Visualisation de fonctions générant un point de selle multiple dans ℝn

Le présent rapport est la conclusion d'un project de visualisation de fonctions allant de Rn dans R et générant des points de selle multiple. Le choix des fonctions étudiées est motivé par une famille de fonctions discutée dans [2] ; elles se trouvent à être une généralisation de cette famille. Le logiciel utilisé est Mathematica 7. On y présente en premier lieu, aussi assisté par Mathematica, le calcul du degré topologique des points de selle, qui sont des points critiques dégénérés. Ensuite viennent plusieurs images, des cas n = 2 à n = 4, visant à montrer certaines de leur caractéristiques. Ce travail se veut un d'expérimentation ; par conséquent, aucun résultat original de mathématiques fondamentales n'y est démontré

Thyroid hormone-regulated gene expression in juvenile mouse liver: identification of thyroid response elements using microarray profiling and in silico analyses

<p>Abstract</p> <p>Background</p> <p>Disruption of thyroid hormone signalling can alter growth, development and energy metabolism. Thyroid hormones exert their effects through interactions with thyroid receptors that directly bind thyroid response elements and can alter transcriptional activity of target genes. The effects of short-term thyroid hormone perturbation on hepatic mRNA transcription in juvenile mice were evaluated, with the goal of identifying genes containing active thyroid response elements. Thyroid hormone disruption was induced from postnatal day 12 to 15 by adding goitrogens to dams' drinking water (hypothyroid). A subgroup of thyroid hormone-disrupted pups received intraperitoneal injections of replacement thyroid hormones four hours prior to sacrifice (replacement). An additional group received only thyroid hormones four hours prior to sacrifice (hyperthyroid). Hepatic mRNA was extracted and hybridized to Agilent mouse microarrays.</p> <p>Results</p> <p>Transcriptional profiling enabled the identification of 28 genes that appeared to be under direct thyroid hormone-regulation. The regulatory regions of the genome adjacent to these genes were examined for half-site sequences that resemble known thyroid response elements. A bioinformatics search identified 33 thyroid response elements in the promoter regions of 13 different genes thought to be directly regulated by thyroid hormones. Thyroid response elements found in the promoter regions of Tor1a, 2310003H01Rik, Hect3d and Slc25a45 were further validated by confirming that the thyroid receptor is associated with these sequences <it>in vivo </it>and that it can bind directly to these sequences <it>in vitro</it>. Three different arrangements of thyroid response elements were identified. Some of these thyroid response elements were located far up-stream (> 7 kb) of the transcription start site of the regulated gene.</p> <p>Conclusions</p> <p>Transcriptional profiling of thyroid hormone disrupted animals coupled with a novel bioinformatics search revealed new thyroid response elements associated with genes previously unknown to be responsive to thyroid hormone. The work provides insight into thyroid response element sequence motif characteristics.</p

Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring

Understanding the effects of environmental exposures on germline mutation rates has been a decades-long pursuit in genetics. We used next-generation sequencing and comparative genomic hybridization arrays to investigate genome-wide mutations in the offspring of male mice exposed to benzo(a)pyrene (BaP), a common environmental pollutant. We demonstrate that offspring developing from sperm exposed during the mitotic or post-mitotic phases of spermatogenesis have significantly more de novo single nucleotide variants (1.8-fold; P < 0.01) than controls. Both phases of spermatogenesis are susceptible to the induction of heritable mutations, although mutations arising from post-fertilization events are more common after post-mitotic exposure. In addition, the mutation spectra in sperm and offspring of BaP-exposed males are consistent. Finally, we report a significant increase in transmitted copy number duplications (P = 0.001) in BaP-exposed sires. Our study demonstrates that germ cell mutagen exposures induce genome-wide mutations in the offspring that may be associated with adverse health outcomes

Visualisation de fonctions générant un point de selle multiple dans ℝn

Le présent rapport est la conclusion d'un project de visualisation de fonctions allant de Rn dans R et générant des points de selle multiple. Le choix des fonctions étudiées est motivé par une famille de fonctions discutée dans [2] ; elles se trouvent à être une généralisation de cette famille. Le logiciel utilisé est Mathematica 7. On y présente en premier lieu, aussi assisté par Mathematica, le calcul du degré topologique des points de selle, qui sont des points critiques dégénérés. Ensuite viennent plusieurs images, des cas n = 2 à n = 4, visant à montrer certaines de leur caractéristiques. Ce travail se veut un d'expérimentation ; par conséquent, aucun résultat original de mathématiques fondamentales n'y est démontré

Transcriptional profiling of the mouse hippocampus supports an NMDAR-mediated neurotoxic mode of action for benzo[a]pyrene

Benzo[a]pyrene (BaP) is a genotoxic carcinogen and a neurotoxicant. The neurotoxicity of BaP is proposed to arise from either genotoxicity leading to neuronal cell death, or perturbed expression of N‐methyl‐d‐aspartate receptor (NMDAR) subunits. To explore these hypotheses, we profiled hippocampal gene expression of adult male Muta(™)Mouse administered 0, 1, 35, or 70 mg BaP/kg bw per day by oral gavage for 3 days. Transcriptional profiles were examined by RNA‐sequencing (RNA‐seq), DNA microarrays, and real‐time quantitative reverse transcription polymerase chain reaction (RT‐PCR). BaP‐DNA adducts in the cerebellum were quantified by (32)P‐post‐labeling to measure genotoxicity. RNA‐seq revealed altered expression of 0, 260, and 219 genes (P‐value < 0.05, fold‐change ≥ ± 1.5) following exposure to the low, medium, and high doses, respectively; 54 genes were confirmed by microarrays. Microarray and RT‐PCR analysis showed increased expression of NMDAR subunits Grina and Grin2a. In contrast, no effects on DNA‐damage response genes were observed despite comparable BaP‐DNA adduct levels in the cerebellum and in the lungs and livers of mice at similar BaP doses in previous studies. The results suggest that DNA‐damage response does not play a major role in BaP‐induced adult neurotoxicity. Meta‐analysis revealed that BaP‐induced transcriptional profiles are highly correlated with those from the hippocampus of transgenic mice exhibiting similar neurotoxicity outcomes to BaP‐exposed mice and rats (i.e., defects in learning and memory). Overall, we suggest that BaP‐induced neurotoxicity is more likely to be a consequence of NMDAR perturbation than genotoxicity, and identify other important genes potentially mediating this adverse outcome. Environ. Mol. Mutagen. 57:350–363, 2016. © 2016 Her Majesty the Queen in Right of Canada. Environmental and Molecular Mutagenesis © 2016 Environmental Mutagen Society

Additional file 1: of Characterizing Benzo[a]pyrene-induced lacZ mutation spectrum in transgenic mice using next-generation sequencing

Figure S1. Comparison of mutant read proportions for substitutions at each nucleotide position across all samples. Figure S2. Example density graphs (smoothed histograms) for variant calls at two different nucleotide positions. Figure S3. Distribution of read starts and ends. Figure S4. Comparison of the density of false mutation proportions between base substitutions (red) and indels (blue). Figure S5. Relative proportion of control and BaP-induced lacI mutations in liver from reference [29]. Figure S6. Bone marrow mutation spectra of control and BaP treatments. Figure S7. Comparison of spontaneous mutation spectra between our NGS dataset and other published datasets [4, 5, 7, 9-11]. Figure S8. Comparison of BaP-induced mutation spectrum in bone marrow measured using NGS with the mean mutation spectrum measured from four tissues (forestomach, spleen, colon, glandular stomach) using Sanger sequencing [6]. Figure S9. Distribution of non-unique base substitutions across the lacZ transgene for control and BaP samples. Figure S10. Comparison of lacZ mutation hotspots identified using Sanger sequencing [5-10] with mutations identified using NGS at the same nucleotide positions in the present study. Figure S11. Distribution of non-unique indels across the lacZ transgene for control and BaP samples. Figure S12. Results of simulations that use random sampling of BaP mutants to approximate the number of mutants per sample required to achieve a consistent mutation spectrum. Table S1. Thresholds used to detect mutations from each sample library. Table S2. Comparison of expected and observed mutant count when the number of each mutant plaque was controlled for in each NGS library. Table S3. Percent Clonality and Adjusted Mutant Frequencies in Control and BaP-treated samples using the LOD/linear model to adjust mutant counts. Table S4. Comparison of BaP-induced and spontaneous mutation spectra. (DOCX 418 kb

Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD).

Many regulatory agencies are exploring ways to integrate toxicogenomic data into their chemical risk assessments. The major challenge lies in determining how to distill the complex data produced by high-content, multi-dose gene expression studies into quantitative information. It has been proposed that benchmark dose (BMD) values derived from toxicogenomics data be used as point of departure (PoD) values in chemical risk assessments. However, there is limited information regarding which genomics platforms are most suitable and how to select appropriate PoD values. In this study, we compared BMD values modeled from RNA sequencing-, microarray-, and qPCR-derived gene expression data from a single study, and explored multiple approaches for selecting a single PoD from these data. The strategies evaluated include several that do not require prior mechanistic knowledge of the compound for selection of the PoD, thus providing approaches for assessing data-poor chemicals. We used RNA extracted from the livers of female mice exposed to non-carcinogenic (0, 2 mg/kg/day, mkd) and carcinogenic (4, 8 mkd) doses of furan for 21 days. We show that transcriptional BMD values were consistent across technologies and highly predictive of the two-year cancer bioassay-based PoD. We also demonstrate that filtering data based on statistically significant changes in gene expression prior to BMD modeling creates more conservative BMD values. Taken together, this case study on mice exposed to furan demonstrates that high-content toxicogenomics studies produce robust data for BMD modelling that are minimally affected by inter-technology variability and highly predictive of cancer-based PoD doses