Search Results (161)

Alzheimer’s disease (AD) is a prevalent neurodegenerative disorder with a pressing need for novel therapeutics. However, current medications only offer symptomatic relief, without tackling the underlying pathology. To explore the bioactive potential of marine-derived fungi, this study focused on Aspergillus terreus C23-3, a strain isolated from the coral Pavona cactus in Xuwen County, China, which showed a richer metabolite fingerprint among the three deposited A. terreus strains. AntiSMASH analysis based on complete genome sequencing predicted 68 biosynthetic gene clusters (BGCs) with 7 BGCs synthesizing compounds reported to have anti-AD potential, including benzodiazepines, benzaldehydes, butenolides, and lovastatin. Liquid chromatography coupled with mass spectrometry (LC-MS)-based combinational metabolomic annotation verified most of the compounds predicted by BGCs with the acetylcholinesterase (AChE) inhibitor territrem B characterized from its fermentation extract. Subsequently, molecular docking showed that these compounds, especially aspulvione B1, possessed strong interactions with AD-related targets including AChE, cyclin-dependent kinase 5-p25 complex (CDK5/p25), glycogen synthase kinase-3β (GSK-3β), and monoamine oxidase-B (MAO-B). In conclusion, the genomic–metabolomic analyses and molecular docking indicated that C23-3 is a high-value source strain for anti-AD natural compounds. Full article

Brachial plexus root avulsion [BPRA] and concomitant spinal cord injury [SCI] represent devastating injuries that come with limited hope for recovery owing to the adult spinal cord’s loss of intrinsic ability to spontaneously regenerate. BPRA/SCI is an enormous public health issue the world over, and its catastrophic impact goes beyond the patient, the family, businesses, and national health budgets, draining billions of dollars annually. The rising population and economic growth have seen the incidence of SCI surging. Genomic, transcriptomic, and proteomic studies have yielded loads of information on the various molecular events that precede, regulate, and support both regenerative and degenerative pathways post-SCI. Metabolomics, on the other hand, comes in as the search for a cure and the objective monitoring of SCI severity and prognosis remains on the horizon. Despite the large number of review articles on metabolomics and its application fields such as in cancer and diabetes research, there is no comprehensive review on metabolite profiling to study disease mechanisms, biomarkers, or neuroprotection in SCI. First, we present a short review on BPRA/SCI. Second, we discuss potential benefits of metabolomics as applied in BPRA/SCI cases. Next, a look at the analytical techniques that are used in metabolomics. Next, we present an overview of the studies that have used metabolomics to reveal SCI metabolic fingerprints and point out areas of further investigation. Finally, we discuss future research directions. Full article

Insects are often associated with diverse microorganisms that enhance their metabolism and nutrient assimilation. These microorganisms, residing in the insect’s gut, play a crucial role in breaking down complex molecules into simpler compounds essential for the host’s growth. This study investigates the diversity and functional potential of symbiotic bacteria in the gut of Arsenura armida (Lepidoptera: Saturniidae) larvae, an edible insect from southeastern Mexico, using culture-dependent and metagenomic approaches. Bacterial strains were isolated from different gut sections (foregut, midgut, and hindgut) and cultured on general-purpose media. Isolates were identified through 16S rRNA gene sequencing and genomic fingerprinting. Metagenomics revealed the bacterial community structure and diversity, along with their functional potential. A total of 96 bacterial strains were isolated, predominantly Gram-negative bacilli. Rapidly growing colonies exhibited enzymatic activity, cellulose degradation, and sugar production. Phylogenetic analysis identified eight genera, including Acinetobacter, Bacillus, Enterobacter, Pseudomonas, and others, with significant cellulose-degrading capabilities. Metagenomics confirmed Bacillota as the most abundant phylum. These complementary methods revealed abundant symbiotic bacteria with key metabolic roles in A. armida, offering promising biotechnological applications in enzymatic bioconversion and cellulose degradation. Full article

Wine DNA fingerprinting (WDF), retrieved from the amplification of a wider panel of Simple Sequence Repeat (SSR) marker mappings in the Vitis vinifera L. genome, was used to assess the monovarietal nature of Brunello di Montalcino wine. The reliability of the varietal assessment was carried out by estimating the PI values associated with resolutive unrooted dendrograms depicting the correct varietal nature of different wines. As few as five SSR DNA markers associated with a PI value of one over a million or less, PI ≤ 10⁻⁶, can identify the purity of Sangiovese against Merlot, Pinot Noir, Cabernet Sauvignon, Primitivo (Zinfandel), and genetic variants of the Sangiovese as plant references. WDF was used on other monovarietal wines obtained from Cabernet Sauvignon, Merlot, Chardonnay, and Pinot Noir to test the feasibility of the method. In blended wines, the test was able to trace the main varietal component in a three-variety blend, keeping the varietal fingerprint detectable when the main variety was at least 75% (v/v). The data confirm how local genetic variants of Sangiovese can be tracked in commercial wines, becoming, at wine makers’ demand, part of an evidence synthesis of geographical origin. Full article

Tilapia (Oreochromis spp.) is a globally important farmed fish. Analyses of genetic variation across different types of tilapia are essential for the development of superior breeding populations. We investigated the genetic structures of breeding populations of blue tilapia (Oreochromis aureus) (OA), Nile tilapia (Oreochromis niloticus) (ON), and red tilapia (Oreochromis spp.) (OS) by whole-genome resequencing. The results showed that the OS population had maintained high genetic diversity but significant genetic differentiation from the OA population. Principal component analysis, phylogenetic analysis, and genetic clustering analysis revealed a clear pattern of genetic differentiation among the three populations. The genetic structure of the ON population differed from that of the OA population but was similar to that of the OS population. Population kinship analysis revealed a close relationship between the ON and OS populations. Selective scanning analyses of three comparison groups (OA vs. ON, OA vs. OS, and ON vs. OS) revealed population-selected regions related to metabolism, endocrine, and immune systems, harboring key genes (qrsl1, pde4d, hras, ikbkb, prkag1, prkaa2, prkacb, irs2, and eif4e2). These key genes were related to growth, reproduction, and disease resistance, indicating that breeding programs have selected for these traits. Due to the lack of stable morphological characteristics of juvenile fish and the changes in external environmental conditions that lead to changes in individual morphological characteristics, SNP fingerprints were successfully constructed for the identification of the three populations based on the differences in SNPs. Based on the five core SNP markers, two combinations of SNP markers were developed to accurately identify the three populations of tilapia at the genomic level. These results provide new information about tilapia genetic resources and reference data for identification and breeding purposes. Full article

The analysis and identification of the genetic diversity of plant germplasm resources and varieties are crucial for plant breeding. DNA fingerprinting using genomic molecular markers is crucial for precisely identifying germplasm resources. In this study, the SLAF-seq was performed using 47 germplasm resources of the Wanzhou tea plant population and 5 common cultivated varieties from the Yunnan, Sichuan, and Fujian provinces. A total of 7,447,940 SNPs were identified from 1,641,569 SLAF tags with an averaged sequencing depth of 11.73 (Q30 94.93% and GC 41.37%), which were used to analyze the population composition and genetic diversity. Results showed a large degree of genetic diversity and genetic variation among the samples. The cluster analysis showed that the tea plant population was categorized into three groups, indicating that these germplasms could not be fully classified by their geographical origin, and the linkage disequilibrium analysis indicates that the population resources of the XJ production area are more modern in evolution. A total of 371 uniformly distributed SNP loci were selected and successfully employed to construct the first SNP fingerprint and quick response code (QR code) for tea resources in Wanzhou. These findings offer new insights for genotyping, classifying, and identifying germplasm and genetic resources in the breeding of the Wanzhou tea population. Full article

Auricularia heimuer is the second most widely cultivated edible fungus in China, with significant food and medicinal value, and is highly popular throughout Asia and globally. However, the differentiation of A. heimuer is simple, as its morphology is characterized by a small “black disc”, making it difficult to distinguish among germplasms with highly similar agronomic traits, thus posing challenges for germplasm identification. To address this issue, this study conducted whole-genome resequencing analysis on 150 A. heimuer germplasms. Through filtering 9,589,911 SNPs obtained from 280 G resequencing data, a total of 1,202,947 high-quality SNP sites were identified. Based on these high-quality SNPs, population structure analysis, principal component analysis (PCA), and phylogenetic tree analysis revealed that the 150 A. heimuer germplasms could be divided into five groups, with wild strains from the same geographical origin exhibiting significant geographical clustering patterns. This finding underscores the relationship between the genetic diversity of wild A. heimuer and its geographical distribution in China. A further selection of 71 SNP sites was made, and 61 KASP markers were successfully developed using kompetitive allele-specific PCR (KASP) technology, with 54 of them demonstrating good polymorphism. The average values for the polymorphism information content (PIC), minor allele frequency (MAF), gene diversity, and heterozygosity of these core KASP markers were 0.34, 0.35, 0.34, and 0.43, respectively. Based on the 54 core KASP markers, a DNA fingerprinting map of the 150 A. heimuer germplasms was constructed in this study. The findings provide important molecular marker resources and theoretical support for the identification of A. heimuer germplasm, molecular marker-assisted breeding, and the selection of superior varieties. Full article

Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy–Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM. Full article

Aflatoxin B₁ (AFB₁) and sterigmatocystin (ST) are mycotoxins that pose significant threats to human and animal health owing to their mutagenic, carcinogenic, and toxic properties. They are structurally similar and widely believed to exert their biological effects via the generation of DNA-damaging epoxides at their respective terminal furan rings. Despite structural identity in the warhead portion of each toxin, this work shows that distal parts of each molecule are responsible for the distinctive mutational fingerprints seen in gptΔ C57BL/6J mouse embryo fibroblasts (MEFs). The two toxins differ structurally in the puckered cyclopentenone ring of AFB₁ and in the planar xanthone functionality of ST. While both toxins mainly induce GC→TA mutations, the aforementioned differences in structure apparently trigger unique patterns of mutations, as revealed by high-resolution duplex sequencing of MEF genomes. AFB₁ is more mutagenic than ST and displays its transversion mutations in a pattern with primary and secondary hotspots (underscored) in 5′-CGC-3′ and 5′-CGG-3′ contexts, respectively. ST displays a modest 5′-CGG-3′ hotspot while its other GC→TA transversions are more uniformly distributed in a pattern resembling established oxidative stress mutational spectra. This research delineates the mutational spectra of AFB₁ and ST, establishing these patterns as possible early-onset biomarkers of exposure. Full article

Background/Objectives: The surgeon’s subjective intraoperative evaluation is the standard of care to assess postoperative residual disease (RD) in advanced epithelial ovarian cancer (EOC). We investigated the feasibility of ctDNA as an objective marker for postoperative RD. Methods: This prospective study included 27 patients with advanced ovarian cancer (FIGO IIIA1–IVB) who underwent primary surgery between July 2021 and July 2022. Blood samples were analyzed preoperatively and on days 2 (d2) and 10 (d10) postoperatively. Low-coverage whole genome sequencing (WGS) was used to identify structural variants (SVs) at single-base pair resolution, single nucleotide variants (SNVs), and indels in tumor tissue to develop personalized, tumor-informed digital polymerase chain reaction (dPCR) fingerprint assays for each patient. Results: dPCR fingerprint assays were successfully developed for all patients by identifying one to eight SVs/SNVs per patient. ctDNA was detected in 96% (n = 26/27) of patients preoperatively and in 81% (n = 22/27) of patients at d10. Median ctDNA levels at d10 were significantly higher in patients with postoperative RD (median 367.38 copies (cps)/mL, 2.84% variant allele frequency; VAF) than in patients without postoperative RD (median 0.92 cps/mL, 0.017% VAF, p < 0.001). In patients with postoperative RD, ctDNA levels increased from the preoperative stage to d10 in seven out of eight patients (p = 0.016). In patients with complete tumor resection, ctDNA levels decreased from the preoperative stage to d10 in 17/19 patients (p < 0.001). Conclusions: A tumor-informed personalized ctDNA approach demonstrated feasibility, providing extremely high detection rates pre- and postoperatively. These results indicate that this approach could potentially be used for postoperative RD assessment in patients with primary advanced EOC. Full article

Leymus chinensis, a major component of the plant community in the eastern Eurasian grasslands with a wide distribution, provides stability to grassland ecosystems and supports animal husbandry. This study aimed to bridge the gap between the molecular breeding and industrial application of L. chinensis by conducting a comprehensive simple sequence repeat (SSR) analysis. A total of 973,129 SSRs were identified in the L. chinensis whole genome, which was used to design 20 polymorphic pairs of SSR primers to further assess 105 L. chinensis accessions. On average, 33.55 alleles were detected per locus, with an average Shannon index of 2.939 and a polymorphic information content value of 0.910. Principal coordinate, maximum likelihood, and structure analyses consistently showed that all samples were coincidentally divided into four subclasses. In addition, Mantel test data indicated a weak correlation between genetic and geographical distances in L. chinensis, whose variability may be related to the pollination mode and natural selection pressures. Finally, we used the 20 pairs of selected markers to scan 105 accessions, constructing a fingerprint for them. These findings provide new foundations for identifying superior varieties, improving the management of genetic resources, and constructing a germplasm resource database for L. chinensis. Full article

Palm trees (Arecaceae) are among the most popular ornamental plants worldwide. Despite extensive research on the fungi associated with Arecaceae, the diversity and ecological dynamics of fungi affecting ornamental palms remain poorly studied, although they have significant impact on palm health and economic value. Furthermore, while research on palm fungal diversity has traditionally focused on tropical assemblages, ornamental palms in temperate climates offer a unique opportunity to explore the diversity of palm fungi in non-native habitats. The present study conducted a preliminary assessment of the diversity and ecology of potential phytopathogenic fungi associated with foliar lesions on various ornamental palm host species in Portugal, combining morphological examination, PCR-based genomic fingerprinting, and biodiversity data analysis. The examination of 134 foliar lesions sampled from 100 palm trees resulted in a collection of 2064 palm leaf spotting fungi (PLSF), representing a diverse fungal assemblage of 320 molecular operational taxonomic units (MOTUs) across 97 genera. The overall fungal community composition revealed a distinct assemblage dominated by Neosetophoma, Alternaria, Phoma, and Cladosporium, with a profusion of infrequent and rare taxa consistent with a logseries distribution. Significantly positive co-occurrence (CO) patterns among prevalent and uncommon taxa suggest potential synergistic interactions enhancing fungal colonisation, persistence, and pathogenicity. The taxonomic structures of the PLSF contrasted markedly from tropical palm fungi, especially in the prevalence of pleosporalean coelomycetes of the Didymellaceae and Phaeosphaeriaceae, including recently introduced or not previously documented genera on Arecaceae. This novel assemblage suggests that climatic constraints shape the structure of palm fungal communities, resulting in distinctive temperate and tropical assemblages. In addition, the fungal assemblages varied significantly across palm host species, with temperate-native palms hosting more diverse, coelomycete-enriched communities. The present findings highlight foliar lesions as hyperdiverse microhabitats harbouring fungal communities with intricate interactions and a complex interplay of climatic, host, and ecological factors. With climate change altering environmental conditions, the identification of fungi thriving in or inhabiting these microhabitats becomes crucial for predicting shifts in pathogen dynamics and mitigating future fungal disease outbreaks. Understanding these complex ecological dynamics is essential for identifying potential phytopathogenic threats and developing effective management strategies for the health and sustainability of ornamental plants. Full article

Mango (Mangifera indica L.) (2n = 40) is an important perennial fruit tree in tropical and subtropical regions. The lack of information on genetic diversity at the molecular level hinders efforts in mango genetic improvement and molecular marker-assisted breeding. In this study, a genome-wide screening was conducted to develop simple sequence repeat (SSR) markers using the Alphonso reference genome. A total of 187 SSR primer pairs were designed based on SSR loci with consisting of tri- to hexa-nucleotide motifs, and 34 highly polymorphic primer pairs were selected to analyze the diversity of 231 germplasm resources. These primers amplified 219 alleles (Na) across 231 accessions, averaging of 6.441 alleles for per marker. The polymorphic information content (PIC) values ranged from 0.509 to 0.757 with a mean of 0.620. Genetic diversity varied among populations, with Southeast Asia showing the highest diversity, and Australia the lowest. Population structure analysis, divided the accessions into two groups, Group I (India) and Group II (Southeast Asia), containing 104 and 127 accessions, respectively, consistent with results from phylogenetic analysis and principal component analysis (PCA). Sixteen SSR primer pairs capable of distinguishing all tested accessions, were selected as core primers for constructing fingerprints of 229 mango accessions. These findings offer valuable resources for enhancing the utilization of mango germplasm in breeding programs. Full article

Pleurotus pulmonarius is prized by consumers for its distinct flavor, strong aroma, and dense, crispy texture. Although China has extensive germplasm resources for P. pulmonarius, only a limited number of cultivars are commercially available. A comprehensive evaluation and detailed analysis of P. pulmonarius germplasm, alongside the exploration of superior germplasm resources, are essential for developing new varieties. In this study, we resequenced the genomes of 47 P. pulmonarius strains collected nationwide, identifying a total of 4,430,948 single nucleotide polymorphism (SNP) loci. After filtering based on minor allele frequency and data integrity, 181,731 high-quality SNP markers were retained. Phylogenetic analysis grouped the strains into six clusters, with strains from similar geographical regions clustering together. Most CBS strains formed a single cluster; cultivated varieties exhibited higher genetic similarity, whereas wild strains displayed greater diversity. Principal component analysis (PCA) and population structure analyses, using the same SNP markers, corroborated the phylogenetic findings. DNA fingerprinting, derived from 369 core SNPs, further underscored the genetic diversity among strains. Significant morphological variation was observed, with strains in groups ZP, CBS, and WHLJ exhibiting notably higher yields and cap widths compared to other groups. Correlation analysis revealed associations among various phenotypes, while genome-wide association study (GWAS) identified multiple SNP markers within candidate genes linked to agronomic traits, most of which were controlled by multiple genes. This research offers a molecular-level characterization and evaluation of P. pulmonarius germplasm resources, providing a scientific basis for enriching available germplasm and advancing breeding materials. Full article