A sequence based synteny map between soybean and Arabidopsis thaliana

BACKGROUND: Soybean (Glycine max, L. Merr.) is one of the world's most important crops, however, its complete genomic sequence has yet to be determined. Nonetheless, a large body of sequence information exists, particularly in the form of expressed sequence tags (ESTs). Herein, we report the use of the model organism Arabidopsis thaliana (thale cress) for which the entire genomic sequence is available as a framework to align thousands of short soybean sequences. RESULTS: A series of JAVA-based programs were created that processed and compared 341,619 soybean DNA sequences against A. thaliana chromosomal DNA. A. thaliana DNA was probed for short, exact matches (15 bp) to each soybean sequence, and then checked for the number of additional 7 bp matches in the adjacent 400 bp region. The position of these matches was used to order soybean sequences in relation to the A. thaliana genome. CONCLUSION: Reported associations between soybean sequences and A. thaliana were within a 95% confidence interval of e(-30 )– e(-100). In addition, the clustering of soybean expressed sequence tags (ESTs) based on A. thaliana sequence was accurate enough to identify potential single nucleotide polymorphisms (SNPs) within the soybean sequence clusters. An EST, bacterial artificial chromosome (BAC) end sequence and marker amplicon sequence synteny map of soybean and A. thaliana is presented. In addition, all JAVA programs used to create this map are available upon request and on the WEB

Protein Fingerprinting: A Domain-Free Approach to Protein Analysis

An alternative method for analyzing proteins is proposed. Currently, protein search engines available on the internet utilize domains (predefined sequences of amino acids) to align proteins. The method presented converts a protein sequence with the use of 1200 numeric codes that represent a unique three—amino-acid protein sequence. Each numeric code starts with one of three specific amino acids, followed by any two additional amino acids. With the use of the FPC (FingerPrinted Contig) program, the total protein database (including “redundant” records) from the National Center for Biotechnology Information (NCBI) has been processed and placed into “bins/contigs” based on associations of these triplet codes. When analyzed with FPC, proteins are “contigged” together based on the number of shared fragments, regardless of order. These associations were supported by additional analysis with the standard BLASTP utility from NCBI. Within the created contig sets, there are numerous examples of proteins (allotypes and orthotypes) that have evolved into different, seemingly unrelated proteins. The power of this domain-free technique has yet to be explored; however, the ability to bin proteins together with no a priori knowledge of domains may prove a powerful tool in the characterization of the hundreds of thousands of available, yet undescribed expressed protein and open reading frame sequences

Presence of intestinal intraepithelial lymphocytes in mice with severe combined immunodeficiency disease.

The murine intestinal epithelium contains a heterogeneous population of intraepithelial leukocytes (IEL) most of which are granulated, Thy-1-CD5-CD8+. In order to assess the lineage relationship of this subgroup of IEL to peripheral T cells, we examined IEL in mice with the severe combined immunodeficiency (scid/scid) mutation, which lack T and B cells in peripheral lymphoid tissues. Electron and light microscopy showed that the intestine from scid/scid mice had granulated IEL similar to IEL in normal C.B-17 mice. Flow cytometry of isolated IEL stained with monoclonal antibodies against Thy-1, CD3, CD4, CD5 and CD8 showed that scid/scid mice IEL contained cells with the Thy-1-CD4-CD5-CD8+ phenotype. Immunohistochemical staining of IEL in tissue sections with antibodies to Thy-1 and CD8 confirmed that the Thy-1-CD8+ cells were in the intestinal epithelium. These scid/scid IEL also lacked CD3 expression and mRNA for the V gamma 7 V region gene of the gamma T cell receptor. We conclude that scid/scid mice contain precursors for IEL that can differentiate into a granulated Thy-1-CD5-CD8+ IEL in the intestine. The absence of CD8+ peripheral T cells in these mice suggests that these IEL differ from classical T cells in their ability to differentiate and express CD8 and do not require T cell receptor expression for their localization to the intestine