Ecological and evolutionary dynamics of CRISPR-Cas systems in Clostridium botulinum: Insights from genome mining and comparative analysis.

Understanding the prevalence and distribution of CRISPR-Cas systems across different strains can illuminate the ecological and evolutionary dynamics of Clostridium botulinum populations. In this study, we conducted genome mining to characterize the CRISPR-Cas systems of C. botulinum strains. Our analysis involved retrieving complete genome sequences of these strains and assessing the diversity, prevalence, and evolution of their CRISPR-Cas systems. Subsequently, we performed an analysis of homology in spacer sequences from identified CRISPR arrays to investigate and characterize the range of targeted phages and plasmids. Additionally, we investigated the evolutionary trajectory of C. botulinum strains under selective pressures from foreign invasive DNA. Our findings revealed that 306 strains possessed complete CRISPR-Cas structures, comprising 58% of the studied C. botulinum strains. Secondary structure prediction of consensus repeats indicated that subtype II-C, with longer stems compared to subtypes ID and IB, tended to form more stable RNA secondary structures. Moreover, protospacer motif analysis demonstrated that strains with subtype IB CRISPR-Cas systems exhibited 5'-CGG-3', 5'-CC-3', and 5'-CAT-3' motifs in the 3' flanking regions of protospacers. The diversity observed in CRISPR-Cas systems indicated their classification into subtypes IB, ID, II-C, III-B, and III-D. Furthermore, our results showed that systems with subtype ID and III-D frequently harbored similar spacer patterns. Moreover, analysis of spacer sequences homology with phage and prophage genomes highlighted the specific activities exhibited by subtype IB and III-B against phages and plasmids, providing valuable insights into the functional specialization within these systems.

Apoptosis induction in cancer cell lines and anti-inflammatory and anti-pathogenic properties of proteinaceous metabolites secreted from potential probiotic Enterococcus faecalis KUMS-T48.

Potential probiotic Enterococcus faecalis KUMS-T48, isolated from a kind of Iranian traditional dairy product (Tarkhineh), was assessed for its anti-pathogenic, anti-inflammatory and anti-proliferative properties against HT-29 and AGS cancer cell lines. This strain showed strong effects on Bacillus subtilis and Listeria monocytogenes and moderate effect on Yersinia enterocolitica, while indicated weak effect on Klebsiella pneumoniae and Escherichia coli. Also, neutralizing the cell-free supernatant and treating it with catalase and proteinase K enzymes reduced the antibacterial effects. Similar to Taxol, the cell-free supernatant of E. faecalis KUMS-T48 inhibited the in vitro proliferation of both cancer cells in a dose-dependent manner, but unlike Taxol, they had no activity against normal cell line (FHs-74). Pronase-treatment of the CFS of E. faecalis KUMS-T48 abrogated its anti-proliferative capacity, thereby showing the proteinaceous nature of the cell-free supernatant. Further, induction of apoptosis-based cytotoxic mechanism by E. faecalis KUMS-T48 cell-free supernatant is related to anti-apoptotic genes ErbB-2 and ErbB-3, which is different from Taxol's apoptosis induction (intrinsic mitochondria apoptosis pathway). Also, as evidenced by a decline in interleukin 1ß inflammation-promoting gene expression and a rise in the anti-inflammatory interleukin-10 gene expression in the HT-29 cell line, probiotic E. faecalis KUMS-T48 cell-free supernatant demonstrated a significant anti-inflammatory impact.

In-situ formation/decomposition of deep eutectic solvent during solidification of floating organic droplet-liquid-liquid microextraction method for the extraction of some antibiotics from honey prior to high performance liquid chromatography-tandem mass spectrometry.

A new liquid-liquid microextraction approach by applying a deep eutectic solvent was adopted for the extraction of four antibiotics (penicillin G, dihydrostreptomycin, enrofloxacin, and ciprofloxacin) from honey samples. The enriched analytes were analyzed by HPLC-MS/MS. The procedure was carried out by synthesis of tetrabutylammonium chloride: p-cresol deep eutectic solvent in the sample solution and then its decomposition in the presence of an acid. In-solution formation of deep eutectic solvent provided wide contact areas among the extractant and sample solution, and accelerated sample preparation. Also, its decomposition enabled collection of the final extraction phase without centrifugation. Low LODs (0.55-0.79 ng/g) and LOQs (1.9-2.6 ng/g), high ERs (70-92%), and suitable RSDs (≤ 6.9%) were obtained. After performing the method on real samples, dihydrostreptomycin was found in several honey samples.

Combination of dispersive solid phase extraction with solidification organic drop-dispersive liquid-liquid microextraction based on deep eutectic solvent for extraction of organophosphorous pesticides from edible oil samples.

A dispersive solid phase extraction method was combined with deep eutectic solvent-based solidification of floating organic drop-dispersive liquid-liquid microextraction and used for the extraction/preconcentration of some organophosphorus pesticides residues from edible oil samples. The extracted analytes were quantified with gas chromatography-nitrogen phosphorous detector. In this procedure, the sample lipids are saponified with a sodium hydroxide solution and then the analytes are adsorbed onto a primary secondary amine sorbent. After that the analytes are desorbed with acetone as an elution/dispersive solvent and mixed with choline chloride: 3,3-dimethyl butyric acid deep eutectic solvent and the mixture is rapidly dispersed into deionized water. Then, the obtained cloudy solution is centrifuged and placed into an ice bath. The extraction solvent is solidified on the top of the solution. Finally, it is removed and dissolved in acetonitrile, and 1 µL of the solution is injected into the separation system. Validation of the method showed that limits of detection and quantification were in the ranges of 0.06-0.24 and 0.20-0.56 ng mL-1, respectively. Enrichment factors and extraction recoveries of the analytes ranged from 170-192 and 68-77%, respectively. The method had an acceptable precision with relative standard deviations less than ≤9.2% for intra- (n=6) and inter-day (n=6) precisions at four concentrations (3, 10, 50, and 250 ng mL-1, each analyte). Finally the method was used for determination of the analytes in five edible oil samples.