an intervariety F 2 mapping population, and found that the F 2 individuals could be divided into two groups mainly based on the awn length at the middle of spike, namely short and long awn groups, significantly fitting a 3:1 segregation ratio, which indicated that a single locus controls the awnless phenotype. The awnless locus, Anathera (Antr), was assigned to the distal region of the short arm of chromosome 5D. Quantitative trait locus analysis using the awn length data of each F 2 individual showed that only one major locus was at the same chromosomal position as Antr. These results suggest that a single dominant allele determines the awnless diagnostic character in the variety anathera. The Antr dominant allele is a novel gene inhibiting awn elongation in wheat and its relatives.

  5. Hsp90 inhibition differentially destabilises MAP kinase and TGF-beta signalling components in cancer cells revealed by kinase-targeted chemoproteomics

    International Nuclear Information System (INIS)

    Haupt, Armin; Dahl, Andreas; Lappe, Michael; Lehrach, Hans; Gonzalez, Cayetano; Drewes, Gerard; Lange, Bodo MH; Joberty, Gerard; Bantscheff, Marcus; Fröhlich, Holger; Stehr, Henning; Schweiger, Michal R; Fischer, Axel; Kerick, Martin; Boerno, Stefan T

    2012-01-01

    The heat shock protein 90 (Hsp90) is required for the stability of many signalling kinases. As a target for cancer therapy it allows the simultaneous inhibition of several signalling pathways. However, its inhibition in healthy cells could also lead to severe side effects. This is the first comprehensive analysis of the response to Hsp90 inhibition at the kinome level. We quantitatively profiled the effects of Hsp90 inhibition by geldanamycin on the kinome of one primary (Hs68) and three tumour cell lines (SW480, U2OS, A549) by affinity proteomics based on immobilized broad spectrum kinase inhibitors ('kinobeads'). To identify affected pathways we used the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway classification. We combined Hsp90 and proteasome inhibition to identify Hsp90 substrates in Hs68 and SW480 cells. The mutational status of kinases from the used cell lines was determined using next-generation sequencing. A mutation of Hsp90 candidate client RIPK2 was mapped onto its structure. We measured relative abundances of > 140 protein kinases from the four cell lines in response to geldanamycin treatment and identified many new potential Hsp90 substrates. These kinases represent diverse families and cellular functions, with a strong representation of pathways involved in tumour progression like the BMP, MAPK and TGF-beta signalling cascades. Co-treatment with the proteasome inhibitor MG132 enabled us to classify 64 kinases as true Hsp90 clients. Finally, mutations in 7 kinases correlate with an altered response to Hsp90 inhibition. Structural modelling of the candidate client RIPK2 suggests an impact of the mutation on a proposed Hsp90 binding domain. We propose a high confidence list of Hsp90 kinase clients, which provides new opportunities for targeted and combinatorial cancer treatment and diagnostic applications

  6. Laser-scanning astrocyte mapping reveals increased glutamate-responsive domain size and disrupted maturation of glutamate uptake following neonatal cortical freeze-lesion

    Directory of Open Access Journals (Sweden)

    Mortiz eArmbruster

    2014-09-01

    Full Text Available Astrocytic uptake of glutamate shapes extracellular neurotransmitter dynamics, receptor activation, and synaptogenesis. During development, glutamate transport becomes more robust. How neonatal brain insult affects the functional maturation of glutamate transport remains unanswered. Neonatal brain insult can lead to developmental delays, cognitive losses, and epilepsy; the disruption of glutamate transport is known to cause changes in synaptogenesis, receptor activation, and seizure. Using the neonatal freeze-lesion (FL model, we have investigated how insult affects the maturation of astrocytic glutamate transport. As lesioning occurs on the day of birth, a time when astrocytes are still functionally immature, this model is ideal for identifying changes in astrocyte maturation following insult. Reactive astrocytosis, astrocyte proliferation, and in vitro hyperexcitability are known to occur in this model. To probe astrocyte glutamate transport with better spatial precision we have developed a novel technique, Laser Scanning Astrocyte Mapping (LSAM, which combines glutamate transport current (TC recording from astrocytes with laser scanning glutamate photolysis. LSAM allows us to identify the area from which a single astrocyte can transport glutamate and to quantify spatial heterogeneity in the rate of glutamate clearance kinetics within that domain. Using LSAM, we report that cortical astrocytes have an increased glutamate-responsive area following FL and that TCs have faster decay times in distal, as compared to proximal processes. Furthermore, the developmental shift from GLAST- to GLT-1-dominated clearance is disrupted following FL. These findings introduce a novel method to probe astrocyte glutamate uptake and show that neonatal cortical FL disrupts the functional maturation of cortical astrocytes.

  7. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    Directory of Open Access Journals (Sweden)

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  8. Hybrid-Based Dense Stereo Matching

    Science.gov (United States)

    Chuang, T. Y.; Ting, H. W.; Jaw, J. J.

    2016-06-01

    Stereo matching generating accurate and dense disparity maps is an indispensable technique for 3D exploitation of imagery in the fields of Computer vision and Photogrammetry. Although numerous solutions and advances have been proposed in the literature, occlusions, disparity discontinuities, sparse texture, image distortion, and illumination changes still lead to problematic issues and await better treatment. In this paper, a hybrid-based method based on semi-global matching is presented to tackle the challenges on dense stereo matching. To ease the sensitiveness of SGM cost aggregation towards penalty parameters, a formal way to provide proper penalty estimates is proposed. To this end, the study manipulates a shape-adaptive cross-based matching with an edge constraint to generate an initial disparity map for penalty estimation. Image edges, indicating the potential locations of occlusions as well as disparity discontinuities, are approved by the edge drawing algorithm to ensure the local support regions not to cover significant disparity changes. Besides, an additional penalty parameter 𝑃𝑒 is imposed onto the energy function of SGM cost aggregation to specifically handle edge pixels. Furthermore, the final disparities of edge pixels are found by weighting both values derived from the SGM cost aggregation and the U-SURF matching, providing more reliable estimates at disparity discontinuity areas. Evaluations on Middlebury stereo benchmarks demonstrate satisfactory performance and reveal the potency of the hybrid-based dense stereo matching method.

  9. Helper T cell epitope-mapping reveals MHC-peptide binding affinities that correlate with T helper cell responses to pneumococcal surface protein A.

    Directory of Open Access Journals (Sweden)

    Rajesh Singh

    2010-02-01

    Full Text Available Understanding the requirements for protection against pneumococcal carriage and pneumonia will greatly benefit efforts in controlling these diseases. Several proteins and polysaccharide capsule have recently been implicated in the virulence of and protective immunity against Streptococcus pneumonia. Pneumococcal surface protein A (PspA is highly conserved among S. pneumonia strains, inhibits complement activation, binds lactoferrin, elicits protective systemic immunity against pneumococcal infection, and is necessary for full pneumococcal virulence. Identification of PspA peptides that optimally bind human leukocyte antigen (HLA would greatly contribute to global vaccine efforts, but this is hindered by the multitude of HLA polymorphisms. Here, we have used an experimental data set of 54 PspA peptides and in silico methods to predict peptide binding to HLA and murine major histocompatibility complex (MHC class II. We also characterized spleen- and cervical lymph node (CLN-derived helper T lymphocyte (HTL cytokine responses to these peptides after S. pneumonia strain EF3030-challenge in mice. Individual, yet overlapping peptides, 15 amino acids in length revealed residues 199 to 246 of PspA (PspA(199-246 consistently caused the greatest IFN-gamma, IL-2, IL-5 and proliferation as well as moderate IL-10 and IL-4 responses by ex vivo stimulated splenic and CLN CD4(+ T cells isolated from S. pneumonia strain EF3030-challeged F(1 (B6xBALB/c mice. IEDB, RANKPEP, SVMHC, MHCPred, and SYFPEITHI in silico analysis tools revealed peptides in PspA(199-246 also interact with a broad range of HLA-DR, -DQ, and -DP allelles. These data suggest that predicted MHC class II-peptide binding affinities do not always correlate with T helper (Th cytokine or proliferative responses to PspA peptides, but when used together with in vivo validation can be a useful tool to choose candidate pneumococcal HTL epitopes.

  10. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    Directory of Open Access Journals (Sweden)

    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  11. Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6

    Directory of Open Access Journals (Sweden)

    An Chung-Il

    2011-10-01

    Full Text Available Abstract Background Sox6 is a multi-faceted transcription factor involved in the terminal differentiation of many different cell types in vertebrates. It has been suggested that in mice as well as in zebrafish Sox6 plays a role in the terminal differentiation of skeletal muscle by suppressing transcription of slow fiber specific genes. In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes in mouse fetal myotubes and generated muscle-specific Sox6 knockout (KO mice to determine the Sox6 null muscle phenotype in adult mice. Results We have identified 1,066 Sox6 binding sites using mouse fetal myotubes. The Sox6 binding sites were found to be associated with slow fiber-specific, cardiac, and embryonic isoform genes that are expressed in the sarcomere as well as transcription factor genes known to play roles in muscle development. The concurrently performed RNA polymerase II (Pol II ChIP-seq analysis revealed that 84% of the Sox6 peak-associated genes exhibited little to no binding of Pol II, suggesting that the majority of the Sox6 target genes are transcriptionally inactive. These results indicate that Sox6 directly regulates terminal differentiation of muscle by affecting the expression of sarcomere protein genes as well as indirectly through influencing the expression of transcription factors relevant to muscle development. Gene expression profiling of Sox6 KO skeletal and cardiac muscle revealed a significant increase in the expression of the genes associated with Sox6 binding. In the absence of the Sox6 gene, there was dramatic upregulation of slow fiber-specific, cardiac, and embryonic isoform gene expression in Sox6 KO skeletal muscle and fetal isoform gene expression in Sox6 KO cardiac muscle, thus confirming the role Sox6 plays as a transcriptional suppressor in muscle development

  12. A protein interaction map of the kalimantacin biosynthesis assembly line

    Directory of Open Access Journals (Sweden)

    Birgit Uytterhoeven

    2016-11-01

    Full Text Available The antimicrobial secondary metabolite kalimantacin is produced by a hybrid polyketide/ non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein-protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites.This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters.

  13. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.

    Directory of Open Access Journals (Sweden)

    Sarit Edelheit

    2013-06-01

    Full Text Available The presence of 5-methylcytidine (m(5C in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago. However, detection of this modification was limited to specific, abundant, RNA species, due to the usage of low-throughput methods. To obtain a high resolution, systematic, and comprehensive transcriptome-wide overview of m(5C across the three domains of life, we used bisulfite treatment on total RNA from both gram positive (B. subtilis and gram negative (E. coli bacteria, an archaeon (S. solfataricus and a eukaryote (S. cerevisiae, followed by massively parallel sequencing. We were able to recover most previously documented m(5C sites on rRNA in the four organisms, and identified several novel sites in yeast and archaeal rRNAs. Our analyses also allowed quantification of methylated m(5C positions in 64 tRNAs in yeast and archaea, revealing stoichiometric differences between the methylation patterns of these organisms. Molecules of tRNAs in which m(5C was absent were also discovered. Intriguingly, we detected m(5C sites within archaeal mRNAs, and identified a consensus motif of AUCGANGU that directs methylation in S. solfataricus. Our results, which were validated using m(5C-specific RNA immunoprecipitation, provide the first evidence for mRNA modifications in archaea, suggesting that this mode of post-transcriptional regulation extends beyond the eukaryotic domain.

  14. Behavioural mapping of a pelagic seabird: combining multiple sensors and a hidden Markov model reveals the distribution of at-sea behaviour

    Science.gov (United States)

    Dean, Ben; Freeman, Robin; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

    2013-01-01

    The use of miniature data loggers is rapidly increasing our understanding of the movements and habitat preferences of pelagic seabirds. However, objectively interpreting behavioural information from the large volumes of highly detailed data collected by such devices can be challenging. We combined three biologging technologies—global positioning system (GPS), saltwater immersion and time–depth recorders—to build a detailed picture of the at-sea behaviour of the Manx shearwater (Puffinus puffinus) during the breeding season. We used a hidden Markov model to explore discrete states within the combined GPS and immersion data, and found that behaviour could be organized into three principal activities representing (i) sustained direct flight, (ii) sitting on the sea surface, and (iii) foraging, comprising tortuous flight interspersed with periods of immersion. The additional logger data verified that the foraging activity corresponded well to the occurrence of diving. Applying this approach to a large tracking dataset revealed that birds from two different colonies foraged in local waters that were exclusive, but overlapped in one key area: the Irish Sea Front (ISF). We show that the allocation of time to each activity differed between colonies, with birds breeding furthest from the ISF spending the greatest proportion of time engaged in direct flight and the smallest proportion of time engaged in foraging activity. This type of analysis has considerable potential for application in future biologging studies and in other taxa. PMID:23034356

  15. Mapped clone and functional analysis of leaf-color gene Ygl7 in a rice hybrid (Oryza sativa L. ssp. indica).

    Science.gov (United States)

    Deng, Xiao-juan; Zhang, Hai-qing; Wang, Yue; He, Feng; Liu, Jin-ling; Xiao, Xiao; Shu, Zhi-feng; Li, Wei; Wang, Guo-huai; Wang, Guo-liang

    2014-01-01

    Leaf-color is an effective marker to identify the hybridization of rice. Leaf-color related genes function in chloroplast development and the photosynthetic pigment biosynthesis of higher plants. The ygl7 (yellow-green leaf 7) is a mutant with spontaneous yellow-green leaf phenotype across the whole lifespan but with no change to its yield traits. We cloned gene Ygl7 (Os03g59640) which encodes a magnesium-chelatase ChlD protein. Expression of ygl7 turns green-leaves to yellow, whereas RNAi-mediated silence of Ygl7 causes a lethal phenotype of the transgenic plants. This indicates the importance of the gene for rice plant. On the other hand, it corroborates that ygl7 is a non-null mutants. The content of photosynthetic pigment is lower in Ygl7 than the wild type, but its light efficiency was comparatively high. All these results indicated that the mutational YGL7 protein does not cause a complete loss of original function but instead acts as a new protein performing a new function. This new function partially includes its preceding function and possesses an additional feature to promote photosynthesis. Chl1, Ygl98, and Ygl3 are three alleles of the OsChlD gene that have been documented previously. However, mutational sites of OsChlD mutant gene and their encoded protein products were different in the three mutants. The three mutants have suppressed grain output. In our experiment, plant materials of three mutants (ygl7, chl1, and ygl98) all exhibited mutational leaf-color during the whole growth period. This result was somewhat different from previous studies. We used ygl7 as female crossed with chl1 and ygl98, respectively. Both the F1 and F2 generation display yellow-green leaf phenotype with their chlorophyll and carotenoid content falling between the values of their parents. Moreover, we noted an important phenomenon: ygl7-NIL's leaf-color is yellow, not yellowy-green, and this is also true of all back-crossed offspring with ygl7.

  16. Mapped clone and functional analysis of leaf-color gene Ygl7 in a rice hybrid (Oryza sativa L. ssp. indica.

    Directory of Open Access Journals (Sweden)

    Xiao-juan Deng

    Full Text Available Leaf-color is an effective marker to identify the hybridization of rice. Leaf-color related genes function in chloroplast development and the photosynthetic pigment biosynthesis of higher plants. The ygl7 (yellow-green leaf 7 is a mutant with spontaneous yellow-green leaf phenotype across the whole lifespan but with no change to its yield traits. We cloned gene Ygl7 (Os03g59640 which encodes a magnesium-chelatase ChlD protein. Expression of ygl7 turns green-leaves to yellow, whereas RNAi-mediated silence of Ygl7 causes a lethal phenotype of the transgenic plants. This indicates the importance of the gene for rice plant. On the other hand, it corroborates that ygl7 is a non-null mutants. The content of photosynthetic pigment is lower in Ygl7 than the wild type, but its light efficiency was comparatively high. All these results indicated that the mutational YGL7 protein does not cause a complete loss of original function but instead acts as a new protein performing a new function. This new function partially includes its preceding function and possesses an additional feature to promote photosynthesis. Chl1, Ygl98, and Ygl3 are three alleles of the OsChlD gene that have been documented previously. However, mutational sites of OsChlD mutant gene and their encoded protein products were different in the three mutants. The three mutants have suppressed grain output. In our experiment, plant materials of three mutants (ygl7, chl1, and ygl98 all exhibited mutational leaf-color during the whole growth period. This result was somewhat different from previous studies. We used ygl7 as female crossed with chl1 and ygl98, respectively. Both the F1 and F2 generation display yellow-green leaf phenotype with their chlorophyll and carotenoid content falling between the values of their parents. Moreover, we noted an important phenomenon: ygl7-NIL's leaf-color is yellow, not yellowy-green, and this is also true of all back-crossed offspring with ygl7.

  17. Multimodal hybrid imaging agents for sentinel node mapping as a means to (re)connect nuclear medicine to advances made in robot-assisted surgery.

    Science.gov (United States)

    KleinJan, Gijs H; van den Berg, Nynke S; de Jong, Jeroen; Wit, Esther M; Thygessen, Helene; Vegt, Erik; van der Poel, Henk G; van Leeuwen, Fijs W B

    2016-07-01

    Radical prostatectomy and complementary extended pelvic lymph node dissection (ePLND) of sentinel lymph nodes (SNs) and non-sentinel lymph nodes (LNs) at risk of containing metastases are increasingly being performed using high-tech robot-assisted approaches. Although this technological evolution has clear advantages, the physical nature of robotic systems limits the integrated use of routine radioguided surgery technologies. Hence, engineering effort in robotics are focused on the integration of fluorescence guidance technologies. Using the hybrid SN tracer indocyanine green-(99m)Tc-nanocolloid (radioactive and fluorescent), for the first time in combination with a robot-integrated laparoscope, we investigated whether the robot-assisted approach affects the accuracy of fluorescence detection of SNs identified preoperatively using nuclear medicine. The study included 55 patients (Briganti nomogram-based risk >5 % on LN metastases) scheduled for robot-assisted radical prostatectomy, SN biopsy and ePLND. Following indocyanine green-(99m)Tc-nanocolloid injection, preoperative nuclear imaging (lymphoscintigraphy and SPECT/CT) was used to locate the SN(s). The fluorescence laparoscope was used intraoperatively to identify the SN(s) with standard fluorescence settings (in 50 patients) and with customized settings (in 5 patients). The number and location of the SNs, the radioactive, fluorescence (both in vivo and ex vivo) and tumour status of the resected SNs/LNs, and postoperative complications were recorded and analysed. Combined, preoperative lymphoscintigraphy and SPECT/CT imaging identified 212 SNs (median 4 per patient). Intraoperative fluorescence imaging using standard fluorescence settings visualized 80.4 % (148/184 SNs; 50 patients; ex vivo 97.8 %). This increased to 85.7 % (12/14 SNs; 5 patients; ex vivo 100 %) with customized fluorescence settings. SPECT/CT images provided guidance towards the residual SNs. Ex vivo all removed SNs were radioactive. SNs

  18. Multimodal hybrid imaging agents for sentinel node mapping as a means to (re)connect nuclear medicine to advances made in robot-assisted surgery

    Energy Technology Data Exchange (ETDEWEB)

    KleinJan, Gijs H. [Leiden University Medical Hospital, Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Nuclear Medicine, Amsterdam (Netherlands); Berg, Nynke S. van den [Leiden University Medical Hospital, Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); Jong, Jeroen de [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Pathology, Amsterdam (Netherlands); Wit, Esther M.; Poel, Henk G. van der [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); Thygessen, Helene [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Biostatistics, Amsterdam (Netherlands); Vegt, Erik [The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Nuclear Medicine, Amsterdam (Netherlands); Leeuwen, Fijs W.B. van [Leiden University Medical Hospital, Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Urology, Amsterdam (Netherlands); The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Department of Head and Neck Surgery and Oncology, Amsterdam (Netherlands)

    2016-07-15

    Radical prostatectomy and complementary extended pelvic lymph node dissection (ePLND) of sentinel lymph nodes (SNs) and non-sentinel lymph nodes (LNs) at risk of containing metastases are increasingly being performed using high-tech robot-assisted approaches. Although this technological evolution has clear advantages, the physical nature of robotic systems limits the integrated use of routine radioguided surgery technologies. Hence, engineering effort in robotics are focused on the integration of fluorescence guidance technologies. Using the hybrid SN tracer indocyanine green-{sup 99m}Tc-nanocolloid (radioactive and fluorescent), for the first time in combination with a robot-integrated laparoscope, we investigated whether the robot-assisted approach affects the accuracy of fluorescence detection of SNs identified preoperatively using nuclear medicine. The study included 55 patients (Briganti nomogram-based risk >5 % on LN metastases) scheduled for robot-assisted radical prostatectomy, SN biopsy and ePLND. Following indocyanine green-{sup 99m}Tc-nanocolloid injection, preoperative nuclear imaging (lymphoscintigraphy and SPECT/CT) was used to locate the SN(s). The fluorescence laparoscope was used intraoperatively to identify the SN(s) with standard fluorescence settings (in 50 patients) and with customized settings (in 5 patients). The number and location of the SNs, the radioactive, fluorescence (both in vivo and ex vivo) and tumour status of the resected SNs/LNs, and postoperative complications were recorded and analysed. Combined, preoperative lymphoscintigraphy and SPECT/CT imaging identified 212 SNs (median 4 per patient). Intraoperative fluorescence imaging using standard fluorescence settings visualized 80.4 % (148/184 SNs; 50 patients; ex vivo 97.8 %). This increased to 85.7 % (12/14 SNs; 5 patients; ex vivo 100 %) with customized fluorescence settings. SPECT/CT images provided guidance towards the residual SNs. Ex vivo all removed SNs were radioactive. SNs

  19. Multimodal hybrid imaging agents for sentinel node mapping as a means to (re)connect nuclear medicine to advances made in robot-assisted surgery

    International Nuclear Information System (INIS)

    KleinJan, Gijs H.; Berg, Nynke S. van den; Jong, Jeroen de; Wit, Esther M.; Poel, Henk G. van der; Thygessen, Helene; Vegt, Erik; Leeuwen, Fijs W.B. van

    2016-01-01

    Radical prostatectomy and complementary extended pelvic lymph node dissection (ePLND) of sentinel lymph nodes (SNs) and non-sentinel lymph nodes (LNs) at risk of containing metastases are increasingly being performed using high-tech robot-assisted approaches. Although this technological evolution has clear advantages, the physical nature of robotic systems limits the integrated use of routine radioguided surgery technologies. Hence, engineering effort in robotics are focused on the integration of fluorescence guidance technologies. Using the hybrid SN tracer indocyanine green- 99m Tc-nanocolloid (radioactive and fluorescent), for the first time in combination with a robot-integrated laparoscope, we investigated whether the robot-assisted approach affects the accuracy of fluorescence detection of SNs identified preoperatively using nuclear medicine. The study included 55 patients (Briganti nomogram-based risk >5 % on LN metastases) scheduled for robot-assisted radical prostatectomy, SN biopsy and ePLND. Following indocyanine green- 99m Tc-nanocolloid injection, preoperative nuclear imaging (lymphoscintigraphy and SPECT/CT) was used to locate the SN(s). The fluorescence laparoscope was used intraoperatively to identify the SN(s) with standard fluorescence settings (in 50 patients) and with customized settings (in 5 patients). The number and location of the SNs, the radioactive, fluorescence (both in vivo and ex vivo) and tumour status of the resected SNs/LNs, and postoperative complications were recorded and analysed. Combined, preoperative lymphoscintigraphy and SPECT/CT imaging identified 212 SNs (median 4 per patient). Intraoperative fluorescence imaging using standard fluorescence settings visualized 80.4 % (148/184 SNs; 50 patients; ex vivo 97.8 %). This increased to 85.7 % (12/14 SNs; 5 patients; ex vivo 100 %) with customized fluorescence settings. SPECT/CT images provided guidance towards the residual SNs. Ex vivo all removed SNs were radioactive. SNs were

  20. Mapping the spatiotemporal evolution of solute transport in articular cartilage explants reveals how cartilage recovers fluid within the contact area during sliding.

    Science.gov (United States)

    Graham, Brian T; Moore, Axel C; Burris, David L; Price, Christopher

    2018-04-11

    The interstitial fluid within articular cartilage shields the matrix from mechanical stresses, reduces friction and wear, enables biochemical processes, and transports solutes into and out of the avascular extracellular matrix. The balanced competition between fluid exudation and recovery under load is thus critical to the mechanical and biological functions of the tissue. We recently discovered that sliding alone can induce rapid solute transport into buried cartilage contact areas via a phenomenon termed tribological rehydration. In this study, we use in situ confocal microscopy measurements to track the spatiotemporal propagation of a small neutral solute into the buried contact area to clarify the fluid mechanics underlying the tribological rehydration phenomenon. Sliding experiments were interrupted by periodic static loading to enable scanning of the entire contact area. Spatiotemporal patterns of solute transport combined with tribological data suggested pressure driven flow through the extracellular matrix from the contact periphery rather than into the surface via a fluid film. Interestingly, these testing interruptions also revealed dynamic, repeatable and history-independent fluid loss and recovery processes consistent with those observed in vivo. Unlike the migrating contact area, which preserves hydration by moving faster than interstitial fluid can flow, our results demonstrate that the stationary contact area can maintain and actively recover hydration through a dynamic competition between load-induced exudation and sliding-induced recovery. The results demonstrate that sliding contributes to the recovery of fluid and solutes by cartilage within the contact area while clarifying the means by which it occurs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  1. Surface morphology of caldera-forming eruption deposits revealed by lidar mapping of Crater Lake National Park, Oregon- Implications for emplacement and surface modification

    Science.gov (United States)

    Robinson, Joel E.; Bacon, Charles R.; Major, Jon J.; Wright, Heather M.; Vallance, James W.

    2017-01-01

    Large explosive eruptions of silicic magma can produce widespread pumice fall, extensive ignimbrite sheets, and collapse calderas. The surfaces of voluminous ignimbrites are rarely preserved or documented because most terrestrial examples are heavily vegetated, or severely modified by post-depositional processes. Much research addresses the internal sedimentary characteristics, flow processes, and depositional mechanisms of ignimbrites, however, surface features of ignimbrites are less well documented and understood, except for comparatively small-volume deposits of historical eruptions. The ~7,700 calendar year B.P. climactic eruption of Mount Mazama, USA vented ~50 km3 of magma, deposited first as rhyodacite pumice fall and then as a zoned rhyodacite-to-andesite ignimbrite as Crater Lake caldera collapsed. Lidar collected during summer 2010 reveals the remarkably well-preserved surface of the Mazama ignimbrite and related deposits surrounding Crater Lake caldera in unprecedented detail despite forest cover. The ±1 m lateral and ±4 cm vertical resolution lidar allows surface morphologies to be classified. Surface morphologies are created by internal depositional processes and can point to the processes at work when pyroclastic flows come to rest. We describe nine surface features including furrow-ridge sets and wedge-shaped mounds in pumice fall eroded by high-energy pyroclastic surges, flow- parallel ridges that record the passage of multiple pyroclastic flows, perched benches of marginal deposits stranded by more-mobile pyroclastic-flow cores, hummocks of dense clasts interpreted as lag deposit, transverse ridges that mark the compression and imbrication of flows as they came to rest, scarps indicating ignimbrite remobilization, fields of pit craters caused by phreatic explosions, fractures and cracks caused by extensional processes resulting from ignimbrite volume loss, and stream channels eroded in the newly formed surface. The nine morphologies presented

  2. Mapping of a Cellulose-Deficient Mutant Named dwarf1-1 in Sorghum bicolor to the Green Revolution Gene gibberellin20-oxidase Reveals a Positive Regulatory Association between Gibberellin and Cellulose Biosynthesis.

    Science.gov (United States)

    Petti, Carloalberto; Hirano, Ko; Stork, Jozsef; DeBolt, Seth

    2015-09-01

    Here, we show a mechanism for expansion regulation through mutations in the green revolution gene gibberellin20 (GA20)-oxidase and show that GAs control biosynthesis of the plants main structural polymer cellulose. Within a 12,000 mutagenized Sorghum bicolor plant population, we identified a single cellulose-deficient and male gametophyte-dysfunctional mutant named dwarf1-1 (dwf1-1). Through the Sorghum propinquum male/dwf1-1 female F2 population, we mapped dwf1-1 to a frameshift in GA20-oxidase. Assessment of GAs in dwf1-1 revealed ablation of GA. GA ablation was antagonistic to the expression of three specific cellulose synthase genes resulting in cellulose deficiency and growth dwarfism, which were complemented by exogenous bioactive gibberellic acid application. Using quantitative polymerase chain reaction, we found that GA was positively regulating the expression of a subset of specific cellulose synthase genes. To cross reference data from our mapped Sorghum sp. allele with another monocotyledonous plant, a series of rice (Oryza sativa) mutants involved in GA biosynthesis and signaling were isolated, and these too displayed cellulose deficit. Taken together, data support a model whereby suppressed expansion in green revolution GA genes involves regulation of cellulose biosynthesis. © 2015 American Society of Plant Biologists. All Rights Reserved.

  3. The Europa Global Geologic Map

    Science.gov (United States)

    Leonard, E. J.; Patthoff, D. A.; Senske, D. A.; Collins, G. C.

    2018-06-01

    The Europa Global Geologic Map reveals three periods in Europa's surface history as well as an interesting distribution of microchaos. We will discuss the mapping and the interesting implications of our analysis of Europa's surface.

  4. Hybrid reactors

    International Nuclear Information System (INIS)

    Moir, R.W.

    1980-01-01

    The rationale for hybrid fusion-fission reactors is the production of fissile fuel for fission reactors. A new class of reactor, the fission-suppressed hybrid promises unusually good safety features as well as the ability to support 25 light-water reactors of the same nuclear power rating, or even more high-conversion-ratio reactors such as the heavy-water type. One 4000-MW nuclear hybrid can produce 7200 kg of 233 U per year. To obtain good economics, injector efficiency times plasma gain (eta/sub i/Q) should be greater than 2, the wall load should be greater than 1 MW.m -2 , and the hybrid should cost less than 6 times the cost of a light-water reactor. Introduction rates for the fission-suppressed hybrid are usually rapid

  5. Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine

    Science.gov (United States)

    2013-01-01

    Background Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esculentus complex) represent an appropriate model for studying interspecies hybridization, processes of hemiclonal inheritance and polyploidization. P. esculentus complex consists of two parental species, P. ridibundus (the lake frog) and P. lessonae (the pool frog), and their hybridogenetic hybrid – P. esculentus (the edible frog). Parental and hybrid frogs can reproduce syntopically and form hemiclonal population systems. For studying mechanisms underlying the maintenance of water frog population systems it is required to characterize the karyotypes transmitted in gametes of parental and different hybrid animals of both sexes. Results In order to obtain an instrument for characterization of oocyte karyotypes in hybrid female frogs, we constructed cytological maps of lampbrush chromosomes from oocytes of both parental species originating in Eastern Ukraine. We further identified certain molecular components of chromosomal marker structures and mapped coilin-rich spheres and granules, chromosome associated nucleoli and special loops accumulating splicing factors. We recorded the dissimilarities between P. ridibundus and P. lessonae lampbrush chromosomes in the length of orthologous chromosomes, number and location of marker structures and interstitial (TTAGGG)n-repeat sites as well as activity of nucleolus organizer. Satellite repeat RrS1 was mapped in centromere regions of lampbrush chromosomes of the both species. Additionally, we discovered transcripts of RrS1 repeat in oocytes of P. ridibundus and P. lessonae. Moreover, G-rich transcripts of telomere repeat were revealed in association with terminal regions of P. ridibundus and P. lessonae lampbrush chromosomes. Conclusions The constructed cytological maps of lampbrush chromosomes of P

  6. A rice kinase-protein interaction map.

    Science.gov (United States)

    Ding, Xiaodong; Richter, Todd; Chen, Mei; Fujii, Hiroaki; Seo, Young Su; Xie, Mingtang; Zheng, Xianwu; Kanrar, Siddhartha; Stevenson, Rebecca A; Dardick, Christopher; Li, Ying; Jiang, Hao; Zhang, Yan; Yu, Fahong; Bartley, Laura E; Chern, Mawsheng; Bart, Rebecca; Chen, Xiuhua; Zhu, Lihuang; Farmerie, William G; Gribskov, Michael; Zhu, Jian-Kang; Fromm, Michael E; Ronald, Pamela C; Song, Wen-Yuan

    2009-03-01

    Plants uniquely contain large numbers of protein kinases, and for the vast majority of the 1,429 kinases predicted in the rice (Oryza sativa) genome, little is known of their functions. Genetic approaches often fail to produce observable phenotypes; thus, new strategies are needed to delineate kinase function. We previously developed a cost-effective high-throughput yeast two-hybrid system. Using this system, we have generated a protein interaction map of 116 representative rice kinases and 254 of their interacting proteins. Overall, the resulting interaction map supports a large number of known or predicted kinase-protein interactions from both plants and animals and reveals many new functional insights. Notably, we found a potential widespread role for E3 ubiquitin ligases in pathogen defense signaling mediated by receptor-like kinases, particularly by the kinases that may have evolved from recently expanded kinase subfamilies in rice. We anticipate that the data provided here will serve as a foundation for targeted functional studies in rice and other plants. The application of yeast two-hybrid and TAPtag analyses for large-scale plant protein interaction studies is also discussed.

  7. X chromosome control of meiotic chromosome synapsis in mouse inter-subspecific hybrids.

    Directory of Open Access Journals (Sweden)

    Tanmoy Bhattacharyya

    2014-02-01

    Full Text Available Hybrid sterility (HS belongs to reproductive isolation barriers that safeguard the integrity of species in statu nascendi. Although hybrid sterility occurs almost universally among animal and plant species, most of our current knowledge comes from the classical genetic studies on Drosophila interspecific crosses or introgressions. With the house mouse subspecies Mus m. musculus and Mus m. domesticus as a model, new research tools have become available for studies of the molecular mechanisms and genetic networks underlying HS. Here we used QTL analysis and intersubspecific chromosome substitution strains to identify a 4.7 Mb critical region on Chromosome X (Chr X harboring the Hstx2 HS locus, which causes asymmetrical spermatogenic arrest in reciprocal intersubspecific F1 hybrids. Subsequently, we mapped autosomal loci on Chrs 3, 9 and 13 that can abolish this asymmetry. Combination of immunofluorescent visualization of the proteins of synaptonemal complexes with whole-chromosome DNA FISH on pachytene spreads revealed that heterosubspecific, unlike consubspecific, homologous chromosomes are predisposed to asynapsis in F1 hybrid male and female meiosis. The asynapsis is under the trans- control of Hstx2 and Hst1/Prdm9 hybrid sterility genes in pachynemas of male but not female hybrids. The finding concurred with the fertility of intersubpecific F1 hybrid females homozygous for the Hstx2(Mmm allele and resolved the apparent conflict with the dominance theory of Haldane's rule. We propose that meiotic asynapsis in intersubspecific hybrids is a consequence of cis-acting mismatch between homologous chromosomes modulated by the trans-acting Hstx2 and Prdm9 hybrid male sterility genes.

  8. X chromosome control of meiotic chromosome synapsis in mouse inter-subspecific hybrids.

    Science.gov (United States)

    Bhattacharyya, Tanmoy; Reifova, Radka; Gregorova, Sona; Simecek, Petr; Gergelits, Vaclav; Mistrik, Martin; Martincova, Iva; Pialek, Jaroslav; Forejt, Jiri

    2014-02-01

    Hybrid sterility (HS) belongs to reproductive isolation barriers that safeguard the integrity of species in statu nascendi. Although hybrid sterility occurs almost universally among animal and plant species, most of our current knowledge comes from the classical genetic studies on Drosophila interspecific crosses or introgressions. With the house mouse subspecies Mus m. musculus and Mus m. domesticus as a model, new research tools have become available for studies of the molecular mechanisms and genetic networks underlying HS. Here we used QTL analysis and intersubspecific chromosome substitution strains to identify a 4.7 Mb critical region on Chromosome X (Chr X) harboring the Hstx2 HS locus, which causes asymmetrical spermatogenic arrest in reciprocal intersubspecific F1 hybrids. Subsequently, we mapped autosomal loci on Chrs 3, 9 and 13 that can abolish this asymmetry. Combination of immunofluorescent visualization of the proteins of synaptonemal complexes with whole-chromosome DNA FISH on pachytene spreads revealed that heterosubspecific, unlike consubspecific, homologous chromosomes are predisposed to asynapsis in F1 hybrid male and female meiosis. The asynapsis is under the trans- control of Hstx2 and Hst1/Prdm9 hybrid sterility genes in pachynemas of male but not female hybrids. The finding concurred with the fertility of intersubpecific F1 hybrid females homozygous for the Hstx2(Mmm) allele and resolved the apparent conflict with the dominance theory of Haldane's rule. We propose that meiotic asynapsis in intersubspecific hybrids is a consequence of cis-acting mismatch between homologous chromosomes modulated by the trans-acting Hstx2 and Prdm9 hybrid male sterility genes.

  9. X Chromosome Control of Meiotic Chromosome Synapsis in Mouse Inter-Subspecific Hybrids

    Science.gov (United States)

    Bhattacharyya, Tanmoy; Reifova, Radka; Gregorova, Sona; Simecek, Petr; Gergelits, Vaclav; Mistrik, Martin; Martincova, Iva; Pialek, Jaroslav; Forejt, Jiri

    2014-01-01

    Hybrid sterility (HS) belongs to reproductive isolation barriers that safeguard the integrity of species in statu nascendi. Although hybrid sterility occurs almost universally among animal and plant species, most of our current knowledge comes from the classical genetic studies on Drosophila interspecific crosses or introgressions. With the house mouse subspecies Mus m. musculus and Mus m. domesticus as a model, new research tools have become available for studies of the molecular mechanisms and genetic networks underlying HS. Here we used QTL analysis and intersubspecific chromosome substitution strains to identify a 4.7 Mb critical region on Chromosome X (Chr X) harboring the Hstx2 HS locus, which causes asymmetrical spermatogenic arrest in reciprocal intersubspecific F1 hybrids. Subsequently, we mapped autosomal loci on Chrs 3, 9 and 13 that can abolish this asymmetry. Combination of immunofluorescent visualization of the proteins of synaptonemal complexes with whole-chromosome DNA FISH on pachytene spreads revealed that heterosubspecific, unlike consubspecific, homologous chromosomes are predisposed to asynapsis in F1 hybrid male and female meiosis. The asynapsis is under the trans- control of Hstx2 and Hst1/Prdm9 hybrid sterility genes in pachynemas of male but not female hybrids. The finding concurred with the fertility of intersubpecific F1 hybrid females homozygous for the Hstx2Mmm allele and resolved the apparent conflict with the dominance theory of Haldane's rule. We propose that meiotic asynapsis in intersubspecific hybrids is a consequence of cis-acting mismatch between homologous chromosomes modulated by the trans-acting Hstx2 and Prdm9 hybrid male sterility genes. PMID:24516397

  10. Hybrid composites

    CSIR Research Space (South Africa)

    Jacob John, Maya

    2009-04-01

    Full Text Available mixed short sisal/glass hybrid fibre reinforced low density polyethylene composites was investigated by Kalaprasad et al [25].Chemical surface modifications such as alkali, acetic anhydride, stearic acid, permanganate, maleic anhydride, silane...

  11. Hybrid intermediaries

    OpenAIRE

    Cetorelli, Nicola

    2014-01-01

    I introduce the concept of hybrid intermediaries: financial conglomerates that control a multiplicity of entity types active in the "assembly line" process of modern financial intermediation, a system that has become known as shadow banking. The complex bank holding companies of today are the best example of hybrid intermediaries, but I argue that financial firms from the "nonbank" space can just as easily evolve into conglomerates with similar organizational structure, thus acquiring the cap...

  12. Mapping of repair genes

    International Nuclear Information System (INIS)

    Hori, Tadaaki

    1985-01-01

    Chromosome mapping of repair genes involved in U.V. sensitivity is reported. Twenty-three of 25 hybrid cells were resistant to U.V. light. Survival curves of 2 U.V.-resistant cell strains, which possessed mouse chromosomes and human chromosome No.7 - 16, were similar to those of wild strain (L5178Y). On the other hand, survival curves of U.V.-sensitive hybrid cells was analogous to those of Q31. There was a definitive difference in the frequency of inducible chromosome aberrations between U.V. resistant and sensitive mouse-human hybrid cells. U.V.-resistant cell strains possessed the ability of excision repair. Analysis of karyotype in hybrid cells showed that the difference in U.V. sensitivity is dependent upon whether or not human chromosome No.13 is present. Synteny test on esterase D-determining locus confirmed that there is an agreement between the presence of chromosome No.13 and the presence of human esterase D activity. These results led to a conclusion that human genes which compensate recessive character of U.V.-sensitive mutant strain, Q31, with mouse-human hybrid cells are located on the locus of chromosome No.13. (Namekawa, K.)

  13. Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

    Science.gov (United States)

    Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal

    2016-04-01

    The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

  14. Hybrid stars

    Indian Academy of Sciences (India)

    Hybrid stars. AsHOK GOYAL. Department of Physics and Astrophysics, University of Delhi, Delhi 110 007, India. Abstract. Recently there have been important developments in the determination of neutron ... number and the electric charge. ... available to the system to rearrange concentration of charges for a given fraction of.

  15. Hybrid Fuel Cell Technology Overview

    Energy Technology Data Exchange (ETDEWEB)

    None available

    2001-05-31

    For the purpose of this STI product and unless otherwise stated, hybrid fuel cell systems are power generation systems in which a high temperature fuel cell is combined with another power generating technology. The resulting system exhibits a synergism in which the combination performs with an efficiency far greater than can be provided by either system alone. Hybrid fuel cell designs under development include fuel cell with gas turbine, fuel cell with reciprocating (piston) engine, and designs that combine different fuel cell technologies. Hybrid systems have been extensively analyzed and studied over the past five years by the Department of Energy (DOE), industry, and others. These efforts have revealed that this combination is capable of providing remarkably high efficiencies. This attribute, combined with an inherent low level of pollutant emission, suggests that hybrid systems are likely to serve as the next generation of advanced power generation systems.

  16. Assessment on Hybrid E-Learning Instrument

    OpenAIRE

    Intan Farahana Kamsin; Rosseni Din

    2015-01-01

    This study aims to improve Hybrid e-Learning 9.3. A total of 233 students of International Islamic University Malaysia, Gombak who have the experience in hybrid teaching and learning were involved as respondents. Rasch Measurement Model was used for this study. Validity analyses conducted were on (i) the compatibility of the items, (ii) mapping of items and respondents, (iii) scaling of instruments, and (iv) unidimentional items. The findings of the study show that (i) the items developed cor...

  17. Active and Passive Hybrid Sensor

    Science.gov (United States)

    Carswell, James R.

    2010-01-01

    A hybrid ocean wind sensor (HOWS) can map ocean vector wind in low to hurricane-level winds, and non-precipitating and precipitating conditions. It can acquire active and passive measurements through a single aperture at two wavelengths, two polarizations, and multiple incidence angles. Its low profile, compact geometry, and low power consumption permits installation on air craft platforms, including high-altitude unmanned aerial vehicles (UAVs).

  18. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

    KAUST Repository

    Liu, Guozheng

    2016-07-06

    Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population.

  19. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat.

    Directory of Open Access Journals (Sweden)

    Guozheng Liu

    Full Text Available Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1 examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2 explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3 investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L. and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs, but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population.

  20. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

    KAUST Repository

    Liu, Guozheng; Zhao, Yusheng; Gowda, Manje; Longin, C. Friedrich H.; Reif, Jochen C.; Mette, Michael F.

    2016-01-01

    Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population.

  1. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

    Science.gov (United States)

    Liu, Guozheng; Zhao, Yusheng; Gowda, Manje; Longin, C. Friedrich H.; Reif, Jochen C.; Mette, Michael F.

    2016-01-01

    Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population. PMID:27383841

  2. Bodily maps of emotions.

    Science.gov (United States)

    Nummenmaa, Lauri; Glerean, Enrico; Hari, Riitta; Hietanen, Jari K

    2014-01-14

    Emotions are often felt in the body, and somatosensory feedback has been proposed to trigger conscious emotional experiences. Here we reveal maps of bodily sensations associated with different emotions using a unique topographical self-report method. In five experiments, participants (n = 701) were shown two silhouettes of bodies alongside emotional words, stories, movies, or facial expressions. They were asked to color the bodily regions whose activity they felt increasing or decreasing while viewing each stimulus. Different emotions were consistently associated with statistically separable bodily sensation maps across experiments. These maps were concordant across West European and East Asian samples. Statistical classifiers distinguished emotion-specific activation maps accurately, confirming independence of topographies across emotions. We propose that emotions are represented in the somatosensory system as culturally universal categorical somatotopic maps. Perception of these emotion-triggered bodily changes may play a key role in generating consciously felt emotions.

  3. Geological mapping of the vertical southeast face of El Capitan, Yosemite Valley, California (Invited)

    Science.gov (United States)

    Stock, G. M.; Glazner, A. F.; Ratajeski, K.; Law, B.

    2010-12-01

    El Capitan in Yosemite Valley, California, is one of the world’s most accessible large granitic rock faces. At nearly 1 km tall, the vertical southeast face of El Capitan provides unique insight into igneous processes contributing to the assembly of the Sierra Nevada batholith ~103 million years ago. Although the base and summit dome of El Capitan have been mapped in detail, the vertical face has so far eluded comprehensive attempts at geologic mapping. We have combined field mapping by technical rock climbing with high-resolution gigapixel photography to develop the first detailed digital geologic map of the southeast face (North America Wall). Geologic units exposed on the face include the El Capitan and Taft Granites, at least two phases of dioritic intrusions, hybridized rocks, and late-stage aplite/pegmatite dikes and pods. We map these units on a high resolution far-range base image derived from a high-resolution panoramic photograph, and verify contact relationships with close-range field photographs and visual observations from anchor points along major climbing routes. Mapping of contact relationships between these units reveals the sequence of intrusion of the various units, as well as the relationship of the mafic intrusions with the more voluminous granites. Geologic mapping of the southeast face also informs geologic hazards by constraining the source area for lithologically distinct rock falls; for example, geologic mapping confirms that a 2.2 x 106 m3 rock avalanche that occurred circa 3,600 years ago originated from near the summit of El Capitan, within an area dominated by Taft Granite. In addition to expanding mapping to the southwest face, future mapping efforts will focus on integrating the high resolution base map with airborne and terrestrial LiDAR data to produce a three-dimensional geologic map of one of the most iconic rock formations in the world.

  4. Hybrid fixed point in CAT(0 spaces

    Directory of Open Access Journals (Sweden)

    Hemant Kumar Pathak

    2018-02-01

    Full Text Available In this paper, we introduce an ultrapower approach to prove fixed point theorems for $H^{+}$-nonexpansive multi-valued mappings in the setting of CAT(0 spaces and prove several hybrid fixed point results in CAT(0 spaces for families of single-valued nonexpansive or quasinonexpansive mappings and multi-valued upper semicontinuous, almost lower semicontinuous or $H^{+}$-nonexpansive mappings which are weakly commuting. We also establish a result about structure of the set of fixed points of $H^{+}$-quasinonexpansive mapping on a CAT(0 space.

  5. Model Predictive Control for Connected Hybrid Electric Vehicles

    Directory of Open Access Journals (Sweden)

    Kaijiang Yu

    2015-01-01

    Full Text Available This paper presents a new model predictive control system for connected hybrid electric vehicles to improve fuel economy. The new features of this study are as follows. First, the battery charge and discharge profile and the driving velocity profile are simultaneously optimized. One is energy management for HEV for Pbatt; the other is for the energy consumption minimizing problem of acc control of two vehicles. Second, a system for connected hybrid electric vehicles has been developed considering varying drag coefficients and the road gradients. Third, the fuel model of a typical hybrid electric vehicle is developed using the maps of the engine efficiency characteristics. Fourth, simulations and analysis (under different parameters, i.e., road conditions, vehicle state of charge, etc. are conducted to verify the effectiveness of the method to achieve higher fuel efficiency. The model predictive control problem is solved using numerical computation method: continuation and generalized minimum residual method. Computer simulation results reveal improvements in fuel economy using the proposed control method.

  6. Case for the fusion hybrid

    International Nuclear Information System (INIS)

    Rose, R.P.

    1981-01-01

    The use of nuclear fusion to produce fuel for nuclear fission power stations is discussed in the context of a crucial need for future energy options. The fusion hybrid is first considered as an element in the future of nuclear fission power to provide long term assurance of adequate fuel supplies for both breeder and convertor reactors. Generic differences in neutronic characteristics lead to a fuel production potential of fusion-fission hybrid systems which is significantly greater than that obtainable with fission systems alone. Furthermore, cost benefit studies show a variety of scenarios in which the hybrid offers sufficient potential to justify development costs ranging in the tens of billions of dollars. The hybrid is then considered as an element in the ultimate development of fusion electric power. The hybrid offers a near term application of fusion where experience with the requisite technologies can be derived as a vital step in mapping a credible route to eventual commercial feasibility of pure fusion systems. Finally, the criteria for assessment of future energy options are discussed with prime emphasis on the need for rational comparision of alternatives

  7. Involvement of an ABI-like protein and a Ca2+-ATPase in drought tolerance as revealed by transcript profiling of a sweetpotato somatic hybrid and its parents Ipomoea batatas (L.) Lam. and I. triloba L.

    Science.gov (United States)

    Yang, Yufeng; Wang, Yannan; Jia, Licong; Yang, Guohong; Xu, Xinzhi; Zhai, Hong; He, Shaozhen; Li, Junxia; Dai, Xiaodong; Qin, Na; Zhu, Cancan; Liu, Qingchang

    2018-01-01

    Previously, we obtained the sweetpotato somatic hybrid KT1 from a cross between sweetpotato (Ipomoea batatas (L.) Lam.) cv. Kokei No. 14 and its drought-tolerant wild relative I. triloba L. KT1 not only inherited the thick storage root characteristic of Kokei No. 14 but also the drought-tolerance trait of I. triloba L. The aim of this study was to explore the molecular mechanism of the drought tolerance of KT1. Four-week-old in vitro-grown plants of KT1, Kokei No. 14, and I. triloba L. were subjected to a simulated drought stress treatment (30% PEG6000) for 0, 6, 12 and 24 h. Total RNA was extracted from samples at each time point, and then used for transcriptome sequencing. The gene transcript profiles of KT1 and its parents were compared to identify differentially expressed genes, and drought-related modules were screened by a weighted gene co-expression network analysis. The functions of ABI-like protein and Ca2+-ATPase, two proteins screened from the cyan and light yellow modules, were analyzed in terms of their potential roles in drought tolerance in KT1 and its parents. These analyses of the drought responses of KT1 and its somatic donors at the transcriptional level provide new annotations for the molecular mechanism of drought tolerance in the somatic hybrid KT1 and its parents.

  8. Conditions that impact artificial hybridization of Arachis hypogaea L.

    Science.gov (United States)

    Modern farming is dependent on continual development of improved cultivars and efficient cultural management practices. In addition, dissecting genetic components of heritable traits also relies on the development of large mapping populations. Artificial hybridization is the critical initial step ...

  9. Topographic mapping

    Science.gov (United States)

    ,

    2008-01-01

    The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

  10. Quantitative magneto-optical investigation of superconductor/ferromagnet hybrid structures.

    Science.gov (United States)

    Shaw, G; Brisbois, J; Pinheiro, L B G L; Müller, J; Blanco Alvarez, S; Devillers, T; Dempsey, N M; Scheerder, J E; Van de Vondel, J; Melinte, S; Vanderbemden, P; Motta, M; Ortiz, W A; Hasselbach, K; Kramer, R B G; Silhanek, A V

    2018-02-01

    We present a detailed quantitative magneto-optical imaging study of several superconductor/ferromagnet hybrid structures, including Nb deposited on top of thermomagnetically patterned NdFeB and permalloy/niobium with erasable and tailored magnetic landscapes imprinted in the permalloy layer. The magneto-optical imaging data are complemented with and compared to scanning Hall probe microscopy measurements. Comprehensive protocols have been developed for calibrating, testing, and converting Faraday rotation data to magnetic field maps. Applied to the acquired data, they reveal the comparatively weaker magnetic response of the superconductor from the background of larger fields and field gradients generated by the magnetic layer.

  11. Quantitative magneto-optical investigation of superconductor/ferromagnet hybrid structures

    Science.gov (United States)

    Shaw, G.; Brisbois, J.; Pinheiro, L. B. G. L.; Müller, J.; Blanco Alvarez, S.; Devillers, T.; Dempsey, N. M.; Scheerder, J. E.; Van de Vondel, J.; Melinte, S.; Vanderbemden, P.; Motta, M.; Ortiz, W. A.; Hasselbach, K.; Kramer, R. B. G.; Silhanek, A. V.

    2018-02-01

    We present a detailed quantitative magneto-optical imaging study of several superconductor/ferromagnet hybrid structures, including Nb deposited on top of thermomagnetically patterned NdFeB and permalloy/niobium with erasable and tailored magnetic landscapes imprinted in the permalloy layer. The magneto-optical imaging data are complemented with and compared to scanning Hall probe microscopy measurements. Comprehensive protocols have been developed for calibrating, testing, and converting Faraday rotation data to magnetic field maps. Applied to the acquired data, they reveal the comparatively weaker magnetic response of the superconductor from the background of larger fields and field gradients generated by the magnetic layer.

  12. Hybrid Qualifications

    DEFF Research Database (Denmark)

    Against the background of increasing qualification needs there is a growing awareness of the challenge to widen participation in processes of skill formation and competence development. At the same time, the issue of permeability between vocational education and training (VET) and general education...... has turned out as a major focus of European education and training policies and certainly is a crucial principle underlying the European Qualifications Framework (EQF). In this context, «hybrid qualifications» (HQ) may be seen as an interesting approach to tackle these challenges as they serve «two...

  13. Hybrid Gear

    Science.gov (United States)

    Handschuh, Robert F. (Inventor); Roberts, Gary D. (Inventor)

    2016-01-01

    A hybrid gear consisting of metallic outer rim with gear teeth and metallic hub in combination with a composite lay up between the shaft interface (hub) and gear tooth rim is described. The composite lay-up lightens the gear member while having similar torque carrying capability and it attenuates the impact loading driven noise/vibration that is typical in gear systems. The gear has the same operational capability with respect to shaft speed, torque, and temperature as an all-metallic gear as used in aerospace gear design.

  14. Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

    Science.gov (United States)

    Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

    2013-01-01

    Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

  15. Intuitionistic hybrid logic

    DEFF Research Database (Denmark)

    Braüner, Torben

    2011-01-01

    Intuitionistic hybrid logic is hybrid modal logic over an intuitionistic logic basis instead of a classical logical basis. In this short paper we introduce intuitionistic hybrid logic and we give a survey of work in the area.......Intuitionistic hybrid logic is hybrid modal logic over an intuitionistic logic basis instead of a classical logical basis. In this short paper we introduce intuitionistic hybrid logic and we give a survey of work in the area....

  16. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  17. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  18. Participatory Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    2016-01-01

    practice. In particular, mapping environmental damage, endangered species, and human-made disasters has become one focal point for environmental knowledge production. This type of digital map has been highlighted as a processual turn in critical cartography, whereas in related computational journalism...... of a geo-visualization within information mapping that enhances embodiment in the experience of the information. InfoAmazonia is defined as a digitally created map-space within which journalistic practice can be seen as dynamic, performative interactions between journalists, ecosystems, space, and species...

  19. Hybridized Tetraquarks

    CERN Document Server

    Esposito, A.; Polosa, A.D.

    2016-01-01

    We propose a new interpretation of the neutral and charged X, Z exotic hadron resonances. Hybridized-tetraquarks are neither purely compact tetraquark states nor bound or loosely bound molecules. The latter would require a negative or zero binding energy whose counterpart in h-tetraquarks is a positive quantity. The formation mechanism of this new class of hadrons is inspired by that of Feshbach metastable states in atomic physics. The recent claim of an exotic resonance in the Bs pi+- channel by the D0 collaboration and the negative result presented subsequently by the LHCb collaboration are understood in this scheme, together with a considerable portion of available data on X, Z particles. Considerations on a state with the same quantum numbers as the X(5568) are also made.

  20. A Novel Three-Colour Fluorescence in Situ Hybridization Approach for the Detection of t(7;12)(q36;p13) in Acute Myeloid Leukaemia Reveals New Cryptic Three Way Translocation t(7;12;16)

    Energy Technology Data Exchange (ETDEWEB)

    Naiel, Abdulbasit [Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University, London, Middlesex UB8 3PH (United Kingdom); Vetter, Michael [MetaSystems, Altlussheim 68804 (Germany); Plekhanova, Olga [Regional Children’s Hospital N 1, Ekaterinburg 620149 (Russian Federation); Fleischman, Elena; Sokova, Olga [N.N. Blokhin Russian Cancer Research Center Russian Academy of Medical Science, Moscow 115478 (Russian Federation); Tsaur, Grigory [Regional Children’s Hospital N 1, Ekaterinburg 620149 (Russian Federation); Research Institute of Medical Cell Technologies, Ekaterinburg 620149 (Russian Federation); Harbott, Jochen [Oncogenetic Laboratory, Department of Paediatric Haematology and Oncology, Justus Liebig University, Giessen 35392 (Germany); Tosi, Sabrina, E-mail: sabrina.tosi@brunel.ac.uk [Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University, London, Middlesex UB8 3PH (United Kingdom)

    2013-03-11

    The t(7;12)(q36;p13) translocation is a recurrent chromosome abnormality that involves the ETV6 gene on chromosome 12 and has been identified in 20–30% of infant patients with acute myeloid leukaemia (AML). The detection of t(7;12) rearrangements relies on the use of fluorescence in situ hybridization (FISH) because this translocation is hardly visible by chromosome banding methods. Furthermore, a fusion transcript HLXB9-ETV6 is found in approximately 50% of t(7;12) cases, making the reverse transcription PCR approach not an ideal screening method. Considering the report of few cases of variant translocations harbouring a cryptic t(7;12) rearrangement, we believe that the actual incidence of this abnormality is higher than reported to date. The clinical outcome of t(7;12) patients is believed to be poor, therefore an early and accurate diagnosis is important in the clinical management and treatment. In this study, we have designed and tested a novel three-colour FISH approach that enabled us not only to confirm the presence of the t(7;12) in a number of patients studied previously, but also to identify a cryptic t(7;12) as part of a complex rearrangement. This new approach has proven to be an efficient and reliable method to be used in the diagnostic setting.

  1. Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes

    Science.gov (United States)

    In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approxima...

  2. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

    Directory of Open Access Journals (Sweden)

    Dipnarayan Saha

    2017-10-01

    Full Text Available Corchorus capsularis (white jute and C. olitorius (dark jute are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60% followed by dinucleotide repeats (37.6%. Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR markers were successfully mapped to the existing single-nucleotide polymorphism (SNP linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/ for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.

  3. Continuity controlled Hybrid Automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation

  4. Continuity Controlled Hybrid Automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2004-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  5. Continuity controlled hybrid automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2004-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  6. Continuity controlled hybrid automata

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2006-01-01

    We investigate the connections between the process algebra for hybrid systems of Bergstra and Middelburg and the formalism of hybrid automata of Henzinger et al. We give interpretations of hybrid automata in the process algebra for hybrid systems and compare them with the standard interpretation of

  7. Hybrid discrete-time neural networks.

    Science.gov (United States)

    Cao, Hongjun; Ibarz, Borja

    2010-11-13

    Hybrid dynamical systems combine evolution equations with state transitions. When the evolution equations are discrete-time (also called map-based), the result is a hybrid discrete-time system. A class of biological neural network models that has recently received some attention falls within this category: map-based neuron models connected by means of fast threshold modulation (FTM). FTM is a connection scheme that aims to mimic the switching dynamics of a neuron subject to synaptic inputs. The dynamic equations of the neuron adopt different forms according to the state (either firing or not firing) and type (excitatory or inhibitory) of their presynaptic neighbours. Therefore, the mathematical model of one such network is a combination of discrete-time evolution equations with transitions between states, constituting a hybrid discrete-time (map-based) neural network. In this paper, we review previous work within the context of these models, exemplifying useful techniques to analyse them. Typical map-based neuron models are low-dimensional and amenable to phase-plane analysis. In bursting models, fast-slow decomposition can be used to reduce dimensionality further, so that the dynamics of a pair of connected neurons can be easily understood. We also discuss a model that includes electrical synapses in addition to chemical synapses with FTM. Furthermore, we describe how master stability functions can predict the stability of synchronized states in these networks. The main results are extended to larger map-based neural networks.

  8. A general method for identifying major hybrid male sterility genes in Drosophila.

    Science.gov (United States)

    Zeng, L W; Singh, R S

    1995-10-01

    The genes responsible for hybrid male sterility in species crosses are usually identified by introgressing chromosome segments, monitored by visible markers, between closely related species by continuous backcrosses. This commonly used method, however, suffers from two problems. First, it relies on the availability of markers to monitor the introgressed regions and so the portion of the genome examined is limited to the marked regions. Secondly, the introgressed regions are usually large and it is impossible to tell if the effects of the introgressed regions are the result of single (or few) major genes or many minor genes (polygenes). Here we introduce a simple and general method for identifying putative major hybrid male sterility genes which is free of these problems. In this method, the actual hybrid male sterility genes (rather than markers), or tightly linked gene complexes with large effects, are selectively introgressed from one species into the background of another species by repeated backcrosses. This is performed by selectively backcrossing heterozygous (for hybrid male sterility gene or genes) females producing fertile and sterile sons in roughly equal proportions to males of either parental species. As no marker gene is required for this procedure, this method can be used with any species pairs that produce unisexual sterility. With the application of this method, a small X chromosome region of Drosophila mauritiana which produces complete hybrid male sterility (aspermic testes) in the background of D. simulans was identified. Recombination analysis reveals that this region contains a second major hybrid male sterility gene linked to the forked locus located at either 62.7 +/- 0.66 map units or at the centromere region of the X chromosome of D. mauritiana.

  9. Corporate Hybrid Bonds

    OpenAIRE

    Ahlberg, Johan; Jansson, Anton

    2016-01-01

    Hybrid securities do not constitute a new phenomenon in the Swedish capital markets. Most commonly, hybrids issued by Swedish real estate companies in recent years are preference shares. Corporate hybrid bonds on the other hand may be considered as somewhat of a new-born child in the family of hybrid instruments. These do, as all other hybrid securities, share some equity-like and some debt-like characteristics. Nevertheless, since 2013 the interest for the instrument has grown rapidly and ha...

  10. Common fixed points of single-valued and multivalued maps

    Directory of Open Access Journals (Sweden)

    Yicheng Liu

    2005-01-01

    Full Text Available We define a new property which contains the property (EA for a hybrid pair of single- and multivalued maps and give some new common fixed point theorems under hybrid contractive conditions. Our results extend previous ones. As an application, we give a partial answer to the problem raised by Singh and Mishra.

  11. Quantitative trait loci mapping for stomatal traits in interspecific ...

    Indian Academy of Sciences (India)

    Dr.YASODHA

    seedling raising, field planting and maintenance of the mapping population. ... tereticornis and production of interspecific hybrids displaying hybrid vigour in terms of .... A total of 114, 115 and 129 SSR, ISSR and SRAP markers were generated .... stomatal traits with yield and adaptability would help to improve productivity of ...

  12. Mapping racism.

    Science.gov (United States)

    Moss, Donald B

    2006-01-01

    The author uses the metaphor of mapping to illuminate a structural feature of racist thought, locating the degraded object along vertical and horizontal axes. These axes establish coordinates of hierarchy and of distance. With the coordinates in place, racist thought begins to seem grounded in natural processes. The other's identity becomes consolidated, and parochialism results. The use of this kind of mapping is illustrated via two patient vignettes. The author presents Freud's (1905, 1927) views in relation to such a "mapping" process, as well as Adorno's (1951) and Baldwin's (1965). Finally, the author conceptualizes the crucial status of primitivity in the workings of racist thought.

  13. Hybrid XRF

    International Nuclear Information System (INIS)

    Heckel, J.

    2002-01-01

    Full text: In the last 10 years significant innovations of EDXRF, e.g. total reflection XRF or polarized beam XRF, were utilized in different industrial applications. The decrease of background within the spectra was the goal of these developments. Excellent detection limits and sensitivities demonstrate the success of these new techniques. Nevertheless, further improvements are possible by using Si drift detectors. These detectors allow the processing of input count rates up to 10 6 cps in comparison to 10 5 of Si(Li) detectors. New excitation optics are necessary to produce such count rates. One possibility is the use of doubly curved crystals between tube and sample. These crystals enable the reflection of the primary beam within the given solid angle (0.4π) of an end window tube to the sample. Using such brightness optics excellent sensitivities mainly for light elements are achievable. The combination of a BRAGG crystal as a wavelength dispersive component and a solid state detector as an energy dispersive component creates a new technique: hybrid XRF. Copyright (2002) Australian X-ray Analytical Association Inc. Copyright (2002) Australian X-ray Analytical Association Inc

  14. Hybrid mimics and hybrid vigor in Arabidopsis

    Science.gov (United States)

    Wang, Li; Greaves, Ian K.; Groszmann, Michael; Wu, Li Min; Dennis, Elizabeth S.; Peacock, W. James

    2015-01-01

    F1 hybrids can outperform their parents in yield and vegetative biomass, features of hybrid vigor that form the basis of the hybrid seed industry. The yield advantage of the F1 is lost in the F2 and subsequent generations. In Arabidopsis, from F2 plants that have a F1-like phenotype, we have by recurrent selection produced pure breeding F5/F6 lines, hybrid mimics, in which the characteristics of the F1 hybrid are stabilized. These hybrid mimic lines, like the F1 hybrid, have larger leaves than the parent plant, and the leaves have increased photosynthetic cell numbers, and in some lines, increased size of cells, suggesting an increased supply of photosynthate. A comparison of the differentially expressed genes in the F1 hybrid with those of eight hybrid mimic lines identified metabolic pathways altered in both; these pathways include down-regulation of defense response pathways and altered abiotic response pathways. F6 hybrid mimic lines are mostly homozygous at each locus in the genome and yet retain the large F1-like phenotype. Many alleles in the F6 plants, when they are homozygous, have expression levels different to the level in the parent. We consider this altered expression to be a consequence of transregulation of genes from one parent by genes from the other parent. Transregulation could also arise from epigenetic modifications in the F1. The pure breeding hybrid mimics have been valuable in probing the mechanisms of hybrid vigor and may also prove to be useful hybrid vigor equivalents in agriculture. PMID:26283378

  15. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  16. Genetic Mapping

    Science.gov (United States)

    ... greatly advanced genetics research. The improved quality of genetic data has reduced the time required to identify a ... cases, a matter of months or even weeks. Genetic mapping data generated by the HGP's laboratories is freely accessible ...

  17. Acoustic force mapping in a hybrid acoustic-optical micromanipulation device supporting high resolution optical imaging† †Electronic supplementary information (ESI) available: Additional information about 1D model calculations for a piezoelectric transducer. See DOI: 10.1039/c6lc00182c Click here for additional data file.

    Science.gov (United States)

    McDougall, Craig; MacDonald, Michael Peter; Ritsch-Marte, Monika

    2016-01-01

    Many applications in the life-sciences demand non-contact manipulation tools for forceful but nevertheless delicate handling of various types of sample. Moreover, the system should support high-resolution optical imaging. Here we present a hybrid acoustic/optical manipulation system which utilizes a transparent transducer, making it compatible with high-NA imaging in a microfluidic environment. The powerful acoustic trapping within a layered resonator, which is suitable for highly parallel particle handling, is complemented by the flexibility and selectivity of holographic optical tweezers, with the specimens being under high quality optical monitoring at all times. The dual acoustic/optical nature of the system lends itself to optically measure the exact acoustic force map, by means of direct force measurements on an optically trapped particle. For applications with (ultra-)high demand on the precision of the force measurements, the position of the objective used for the high-NA imaging may have significant influence on the acoustic force map in the probe chamber. We have characterized this influence experimentally and the findings were confirmed by model simulations. We show that it is possible to design the chamber and to choose the operating point in such a way as to avoid perturbations due to the objective lens. Moreover, we found that measuring the electrical impedance of the transducer provides an easy indicator for the acoustic resonances. PMID:27025398

  18. Electrokinetic acceleration of DNA hybridization in microsystems.

    Science.gov (United States)

    Lei, Kin Fong; Wang, Yun-Hsiang; Chen, Huai-Yi; Sun, Jia-Hong; Cheng, Ji-Yen

    2015-06-01

    In this work, electrokinetic acceleration of DNA hybridization was investigated by different combinations of frequencies and amplitudes of actuating electric signals. Because the frequencies from low to high can induce different kinds of electrokinetic forces, i.e., electroosmotic to electrothermal forces, this work provides an in-depth investigation of electrokinetic enhanced hybridization. Concentric circular Cr/Au microelectrodes of 350 µm in diameter were fabricated on a glass substrate and probe DNA was immobilized on the electrode surface. Target DNA labeled with fluorescent dyes suspending in solution was then applied to the electrode. Different electrokinetic forces were induced by the application of different electric signals to the circular microelectrodes. Local microfluidic vortexes were generated to increase the collision efficiency between the target DNA suspending in solution and probe DNA immobilized on the electrode surface. DNA hybridization on the electrode surface could be accelerated by the electrokinetic forces. The level of hybridization was represented by the fluorescent signal intensity ratio. Results revealed that such 5-min dynamic hybridization increased 4.5 fold of signal intensity ratio as compared to a 1-h static hybridization. Moreover, dynamic hybridization was found to have better diff