Given a phylogenetic tree involving Whole Genome Duplication events, we contribute to the problem of computing the rearrangement distance on a branch of a tree linking a duplication node d to a speciation node or a leaf s. In the case of a genome G at s containing exactly two copies of each gene, the genome halving problem is to find a perfectly duplicated genome D at d minimizing the rearrange...

The genome rearrangement problem is to find the most economical explanation for observed differences between the gene orders of two genomes. Such an explanation is provided in terms of events that change the order of genes in a genome. We present a new approach to the genome rearrangement problem, according to which this problem is viewed as the problem of planning rearrangement events that tra...

Synovial sarcomas are aggressive tumors of adolescent and young adults that account for up to 10% of soft tissue sarcomas. Cytogenetically, they are characterized by translocation t(X;18), which is found in more than 95% of tumors. In most cases, it results in fusion of the SYT gene with the SSX1 or SSX2 gene, thus creating SYT-SSX1 or SYT-SSX2 rearrangement. The 2 types of gene fusion have bee...

Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic...

Group A rotaviruses are the main cause of viral gastroenteritis in infants. The viral genome consists of 11 double-stranded RNA (dsRNA) segments. Dysfunction of the viral RNA polymerase can lead to gene rearrangements, which most often consist of partial sequence duplication of a dsRNA segment. Gene rearrangements have been detected in vivo during chronic infection in immunodeficient children o...

The genes encoding the variable (V) region of the B-cell antigen receptor (BCR) are assembled from V, D (diversity), and J (joining) elements through a RAG-mediated recombination process that relies on the recognition of recombination signal sequences (RSSs) flanking the individual elements. Secondary V(D)J rearrangement modifies the original Ig rearrangement if a nonproductive original joint i...

PURPOSE To identify mucosa-associated lymphoid tissue (MALT) type lymphoma in conjunctival infiltrates. METHODS Clinical, histopathologic, immunophenotypic, and immunogenotypic studies were performed on 14 patients with conjunctival lymphoid infiltrates. Surgical biopsy specimens were subjected to histopathologic, immunohistochemical, and gene rearrangement analysis. RESULTS Thirteen of the...

We report a molecular analysis of the chicken Ig loci in single bursal follicles from 3- to 7-week-old chickens. Each follicle contained between 10(5) and 3 X 10(5) cells. The Ig gene rearrangement patterns obtained were compared to the pattern observed with the corresponding total bursal DNA. The results obtained for the light chain locus imply that a very small number (two on average) of rear...

Our previous studies of the translocated MYC gene in Burkitt's lymphoma showed the existence of clustered somatic mutations located in the transcriptional activation domain. We now report that aggressive lymphomas arising in the acquired immunodeficiency syndrome (AIDS) contain similar mutations and that the presence of mutations is correlated with the rearrangement of the oncogene. Mutations w...

The nivea (niv) gene of Antirrhinum majus encodes chalcone synthase, an enzyme involved in synthesis of anthocyanin pigments. The nivfeC:98 allele contains a single copy of the transposon Tamd inserted at the niv locus. A large chromosomal rearrangement derived from this mutant has been shown to be flanked by two copies of Tam3. In this study, we compared sequences involved in this rearrangemen...