Gene rearrangements in human T-cells

One of the most basal requirements of the immune system is that it must be capable of specifically recognizing and responding to foreign antigens, while remaining indifferent to self-components. For T-cells the antigen recognizing function is fulfilled by the TcR. Because of the stochastic nature of antigen receptor formation, selection for appropriate TeR is needed. These selection processes take place in the thymus, presumably in complex interactions with the thymic stromal cells. Negative selection (clonal deletion) prevents self-reactive T-cells from becoming auto-aggressive. Positive selection (clonal selection) prevents the accumulation of useless T-cells with either no antigen receptor at all, or with for the organism useless receptors

Integrating heterogeneous sequence information for transcriptome-wide microarray design; a Zebrafish example

BACKGROUND: A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous sequence information that can be used as input for an up-to-date microarray design. FINDINGS: Our algorithm consists of four steps. In the first step transcripts from different resources are grouped into Transcription Clusters (TCs) by looking at the similarity of all transcripts. TCs are groups of transcripts with a similar length. If a transcript is much smaller than a TC to which it is highly similar, it will be annotated as a subsequence of that TC and is used for probe design only if the probe designed for the TC does not query the subsequence. Secondly, all TCs are mapped to a genome assembly and gene information is added to the design. Thirdly TC members are ranked according to their trustworthiness and the most reliable sequence is used for the probe design. The last step is the actual array design. We have used this strategy to build an up-to-date zebrafish microarray. CONCLUSIONS: With our strategy and the software developed, it is possible to use a set of heterogeneous transcript resources for microarray design, reduce the number of candidate target sequences on which the design is based and reduce redundancy. By changing the parameters in the procedure it is possible to control the similarity within the TCs and thus the amount of candidate sequences for the design. The annotation of the microarray is carried out simultaneously with the design

Site-specific deletions involving the tal-1 and sil genes are restricted to cells of the T cell receptor alpha/beta lineage: T cell receptor delta gene deletion mechanism affects multiple genes

Site-specific deletions in the tal-1 gene are reported to occur in 12-26% of T cell acute lymphoblastic leukemias (T-ALL). So far two main types of tal-1 deletions have been described. Upon analysis of 134 T-ALL we have found two new types of tal-1 deletions. These four types of deletions juxtapose the 5' part of the tal-1 gene to the sil gene promoter, thereby deleting all coding sil exons but leaving the coding tal-1 exons undamaged. The recombination signal sequences (RSS) and fusion regions of the tal-1 deletion breakpoints strongly resemble the RSS and junctional regions of immunoglobulin/T cell receptor (TCR) gene rearrangements, which implies that they are probably caused by the same V(D)J recombinase complex. Analysis of the 134 T-ALL suggested that the occurrence of tal-1 deletions is associated with the CD3 phenotype, because no tal-1 deletions were found in 25 TCR-gamma/delta + T-ALL, whereas 8 of the 69 CD3- T-ALL and 11 of the 40 TCR-alpha/beta + T-ALL contained such a deletion. Careful examination of all TCR genes revealed that tal-1 deletions exclusively occurred in CD3- or CD3+ T-ALL of the alpha/beta lineage with a frequency of 18% in T-ALL with one deleted TCR-delta allele, and a frequency of 34% in T-ALL with TCR-delta gene deletions on both alleles. Therefore, we conclude that alpha/beta lineage commitment of the T-ALL and especially the extent of TCR-delta gene deletions determines the chance of a tal-1 deletion. This suggests that tal-1 deletions are mediated via the same deletion mechanism as TCR-delta gene deletions

Genome sequences of 10 new carnation mottle virus variants

Here, we report the genome sequences of 10 Carnation mottle virus variants. Six variants originated from a single proprietary carnation cultivar, and four were derived from four different proprietary cultivars. All variants showed nucleotide differences, but the last four did not show any variation at the amino acid level