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Carlene Chun,
Todd Scheetz,
Maria Bonaldo,
Bartley Brown,
Anik Clemens,
Wendy Crookes-Goodson,
Keith Crouch,
Tad DeMartini,
Mari Eyestone,
Michael Goodson, [......],
Christina Smith,
Jennifer Stewart,
Deyan Tong,
Joshua Troll,
Sarahrose Webster,
Jane Winhall-Rice,
Cory Yap,
Thomas Casavant,
Margaret McFall-Ngai,
Soares M Bento
[show abstract]
[hide abstract]
ABSTRACT: Abstract
Background
Biologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force for the development of models for the study of beneficial animal-bacterial interactions. In the squid-vibrio model, symbiotic Vibrio fischeri induce dramatic developmental changes in the light organ of host Euprymna scolopes over the first hours to days of their partnership. We report here the creation of a juvenile light-organ specific EST database.
Results
We generated eleven cDNA libraries from the light organ of E. scolopes at developmentally significant time points with and without colonization by V. fischeri . Single pass 3' sequencing efforts generated 42,564 expressed sequence tags (ESTs) of which 35,421 passed our quality criteria and were then clustered via the UIcluster program into 13,962 nonredundant sequences. The cDNA clones representing these nonredundant sequences were sequenced from the 5' end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E-value < -03) and Gene Ontology (GO).
Conclusion
Both the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom.
BMC Genomics. 01/2006;
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Carlene K Chun,
Todd E Scheetz,
Maria de Fatima Bonaldo,
Bartley Brown,
Anik Clemens,
Wendy J Crookes-Goodson,
Keith Crouch,
Tad DeMartini,
Mari Eyestone,
Michael S Goodson, [......],
Christina Smith,
Jennifer J Stewart,
Deyan Tong,
Joshua V Troll,
Sarahrose Webster,
Jane Winhall-Rice,
Cory Yap,
Thomas L Casavant,
Margaret J McFall-Ngai,
M Bento Soares
[show abstract]
[hide abstract]
ABSTRACT: Biologists are becoming increasingly aware that the interaction of animals, including humans, with their coevolved bacterial partners is essential for health. This growing awareness has been a driving force for the development of models for the study of beneficial animal-bacterial interactions. In the squid-vibrio model, symbiotic Vibrio fischeri induce dramatic developmental changes in the light organ of host Euprymna scolopes over the first hours to days of their partnership. We report here the creation of a juvenile light-organ specific EST database.
We generated eleven cDNA libraries from the light organ of E. scolopes at developmentally significant time points with and without colonization by V. fischeri. Single pass 3' sequencing efforts generated 42,564 expressed sequence tags (ESTs) of which 35,421 passed our quality criteria and were then clustered via the UIcluster program into 13,962 nonredundant sequences. The cDNA clones representing these nonredundant sequences were sequenced from the 5' end of the vector and 58% of these resulting sequences overlapped significantly with the associated 3' sequence to generate 8,067 contigs with an average sequence length of 1,065 bp. All sequences were annotated with BLASTX (E-value < -03) and Gene Ontology (GO).
Both the number of ESTs generated from each library and GO categorizations are reflective of the activity state of the light organ during these early stages of symbiosis. Future analyses of the sequences identified in these libraries promise to provide valuable information not only about pathways involved in colonization and early development of the squid light organ, but also about pathways conserved in response to bacterial colonization across the animal kingdom.
BMC Genomics 01/2006; 7:154. · 4.07 Impact Factor
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Jennifer J S Laffin,
Todd E Scheetz,
Maria de Fatima Bonaldo,
Rebecca S Reiter,
Shereen Chang,
Mari Eyestone,
Hakeem Abdulkawy,
Bartley Brown,
Chad Roberts,
Dylan Tack, Tamara Kucaba,
Jim Jung-Ching Lin,
Val C Sheffield,
Thomas L Casavant,
M Bento Soares
[show abstract]
[hide abstract]
ABSTRACT: Congenital heart defects affect approximately 1,000,000 people in the United States, with 40,000 new births contributing to that number every year. A large percentage of these defects can be attributed to septal defects. We assembled a nonredundant collection of over 12,000 expressed sequence tags (ESTs) from a total of 30,000 ESTs, with the ultimate goal of identifying spatially and/or temporally regulated genes during heart septation. These ESTs were compiled from nonnormalized, normalized, and serially subtracted cDNA libraries derived from two sets of tissue samples. The first includes microdissected rat hearts from embryonic (E) days E13, E15, and E16.5-E18.5 and adult heart. The second includes hearts from embryonic days E17, E19, and E21 and postnatal (P) days P1, P12, P74, and P200. Over 6,000 novel ESTs were identified in the libraries derived from these two sets of tissues, all of which have been contributed to the NCBI rat UniGene collection. It is anticipated that such EST and cDNA clone resources will prove invaluable to gene expression studies aimed at the understanding of the molecular mechanisms underlying heart septation defects.
Physiological Genomics 05/2004; 17(2):245-52. · 2.73 Impact Factor
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[show abstract]
[hide abstract]
ABSTRACT: The airway epithelium represents an important barrier between the host and the environment. It is a first site of contact with pathogens, particulates, and other stimuli, and has evolved the means to dynamically respond to these challenges. In an effort to define the transcript profile of airway epithelia, we created and sequenced cDNA libraries from cystic fibrosis (CF) and non-CF epithelia and from human lung tissue. Sequencing of these libraries produced approximately 53,000 3'-expressed sequence tags (3'-ESTs). From these, a nonredundant UniGene set of more than 19,000 sequences was generated. Despite the relatively small contribution of airway epithelia to the total mass of the lung, focused gene discovery in this tissue yielded novel results. The ESTs included several thousand transcripts (6,416) not previously identified from cDNA sequences as expressed in the lung. Among the abundant transcripts were several genes involved in host defense. Most importantly, the set also included 879 3'-ESTs that appear to be novel sequences not previously represented in the National Center for Biotechnology Information UniGene collection. This UniGene set should be useful for studies of pulmonary diseases involving the airway epithelium including cystic fibrosis, respiratory infections and asthma. It also provides a reagent for large-scale expression profiling.
Physiological Genomics 04/2004; 17(1):69-77. · 2.73 Impact Factor
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Todd E Scheetz,
Jennifer J Laffin,
Brian Berger,
Sara Holte,
Susan A Baumes,
Robert Brown,
Shereen Chang,
Justin Coco,
Jim Conklin,
Keith Crouch, [......],
Michael Smith,
Dylan Tack,
Nishank Trivedi, Tamara Kucaba,
Tom Freeman,
Jim J-C Lin,
Maria F Bonaldo,
Thomas L Casavant,
Val C Sheffield,
M Bento Soares
[show abstract]
[hide abstract]
ABSTRACT: The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3' ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to approximately 50,000 rat UniGene clusters. We have identified, arrayed, and derived 5' ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI.
Genome Research 04/2004; 14(4):733-41. · 13.61 Impact Factor
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Methods in molecular biology (Clifton, N.J.) 02/2004; 255:143-56.
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Christopher K Tuggle,
Jon A Green,
Carolyn Fitzsimmons,
Rami Woods,
Randall S Prather,
Sergei Malchenko,
Bento M Soares, Tamara Kucaba,
Keith Crouch,
Christina Smith, [......],
Natalie Robinson,
Brian O'Leary,
Todd Scheetz,
Thomas Casavant,
Daniel Pomp,
Brad J Edeal,
Yuandan Zhang,
Max F Rothschild,
Kevin Garwood,
William Beavis
[show abstract]
[hide abstract]
ABSTRACT: A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3' end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.
Mammalian Genome 09/2003; 14(8):565-79. · 2.89 Impact Factor
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Todd E Scheetz,
Nishank Trivedi,
Chad A Roberts, Tamara Kucaba,
Brian Berger,
Natalie L Robinson,
Clayton L Birkett,
Allen J Gavin,
Brian O'Leary,
Terry A Braun,
Maria F Bonaldo,
John P Robinson,
Val C Sheffield,
Marcelo B Soares,
Thomas L Casavant
[show abstract]
[hide abstract]
ABSTRACT: High accuracy of data always governs the large-scale gene discovery projects. The data should not only be trustworthy but should be correctly annotated for various features it contains. Sequence errors are inherent in single-pass sequences such as ESTs obtained from automated sequencing. These errors further complicate the automated identification of EST-related sequencing. A tool is required to prepare the data prior to advanced annotation processing and submission to public databases.
This paper describes ESTprep, a program designed to preprocess expressed sequence tag (EST) sequences. It identifies the location of features present in ESTs and allows the sequence to pass only if it meets various quality criteria. Use of ESTprep has resulted in substantial improvement in accurate EST feature identification and fidelity of results submitted to GenBank.
The program is freely available for download from http://genome.uiowa.edu/pubsoft/software.html
Bioinformatics 08/2003; 19(11):1318-24. · 5.47 Impact Factor
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Todd E. Scheetz,
Nishank Trivedi,
Chad A. Roberts, Tamara Kucaba,
Brian Berger,
Natalie L. Robinson,
Clayton L. Birkett,
Allen J. Gavin,
Brian O'Leary,
Terry A. Braun,
Maria F. Bonaldo,
John P. Robinson,
Val C. Sheffield,
Marcelo Bento Soares,
Thomas L. Casavant
Bioinformatics. 01/2003; 19:1318-1324.
