| Title |
Investigators | Department | Objectives | Approach Keywords | Progress Reports | Impact Statements | Publications | |
Project * COL00648 | |
| Title | Genomics of Pest Insects, Plant Pathogens, and Plants |
| Investigator(s) | Knudson, DL; |
| Department | Bioagricultural Sciences and Pest Mgmt. |
| Objectives | 1. To establish a repertoire of genomic technologies at Colorado State University. 2. To transfer and apply genomics technologies to important agricultural problems through innovative experimental design and strategic alliances. |
| Approach | The overall project objectives will be accomplished through the subproject objectives. The mosquito genomics subproject provides the primary source of innovation and genomic technology development. The other subprojects are the beneficiaries of the technology transfer through strategic alliances. |
| Keywords | genomes, bacterial ring rot, russian wheat aphid, mosquito, fungus |
| Progress Reports | |
| 1993 | This project is composed of subprograms. The Aedes aegypti genome mapping subprogram made substantial progress during the reporting period and a grant application to NIH NIAID was developed which was entitled, Physical mapping of filarial vector competence in Aedes aegypti. It was reviewed and received a very high score, with funding anticipated from April 1994 for three years. Dog heartworm susceptibility is the target of the proposal. Our genomic mapping technology is being applied to the another important agricultural vector of bluetongue disease, Culicoides variipennis. This work is in a collaboration with the USDA Arthropod Borne Animal Disease Research Laboratory. The target of the midge mapping is the gene(s) controlling vector competence and a NRI competitive grant application is planned. |
| 1994 | This project is composed of 7 subprograms. The Aedes aegypti genomics subprogram has had substantial progress during this reporting period with 2 manuscripts in press or preparation and these data are available via the internet at URL http://klab.agsci.colostate.edu/. The technology established in the laboratory during this period will have direct application to the other subprograms. The Culicoides variipennis genomics collaborative subprogram has been successful in the production of a cosmid library of the genome and the demonstration of FISH mapping to culicoid metaphase chromosomes. In the Clavibacter genomics collaborative subprogram we have assisted in the production of a genomic cosmid library and planning a collaborative NFS grant. In the plant genomics collaborative subprogram, initial FISH imaging work has been undertaken and personnel trained. There has been no work on the remaining 3 lower priority subprograms during this period. Additionally, another manuscript dealing with a previous subprogram is in press. |
| 1995 | This project is composed of 7 subprograms. The Aedes aegypti genomics subprogram has had substantial progress during this reporting period where the physical map has been correlated with the genetic linkage map and these data are available via the internet at URL http://klab .agsci.colostate.edu/. The Culicoides variipennis genomics collaborative subprogram continues with additional clones added to the physical map of the culicoid metaphase chromosomes. In the plant genomics collaborative subprogram, initial FISH imaging work has been undertaken and personnel trained, resulting in a joint grant submission to the USDA NRICGP Plant Genome program. There has been no work on the remaining lower priority subprograms during this period . Three manuscripts are currently in press. |
| 1996 | This project is composed of 7 subprograms. The Aedes aegypti genomics subprogram has had substantial progress during this reporting period where the physical map has been correlated with the genetic linkage map and these data are available via the internet at URL http://klab .agsci.colostate.edu/. The Culicoides variipennis genomics collaborative subprogram continues by identifying chromosome specific tags. In the plant genomics collaborative subprogram, the FISH imaging work has resulted in a successful joint grant from the USDA NRICGP Plant Genome program, entitled "Gene Organization in Barley." There has been no work on the remaining lower priority subprograms during this period. Two manuscripts are currently in press. |
| 1997 | This project is composed of 7 subprograms. This year the Aedes aegypti genomics subprogram is highlighted, and more specifically, our successful application of exon trapping methods to transcript mapping in insects is detailed. Briefly, filarial and malarial parasites are responsible for devastating infections of humans and animals. Since these parasites are vectored in nature by mosquitoes, the elucidation of the molecular mechanism(s) which underlie parasite vector competence has been our goal. Our research efforts in collaboration with others have focused on map-based positional cloning of genes responsible for parasite vector competence in Aedes aegypti. Our efforts have progressed to the point where strategies for transcript mapping of mosquito genomic sequences need to be evaluated. We chose to evaluate the exon trapping (also known as exon amplification) method, which isolates internal and terminal exons from genomic clones, such as, cosmids and BACs. This transcript mapping method has been applied widely in human genetic research, and it represents a primary tool in gene identification because several 100 kb of a recombinant DNA clone can be screened in a single transfection. The applicability of this approach to invertebrates, specifically mosquitoes, however, could have serious shortcomings because the functionality of invertebrate splice signals in a vertebrate system has not been reported. In the last year, we have demonstrated that the vertebrate exon trapping methods do work with mosquito genomic sequences both through a theoretical analysis in software of mosquito splice sites and by a direct physical trapping demonstration of mosquito gene exons from a genomic clone. Hence, these protocols can be employed generally for transcript mapping of mosquito genomic clones. This transcript mapping strategy will be productive in developing transcript maps across genomic regions, and they will yield candidate genes or exons for functional analyses. Not only have we added an important tool to our map-based positional cloning strategies in mosquitoes, but the general application of these methods to other insect genomics programs has also been assured through this demonstration. |
| 1998 | This project is composed of 7 subprograms with major focus to apply molecular technologies to systems of agricultural importance. The problem faced is that systems of great agricultural importance would benefit from the application of molecular tools. To this end, we have had significant success in the application of molecular biotechnologies to several of these subprograms in the past year, and one is highlighted here. We have successfully applied cosmid contig mapping methods that were developed in our Aedes aegypti genomics subprogram to the interdisciplinary, collaborative subprogram on the bacterial ringrot of potato pathogen, Clavibacter michiganensis subsp. sepedonicus (Cms) genomics subprogram (see the Ishimaru report for details on the accomplishments, http://www.colostate.edu/Depts/AES/projs/648.htm). Briefly, we have demonstrated that a physical map of this economically important bacterial plant pathogen can be constructed. More importantly, this demonstration will allow us to focus on identifying potential pathogenicity determinants in Cms, from which new targets for detection can be developed. To this end, a grant proposal detailing this strategy has been submitted to U.S.D.A. N.R.I. Competitive Grants Program, Plant Pathology program in January 1999. The combination of sensitive detection methods and extreme host resistance would greatly improve efforts toward eradicating Cms from the U.S.A. Identification of pathogenicity determinants in plant pathogenic coryneform bacteria will also contribute to the general knowledge of a basic question in plant pathology and may reveal concordances with animal and human pathogenic coryneforms. |
| 1999 | This project is composed of 7 subprojects with a major focus to apply molecular technologies to systems of agricultural importance through technology transfer among the subprojects. A primary finding to be gleaned from this approach is that technology transfer between interdisciplinary research topics can be effective with many substantial benefits accruing to other research areas. This project has been extremely successful in transferring key FISH and genomic mapping technologies developed and established in the mosquito subproject to the bacterial ring rot genomics, barley gene mapping, and bluetongue virus-midge vector competence mapping subprojects. The areas targeted by this project represent key agricultural issues for Colorado and the nation. For example, the mosquito work will impact dog heartworm transmission in Colorado as well as human filarial transmission world-wide. Bluetongue disease of cattle and sheep is enzootic in Colorado and the midge vector competence work may help in future control of the disease. Bacterial ring rot is a plant pathogen of one Colorado's most important crops, potato, and the purpose of these studies is to identify the gene(s) that make the bacteria pathogenic in potato. One offshoot of the barley gene mapping studies will be to use this technology as a strategy to isolate the wheat DN4 and related gene(s) that confer resistance to Russian wheat aphid infestation. |
| 2000 | This project is composed of 7 subprojects with a major focus to apply molecular technologies to systems of agricultural importance through technology transfer among the subprojects. In this year's report, one subproject, a collaboration with Dr. Nora Lapitan, will be highlighted . Briefly, a strategy was taken in the last year to isolate possible wheat gene(s) that confer resistance to Russian wheat aphid infestation. We used a resistant wheat variety developed at Colorado State University as a source of genes because genes must be expressed in this variety that render the plant resistant to Russian wheat aphid infestation. What are those genes and how does one identify them? A wheat cDNA library was prepared from the resistant wheat variety following exposure to Russian wheat aphid. Since there is large number of wheat cDNAs sequences in the sequence databases, genes that are expressed in the resistant wheat variety solely as a result of the Russian wheat aphid infestation may not be found in the existing databases. A random selection of ~1,000 cDNA clones were sequenced and these sequences were compared to existing sequence databases. Eighty-five percent of the cDNAs were known in the existing databases and 15% represented unknown or undescribed, new wheat cDNAs. Fifteen cDNAs were also identified as known disease resistance genes. |
| 2001 | This project is composed of 7 subprojects with a major focus to apply molecular technologies to systems of agricultural importance through technology transfer among the subprojects. In this year's report, one subproject, a collaboration with Dr. Carol Ishimaru, will be highlighted. Over the past several years, we have worked to develop background information that would be essential in developing a grant proposal on the whole genome sequencing of the bacterial potato pathogen, Clavibacter michiganesis subsp. sepedonicus. In our 1998 report, we first mentioned the strategies taken in our efforts to transfer the technologies that we had developed in the Aedes aegypti project to this plant pathogen. In the course of a few years, background information was developed that was indicative that our efforts of technology transfer were successful resulting in manuscripts and presentations at important national and international meetings. More importantly, the USDA Microbial Genome program funded a proposal to do the complete genome sequence of the bacterium in 2001. The funded project is a joint collaboration between Colorado State University, Ohio University, and the Sanger Centre. The Sanger Centre will do the large-scale sequencing, assembly, and annotation of the genome. |
| 2002 | This year the Aedes aegypti genomics subproject is highlighted. Over the years, we have worked to develop background information and essential reagents that would be necessary for the whole genome sequencing of the yellow fever mosquito, Aedes aegypti. Last year, the National Institutes of Health, National Institute for Allergy and Infectious Diseases funded the Aedes aegypti Genome Project (mosquito.colostate.edu). The funded project is a joint collaboration between Colorado State University, University of Notre Dame, University of Iowa and the Institute for Genomic Research. The immediate objective of the A. aegypti genome project is to develop a body of information, including expressed sequence tag (EST) sequences, BAC clone end sequences, and the physical map locations of selected BAC clones that will enhance gene discovery and also provide the critical preliminary tools for an eventual annotated complete genome sequence of Aedes aegypti. Our goal is to sequence and analyze both ends of 40,000 cDNAs derived from normalized libraries produced from 4 specific mRNA sources. Single pass sequence will also be obtained from both ends of 50,000 BAC clones. We will use fluorescent in situ hybridization (FISH) technology to physically map 1,000 A. aegypti BAC clones to metaphase chromosomes. To make this effort even more informative, we will identify and include BAC clones containing ESTs genetically mapped as well as ESTs or known genes deemed of particular interest as our gene discovery project proceeds. |
| 2003 | The Aedes aegypti genomics subproject is highlighted again this year. As a prelude to the whole genome sequencing (WGS) of the yellow fever mosquito, we have collaborated with multiple institutions to lay the foundation for a WGS project. The National Institute for Allergy and Infectious Diseases has funded the initial Aedes aegypti Genome Project (mosquito.colostate .edu), which is a collaboration between Colorado State University, University of Notre Dame, University of Iowa and the Institute for Genomic Research, and the project has met its first objective in the past year. At least, 117,937 BAC end sequences were deposited in GenBank. In addition, these data provided information on the genome structure. Before the project started, there were approximately only 118 repetitive element families known in Ae. aegypti and these studies have added another 1,034 families (in collaboration with Virginia Tech). Further, the frequency and divergence of each family was also recorded. These data will be used to assist in assembling scaffolds for the WGS sequencing project. The initial stages of the EST sequencing began and there is an Aedes aegypti Gene Index (AeGI) maintained at the Institute for Genomic Research online. AeGI contains over 10,000 unique transcript sequences. Generation of EST data is important because it will identify genes expressed at developmental stages and be representative of the entire transcriptome. In addition, the EST data will be essential for training gene-finding software in the annotation phase of the WGS. |
| 2004 | The Aedes aegypti genomics subproject is highlighted again this year. Last year we laid the foundation for development of a plan for the whole genome sequencing (WGS) of the yellow fever mosquito. This past year the WGS project has become a reality. We have collaborated with multiple institutions to accomplish this goal. Based upon a collaborative White Paper that was submitted, the National Institute for Allergy and Infectious Diseases funded the Aedes aegypti Genome Project (see mosquito.colostate.edu). This project is a collaboration between Colorado State University, University of Notre Dame, University of Iowa, the Institute for Genomic Research, and the Broad Institute. Roughly, 9.7 million sequence reads have been completed to date, and this may represent an ~8X genome coverage. This project and its progenitor have released an enormous amount of genomic, EST, and BAC end sequence data to the research community. As these sequences are assembled into contiguous stretches, the genes will initially be annotated via automated procedures. Given the wealth of dipteran genome data, it is anticipated that the product of the annotation will be useful to the research community. |
| 2005 | In the past year, we have been involved in a project that aims to produce a draft genome sequence for the necrotrophic fungus, Alternaria brassicicola. A. brassicicola is the causal organism of black spot disease of Brassicas. Christopher Lawrence (Bioinformatics Institute, Virginia Polytechnic Institute and State University) is the principal investigator for this project and it includes collaborations between Colorado State University, Virginia Polytechnic Institute and State University, Washington University, North Carolina State University and Solexa. Our role in the project has been to produce a large insert BAC library of the A. brassicicola genome and to assist in bioinformatics analyses. We have made 9,600 BAC clones of A. brassicicola where each clone contains a large genome insert, and as such, the library represents 32-fold genome coverage. Using our BAC library, a fingerprint physical map is in preparation and a minimum tile path of BACs by end-sequencing is in progress. These results will provide a framework for genome assembly of shotgun genome sequence data that is being produced by the Washington University Genome Sequencing Center (WUGSC). |
| 2006 | In the past few years, we have actively sought funding to follow up to our funded whole sequence determination of Clavibacter genome (a collaboration with Carol Ishimaru). Resources for post whole genome sequence research are limited resulting in only a few number of funded functional genomes projects. In absence of functional genomics funding on the Clavibacter genome, we have tried to diversify our systems and use our technologies to adapt them to other projects that might benefit from our work on the Clavibacter genome. Briefly, we transferred several bioinformatics strategies to the draft genome sequence for the necrotrophic fungus, Alternaria brassicicola and two medically important mycobacteria and these efforts are reflected in this year's publications. |
| Impact | |
| 1999 | This research lays the foundation upon which future mapping studies on mosquitoes, midges, and a gram-positive bacterial plant pathogen will be based. The finding that genes in barley are located in discrete regions of the chromosomes will influence future map-based positional cloning strategies. |
| 2000 | The areas targeted by this project represent key agricultural issues for Colorado and the nation. New novel wheat genes that are induced due to Russian wheat aphid infestation have been identified and known resistance genes were also identified. These genes represent important new, potential genetic markers that may be used to selectively develop new varieties of wheat that are resistant to Russian wheat aphid infestation. In addition, their analysis at a molecular sequence level may provide insight into the specific resistance mechanism. |
| 2001 | The determination of the whole complete genome sequence represents an important first step in the identification of the pathogenicity determinants in a plant pathogenic coryneform bacteria . In addition, the sequence data may provide new insights for diagnostics and control of this important potato pathogen. |
| 2002 | The Aedes aegypti genome project lays the foundation for whole genome sequence assembly by providing the scaffolding and gene training datasets. These sequence data will provide new insights for diagnostics and control of important mosquito vectored disease. |
| 2003 | The Ae. aegypti WGS is a logical next step because the African malaria disease vector, Anopheles gambiae was completed recently and these two species represent the best characterized members of the two medically-important mosquito subfamilies, Culicinae and Anophelinae. The transmission of arboviruses and lymphatic filariasis is primarily due to culicine mosquitoes and anophelines are primary vectors in malaria transmission. Further, these subfamilies are very different taxonomically and in their genome structure. This WGS project will identify new targets for diagnostics and control of important mosquito vectored disease. |
| 2004 | The WGS of the African malaria disease vector, Anopheles gambiae was completed in 2003 and the Ae. aegypti WGS is in progress. These two species represent the best characterized members of the two medically-important mosquito subfamilies, Culicinae and Anophelinae. The transmission of arboviruses and lymphatic filariasis is primarily due to culicine mosquitoes and anophelines are primary vectors in malaria transmission. Further, these subfamilies are very different taxonomically and in their genome structure. This WGS project will identify new targets for diagnostics and control of important mosquito vectored disease. |
| 2005 | The whole genome sequence of the necrotrophic fungus, Alternaria brassicicola, will likely be completed in 2006. A. brassicicola is representative of pathogens that inflict substantial agricultural damage worldwide. In addition, the genus Alternaria impacts humans, through its association with mycotoxin contamination of food and food products, allergy, asthma, and opportunistic infection of immuno-suppressed patients. Hence, it is anticipated that this work will have far ranging applications. |
| 2006 | Resources for post genome sequence research in agriculture are limited. It is essential that agricultural agencies provide a well-funded plan for future functional genomics projects on agriculturally important pathogens, pests and plants. |
| Publications | |
| 1993 |
BROWN, S.E., B.M. GORMAN, R.B. TESH, & D.L. KNUDSON. 1993. C oltiviruses isolated from mosquitoes collected in Indonesia. Virology 196:363-367. GORDON, S.W. 1993. Molecular Genetics of Aedes aegypti. Ph.D . Thesis, Colorado State University, Fort Collis, 238 pages. |
| 1995 |
BROWN, S.E. and D.L. KNUDSON. 1995. Coltivirus Infections. In: Exotic Viral Infections, J.S. Porterfield, ed., Kass Handbook of Infectious Diseases, J. Sanford, D. Tyrrell, T. Weller & S. Wolff, Series ed., Chap. 17, Chapman and. BROWN, S.E., J. MENNINGER, M. DIFILLIPANTONIO, B.J. BEATY, D.C. WARD AND D.L. KNUDSON. 1995. Toward a physical map of Aedes aegypti. Insect Molecular Biology 4:161-167 |
| 1996 |
Ferguson, M.L., S.E. Brown, and D.L. Knudson (1996) FISH digital imaging microscopy in mosquito genomics. Parasitology Today 12(3):91-96 Knudson, D.L., L. Zheng, S.W. Gordon, S.E. Brown, and F.C. Kafatos (1996) Genome organization of vectors. In: The Biology of Disease Vectors, B.J. Beaty and W.C. Marquardt, Eds., Chap. 13, University Press of Colorado, Niwot, pp. 175-214 Nunamaker, R.A., S.E. Brown, and D.L. Knudson (1996) Metaphase chromosomes of Culicoides variipennis (Diptera: Ceratopogonidae). J. Med. Ent. 33(5):871-873 |
| 1997 |
BROWN, S.E. and KNUDSON, D.L. 1997 FISH landmarks for Aedes aegypti chromosomes. Insect Mol. Biol 6:197-202 LAPITAN, N.L.V., BROWN, S.E., KENNARD, W., STEPHENS, J.L. and KNUDSON, D.L. 1997 FISH physical mapping with barley BAC clones. The Plant Journal 11:149-156 |
| 1998 |
Brown, S.E. and Knudson, D.L. 1996. Abstract Number 468. Second generation FISH physical map of Aedes aegypti. The 45th Annual Meeting of the American Society for Tropical Medicine and Hygiene, The Hyatt Regency, Baltimore, Maryland, December 1-5, 1996, American Journal of Tropical Medicine and Hygiene 55:254 Brown, S.E. and Knudson, D.L. 1997. Abstract Number 600. Exon trapping with Mosquito DNA Aedes aegypti. The 46th Annual Meeting of the American Society of Tropical Medicine and Hygiene, Disney's Coronado Springs Resort, Lake Buena Vista, Florida, December 7-11, 1997, American Journal of Tropical Medicine and Hygiene 57:304-305 Brown, S.E., Reilley, A.A., Knudson, D.L. and Ishimaru, C.A. 1998. Genome fingerprinting of Clavibacter michiganensis subsp. sepedonicus. The American Phytopathological Society and the Entomology Society of American Joint Annual Meeting, Las Vegas, Nevada, November 8-12, 1998, Phytopathology 88:S12 Brown, S.E., Severson, D.W. and Knudson, D.L. 1996. Abstract Number 467. Correlation of the Aedes aegypti genetic linkage and physical maps. The 45th Annual Meeting of the American Society for Tropical Medicine and Hygiene, The Hyatt Regency, Baltimore, Maryland, December 1-5, 1996, American Journal of Tropical Medicine and Hygiene 55:253-254 Brown, S.E., Severson, D.W. and Knudson, D.L. 1997. Abstract Number P327. Correlation of the genetic linkage and FISH physical maps of the Aedes aegypti mosquito. International Plant and Animal Genome V Conference, Town and Country Hotel, San Diego, California, January 12-16, 1997 , Scherago International Inc. (http://www.intl-pag.org/pag/5/abstracts/p-5q-327.html Brown, S.E., Stephens, J.L., Knudson, D.L. and Lapitan, N.L.V. 1997. Abstract Number P154. Do the minor ribosomal DNA loci in barley contain 18S sequences? International Plant and Animal Genome V Conference, Town and Country Hotel, San Diego, California, January 12-16, 1997, Scherago International Inc. (http://www.intl-pag.org/pag/5/abstracts/p-5c-154.html Gordon, S.W., Brown, S.E. and Knudson, D.L. 1994. Detection of genetic variability in Aedes aegypti with RAPD-PCR. The 43th Annual Meeting of the American Society for Tropical Medicine and Hygiene, Cincinnati, Ohio, November 13-17, 1994, American Journal of Tropical Medicine and Hygiene 51:300 Lapitan, N.L.V., Brown, S.E. and Knudson, D.L. 1996. Abstract Number P145. Gene organization in barley. International Plant and Animal Genome IV Conference, Town and Country Hotel, San Diego, California, January 14-18 1996, Scherago International Inc. (http://www.intl-pag .org/pag/4/abstracts/p145.html Lapitan, N.L.V., Brown, S.E., Stephens, J.L. and Knudson, D.L. 1997. Abstract S22. FISH physical mapping in plant species with large genomes. International Plant and Animal Genome V Conference, Town and Country Hotel, San Diego, California, January 12-16, 1997, Scherago International Inc. (http://www.intl-pag.org/pag/5/abstracts/s22.html Nunamaker, R.A., Brown, S.E. and Knudson, D.L. 1996. Physical mapping in an arthropod vector of animal diseases: Culicoides variipennis (Diptera: Ceratopogonidae and bluetongue viruses. The XX International Congress of Entomology, Firenze, Italy, August 25-31, 1996, Finito di stampare dalla Tipografia TAF srl Borgo Stella 21r, Firenze, Proceedings of the XX International Congress of Entomology page 283. Nunamaker, R.A., Brown, S.E. and Knudson, D.L. 1995. Physical mapping of complex traits in an arthropod vector of animal diseases: Culicoides variipennis and the bluetongue viruses. Beltsville Symposium XX: Biotechnology Role in the Genetic Improvement of Farm Animals, Beltsville, Maryland, May 14-17, 1995, American Society of Animal Science, Savoy, Illinois., P40 Rokka, V.-M., Clark, M. S., Knudson, D. L., Pehu, E., and Lapitan, N. L. V. 1998. Cytological and molecular characterization of repetitive DNA sequences of Solanum brevidans and Solanum tuberosum. Genome 41(4):487-494 Rokka, V.-M., Lapitan, N. L. V., Knudson, D. L., and Pehu, E. 1998. Fluorescence in situ hybridization of potato somatohaploids and their somatic hybrid donors using two Solanum brevidens specific sequences. Agricultural and Food Science in Finland 7(1):31-38 Stephens, J.L., Brown, S.E., Knudson, D.L. and Lapitan, N.L.V. 1997. Abstract Number P179. FISH tags for barley chromosomes. International Plant and Animal Genome V Conference, Town and Country Hotel, San Diego, California, January 12-16, 1997, Scherago International Inc. (http://www.intl-pag.org/pag/5/abstracts/p-5c-179.html |
| 1999 |
Brown, S.E., Reilley, A.A., Knudson, D.L. and Ishimaru, C.A. 1999. Clavibacter michiganensis subsp. sepedonicus genomics. International Plant and Animal Genome VII Conference, Scherago International Inc., Town and Country Hotel, San Diego, California, pp. 148 Abstract Number P273 http://www.intl-pag.org/pag/7/abstracts/pag7231.html Brown, S.E., Stephens, J.L., Lapitan, N.L. and Knudson, D.L. 1999. FISH landmarks for barley chromosomes (Hordeum vulgare L.). Genome 42:1-7 Brown, S.E., Stephens, J.L., Lapitan, N.L.V. and Knudson, D.L. 1999. rDNA loci in barley and wheat: Probe pTA71 FISH fact or fiction. International Plant and Animal Genome VII Conference, Scherago International Inc., Town and Country Hotel, San Diego, California, pp. 181 Abstract Number P400 http://www.intl-pag.org/pag/7/abstracts/pag7237.html Brown, S.E., Wood, S.H. and Knudson, D.L. 1999. Vertebrate exon trapping methods: Implications for transcript mapping with mosquito DNA. Insect Biochem. Molec. Biol. 27:643-651 Nunamaker, R.A., Brown, S.E. and Knudson, D.L. 1999. Fluorescence in situ hybridization landmarks for chromosomes for Culicoides variipennis (Diptera: Ceratopogonidae). J. Med. Ent. 36:171-175 Stephens, J.L., Brown, S.E., Severson, D.W. and Knudson, D.L. 1999. Mosquito genomics: Contig construction across parasite vector competence QTL regions using fine scale FISH mapping. International Plant and Animal Genome VII Conference, Scherago International Inc., Town and Country Hotel, San Diego, California, pp. 154 Abstract Number P297 http://www.intl-pag .org/pag/7/abstracts/ag7035.html |
| 2000 |
Brown, S.E., Knudson, D.L., and Ishimaru, C.A. 2000. Genomic analysis of the ring rot bacterium. In "84th Annual Meeting of the Potato Association of America", Vol. 77, pp. 394. American Journal of Potato Research, Colorado Springs, Colorado. Brown, S.E., Reilley, A.A., Knudson, D.L., and Ishimaru, C.A. 2000. Sequence-tagged connectors from a recombinant cosmid library. In "Agricultural Microbes Genome I Conference". Scherago International Inc., Town and Country Hotel, San Diego, California. Abstract Number P1 http://www.intl-pag.org/amg/1/abstracts/. Brown, S.E., Stephens, J.L., and Knudson, D.L. 2000. Mosquito Genomics: Sequence-tagged connectors for the Aedes aegypti FISH physical map. In "International Plant and Animal Genome VIII Conference", pp. 202. Scherago International Inc., Scherago International Inc. Abstract Number P602 http://www.intl-pag.org/pag/8/abstracts/pag8517.html. Hansen, W.R., Nashold, S.W., Docherty, D.E., Brown, S.E., and Knudson, D.L. 2000. Diagnosis of duck plague in waterfowl by polymerase chain reaction. Avian Diseases 44(2), 266-274. Ishimaru, C.A., Brown, S.E., and Knudson, D.L. 2000. Genomic analysis of the plant pathogenic coryneform Clavibacter michiganesis subsp. sepedonicus. In "American Phytopathological Society Annual Meeting", Vol. 90, pp. S93. Phytopathology, New Orleans. Pham, D.Q.-D., Brown, S.E., Knudson, D.L., Winzerling, J.J., Dodson, M.S., and Shaffer, J.J. 2000. Structure and location of the ferritin gene of the yellow fever mosquito Aedes aegypti. European Journal of Biochemistry 267, 1-7. Stephens, J.L., Brown, S.E., Lapitan, N.L.V., and Knudson, D.L. 2000. FISH mapping cDNAs to cereal chromosomes. In "International Plant and Animal Genome VIII Conference", pp. 61. Scherago International Inc., Town and Country Hotel, San Diego, California. Abstract Number P41 http://www.intl-pag.org/pag/8/abstracts/pag8518.html. |
| 2001 |
Brown, S.E., Severson, D.W., Smith, L.A., and Knudson, D.L. 2001. Integration of the Aedes aegypti mosquito genetic linkage and physical maps. Genetics 157(3), 1299-1305. Brown, S.E., Stephens, J.L., Severson, D.W., and Knudson, D.L. 2001. Aedes aegypti genomics: targeting filarial vector competence. In "Keystone Symposia, Genetic Manipulation of Insects", pp. 55, Taos, NM. Poster presentation Lapitan, N.L.V., Stephens, J.L., Brown, S.E., Altinkut, A., and Knudson, D.L. 2001. Integration of the genetic and physical maps of barley and wheat based on FISH with cDNAS and BACS. In "International Plant and Animal Genome IX Conference", Vol. Workshop: Plant Cytogenetics. Scherago International Inc., Town and Country Hotel, San Diego, California. http://www.intl-pag.org/pag/9/abstracts/W46_05.html. Severson, D.W., Brown, S.E., and Knudson, D.L. 2001. Genetic and physical mapping in mosquitoes: molecular approaches. Annual Reviews in Entomology 46, 183-219. |
| 2002 |
Brown, S.E., Reilley, A.A., Knudson, D.L., and Ishimaru, C.A. 2002. Genomic fingerprinting of virulent and avirulent strains of Clavibacter michiganensis subspecies sepedonicus. Current Microbiology 44, 112-119. Ishimaru, C.A., Brown, S.E., and Knudson, D.L. 2002. Linear plasmid in Clavibacter michiganensis subspecies sepedonicus. In "Plant, Animal & Microbe Genomes X Conference". Scherago International Inc, Town & Country Convention Center, San Diego, CA. Poster: Microbial Sequencing and Genome Programs http://www.intl-pag.org/pag/10/abstracts/PAGX_P5.html. Ishimaru, C.A., Brown, S.E., and Knudson, D.L. 2002. Linear plasmid in the genome of Clavibacter michiganensis subspecies sepedonicus. Journal of Bacteriology 10(10), 2841-2844. Ishimaru, C.A., Parkhill, J., Francis, D.M., Brown, S.E., and Knudson, D.L. 2002. Complete genome sequencing of Clavibacter michiganensis subspecies sepedonicus. In "Plant, Animal & Microbe Genomes X Conference". Scherago International Inc, Town & Country Convention Center, San Diego, CA. Workshop: Microbe Genome Awardee 2001 http://www.intl-pag .org/pag/10/abstracts/PAGX_W211.html. Knudson, D.L., Brown, S.E., and Severson, D.W. 2002. Culicine genomics. Insect Biochemistry and Molecular Biology 32, 1193-1197. Knudson, D.L., Brown, S.E., and Severson, D.W. 2002. Programs and Abstracts of the 51st Annual Meeting of the American Society of Tropical Medicine and Hygiene, Denver, Colorado USA. |
| 2003 |
Carlson, J., Lyon, M., Bishop, J., Vaiman, A., Cribiu, E., Mornex, J.-F., Brown, S., Knudson, D., Demartini, J., and Leroux, C. 2003. Chromosomal distribution of endogenous Jaagsiekte sheep retrovirus proviral sequences in the sheep genome. Journal of Virology 77(17), 9662-9668 . Luna, C., Hoa, N.T., Zhang, J., Kanzok, S.M., Brown, S.E., Imler, J.-L., Knudson, D.L., and Zheng, L. 2003. Characterization of three Toll-like genes from mosquito Aedes aegypti. Insect Molecular Biology 12(1), 67-74. Severson, D.W., Knudson, D.L., Soares, M.B., and Loftus, B.J. 2003. Aedes aegypti BAC end sequences: 117,937 deposited. GenBank GSS Division, Accessions 78,411 CC065891-CC144307, 6,138 CC149837-CC155974, 33,388 CC841772-CC875159. Severson,D.W., deBruyn,B., Lovin,D.D., Brown,S.E., Knudson,D.L., Morlais,I. 2003. Comparative genome analysis of the yellow fever mosquito Aedes aegypti with the malaria vector mosquito Anopheles gambiae and Drosophila melanogaster: 8 sequences deposited. GenBank GSS Division, Accessions 2 CC144865-CC144866, 6 CC144559-CC144564 |
| 2004 |
Severson, D.W., deBruyn,B., Lovin,D.D., Brown,S.E., Knudson,D.L. and Morlais,I. 2004. Comparative genome analysis of the yellow fever mosquito Aedes aegypti with Drosophila melanogaster and the malaria vector mosquito Anopheles gambiae. J. Heredity 95:103-113. Severson, D.W., Knudson,D.L., Soares,M.B. and Loftus,B.J. 2004. Aedes aegypti Genomics. Insect Biochem. Molec. Biol. 34:715-721. Stephens, J.L., Brown, S.E., Lapitan, N.L.V. and Knudson,D.L. 2004. Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179-189. Stephens, J.L., Brown,S.E., Lapitan,N.L.V. and Knudson,D.L. 2004. Physical mapping of barley genes using an ultrasensitive fluorescence in situ hybridization technique. Genome 47:179-189. |
| 2005 |
Adelman, Z. N., Jasinskiene, N., Vally, K. J. M., Peek, C., Travanty, E. A., Olson, K. E., Brown, S. E., Stephens, J. L., Knudson, D. L., Coates, C. J., and James, A. A. 2004. Formation and loss of large, unstable tandem arrays of the piggyBac transposable element in the yellow fever mosquito, Aedes aegypti. Transgenic Research 13:411-425. Ishimaru, C. A., Knudson, D. L., Brown, S. E., Francis, D. M., and Parkhill, J. 2004. Genome sequencing of Clavibacter michiganensis subsp. sepedonicus. Phytopathology 94:S123. |
| 2006 |
Cramer, R. A., La Rota, C. M., Cho, Y., Thon, M., Craven, K. D., Knudson, D. L., Mitchell, T. K., and Lawrence, C. B. 2006. Bioinformatic analysis of expressed sequence tag derived from a compatible Alternaria brassicicola-Brassica oleracea interaction. Molecular Plant Pathology 7:113-124. Groathouse, N. A., Amin, A., Marques, M. A. M., Spencer, J. S., Gelber, R., Knudson, D. L., Belisle, J. T., Brennan, P. J., and Slayden, R. A. 2006. Use of protein microarrays to define the humoral immune response in leprosy patients and identification of disease-state-specific antigenic profiles. Infection and Immunity 74:6458-6466. Groathouse, N. A., Brown, S. E., Knudson, D. L., Brennan, P. J., and Slayden, R. A. 2006. Isothermal amplification and molecular typing of the obligate intracellular pathogen Mycobacterium leprae from tissues of unknown origins. Journal of Clinical Microbiology 44:1502-1508. Slayden, R. A., Knudson, D. L., and Belisle, J. T. 2006. Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis. Microbiology 152:1789-1797. |