Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts

BACKGROUND: The Solanaceae is a family of closely related species with diverse phenotypes that have been exploited for agronomic purposes. Previous studies involving a small number of genes suggested sequence conservation across the Solanaceae. The availability of large collections of Expressed Sequence Tags (ESTs) for the Solanaceae now provides the opportunity to assess sequence conservation and divergence on a genomic scale. RESULTS: All available ESTs and Expressed Transcripts (ETs), 449,224 sequences for six Solanaceae species (potato, tomato, pepper, petunia, tobacco and Nicotiana benthamiana), were clustered and assembled into gene indices. Examination of gene ontologies revealed that the transcripts within the gene indices encode a similar suite of biological processes. Although the ESTs and ETs were derived from a variety of tissues, 55–81% of the sequences had significant similarity at the nucleotide level with sequences among the six species. Putative orthologs could be identified for 28–58% of the sequences. This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species. 16–19% of the transcripts within the six Solanaceae gene indices did not have matches among Solanaceae, Arabidopsis, rice or 21 other plant gene indices. CONCLUSION: Results from this genome scale analysis confirmed a high level of sequence conservation at the nucleotide level of the coding sequence among Solanaceae. Additionally, the results indicated that part of the Solanaceae transcriptome is likely to be unique for each species

The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

Antirheumatic agents: CNS toxicity and its avoidance.

Altered drug metabolism, polypharmacy, multiple diseases, and errors in self-medication are all factors seen in the elderly which increase the risk for side effects from antirheumatic drug therapy. The geriatric presentation of central nervous system (CNS) toxicity, which is common yet frequently overlooked, is reviewed as it pertains to various drugs commonly used to treat rheumatic disease. Practical advice on avoiding common pitfalls in antirheumatic prescribing is offered

Plate-assisted Lengthening of the Femur and Tibia in Pediatric Patients.

BACKGROUND: Limb lengthening over a percutaneous plate can be used during pediatric distraction osteogenesis to decrease the time of external fixation. METHODS: A retrospective, consecutive 2-surgeon experience of pediatric femoral and tibial lengthenings with a plate-assisted lengthening (PAL) technique was performed. The plate was placed at the time of index corticotomy. The primary outcome measures of external fixation index, consolidation index, and complications were assessed for each lengthening. RESULTS: From 2005 to 2012, 38 lengthenings (23 femur, 15 tibia) in 30 patients were performed by a PAL technique. All patients experienced successful distraction and consolidation. The average achieved lengthening was 3.80±0.98 cm (range, 2.2 to 6.4) with an average consolidation index of 27 days/cm and a mean external fixation index of 13.1±4.29 days/cm (range, 7.8 to 30). Patients returned to full weight-bearing activity after an average of 98.3±28.5 days. There were an average of 1.08±1.05 total complications and 0.39±0.75 severe complications per lengthening. Complications were encountered most commonly during femoral lengthening, including procurvatum and varus deformity through the regenerate. These deformities were usually corrected by frame adjustment before removal. CONCLUSIONS: PAL is a safe technique that minimizes time of external fixation, accelerates rehabilitation and weight-bearing, and can be successfully used on the femur or tibia. The most common complications are angular deformities of the regenerate that can be treated with adjustment before or at the time of plate locking. LEVEL OF EVIDENCE: Level IV-retrospective case series