Search Results (1,065)

Chilling injury during the germination stage (CIGS) of maize significantly hinders production, particularly in middle- and high-latitude regions, leading to slow germination, seed decay, and increased susceptibility to pathogens. This study dissects the genetic architecture of CIGS resistance expressed in terms of the relative germination rate (RGR) in maize through association mapping using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). A natural panel of 287 maize inbred lines was evaluated across multiple environments. The results revealed a broad-sense heritability of 0.68 for chilling tolerance, with 12 significant QTLs identified on chromosomes 1, 3, 5, 6, and 10. A genomic prediction analysis demonstrated that the rr-BLUP model outperformed other models in accuracy, achieving a moderate prediction accuracy of 0.44. This study highlights the potential of genomic selection (GS) to enhance chilling tolerance in maize, emphasizing the importance of training population size, marker density, and significant markers on prediction accuracy. These findings provide valuable insights for breeding programs aimed at improving chilling tolerance in maize. Full article

Abstract: Campylobacter jejuni (C. jejuni) is a zoonotic foodborne pathogen that is widely distributed worldwide. Its optimal growth environment is microaerophilic conditions (5% O₂, 10% CO₂), but it can spread widely in the atmospheric environment. Biofilms are thought to play an important role in this process. However, there are currently relatively few research works on the regulatory mechanisms of C. jejuni biofilm formation. In this study, a pan-genome analysis, combined with the analysis of biofilm phenotypic information, revealed that the gene cluster Cj0423–Cj0425 is associated with the negative regulation of biofilm formation in C. jejuni. Through gene knockout experiments, it was observed that the Cj0423–Cj0425 mutant strain significantly increased biofilm formation and enhanced flagella formation. Furthermore, pull-down assay revealed that Cj0424 interacts with 93 proteins involved in pathways such as fatty acid synthesis and amino acid metabolism, and it also contains the quorum sensing-related gene luxS. This suggests that Cj0423–Cj0425 affects fatty acid synthesis and amino acid metabolism, influencing quorum sensing and strain motility, ultimately inhibiting biofilm formation. Full article

The effect of crop rotation on soil-borne diseases is a representative case of plant–soil feedback in the sense that plant disease resistance is influenced by soils with different cultivation histories. This study examined the microbial mechanisms inducing the differences in the clubroot (caused by Plasmodiophora brassicae pathogen) damage of Chinese cabbage (Brassica rapa subsp. pekinensis) after the cultivation of different preceding crops. It addresses two key questions in crop rotation: changes in the soil bacterial community induced by the cultivation of different plants and the microbial mechanisms responsible for the disease-suppressive capacity of Chinese cabbage. Twenty preceding crops from different plant families showed significant differences in the disease damage, pathogen density, and bacterial community composition of the host plant. Structural equation modelling revealed that the relative abundance of four key bacterial orders in Chinese cabbage roots can explain 85% and 70% of the total variation in pathogen density and disease damage, respectively. Notably, the relative dominance of Bacillales and Rhizobiales, which have a trade-off relationship, exhibited predominant effects on pathogen density and disease damage. The disease-suppressive soil legacy effects of preceding crops are reflected in compositional changes in key bacterial orders, which are intensified by the bacterial community network. Full article

Kallmann syndrome is a rare disorder characterized by hypogonadotropic hypogonadism and an impaired sense of smell (anosmia or hyposmia) caused by congenital defects in the development of the gonadotropin-releasing hormone (GnRH) and olfactory neurons. Mutations in several genes have been associated with Kallmann syndrome. However, genetic testing of this disorder often reveals variants of uncertain significance (VUS) that remain uninterpreted without experimental validation. The aim of this study was to analyze the functional consequences of a heterozygous missense VUS in the CHD7 gene (c.4354G>T, p.Val1452Leu), in a patient with Kallmann syndrome with reversal of hypogonadism. The variant, located in the first nucleotide of exon 19, was analyzed using minigene assays to determine its effect on ribonucleic acid (RNA) splicing. These showed that the variant generates two different transcripts: a full-length transcript with the missense change (p.Val1452Leu), and an abnormally spliced transcript lacking exon 19. The latter results in an in-frame deletion (p.Val1452_Lys1511del) that disrupts the helicase C-terminal domain of the CHD7 protein. The variant was reclassified as likely pathogenic. These findings demonstrate that missense variants can exert more extensive effects beyond simple amino acid substitutions and underscore the critical role of functional analyses in VUS reclassification and genetic diagnosis. Full article

Infection by retroviruses and the mobilization of transposable elements cause DNA damage that can be catastrophic for a cell. If the cell survives, the mutations generated by retrotransposition may confer a selective advantage, although, more commonly, the effect of new integrants is neutral or detrimental. If retrotransposition occurs in gametes or in the early embryo, it introduces genetic modifications that can be transmitted to the progeny and may become fixed in the germline of that species. PIWI-interacting RNAs (piRNAs) are single-stranded, 21–35 nucleotide RNAs generated by the PIWI clade of Argonaute proteins that maintain the integrity of the animal germline by silencing transposons. The sequence specific manner by which piRNAs and germline-encoded PIWI proteins repress transposons is reminiscent of CRISPR, which retains memory for invading pathogen sequences. piRNAs are processed preferentially from the unspliced transcripts of piRNA clusters. Via complementary base pairing, mature antisense piRNAs guide the PIWI clade of Argonaute proteins to transposon RNAs for degradation. Moreover, these piRNA-loaded PIWI proteins are imported into the nucleus to modulate the co-transcriptional repression of transposons by initiating histone and DNA methylation. How retroviruses that invade germ cells are first recognized as foreign by the piRNA machinery, as well as how endogenous piRNA clusters targeting the sequences of invasive genetic elements are acquired, is not known. Currently, koalas (Phascolarctos cinereus) are going through an epidemic due to the horizontal and vertical transmission of the KoRV-A gammaretrovirus. This provides an unprecedented opportunity to study how an exogenous retrovirus becomes fixed in the genome of its host, and how piRNAs targeting this retrovirus are generated in germ cells of the infected animal. Initial experiments have shown that the unspliced transcript from KoRV-A proviruses in koala testes, but not the spliced KoRV-A transcript, is directly processed into sense-strand piRNAs. The cleavage of unspliced sense-strand transcripts is thought to serve as an initial innate defense until antisense piRNAs are generated and an adaptive KoRV-A-specific genome immune response is established. Further research is expected to determine how the piRNA machinery recognizes a new foreign genetic invader, how it distinguishes between spliced and unspliced transcripts, and how a mature genome immune response is established, with both sense and antisense piRNAs and the methylation of histones and DNA at the provirus promoter. Full article

Bacterial quorum sensing (QS) is a critical communication process that regulates gene expression in response to population density, influencing activities such as biofilm formation, virulence, and antibiotic resistance. This study investigates the inhibitory effects of five phytochemicals—apigenin, carnosol, chlorogenic acid, quercetin, and rosmarinic acid—on the S-ribosylhomocysteinase (LuxS) enzyme, a key player in AI-2 signaling across both Gram-positive and Gram-negative bacteria. Using molecular docking studies, we identified that these phytochemicals interact with the LuxS enzyme, with apigenin, carnosol, chlorogenic acid, and rosmarinic acid binding within the substrate-binding pocket and exhibiting binding scores below −7.0 kcal/mol. Subsequent in vitro assays demonstrated that these compounds inhibited AI-2 signaling and biofilm formation in Escherichia coli MG1655 in a concentration-dependent manner. Notably, carnosol and chlorogenic acid showed the most potent effects, with IC₅₀ values of approximately 60 μM. These findings suggest that these phytochemicals may serve as potential QS inhibitors, providing a foundation for developing new anti-pathogenic agents to combat bacterial infections without promoting antibiotic resistance. Further studies are warranted to explore the therapeutic applications of these compounds in both clinical and agricultural settings. Full article

The functions of bacterial plasmid-encoded toxin–antitoxin (TA) systems are unambiguous in the sense of controlling cells that fail to inherit a plasmid copy. However, its role in chromosomal copies is contradictory, including stress-response-promoting fitness and antibiotic treatment survival. A hybrid pathogenic Escherichia coli strain may have the ability to colonize distinct host niches, facing contrasting stress environments. Herein, we determined the influence of multiple environmental stress factors on the bacterial growth dynamic and expression profile of previously described TA systems present in the chromosome of a hybrid atypical enteropathogenic and extraintestinal E. coli strain. Genomic analysis revealed 26 TA loci and the presence of five type II TA systems in the chromosome. Among the tested stress conditions, osmotic and acid stress significantly altered the growth dynamics of the hybrid strain, enhancing the necessary time to reach the stationary phase. Using qPCR analyses, 80% of the studied TA systems were differentially expressed in at least one of the tested conditions, either in the log or in the stationary phase. These data indicate that type II TA systems may contribute to the physiology of pathogenic hybrid strains, enabling their adaptation to different milieus. Full article

Food safety has recently become a widespread concern among consumers. Surface-enhanced Raman scattering (SERS) is a rapidly developing novel spectroscopic analysis technique with high sensitivity, an ability to provide molecular fingerprint spectra, and resistance to photobleaching, offering broad application prospects in rapid trace detection. With the interdisciplinary development of nanomaterials and biotechnology, the detection performance of SERS biosensors has improved significantly. This review describes the advantages of nanomaterial-based SERS detection technology and SERS’s latest applications in the detection of biological and chemical contaminants, the identification of foodborne pathogens, the authentication and quality control of food, and the safety assessment of food packaging materials. Finally, the challenges and prospects of constructing and applying nanomaterial-based SERS sensing platforms in the field of food safety detection are discussed with the aim of early detection and ultimate control of foodborne diseases. Full article

Many phytopathogens’ gene products that contribute to plant–pathogen interactions remain unexplored. In one of the most harmful phytopathogenic bacterium Pectobacterium atrosepticum (Pba), phosphonate-related genes have been previously shown to be among the most upregulated following host plant colonization. However, phosphonates, compounds characterized by a carbon–phosphorus bond in their composition, have not been described in Pectobacterium species and other phytopathogenic bacteria, with the exception of Pseudomonas syringae and Pantoea ananatis. Our study aimed to determine whether Pba synthesizes extracellular phosphonates and, if so, to analyze their physiological functions. We demonstrated that Pba produces two types of extracellular phosphonates: 2-diethoxyphosphorylethanamine and phenylphosphonic acid. Notably, such structures have not been previously described among natural phosphonates. The production of Pba phosphonates was shown to be positively regulated by quorum sensing and in the presence of pectic compounds. Pba phosphonates were found to have a positive effect on Pba stress resistance and a negative effect on Pba virulence. The discovered Pba phosphonates are discussed as metabolites that enable Pba to control its “harmful properties”, thereby maintaining its ecological niche (the host plant) in a relatively functional state for an extended period. Full article

Pseudomonas aeruginosa is a harmful pathogen that causes a variety of acute and chronic infections through quorum sensing (QS) mechanisms. The increasing resistance of this bacterium to numerous antibiotics has created a demand for new medications that specifically target QS. Endophytes can be the source of compounds with antibacterial properties. This research is the first to examine tannic acid (TA) produced by endophytic fungus as a potential biotherapeutic agent. A novel endophytic fungal isolate identified as Penicillium oxalicum was derived from the cladodes of Opuntia ficus-indica (L.). The species identification for this isolate was confirmed through sequencing of the internal transcribed spacer region. The metabolites from the culture of this isolate were extracted using ethyl acetate, then separated and characterized using chromatographic methods. This led to the acquisition of TA, a compound that shows strong anti-QS and excellent antibacterial effects against extensively drug-resistant P. aeruginosa strains. Furthermore, it was shown that treating P. aeruginosa with the obtained TA reduced the secretion of virulence factors controlled by QS in a dose-dependent manner, indicating that TA inhibited the QS characteristics of P. aeruginosa. Simultaneously, TA significantly inhibited the expression of genes associated with QS, including rhlR/I, lasR/I, and pqsR. In addition, in silico virtual molecular docking showed that TA could efficiently bind to QS receptor proteins. Our results showed that P. oxalicum could be a new source of TA for the treatment of infections caused by extensively drug-resistant P. aeruginosa. Full article

Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease. Full article

Surface-based biosensors have proven to be of particular interest in the monitoring of human pathogens by means of their distinct nucleic acid sequences. Genosensors rely on targeted gene/DNA probe hybridization at the surface of a physical transducer and have been exploited for their high specificity and physicochemical stability. Unfortunately, these sensing materials still face limitations impeding their use in current diagnostic techniques. Most of their shortcomings arise from their suboptimal surface properties, including low hybridization density, inadequate probe orientation, and biofouling. Herein, we describe and compare two functionalization methodologies to immobilize DNA probes on a glass substrate via a thermoresponsive polymer in order to produce genosensors with improved properties. The first methodology relies on the use of a silanization step, followed by PET-RAFT of NIPAM monomers on the coated surface, while the second relies on vinyl sulfone modifications of the substrate, to which the pre-synthetized PNIPAM was grafted to. The functionalized substrates were fully characterized by means of X-ray photoelectron spectroscopy for their surface atomic content, fluorescence assay for their DNA hybridization density, and water contact angle measurements for their thermoresponsive behavior. The antifouling properties were evaluated by fluorescence microscopy. Both immobilization methodologies hold the potential to be applied to the engineering of DNA biosensors with a variety of polymers and other metal oxide surfaces. Full article

Defects of the GNAS gene have been mainly associated with pseudohypoparathyroidism Ia. To date, pathogenic missense, frameshift, non-sense and splicing variants have been described in all the 13 exons of the GNAS gene. Of them, a specific mutation, namely the 4 bp deletion c.565_568delGACT, is currently considered a mutation hotspot. Recent articles performed genotype–phenotype correlations in patients with GNAS-related pseudohypoparathyroidism Ia (PHP1a) but a specific focus on this hotspot is still lacking. We reported two cases, from our department, of PHP1a associated with c.565_568delGACT deletion and performed a literature review of all the previously reported cases of the 4 bp deletion hotspot. We found a higher prevalence of brachydactyly, round face, intellectual disability and subcutaneous/heterotopic ossifications in patients with the c.565_568delGACT as compared to the other variants in the GNAS gene. The present study highlights the different prevalence of some clinical features in patients with the c.565_568delGACT variant in the GNAS gene, suggesting the possibility of a personalized diagnostic follow-up and surveillance for these patients. Full article

Riboswitches are highly structured RNA regulators of gene expression. Although found in all three domains of life, they are particularly abundant and widespread in bacteria, including many human pathogens, thus making them an attractive target for antimicrobial development. Moreover, the functional versatility of riboswitches to recognize a myriad of ligands, including ions, amino acids, and diverse small-molecule metabolites, has enabled the generation of synthetic aptamers that have been used as molecular probes, sensors, and regulatory RNA devices. Generally speaking, a riboswitch consists of a ligand-sensing aptamer domain and an expression platform, whose genetic control is achieved through the formation of mutually exclusive secondary structures in a ligand-dependent manner. For most riboswitches, this involves formation of the aptamer’s P1 helix and the regulation of its stability, whose competing structure turns gene expression ON/OFF at the level of transcription or translation. Structural knowledge of the conformational changes involving the P1 regulatory helix, therefore, is essential in understanding the structural basis for ligand-induced conformational switching. This review provides a summary of riboswitch cases for which ligand-free and ligand-bound structures have been determined. Comparative analyses of these structures illustrate the uniqueness of these riboswitches, not only in ligand sensing but also in the various structural mechanisms used to achieve the same end of regulating switch helix stability. In all cases, the ligand stabilizes the P1 helix primarily through coaxial stacking interactions that promote helical continuity. Full article

Ensuring global food security amid mounting challenges, such as population growth, disease infestations, resource limitations, and climate change, is a pressing concern. Anticipated increases in food demand add further complexity to this critical issue. Plant pathogens, responsible for substantial crop losses (up to 41%) in major crops like wheat, rice, maize, soybean, and potato, exacerbate the situation. Timely disease detection is crucial, yet current practices often identify diseases at advanced stages, leading to severe infestations. To address this, remote sensing and Hyperspectral imaging (HSI) have emerged as robust and nondestructive techniques, exhibiting promising results in early disease identification. Integrating machine learning algorithms with image data sets enables precise spatial–temporal disease identification, facilitating timely detection, predictive modeling, and effective disease management without compromising fitness or climate adaptability. By harnessing these cutting-edge technologies and data-driven decision-making, growers can optimize input costs while achieving enhanced yields, making significant strides toward global food security in the face of climate change risks. This review will discuss some of the foundational concepts of remote sensing, several platforms used for remote sensing data collection, successful application of the approach, and its future perspective. Full article