Search Results (29)

Rapeseed (Brassica napus L.) faces escalating threats from abiotic and biotic stresses, notably blackleg caused by Leptosphaeria maculans. Due to limited chemical control efficacy and stringent GMO regulations, marker-assisted selection (MAS) leveraging natural genetic variation has become an indispensable strategy for crop improvement. This study identified novel molecular markers for blackleg resistance by integrating genome-wide association study (GWAS) results with high-throughput genotyping by Diversity Arrays Technology sequencing. Phenotypic screening across the population demonstrated a wide spectrum of disease severity (scores 0–6), confirming the segregation of key resistance genes. The DArTseq platform identified nearly 104,000 markers, comprising 61% SilicoDArTs and 39% SNPs. Among the 33 most significant markers associated with resistance (p < 0.01), 76% were SilicoDArTs. Transcriptomic data further validated these findings, revealing 13 marker-linked genes expressed during infection, seven of which exhibited significant differential expression. Comprehensive functional annotation of Arabidopsis thaliana orthologs associated these genes with diverse cellular and plant-wide processes, particularly during stress responses. Collectively, these findings emphasize the complex polygenic nature of blackleg resistance and provide robust genomic tools for the accelerated breeding of resilient B. napus cultivars. Full article

The rapid global expansion of genetically modified (GM) crops requires fast, on-site detection methods. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated (CRISPR/Cas) systems offer a promising platform for decentralized GM organism (GMO) monitoring. This review focuses specifically on the application of this technology in agriculture and food supply chains, diverging from previous reviews centered on clinical diagnostics. We examine the mechanisms of key CRISPR effectors (e.g., Cas12a, Cas13a) and their integration into diagnostic platforms (e.g., DETECTR, SHERLOCK) for detecting transgenic elements (e.g., CaMV35S promoter). A dedicated comparison of signal readout modalities, including fluorescence, lateral flow, and electrochemical sensing, highlights their suitability for different GMO detection scenarios, from field screening to laboratory confirmation. Finally, we discuss current challenges, including multiplexing and standardization, and outline future directions, such as the engineering of novel Cas variants and integration with smartphone technology. CRISPR-based diagnostics are poised to become indispensable tools for decentralized, efficient, and reliable GMO detection. Full article

Antisense oligonucleotides (ASOs) are short, synthetic DNA fragments that offer a powerful means of modulating gene expression. By leveraging endogenous regulatory pathways, ASOs enable precise control over gene activity at multiple levels, including genomic DNA, transcription, RNA processing, and translation. Their applications span basic research and translational science, ranging from the generation of epigenetically modified organisms as potential GMO alternatives to the development of therapies for rare or treatment-resistant diseases. This review highlights the molecular mechanisms of ASO action, design and modification strategies, and delivery approaches across diverse cell types. Future directions include elucidating detailed molecular pathways, optimizing experimental conditions, and enhancing the persistence of therapeutic effects. Overall, ASOs represent a versatile and innovative tool in functional genomics, with broad implications for molecular biology, biotechnology, and medicine. Full article

The rapid and sensitive detection of regulatory elements within transgenic constructs of genetically modified organisms (GMOs) is essential for effective monitoring and control of their distribution. In this study, we present several innovative electrochemical biosensing platforms for the detection of regulatory sequences in genetically modified (GM) plants, combining the loop-mediated isothermal amplification (LAMP) method with electrodes functionalized by two-dimensional (2D) nanomaterials. The sensor design exploits the high surface area and excellent conductivity of reduced graphene oxide, Ti₃C₂T_x, and molybdenum disulfide (MoS₂) to enhance signal transduction. Furthermore, we used a “green synthesis” method for Ti₃C₂T_x preparation that eliminates the use of hazardous hydrofluoric acid (HF) and hydrochloric acid (HCl), providing a safer and more sustainable approach for nanomaterial production. Within this framework, the performance of various custom-fabricated electrodes, including laser-patterned gold leaf films, physical vapor deposition (PVD)-deposited gold electrodes, and screen-printed gold electrodes, is evaluated and compared with commercial screen-printed gold electrodes. Additionally, gold and carbon electrodes were electrochemically covered by gold nanoparticles (AuNPs), and their properties were compared. Several electrochemical methods were used during the DNA detection, and their importance and differences in excitation signal were highlighted. Electrochemical properties, sensitivity, selectivity, and reproducibility are characterized for each electrode type to assess the influence of fabrication methods and material composition on sensor performance. The developed biosensing systems exhibit high sensitivity, specificity, and rapid response, highlighting their potential as practical tools for on-site GMO screening and regulatory compliance monitoring. This work advances electrochemical nucleic acid detection by integrating environmentally-friendly nanomaterial synthesis with robust biosensing technology. Full article

Background: Ultra-processed foods (UPFs) represent a substantial part of modern diets, with a growing prevalence in food environments worldwide. Their unfavourable nutritional composition and adverse health effects present growing public health concerns. Methods: This study examines the prevalence of UPFs in the Slovenian food supply, their nutritional quality and the use of different food symbols and labelling schemes on food packaging. A cross-sectional analysis was conducted using the representative Slovenian branded foods database. A total of 23,173 prepacked foods and beverages were categorised into levels of processing according to the NOVA classification system. The nutritional composition of UPFs was compared to less processed products within 16 narrow subcategories. Additionally, the prevalence in the use of front-of-package nutrition labelling (FOPNL) and subjectively nutrition-related elements (SNREs) (such as EU Organic, Vegan labels etc.) were assessed across different food categories and processing levels. Results: Results show that UPFs represent 54.5% of the available products in the Slovenian food supply, with the highest prevalence in Confectionery (93%), Bread and bakery products (83%), Meat, meat products and alternatives (77%) and Convenience foods (74%). Comparison of nutritional composition indicated that UPFs had significantly poorer nutritional composition compared to less processed counterparts, including higher levels of sugar, salt and saturated fats, and a lower protein content. Breakfast cereals, Snack foods, Meat alternatives and Pre-prepared salads and sandwiches showed the most significant differences between UPFs and less processed counterparts. Analysis of the prevalence of symbols and labelling schemes revealed that 33.8% of products carried at least one FOPNL (15.0%) or SNRE (19.1%), with SNREs being more prevalent on less processed products and FOPNL predominantly used on UPFs (p < 0.05). The most prevalent SNRE was the EU Organic logo (12.7%), followed by the Vegan (4.7%) and Non-GMO (3.1%) logos, whereas the most frequent FOPNL was Reference Intakes (RI), presenting only energy value RI-Energy (12.5%), followed by nutrient-specific RI (1.6%), while other FOPNL were scarce and limited to certain categories. An additional comparison of visual presentation highlighted the potentially selective use of voluntary FOPNL to improve product framing. This raises concerns about their role in guiding consumer choices versus serving as marketing tools, especially when it comes to UPFs. Conclusions: Our findings highlight the need for monitoring UPFs in the food supply together with harmonised, mandatory labelling regulations to ensure transparency and empower consumers to make healthier choices. Full article

CRISPR-Cas9 has revolutionized genetic research with bioinformatics tools essential for tasks like guide RNA design, off-target prediction, and data analysis. This systematic review summarizes the functionality and key features of such tools. Studies published after 2012 were selected through searches in PubMed, Google Scholar, and other sources, with the final search conducted on 9 November 2024. Seven studies met the criteria, describing around 45 tools, including databases and functional programs. Tools like CRISPResso, CHOPCHOP, and Cas-OFFinder were commonly highlighted, with a major focus on single-guide RNA (sgRNA) design and optimization. Some tools provided specific solutions, while others offered broader functionality, but most lacked experimental validation. Several tools were developed by the authors of the studies, introducing potential bias. Findings highlight a need for integrated platforms that combine functionalities, reducing reliance on fragmented workflows. Current tools often address narrow tasks, complicating their practical application. Future development should focus on comprehensive, multitasking tools to improve accessibility and streamline research processes. Limitations include the descriptive nature of most studies, potential author bias, and challenges in comparing tools objectively. Nonetheless, this review underscores bioinformatics’ critical role in CRISPR research and emphasizes the need for innovative, standardized platforms. This study received no funding and was not registered. Full article

Gene editing using CRISPR/Cas9 is an innovative tool for developing new mushroom strains, offering a promising alternative to traditional breeding methods that are time-consuming and labor-intensive. However, plasmid-based gene editing presents several challenges, including the need for selecting appropriate promoters for Cas9 expression, optimizing codons for the Cas9 gene, the unintended insertion of fragmented plasmid DNA into genomic DNA (gDNA), and regulatory concerns related to genetically modified organisms (GMOs). To address these issues, we utilized a Ribonucleoprotein (RNP) complex consisting of Cas9 and gRNA for gene editing to modify the A mating-type gene of Lentinula edodes. To overcome the challenges posed by the large size of the Cas9 protein, which limits its penetration through the protoplast membrane, and the susceptibility of sgRNA to degradation, we developed a nanoparticle complex using calcium phosphate and polyacrylic acid. This approach significantly improved gene editing efficiency. Consequently, we successfully edited the mating-controlling genes hd1 and hd2 in L. edodes and examined the effects of their disruption on mating. Disruption of the hd1 gene, which is known to influence mycelial growth, did not significantly affect growth or mating. In contrast, editing the hd2 gene disrupted mating with compatible partners, highlighting its critical role in the mating process. The RNP-based transformation technology presented here offers significant advancement over traditional plasmid-based methods, enhancing the efficiency of targeted gene modification while avoiding the insertion of foreign genetic material, thereby mitigating GMO-related regulatory concerns. Full article

World hunger remains a pressing global issue that demands innovative solutions to ensure food security and alleviate widespread malnutrition. In this context, the role of chemistry in addressing the complex challenges of food production, preservation, and distribution is crucial. Chemistry has the potential to play a significant role in addressing the global issue of world hunger. Through the development of innovative agricultural practices, food preservation technologies, and novel food sources, chemistry can help increase the global food supply and ensure that all people have access to nutritious and affordable food. This paper explores the various ways in which chemistry is being used to tackle world hunger, from the production of drought-resistant crops to the development of sustainable farming methods. The paper also discusses the challenges that must be overcome to fully leverage the potential of chemistry in addressing world hunger, including the need for investment in research and development, as well as greater collaboration between scientists, policymakers, and other stakeholders. Ultimately, this paper argues that chemistry can be a powerful tool in the fight against world hunger and that continued investment in this field has the potential to make a significant impact on global food security. Chemistry plays a fundamental role in improving agricultural practices and increasing crop yields. Through the development of fertilizers, pesticides, and herbicides, chemists can optimize plant growth, enhance soil fertility, and combat pests and diseases that threaten agricultural productivity. Moreover, advancements in genetic engineering and biotechnology allow scientists to create genetically modified organisms (GMOs) as potential food. In conclusion, chemistry holds immense potential in addressing the challenges of world hunger. By leveraging its principles and technologies, including agricultural innovations, food preservation techniques, fortification strategies, and sustainable practices, chemistry can contribute to increasing food production, improving nutrition, and ensuring food security for vulnerable populations. However, it is crucial to prioritize ethical considerations, sustainability, and equitable access to these advancements to ensure a comprehensive and inclusive approach to solving world hunger. Full article

The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed. Full article

The revolutionary CRISPR/Cas9 genome-editing technology has emerged as a powerful tool for plant improvement, offering unprecedented precision and efficiency in making targeted gene modifications. This powerful and practical approach to genome editing offers tremendous opportunities for crop improvement, surpassing the capabilities of conventional breeding techniques. This article provides an overview of recent advancements and challenges associated with the application of CRISPR/Cas9 in plant improvement. The potential of CRISPR/Cas9 in terms of developing crops with enhanced resistance to biotic and abiotic stresses is highlighted, with examples of genes edited to confer disease resistance, drought tolerance, salt tolerance, and cold tolerance. Here, we also discuss the importance of off-target effects and the efforts made to mitigate them, including the use of shorter single-guide RNAs and dual Cas9 nickases. Furthermore, alternative delivery methods, such as protein- and RNA-based approaches, are explored, and they could potentially avoid the integration of foreign DNA into the plant genome, thus alleviating concerns related to genetically modified organisms (GMOs). We emphasize the significance of CRISPR/Cas9 in accelerating crop breeding processes, reducing editing time and costs, and enabling the introduction of desired traits at the nucleotide level. As the field of genome editing continues to evolve, it is anticipated that CRISPR/Cas9 will remain a prominent tool for crop improvement, disease resistance, and adaptation to challenging environmental conditions. Full article

This is the third part of the paper presenting a miniature, combustion-type gas sensor (dubbed GMOS) based on a novel thermal sensor (dubbed TMOS). The TMOS is a micromachined CMOS-SOI transistor, which acts as the sensing element and is integrated with a catalytic reaction plate, where ignition of the gas takes place. The first part was focused on the chemical and technological aspects of the sensor. In Part 2, the emphasis was on the physical aspects of the reaction micro-hot plate on which the catalytic layer is deposited. The present study focuses on applying several advanced simulation tools, which extend our understanding of the GMOS performance, as well as pellistor sensors in general. The three main challenges in simulating the performance are: (i) how to define the operating temperature based on the input parameters; (ii) how to measure the dynamics of the temperature increase during cyclic operation at a given duty cycle; (iii) how to model the correlation between the operating temperature and the sensing response. The simulated and analytical models and measured results are shown to be in good agreement. Full article

Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs. Full article

Genetic transformation has emerged as an important tool for the genetic improvement of valuable plants by incorporating new genes with desirable traits. These strategies are useful especially in crops to increase yields, disease resistance, tolerance to environmental stress (cold, heat, drought, salinity, herbicides, and insects) and increase biomass and medicinal values of plants. The production of healthy plants with more desirable products and yields can contribute to sustainable development goals. The introduction of genetically modified food into the market has raised potential risks. A proper assessment of their impact on the environment and biosafety is an important step before their commercialization. In this paper, we summarize and discuss the risks and benefits of genetically modified plants and products, human health hazards by genetically transformed plants, environmental effects, Biosafety regulations of GMO foods and products, and improvement of medicinal values of plants by the genetic transformation process. The mechanisms of action of those products, their sources, and their applications to the healthcare challenges are presented. The present studies pointed out the existence of several controversies in the use of GMOs, mainly related to the human health, nutritions, environmental issues. Willingness to accept genetically modified (GM) products and the adoption of biosafety regulations varies from country to country. Knowledge about the gene engineering technology, debate between the government agencies, scientist, environmentalist and related NGOs on the GM products are the major factors for low adoptions of biosafety regulation. Therefore, the genetic transformation will help in the advancement of plant species in the future; however, more research and detailed studies are required. Full article

The tomato is one of the most important vegetables in the world. The demand for tomatoes is high in virtually any country, owing to their gastronomic versatility and nutritional and aromatic value. Drought, salinity, and inadequate temperature can be major factors in diminishing yield, affecting physiological and biochemical processes and altering various metabolic pathways, from the aggregation of low molecular–weight substances to the transcription of specific genes. Various biotechnological tools can be used to alter the tomato genes so that this species can more rapidly or better adapt to abiotic stress. These approaches range from the introgression of genes coding for specific enzymes for mitigating a prevailing stress to genetic modifications that alter specific metabolic pathways to help tomato perceive environmental cues and/or withstand adverse conditions. In recent years, environmental and social concerns and the high complexity of the plant response may increase the attention of applied plant biotechnology toward biomimetic strategies, generally defined as all the approaches that seek to develop more sustainable and acceptable strategies by imitating nature’s time-tested solutions. In this review, we provide an overview of some of the genetic sequences and molecules that were the objects of biotechnological intervention in tomato as examples of approaches to achieve tolerance to abiotic factors, improving existing nature-based mechanisms and solutions (biomimetic biotechnological approaches (BBA)). Finally, we discuss implications and perspectives within the GMO debate, proposing that crops modified with BBA should receive less stringent regulation. Full article

Environmental abiotic stresses challenge food security by depressing crop yields often exceeding 50% of their annual production. Different methods, including conventional as well as genomic-assisted breeding, mutagenesis, and genetic engineering have been utilized to enhance stress resilience in several crop species. Plant breeding has been partly successful in developing crop varieties against abiotic stresses owning to the complex genetics of the traits as well as the narrow genetic base in the germplasm. Irrespective of the fact that genetic engineering can transfer gene(s) from any organism(s), transgenic crops have become controversial mainly due to the potential risk of transgene-outcrossing. Consequently, the cultivation of transgenic crops is banned in certain countries, particularly in European countries. In this scenario, the discovery of the CRISPR tool provides a platform for producing transgene-free genetically edited plants—similar to the mutagenized crops that are not extensively regulated such as genetically modified organisms (GMOs). Thus, the genome-edited plants without a transgene would likely go into the field without any restriction. Here, we focused on the deployment of CRISPR for the successful development of abiotic stress-tolerant crop plants for sustaining crop productivity under changing environments. Full article