Newcombe, P. | Search bioRxiv

bioRxiv2018

Developmental Effects of the Pesticide Imidacloprid on Zebrafish Body Length and Mortality

The pesticide imidacloprid, a Neonicotinoid, is widely used and commercially available. Neonicotinoids are antagonists at nicotinic acetylcholine receptors, which can cause neurobehavioral effects in developing organisms. While the effects of other insecticides such as Malathion and Fipronil on zebrafish Danio rerio development have been studied, few studies describe the morphological effects of imidacloprid during zebrafish development. To test the hypothesis that imidacloprid concentration positively correlates to increased mortality and decreased body length, we exposed zebrafish to imidacloprid for five days post fertilization. Body length and embryo mortality were recorded at 1, 2, 3, 4, and 5 days post fertilization in 0 ug/L, 100 ug/L, 1,000 ug/L, and 10,000 ug/L imidacloprid concentrations. These concentrations were chosen to mimic levels that could be reached in the environment especially soon after application. Our results demonstrate statistically increased embryo mortality, with a f crit value of 3.193 and a f value of 3.098 from an ANOVA test, and impaired body length with a dose dependent correlation to the concentration of imidacloprid and a P value of less than 0.01 from a T test. Given the pesticides high prevalence, future studies should be considered to determine if this effect may impact livestock and human development.

developmental biology↗

bioRxiv2018

Fine mapping chromatin contacts in capture Hi-C data

Hi-C and capture Hi-C (CHi-C) are used to map physical contacts between chromatin regions in cell nuclei using high-throughput sequencing. Analysis typically proceeds considering the evidence for contacts between each possible pair of fragments independent from other pairs. This can produce long runs of fragments which appear to all make contact with the same baited fragment of interest. We hypothesised that these long runs could result from a smaller subset of direct contacts and propose a new method, based on a Bayesian sparse variable selection approach, which attempts to fine map these direct contacts.\n\nOur model is conceptually novel, exploiting the spatial pattern of counts in CHi-C data, and prioritises fragments with biological properties that would be expected of true contacts. For bait fragments corresponding to gene promoters, we identify contact fragments with active chromatin and contacts that correspond to edges found in previously defined enhancer-target networks; conversely, for intergenic bait fragments, we identify contact fragments corresponding to promoters for genes expressed in that cell type. We show that long runs of apparently co-contacting fragments can typically be explained using a subset of direct contacts consisting of < 10% of the number in the full run, suggesting that greater resolution can be extracted from existing datasets. Our results appear largely complementary to the those from a per-fragment analytical approach, suggesting that they provide an additional level of interpretation that may be used to increase resolution for mapping direct contacts in CHi-C experiments.

genomics↗