Analysis of angiogenesis using in vitro experiments and stochastic growth models.

The global properties of vascular networks grown with an in vitro angiogenesis assay are compared quantitatively, using automated image analysis, with the global properties of networks obtained with discrete, stochastic growth models. The model classes that are investigated are invasion percolation and diffusion limited aggregation. By matching global properties to experimental data, one can infer which model classes and parameters are most reflective of angiogenesis in experimental cells.

The SHREW1 gene, frequently deleted in oligodendrogliomas, functions to inhibit cell adhesion and migration.

Allelic loss of the short arm of chromosome 1 has been observed frequently in oligodendroglioma (60-80%). We evaluated 177 oligodendroglial tumor samples and defined a consensus region of deletion of approximately 630 kb. This region contains a single gene, SHREW1, which encodes a novel transmembrane protein in adherens junctions.

Attenuated expression of DFFB is a hallmark of oligodendrogliomas with 1p-allelic loss.

Allelic loss of chromosome 1p is frequently observed in oligodendroglioma. We screened 177 oligodendroglial tumors for 1p deletions and found 6 tumors with localized 1p36 deletions. Several apoptosis regulation genes have been mapped to this region, including Tumor Protein 73 (p73), DNA Fragmentation Factor subunits alpha (DFFA) and beta (DFFB), and Tumor Necrosis Factor Receptor Superfamily Members 9 and 25 (TNFRSF9, TNFRSF25).

Robust quantification of in vitro angiogenesis through image analysis.

An automated image analysis method for quantification of in vitro angiogenesis is presented. The method is designed for in vitro angiogenesis assays that are based on co-culturing endothelial cells with fibroblasts. Such assays are used in many current studies in which anti-angiogenic agents for the treatment of cancer are being sought.

In silico microdissection of microarray data from heterogeneous cell populations.

Background: Very few analytical approaches have been reported to resolve the variability in microarray measurements stemming from sample heterogeneity. For example, tissue samples used in cancer studies are usually contaminated with the surrounding or infiltrating cell types. This heterogeneity in the sample preparation hinders further statistical analysis, significantly so if different samples contain different proportions of these cell types.

Improving signal intensities for genes with low-expression on oligonucleotide microarrays.

Background: DNA microarrays using long oligonucleotide probes are widely used to evaluate gene expression in biological samples. These oligonucleotides are pre-synthesized and sequence-optimized to represent specific genes with minimal cross-hybridization to homologous genes. Probe length and concentration are critical factors for signal sensitivity, particularly when genes with various expression levels are being tested.

Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis.

Background: Metastatic disease is a major adverse prognostic factor in breast carcinoma. Lymph node metastases often represent the first step in the metastatic process.

Methods: To gain insight into the molecular events that underlie breast carcinoma metastasis, the authors compared gene expression profiles, obtained by cDNA microarray analysis, of nine matched primary tumors and metastases after screening for enrichment of tumor cells.

Increased yield of total RNA from fine-needle aspirates for use in expression microarray analysis.

Fine-needle aspirate samples hold the potential for gaining valuable insight into the molecular details and prognostic indicators for certain types of cancer in a limited volume of relatively pure tumor cells. Although limited, such clinical samples can be used with high efficiency when analyzed in conjunction with gene-dense expression microarrays. For this reason, it is essential to retrieve as much high-quality genetic material as possible from each fine-needle aspirate sample.

Clonal heterogeneity in mycosis fungoides and its relationship to clinical course.

Mycosis fungoides (MF) is a cutaneous T-cell lymphoma characterized by multifocal disease and protracted clinical course. The few studies that have assessed T-cell receptor (TCR) gene rearrangements (GRs) present at different anatomic sites in MF have generally reported a common clone. We used a previously validated 4-color polymerase chain reaction (PCR) assay to assess the size and V-family usage of TCR-gamma GRs in 102 concurrent and/or sequential morphologically involved biopsy specimens (91 skin and 11 lymph nodes) from 39 MF patients.

Genetic suppression analysis of an asgA missense mutation in Myxococcus xanthus.

The asgA gene is required for generation of extracellular A signal, which serves as a cell-density signal for fruiting body development in Myxococcus xanthus. The AsgA protein is a histidine protein kinase and consists of a receiver domain that is conserved among response regulators of two-component signal transduction systems, followed by a histidine protein kinase domain that is conserved among sensor proteins of two-component systems. AsgA is thought to function in a signal transduction pathway that leads to expression of genes required for A-signal generation.