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489 results on '"Rusch, Douglas B"'

4. Nitric oxide stimulates type IV MSHA pilus retraction in Vibrio cholerae via activation of the phosphodiesterase CdpA

Author

Hughes, Hannah Q., Floyd, Kyle A., Hossain, Sajjad, Anantharaman, Sweta, Kysela, David T., Zöldi, Mikls, Barna, Lászl, Yu, Yuanchen, Kappler, Michael P., Dalia, Triana N., Podicheti, Ram C., Rusch, Douglas B., Zhuang, Meng, Fraser, Cassandra L., Brun, Yves V., Jacobson, Stephen C., McKinlay, James B., Yildiz, Fitnat H., Boon, Elizabeth M., and Dalia, Ankur B.

Published
2022

11. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean‐specific genes

Author

Orsini, Luisa, Brown, James B, Solari, Omid Shams, Li, Dong, He, Shan, Podicheti, Ram, Stoiber, Marcus H, Spanier, Katina I, Gilbert, Donald, Jansen, Mieke, Rusch, Douglas B, Pfrender, Michael E, Colbourne, John K, Frilander, Mikko J, Kvist, Jouni, Decaestecker, Ellen, De Schamphelaere, Karel AC, and De Meester, Luc

Subjects
Genetics, 2.1 Biological and endogenous factors, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, Animals, Conserved Sequence, Daphnia, Gene Expression Regulation, Gene Regulatory Networks, Genome, Genotype, Multigene Family, Transcription, Genetic, abiotic stressors, biotic stressors, differential co-expression networks, differential gene expression, ecological gene annotation, ecoresponsive genes, waterflea, Biological Sciences, Evolutionary Biology
Abstract

Natural habitats are exposed to an increasing number of environmental stressors that cause important ecological consequences. However, the multifarious nature of environmental change, the strength and the relative timing of each stressor largely limit our understanding of biological responses to environmental change. In particular, early response to unpredictable environmental change, critical to survival and fitness in later life stages, is largely uncharacterized. Here, we characterize the early transcriptional response of the keystone species Daphnia magna to twelve environmental perturbations, including biotic and abiotic stressors. We first perform a differential expression analysis aimed at identifying differential regulation of individual genes in response to stress. This preliminary analysis revealed that a few individual genes were responsive to environmental perturbations and they were modulated in a stressor and genotype-specific manner. Given the limited number of differentially regulated genes, we were unable to identify pathways involved in stress response. Hence, to gain a better understanding of the genetic and functional foundation of tolerance to multiple environmental stressors, we leveraged the correlative nature of networks and performed a weighted gene co-expression network analysis. We discovered that approximately one-third of the Daphnia genes, enriched for metabolism, cell signalling and general stress response, drives transcriptional early response to environmental stress and it is shared among genetic backgrounds. This initial response is followed by a genotype- and/or condition-specific transcriptional response with a strong genotype-by-environment interaction. Intriguingly, genotype- and condition-specific transcriptional response is found in genes not conserved beyond crustaceans, suggesting niche-specific adaptation.

Published
2018

13. The coral pathogen Vibrio coralliilyticus uses a T6SS to secrete a group of novel anti-eukaryotic effectors that contribute to virulence.

Author

Mass, Shir, Cohen, Hadar, Podicheti, Ram, Rusch, Douglas B., Gerlic, Motti, Ushijima, Blake, van Kessel, Julia C., Bosis, Eran, and Salomon, Dor

Subjects
OCEAN temperature, AQUATIC organisms, HIGH temperatures, VIBRIO, TOXINS
Abstract

Vibrio coralliilyticus is a pathogen of coral and shellfish, leading to devastating economic and ecological consequences worldwide. Although rising ocean temperatures correlate with increased V. coralliilyticus pathogenicity, the specific molecular mechanisms and determinants contributing to virulence remain poorly understood. Here, we systematically analyzed the type VI secretion system (T6SS), a contact-dependent toxin delivery apparatus, in V. coralliilyticus. We identified 2 omnipresent T6SSs that are activated at temperatures in which V. coralliilyticus becomes virulent; T6SS1 is an antibacterial system mediating interbacterial competition, whereas T6SS2 mediates anti-eukaryotic toxicity and contributes to mortality during infection of an aquatic model organism, Artemia salina. Using comparative proteomics, we identified the T6SS1 and T6SS2 toxin arsenals of 3 V. coralliilyticus strains with distinct disease etiologies. Remarkably, T6SS2 secretes at least 9 novel anti-eukaryotic toxins comprising core and accessory repertoires. We propose that T6SSs differently contribute to V. coralliilyticus's virulence: T6SS2 plays a direct role by targeting the host, while T6SS1 plays an indirect role by eliminating competitors. Vibrio coralliilyticus is a pathogen of coral and shellfish that is becoming more virulent as ocean temperatures rise, causing significant damage. This study shows that V. coralliilyticus has two type VI secretion systems (T6SSs) that are activated at high temperatures; one targets bacterial competitors, while the other launches up to 9 novel toxins against eukaryotic hosts like shrimps. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Author

Orsini, Luisa, Gilbert, Donald, Podicheti, Ram, Jansen, Mieke, Brown, James B, Solari, Omid Shams, Spanier, Katina I, Colbourne, John K, Rusch, Douglas B, Decaestecker, Ellen, Asselman, Jana, De Schamphelaere, Karel AC, Ebert, Dieter, Haag, Christoph R, Kvist, Jouni, Laforsch, Christian, Petrusek, Adam, Beckerman, Andrew P, Little, Tom J, Chaturvedi, Anurag, Pfrender, Michael E, De Meester, Luc, and Frilander, Mikko J

Published
2017

15. Erratum: Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

Author

Orsini, Luisa, Gilbert, Donald, Podicheti, Ram, Jansen, Mieke, Brown, James B, Solari, Omid Shams, Spanier, Katina I, Colbourne, John K, Rusch, Douglas B, Decaestecker, Ellen, Asselman, Jana, De Schamphelaere, Karel AC, Ebert, Dieter, Haag, Christoph R, Kvist, Jouni, Laforsch, Christian, Petrusek, Adam, Beckerman, Andrew P, Little, Tom J, Chaturvedi, Anurag, Pfrender, Michael E, De Meester, Luc, and Frilander, Mikko J

Subjects
Biological Sciences, Genetics
Abstract

Scientific Data 3:160030 doi:10.1038/sdata.2016.30 (2016); Published 10 May 2016; Updated 31 Jan 2017 The original version of this Data Descriptor contained a typographical error in the spelling of the author Douglas B. Rusch, which was incorrectly given as Douglas Rush. This has now been corrected in the PDF and HTML versions of the Data Descriptor.

Published
2017

16. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.

Author

Orsini, Luisa, Gilbert, Donald, Podicheti, Ram, Jansen, Mieke, Brown, James B, Solari, Omid Shams, Spanier, Katina I, Colbourne, John K, Rusch, Douglas B, Decaestecker, Ellen, Asselman, Jana, De Schamphelaere, Karel AC, Ebert, Dieter, Haag, Christoph R, Kvist, Jouni, Laforsch, Christian, Petrusek, Adam, Beckerman, Andrew P, Little, Tom J, Chaturvedi, Anurag, Pfrender, Michael E, De Meester, Luc, and Frilander, Mikko J

Subjects
Animals, Daphnia, RNA, Base Sequence, Genome, Databases, Genetic, Gene-Environment Interaction, Transcriptome, Databases, Genetic
Abstract

The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

Published
2016

23. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees.

Author

Wu, Dongying, Wu, Martin, Halpern, Aaron, Rusch, Douglas B, Yooseph, Shibu, Frazier, Marvin, Venter, J Craig, and Eisen, Jonathan A

Subjects
Rec A Recombinases, Bacterial Proteins, RNA, Ribosomal, Evolution, Molecular, Phylogeny, Base Sequence, Multigene Family, Databases, Genetic, Oceans and Seas, Metagenomics, RNA, Ribosomal, Evolution, Molecular, Databases, Genetic, General Science & Technology
Abstract

BackgroundMost of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.Methodology/principal findingsWe designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.Conclusions/significanceOf the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.

Published
2011

25. The Genome Sequence of the Malaria Mosquito Anopheles gamblae

Author

Holt, Robert A., Subramanian, G. Mani, Halpern, Aaron, Sutton, Granger G., Charlab, Rosane, Nusskern, Deborah R., Wincker, Patrick, Clark, Andrew G., Wides, Ron, Salzberg, Steven L., Loftus, Brendan, Yandell, Mark, Majoros, William H., Rusch, Douglas B., Lai, Zhongwu, Kraft, Cheryl L., Abril, Josep F., Anthouard, Veronique, Arensburger, Peter, Atkinson, Peter W., Baden, Holly, de Berardinis, Veronique, Baldwin, Danita, Benes, Vladimir, Biedler, Jim, Blass, Claudia, Bolanos, Randall, Boscus, Didier, Barnstead, Mary, Cai, Shuang, Chatuverdi, Kabir, Christophides, George K., Chrystal, Mathew A., Clamp, Michele, Cravchik, Anibal, Curwen, Val, Dana, Ali, Delcher, Art, Dew, Ian, Evans, Cheryl A., Flanigan, Michael, Grundschober-Freimoser, Anne, Friedli, Lisa, Gu, Zhiping, Guan, Ping, Guigo, Roderic, Hillenmeyer, Maureen E., Hladun, Susanne L., Hogan, James R., Hong, Young S., Hoover, Jeffrey, Jaillon, Olivier, Ke, Zhaoxi, Kodira, Chinnappa, Kokoza, Elena, Koutsos, Anastasios, Letunic, Ivica, Levitsky, Alex, Liang, Yong, Lin, Jhy-Jhu, Lobo, Neil F., Lopez, John R., Malek, Joel A., McIntosh, Tina C., Meister, Stephan, Miller, Jason, Mobarry, Clark, Mongin, Emmanuel, Murphy, Sean D., O'Brochta, David A., Pfannkoch, Cynthia, Qi, Rong, Regier, Megan A., Remington, Karin, Shao, Hongguang, Sharakhova, Maria V., Sitter, Cynthia D., Shetty, Jyoti, Smith, Thomas J., Strong, Renee, Sun, Jingtao, Thomasova, Dana, Ton, Lucas Q., Topalis, Pantelis, Tu, Zhijian, Unger, Maria F., Walenz, Brian, Wang, Aihui, Wang, Jian, Wang, Mei, Wang, Xuelan, Woodford, Kerry J., Wortman, Jennifer R., Wu, Martin, Yao, Alison, Zdobnov, Evgeny M., Zhang, Hongyu, Zhao, Qi, Zhao, Shaying, Zhu, Shiaoping C., Zhimulev, Igor, Coluzzi, Mario, della Torre, Alessandra, Roth, Charles W., Louis, Christos, Kalush, Francis, Mural, Richard J., Myers, Eugene W., Adams, Mark D., Smith, Hamilton O., Broder, Samuel, Gardner, Malcolm J., Fraser, Claire M., Birney, Ewan, Bork, Peer, Brey, Paul T., Venter, J. Craig, Weissenbach, Jean, Kafatos, Fotis C., Collins, Frank H., and Hoffman, Stephen L.

Published
2002

26. A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome

Author

Mural, Richard J., Adams, Mark D., Myers, Eugene W., Smith, Hamilton O., Wides, Ron, Halpern, Aaron, Li, Peter W., Sutton, Granger G., Nadeau, Joe, Salzberg, Steven L., Holt, Robert A., Kodira, Chinnappa D., Lu, Fu, Chen, Lin, Deng, Zuoming, Evangelista, Carlos C., Gan, Weiniu, Heiman, Thomas J., Li, Jiayin, Li, Zhenya, Merkulov, Gennady V., Milshina, Natalia V., Naik, Ashwinikumar K., Qi, Rong, Shue, Bixiong Chris, Wang, Aihui, Wang, Jian, Wang, Xin, Yan, Xianghe, Ye, Jane, Yooseph, Shibu, Zhao, Qi, Zheng, Liansheng, Zhu, Shiaoping C., Biddick, Kendra, Bolanos, Randall, Delcher, Arthur L., Dew, Ian M., Fasulo, Daniel, Flanigan, Michael J., Huson, Daniel H., Kravitz, Saul A., Miller, Jason R., Mobarry, Clark M., Reinert, Knut, Remington, Karin A., Zhang, Qing, Zheng, Xiangqun H., Nusskern, Deborah R., Lai, Zhongwu, Lei, Yiding, Zhong, Wenyan, Yao, Alison, Guan, Ping, Ji, Rui-Ru, Gu, Zhiping, Wang, Zhen-Yuan, Zhong, Fei, Xiao, Chunlin, Chiang, Chia-Chien, Yandell, Mark, Wortman, Jennifer R., Amanatides, Peter G., Hladun, Suzanne L., Pratts, Eric C., Johnson, Jeffery E., Dodson, Kristina L., Woodford, Kerry J., Evans, Cheryl A., Gropman, Barry, Rusch, Douglas B., Venter, Eli, Wang, Mei, Smith, Thomas J., Houck, Jarrett T., Tompkins, Donald E., Haynes, Charles, Jacob, Debbie, Chin, Soo H., Allen, David R., Dahlke, Carl E., Sanders, Robert, Li, Kelvin, Liu, Xiangjun, Levitsky, Alexander A., Majoros, William H., Chen, Quan, Xia, Ashley C., Lopez, John R., Donnelly, Michael T., Newman, Matthew H., Glodek, Anna, Kraft, Cheryl L., Nodell, Marc, Ali, Feroze, An, Hui-Jin, Baldwin-Pitts, Danita, Beeson, Karen Y., Cai, Shuang, Carnes, Mark, Carver, Amy, Caulk, Parris M., Chen, Yen-Hui, Cheng, Ming-Lai, Coyne, My D., Crowder, Michelle, Danaher, Steven, Davenport, Lionel B., Desilets, Raymond, Dietz, Susanne M., Doup, Lisa, Dullaghan, Patrick, Ferriera, Steven, Fosler, Carl R., Gire, Harold C., Gluecksmann, Andres, Gocayne, Jeannine D., Gray, Jonathan, Hart, Brit, Haynes, Jason, Hoover, Jeffery, Howland, Tim, Ibegwam, Chinyere, Jalali, Mena, Johns, David, Kline, Leslie, Ma, Daniel S., MacCawley, Steven, Magoon, Anand, Mann, Felecia, May, David, McIntosh, Tina C., Mehta, Somil, Moy, Linda, Moy, Mee C., Murphy, Brian J., Murphy, Sean D., Nelson, Keith A., Nuri, Zubeda, Parker, Kimberly A., Prudhomme, Alexandre C., Puri, Vinita N., Qureshi, Hina, Raley, John C., Reardon, Matthew S., Regier, Megan A., Rogers, Yu-Hui C., Romblad, Deanna L., Schutz, Jakob, Scott, John L., Scott, Richard, Sitter, Cynthia D., Smallwood, Michella, Sprague, Arlan C., Stewart, Erin, Strong, Renee V., Suh, Ellen, Sylvester, Karena, Thomas, Reginald, Tint, Tsonis, Christopher, Wang, Gary, Wang, George, Williams, Monica S., Williams, Sherita M., Windsor, Sandra M., Wolfe, Keriellen, Wu, Mitchell M., Zaveri, Jayshree, Chaturvedi, Kabir, Gabrielian, Andrei E., Ke, Zhaoxi, Sun, Jingtao, Subramanian, Gangadharan, and Venter, J. Craig

Published
2002

27. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

Author

Rusch, Douglas B, Halpern, Aaron L, Sutton, Granger, Heidelberg, Karla B, Williamson, Shannon, Yooseph, Shibu, Wu, Dongying, Eisen, Jonathan A, Hoffman, Jeff M, Remington, Karin, Beeson, Karen, Tran, Bao, Smith, Hamilton, Baden-Tillson, Holly, Stewart, Clare, Thorpe, Joyce, Freeman, Jason, Andrews-Pfannkoch, Cynthia, Venter, Joseph E, Li, Kelvin, Kravitz, Saul, Heidelberg, John F, Utterback, Terry, Rogers, Yu-Hui, Falcón, Luisa I, Souza, Valeria, Bonilla-Rosso, Germán, Eguiarte, Luis E, Karl, David M, Sathyendranath, Shubha, Platt, Trevor, Bermingham, Eldredge, Gallardo, Victor, Tamayo-Castillo, Giselle, Ferrari, Michael R, Strausberg, Robert L, Nealson, Kenneth, Friedman, Robert, Frazier, Marvin, and Venter, J Craig

Subjects
Genetics, Human Genome, Biotechnology, Life Below Water, Computational Biology, Food Chain, Oceans and Seas, Plankton, Species Specificity, Water Microbiology, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology
Abstract

The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

Published
2007

28. The Sequence of the Human Genome

Author

Venter, J. Craig, Adams, Mark D., Myers, Eugene W., Li, Peter W., Mural, Richard J., Sutton, Granger G., Smith, Hamilton O., Yandell, Mark, Evans, Cheryl A., Holt, Robert A., Gocayne, Jeannine D., Amanatides, Peter, Ballew, Richard M., Huson, Daniel H., Wortman, Jennifer Russo, Zhang, Qing, Kodira, Chinnappa D., Zheng, Xiangqun H., Chen, Lin, Skupski, Marian, Subramanian, Gangadharan, Thomas, Paul D., Zhang, Jinghui, Nelson, Catherine, Broder, Samuel, Clark, Andrew G., Nadeau, Joe, McKusick, Victor A., Zinder, Norton, Levine, Arnold J., Roberts, Richard J., Simon, Mel, Slayman, Carolyn, Hunkapiller, Michael, Bolanos, Randall, Delcher, Arthur, Dew, Ian, Fasulo, Daniel, Flanigan, Michael, Florea, Liliana, Halpern, Aaron, Hannenhalli, Sridhar, Kravitz, Saul, Levy, Samuel, Mobarry, Clark, Reinert, Knut, Remington, Karin, Abu-Threideh, Jane, Beasley, Ellen, Biddick, Kendra, Bonazzi, Vivien, Brandon, Rhonda, Cargill, Michele, Chandramouliswaran, Ishwar, Charlab, Rosane, Chaturvedi, Kabir, Deng, Zuoming, Di Francesco, Valentina, Dunn, Patrick, Eilbeck, Karen, Evangelista, Carlos, Gabrielian, Andrei E., Gan, Weiniu, Ge, Wangmao, Gong, Fangcheng, Gu, Zhiping, Guan, Ping, Heiman, Thomas J., Higgins, Maureen E., Ji, Rui-Ru, Ke, Zhaoxi, Ketchum, Karen A., Lai, Zhongwu, Lei, Yiding, Li, Zhenya, Li, Jiayin, Liang, Yong, Lin, Xiaoying, Lu, Fu, Merkulov, Gennady V., Milshina, Natalia, Moore, Helen M., Naik, Ashwinikumar K, Narayan, Vaibhav A., Neelam, Beena, Nusskern, Deborah, Rusch, Douglas B., Salzberg, Steven, Shao, Wei, Shue, Bixiong, Sun, Jingtao, Wang, Zhen Yuan, Wang, Aihui, Wang, Xin, Wang, Jian, Wei, Ming-Hui, Wides, Ron, Xiao, Chunlin, Yan, Chunhua, Yao, Alison, Ye, Jane, Zhan, Ming, Zhang, Weiqing, Zhang, Hongyu, Zhao, Qi, Zheng, Liansheng, Zhong, Fei, Zhong, Wenyan, Zhu, Shiaoping C., Zhao, Shaying, Gilbert, Dennis, Baumhueter, Suzanna, Spier, Gene, Carter, Christine, Cravchik, Anibal, Woodage, Trevor, Ali, Feroze, An, Huijin, Awe, Aderonke, Baldwin, Danita, Baden, Holly, Barnstead, Mary, Barrow, Ian, Beeson, Karen, Busam, Dana, Carver, Amy, Cheng, Ming Lai, Curry, Liz, Danaher, Steve, Davenport, Lionel, Desilets, Raymond, Dietz, Susanne, Dodson, Kristina, Doup, Lisa, Ferriera, Steven, Garg, Neha, Gluecksmann, Andres, Hart, Brit, Haynes, Jason, Haynes, Charles, Heiner, Cheryl, Hladun, Suzanne, Hostin, Damon, Houck, Jarrett, Howland, Timothy, Ibegwam, Chinyere, Johnson, Jeffery, Kalush, Francis, Kline, Lesley, Koduru, Shashi, Love, Amy, Mann, Felecia, May, David, McCawley, Steven, Mclntosh, Tina, McMullen, Ivy, Moy, Mee, Moy, Linda, Murphy, Brian, Nelson, Keith, Pfannkoch, Cynthia, Pratts, Eric, Puri, Vinita, Qureshi, Hina, Reardon, Matthew, Rodriguez, Robert, Rogers, Yu-Hui, Romblad, Deanna, Ruhfel, Bob, Scott, Richard, Sitter, Cynthia, Smallwood, Michelle, Stewart, Erin, Strong, Renee, Suh, Ellen, Thomas, Reginald, Tint, Tse, Sukyee, Vech, Claire, Wang, Gary, Wetter, Jeremy, Williams, Sherita, Williams, Monica, Windsor, Sandra, Winn-Deen, Emily, Wolfe, Keriellen, Zaveri, Jayshree, Zaveri, Karena, Abril, Josep F., Guigó, Roderic, Campbell, Michael J., Sjolander, Kimmen V., Karlak, Brian, Kejariwal, Anish, Mi, Huaiyu, Lazareva, Betty, Hatton, Thomas, Narechania, Apurva, Diemer, Karen, Muruganujan, Anushya, Guo, Nan, Sato, Shinji, Bafna, Vineet, Istrail, Sorin, Lippert, Ross, Schwartz, Russell, Walenz, Brian, Yooseph, Shibu, Allen, David, Basu, Anand, Baxendale, James, Blick, Louis, Caminha, Marcelo, Carnes-Stine, John, Caulk, Parris, Chiang, Yen-Hui, Coyne, My, Dahlke, Carl, Mays, Anne Deslattes, Dombroski, Maria, Donnelly, Michael, Ely, Dale, Esparham, Shiva, Fosler, Carl, Gire, Harold, Glanowski, Stephen, Glasser, Kenneth, Glodek, Anna, Gorokhov, Mark, Graham, Ken, Gropman, Barry, Harris, Michael, Heil, Jeremy, Henderson, Scott, Hoover, Jeffrey, Jennings, Donald, Jordan, Catherine, Jordan, James, Kasha, John, Kagan, Leonid, Kraft, Cheryl, Levitsky, Alexander, Lewis, Mark, Liu, Xiangjun, Lopez, John, Ma, Daniel, Majoros, William, McDaniel, Joe, Murphy, Sean, Newman, Matthew, Nguyen, Trung, Nguyen, Ngoc, Nodell, Marc, Pan, Sue, Peck, Jim, Peterson, Marshall, Rowe, William, Sanders, Robert, Scott, John, Simpson, Michael, Smith, Thomas, Sprague, Arlan, Stockwell, Timothy, Turner, Russell, Venter, Eli, Wang, Mei, Wen, Meiyuan, Wu, David, Wu, Mitchell, Xia, Ashley, Zandieh, Ali, and Zhu, Xiaohong

Published
2001

29. The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Author

Yooseph, Shibu, Sutton, Granger, Rusch, Douglas B., Halpern, Aaron L., Williamson, Shannon J., Remington, Karin, Eisen, Jonathan A., Heidelberg, Karla B., Manning, Gerard, Li, Weizhong, Jaroszewski, Lukasz, Cieplak, Piotr, Miller, Christopher S., Li, Huiying, Mashiyama, Susan T., Joachimiak, Marcin P., van Belle, Christopher, Chandonia, John-Marc, Soergel, David A., Zhai, Yufeng, Natarajan, Kannan, Lee, Shaun, Raphael, Benjamin J., Bafna, Vineet, Friedman, Robert, Brenner, Steven E., Godzik, Adam, Eisenberg, David, Dixon, Jack E., Taylor, Susan S., Strausberg, Robert L., Frazier, Marvin, and Venter, J.Craig

Published
2006

30. A novel screening approach comparing kinase activity of small molecule inhibitors with similar molecular structures and distinct biologic effects in triple-negative breast cancer to identify targetable signaling pathways

Author

Matossian, Margarite D., Burks, Hope E., Elliott, Steven, Hoang, Van T., Zuercher, William J., Wells, Carrow, Drewry, David H., Kapadia, Nirav, Chang, Tiffany, Yan, Thomas, Windsor, Gabrielle O., Nguyen, Khoa, Fang, Fang, Nephew, Kenneth P., Buechlein, Aaron, Rusch, Douglas B., Sabol, Rachel A., Ucar, Deniz A., Zabaleta, Jovanny, Miele, Lucio, Bunnell, Bruce A., Collins-Burow, Bridgette M., and Burow, Matthew E.

Published
2020
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38. Transcriptomics analysis of allergen-induced inflammatory gene expression in the Four-Core Genotype mouse model.

Author

Ekpruke, Carolyn Damilola, Alford, Rachel, Rousselle, Dustin, Babayev, Maksat, Sharma, Shikha, Commodore, Sarah, Buechlein, Aaron, Rusch, Douglas B., and Silveyra, Patricia

Subjects
GENE expression, GENE expression profiling, TRANSCRIPTOMES, LABORATORY mice, HOUSE dust mites, GENOTYPES, SEX chromosomes, IMMUNOGLOBULIN E
Abstract

Sex differences in allergic inflammation have been reported, but the mechanisms underlying these differences remain unknown. Contributions of both sex hormones and sex-related genes to these mechanisms have been previously suggested in clinical and animal studies. Here, Four-Core Genotypes (FCG) mouse model was used to study the inflammatory response to house dust mite (HDM) challenge and identify differentially expressed genes (DEGs) and regulatory pathways in lung tissue. Briefly, adult mice (8–10 wk old) of the FCG (XXM, XXF, XYM, XYF) were challenged intranasally with 25 μg of HDM or vehicle (PBS-control group) 5 days/wk for 5 wk (n ¼ 3/10 group). At 72 h after the last exposure, we analyzed the eosinophils and neutrophils in the bronchoalveolar lavage (BAL) of FCG mice. We extracted lung tissue and determined DEGs using Templated Oligo-Sequencing (TempO-Seq). DEG analysis was performed using the DESeq2 package and gene enrichment analysis was done using Ingenuity Pathway Analysis. A total of 2,863 DEGs were identified in the FCG. Results revealed increased eosinophilia and neutrophilia in the HDM-treated group with the most significantly expressed genes in XYF phenotype and a predominant effect of female hormones vs. chromosomes. Regardless of the sex hormones, mice with female chromosomes had more downregulated genes in the HDM group but this was reversed in the control group. Interestingly, genes associated with inflammatory responses were overrepresented in the XXM and XYF genotypes treated with HDM. Sex hormones and chromosomes contribute to inflammatory responses to HDM challenge, with female hormones exerting a predominant effect mediated by inflammatory DEGs. NEW & NOTEWORTHY Gene expression profiling helps to provide deep insight into the global view of disease-related mechanisms and responses to therapy. Using the Four-Core Genotype mouse model, our findings revealed the influence of sex hormones and sex chromosomes in the gene expression of lungs exposed to an aeroallergen (House Dust Mite) and identified sexspecific pathways to better understand sex disparities associated with allergic airway inflammation. [ABSTRACT FROM AUTHOR]

Published
2024
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39. Supplementary Table S5 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
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40. Data from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
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41. Supplementary Figures S1-S6, Table S4, Table S6 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
Full Text
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49. A unique microbiota for normal breast tissue

Author

German, Rana, primary, Marino, Natascia, additional, Hemmerich, Chris, additional, Podicheti, Ram, additional, Rusch, Douglas B., additional, Stiemsma, Leah T., additional, Gao, Hongyu, additional, Xuei, Xiaoling, additional, Rockey, Pam, additional, and Storniolo, Anna Maria, additional

Published
2022
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