Current Issues in Molecular Biology最新文献

The genome sequence of Pantoea agglomerans UADEC20 is presented, which is a strain isolated from agricultural fields in northeast Mexico. The genome was assembled into 13 scaffolds, constituting a total chromosome size of 4.2 Mbp, with two of the scaffolds representing closed plasmids. The strain exhibits activity in phosphate solubilization and exopolysaccharide (EPS) production and secretion; therefore, we explored its biotechnological potential via its genome sequencing and annotation. Genomic analyses showed that a total of 57 and 58 coding sequences (CDSs) related to phosphate solubilization and EPS production were identified within its genome, in addition to a reduced number of CDSs related to drug resistance and phages. The comprehensive set of genes supporting phosphate solubilization, EPS synthesis, and secretion, along with its low virulence and antibiotic resistance levels, justify further research for its potential biotechnological application and possible use as a plant growth-promoting agent in the field. These findings suggest a unique genetic background in the P. agglomerans UADEC20 strain.

Wound healing incurs various challenges, making it an important topic in medicine. Short-chain peptides from fish protein hydrolysates possess wound healing properties that may represent a solution. In this study, perch hydrolysates were produced from perch side steams using a designed commercial complex enzyme via a proprietary pressure extraction technique. The average molecular weight of the perch peptides was 1289 kDa, and 62.60% of the peptides had a low molecular weight (≤1 kDa). Similarly to the beneficial amino acid sequence FPSIVGRP, FPSLVRGP accounted for 6.21% abundance may have a potential antihypertensive effect. The concentrations of collagen composition and branched-chain amino acids were 1183 and 1122 mg/100 g, respectively. In a fibroblast model, active perch peptides accelerated wound healing mainly by increasing the secretion of procollagen I, fibronectin, and hyaluronan. In an SD rat model established to mimic human wounds, orally administered perch hydrolysates with a molecular weight below 2.3 kDa accelerated wound healing, which mainly resulted from collagen-forming amino acids, branched-chain amino acids, and matrikine. Collectively, the residue of perch extract can be upcycled via a hydrolysis technique to produce not only bioactive sequences but also short-chain peptides. Considering the therapeutic potential to promote wound healing, such by-products are of great value and may be developed as dietary nutraceuticals.

Understanding the ammonium (NH₄⁺) uptake and transport systems, particularly AMT1 genes, is important for plant growth and defense. However, there is a lack of research on identifying and analyzing AMT1 genes in pomegranate, emphasizing the need for further investigation in this area. Five AMT1 genes (PgAMT1-1 to PgAMT1-5) were identified, all of which contain the PF00909 domain, a feature of ammonium transporters. Various characteristics of these genes, including gene length, coding sequence length, and chromosomal locations, were examined. This study evaluated the isoelectric point, hydropathicity, conserved domains, motifs, and synteny of the PgAMT1 proteins. Phylogenetic analysis confirmed the homology of PgAMT1 genes with previously reported AMT in Arabidopsis and tomato. The tissue-specific expression analysis of PgAMT1 genes revealed distinct patterns: PgAMT1-1 and PgAMT1-2 were predominantly expressed in flowers, PgAMT1-3 exhibited notable expression in roots, leaves, and flowers, PgAMT1-4 was primarily expressed in leaf tissue, while the expression of PgAMT1-5 was detected in both leaves and roots. The impact of salt-induced stress on AMT1 gene expression was also examined, revealing that PgAMT1-1, PgAMT1-2, and PgAMT1-4 expression is reduced under increased salt stress. These expression modifications can help regulate NH₄+ assimilation in conditions of elevated salinity, maintaining cellular homeostasis and ion balance. This study contributes to the comprehensive identification of the AMT1s gene family in pomegranate; however, further research on the functional characterization of the identified PgAMT1s is needed.

Loquat leaves, flowers, and other organs contain abundant antioxidant substances, which have wide applications in medicine, health, and food industries. This study aims to provide theoretical guidance for loquat hybrid parent and combination selection and a basis for high-quality loquat strain screening and development. For comprehensive antioxidant profiling, we used "Ninghaibai" and "Oobusa" loquat and their F₁ generation as experimental materials to determine the total phenol, flavonoid, DPPH, ABTS, and FRAP content in the leaves and flowers of 56 strains. Five traits, including total phenols, flavonoids, DPPH, ABTS, and FRAP, were widely separated and normally distributed in the flowers of 56 F₁ loquat strains, exhibiting the genetic basis of these quantitative traits. However, these traits displayed widely separated and slightly skewed distribution in the leaves of the F₁ generation. The total phenols, flavonoids, DPPH, and FRAP showed a trend of small inheritance in the leaves. However, the ABTS showed a trend of medium and high inheritance in leaves and flowers, respectively. Through cluster and principal component analyses, a comprehensive antioxidant activity evaluation was conducted. Ten strains with comprehensive scores greater than 1 for antioxidant activity in leaves and flowers were selected. Among them, the top three strains with high antioxidant capacity were ND107, "Oobusa", and ND128. These results suggest that hybrid breeding guided by the genetic characteristics of each trait can improve the possibility of cultivating new varieties with high antioxidant activity.

Considering that fungi display a great morphological, ecological, metabolic, and phylogenetic diversity, their taxonomic identification is extremely important because it helps us establish important information about each species and its possible biochemical and ecological roles. Traditionally, the identification of fungi at the species level has been carried out with molecular tools such as DNA sequencing, but it still represents a huge challenge today due to the heterogeneity of the fungal kingdom, making the task of identification a complex and difficult process. Biotyping, a type of chemotaxonomy, has been developed in the field of the identification/differentiation and classification of micro-fungi through tools such as mass spectrometry (MS). Here, two endophytic strains isolated from two different hosts were cultivated and studied regarding their morphology and molecular biology. Morphology analysis determined the strains as Diaporthe, and the molecular analysis results grouped them as D. melongenae. We sought a faster and less complex way of differentiating these fungal strains of interest through an MS chemical profile and MS/MS data using a low-resolution mass spectrometer. Additionally, we linked this information with the structure of compounds previously isolated in the genus Diaporthe. Studies conducted using this technique allowed us to propose the structure of distinctive molecules that are unique to each strain and share compounds common to this genus (13 compounds in total). In addition, this is the first report of secondary metabolites in D. melongenae. The dataset demonstrates that the two strains under investigation can be distinguished via mass spectrometry, suggesting host affinity; both exhibits pronounced differences in their chemical profiles across all culture media and incubation periods with the parameters described herein.

Tribulus terrestris is a rich source of bioactive molecules and thrives in Mediterranean and desert climate regions worldwide. In this study, Tribulus terrestris methanolic HPLC fractions were evaluated for bioactive compounds and PBP2a transpeptidase inhibitors against methicillin-resistant Staphylococcus epidermidis (MRSE). Among the collected HPLC fractions, F02 of the methanol extract demonstrated potential activity against MRSE01 (15 ± 0.13 mm), MRSE02 (13 ± 0.21 mm), and MRSE03 (16 ± 0.14 mm) isolates. GC-MS analysis of the F02 fraction identified seventeen compounds. Among seventeen compounds, eight have favorable pharmacokinetics and medicinal chemistry; however, on the basis of in silico high water solubility, high GI absorption, blood-brain barrier non-permeability, lack of toxicity, and potential drug-likeness, 1-ethylsulfanylmethyl-2,8,9-trioxa-5-aza-1-sila-bicyclo[3.3.3]undecane and phthalimide, N-(1-hydroxy-2-propyl), were processed for molecular docking. 1-ethylsulfanylmethyl-2,8,9-trioxa-5-aza-1-sila-bicyclo[3.3.3]undecane formed three hydrogen bonds with Ser-452, Thr-584, and Asn-454 residues of the PBP2a transpeptidase. Similarly, phthalimide, N-(1-hydroxy-2-propyl)-formed four hydrogen bonds with Ser-396, Asn-454, Lys-399, and Ser-452 residues of PBP2a transpeptidase. These two compounds are proposed as novel putative PBP2a transpeptidase inhibitors. Further characterization of compounds extracted from Tribulus terrestris may aid in identifying novel PBP2a inhibitory agents for managing MRSE infections.

Pseudomonas aeruginosa (PA), as a common pathogen of nosocomial infections, has been experiencing an increasing rate of drug resistance with the widespread use and abuse of antimicrobial drugs. High-drug-resistance and high-virulence phenotypes are two distinctive features of the strong pathogenicity of multi-drug-resistant PA. Exploring the characterization of virulence factor expression and its relationship with the multi-drug resistance phenotype is essential to reduce the further development of resistance as well as a high standard of infection prevention and control. A total of 50 PA isolated from clinical practice were collected. The Kirby-Bauer test was used for drug-sensitive screening, and the results showed that 16 strains were resistant and 16 strains were sensitive. The drug resistance rate of multi-drug-resistant PA against cefepime, cefazolin, ampicillin, and imipenem was up to 100%. The multi-drug-resistant groups were superior in producing pyocyanin and forming biofilm to the sensitive groups. The distribution of isolates with different swarming motility capacities and elastase levels did not show pronounced differences among the multi-drug-resistant and sensitive groups. In addition, biofilm formation was moderately associated with imipenem resistance. Among the strains with strong virulence factor expression, the gene bands showed little difference, suggesting that the gene is highly homologous. The virulence factor matrix analysis showed that there were different degrees of correlation among the 4 virulence factors. The correlation between multidrug-resistant PA and virulence factor expression is complex. PA, which were good at producing pyocyain and forming biofilm, were highly resistant to cephalosporins, beta-lactams and carbepenems; hence, such drugs are not proper for anti-infective treatment in clinics.

Circulating endothelial cells (CECs) and endothelial progenitor cells (EPCs) are promising markers of vascular damage and endothelial regeneration potential. We focused on the detection of CECs and EPCs using flow cytometry with regard to analytical challenges and its suitability for routine testing. As part of a clinical validation, CECs and EPCs were measured in blood samples from 83 subjects with type 1 diabetes (T1DM), evaluating an adjuvant intervention with two different antidiabetic drugs, empagliflozin (N = 28) and semaglutide (N = 29). Both groups receiving adjuvant therapy were compared with the insulin-only group (N = 26) at two time points: before the start of therapy and after 12 weeks of adjuvant therapy. All three groups were comparable regarding demographic characteristics and concomitant risk factors. Absolute and relative endothelial cell count at baseline were low and comparable to those of healthy individuals. In the group receiving empagliflozin or semaglutide, a significant increase in EPC was observed after 12 weeks of treatment. We demonstrated that EPCs have the potential to serve as markers for monitoring the efficacy of adjuvant therapy in T1DM patients. However, before their implementation in clinical practice, the flow cytometry protocol for CEC and EPC identification and quantification must be standardized.

Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease without an approved pharmacological approach for its prevention/treatment. Based on the modified Delphi process, NAFLD was redefined as metabolic dysfunction-associated steatotic liver disease (MASLD) to highlight the metabolic aspect of liver pathogenesis. Chios mastiha (Pistacia lentiscus var. Chia, Anacardiaceae) resin demonstrated promising results in MASLD treatment. In this paper, molecular docking was applied to test 16 compounds from Chios mastiha as potential ligands for the receptors GR, LXRα, LXRβ, PPARα PPARγ, MC4R, AMPK, and VEGFR2, whose up- and down-regulation interfere with MASLD development and progression. The observed compounds had moderate and high affinity for LXR, GR, MC4R, and PPARγ in comparison to proven ligands, while their affinity for PPARα, AMPK, and VEGFR was less pronounced. The combination of active compounds from Chios mastiha rather than a single molecule may have a superior ability to control the intertwined MASLD metabolic pathways.

Teucrium polium L. is a plant with various claims of ethnobotanical use, primarily for inflammatory diseases. Chemical studies have already isolated different types of terpenes from the species, and studies have established its pharmacological potential. The present study evaluates the components of T. polium essential oil cultivated in the Algerian Saharan Atlas. GC-MS identified the major components as fenchone (31.25%), 3-carene (15.77%), cis-limonene oxide (9.77%), and myrcene (9.15%). In the in silico prediction, molecules with more than 1% abundance were selected. Regarding Lipinski's rule, all molecules followed the rule. All molecules were found to be toxic in at least one model, with some molecules being non-genotoxic (6, 8, 10, 11, 12, 13) and others being non-mutagenic (5, 7, 9, 14). Three molecules were selected that showed the best results in pharmacokinetic and toxicity studies: the molecules that did not present carcinogenic potential (7-myrtenal; 9-myrtenol; 14-verbenol). The molecular target was established, and it seems that all three bound to the nuclear factor NF-kappa-B. Based on the docking and molecular dynamics results, these molecules have potential as anti-inflammatory and antitumor therapies, with further in vitro and in vivo studies needed to evaluate their activity and toxicity.