Publications – Publikationen

Sabel B. and Larhammar D. (2025): Reformation of science publishing: the Stockholm Declaration. R. Soc. Open Sci.

12251805 | http://doi.org/10.1098/rsos.251805

Science relies on integrity and trustworthiness. But scientists under career pressure are lured to purchase fake publications from ‘paper mills’ that use AI-generated data, text and image fabrication. The number of low-quality or fraudulent publications is rising to hundreds of thousands per year, which—if unchecked—will damage the scientific and economic progress of our societies. The result is editor and reviewer fatigue, irreproducible experiments, misguided experiments, disinformation and escalating costs that devour funding from taxpayers intended for research. It is high time to reevaluate current publishing models and outline a global plan to stop this unhealthy development. A conference was therefore organized by the Royal Swedish Academy of Sciences to draft an action plan with specific recommendations, as follows. (i) Academia should resume control of publishing using non-profit publishing models (e.g. diamond open-access). (ii) Adjust incentive systems to merit quality, not quantity, in a reputation economy where the gaming of publication numbers and citation metrics distorts the perception of academic excellence. (iii) Implement mechanisms to prevent and detect fake publications and fraud which are independent of publishers. (iv) Draft and implement legislations, regulations and policies to increase publishing quality and integrity. This is a call to action for universities, academies, science organizations and funders to unite and join this effort.

https://royalsocietypublishing.org/doi/10.1098/rsos.251805

Für die Mitzeichnung: https://sciii-it.org/stockholm-declaration/

Sabel, B.A., Knaack, E., Gigerenzer, G. et al. (2025): Fake publications in biomedical science: red-flagging method indicates

mass production. Naunyn-Schmiedeberg's Arch Pharmacol | https://doi.org/10.1007/s00210-025-04275-9

Integrity of academic publishing is increasingly undermined by fake publications massively produced by commercial “editing services” (so-called “paper mills”). These services use AI-supported production techniques at scale and sell fake publications to students, scientists, and physicians under pressure to advance their careers. Because the scale of fake publications in biomedicine is unknown, we developed an easy-to-apply rule to red-flag potentially fake publications and estimate their number. After analyzing questionnaires sent to authors of published papers, we developed simple classification rules and tested them in a 9-step bibliometric analysis in a sample of 17,120 publications listed in PubMed®. We first validated various simple rules and finally applied a multifactorial tallying rule comparing 400 known fakes with 400 random (presumed) non-fakes. This rule was then applied to 1,000 random publications each from 2020 and 2023. The multifactorial tallying rule was the best red-flagging method, with a 94% sensitivity and only a 11.5% false-alarm rate. The rate of red-flagged articles increased during the last decade, reaching an estimated 14.9% in 2020 and 16.3% in 2023. Countries with the highest proportion of read-flagged publications were China, India, Iran, Russia, and Turkey, with China and India the largest absolute contributors globally. Applying Bayes’ rule resulted in an estimate of 5.8% actual fakes in the biomedical literature. Given 1.86 million Scimago-listed biomedical publications in 2023, we estimate the actual number of true fakes at 107.800 articles per year, growing steadily. Scientific publications in biomedicine can be red-flagged as potentially fake using fast-and-frugal classification rules to earmark them for subsequent scrutiny. When applying Bayes´rule, the annual true scale of fake publishing in biomedicine is about 19 times that of the 5.671 biomedicine retractions in 2023. This scale of fraudulent publishing is concerning as it can damage trust in science, endanger public health, and impact economic spending. But fake detection tools can enable retractions of fake publications at scale and help prevent further damage to the permanent scientific record.

https://link.springer.com/article/10.1007/s00210-025-04275-9

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Luo, Y., Ceasar, S.A. & Benabdellah, K. (2025): Trajectory of genome editing technology. BMC Biol 23, 351 |

https://doi.org/10.1186/s12915-025-02450-1

https://link.springer.com/article/10.1186/s12915-025-02450-1

Venkataraman S.:, Hefferon K. (2025): Editorial: Social aspects of crop genome editing. Front. Genome Ed., Sec. Genome

Editing in Plants Volume 7 - 2025 | https://doi.org/10.3389/fgeed.2025.1740380

Koller F.:(2025): The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications .

Int. J. Mol. Sci. 2025, 26(23), 11391; https://doi.org/10.3390/ijms262311391

Conventional plant breeding relies on the occurrence of chromosomal crossover and spontaneous or non-targeted mutations in the genome induced by physical or chemical stressors. However, constraints exist concerning the number and variation of genotypes that can be achieved in this way, as the occurrence and combination of mutations are not equally distributed across the genome. The underlying mechanisms and causes of reproductive constraints can be considered the result of evolution to maintain the genomic stability of a species while at the same time allowing necessary adaptations. A continuous horizon scan was carried out to identify plants derived from new genomic techniques (NGTs), which show that CRISPR/Cas is able to circumvent at least some of these mechanisms and constraints. The reason for this is the specific mode of action: While physico-chemical mutagens such as radiation or chemicals merely cause a break in DNA, recombinant enzymatic mutagens (REMs), such as CRISPR/Cas, additionally interfere with cellular repair mechanisms. More recently developed REMs even expand the capabilities of NGTs to introduce new genetic variations within the target sequences. Thus, NGTs introduce genetic changes and combinations that are unknown in the current breeding pool and that are also unlikely to occur as a result of any previously used breeding methods. The resulting genotypes may need to be considered as ‘new to the environment’. The technical potential of NGTs should also be taken into account in regulatory provisions. Previously unknown genotypes and phenotypes may negatively impact plant health, ecosystems, biodiversity, and plant breeding. It must further be acknowledged that the different outcomes of NGTs and conventional breeding are not always evident at first sight. As a starting point, within a process-oriented approval process, molecular characterization can inform the following steps in risk assessment and guide requests for further data.

https://www.mdpi.com/1422-0067/26/23/11391

Avni, R., Kamal, N., Bitz, L. et al. (2025): A pangenome and pantranscriptome of hexaploid oat. Nature (2025) |

https://doi.org/10.1038/s41586-025-09676-7

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health^1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues³. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales⁴. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

https://www.nature.com/articles/s41586-025-09676-7

Yan J., Zhou Z., Gatehouse A.M.R., Ma W., Gao Y. (2025): Potato expressing Cry1C and Cry2A confers resistance to

Phthorimaea operculella (Lepidoptera: Gelechiidae). Pest Management Science | https://doi.org/10.1002/ps.70403

BACKGROUND: As the third most important global food crop, potato plays a vital role in ensuring food security and poverty alleviation. However, its production is severely threatened by the potato tuber moth (Phthorimaea operculella; PTM), a destructive pest that damages foliage during growth and bores into tubers during storage, causing yield losses of 85–100% under severe infestations. Traditional reliance on chemical pesticides poses challenges such as environmental pollution, pesticide residues, and increased production costs, highlighting the need for sustainable alternatives.

RESULT:In this study, Cry1C and Cry2A genes were expressed in potato cultivar E3 via Agrobacterium-mediated transformation, generating single-copy transgenic lines with high gene expression. Bioassays showed that PTM larvae feeding on transgenic leaves exhibited significantly elevated mortality (>35.4%), with the Cry1C-2 line achieving 60.4% mortality within 24 h. Notably, the highest-expressing Cry1C and Cry2A transgenic lines caused 100% larval mortality within 4 and 7 days, respectively, demonstrating complete lethality against PTM. Histological analysis confirmed that Bt proteins induced midgut epithelial cell lysis and peritrophic membrane disruption, directly leading to insect death.

CONCLUSION: This study is the first to demonstrate that Cry2A expression in potato confers resistance to PTM. It provides novel genetic resources for insect-resistant potato breeding and proposes a gene pyramiding strategy to delay the onset of resistance evolution in pest populations. Future research should focus on evaluating field resistance durability and investigating potential synergistic effects between Cry1C/Cry2A and other Bt proteins to develop multi-target pest management systems.

https://scijournals.onlinelibrary.wiley.com/doi/10.1002/ps.70403

Yu, D.; Meng, Z.; Kong, F.; Gao, N.et al.(2025): Increasing γ-Aminobutyric Acid Content in Dwarf Cherry Tomato Using

CRISPR/Cas9-Mediated Gene Editing. Horticulturae 2025, 11, 1423.https://doi.org/10.3390/horticulturae11121423

Gamma-aminobutyric acid (GABA) is considered an important bioactive compound that improves sleep quality and regulates blood pressure. Tomatoes are an ideal horticultural crop that can accumulate a high level of GABA in fruits. The development of higher-GABA tomatoes has significant market potential. In this study, we edited the SlGAD3 gene to increase GABA content in the dwarf cherry tomato, WEIMEI T102. After transformation using the Agrobacterium-mediated method, we identified several SlGAD3 mutation lines, which showed changed GABA levels compared to the recipient line. Molecular characterization showed stable trait inheritance for multiple generations. The GABA level in fruits also stably accumulated for multiple generations, which significantly increased up to about 1.9 mg/g FW in E13-13. These results indicate that it is feasible to increase the GABA content in dwarf cherry tomatoes by using gene editing technology.

https://www.mdpi.com/2311-7524/11/12/1423

Rajendran, P., Saravanan, K., Jagadhesan, B. et al. (2025): Stress Resilience in Tuber Crops: A Closer View on Genome Editing

and Molecular Approaches. J Plant Growth Regul | https://doi.org/10.1007/s00344-025-11936-9

The increasing population raises concerns about food scarcity in the future. Tuber crops, which meet a significant fraction of the global food demand, are also valuable sources of animal feed. Their production is hampered by various abiotic (drought, salinity, heavy metal toxicity, etc.) and biotic stresses (viruses, bacteria, fungi, nematodes, weeds, insect pests, etc.). The severity of these stresses is further exacerbated by the changing climatic conditions, which threaten food security. This review examines recent advances in genome editing technologies, particularly CRISPR/Cas systems, to improve stress resilience in major tuber crops like potato, cassava, and sweet potato. Key abiotic stresses addressed include salinity, drought, and heavy metal toxicity. For biotic stresses, the focus is on developing resistance to major diseases and insect pests. The review highlights potential gene targets identified through omics approaches that could be manipulated via genome editing to enhance stress tolerance. Recent improvements in CRISPR technology, including base editors and smaller Cas variants, offer increased precision and versatility for tuber crop improvement. While genome editing shows great promise, challenges remain in identifying optimal gene targets and improving editing efficiency in some tuber species. Overall, genome editing presents a powerful tool to rapidly develop climate-resilient, high-yielding tuber crop varieties to meet growing global food demand.

https://link.springer.com/article/10.1007/s00344-025-11936-9

Palange, N.J., Obua, T., Sserumaga, J.P. et al. (2025): Unraveling the genetic architecture of anti-nutritional factors in

soybean (Glycine max.) for nutritional enhancement. Sci Rep 15, 42787 | https://doi.org/10.1038/s41598-025-27132-4

Anti-nutritional factors (ANFs) can reduce nutrient bioavailability for monogastric animals. Therefore, this study aimed to understand the genetic architecture underlying ANF accumulation in soybean. Diversity arrays technology and a spectrophotometric method were employed to generate genotypic and phenotypic data, respectively, and gene mining was performed within 100-kb genomic window. A significant difference was found regarding ANFs content in the genotypes (p < 0.001). Significant SNP markers for phytate were identified on chromosomes 3, 4, 13, and 20 by FarmCPU, and for total trypsin inhibitors (TTI) on 6, 12, and 14 by CMLM models, whereas mrMLM model detected markers on chromosome 3, 12 and 15 for phytate, 4, 9, 13, 17 and 18 for TTI. Genes associated with phytate content include Glyma.03G001600, Glyma.04G194600, Glyma.13G128200, Glyma.20G118700, Glyma.14G213400, and Glyma.16G126400. For TTI, the genes are Glyma.06G074700, Glyma.12G241600, Glyma.14G176700, Glyma.13G052700, and Glyma.18G050400. These genes are primarily linked to plant defense and substrate interactions. Most promising SNP markers for marker-assisted selection aimed at reducing phytate levels include Soy_3_218818 (218,818 bp), Soy_3_241209 (241,209 bp), Soy_4_45462019 (45,462,019 bp), Soy_14_48672982 (48,672,982 bp), and Soy_6_5695090 (5,695,090 bp). For TTI, key markers include Soy_14_43649238 (43,649,238 bp), Soy_12_41339023 (41,339,023 bp), Soy_18_4301721 (4,301,721 bp), and Soy_13_14029215 (14,029,215 bp). These findings offer a valuable foundation for marker-assisted breeding aimed at improving soybean nutritional quality.

https://www.nature.com/articles/s41598-025-27132-4

Xu, G., Chen, Y., Martins, L.M. et al. (2025): Transcription factors instruct DNA methylation patterns in plant reproductive

tissues. Nat Cell Biol | https://doi.org/10.1038/s41556-025-01808-5

DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. In Arabidopsis, CLASSY3 targets the RNA-directed DNA methylation machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLASSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCTS METHYLATION (RIMs) and demonstrate that disruption of their DNA-binding domains, or the motifs they recognize, blocks RNA-directed DNA methylation. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information.

https://www.nature.com/articles/s41556-025-01808-5

Park B.J. Hua S., Casler K.D., Vertino P.M. et al. (2025): CUT&Tag overcomes biases of ChIP and establishes chromatin patterns for repetitive genomic loci, iScience 28, 113757 | https://doi.org/10.1016/j.isci.2025.113757

New in situ chromatin profiling methods, such as CUT&Tag, have streamlined studies of chromatin features by eliminating the need for up-front purification, but we find that some features are not equally detectable when comparing with previous methods. ChIP-Seq and CUT&Tag identify similar chromatin enrichment profiles for genic loci, such as promoters, but major differences are detected at heterochromatin-associated regions. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 over a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. For example, mouse IAPEz-int elements exhibit strong enrichment using CUT&Tag but underrepresentation using ChIP-Seq. Additionally, several euchromatin-associated proteins, such as RUNX1, co-purify with insoluble heterochromatin in ChIP studies, but are detectible at repetitive elements when applying in situ fragmentation methods. Our study reveals that the current understanding of chromatin states is extensively incomplete, and newer in situ chromatin fragmentation-based techniques are preferred for investigating repetitive

https://www.cell.com/iscience/fulltext/S2589-0042(25)02018-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2589004225020188%3Fshowall%3Dtrue

Lee, HJ., Lee, TG., Cho, C. et al.(2025): Enhanced heme production in industrial Saccharomyces cerevisiae through

metabolic engineering. npj Sci Food 9, 244 | https://doi.org/10.1038/s41538-025-00618-1

This study aimed to develop an efficient Saccharomyces cerevisiae-based cell factory for heme production. The industrial strain S. cerevisiae KCCM 12638, a starter strain used in American whisky production, was selected for its naturally high heme concentration, and its medium composition was optimized. Next, CRISPR/Cas9-based genome editing was employed to enhance carbon flux through the heme biosynthetic pathway by overexpressing HEM2, HEM3, HEM12, and HEM13 genes, which encode key enzymes involved in heme synthesis. Additionally, the HMX1 gene, which encodes heme oxygenase 1, was inactivated to prevent heme degradation. The resulting ΔHMX1_H2/3/12/13 strain achieved a heme titer of 9 mg/L in batch fermentation, a 1.7-fold improvement over the wild-type KCCM 12638 strain. In a glucose-limited fed-batch fermentation, the ΔHMX1_H2/3/12/13 strain produced 67 mg/L heme. This study demonstrates that engineering industrial yeast strains can significantly enhance heme production, with promising applications in food, pharmaceuticals, and bioenergy.

https://www.nature.com/articles/s41538-025-00618-1

EFSA

GMO Panel (2025): Assessment of genetically modified maize NK603 × T25 for renewal authorisation under Regulation (EC)

No 1829/2003 (dossier GMFF-2023-21252). EFSA Journal, 23(11), e9745 | https://doi.org/10.2903/j.efsa.2025.9745

https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2025.9745