Biomedical subjects

Jonathan Clarke

Publications and source records attributed to Jonathan Clarke.

5 recordsLinked to original sources

PubMed2006

SERRATE: a new player on the plant microRNA scene.

MicroRNAs (miRNAs) function as sequence-specific guides that control gene expression by post-transcriptional gene silencing. Many miRNAs influence plant development by regulating the accumulation of transcripts that encode transcription factors. Mutants defective in miRNA accumulation, such as dcl1, hen1, hyl1 and ago1, have pleiotropic developmental phenotypes. The serrate-1 (se-1) mutant of Arabidopsis also shows a highly pleiotropic phenotype, which overlaps with the phenotypes of mutants defective in miRNA accumulation. Although it has been proposed that SERRATE (SE) functions specifically in miRNA-mediated repression of the leaf polarity genes PHABULOSA and PHAVOLUTA, microarray analysis shows upregulation of many genes known to be the targets of miRNAs in se-1. We show that SE is a general regulator of miRNA levels affecting the processing of primary miRNA to miRNA.

Alleles↗

PubMed2006

High-frequency sonographic patterns of the spleen in children.

PURPOSE: To retrospectively evaluate the normal sonographic appearance of splenic parenchyma in children of various ages with high-frequency transducer sonography. MATERIALS AND METHODS: Research ethics committee board approval was obtained, with waiver of informed consent. We evaluated in vivo sagittal and transverse sonograms of spleens obtained with 13-MHz linear-array transducers in 100 children (age range, 1 day to 17 years) with clinically diagnosed disease that did not affect the lymphoid system. Three radiologists working in consensus defined the grading system for the splenic parenchyma. Thereafter, these same radiologists graded the sonographic reticulonodular pattern independently as granular, mild, or marked. These grades were cross correlated with clinical data by using logistic regression analysis and chi(2) tests. Sonographic measurements of the splenic parenchyma in nine pediatric cadavers separate from the in vivo cohort of the study were compared with those of corresponding histologic slices by means of linear correlation. RESULTS: Both grade 2 and grade 3 patterns occurred more frequently in children older than 1 year but no older than 5 years, whereas grade 1 pattern occurred most frequently in neonates (P < .001). As patients' age (odds ratio, 1.6; P < .001) and splenic dimensions (odds ratio, 3.1; P < .001) increased, the frequency with which the reticulonodular pattern was classified as either grade 2 or grade 3 increased. No association was noted between sonographic patterns and body mass index (P = .85) or sex (P = .07). The parenchymal nodules graded as 2 or 3 on sonograms correlated well with the presence of lymphoid follicles (white pulp) at histologic analysis (r = .71, P = .03). CONCLUSION: High-frequency transducer sonography of the spleen in children can demonstrate normal echo patterns that should not be misinterpreted as indicative of disease.

Adolescent↗

PubMed2005

Recent advances in trabeculectomy technique.

PURPOSE OF REVIEW: Trabeculectomy is an effective operation for lowering intraocular pressure. However, success is limited by complications such as infection, hypotony, and scarring. RECENT FINDINGS: These complications, which are increased by antifibrotic use, can be reduced with attention to surgical technique. We highlight the benefit of sub-Tenon anaesthesia, careful choice of the surgical site, fashioning of the scleral flap to produce diffuse aqueous flow, and better intraocular pressure control, maintenance of intraocular pressure, a formed anterior chamber, with outflow control during surgery using an infusion, optimal method of antimetabolites application, new adjustable sutures, and corneal-conjunctival closure techniques. SUMMARY: These techniques reduce hypotony, producing a diffuse noncystic bleb with long-term pressure control.

Glaucoma↗

PubMed2003

ATIDB: Arabidopsis thaliana insertion database.

Insertional mutagenesis techniques, including transposon- and T-DNA-mediated mutagenesis, are key resources for systematic identification of gene function in the model plant species Arabidopsis thaliana. We have developed a database (http://atidb.cshl.org/) for archiving, searching and analyzing insertional mutagenesis lines. Flanking sequences from approximately 10 500 insertion lines (including transposon and T-DNA insertions) from several tagging programs in Arabidopsis were mapped to the genome sequence through our annotation system before being entered into the database. The database front end provides World Wide Web searching and analyzing interfaces for genome researchers and other biologists. Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions. Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function. The database is based on open source components and is available under an open source license.

Amino Acid Sequence↗

PubMed2002

GARNet, the Genomic Arabidopsis Resource Network.

GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana. In addition, GARNet provides a platform for international Arabidopsis research and for research on other plant species. To use the GARNet facilities apply via the website: http://garnet.arabidopsis.org.uk. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases held at the Nottingham Arabidopsis Stock Centre and the John Innes Centre.

Arabidopsis↗