Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach

Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Different environmental toxicants have been shown to promote exposure (i.e., toxicant) specific signatures of germline epimutations. Analysis of genomic features associated with these epimutations identified low-density CpG regions (<3 CpG / 100bp) termed CpG deserts and a number of unique DNA sequence motifs. The rat genome was annotated for these and additional relevant features. The objective of the current study was to use a machine learning computational approach to predict all potential epimutations in the genome. A number of previously identified sperm epimutations were used as training sets. A novel machine learning approach using a sequential combination of Active Learning and Imbalance Class Learner analysis was developed. The transgenerational sperm epimutation analysis identified approximately 50K individual sites with a 1 kb mean size and 3,233 regions that had a minimum of three adjacent sites with a mean size of 3.5 kb. A select number of the most relevant genomic features were identified with the low density CpG deserts being a critical genomic feature of the features selected. A similar independent analysis with transgenerational somatic cell epimutation training sets identified a smaller number of 1,503 regions of genome-wide predicted sites and differences in genomic feature contributions. The predicted genome-wide germline (sperm) epimutations were found to be distinct from the predicted somatic cell epimutations. Validation of the genome-wide germline predicted sites used two recently identified transgenerational sperm epimutation signature sets from the pesticides dichlorodiphenyltrichloroethane (DDT) and methoxychlor (MXC) exposure lineage F3 generation. Analysis of this positive validation data set showed a 100% prediction accuracy for all the DDT-MXC sperm epimutations. Observations further elucidate the genomic features associated with transgenerational germline epimutations and identify a genome-wide set of potential epimutations that can be used to facilitate identification of epigenetic diagnostics for ancestral environmental exposures and disease susceptibility.     

Effects of seed-irradiation on meiosis in M1 plants of Lactuca and related plants

Meiosis was studied in control and seed-irradiated materials of Lactuca sativa, cultivars Tom, Cos and Webbs, L. serriola from the wild, and Cichorium intybus. In meiosis of the M₁ plants from irradiated seed, observations of univalent and multivalent formation, bridge formation at Anaphase I and II, micronucleus formation and persistence, and pollen fertility, were carried out, and compared with controls. Quantitative estimations of bridge formation were made in L. sativa Tom and Cos and in L. serriola, at anaphase I only. It was found that the frequency of anaphase I bridges and reduction of pollen fertility in the M₁ and also M₂ generation, were different for each variety or species; these could be sequenced radiation-resistant to sensitive in the order Tom, Cos and L. serriola.     

Cell division study in ‘pollen mother cells’ and ‘pollen grains’ of in vivo and ex vitro plants in Drimiopsis botryoides

The various normal and abnormal stages of meiosis and pollen mitosis of Drimiopsis botryoides are described, and a comparison between naturally propagated in vivo and tissue culture derived ex vitro plants in respect to their cytological behaviour presented. We also describe the floral morphology and investigate the relationship between the floral developmental stages and the progression of microgametogenesis. In total, 33 bivalents are observed in diakinesis, which indicate the diploid number 2n = 66 and this number is cross-checked by a haploid set of n = 33 chromosomes in pollen mitosis. Only 6.8% and 4.9% meiotic abnormalities were recorded on in vivo and ex vitro plants, respectively, which led to the formation of non-viable pollen. Finally, the microspores have to develop into tri-cellular male gametophyte. Only 0.2% pollen grains are found with a micro-nucleus. Though the higher pollen viability was recorded on both in vivo (89.3 ± 4.1%) and ex vitro (92.1 ± 4.6%) plants, but surprisingly the pollen germination rate is extremely low with 13.6 ± 1.74% and 21.3 ± 1.55%, respectively. The present study obviously enriches the cytological database of D. botryoides and may help future research on androgenesis and genetic improvement.     

Effect of nitrogen,phosphorus and potassium on spikelet sterility induced by low temperature at the reproductive stage of rice

Spikelet sterility induced by low temperature at the reproductive stage of rice increased further with the increase of nitrogen supply. Spikelet sterility in Fujisaka-5 did not increase due to low temperature when nitrogen supply was increased from 10 to 40 ppm and at 80 ppm nitrogen supply it was less affected than IR36. Total nitrogen content in the leaves increased with the increase of nitrogen supply and was forced to be associated with the spikelet sterility induced by low temperature. Based on auricle distance between the last two leaves, the most sensitive stage to low temperature damage differed in Fujisaka-5 and IR36. Spikelet sterility induced by low temperature for 10 days was very high in both the varieties and the effect of nitrogen was not clear.The effect of phosphorus on the spikelet sterility induced by low temperature at reproductive stage was not clear except that at the highest phosphorus (P) level (10 ppm) the spikelet sterility increased both in Fujisaka-5 and IR36.Spikelet sterility induced by low temperature at the reproductive stage of rice decreased with the increase of Potassium (K) supply in both Fujisaka-5 and IR36. With an increase of potassium supply, nitrogen (N) content decreased in the leaves and panicles and spikelet sterility induced by low temperature decreased with an increase of the K to N ratio in the leaves and panicles. The results suggest that potassium might play a major role to counteract the low temperature damage at the reproductive stage of rice.     

Influence of host plants on development, fecundity and egg hatchability of the arctiid moth Diacrisia casignetum

Measurements were made of the differences between sunflower and climbing hempweed leaves for development, fecundity and egg hatchability of Diacrisia casignetum Kollar. Developmental time and weight gains of sunflower-fed larvae were respectively longer and greater than those of hempweed-fed ones. The development time and weight gain, attributable to differences in host plants, were statistically heterogeneous (P<0.05-<0.10). Relative fecundity and egg hatchability of sunflower reared insects were greater than those of hempweed reared ones, and these were also statistically heterogeneous (P<0.1 and <0.05, respectively). Hempweed leaves contained relatively high titres of phenols and low ratios of proteins to phenols. Ovaries were heavier in insects reared on sunflower than on hempweed, whereas the level of phenols incorporated into the ovary was higher in insects fed on hempweed than those on sunflower. The differences in these parameters may be due to variations in nutritional quality of these hosts and incorporation of ingested phenolic materials to ovary and insect biomass.

---

Résumé L'étude a porté sur l'évaluation de l'influence des feuilles de tournesol (Helianthus annuus) et de Mikana cordata sur le développement, la fécondité et l'éclosion des oeufs de D. casignetum Kollaz. La durée de développement et le gain de poids sur tournesol étaient plus importants que sur M. cordata. La durée de développement était statistiquement hétérogène (P<0.05), ce qui peut être dû à des différences entre plantes. La fécondité et le taux d'éclosion chez les insectes élevés sur tournesol étaient plus élevés que ceux observés sur M. cordata, dont les résultats étaient aussi hétérogènes (P<0.1 et<0.05 respectivement). Les feuilles de M. cordata contenaient des taux relativement élevés de phénols et des rapports protéines sur phénols bas. Tout ceci suggère que les différences observées sont attribuables à des variations dans la qualité nutritive de ces hôtes et dans l'incorporation à la biomasse de l'insecte de matériaux phénologiques ingérés.