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1. The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

Author

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

Subjects
Basic biological sciences
Abstract

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (3). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (2).

Published
2008

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

Author

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

Subjects
Basic biological sciences, Comparative analysis genomics evolution virulence opportunistic pathogen
Abstract

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

Published
2005

3. The sequence and analysis of duplication rich human chromosome 16

Author

Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, Xie, Gary, Hellsten, Uffe, Man Chan, Yee, Altherr, Michael, Couronne, Olivier, Aerts, Andrea, Bajorek, Eva, Black, Stacey, Blumer, Heather, Branscomb, Elbert, Brown, Nancy C., Bruno, William J., Buckingham, Judith M., Callen, David F., Campbell, Connie S., Campbell, Mary L., Campbell, Evelyn W., Caoile, Chenier, Challacombe, Jean F., Chasteen, Leslie A., Chertkov, Olga, Chi, Han C., Christensen, Mari, Clark, Lynn M., Cohn, Judith D., Denys, Mirian, Detter, John C., Dickson, Mark, Dimitrijevic-Bussod, Mira, Escobar, Julio, Fawcett, Joseph J., Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Goodwin, Lynne A., Grady, Deborah L., Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Hildebrand, Carl E., Huang, Wayne, Israni, Sanjay, Jett, Jamie, Jewett, Phillip E., Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Krawczyk, Marie-Claude, Leyba, Tina, Longmire, Jonathan L., Lopez, Frederick, Lou, Yunian, Lowry, Steve, Ludeman, Thom, Mark, Graham A., Mcmurray, Kimberly L., Meincke, Linda J., Morgan, Jenna, Moyzis, Robert K., Mundt, Mark O., Munk, A. Christine, Nandkeshwar, Richard D., Pitluck, Sam, Pollard, Martin, Predki, Paul, Parson-Quintana, Beverly, Ramirez, Lucia, Rash, Sam, Retterer, James, Ricke, Darryl O., Robinson, Donna L., Rodriguez, Alex, Salamov, Asaf, Saunders, Elizabeth H., Scott, Duncan, Shough, Timothy, Stallings, Raymond L., Stalvey, Malinda, Sutherland, Robert D., Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Torney, David C., Tran-Gyamfi, Mary, Tsai, Ming, Ulanovsky, Levy E., and Ustaszewska, Anna

Subjects
Applied life sciences
Abstract

We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

Published
2004

4. The complete sequence of human chromosome 5

Author

Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, Gordon, Laurie A., Scott, Duncan, Xie, Gary, Huang, Wayne, Hellsten, Uffe, Tran-Gyamfi, Mary, She, Xinwei, Prabhakar, Shyam, Aerts, Andrea, Altherr, Michael, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caoile, Chenier, Challacombe, Jean F., Chan, Yee Man, Denys, Mirian, Detter, Chris, Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstenin, David, Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimbal, Heather, Kobayashi, Arthur, Lopez, Frederick, Lou, Yunian, Martinez, Diego, Medina, Catherine, Morgan, Jenna, Nandkeshwar, Richard, Noonan, James P., Pitluck, Sam, Pollard, Martin, Predki, Paul, Priest, James, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanie, Salamov, Asaf, Salazar, Angelica, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wheeler, Jeremy, Wu, Kevin, Yang, Joan, Dickson, Mark, Cheng, Jan-Fang, Eichler, Evan E., Olsen, Anne, Pennacchio, Len A., Rokhsar, Daniel S., Richardson, Paul, Lucas, Susan M., Myers, Richard M., and Rubin, Edward M.

Subjects
Applied life sciences
Abstract

Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA).

Published
2004

5. Complete genome sequence of Haemophilus somnus (Histophilus somni) strain 129Pt and comparison to Haemophilus ducreyi 35000HP and Haemophilus influenzae Rd

Author

Challacombe, Jean F., Duncan, A.J., Brettin, Thomas S., Bruce, David, Chertkov, Olga, Detter, J. Chris, Han, Cliff S., Misra, Monica, Richardson, Paul, Tapia, Roxanne, Thayer, Nina, Xie, Gary, and Inzana, Thomas J.

Subjects
Hemophilus infections -- Genetic aspects, Hemophilus infections -- Research, Hemophilus influenzae -- Genetic aspects, Hemophilus influenzae -- Research, Genomes -- Research, Biological sciences
Abstract

Haemophilus somnus can be either a commensal of bovine mucosal surfaces or an opportunistic pathogen. Pathogenic strains of H. somnus are a significant cause of systemic disease in cattle. We report the genome sequence of H. somnus 129Pt, a nonpathogenic commensal preputial isolate, and the results of a genome-wide comparative analysis of H. somnus 129Pt, Haemophilus influenzae Rd, and Haemophilus ducreyi 35000HP. We found unique genes in H. somnus 129Pt involved in lipooligosaccharide biosynthesis, carbohydrate uptake and metabolism, cation transport, amino acid metabolism, ubiquinone and menaquinone biosynthesis, cell surface adhesion, biosynthesis of cofactors, energy metabolism, and electron transport. There were also many genes in common among the three organisms. Our comparative analyses of H. somnus 129Pt, H. influenzae Rd, and H. ducreyi 35000HP revealed similarities and differences in the numbers and compositions of genes involved in metabolism, host colonization, and persistence. These results lay a foundation for research on the host specificities and niche preferences of these organisms. Future comparisons between H. somnus 129Pt and virulent strains will aid in the development of protective strategies and vaccines to protect cattle against H. somnus disease.

Published
2007

6. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis

Author

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

Subjects
Bacillus cereus -- Environmental aspects, Bacillus cereus -- Genetic aspects, Bacillus thuringiensis -- Environmental aspects, Bacillus thuringiensis -- Genetic aspects, Bacillus anthracis -- Environmental aspects, Bacillus anthracis -- Genetic aspects, Genetic research, Biological sciences
Abstract

Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp, konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27 and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.

Published
2006

7. The DNA sequence and biology of human chromosome 19

Author

Grimwood, Jane, Gordon, Laurie A., Olsen, Anne, Terry, Astrid, Schmutz, Jeremy, Lamerdin, Jane, Hellsten, Uffe, Goodstein, David, Couronne, Olivier, Tran-Gyamfi, Mary, Aerts, Andrea, Altherr, Michael, Ashworth, Linda, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caenepeel, Sean, Carrano, Anthony, Caoile, Chenier, Man Chan, Yee, Christensen, Mari, Cleland, Catherine A., Copeland, Alex, Dalin, Eileen, Dehal, Paramvir, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Garcia, Carmen, Georgescu, Anca M., Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Ho, Isaac, Huang, Wayne, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Larionov, Vladimer, Leem, Sun-Hee, Lopez, Frederick, Lou, Yunian, Lowry, Steve, Malfatti, Stephanie, Martinez, Diego, McCready, Paula, Medina, Catherine, Morgan, Jenna, Nelson, Kathryn, Nolan, Matt, Ovcharenko, Ivan, Pitluck, Sam, Pollard, Martin, Popkie, Anthony P., Predki, Paul, Quan, Glenda, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanine, Salamov, Asaf, Salazar, Angelica, She, Xinwei, Smith, Doug, Slezak, Tom, Solovyev, Victor, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wagner, Mark, Wheeler, Jeremy, Wu, Kevin, Xie, Gary, Yang, Joan, Dubchak, Inna, Furey, Terrence S., DeJong, Pieter, Dickson, Mark, Gordon, David, Eichler, Evan E., Pennacchio, Len A., Richardson, Paul, Stubbs, Lisa, Rokhsar, Daniel S., Myers, Richard M., Rubin, Edward M., and Lucas, Susan M.

Published
2004
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8. The DNA sequence and comparative analysis of human chromosome 5

Author

Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, Steve, Gordon, Laurie A., Scott, Duncan, Xie, Gary, Huang, Wayne, Hellsten, Uffe, Tran-Gyamfi, Mary, She, Xinwei, Prabhakar, Shyam, Aerts, Andrea, Altherr, Michael, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caoile, Chenier, Challacombe, Jean F., Man Chan, Yee, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Lopez, Frederick, Lou, Yunian, Martinez, Diego, Medina, Catherine, Morgan, Jenna, Nandkeshwar, Richard, Noonan, James P., Pitluck, Sam, Pollard, Martin, Predki, Paul, Priest, James, Ramirez, Lucia, Retterer, James, Rodriguez, Alex, Rogers, Stephanie, Salamov, Asaf, Salazar, Angelica, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wheeler, Jeremy, Wu, Kevin, Yang, Joan, Dickson, Mark, Cheng, Jan-Fang, Eichler, Evan E., Olsen, Anne, Pennacchio, Len A., Rokhsar, Daniel S., Richardson, Paul, Lucas, Susan M., Myers, Richard M., and Rubin, Edward M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jeremy Schmutz (corresponding author) [1]; Joel Martin [2]; Astrid Terry [2]; Olivier Couronne [3]; Jane Grimwood [1]; Steve Lowry [2]; Laurie A. Gordon [2, 4]; Duncan Scott [2]; Gary [...]

Published
2004
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9. Preserve the ITFS Spectrum for ITFS Systems.

Author

Curtis, John A. and Thayer, Nina J.

Abstract

Reports on the Instructional Television Fixed Service (ITFS) and its use in the United States. Included are highlights of the study, discussion of the technology of modern ITFS systems, description of the National University of the Air, Inc., and some recommendations to the Federal Communications Commission. (JN)

Published
1983

10. Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii

Author

Xie, Gary, Bruce, David C., Challacombe, Jean F., Chertkov, Olga, Detter, John C., Gilna, Paul, Han, Cliff S., Lucas, Susan, Misra, Monica, Myers, Gerald L., Richardson, Paul, Tapia, Roxanne, Thayer, Nina, Thompson, Linda S., Henrissat, Bernard, Wilson, David B., McBride, Mark J., and Brettin, Thomas S.

Subjects
Nucleotide sequence -- Research, DNA -- Research, Anaerobic bacteria -- Genetic aspects, Biological sciences
Abstract

The complete DNA and genome sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii that belongs to the phylum Bacteroidetes is studied. The bacterium is found to have cellobiohydrolases or other enzymes that facilitate the efficient cellulose digestion exhibited by it.

Published
2007

11. The complete genome sequence of Bacillus thuringiensis Al Hakam

Author

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

Subjects
Bacillus thuringiensis -- Genetic aspects, Bacillus thuringiensis -- Research, Genomes -- Research, Biological sciences
Abstract

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003). doi:10.1128/JB.00241-07

Published
2007

12. Erratum: Corrigendum: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Author

Martinez, Diego, primary, Berka, Randy M, additional, Henrissat, Bernard, additional, Saloheimo, Markku, additional, Arvas, Mikko, additional, Baker, Scott E, additional, Chapman, Jarod, additional, Chertkov, Olga, additional, Coutinho, Pedro M, additional, Cullen, Dan, additional, Danchin, Etienne G J, additional, Grigoriev, Igor V, additional, Harris, Paul, additional, Jackson, Melissa, additional, Kubicek, Christian P, additional, Han, Cliff S, additional, Ho, Isaac, additional, Larrondo, Luis F, additional, de Leon, Alfredo Lopez, additional, Magnuson, Jon K, additional, Merino, Sandy, additional, Misra, Monica, additional, Nelson, Beth, additional, Putnam, Nicholas, additional, Robbertse, Barbara, additional, Salamov, Asaf A, additional, Schmoll, Monika, additional, Terry, Astrid, additional, Thayer, Nina, additional, Westerholm-Parvinen, Ann, additional, Schoch, Conrad L, additional, Yao, Jian, additional, Barabote, Ravi, additional, Nelson, Mary Anne, additional, Detter, Chris, additional, Bruce, David, additional, Kuske, Cheryl R, additional, Xie, Gary, additional, Richardson, Paul, additional, Rokhsar, Daniel S, additional, Lucas, Susan M, additional, Rubin, Edward M, additional, Dunn-Coleman, Nigel, additional, Ward, Michael, additional, and Brettin, Thomas S, additional

Published
2008
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13. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

Author

Martinez, Diego, primary, Berka, Randy M, additional, Henrissat, Bernard, additional, Saloheimo, Markku, additional, Arvas, Mikko, additional, Baker, Scott E, additional, Chapman, Jarod, additional, Chertkov, Olga, additional, Coutinho, Pedro M, additional, Cullen, Dan, additional, Danchin, Etienne G J, additional, Grigoriev, Igor V, additional, Harris, Paul, additional, Jackson, Melissa, additional, Kubicek, Christian P, additional, Han, Cliff S, additional, Ho, Isaac, additional, Larrondo, Luis F, additional, de Leon, Alfredo Lopez, additional, Magnuson, Jon K, additional, Merino, Sandy, additional, Misra, Monica, additional, Nelson, Beth, additional, Putnam, Nicholas, additional, Robbertse, Barbara, additional, Salamov, Asaf A, additional, Schmoll, Monika, additional, Terry, Astrid, additional, Thayer, Nina, additional, Westerholm-Parvinen, Ann, additional, Schoch, Conrad L, additional, Yao, Jian, additional, Barabote, Ravi, additional, Nelson, Mary Anne, additional, Detter, Chris, additional, Bruce, David, additional, Kuske, Cheryl R, additional, Xie, Gary, additional, Richardson, Paul, additional, Rokhsar, Daniel S, additional, Lucas, Susan M, additional, Rubin, Edward M, additional, Dunn-Coleman, Nigel, additional, Ward, Michael, additional, and Brettin, Thomas S, additional

Published
2008
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14. The sequence and analysis of duplication-rich human chromosome 16

Author

Martin, Joel, primary, Han, Cliff, additional, Gordon, Laurie A., additional, Terry, Astrid, additional, Prabhakar, Shyam, additional, She, Xinwei, additional, Xie, Gary, additional, Hellsten, Uffe, additional, Chan, Yee Man, additional, Altherr, Michael, additional, Couronne, Olivier, additional, Aerts, Andrea, additional, Bajorek, Eva, additional, Black, Stacey, additional, Blumer, Heather, additional, Branscomb, Elbert, additional, Brown, Nancy C., additional, Bruno, William J., additional, Buckingham, Judith M., additional, Callen, David F., additional, Campbell, Connie S., additional, Campbell, Mary L., additional, Campbell, Evelyn W., additional, Caoile, Chenier, additional, Challacombe, Jean F., additional, Chasteen, Leslie A., additional, Chertkov, Olga, additional, Chi, Han C., additional, Christensen, Mari, additional, Clark, Lynn M., additional, Cohn, Judith D., additional, Denys, Mirian, additional, Detter, John C., additional, Dickson, Mark, additional, Dimitrijevic-Bussod, Mira, additional, Escobar, Julio, additional, Fawcett, Joseph J., additional, Flowers, Dave, additional, Fotopulos, Dea, additional, Glavina, Tijana, additional, Gomez, Maria, additional, Gonzales, Eidelyn, additional, Goodstein, David, additional, Goodwin, Lynne A., additional, Grady, Deborah L., additional, Grigoriev, Igor, additional, Groza, Matthew, additional, Hammon, Nancy, additional, Hawkins, Trevor, additional, Haydu, Lauren, additional, Hildebrand, Carl E., additional, Huang, Wayne, additional, Israni, Sanjay, additional, Jett, Jamie, additional, Jewett, Phillip B., additional, Kadner, Kristen, additional, Kimball, Heather, additional, Kobayashi, Arthur, additional, Krawczyk, Marie-Claude, additional, Leyba, Tina, additional, Longmire, Jonathan L., additional, Lopez, Frederick, additional, Lou, Yunian, additional, Lowry, Steve, additional, Ludeman, Thom, additional, Manohar, Chitra F., additional, Mark, Graham A., additional, McMurray, Kimberly L., additional, Meincke, Linda J., additional, Morgan, Jenna, additional, Moyzis, Robert K., additional, Mundt, Mark O., additional, Munk, A. Christine, additional, Nandkeshwar, Richard D., additional, Pitluck, Sam, additional, Pollard, Martin, additional, Predki, Paul, additional, Parson-Quintana, Beverly, additional, Ramirez, Lucia, additional, Rash, Sam, additional, Retterer, James, additional, Ricke, Darryl O., additional, Robinson, Donna L., additional, Rodriguez, Alex, additional, Salamov, Asaf, additional, Saunders, Elizabeth H., additional, Scott, Duncan, additional, Shough, Timothy, additional, Stallings, Raymond L., additional, Stalvey, Malinda, additional, Sutherland, Robert D., additional, Tapia, Roxanne, additional, Tesmer, Judith G., additional, Thayer, Nina, additional, Thompson, Linda S., additional, Tice, Hope, additional, Torney, David C., additional, Tran-Gyamfi, Mary, additional, Tsai, Ming, additional, Ulanovsky, Levy E., additional, Ustaszewska, Anna, additional, Vo, Nu, additional, Scott White, P., additional, Williams, Albert L., additional, Wills, Patricia L., additional, Wu, Jung-Rung, additional, Wu, Kevin, additional, Yang, Joan, additional, DeJong, Pieter, additional, Bruce, David, additional, Doggett, Norman A., additional, Deaven, Larry, additional, Schmutz, Jeremy, additional, Grimwood, Jane, additional, Richardson, Paul, additional, Rokhsar, Daniel S., additional, Eichler, Evan E., additional, Gilna, Paul, additional, Lucas, Susan M., additional, Myers, Richard M., additional, Rubin, Edward M., additional, and Pennacchio, Len A., additional

Published
2004
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17. A comparison of multiple-choice test response modes and scoring methods

Author

Thayer, Nina and Educational Research and Evaluation

Subjects
LD5655.V856 1982.T529, Educational tests and measurements
Abstract

This study reports the comparison of seven different response/scoring methods used with multiple-choice tests in an academic setting with students enrolled in a required undergraduate art appreciation course at a medium-sized state university. The number of correct responses, based on a single choice per item, constituted the score on a preliminary test in each section of 35 to 40 students. Then, a distinct response/scoring method was randomly assigned to each section for two additional tests. One section continued to use number-right scoring and six sections used methods requiring or permitting multiple marks per item. All test scores counted toward course grades and examinees were so informed. Responses were used to determine estimates of internal consistency reliability and of validity with the previous quarter's grade-point average and subscores of the Scholastic Aptitude Test. An Evaluation Questionnaire, administered in each section, obtained for each response/scoring method self-report information about examinee study habits, testing preferences and experience, and responding behaviors. Observations of examinee behavior, subjective in nature, helped explain or confirm various empirical findings from this study or from the literature. Based on the findings from this study, it was concluded that: 1. observed differences in estimates of reliability or validity were not sufficient to justify the effort expended in administering and hand-scoring multiple-mark tests. 2. examinees experienced substantial difficulty becoming familiar with response/scoring methods which permit multiple marks. These methods require more than casual explanation and practice before examinees become adept in their use. 3. Item mark totals from methods scoring all the levels of information can provide more feedback to instructors regarding the performance of examinees on specific test items than could be acquired from the NR method. This feedback can help the instructor identify areas of content needing revision or test items needing rewording. When the examinees receive feedback, they have the opportunity to observe, score and learn from their own item performance, Pressey's initial consideration in 1950. Ph. D.

Published
1982

21. The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes

Author

Harger, Carol, Skupski, Marian, Allen, Ethan, Clark, Christopher, Crowley, David, Dickinson, Emily, Easley, David, Espinosa-Lujan, Ada, Farmer, Andrew, Fields, Chris, Flores, Leandrita, Harris, Lynn, Keen, Gifford, Manning, Maurice, McLeod, Mia, O'Neill, John, Pumilia, Maria, Reinert, Rhonda, Rider, David, Rohrlich, John, Romero, Yolanda, Schwertfeger, Jolene, Seluja, Gustavo, Siepel, Adam, Singh, Gautam, Smyth, Linda, Stamper, David, Stein, Judy, Suggs, Randy, Takkallapalli, Rajini, Thayer, Nina, Thompson, Gary, Walsh, Colleen, Wedgeworth, Frederick, and Schad, Peter A.

Abstract

The Genome Sequence DataBase (GSDB) has completed its conversion to an improved relational database. The new database, GSDB 1.0, is fully operational and publicly available. Data contributions, including both original sequence submissions and community annotation, are being accomplished through the use of a graphical client-server interface tool, the GSDB Annotator, and via GIO (GSDB Input/Output) files. Data retrieval services are being provided through a new Web Query Tool and direct SQL. All methods of data contribution and data retrieval fully support the new data types that have been incorporated into GSDB, including discontiguous sequences, multiple sequence alignments, and community annotation.

Published
1997
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22. Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsonii.

Author

Gary Xie, Bruce, David C., Challacombe, Jean F., Chertkov, Olga, Detter, John C., Gilna, Paul, Han, Cliff S., Lucas, Susan, Misra, Monica, Myers, Gerald L., Richardson, Paul, Tapia, Roxanne, Thayer, Nina, Thompson, Linda S., Brettin, Thomas S., Henrissat, Bernard, Wilson, David B., and McBride, Mark J.

Subjects
*CYTOPHAGALES, *BACTERIA, *CYTOPHAGA, *NUCLEOTIDE sequence, *GENETIC code, *NUCLEIC acid analysis, *GLYCOSIDASES, *CELLULOSE, *NUCLEIC acids
Abstract

The complete DNA sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii, which belongs to the phylum Bacteroidetes, is presented. The genome consists of a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 of which have been assigned a tentative function. Two of the most striking characteristics of C. hutchinsonii are its rapid gliding motility over surfaces and its contact-dependent digestion of crystalline cellulose. The mechanism of C. hutchinsonii motility is not known, but its genome contains homologs for each of the gld genes that are required for gliding of the distantly related bacteroidete Flavobacterium johnsoniae. Cytophaga-Flavobacterium gliding appears to be novel and does not involve well-studied motility organelles such as flagella or type IV pili. Many genes thought to encode proteins involved in cellulose utilization were identified. These include candidate endo-β-1,4-glucanases and β-glucosidases. Surprisingly, obvious homologs of known cellobiohydrolases were not detected. Since such enzymes are needed for efficient cellulose digestion by well-studied cellulolytic bacteria, C. hutchinsonii either has novel cellobiohydrolases or has an unusual method of cellulose utilization. Genes encoding proteins with cohesin domains, which are characteristic of cellulosomes, were absent, but many proteins predicted to be involved in polysaccharide utilization had putative D5 domains, which are thought to be involved in anchoring proteins to the cell surface. [ABSTRACT FROM AUTHOR]

Published
2007
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