Bernard W Futscher

PMID: 17674622;Abstract:

High dimensionality has been a major problem for gene array-based cancer classification. It is critical to identify marker genes for cancer diagnoses. We developed a framework of gene selection methods based on previous studies. This paper focuses on optimal search-based subset selection methods because they evaluate the group performance of genes and help to pinpoint global optimal set of marker genes. Notably, this paper is the first to introduce tabu search (TS) to gene selection from high-dimensional gene array data. Our comparative study of gene selection methods demonstrated the effectiveness of optimal search-based gene subset selection to identify cancer marker genes. TS was shown to be a promising tool for gene subset selection. © 2007 IEEE.

PMID: 1548483;Abstract:

Although immediate cholinergic deficits produced by AF64A can be explained adequately by inhibition of enzymes involved in acetylcholine metabolism, the structural similarity of AF64A to a number of DNA-damaging antitumor agents suggested that the observed long-term cholinergic deficits may involve damage to the cell's informational molecules. This study was initiated to determine if AF64A can damage DNA and prematurely terminate RNA transcription in vitro, and to produce cytotoxic and DNA damaging effects in cells exposed to the drug in vivo. The ability of AF64A to produce N-7 guanine alkylations in DNA in vitro was assessed using a modified Maxam and Gilbert DNA sequencing technique, and the ability of AF64A to terminate RNA transcription was assessed by an in vitro RNA transcription system. AF64A was capable of producing extensive dose-dependent N-7 guanine alkylations in DNA fragments exposed to AF64A in vitro, although no sequence specificity of AF64A attack could be discerned. Furthermore, AF64A was able to produce RNA transcription-terminating lesions in vitro, also in a dose-dependent fashion. Transcription of AF64A-damaged DNA resulted in RNA molecules terminated not at every alkylated guanine, but at various discrete sites along the DNA template. AF64A was also found to be cytotoxic in a dose-dependent manner in cultured mouse leukemia L1210 cells. The induced cytotoxicity was accompanied by DNA lesions which were detected as DNA single strand breaks using the DNA alkaline elution technique. The results of these experiments support the hypothesis that AF64A may alter the structure and function of cellular DNA and may help explain the observed long-term cholinergic deficits.

PMID: 24024150;PMCID: PMC3757676;Abstract:

Manganese superoxide dismutase, encoded by the Sod2 gene, is a ubiquitously expressed mitochondrial antioxidant enzyme that is essential for mammalian life. Mice born with constitutive genetic knockout of Sod2 do not survive the neonatal stage, which renders the longitudinal study of the biochemical and metabolic effects of Sod2 loss difficult. However, multiple studies have demonstrated that tissue-specific knockout of Sod2 in murine liver yields no observable gross pathology or injury to the mouse. We hypothesized that Sod2 loss may have sub-pathologic effects on liver biology, including the acquisition of reactive oxygen species-mediated mitochondrial DNA mutations. To evaluate this, we established and verified a hepatocyte-specific knockout of Sod2 in C57/B6 mice using Cre-LoxP recombination technology. We utilized deep sequencing to identify possible mutations in Sod2 mitochondrial DNA as compared to wt, and both RT-PCR and traditional biochemical assays to evaluate baseline differences in redox-sensitive pathways in Sod2^-/- hepatocytes. Surprisingly, no mutations in Sod2^-/- mitochondrial DNA were detected despite measurable increases in dihydroethidium staining in situ and concomitant decreases in complex II activity indicative of elevated superoxide in the Sod2^-/- hepatocytes. In contrast, numerous compensatory alterations in gene expression were identified that suggest hepatocytes havea remarkable capacity to adapt and overcome the loss of Sod2 through transcriptional means. Taken together, these results suggest that murine hepatocytes have a large reserve capacity to cope with the presence of additional mitochondrial reactive oxygen species. © 2013 The Authors.

PMID: 1352887;PMCID: PMC49508;Abstract:

An activated Ha-ras oncogene has been consistently found in chemically initiated benign and malignant mouse skin tumors, and an activated ras oncogene has been shown to initiate the process of mouse skin carcinogenesis. However, the exact timing of mutational activation of the Ha-ras gene relative to application of the chemical carcinogen is not known. A sensitive mutation-specific PCR technique was used to experimentally address the timing of Ha-ras gene mutational activation. This technique can detect mutant Ha-ras alleles in the presence of a very large excess of normal ras alleles. Activated Ha-ras genes with 61st codon A → T mutations were found in the epidermis of mice 1 week after topical initiation with 7,12-dimethylbenz[a]anthracene or urethane by using this assay. These results were confirmed by Xba I restriction fragment length polymorphism analysis and direct DNA sequencing. One week after initiation is 1-2 months before the appearance of benign papillomas that harbor activated Ha-ras oncogenes when the initiated mice are promoted with the tumor promoter phorbol 12-myristate 13-acetate. Our data support the hypothesis that initiated epidermal cells containing an activated Ha-ras gene can remain dormant in the skin until a tumor promoter induces regenerative hyperplasia that allows for outgrowth of these cells with an activated ras oncogene to give rise to a benign papilloma.