Genetic analysis of enzyme polymorphisms in plaice (Pleuronectes platessa)

Genetic analysis was performed on five enzyme systems (G3PDH; GPI-A; GPI-B; PGM; MDH-A) in plaice (Pleuronectes platessa) collected in spawning condition from the North Sea. Conventional crosses, induced gynogenesis and induced triploidy were performed. The data conclusively demonstrated the inheritance of isozymes by co-dominant alleles at individual loci for each system. No linkage was observed but tests did not include MDH nor the possibility of linkage between G3PDH and GPI-A. Some anomalous segregation ratios were observed, particularly a deficiency of heterozygotes for GPI-A, but the data were largely in conformity with Mendelian expectations. At the PGM locus, five independent anomalous individuals were scored and interpreted as mutations with a mutation rate of 1·1 × 10−3 per gamete. Recombination with the centromere was assessed and induced triploidy and cross-over values of 41 per cent for PGM, 19 per cent for MDH-A and 9 per cent for GPI-B were derived on the assumption of complete interference. Amongst the parent fish, genotypic and phenotypic frequencies were largely consistent with the expectations of the Hardy-Weinberg Law, and allelic frequencies were not significantly different between year of collection or location of collection ground

Identifying differential exon splicing using linear models and correlation coefficients

Background: With the availability of the Affymetrix exon arrays a number of tools have been developed to enable the analysis. These however can be expensive or have several pre-installation requirements. This led us to develop an analysis workflow for analysing differential splicing using freely available software packages that are already being widely used for gene expression analysis. The workflow uses the packages in the standard installation of R and Bioconductor (BiocLite) to identify differential splicing. We use the splice index method with the LIMMA framework. The main drawback with this approach is that it relies on accurate estimates of gene expression from the probe-level data. Methods such as RMA and PLIER may misestimate when a large proportion of exons are spliced. We therefore present the novel concept of a gene correlation coefficient calculated using only the probeset expression pattern within a gene. We show that genes with lower correlation coefficients are likely to be differentially spliced.Results: The LIMMA approach was used to identify several tissue-specific transcripts and splicing events that are supported by previous experimental studies. Filtering the data is necessary, particularly removing exons and genes that are not expressed in all samples and cross-hybridising probesets, in order to reduce the false positive rate. The LIMMA approach ranked genes containing single or few differentially spliced exons much higher than genes containing several differentially spliced exons. On the other hand we found the gene correlation coefficient approach better for identifying genes with a large number of differentially spliced exons.Conclusion: We show that LIMMA can be used to identify differential exon splicing from Affymetrix exon array data. Though further work would be necessary to develop the use of correlation coefficients into a complete analysis approach, the preliminary results demonstrate their usefulness for identifying differentially spliced genes. The two approaches work complementary as they can potentially identify different subsets of genes (single/few spliced exons vs. large transcript structure differences)

Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735

A critical review of the formation of mono- and dicarboxylated metabolic intermediates of alkylphenol polyethoxylates during wastewater treatment and their environmental significance

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2010 Taylor & Francis.Alkylphenoxyacetic acids, the metabolic biodegradation products of alkylphenol ethoxylates, are commonly found in wastewaters and sewage effluents. These persistent hydrophilic derivatives possess intrinsic estrogenic activity, which can mimic natural hormones. Their concentrations increase through the sewage treatment works as a result of biodegradation and biotransformation, and when discharged can disrupt endocrine function in fish. These acidic metabolites represent the dominant alkylphenolic compounds found in wastewater effluent and their presence is cause for concern as, potentially, through further biotransformation and biodegradation, they can act as sources of nonylphenol, which is toxic and estrogenic. The authors aim to assess the mechanisms of formation as well as elimination of alkylphenoxyacetic acids within conventional sewage treatment works with the emphasis on the activated sludge process. In addition, they evaluate the various factors influencing their degradation and formation in laboratory scale and full-scale systems. The environmental implications of these compounds are considered, as is the need for tertiary treatment processes for their removal

Differential splicing using whole-transcript microarrays

<p>Abstract</p> <p>Background</p> <p>The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target) platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events.</p> <p>Results</p> <p>We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis). RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of <it>differential </it>splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms.</p> <p>Conclusion</p> <p>We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data.</p> <p>Software implementing our methods is freely available as an <monospace>R</monospace> package.</p

Verified Efficient Implementation of Gabow’s Strongly Connected Component Algorithm

Abstract. We present an Isabelle/HOL formalization of Gabow’s al-gorithm for finding the strongly connected components of a directed graph. Using data refinement techniques, we extract efficient code that performs comparable to a reference implementation in Java. Our style of formalization allows for reusing large parts of the proofs when defining variants of the algorithm. We demonstrate this by verifying an algorithm for the emptiness check of generalized Büchi automata, reusing most of the existing proofs.

Splice variants as novel targets in pancreatic ductal adenocarcinoma

The study was funded by the MolDiagPaCa European Union Framework Programme and CR-UK Programme grant A12008 from CR-UK (C. Chelala, T. Crnogorac-Jurcevic, and N.R. Lemoine). Italian Cancer Genome Project – Ministry of University [FIRB RBAP10AHJB]; Associazione Italiana Ricerca Cancro [grant number: 12182]; FP7 European Community Grant Cam-Pac [no: 602783]; Italian Ministry of Health [FIMPCUP_J33G13000210001]. The funders were not involved in the design of the study, collection, analysis, and interpretation of data and in writing of the manuscript. We thank Tracy Chaplin-Perkins for help with running the Affymetrix experiments

Estrogens Can Disrupt Amphibian Mating Behavior

The main component of classical contraceptives, 17α-ethinylestradiol (EE2), has high estrogenic activity even at environmentally relevant concentrations. Although estrogenic endocrine disrupting compounds are assumed to contribute to the worldwide decline of amphibian populations by adverse effects on sexual differentiation, evidence for EE2 affecting amphibian mating behaviour is lacking. In this study, we demonstrate that EE2 exposure at five different concentrations (0.296 ng/L, 2.96 ng/L, 29.64 ng/L, 2.96 µg/L and 296.4 µg/L) can disrupt the mating behavior of adult male Xenopus laevis. EE2 exposure at all concentrations lowered male sexual arousal, indicated by decreased proportions of advertisement calls and increased proportions of the call type rasping, which characterizes a sexually unaroused state of a male. Additionally, EE2 at all tested concentrations affected temporal and spectral parameters of the advertisement calls, respectively. The classical and highly sensitive biomarker vitellogenin, on the other hand, was only induced at concentrations equal or higher than 2.96 µg/L. If kept under control conditions after a 96 h EE2 exposure (2.96 µg/L), alterations of male advertisement calls vanish gradually within 6 weeks and result in a lower sexual attractiveness of EE2 exposed males toward females as demonstrated by female choice experiments. These findings indicate that exposure to environmentally relevant EE2 concentrations can directly disrupt male mate calling behavior of X. laevis and can indirectly affect the mating behavior of females. The results suggest the possibility that EE2 exposure could reduce the reproductive success of EE2 exposed animals and these effects might contribute to the global problem of amphibian decline

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

Two bursts of gene gains occurred on the mammalian X chromosome contribute to an age-dependent chromosomal distribution of male-biased genes