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1. The Interface Region Imaging Spectrograph (IRIS)

Author

De Pontieu, B., Title, A. M., Lemen, J., Kushner, G. D., Akin, D. J., Allard, B., Berger, T., Boerner, P., Cheung, M., Chou, C., Drake, J. F., Duncan, D. W., Freeland, S., Heyman, G. F., Hoffman, C., Hurlburt, N. E., Lindgren, R. W., Mathur, D., Rehse, R., Sabolish, D., Seguin, R., Schrijver, C. J., Tarbell, T. D., Wuelser, J. -P., Wolfson, C. J., Yanari, C., Mudge, J., Nguyen-Phuc, N., Timmons, R., van Bezooijen, R., Weingrod, I., Brookner, R., Butcher, G., Dougherty, B., Eder, J., Knagenhjelm, V., Larsen, S., Mansir, D., Phan, L., Boyle, P., Cheimets, P. N., DeLuca, E. E., Golub, L., Gates, R., Hertz, E., McKillop, S., Park, S., Perry, T., Podgorski, W. A., Reeves, K., Saar, S., Testa, P., Tian, H., Weber, M., Dunn, C., Eccles, S., Jaeggli, S. A., Kankelborg, C. C, Mashburn, K., Pust, N., Springer, L., Carvalho, R., Kleint, L., Marmie, J., Mazmanian, E., Pereira, T. M. D., Sawyer, S., Strong, J., Worden, S. P., Carlsson, M., Hansteen, V. H., Leenaarts, J., Wiesmann, M., Aloise, J., Chu, K. -C., Bush, R. I., Scherrer, P. H., Brekke, P., Martinez-Sykora, J., Lites, B. W., McIntosh, S. W., Uitenbroek, H., Okamoto, T. J., Gummin, M. A., Auker, G., Jerram, P., Pool, P., and Waltham, N.

Subjects
Astrophysics - Solar and Stellar Astrophysics
Abstract

The Interface Region Imaging Spectrograph (IRIS) small explorer spacecraft provides simultaneous spectra and images of the photosphere, chromosphere, transition region, and corona with 0.33-0.4 arcsec spatial resolution, 2 s temporal resolution and 1 km/s velocity resolution over a field-of-view of up to 175 arcsec x 175 arcsec. IRIS was launched into a Sun-synchronous orbit on 27 June 2013 using a Pegasus-XL rocket and consists of a 19-cm UV telescope that feeds a slit-based dual-bandpass imaging spectrograph. IRIS obtains spectra in passbands from 1332-1358, 1389-1407 and 2783-2834 Angstrom including bright spectral lines formed in the chromosphere (Mg II h 2803 Angstrom and Mg II k 2796 Angstrom) and transition region (C II 1334/1335 Angstrom and Si IV 1394/1403 Angstrom). Slit-jaw images in four different passbands (C II 1330, Si IV 1400, Mg II k 2796 and Mg II wing 2830 Angstrom) can be taken simultaneously with spectral rasters that sample regions up to 130 arcsec x 175 arcsec at a variety of spatial samplings (from 0.33 arcsec and up). IRIS is sensitive to emission from plasma at temperatures between 5000 K and 10 MK and will advance our understanding of the flow of mass and energy through an interface region, formed by the chromosphere and transition region, between the photosphere and corona. This highly structured and dynamic region not only acts as the conduit of all mass and energy feeding into the corona and solar wind, it also requires an order of magnitude more energy to heat than the corona and solar wind combined. The IRIS investigation includes a strong numerical modeling component based on advanced radiative-MHD codes to facilitate interpretation of observations of this complex region. Approximately eight Gbytes of data (after compression) are acquired by IRIS each day and made available for unrestricted use within a few days of the observation., Comment: 53 pages, 15 figures

Published
2014
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3. Human Factors in the Design of a Computer-Assisted Instruction System. Technical Progress Report.

Author

North Carolina Univ., Chapel Hill. Dept. of Computer Science. and Mudge, J. C.

Abstract

A research project built an author-controlled computer-assisted instruction (CAI) system to study ease-of-use factors in student-system, author-system, and programer-system interfaces. Interfaces were designed and observed in use and systematically revised. Development of course material by authors, use by students, and administrative tasks were integrated into one system whose nucleus was a display-based interactive author language (DIAL). The design permitted systematic language implementation and easy language modification and used a translator writing system (TWS) to generate compilers. Authoring by teachers required simplicity of the language and its operational environment. A measured high level of user acceptance proved the design to be sound, and a significant reduction in authoring time was achieved. DIAL was observed to be a superior language, for machine intrusion was low and other syntactic improvements were possible. An answer-evaluating technique, called the sieve, was devised and a syntactically improved DIAL/2 language derived. The TWS helped to implement DIAL and to remediate language weaknesses. Although the TWS was not available for the command language of the operational environment, the human-factors debugging period revealed the desirability of such. (Author/PB)

Published
1973

4. Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

A Correction to this paper has been published: https://doi.org/10.1038/s41586-021-03473-8.

Published
2021

5. Dense sampling of bird diversity increases power of comparative genomics

Author

Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, Zhang, G, Feng, S, Stiller, J, Deng, Y, Armstrong, J, Fang, Q, Reeve, AH, Xie, D, Chen, G, Guo, C, Faircloth, BC, Petersen, B, Wang, Z, Zhou, Q, Diekhans, M, Chen, W, Andreu-Sanchez, S, Margaryan, A, Howard, JT, Parent, C, Pacheco, G, Sinding, M-HS, Puetz, L, Cavill, E, Ribeiro, AM, Eckhart, L, Fjeldsa, J, Hosner, PA, Brumfield, RT, Christidis, L, Bertelsen, MF, Sicheritz-Ponten, T, Tietze, DT, Robertson, BC, Song, G, Borgia, G, Claramunt, S, Lovette, IJ, Cowen, SJ, Njoroge, P, Dumbacher, JP, Ryder, OA, Fuchs, J, Bunce, M, Burt, DW, Cracraft, J, Meng, G, Hackett, SJ, Ryan, PG, Jonsson, KA, Jamieson, IG, da Fonseca, RR, Braun, EL, Houde, P, Mirarab, S, Suh, A, Hansson, B, Ponnikas, S, Sigeman, H, Stervander, M, Frandsen, PB, van der Zwan, H, van der Sluis, R, Visser, C, Balakrishnan, CN, Clark, AG, Fitzpatrick, JW, Bowman, R, Chen, N, Cloutier, A, Sackton, TB, Edwards, SV, Foote, DJ, Shakya, SB, Sheldon, FH, Vignal, A, Soares, AER, Shapiro, B, Gonzalez-Solis, J, Ferrer-Obiol, J, Rozas, J, Riutort, M, Tigano, A, Friesen, V, Dalen, L, Urrutia, AO, Szekely, T, Liu, Y, Campana, MG, Corvelo, A, Fleischer, RC, Rutherford, KM, Gemmell, NJ, Dussex, N, Mouritsen, H, Thiele, N, Delmore, K, Liedvogel, M, Franke, A, Hoeppner, MP, Krone, O, Fudickar, AM, Mila, B, Ketterson, ED, Fidler, AE, Friis, G, Parody-Merino, AM, Battley, PF, Cox, MP, Lima, NCB, Prosdocimi, F, Parchman, TL, Schlinger, BA, Loiselle, BA, Blake, JG, Lim, HC, Day, LB, Fuxjager, MJ, Baldwin, MW, Braun, MJ, Wirthlin, M, Dikow, RB, Ryder, TB, Camenisch, G, Keller, LF, DaCosta, JM, Hauber, ME, Louder, MIM, Witt, CC, McGuire, JA, Mudge, J, Megna, LC, Carling, MD, Wang, B, Taylor, SA, Del-Rio, G, Aleixo, A, Vasconcelos, ATR, Mello, CV, Weir, JT, Haussler, D, Li, Q, Yang, H, Wang, J, Lei, F, Rahbek, C, Gilbert, MTP, Graves, GR, Jarvis, ED, Paten, B, and Zhang, G

Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Published
2020

6. Compensatory indirect effects of an herbicide on wetland communities

Author

Edge, C. B., Baker, L. F., Lanctôt, C. M., Melvin, S. D., Gahl, M. K., Kurban, L., Navarro-Martín, Laia, Kidd, K. A., Trudeau, V. L., Thompson, D. G., Mudge, J. F., Houlahan, J. E., Edge, C. B., Baker, L. F., Lanctôt, C. M., Melvin, S. D., Gahl, M. K., Kurban, L., Navarro-Martín, Laia, Kidd, K. A., Trudeau, V. L., Thompson, D. G., Mudge, J. F., and Houlahan, J. E.

Abstract

The direct effects of large-scale disturbances are readily studied because their effects are often apparent and result in large changes to ecosystems. Direct effects can cascade through the ecosystem, leading to indirect effects that are often subtle and difficult to detect. Managing anthropogenic disturbances, such as chemical contamination, requires an understanding of both direct and indirect effects to predict, measure, and characterize the impact. Using a replicated whole-ecosystem experiment and path analyses (assesses the effects of a set of variables on a specified outcome, similar to multiple regression), we examined the direct and indirect effects of a glyphosate-based herbicide and nutrient enrichment on wetland communities. The latter did not impact any measured endpoints. The strongest drivers of macrophyte, benthic invertebrate, and amphibian assemblages were the ephemerality and the size of wetlands, factors which were not altered by herbicide applications. The herbicide had a direct negative effect on macrophyte cover, amphibian larval abundance, and the proportion of predatory benthic invertebrates. However, both amphibians and invertebrates were positively affected by the reduction in the macrophyte cover caused by the herbicide applications. The opposing directions of the direct and indirect effects lead to no net change in either group. The compensatory dynamics observed herein highlight the need for a better understanding of indirect effects pathways to determine whether common anthropogenic disturbances alter the ecological communities in small wetland ecosystems.

Published
2020

11. A plant DNA isolation protocol suitable for polymerase chain reaction based marker-assisted breeding

Author

Lange, D.A., Penuela, S., Denny, R.L., Mudge, J., Concibido, V.C., Orf, J.H., and Young, N.D.

Subjects
Plant genetics -- Research -- Genetic aspects, Plant breeding -- Genetic aspects -- Research, Polymerase chain reaction -- Research -- Genetic aspects, Agricultural industry, Business, Genetic aspects, Research
Abstract

An important, but often limiting step in marker-assisted breeding is the efficient isolation of plant DNA for polymerase chain reaction (PCR) amplification. While there are many protocols for plant DNA isolation, they tend to be time consuming or difficult to use on many samples simultaneously. We have optimized an alternative approach to plant DNA isolation that immobilizes DNA on a solid matrix, followed by processing in a 96-well microtiter plate. A single person can isolate DNA and initiate PCR-based analyses for 96 individuals in one day. The DNA samples are suitable for several PCR-based procedures, including random amplified polymorphic DNA (RAPD), microsatellite (simple sequence repeats), and amplified fragment length polymorphism (AFLP) analyses. Because the DNA is immobilized on a solid matrix and processed in 96-well plates, this protocol could be modified for robotic manipulation., Polymerase chain reaction-based marker-assisted selection (MAS) requires a method for fast and efficient DNA isolation. Typically, plant breeding programs require thousands of samples to be analyzed in a short time. [...]

Published
1998

13. Two microsatellite markers that flank the major soybean cyst nematode resistance locus

Author

Mudge, J., Cregan, P.B., Kenworthy, J.P., Kenworthy, W.J., Orf, J.H., and Young, N.D.

Subjects
Plant nematodes -- Analysis -- Research, Soybean -- Research -- Analysis, Agricultural industry, Business, Analysis, Research
Abstract

The use of resistant cultivars is the most effective method for controlling soybean cyst nematode (Heterodera glycines Ichinoe; SCN) on soybean [Glycine max (L.) Merrill]. However, resistance to SCN is oligogenic, making inheritance patterns complex and breeding difficult. One major partial-resistance locus for SCN resistance is located on molecular linkage group (MLG) `G'. This locus controls more than 50% of variation associated with response to SCN and resistant alleles are present in many important sources of SCN resistance, including PI 209332, PI 88788, PI 90763, PI 437654, and `Peking'. Restriction fragment length polymorphisms (RFLPs) linked to the major SCN resistance alleles on MLG G have proven effective in tracking the alleles and predicting SCN response. These RFLPs are much more efficient in terms of time and labor than greenhouse assays for SCN. Nevertheless, more efficient DNA markers are needed to screen the many Hues required for marker-assisted selection. Polymerase chain reaction-based markers, such as microsatellites (simple sequence repents), have been sought because they. are faster, less expensive, more polymorphic, and require less labor than RFLPs. In this study, we report two microsatellites, BARC-Satt038 and BARC-Satt130, that flank the major SCN resistance locus on MLG G. These microsatellites efficiently Identify the chromosome fragment carrying the resistance allele and are also good predictors of SCN phenotype response., The soybean cyst nematode is one of the most economically destructive pathogens of soybean (Noel, 1992). Breeding for SCN resistance is difficult because the trait is controlled by multiple genes [...]

Published
1997

14. A RAPD genetic map of Saccharum officinarum

Author

Mudge, J., Andersen, W.R., Kehrer, R.L., and Fairbanks, D.J.

Subjects
Sugarcane -- Genetic aspects, Genetic polymorphisms -- Research, Genetic markers -- Research, Agricultural industry, Business
Abstract

Saccharum officinarum L. is the major contributing species to modern sugarcane varieties. It is a polyploid where 2n = 80, although the basic chromosome number and level of ploidy have not been conclusively determined. A genetic map in S. officinarum could benefit breeding programs through marker-assisted selection and could provide information about the genetic structure of sugarcane. The objective of this research was to develop a genetic linkage map by means of random amplified polymorphic DNA (RAPD) single-dose markers in S. officinarum. The map was constructed with 84 [F.sub.1] progeny from the cross 'La Purple' (S. officinarum) x 'Molokai 5829' (S. robustum Brandes and Jeswiet ex Grassl.). Single-dose markers should segregate in a 1:1 fashion in the progeny of this cross. Primers were first screened in the parental genotypes, and those revealing polymorphisms were then tested in six progeny selected at random to identify putative single-dose markers. All resulting markers were then tested in 84 progeny and those showing a 1:1 segregation pattern were considered single-dose markers and were used for mapping. Among 279 single-dose markers identified from initial screening with 1840 primers, 161 markers were linked in 50 linkage groups with a minimum LOD of 5.0 and a maximum recombination value of 0.28. The detection of 12 repulsion linkages suggested the occurrence of limited preferential chromosome pairing in this species. Linkage of eyespot susceptibility to a RAPD marker identified an additional linkage group and indicated that linkages identified in this map could potentially be used for marker-assisted selection.

Published
1996

17. The Interface Region Imaging Spectrograph (IRIS)

Author

De, Pontieu B., Title, A. M., Lemen, J. R., Kushner, G. D., Akin, D. J., Allard, B., Berger, T., Boerner, P., Cheung, M., Chou, C., Drake, J. F., Duncan, D. W., Freeland, S., Heyman, G. F., Hoffman, C., Hurlburt, N. E., Lindgren, R. W., Mathur, D., Rehse, R., Sabolish, D., Seguin, R., Schrijver, C. J., Tarbell, T. D., Wulser, J.-P., Wolfson, C. J., Yanari, C., Mudge, J., Nguyen-Phuc, N., Timmons, R., van, Bezooijen R., Weingrod, I., Brookner, R., Butcher, G., Dougherty, B., Eder, J., Knagenhjelm, V., Larsen, S., Mansir, D., Phan, L., Boyle, P., Cheimets, P. N., DeLuca, E. E., Golub, L., Gates, R., Hertz, E., McKillop, S., Park, S., Perry, T., Podgorski, W. A., Reeves, K., Saar, S., Testa, P., Tian, H., Weber, M., Dunn, C., Eccles, S., Jaeggli, S. A., Kankelborg, C. C., Mashburn, K., Pust, N., Springer, L., Carvalho, R., Kleint, L., Marmie, J., Mazmanian, E., Pereira, T. M. D., Sawyer, S., Strong, J., Worden, S. P., Carlsson, M., Hansteen, V. H., Leenaarts, J., Wiesmann, M., Aloise, J., Chu, K.-C., Bush, R. I., Scherrer, P. H., Brekke, P., Martinez-Sykora, J., Lites, B. W., McIntosh, S. W., Uitenbroek, H., Gummin, M. A., Auker, G., Jerram, P., Pool, P., Waltham, N., and Okamoto, Takenori J.

Subjects
Physics, Photosphere, Solar transition region, FOS: Physical sciences, Astronomy and Astrophysics, Astrophysics, Corona, Heating, Solar wind, Astrophysics - Solar and Stellar Astrophysics, Space and Planetary Science, Temporal resolution, Coronal rain, Chromosphere, Spectrograph, Solar and Stellar Astrophysics (astro-ph.SR)
Abstract

著者人数: 88名, Accepted: 2014-01-24, 資料番号: SA1140010000

Published
2014

18. GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

Author

Bignell, A., Frankish, A., Aken, B., Diekhans, M., Kokocinski, F., Lin, M., Tress, M., Van Baren, J., Barnes, I., Hunt, T., Carvalho-Silva, D., Davidson, C., Donaldson, S., Gilbert, J., Hart, E., Kay, M., Kinsella, R., Lloyd, D., Loveland, J., Mudge, J., Snow, C., Vamathevan, J., Wilming, L., Brent, M., Gerstein, M., Guigó, R., Harte, R., Kellis, M., Searle, S., Harrow, J., and Hubbard, T.

Published
2009
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22. Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes

Author

Suh, A., Witt, C.C., Menger, Juliana, Sadanandan, K.R., Podsiadlowski, L., Gerth, M., Weigert, A., McGuire, J.A., Mudge, J., Edwards, S.V., Rheindt, F.E., Suh, A., Witt, C.C., Menger, Juliana, Sadanandan, K.R., Podsiadlowski, L., Gerth, M., Weigert, A., McGuire, J.A., Mudge, J., Edwards, S.V., and Rheindt, F.E.

Abstract

Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83–99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25–22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20–17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.

Published
2016

23. The Interface Region Imaging Spectrograph (IRIS)

Author

De Pontieu, B., Title, A. M., Lemen, J. R., Kushner, G. D., Akin, D. J., Allard, B., Berger, T., Boerner, P., Cheung, M., Chou, C., Drake, J. F., Duncan, D. W., Freeland, S., Heyman, G. F., Hoffman, C., Hurlburt, N. E., Lindgren, R. W., Mathur, D., Rehse, R., Sabolish, D., Seguin, R., Schrijver, C. J., Tarbell, T. D., Wulser, J.-P., Wolfson, C. J., Yanari, C., Mudge, J., Nguyen-Phuc, N., Timmons, R., van Bezooijen, R., Weingrod, I., Brookner, R., Butcher, G., Dougherty, B., Eder, J., Knagenhjelm, V., Larsen, S., Mansir, D., Phan, L., Boyle, P., Cheimets, P. N., DeLuca, E. E., Golub, L., Gates, R., Hertz, E., McKillop, S., Park, S., Perry, T., Podgorski, W. A., Reeves, K., Saar, S., Testa, P., Tian, H., Weber, M., Dunn, C., Eccles, S., Jaeggli, S. A., Kankelborg, C. C., Mashburn, K., Pust, N., Springer, L., Carvalho, R., Kleint, L., Marmie, J., Mazmanian, E., Pereira, T. M. D., Sawyer, S., Strong, J., Worden, S. P., Carlsson, M., Hansteen, V. H., Leenaarts, J., Wiesmann, M., Aloise, J., Chu, K.-C., Bush, R. I., Scherrer, P. H., Brekke, P., Martinez-Sykora, J., Lites, B. W., McIntosh, S. W., Uitenbroek, H., 岡本, 丈典, Gummin, M. A., Auker, G., Jerram, P., Pool, P., Waltham, N., Okamoto, Takenori J., De Pontieu, B., Title, A. M., Lemen, J. R., Kushner, G. D., Akin, D. J., Allard, B., Berger, T., Boerner, P., Cheung, M., Chou, C., Drake, J. F., Duncan, D. W., Freeland, S., Heyman, G. F., Hoffman, C., Hurlburt, N. E., Lindgren, R. W., Mathur, D., Rehse, R., Sabolish, D., Seguin, R., Schrijver, C. J., Tarbell, T. D., Wulser, J.-P., Wolfson, C. J., Yanari, C., Mudge, J., Nguyen-Phuc, N., Timmons, R., van Bezooijen, R., Weingrod, I., Brookner, R., Butcher, G., Dougherty, B., Eder, J., Knagenhjelm, V., Larsen, S., Mansir, D., Phan, L., Boyle, P., Cheimets, P. N., DeLuca, E. E., Golub, L., Gates, R., Hertz, E., McKillop, S., Park, S., Perry, T., Podgorski, W. A., Reeves, K., Saar, S., Testa, P., Tian, H., Weber, M., Dunn, C., Eccles, S., Jaeggli, S. A., Kankelborg, C. C., Mashburn, K., Pust, N., Springer, L., Carvalho, R., Kleint, L., Marmie, J., Mazmanian, E., Pereira, T. M. D., Sawyer, S., Strong, J., Worden, S. P., Carlsson, M., Hansteen, V. H., Leenaarts, J., Wiesmann, M., Aloise, J., Chu, K.-C., Bush, R. I., Scherrer, P. H., Brekke, P., Martinez-Sykora, J., Lites, B. W., McIntosh, S. W., Uitenbroek, H., 岡本, 丈典, Gummin, M. A., Auker, G., Jerram, P., Pool, P., Waltham, N., and Okamoto, Takenori J.

Abstract

著者人数: 88名, Accepted: 2014-01-24

Published
2015

32. Performance

Author

BELL, C. GORDON, primary, MUDGE, J. CRAIG, additional, and McNAMARA, JOHN E., additional

Published
1978
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35. Intercept Panel Trap (Intercept PTBB) for bark beetles and longhorn beetles. Updated design and recent field data

Author

Czokajlo, Darek, McLaughlin, John, Teale, Stephen R., Hoffman, Warren R., Hrasovec, Boris, Pernek, Milan, Aukema, Brian H., Raffa, Kenneth F., and Kirsch, Philipp Mudge, J. LaBonte, F. Noguera.

Subjects
pheromone trap, bark beetles, longorn beetles
Abstract

U radu se prikazuju svojstav nove klopke za lov potkornjaka i ostalih ksilofagnih kornjaša-štetnika u šumarstvu. Rezultati komparativnih ulova pokazuju da se ovaj tip vertikalne klopke pokazuje nadmoćniji prema ostalim rješenjima koja se za sada nalaze u praktičnoj uporabi.

Published
2002

36. The GENCODE human gene set

Author

Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kellis, Manolis, Lin, M., Searle, S., Frankish, A., Bignell, A., Aken, B., Derrien, Thomas, Diekhans, M., Harte, R., Howald, C., Kokocinski, F., Tress, M., Van Baren, M., Barnes, I., Hunt, T., Carvalho-Silva, D., Davidson, C., Donaldson, S., Gilbert, J., Kay, M., Lloyd, D., Loveland, J., Mudge, J., Snow, C., Vamathevan, J., Wilming, L., Brent, M., Gerstein, Mark B., Guigo, Roderic, Reymond, A., Zadissa, A., Valencia, A., Harrow, J., Hubbard, T., Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Kellis, Manolis, Lin, M., Searle, S., Frankish, A., Bignell, A., Aken, B., Derrien, Thomas, Diekhans, M., Harte, R., Howald, C., Kokocinski, F., Tress, M., Van Baren, M., Barnes, I., Hunt, T., Carvalho-Silva, D., Davidson, C., Donaldson, S., Gilbert, J., Kay, M., Lloyd, D., Loveland, J., Mudge, J., Snow, C., Vamathevan, J., Wilming, L., Brent, M., Gerstein, Mark B., Guigo, Roderic, Reymond, A., Zadissa, A., Valencia, A., Harrow, J., and Hubbard, T.

Abstract

This article is part of the supplement: Beyond the Genome: The true gene count, human evolution and disease genomics, Boston, MA, USA. 11-13 October 2010., The GENCODE consortium is a sub group of the ENCODE consortium. Its aim is to provide complete annotation of genes in the human genome including protein-coding loci, non-coding loci and pseudogenes, based on experimental evidence. The final aim is for the HAVANA team to manually annotate the complete genome. This is a time-consuming process which will be completed over the course of the ENCODE project. Currently, to provide a set of annotation covering the complete genome, rather than just the regions that have been manually annotated, a merge of manual annotation from HAVANA with automatic annotation from the Ensembl automatically annotated gene set is created. This process also adds unique full-length CDS predictions from the Ensembl protein coding set into manually annotated genes, to provide the most complete up to date annotation of the genome possible. Also included in the set are short and long ncRNA genes predicted by the Ensembl prediction pipelines and a consensus set of pseudogene predictions agreed between Havana, Yale and UCSC. The CCDS set is also fully represented within the GENCODE set. The GENCODE set is the default annotation available in Ensembl and is also available in the UCSC genome browser. All the annotation is tagged as to whether it is produced by manual annotation alone, automatic annotation alone, or by both approaches. We are currently working to provide confidence levels for annotation, based on depth and type of evidence supporting it.

Published
2012

40. The GENCODE human gene set

Author

Searle, S, primary, Frankish, A, additional, Bignell, A, additional, Aken, B, additional, Derrien, T, additional, Diekhans, M, additional, Harte, R, additional, Howald, C, additional, Kokocinski, F, additional, Lin, M, additional, Tress, M, additional, Van Baren, M, additional, Barnes, I, additional, Hunt, T, additional, Carvalho-Silva, D, additional, Davidson, C, additional, Donaldson, S, additional, Gilbert, J, additional, Kay, M, additional, Lloyd, D, additional, Loveland, J, additional, Mudge, J, additional, Snow, C, additional, Vamathevan, J, additional, Wilming, L, additional, Brent, M, additional, Gerstein, M, additional, Guigó, R, additional, Kellis, M, additional, Reymond, A, additional, Zadissa, A, additional, Valencia, A, additional, Harrow, J, additional, and Hubbard, T, additional

Published
2010
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48. Evolutionary implications of pericentromeric gene expression in humans.

Author

Mudge, J. M. and Jackson, M. S.

Subjects
*GENE expression, *HUMAN genetics, *HUMAN chromosomes, *NUCLEOTIDE sequence, *GENES, *HUMAN genome
Abstract

Human pericentromeric sequences are enriched for recent sequence duplications. The continual creation and shuffling of these duplications can create novel intron-exon structures and it has been suggested that these regions have a function as gene nurseries. However, these sequences are also rich in satellite repeats which can repress transcription, and analyses of chromosomes 10 and 21 have suggested that they are transcript poor. Here, we investigate the relationship between pericentromeric duplication and transcription by analyzing the in silico transcriptional profiles within the proximal 1.5 Mb of genomic sequence on all human chromosome arms in relation to duplication status. We identify an ∼5× excess of transcripts specific to cancer and/or testis in pericentromeric duplications compared to surrounding single copy sequence, with the expression of >50% of all transcripts in duplications being restricted to these tissues. We also identify an ∼5× excess of transcripts in duplications which contain large quantities of interspersed repeats. These results indicate that the transcriptional profiles of duplicated and single copy sequences within pericentromeric DNA are distinct, suggesting that pericentromeric instability is unlikely to represent a common route for gene creation but may have a disproportionate effect upon genes whose function is restricted to the germ line. Copyright © 2005 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Published
2005
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