White, T. B. | bioRxiv Science

bioRxiv2024

Megabase-scale loss of heterozygosity provoked by CRISPR-Cas9 DNA double-strand breaks

Harnessing DNA double-strand breaks (DSBs) is a powerful approach for gene editing, but it may provoke loss of heterozygosity (LOH), which predisposes to tumorigenesis. To interrogate this risk, we developed a two- color flow cytometry-based system (Flo-LOH), detecting LOH in [~]5% of cells following a DSB. After this initial increase, cells with LOH decrease due to a competitive disadvantage with parental cells, but if isolated, they stably propagate. Segmental loss from terminal deletions with de novo telomere addition and nonreciprocal translocations is observed as well as whole chromosome loss, especially following a centromeric DSB. LOH spans megabases distal from the DSB, but also frequently tens of megabases centromere-proximal. Inhibition of microhomology-mediated end joining massively increases LOH, which is synergistically increased with concomitant inhibition of canonical nonhomologous end joining. The capacity for large-scale LOH must therefore be considered when using DSB-based gene editing, especially in conjunction with end joining inhibition.

molecular biology↗

bioRxiv2021

Reducing publication delay to improve the efficiency and impact of conservation science

Evidence-based decision making is most effective with comprehensive access to scientific studies. If studies face delays or barriers to being published, the useful information they contain may not reach decision-makers in a timely manner. This represents a potential problem for mission-oriented disciplines where access to the latest data is paramount to ensure effective actions are deployed. We sought to analyse the severity of publication delay in conservation science -- a field that requires urgent action to prevent the loss of biodiversity. We used the Conservation Evidence database to assess the length of publication delay (time from finishing data collection to publication) in the literature that tests the effectiveness of conservation interventions. From 7,415 peer-reviewed and non-peer-reviewed studies of conservation interventions published over eleven decades, we find that the mean publication delay (time from completing data collection to publication) was 3.6 years and varied by conservation subject -- a smaller delay was observed for studies focussed on the management of captive animals. Publication delay was significantly smaller for studies in the non-journal literature (typically non-peer-reviewed) compared to studies published in scientific journals. Although we found publication delay has marginally increased over time (1912-2020), this change was weak post-1980s. Publication delay also varied inconsistently between studies on species with different IUCN Red List statuses and there was little evidence that studies on more threatened species were subject to a smaller delay. We discuss the possible drivers of publication delay and present suggestions for scientists, funders, publishers, and practitioners to reduce the time taken to publish studies. Although our recommendations are aimed at conservation science, they are highly relevant to other mission-driven disciplines where the rapid dissemination of scientific findings is important.

scientific communication and education↗