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Tumor-suppressor genes (TSGs) have been classically defined as genes whose loss of function in tumor cells contributes to the formation and/or maintenance of the tumor phenotype. TSGs containing nonsense mutations may not be expressed because of nonsense-mediated RNA decay (NMD). We combined inhibition of the NMD process, which clears transcripts that contain nonsense mutations, with the application of high-density single-nucleotide polymorphism arrays analysis to discriminate allelic content in order to identify candidate TSGs in five breast cancer cell lines. We identified ARID1A as a target of NMD in the T47D breast cancer cell line, likely as a consequence of a mutation in exon-9, which introduces a premature stop codon at position Q944. ARID1A encodes a human homolog of yeast SWI1, which is an integral member of the hSWI/SNF complex, an ATP-dependent, chromatin-remodeling, multiple-subunit enzyme. Although we did not find any somatic mutations in 11 breast tumors, which show DNA copy-number loss at the 1p36 locus adjacent to ARID1A, we show that low ARID1A RNA or nuclear protein expression is associated with more aggressive breast cancer phenotypes, such as high tumor grade, in two independent cohorts of over 200 human breast cancer cases each. We also found that low ARID1A nuclear expression becomes more prevalent during the later stages of breast tumor progression. Finally, we found that ARID1A re-expression in the T47D cell line results in significant inhibition of colony formation in soft agar. These results suggest that ARID1A may be a candidate TSG in breast cancer.

This study presents a method for estimating the spatial variations in material properties of elastic membranes, such as biological tissue, which contain both inhomogeneous strain fields and inhomogeneous material properties. In order to validate the method, an inhomogeneous, isotropic rubber membrane was biaxially loaded to obtain a set of states. A neo-Hookean finite element model, together with the measured strains, was used to estimate the material parameters by minimizing the residuals between the measured and modelled residual on surface tractions.

A bacterial gene encoding hygromycin phosphotransferase has been modified for expression in tobacco cells. The aphIV gene from Escherichia coli was inserted between the 5' sequence of an octopine synthase gene and the 3' sequence from a nopaline synthase gene. The new gene was incorporated between T-DNA border fragments in the broad-host-range vector pKT210 to form a micro-Ti plasmid. Agrobacterium tumefaciens containing this plasmid and a Ti plasmid as helper was used to incite crown gall tumors on aseptic tobacco plants. Samples of these galls could grow in the presence of hygromycin B, provided that the aph gene had been fused with the ocs gene to maintain the sense of the coding sequences. When the genes had been fused in the reverse 'antisense' orientation none of the gall samples could grow on hygromycin. Unlike wild-type galls the hygromycin-resistant tissue contained DNA sequences homologous to the aphIV gene. Thus the modified gene can be introduced into tobacco cells and confer on them the ability to grow in the presence of hygromycin B.