SC²ATmd: a tool for integration of the figure of merit with cluster analysis for gene expression data

Standard and Consensus Clustering Analysis Tool for Microarray Data (SC2ATmd) is a MATLAB-implemented application specifically designed for the exploration of microarray gene expression data via clustering. Implementation of two versions of the clustering validation method figure of merit allows for performance comparisons between different clustering algorithms, and tailors the cluster analysis process to the varying characteristics of each dataset. Along with standard clustering algorithms this application also offers a consensus clustering method that can generate reproducible clusters across replicate experiments or different clustering algorithms. This application was designed specifically for the analysis of gene expression data, but may be used with any numerical data as long as it is in the right format. AVAILABILITY: SC2ATmd may be freely downloaded from http://www.compbiosci.wfu.edu/tools.htm.     

Redox control of gene expression and the function of chloroplast genomes — an hypothesis

Two-component regulatory systems that respond to changes in redox potential have recently been discovered in bacteria. Redox sensors are defined as electron carriers which initiate control of gene expression upon oxidation or reduction. Redox response regulators are defined as DNA-binding proteins which modify gene expression as a result of the action of redox sensors. Redox sensors and redox response regulators may comprise a mechanism for feedback control of redox potential in photosynthetic electron transport chains, thereby protecting plants, algae and photosynthetic bacteria from damage caused by electrochemistry operating on inappropriate electron donors and acceptors. Chloroplast redox sensors and redox response regulators, themselves encoded in the nucleus, may place chloroplast gene expression under redox regulatory control. This may account for the persistence, in evolution, of chloroplast genomes, and for the constancy of the sub-set of chloroplast proteins encoded and synthesised in situ. These and other predictions are discussed.     

Genomic organization and refined mapping of the mouse β-dystrobrevin gene

β-Dystrobrevin, a dystrophin-related protein that is expressed in non-muscle tissues, is highly homologous to α-dystrobrevin, a member of the dystrophin-associated protein complex (DPC). β-Dystrobrevin associates with Dp71 and syntrophin and is believed to have a role in non-muscle DPCs. Here we report the characterization and mapping of the mouse β-dystrobrevin gene. The mouse β-dystrobrevin gene is organized into 21 exons spanning over 130 kb of DNA. We provide evidence that this gene is transcribed from at least two promoter regions but appears to utilize a common translation initiation site. We show that the similarity between β-dystrobrevin and α-dystrobrevin is reflected in the conservation of their exon-intron junctions. β-Dystrobrevin has been localized to proximal mouse Chromosome (Chr) 12 by backcross mapping. A database search revealed that two mouse genetic diseases involving tissues expressing β-dystrobrevin have been mapped to this region, namely, congenital polycystic kidneys (cpk) and fatty liver dystrophy (fld). However, refined mapping analysis has excluded β-dystrobrevin as a candidate gene for either disease. Received: 1 June 1998 / Accepted: 16 July 1998     

Subunit structure and gene control of mouse NADP—malate dehydrogenase

The NADP-dependent malate dehydrogenase (MDH) in the supernatant fraction of mouse tissues is known to occur in two allelic forms which are electrophoretically distinguishable; each produces a single band in starch gel. We have investigated the subunit structure and synthesis of NADP—MDH through electrophoretic patterns obtained from several experimental sources. (1) Heterozygotes containing both alleles yield a five-banded pattern. The bands are in an approximate frequency of 1:4:6:4:1; the two extremes correspond to the pure types and the three intermediates are presumably hybrid enzymes. The NADP—MDH molecule therefore appears to be a tetramer. (2) In muscle heterokaryons of allophenic mice (with homozygous nuclei of each genotype within a common cytoplasm), hybrid enzymes are formed; they are not formed in other allophenic tissues. Therefore the gene at this locus codes only for monomeric subunits and the tetramer is assembled in a second step in the cytoplasm. Also, both genes must function in a nucleus when the locus is active (e.g., in F₁ uninucleated cells). (3) Dissociation in vitro of mixtures of both pure types of enzymes, followed by reassociation among fragments, leads to a three-banded pattern, even after repeated cycles. Thus the tetramer must cleave in a fixed plane, to form dimers, which reassociate, rather than in a random fashion to form monomers. The most likely interpretation is that mouse NADP—MDH is an example of the type of tetramer postulated by Monod et al. (1965) and termed isologous. The dimers are held symmetrically in the tetrameric conformation by relatively weak forces; the monomeric subunits comprising the dimer are held together by stronger forces.These investigations were supported by U.S.P.H.S. grants No. HD-01646, CA-06927, and FR-05539, and by an appropriation from the Commonwealth of Pennsylvania.     

Microenvironment-regulated gene expression,morphology, and in vivo performance of mouse pancreatic β-cells

Cell behavior is determined by intrinsic characteristics and complex interactions with microenvironments. This study demonstrated the performance of a murine pancreatic β-cell line, MIN-6, cultured on tissue-culture polystyrene (TCPS), gelatin, type I collagen, and type IV collagen dishes. MIN-6 cells aggregated as clusters on gelatin, type I collagen, and type IV collagen, which was different from the epithelial morphology of cells grown on TCPS. The diameter and survival rate of aggregated cells did not differ significantly regardless of whether the cells were grown on gelatin or type I collagen, while smaller clusters were observed on type IV collagen. Compared with the monolayers on TCPS, the clusters had a higher insulin stimulation index. The mRNA expression levels of Ins1, Pdx-1, NeuroD1 and connexin 36 were upregulated in clusters relative to monolayers. Conversely, E-cadherin and MafA were downregulated when cells were grown on type IV collagen. Monolayers or cell aggregates grown on type IV collagen were subsequently transplanted into diabetic C57BL/6 mice. Animals that received both monolayers and clusters had decreased blood glucose levels and regained body weight. However, the area under curve for the intraperitoneal glucose tolerance test showed that clusters exhibited superior in vivo performance. This study reveals that a type IV collagen substrate promotes β-cell clustering, regulates gene expression and enhances in vivo performance.     

Cloning and expression of the 3′ portion of the T4 denV gene as a lacZ fusion gene

Polyclonal antibodies have been raised against endonuclease V from the bacteriophage T4. This rabbit serum, from which endemic E. coli antibodies have been removed, reacts with a single protein from T4-infected E. coli with a molecular weight of 16078 dalton. It was confirmed that these antibodies were directed against endonuclease V through the inhibition of the pyrimidine dimer specific nicking activity of endonuclease V in an in vitro nicking assay. A phage λgt11 T4 dC DNA library was screened for phage which produced a β-galactosidase-endonuclease V fusion protein. Immunopositive clones were detected at a frequency of 0.25 % of the plaques in the library. Restriction enzyme analyses of the DNA from 45 of these phage showed that all contained a 1.8 kb T4 EcoRI fragment which had been inserted within λgt11 in a single orientation. Western analysis of proteins which were produced from an induction of lysogens made from these phage reveals a single fusion protein band with a molecular weight slightly larger than native β-galactosidase.     

Do changes in gene expression contribute to sexual isolation and reinforcement in the house mouse?

Expression divergence, rather than sequence divergence, has been shown to be important in speciation, particularly in the early stages of divergence of traits involved in reproductive isolation. In the two European subspecies of house mice, Mus musculus musculus and Mus musculus domesticus, earlier studies have demonstrated olfactory‐based assortative mate preference in populations close to their hybrid zone. It has been suggested that this behaviour evolved following the recent secondary contact between the two taxa (~3,000 years ago) in response to selection against hybridization. To test for a role of changes in gene expression in the observed behavioural shift, we conducted a RNA sequencing experiment on mouse vomeronasal organs. Key candidate genes for pheromone‐based subspecies recognition, the vomeronasal receptors, are expressed in these organs. Overall patterns of gene expression varied significantly between samples from the two subspecies, with a large number of differentially expressed genes between the two taxa. In contrast, only ~200 genes were found repeatedly differentially expressed between populations within M. m. musculus that did or did not display assortative mate preferences (close to or more distant from the hybrid zone, respectively), with an overrepresentation of genes belonging to vomeronasal receptor family 2. These receptors are known to play a key role in recognition of chemical cues that handle information about genetic identity. Interestingly, four of five of these differentially expressed receptors belong to the same phylogenetic cluster, suggesting specialization of a group of closely related receptors in the recognition of odorant signals that may allow subspecies recognition and assortative mating.     

Biodiesel production—current state of the art and challenges

Biodiesel is a clean-burning fuel produced from grease, vegetable oils, or animal fats. Biodiesel is produced by transesterification of oils with short-chain alcohols or by the esterification of fatty acids. The transesterification reaction consists of transforming triglycerides into fatty acid alkyl esters, in the presence of an alcohol, such as methanol or ethanol, and a catalyst, such as an alkali or acid, with glycerol as a byproduct. Because of diminishing petroleum reserves and the deleterious environmental consequences of exhaust gases from petroleum diesel, biodiesel has attracted attention during the past few years as a renewable and environmentally friendly fuel. Since biodiesel is made entirely from vegetable oil or animal fats, it is renewable and biodegradable. The majority of biodiesel today is produced by alkali-catalyzed transesterification with methanol, which results in a relatively short reaction time. However, the vegetable oil and alcohol must be substantially anhydrous and have a low free fatty acid content, because the presence of water or free fatty acid or both promotes soap formation. In this article, we examine different biodiesel sources (edible and nonedible), virgin oil versus waste oil, algae-based biodiesel that is gaining increasing importance, role of different catalysts including enzyme catalysts, and the current state-of-the-art in biodiesel production. JIMB 2008: BioEnergy—special issue.