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The RGM 2450 and RGM 2529 strains were isolated from the rhizosphere of plants presenting resilience to abiotic and biotic stress conditions. To understand the implications of bacteria in resilience, a genomic and experimental analysis was carried out on their biostimulant and phytopathogenic antagonist properties. Genome analyses of both strains indicated that they have the potential to synthesize bioactive compounds such as the battery of non-ribosomal peptides, polyketides, extracellular enzymes and phytohormones. These results were consistent with the antagonistic activities of both strains against the phytopathogens , , and . They also showed the capacity to solubilize phosphorus, fix nitrogen and produce indole acetic acid. This was observed in tomato seedlings grown from seeds inoculated with the mixture of strains which presented significantly greater length as well as wet and dry weight in comparison with the treatments individually inoculated with each strain and the control. Accordingly, the combination of RGM 2450 and RGM 2529 showed synergistic biostimulant activity. These findings contribute new knowledge of the genomic and metabolomic properties taking part in the symbiotic interactions between these strains and the plants and uphold the combined use of both strains as a biostimulant.
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http://dx.doi.org/10.3390/microorganisms10040670 | DOI Listing |
Front Immunol
December 2024
Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.
Introduction: Fungi, including , may be a trigger or exacerbate psoriasis, especially in difficult to treat (DTT) areas, through the activation of IL-17/23 axis.
Methods: In this study, seventy patients with DDT psoriasis were enrolled to evaluate species and/or other opportunistic fungi colonization rate at baseline (T0) and the impact of apremilast on fungal load, clinical outcome, serum cytokine levels and biochemical serum profile of patients after 16, 24 and 52 weeks of treatment.
Results: In our population, 33 (47%) patients were colonized by spp.
iScience
December 2024
Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
As an essential regulator of higher-order chromatin structures, CCCTC-binding factor (CTCF) is a highly conserved protein with a central DNA-binding domain of 11 tandem zinc fingers (ZFs), which are flanked by amino (N-) and carboxy (C-) terminal domains of intrinsically disordered regions. Here we report that CRISPR deletion of the entire C-terminal domain of alternating charge blocks decreases CTCF DNA binding but deletion of the C-terminal fragment of 116 amino acids results in increased CTCF DNA binding and aberrant gene regulation. Through a series of genetic targeting experiments, in conjunction with electrophoretic mobility shift assay (EMSA), circularized chromosome conformation capture (4C), qPCR, chromatin immunoprecipitation with sequencing (ChIP-seq), and assay for transposase-accessible chromatin with sequencing (ATAC-seq), we uncovered a negatively charged region (NCR) responsible for weakening CTCF DNA binding and chromatin accessibility.
View Article and Find Full Text PDFPlant Methods
December 2024
Department of Molecular Genetics, Dong-A University, Saha-gu Nakdong-Daero 550 beongil 37, Busan, 49315, Republic of Korea.
Background: Genetic markers are crucial for breeding crops with desired agronomic traits, and their development can be expedited using next-generation sequencing (NGS) and bioinformatics tools. Numerous tools have been developed to design molecular markers, enhancing the convenience, accuracy, and efficiency of molecular breeding. However, these tools primarily focus on genetic variants within short user-input sequences, despite the availability of extensive omics data for genomic variants.
View Article and Find Full Text PDFBMC Bioinformatics
December 2024
Albert Szent-Györgyi Health Centre, University of Szeged, Korányi fasor 14-15, Szeged, H-6725, Csongrád-Csanád, Hungary.
Background: Accurate prediction of copy number variations (CNVs) from targeted capture next-generation sequencing (NGS) data relies on effective normalization of read coverage profiles. The normalization process is particularly challenging due to hidden systemic biases such as GC bias, which can significantly affect the sensitivity and specificity of CNV detection. In many cases, the kit manifests provide only the genome coordinates of the targeted regions, and the exact bait design of the oligo capture baits is not available.
View Article and Find Full Text PDFNPJ Genom Med
December 2024
Experimental Center of Clinical Research, the First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
Wilson's disease (WD) typically manifests in children and young adults, with little knowledge of its late-onset forms. In this study, we performed a retrospective cohort study of 105 WD patients (99 index cases, 6 siblings) with an onset age ≥35 years. We compared 99 index late-onset patients with 1237 early-onset patients and analyzed the ATP7B variant penetrance referring to the Genome Aggregation Database (gnomAD).
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