Nesting biology and food habits of the endangered Sakalava Rail Amaurornis olivieri in the Mandrozo Protected Area,western Madagascar§

We studied the nesting biology and food habits of the endangered and endemic Sakalava Rail Amaurornis olivieri from July to November 2015 in the Mandrozo Protected Area, western Madagascar. Three nesting pairs were observed and their nests were constructed in a dense mat of reeds Phragmites mauritianus and averaged 56.7 ± 15.3 cm above the water (n = 3 nests). Nests were built by both adults and it took 3 d on average to complete a nest (n = 2 nests). Thirteen matings were observed and lasted 4.1 s on average (n = 2 pairs). Average clutch size was three eggs (n = 2 nests). Both sexes incubated; the incubation period was 15–17 d (n = 2 nests). Both male and female participated in brooding and feeding the young, which remained for 3 d in the nest and became independent of their parents at 45 d of age. Based on 194 identified food items, the Sakalava Rail’s diet was composed of invertebrates: spiders (53.1%), insects (32%), crustaceans (10.8%) and molluscs (4.1%). The home ranges of two radio-tagged individuals were 0.95 and 1.98 ha.     

Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips

Hepatocellular carcinoma (HCC) incidence has increased in the US and also has one of the fastest growing death rates of any cancer. The purpose of the current study was to discover novel genome-wide aberrant DNA methylation patterns in HCC tumors that are predominantly HCV-related. Infinium HumanMethylation 450K BeadChip arrays were used to examine genome-wide DNA methylation profiles in 66 pairs of HCC tumor and adjacent non-tumor tissues. After Bonferroni adjustment, a total of 130,512 CpG sites significantly differed in methylation level in tumor compared with non-tumor tissues, with 28,017 CpG sites hypermethylated and 102,495 hypomethylated in tumor tissues. Absolute tumor/non-tumor methylation differences ≥ 20% were found in 24.9% of the hypermethylated and 43.1% of the hypomethylated CpG sites; almost 10,000 CpG sites have ≥ 30% DNA methylation differences. Most (60.1%) significantly hypermethylated CpG sites are located in CpG islands, with 21.6% in CpG shores and 3.6% in shelves. In contrast, only a small proportion (8.2%) of significantly hypomethylated CpG sites are situated in islands, while most are found in open sea (60.2%), shore (17.3%) or shelf (14.3%) regions. A total of 2,568 significant CpG sites (2,441 hypermethylated and 127 hypomethylated) covering 589 genes are located within 684 differentially methylated regions defined as regions with at least two significant CpG sites displaying > 20% methylation differences in the same direction within 250-bp. The top 500 significant CpG sites can significantly distinguish HCC tumor from adjacent tissues with one misclassification. Within adjacent non-tumor tissues, we also identified 75 CpG sites significantly associated with gender, 228 with HCV infection, 17,207 with cirrhosis, and 56 with both HCV infection and cirrhosis after multiple comparisons adjustment. Aberrant DNA methylation profiles across the genome were identified in tumor tissues from US HCC cases that are predominantly related to HCV infection. These results demonstrate the significance of aberrant DNA methylation in HCC tumorigenesis.