Search

Abstract Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6-week wet-lab and bioinformatics course for undergraduates was implemented through the project-based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step-by-step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.

The fishy odor of fish oil, a popular nutritional supplement, affects its quality as well as consumer acceptance and eating experience. An objective or scientific method for analyzing fish oil's olfactory characteristics is still lacking. This study examined anchovy oil to develop qualitative and quantitative approaches for identifying fishy odor components. Multiple fish oil refining samples were analyzed using gas chromatography-ion mobility spectrometry (GC-IMS). Due to their significant alterations during fish oil refining, low threshold values, and distinct olfactory properties, the unsaturated aldehydes (E)-2-pentenal and (E,E)-2,4-heptadienal and the unsaturated ketone 1-penten-3-one may contribute to the fishy odor. Among the chemicals, (E,E)-2,4-heptadienal was chosen as the marker for developing a method to quantify fishy odor and analyze deodorization samples using headspace solid-phase micro-extraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). The quantitative study of fishy odor in fish oil is a pioneering approach that can help improve quality assurance and refining process. [ABSTRACT FROM AUTHOR]

Four dimeric diketopiperazine stereoisomers (1–4) including two new ones (1–2) had been isolated from the culture broth of one marine-derived fungus Aspergillus sp. Z3, which was found in the gut of a marine isopod Ligia exotica. The planner structures and absolute configurations of the new compounds were determined by combination of NMR, HRESIMS, electronic circular dichroism calculation, Marfey's method as well as single-crystal X-ray diffraction. Their cytotoxicity against the prostate cancer PC3 cell line was assayed by the MTT method. [ABSTRACT FROM AUTHOR]

Mycotoxin contamination in food poses health hazards to humans. Current methods of controlling mycotoxins still have limitations and more effective approaches are needed. During the past decades of years, variable environmental factors have been tested for their influence on mycotoxin production leading to elucidation of a complex regulatory network involved in mycotoxin biosynthesis. These regulators are putative targets for screening molecules that could inhibit mycotoxin synthesis. Here, we summarize the regulatory mechanisms of hierarchical regulators, including pathway-specific regulators, global regulators and epigenetic regulators, on the production of the most critical mycotoxins (aflatoxins, patulin, citrinin, trichothecenes and fumonisins). Future studies on regulation of mycotoxins will provide valuable knowledge for exploring novel methods to inhibit mycotoxin biosynthesis in a more efficient way. [ABSTRACT FROM AUTHOR]

Abstract Background Responses to extracellular stress are required for microbes to survive in changing environments. Although the stress response mechanisms have been characterized extensively, the evolution of stress response pathway remains poorly understood. Here, we studied the evolution of High Osmolarity Glycerol (HOG) pathway, one of the important osmotic stress response pathways, across 10 yeast species and underpinned the evolutionary forces acting on the pathway evolution. Results Although the HOG pathway is well conserved across the surveyed yeast species, the evolutionary rate of the genes in this pathway varied substantially among or within different lineages. The fast divergence of MSB2 gene indicates that this gene is subjected to positive selection. Moreover, transcription factors in HOG pathway tend to evolve more rapidly, but the genes in conserved MAPK cascade underwent stronger functional selection. Remarkably, the dN/dS values are negatively correlated with pathway position along HOG pathway from Sln1 (Sho1) to Hog1 for transmitting external signal into nuclear. The increased gradient of selective constraints from upstream to downstream genes suggested that the downstream genes are more pleiotropic, being required for a wider range of pathways. In addition, protein length, codon usage, gene expression, and protein interaction appear to be important factors to determine the evolution of genes in HOG pathway. Conclusions Taken together, our results suggest that functional constraints play a large role in the evolutionary rate variation in HOG pathway, but the genetic variation was influenced by quite complicated factors, such as pathway position, protein length and so on. These findings provide some insights into how HOG pathway genes evolved rapidly for responding to environmental osmotic stress changes. Reviewers This article was reviewed by Han Liang (nominated by Laura Landweber), Georgy Bazykin (nominated by Mikhail Gelfand) and Zhenguo Lin (nominated by John Logsdon).

Four novel stemphol derivatives, pleosporols A–D (1, 2 and mixture of 3 and 4) together with known compounds stemfolones (mixture of 5 and 6), stemphol (7) were isolated from a marine fungus Pleospora sp. (PO4) derived from the gut of marine isopod Ligia oceanica. The planar structures of novel compounds were elucidated on the basis of mass and NMR spectral analysis. The stereo-chemistries of 1–2 were determined by CD spectra, NOESY data, coupling constants analysis and modified Mosher's method while the absolute configurations of 3–6 were not clear. Novel compounds contained α, β-unsaturated cyclohexanone ring and possibly derived from the oxidation of stemphol. All novel ones showed strong antimicrobial activity against Staphylococcus epidermidis CMCC26069 with MIC values less than 10 μg/mL. [ABSTRACT FROM AUTHOR]

Known diketopiperazine WIN 64821 and its asymmetric stereoisomers (1–3) had been isolated from the culture broth of a marine gut fungusAspergillussp. DX4H. The planar and stereochemistry for new compounds were determined by a suite of techniques including mass, NMR and CD spectra together with Marfey’s method. Their inhibitory activity against PC3 cell line had been tested. [ABSTRACT FROM PUBLISHER]

Marine-derived fungi have been reported to have great potential to produce structurally unique metabolites. Our investigation on secondary metabolites from marine-derived fungi resulted in the isolation of seven new polyketides (phomopsiketones D–G (1–4) and letendronols A–C (5–7)) as well as one known xylarinol (8) in the cultural broth of Letendraea sp. Their structures and absolute configurations were elucidated using a set of spectroscopic and chemical methods, including HRESIMS, NMR, single-crystal X-ray diffraction, ECD calculation, and a modified version of Mosher's method. Compound 2 showed weak inhibition against nitric oxide production in lipopolysaccaride-activated macrophages with an IC50 value of 86 μM. [ABSTRACT FROM AUTHOR]

Filamentous fungi's secondary metabolites (SMs) possess significant application owing to their distinct structure and diverse bioactivities, yet their restricted yield levels often hinder further research and application. The study developed a response surface methodology-artificial neural network (RSM-ANN) strategy with multi-parameter optimizations of the ANN model to optimize medium for the production of two high-value fungal SMs, echinocandin E and paraherquamide A. Multi-parameter optimization of the ANN model was achieved through stratifying experimental data, fully adjusting neural network internals, and evaluating metaheuristic algorithms for optimal initial weights and biases. Experimental validation of models revealed that ANN-genetic algorithm models outperformed traditional RSM models in terms of determination coefficients, accuracy, and mean squared errors. ANN models showed outstanding robustness across a variety of fungal species, mediums, and experimental designs (Central Composite Design or Box-Behnken Design). This work refines the RSM-ANN optimization technique to increase fungal SM production efficiency, enabling industrial-scale production and applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Background: Responses to extracellular stress are required for microbes to survive in changing environments. Although the stress response mechanisms have been characterized extensively, the evolution of stress response pathway remains poorly understood. Here, we studied the evolution of High Osmolarity Glycerol (HOG) pathway, one of the important osmotic stress response pathways, across 10 yeast species and underpinned the evolutionary forces acting on the pathway evolution., Results: Although the HOG pathway is well conserved across the surveyed yeast species, the evolutionary rate of the genes in this pathway varied substantially among or within different lineages. The fast divergence of MSB2 gene indicates that this gene is subjected to positive selection. Moreover, transcription factors in HOG pathway tend to evolve more rapidly, but the genes in conserved MAPK cascade underwent stronger functional selection. Remarkably, the dN/dS values are negatively correlated with pathway position along HOG pathway from Sln1 (Sho1) to Hog1 for transmitting external signal into nuclear. The increased gradient of selective constraints from upstream to downstream genes suggested that the downstream genes are more pleiotropic, being required for a wider range of pathways. In addition, protein length, codon usage, gene expression, and protein interaction appear to be important factors to determine the evolution of genes in HOG pathway., Conclusions: Taken together, our results suggest that functional constraints play a large role in the evolutionary rate variation in HOG pathway, but the genetic variation was influenced by quite complicated factors, such as pathway position, protein length and so on. These findings provide some insights into how HOG pathway genes evolved rapidly for responding to environmental osmotic stress changes., Reviewers: This article was reviewed by Han Liang (nominated by Laura Landweber), Georgy Bazykin (nominated by Mikhail Gelfand) and Zhenguo Lin (nominated by John Logsdon).