Agricultural nanotechnology for a safe and sustainable future: current status, challenges, and beyond.

Nanotechnology, which involves manipulating matter at the atomic and molecular scales to produce structures and devices ranging from 1 to 100 nm, is increasingly being applied in agriculture. Nanoscale materials possess distinct optical, electrochemical, and mechanical properties that enable the smart, targeted delivery of pesticides, fertilizers, and genetic materials to plants, as well as rapid sensing and on-site monitoring of plant health, soil fertility, and water quality in a digital format. This review explores the application of nanotechnology in agriculture, examining the challenges and benefits related to all aspects of crop production, with a particular focus on regulatory issues. Key findings indicate that nanotechnology can improve crop production and reduce the environmental footprint of agriculture through precise input management. However, several critical issues need to be addressed, including the limited knowledge of the long-term environmental impacts associated with agricultural nanotechnology and the ambiguity of current regulations. This underscores the need for further research to elucidate its impact on soil, water, and environmental and human health, to inform evidence-based regulations. © 2024 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Oxford nanopore sequencing-based assay for BTD gene screening: Design, clinical validation, and variant frequency assessment in the Turkish population.

Biotinidase deficiency (BTD) is an autosomal recessive disorder characterized by impaired recycling of the water-soluble vitamin biotin which leads to a spectrum of clinical manifestations ranging from mild to severe, including mainly neurological and cutaneous symptoms. Biotin supplementation is a cornerstone of treatment, but diagnosis often relies on measuring serum enzyme activity, which needs to be confirmed by genetic analysis. Thus, molecular methods become necessary in the differential diagnosis of BTD. Accordingly, countries with a high-incidence have implemented next-generation sequencing (NGS) techniques to newborn screening programs for BT. Nevertheless, NGS platforms, while well-established, present challenges in cost, labor, accessibility, and duration for newborn screening programs targeting BTD, therefore these limitations necessitate the exploration of alternative systems to ensure efficient and widespread screening. Here, third-generation sequencing platforms, notably Oxford Nanopore Technology (ONT), present promising solutions to the associated challenges. Hence, in the present study, we aimed to develop an ONT-based assay for the screening of BTD gene. After designing and optimizing primers for long-PCR using reference DNA, we assessed the performance of the ONT assay in BTD patients previously diagnosed by enzyme assay and confirmed using Illumina-based sequencing. The results demonstrate a strong correlation between the two methods, indicating the reliability of the ONT-based assay. Moreover, this first in-house single gene testing specifically tailored for BTD successfully detected previously known genetic variants with high sequencing depths, affirming the effectiveness of ONT-based sequencing in human genetics.

Clinical Validation and Evaluation of a Colorimetric SARS-CoV-2 RT-LAMP Assay Against RT-PCR.

Objective: Reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) is one of the time-saving, accurate, and cost-effective alternative methods to real-time polymerase chain reaction (RT-PCR). This study aimed to identify the robustness of a colorimetric RT-LAMP assay kit that we developed, detecting SARS-COV-2 viral RNA within 30 minutes using a primer set special to the N gene against RT-PCR, the gold standard. Materials and Methods: Both symptomatic and asymptomatic subjects were included from a single university hospital and the status of both RT-PCR and RT-LAMP assay results were compared, and the consistency of these two assays was analyzed. Results: We showed that the RT-LAMP and RT-PCR assay results confirmed 90% consistency. When we consider the epidemiologic, clinical, and radiologic evaluation, the consistency reached 97%. Conclusion: The results revealed that the colorimetric RT-LAMP assay was efficient, robust, and rapid to be used as in vitro diagnostic tool to display competitiveness compared with RT-PCR.

Puccinia striiformis f. sp. tritici effectors in wheat immune responses.

The obligate biotrophic fungus Puccinia striiformis f. sp. tritici, which causes yellow (stripe) rust disease, is among the leading biological agents resulting in tremendous yield losses on global wheat productions per annum. The combatting strategies include, but are not limited to, fungicide applications and the development of resistant cultivars. However, evolutionary pressure drives rapid changes, especially in its "effectorome" repertoire, thus allowing pathogens to evade and breach resistance. The extracellular and intracellular effectors, predominantly secreted proteins, are tactical arsenals aiming for many defense processes of plants. Hence, the identity of the effectors and the molecular mechanisms of the interactions between the effectors and the plant immune system have long been targeted in research. The obligate biotrophic nature of P. striiformis f. sp. tritici and the challenging nature of its host, the wheat, impede research on this topic. Next-generation sequencing and novel prediction algorithms in bioinformatics, which are accompanied by in vitro and in vivo validation approaches, offer a speedy pace for the discovery of new effectors and investigations of their biological functions. Here, we briefly review recent findings exploring the roles of P. striiformis f. sp. tritici effectors together with their cellular/subcellular localizations, host responses, and interactors. The current status and the challenges will be discussed. We hope that the overall work will provide a broader view of where we stand and a reference point to compare and evaluate new findings.

Increased levels of cell wall degrading enzymes and peptidases are associated with aggressiveness in a virulent isolate of Pyrenophora teres f. maculata.

Pyrenophora teres f. maculata (Ptm) is a fungal pathogen that causes the spot form of net blotch on barley and leads to economic losses in many of the world's barley-growing regions. Isolates of Ptm exhibit varying levels of aggressiveness that result in quantifiable changes in the severity of the disease. Previous research on plant-pathogen interactions has shown that such divergence is reflected in the proteome and secretome of the pathogen, with certain classes of proteins more prominent in aggressive isolates. Here we have made a detailed comparative analysis of the secretomes of two Ptm isolates, GPS79 and E35 (highly and mildly aggressive, respectively) using a proteomics-based approach. The secretomes were obtained in vitro using media amended with barley leaf sections. Secreted proteins therein were harvested, digested with trypsin, and fractionated offline by HPLC prior to LC-MS in a high-resolution instrument to obtain deep coverage of the proteome. The subsequent analysis used a label-free quantitative proteomics approach with relative quantification of proteins based on precursor ion intensities. A total of 1175 proteins were identified, 931 from Ptm and 244 from barley. Further analysis revealed 160 differentially abundant proteins with at least a two-fold abundance difference between the isolates, with the most enriched in the aggressive GPS79 secretome. These proteins were mainly cell-wall (carbohydrate) degrading enzymes and peptidases, with some oxidoreductases and other pathogenesis-related proteins also identified, suggesting that aggressiveness is associated with an improved ability of GPS79 to overcome cell wall barriers and neutralize host defense responses.

Selenophene-Modified Boron Dipyrromethene-Based Photosensitizers Exhibit Photodynamic Inhibition on a Broad Range of Bacteria.

Microorganisms are crucial for human survival in view of both mutualistic and pathogen interactions. The control of the balance could be achieved by use of the antibiotics. There is a continuous arms race that exists between the pathogen and the antibiotics. The emergence of multidrug-resistant (MDR) bacteria threatens health even for insignificant injuries. However, the discovery of new antibiotics is not a fast process, and the healthcare system will suffer if the evolution of MDR lingers in its current frequency. The cationic photosensitizers (PSs) provide a unique approach to develop novel, light-inducible antimicrobial drugs. Here, we examine the antimicrobial activity of innovative selenophene-modified boron dipyrromethene (BODIPY)-based PSs on a variety of Gram (+) and Gram (-) bacteria. The candidates demonstrate a level of confidence in both light-dependent and independent inhibition of bacterial growth. Among them, selenophene conjugated PS candidates (BOD-Se and BOD-Se-I) are promising agents to induce photodynamic inhibition (PDI) on all experimented bacteria: E. coli, S. aureus, B. cereus, and P. aeruginosa. Further characterizations revealed that photocleavage ability on DNA molecules could be potentially advantageous over extracellular DNA possessing biofilm-forming bacteria such as B. cereus and P. aeruginosa. Microscopy analysis with fluorescent BOD-H confirmed the colocalization on GFP expressing E. coli.

In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions.

The importance of wheat yellow rust disease, caused by Puccinia striiformis f. sp. tritici (Pst), has increased substantially due to the emergence of aggressive new Pst races in the last couple of decades. In an era of escalating human populations and climate change, it is vital to understand the infection mechanism of Pst in order to develop better strategies to combat wheat yellow disease. The present study focuses on the identification of small secreted proteins (SSPs) and candidate-secreted effector proteins (CSEPs) that are used by the pathogen to support infection and control disease development. We generated de novo assembled transcriptomes of Pst collected from wheat fields in central Anatolia. We inoculated both susceptible and resistant seedlings with Pst and analyzed haustoria formation. At 10 days post-inoculation (dpi), we analyzed the transcriptomes and identified 10550 Differentially Expressed Unigenes (DEGs), of which 6072 were Pst-mapped. Among those Pst-related genes, 227 were predicted as PstSSPs. In silico characterization was performed using an approach combining the transcriptomic data and data mining results to provide a reliable list to narrow down the ever-expanding repertoire of predicted effectorome. The comprehensive analysis detected 14 Differentially Expressed Small-Secreted Proteins (DESSPs) that overlapped with the genes in available literature data to serve as the best CSEPs for experimental validation. One of the CSEPs was cloned and studied to test the reliability of the presented data. Biological assays show that the randomly selected CSEP, Unigene17495 (PSTG_10917), localizes in the chloroplast and is able to suppress cell death induced by INF1 in a Nicotiana benthamiana heterologous expression system.

A Puccinia striiformis f. sp. tritici secreted protein activates plant immunity at the cell surface.

Pathogens secrete effector proteins to suppress host immunity, mediate nutrient uptake and subsequently enable parasitism. However, on non-adapted hosts, effectors can be detected as non-self by host immune receptors and activate non-host immunity. Nevertheless, the molecular mechanisms of effector triggered non-host resistance remain unknown. Here, we report that a small cysteine-rich protein PstSCR1 from the wheat rust pathogen Puccinia striiformis f. sp. tritici (Pst) activates immunity in the non-host solanaceous model plant Nicotiana benthamiana. PstSCR1 homologs were found to be conserved in Pst, and in its closest relatives, Puccinia graminis f. sp. tritici and Puccinia triticina. When PstSCR1 was expressed in N. benthamiana with its signal peptide, it provoked the plant immune system, whereas no stimulation was observed when it was expressed without its signal peptide. PstSCR1 expression in N. benthamiana significantly reduced infection capacity of the oomycete pathogens. Moreover, apoplast-targeted PstSCR1 triggered plant cell death in a dose dependent manner. However, in Brassinosteroid insensitive 1-Associated Kinase 1 (SERK3/BAK1) silenced N. benthamiana, cell death was remarkably decreased. Finally, purified PstSCR1 protein activated defence related gene expression in N. benthamiana. Our results show that a Pst-secreted protein, PstSCR1 can activate surface mediated immunity in non-adapted hosts and contribute to non-host resistance.