Sunday Evening News 394 - Week 39 - 2024
Weekly report on genetic engineering, genome editing, biotechnology and legal regulation.
September 2024-09-23 - 2024-09-29
„Glauben und Wissen verhalten sich wie die zwei Schalen einer Waage:
In dem Maße, als eine steigt, sinkt die andere.“
Arthur Schopenhauer (1788 – 1860)
deutscher Philosoph und Schriftsteller
"Faith and knowledge are like scales of a balance:
As one rises, the other falls. "
Arthur Schopenhauer (1788 - 1860)
German philosopher and writer
Meetings - Tagungen
Die Genschere geht auf Roadshow - CRISPR-Whisper mit Mitmach-Experimenten & Science Café
10. Kongress Lebensmitteltechnologie 2024
10.-12. Oktober 2024, Lemgo
https://www.gdl-ev.org/veranstaltungen/gdl-veranstaltungen/336-kongress-2024
VLOG: „Ohne Gentechnik“-Wirtschaft trifft sich zum „International Non-GMO Summit“
KALS 2024 - 9. Karlsruher Lebensmittelsymposium
20.11 - 21.11.2024 im GenoHotel Karlsruhe
https://www.cp-management.de/kals-2024
Press Releases - Media / Presse- und Medienberichte
Hungarian Presidency debriefs EP committees on priorities
Regalado A.: Two Nobel Prize winners want to cancel their own CRISPR patents in Europe
Testbiotech: European basic patents on CRISPR/Cas gene scissors withdrawn, Patent holders request the revocation
of their patents
https://www.testbiotech.org/en/news/european-basic-patents-on-crispr-cas-gene-scissors-withdrawn/
ARGE Gentechnik-frei Parteien-Check: Breiter Parteien-Konsens für Weiterführung Österreichs kritischer Gentech-Haltung
Informationsdienst Gentechnik: Gentechnik-Weizen breitet sich weltweit aus
https://www.keine-gentechnik.de/nachricht/34961?cHash=07f300fb0f00a08794718eb022c8ccc3
Gillam C., Margot Gibbs M., DeBre E.: Revealed: the US government-funded ‘private social network’ attacking pesticide
critics
v-Fluence response to Lighthouse NGO and collaborators’ claims
https://www.v-fluence.com/2024/09/v-fluence-response-to-lighthouse-ngo-and-collaborators-claims/
RiskMonger: Bonus Eventus and Bonehead Activists
https://risk-monger.com/2024/09/27/bonus-eventus-and-bonehead-activists/
Only some selected press releases or media reports are listed here. The daily up-date of the press releases and
media reports are ►here: September week 39
Publications – Publikationen
Marquart, K.F., Mathis, N., Mollaysa, A. et al. (2024): Effective genome editing with an enhanced ISDra2 TnpB system and
deep learning-predicted ωRNAs. Nat Methods | https://doi.org/10.1038/s41592-024-02418-z
Transposon (IS200/IS605)-encoded TnpB proteins are predecessors of class 2 type V CRISPR effectors and have emerged as one of the most compact genome editors identified thus far. Here, we optimized the design of Deinococcus radiodurans (ISDra2) TnpB for application in mammalian cells (TnpBmax), leading to an average 4.4-fold improvement in editing. In addition, we developed variants mutated at position K76 that recognize alternative target-adjacent motifs (TAMs), expanding the targeting range of ISDra2 TnpB. We further generated an extensive dataset on TnpBmax editing efficiencies at 10,211 target sites. This enabled us to delineate rules for on-target and off-target editing and to devise a deep learning model, termed TnpB editing efficiency predictor (TEEP; https://www.tnpb.app), capable of predicting ISDra2 TnpB guiding RNA (ωRNA) activity with high performance (r > 0.8). Employing TEEP, we achieved editing efficiencies up to 75.3% in the murine liver and 65.9% in the murine brain after adeno-associated virus (AAV) vector delivery of TnpBmax. Overall, the set of tools presented in this study facilitates the application of TnpB as an ultracompact programmable endonuclease in research and therapeutics.
https://www.nature.com/articles/s41592-024-02418-z
Mascher, M., Jayakodi, M., Shim, H. et al. (2024): Promises and challenges of crop translational genomics.
Nature | https://doi.org/10.1038/s41586-024-07713-5
Crop translational genomics applies breeding techniques based on genomic datasets to improve crops. Technological breakthroughs in the past ten years have made it possible to sequence the genomes of increasing numbers of crop varieties and have assisted in the genetic dissection of crop performance. However, translating research findings to breeding applications remains challenging. Here we review recent progress and future prospects for crop translational genomics in bringing results from the laboratory to the field. Genetic mapping, genomic selection and sequence-assisted characterization and deployment of plant genetic resources utilize rapid genotyping of large populations. These approaches have all had an impact on breeding for qualitative traits, where single genes with large phenotypic effects exert their influence. Characterization of the complex genetic architectures that underlie quantitative traits such as yield and flowering time, especially in newly domesticated crops, will require further basic research, including research into regulation and interactions of genes and the integration of genomic approaches and high-throughput phenotyping, before targeted interventions can be designed. Future priorities for translation include supporting genomics-assisted breeding in low-income countries and adaptation of crops to changing environments.
https://www.nature.com/articles/s41586-024-07713-5
Sun L., Lai M., Ghoui F., Nawaz M.A. et al. (2024): Modern Plant Breeding Techniques in Crop Improvement and Genetic
Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence—A Critical Review. Plants 13 (19), 2676 | https://doi.org/10.3390/plants13192676
With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops’ audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.
https://www.mdpi.com/2223-7747/13/19/2676
Noack F., Engist D., Gantois J., Gaur V., Hyjazie B.F., Larsen A., M’Gonigle L.K., Missirian A., Qaim M., [...] , and Kremen C. +
2 authors (2024): Environmental impacts of genetically modified crops, Science 385, Issue 6712 | DOI: 10.1126/science.ado9340
Genetically modified (GM) crops have been adopted by some of the world’s leading agricultural nations, but the full extent of their environmental impact remains largely unknown. Although concerns regarding the direct environmental effects of GM crops have declined, GM crops have led to indirect changes in agricultural practices, including pesticide use, agricultural expansion, and cropping patterns, with profound environmental implications. Recent studies paint a nuanced picture of these environmental impacts, with mixed effects of GM crop adoption on biodiversity, deforestation, and human health that vary with the GM trait and geographic scale. New GM or gene-edited crops with different traits would likely have different environmental and human health impacts.
https://www.science.org/doi/10.1126/science.ado9340 pdf-file available
Collins, M., Lau, M.B., Ma, W. et al. (2024): A frugal CRISPR kit for equitable and accessible education in gene editing and
synthetic biology. Nat Commun 15, 6563 | https://doi.org/10.1038/s41467-024-50767-2
Equitable and accessible education in life sciences, bioengineering, and synthetic biology is crucial for training the next generation of scientists, fostering transparency in public decision-making, and ensuring biotechnology can benefit a wide-ranging population. As a groundbreaking technology for genome engineering, CRISPR has transformed research and therapeutics. However, hands-on exposure to this technology in educational settings remains limited due to the extensive resources required for CRISPR experiments. Here, we develop CRISPRkit, an affordable kit designed for gene editing and regulation in high school education. CRISPRkit eliminates the need for specialized equipment, prioritizes biosafety, and utilizes cost-effective reagents. By integrating CRISPRi gene regulation, colorful chromoproteins, cell-free transcription-translation systems, smartphone-based quantification, and an in-house automated algorithm (CRISPectra), our kit offers an inexpensive (~$2) and user-friendly approach to performing and analyzing CRISPR experiments, without the need for a traditional laboratory setup. Experiments conducted by high school students in classroom settings highlight the kit’s utility for reliable CRISPRkit experiments. Furthermore, CRISPRkit provides a modular and expandable platform for genome engineering, and we demonstrate its applications for controlling fluorescent proteins and metabolic pathways such as melanin production. We envision CRISPRkit will facilitate biotechnology education for communities of diverse socioeconomic and geographic backgrounds.
https://www.nature.com/articles/s41467-024-50767-2
Sisharmini, A., Wihardjaka, A., Enggarini, W. et al. (2024): Field performance and nitrous oxide emissions of transgenic
nitrogen use efficient rice lines cultivated in tropical paddy fields. Transgenic Res | https://doi.org/10.1007/s11248-024-00410-z
Nitrogen (N) fertilizers make up the majority of the input used in rice production, and their excess application leads to significant environmental pollution. Developing rice varieties with improved nitrogen use efficiency (NUE) is essential to maintain the sustainability of rice production. This study aims to evaluate the performance of transgenic Oryza sativa japonica cv. Kitaake expressing the barley (Hordeum vulgare) alanine aminotransferase (HvAlaAT) gene in response to different levels of N fertilizer application under tropical paddy field conditions. Results from this study demonstrate that transgenic nitrogen use efficient Kitaake rice (Kitaake NUE) displays a grain yield increase of up to 41% compared to Kitaake null. Transgenic Kitaake NUE expressing the HvAlaAT gene displays a higher N uptake and achieves a higher nitrogen use efficiency compared to control plants while maintaining lower nitrous oxide (N2O) fluxes. The reduction in N2O emissions in Kitaake NUE compared to Kitaake null ranges from 37.5 to 96.3%. The transgenic Kitaake NUE used in this study has potential as a donor to improve the nitrogen use efficiency of indica rice for better adaptability to tropical conditions.
https://link.springer.com/article/10.1007/s11248-024-00410-z
Schmartz, G.P., Rehner, J., Schuff, M.J. et al. (2024): Exploring microbial diversity and biosynthetic potential in zoo and
wildlife animal microbiomes. Nat Commun 15, 8263 | https://doi.org/10.1038/s41467-024-52669-9
Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the ‘One Health’ approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.
https://www.nature.com/articles/s41467-024-52669-9
Costello, A., Peterson, A.A., Lanster, D.L. et al. (2024): Efficient genetic code expansion without host genome modifications.
Nat Biotechnol | https://doi.org/10.1038/s41587-024-02385-y
Supplementing translation with noncanonical amino acids (ncAAs) can yield protein sequences with new-to-nature functions but existing ncAA incorporation strategies suffer from low efficiency and context dependence. We uncover codon usage as a previously unrecognized contributor to efficient genetic code expansion using non-native codons. Relying only on conventional Escherichia coli strains with native ribosomes, we develop a plasmid-based codon compression strategy that minimizes context dependence and improves ncAA incorporation at quadruplet codons. We confirm that this strategy is compatible with all known genetic code expansion resources, which allowed us to identify 12 mutually orthogonal transfer RNA (tRNA)–synthetase pairs. Enabled by these findings, we evolved and optimized five tRNA–synthetase pairs to incorporate a broad repertoire of ncAAs at orthogonal quadruplet codons. Lastly, we extend these resources to an in vivo biosynthesis platform that can readily create >100 new-to-nature peptide macrocycles bearing up to three unique ncAAs. Our approach will accelerate innovations in multiplexed genetic code expansion and the discovery of chemically diverse biomolecules.
https://www.nature.com/articles/s41587-024-02385-y
Stammnitz M.R., Scholz A.H. , Duffy D.J. (2024): Environmental DNA without borders: Let’s embrace decentralised
genomics to meet the UN’s biodiversity targets. EMBO Rep (2024) | https://doi.org/10.1038/s44319-024-00264-w
https://www.embopress.org/doi/full/10.1038/s44319-024-00264-w
Wray-Cahen D., Hallerman E., Tizard M. (2024): Global regulatory policies for animal biotechnology: overview, opportunities
and challenges. Front. Genome Ed. 6:1467080. | https://doi.org/10.3389/fgeed.2024.1467080
Genome editing (GnEd) has the potential to provide many benefits to animal agriculture, offering a means for achieving rapid growth, disease resistance, and novel phenotypes. The technology has the potential to be useful for rapidly incorporating traits into existing selectively bred animals without the need for crossbreeding and backcrossing. Yet only four products from animals created via biotechnology, all growth-enhanced fishes, have reached commercialization and only on a limited scale. The past failure of genetically engineered (or GM) products to reach conventional producers can largely be attributed to the high cost of meeting GMO regulatory requirements. We review the history of GMO regulations internationally, noting the influence of Codex Alimentarius on the development of many existing regulatory frameworks. We highlight new regulatory approaches for GnEd organisms, first developed by Argentina, and the adoption of similar approaches by other countries. Such new regulatory approaches allow GnEd organisms that could have been developed by conventional means to be regulated under the same rules as conventional organisms and in the future is likely to enhance the opportunity for biotech animals to enter production. Treating certain GnEd products as conventional has had a large impact on the variety of biotechnological innovations successfully navigating regulatory processes. We suggest that for the full potential of GnEd technologies to be realized, enabling public policies are needed to facilitate use of GnEd as a breeding tool to incorporate new traits within existing animal breeding programs, rather than only a tool to create distinct new products.
https://www.frontiersin.org/journals/genome-editing/articles/10.3389/fgeed.2024.1467080/full
Mäkelin M., Helosvuori E., Meskus M. (2024): Strategic naturalizing in the Anthropocene: Managing cells, bodies and
ecosystems. The Sociological Review | https://doi.org/10.1177/00380261241261815
Discussions on the Anthropocene have called for increased attention to how the effects of human actions on the planet are accounted for. While much of this debate remains at a theoretical level, more studies on situated Anthropocene realities have been called for. Contributing to the latter, this article explores how experimental and clinical interventions are being accounted for in life science laboratories. Drawing on three research cases, genetically modified mosquitoes, laboratory-grown stem cell lines and assisted reproduction in the IVF clinic, the article traces how ‘strategic naturalizing’ is conducted to make sense of and justify human interventions on cells, bodies and ecosystems. Strategic naturalizing in laboratory work is situated, fluid, and also implicates the presence of the social scientist. Although naturalizing biotechnologies is not a new phenomenon, according to our observations scientists increasingly draw on notions of a planet profoundly transformed by human intervention as they conceptualize their own accountability. Consequently, we propose that strategic naturalizing is emerging as an elemental logic in the patchy local enactments of the Anthropocene and its concerns. In the context of experimental and clinical laboratory work, it is a key element in enacting good science and orienting the work towards making biotechnology acceptable in wider society. In studying this, the social scientist also is implicated in situated local enactments of the Anthropocene.
https://journals.sagepub.com/doi/full/10.1177/00380261241261815
EFSA
Pinotti L., Pastorelli G., Varese G., Cheli F., Di Lorenzo C., Montanelli S. Landolfi C., Mangano G., Gazerro C., Perricone V., Ottoboni M.,
Moradei A., Abbate R., Luciano A., Mercogliano F. (2024): A proposal for the development of a feed consumption database using a standardised feed classification system. EFSA supporting publication 21(9): EN-9036. 136 pp. doi:10.2903/sp.efsa.2024.EN-9036
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2024.EN-9036
England
Freisetzungsantrag für Weizen und Gerste:
Demonstration of low asparagine, low acrylamide, genome edited wheat (Triticum aestivum) and high lipid genome edited barley (Hordeum vulgare) at an agricultural show.