Relationship of gene expression and chromosomal abnormalities in colorectal cancer.

Several studies have verified the existence of multiple chromosomal abnormalities in colon cancer. However, the relationships between DNA copy number and gene expression have not been adequately explored nor globally monitored during the progression of the disease. In this work, three types of array-generated data (expression, single nucleotide polymorphism, and comparative genomic hybridization) were collected from a large set of colon cancer patients at various stages of the disease.

Identification of a proliferation gene cluster associated with HPV E6/E7 expression level and viral DNA load in invasive cervical carcinoma.

Specific HPV DNA sequences are associated with more than 90% of invasive carcinomas of the uterine cervix. Viral E6 and E7 oncogenes are key mediators in cell transformation by disrupting TP53 and RB pathways. To investigate molecular mechanisms involved in the progression of invasive cervical carcinoma, we performed a gene expression study on cases selected according to viral and clinical parameters.

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices.

Summary: We introduce a novel unsupervised approach for the organization and visualization of multidimensional data. At the heart of the method is a presentation of the full pairwise distance matrix of the data points, viewed in pseudocolor. The ordering of points is iteratively permuted in search of a linear ordering, which can be used to study embedded shapes.

Budding and tubulation in highly oblate vesicles by anchored amphiphilic molecules.

We studied local budding and tubulation induced in highly oblate lipid vesicles by the anchoring of either polymers having a hydrophilic backbone and grafted hydrophobic anchor groups, or by oleoyl-coenzyme A, an amphiphilic molecule important in lipid metabolism. The dynamics of bud formation, shrinkage, and readsorption is consistent with an induced spontaneous curvature coupled with local amphiphile diffusion on the membrane. We report a novel metastable state prior to bud readsorption.

Coiling instability of multilamellar membrane tubes with anchored polymers.

We study experimentally a coiling instability of cylindrical multilamellar stacks of phospholipid membranes, induced by polymers with hydrophobic anchors grafted along their hydrophilic backbone. Our system is unique in that coils form in the absence of both twist and adhesion. We interpret our experimental results in terms of a model in which local membrane curvature and polymer concentration are coupled.