Laboratory of Molecular Biology

About: Laboratory of Molecular Biology is a facility organization based out in Cambridge, Cambridgeshire, United Kingdom. It is known for research contribution in the topics: Gene & RNA. The organization has 19395 authors who have published 24236 publications receiving 2101480 citations.

Automation of the computer handling of gel reading data produced by the shotgun method of DNA sequencing.

Abstract: This paper describes a computer method for handling gel reading data produced by the shotgun method of DNA sequencing. The method greatly reduces the time the sequencer needs to spend checking and editing his data and yet it produces a consensus sequence for which the accuracy of determination of every base can be clearly shown. The program can take a batch of new gel readings, screen them against vector sequences removing any that match, and then compare and align all the sequences to produce a final consensus. No information is lost in this process as alignments are achieved by making only insertions and because all the individual gel readings are added to a database from which they can be retrieved and displayed lined up one above the other. This allows the user to check on the alignments achieved by the program and if necessary change them. As each gel reading is added to the database the consensus is automatically updated accordingly and used for the next comparisons. This is a much faster process than comparing each new gel against every individual gel in the database.

High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma.

Abstract: In a recent issue of Genes, Chromosomes & Cancer, van den Berg et al. (2003) reported on the high expression of human BIC RNA in Hodgkin lymphoma by means of the serial analysis of gene expression (SAGE) technique. In addition, using a combination of RNA in situ hybridization and immunostaining, they found that the expression of BIC is specific for Reed–Sternberg (RS) cells and that the BIC transcripts were in the nuclei of the RS cells. In contrast to their findings in Hodgkin lymphoma, an analysis of 43 cases of non-Hodgkin lymphoma (NHL; 15 follicular lymphomas, 7 diffuse large B-cell lymphomas, 9 Burkitt lymphomas, 7 anaplastic large cell lymphomas, and 5 T-cell-rich B-cell lymphomas) did not reveal any remarkable up-regulation of BIC expression, although one case of Burkitt lymphoma (BL) showed weak expression of BIC in a minority of its tumor cells. The BIC locus was originally identified as a common retroviral integration site in avian-leukosis virus–induced B–cell lymphomas (Clurman and Hayward, 1989; Tam et al., 1997). It should be stressed that the human BIC gene encodes a microRNA, miR-155. This microRNA is encoded by nucleotides 241–262 of BIC, which spans 1,421 bp in total and is on chromosome 21 (GenBank accession number: AF402776). MicroRNAs (miRNAs) are an abundant class of noncoding RNAs that interact with coding mRNA and trigger either translation repression or direct RNA cleavage via RNA interference, depending on the degree of complementarity with the specific target mRNA (Ambros, 2001; Lagos-Quintana et al., 2001; Ruvkun, 2001; Lai, 2002; Pasquinelli, 2002; Ambros et al., 2003; Lagos-Quintana et al., 2003). Mature miRNAs are 21–23 nt long and are excised from an approximately 60to 80-nt double-stranded RNA hairpin by Dicer RNase III (Hutvagner et al., 2001). In the last 2 years, more than 200 human microRNA genes have been described, but the prediction and validation of their target mRNAs by computerized means and experimental approaches is a tantalizing and still unresolved task (Ambros et al., 2003). Apart from this open question, it was recently hypothesized that microRNA genes might play an important role in oncogenesis (McManus, 2003). We support the idea advanced by van den Berg et al. that BIC might play a role in the selection of B cells, but here we also extend their data by demonstrating that miR-155/BIC is highly expressed in pediatric BL but not in other hematologic malignancies, for example, pre-B/common or T-cell leukemia. The conditio sine qua non for the development of BL is activation of the MYC oncogene, mostly by chromosomal translocations in which MYC is juxtaposed to an immunoglobulin enhancer. On the other hand, there is a body of evidence that the activation of MYC alone is not sufficient for full malignancy. Providing support for this contention was the demonstration that MYC cooperates with BMI1, PIM1, RAF, BCL2, or, as shown in a very recent report, with the Werner syndrome protein WRN (Grandori et al., 2003) We analyzed tumor cells from 21 children (ages 2–13 years, with a median age of 6 years) with BL (n 11), common/pre-B acute lymphoblastic leukemia (ALL; n 6), or T-cell ALL (n 4). In all cases selected, the proportion of tumor cells was 80% or greater. The presence of an IGH/MYC rearrangement was demonstrated by long-distance polymerase chain reaction (PCR) in all BL cases, whereas neither the common/pre-B nor T-cell ALLs had such a recombination (Busch et al., unpublished data). All patients were treated according to the NHL-BFM 90, 95, or the ALL-BFM 90, 95 multicenter therapy study (Reiter et al., 1999; Schrappe et al., 2000). Immunophenotyping was done according to standard procedures (Ludwig et al., 1994). Informed parental consent was obtained in all cases. RNA isolated from peripheral blood from 11 healthy volunteers served as an additional control.