DNA sequencing by indexer walking

Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions

The phenomenon of contact-dependent growth inhibition (CDI) and the genes required for CDI (cdiBAI) were identified and isolated in 2005 from an Escherichia coli isolate (EC93) from rats. Although the cdiBAIEC93 locus has been the focus of extensive research during the past 15 years, little is known about the EC93 isolate from which it originates. Here we sequenced the EC93 genome and find two complete and functional cdiBAI loci (including the previously identified cdi locus), both carried on a large 127 kb plasmid. These cdiBAI systems are differentially expressed in laboratory media, enabling EC93 to outcompete E. coli cells lacking cognate cdiI immunity genes. The two CDI systems deliver distinct effector peptides that each dissipate the membrane potential of target cells, although the two toxins display different toxic potencies. Despite the differential expression and toxic potencies of these CDI systems, both yielded similar competitive advantages against E. coli cells lacking immunity. This can be explained by the fact that the less expressed cdiBAI system (cdiBAIEC93-2) delivers a more potent toxin than the highly expressed cdiBAIEC93-1 system. Moreover, our results indicate that unlike most sequenced CDI+ bacterial isolates, the two cdi loci of E. coli EC93 are located on a plasmid and are expressed in laboratory media.

Molecular monitoring of response to imatinib (Glivec) in chronic myeloid leukemia patients: experience at a tertiary care hospital in Saudi Arabia

AIM

The aim of this study was to evaluate the response and resistance of cases to chronic myeloid leukemia (CML) therapy with tyrosine kinase (TK) inhibitors (imatinib mesylate) and to search for mutations in the breakpoint cluster region (BCR)-Abelson murine leukemia (ABL) kinase domain prior to and during therapy.

METHODS

Molecular response was assessed with real-time quantitative reverse transcription-polymerase chain reaction and was expressed as the ratio between BCR-ABL and ABL (k562 cell line) x 100. In addition, we searched for mutations in BCR-ABL kinase domain by amplification and direct sequencing of cDNA products of archived RNA samples.

RESULTS

There were 85 cases of CML Philadelphia-chromosome-positive patients. Major molecular response [corrected] (MMR) of 0.05% was achieved in 40 (47%) of 85 patients and 3-log reduction was achieved in 37 (44%) after 6 months of imatinib therapy. When molecular monitoring was extended to 12 months in a subset of delayed responsive cases (17 cases) who did not achieve an MMR at 6 months, significant changes in BCR-ABL/ABL ratio were noticed. Fifteen de novo CML patients were started directly on treatment and were monitored for BCR-ABL/ABL ratio for a further period of up to 24 months. Their median of BCR-ABL/ABL ratio was 18% at diagnosis, 0.3% after 6 months, 0.2% after 12 months, and 0.01% after 18 and 24 months. Four (27%) of 15 patients achieved MMR as 3-log reduction after 6 months, 6 (40%) after 12 months, 9 (60%) after 18 months, and 7 (46%) after 24 months. No mutation(s) or polymorphism(s) were detected in all tested patients at diagnosis, at 6 months following imatinib and following 12 months for patients showing delayed response.

CONCLUSION

BCR-ABL mutations are rare in early chronic phase and increases with CML disease progression. Therefore, search for other causes in resistant cases at this phase should be sought.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome

BACKGROUND

Recent studies of the mammalian transcriptome have revealed a large number of additional transcribed regions and extraordinary complexity in transcript diversity. However, there is still much uncertainty regarding precisely what portion of the genome is transcribed, the exact structures of these novel transcripts, and the levels of the transcripts produced.

RESULTS

We have interrogated the transcribed loci in 420 selected ENCyclopedia Of DNA Elements (ENCODE) regions using rapid amplification of cDNA ends (RACE) sequencing. We analyzed annotated known gene regions, but primarily we focused on novel transcriptionally active regions (TARs), which were previously identified by high-density oligonucleotide tiling arrays and on random regions that were not believed to be transcribed. We found RACE sequencing to be very sensitive and were able to detect low levels of transcripts in specific cell types that were not detectable by microarrays. We also observed many instances of sense-antisense transcripts; further analysis suggests that many of the antisense transcripts (but not all) may be artifacts generated from the reverse transcription reaction. Our results show that the majority of the novel TARs analyzed (60%) are connected to other novel TARs or known exons. Of previously unannotated random regions, 17% were shown to produce overlapping transcripts. Furthermore, it is estimated that 9% of the novel transcripts encode proteins.

CONCLUSION

We conclude that RACE sequencing is an efficient, sensitive, and highly accurate method for characterization of the transcriptome of specific cell/tissue types. Using this method, it appears that much of the genome is represented in polyA+ RNA. Moreover, a fraction of the novel RNAs can encode protein and are likely to be functional.

Long PCR Product Sequencing (LoPPS): a shotgun-based approach to sequence long PCR products

Here we describe a practical procedure for sequencing long PCR products. The method relies on ultrasonic shearing of PCR products, resulting in fragments 700-1,000 nt long. Termini are subsequently repaired to obtain blunt ends and 3' A-overhangs are added before TA cloning. A predetermined number of clones are sequenced using an insert-independent primer to obtain an overlapping contig covering the full length of the PCR product. This method is cost effective and enables the complete sequencing of any large PCR product in a high-throughput format. Processing of amplified DNA requires 3 h handling time prior to the ligation step, and the clone library is available 2 d later. The complete sequence information is obtained approximately 5 d after the PCR step, depending on the sequencing procedure adopted.