Glassman, D. | Search bioRxiv

bioRxiv2021

Pancreatic cancer prognosis is predicted by a novel ATAC-array technology for assessing chromatin accessibility

We investigated tumor-cell-intrinsic chromatin accessibility patterns of pancreatic ductal adenocarcinoma (PDAC) by ATAC-seq on EpCAM+ PDAC malignant epithelial cells, sorted from 54 freshly resected human tumors, and discovered a signature of 1092 chromatin loci displaying differential accessibility between patients with disease free survival (DFS) < 1 year and patients with DFS > 1 year. Analyzing transcription factor (TF) binding motifs within these loci, we identified two TFs (ZKSCAN1 and HNF1b) displaying differential nuclear localization between patients with short vs. long DFS. We further developed a novel chromatin accessibility microarray methodology termed "ATAC-Array", an easy-to-use platform obviating the time and cost of next generation sequencing. Applying this novel methodology to the original ATAC-seq libraries as well as independent libraries generated from patient-derived organoids, we validated ATAC-array technology in both the original ATAC-Seq cohort as well as in an independent validation cohort. We conclude that PDAC prognosis can be predicted by ATAC-array, which represents a novel, lowcost, clinically feasible technology for assessing chromatin accessibility profiles.

cancer biology↗

bioRxiv2020

Do carbonated beverages reduce bleeding from gill injuries in angled Northern Pike?

The premise of catch-and-release angling is that most fish survive fisheries interactions. Therefore, it is common for anglers, management agencies, and other organizations to share information on handling practices and other strategies that are believed to improve fish welfare and survival. Recent media coverage has sensationalized the use of carbonated beverages to treat bleeding fish, an intervention that is purported to stop bleeding but has yet to be validated scientifically. We captured Northern Pike (Esox lucius) via hook and line, experimentally injured their gills in a standardized manner, and treated them with either Mountain Dew, Coca Cola, or carbonated lake water and observed the duration and intensity of bleeding, as well as overall blood loss (using gill colour as a proxy) while the fish was held in a lake water bath. As a control, we had a group of experimentally injured fish that did not have liquid poured over their gills before the observation period. All treatments and the control were conducted at two different water temperatures (11-18 {degrees}C and 24-27 {degrees}C) to determine if the effects of pouring carbonated beverages over injured gills is temperature dependent. When compared to the control, we found that the duration and intensity of bleeding increased regardless of the type of carbonated beverages used in this study, and there was no effect of water temperature. Use of chilled versus ambient temperature beverages similarly had no influence on outcomes. As such, there is no scientific evidence to support the use of carbonated beverages for reducing or stopping blood loss for fish that have had their gills injured during recreational angling based on the context studied here. This study reinforced the need to scientifically test angler anecdotes and theories when it comes to best practices for catch-and-release fishing.

ecology↗