GenØk

<strong>Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning</strong> Ruxandra A. Lambuta, Luca Nanni, Yuanlong Liu, Juan Diaz-Miyar, Arvind Iyer, Daniele Tavernari, Natalya Katanayeva, Giovanni Ciriello and Elisa Oricchio <em>Supplementary data (part 2)</em> <strong>HOW TO DOWNLOAD</strong> The data is distributed in two Zenodo repositories (part 1 and 2) as a multi-split zip archive. Part 1: https://doi.org/10.5281/zenodo.7101409 Part 2: https://doi.org/10.5281/zenodo.7101412 Please, download both repositories and place both files in the same directory. Then run <pre><code class="language-bash">zip -F Lambuta_Nanni_et_al_2022.zip --out full.zip unzip full.zip</code></pre> to first merge the files together and then decompress the archive. Inside the archive, you will find a README file containing all the information regarding the repository's content.

<strong>Whole genome doubling promotes tumorigenesis through loss of chromatin segregation and compartment repositioning</strong> <strong>PART 1</strong> Hi-C files of RPE TP53-/-, CP-A TP53-/- and CP-A WT cell lines <strong>hic_maps_RPE.zip</strong>: Hi-C maps (in .hic format) for all RPE TP53-/- samples <strong>hic_maps_CPA.zip</strong>: Hi-C maps (in .hic format) for all CP-A TP53-/- and CP-A WT samples

Abstract Monitoring the presence of transgenes in the environment depends on analytical detection methods and their measurement uncertainties. In this chapter, we aim to identify key methodological aspects and pinpoint the research bottlenecks and needs for building the capacity to effectively monitor transgene escape from genetically modified (GM) crops to wild relatives or landraces. We reviewed the iconic debate concerning the presence of transgenes in landraces of Mexican maize (with both positive and negative results for GM contamination shown over the years) to examine the impact of using different approaches to monitoring and detecting transgenes in landraces. Despite the lack of clear international guidelines that are specific for sampling and testing heterogeneous and dispersed landraces and wild relatives, transgene detection methods have developed significantly over the past decades. There is now an immensely valuable set of tools, approaches, and harmonized protocols that continue to develop and provide a way to evaluate transgene presence. To support this ongoing development and to steer it in directions that are particularly useful for addressing the challenges associated with detection in landraces and wild relatives, we offer lessons from our review for future work in this area particularly useful for addressing the challenges associated with detection in landraces and wild relatives, we offer lessons from our review for future work in this area.

The promised disruptive potential of genome editing for producing novel agri- and aquaculture products with enhanced qualities has refocused the discussion on non-safety assessments of biotechnological inventions. Since such assessments are based in societal values, the public or their representatives should be involved in handling the normative issues at stake. A starting point of this paper is that such assessments are feasible and justified, given the proper form and level of engagement. Public engagement includes different forms of surveys, focus group interviews, dialogues, and consultations. In this paper we present two recent Norwegian surveys, both with the intention to identify public perspectives on the use of genome editing in animals and plants to be used within agri- and aquaculture. Through an analysis of these two recent surveys, we will show that such approaches tend to fall short when it comes to providing a normative basis for non-safety assessments. For surveys to be appropriate tools for public engagement, it is important that the forming includes a multitude of perspectives on the use of the technology in question. The information material should not be simplified or provide a biased knowledge basis, and the survey should avoid leading questions. By enhancing the research-based framing of public engagement processes, including reflection on and research into the ethical values at stake, these shortcomings could be amended. We argue that in highly contested areas of research such as genome-editing in agri- and aquaculture, public engagement approaches should be based in transparent scientific and normative analyses.

The opinion expressed by Eriksson and colleagues’ fails to recognise that there are no standard experimental designs for academic investigations involving omics analyses of genetically modified crops and that the only valid comparator to determine the effect of the process of transgenesis is a near isogenic variety grown at the same time and location, as was the case in our investigation of NK603 maize. Eriksson does not acknowledge that the quality of the rat liver tissues in our chronic Roundup toxicity study has neither been questioned nor branded as unsuitable for further investigation. In addition, Eriksson fails to appreciate that the statistical methods we used to analyse the liver metabolomics dataset are recognised as appropriate as some of a number of approaches that can be taken. Moreover, Eriksson neglects to mention that the proteomics analysis of the liver tissues highlights structural and functional damage from Roundup exposure. Thus our results are sound and the claims by Eriksson and colleagues of experimental flaws are unfounded.Replying to: Eriksson et al. Sci Rep 8 (2018); https://doi.org/10.1038/s41598-018-30440-7.