Reactive oxygen species may play an essential role in driving biological evolution: The Cambrian Explosion as an example

Deciphering the biosynthetic potential of microbial genomes using a BGC language processing neural network model

Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC prediction and classification. Leveraging the transformer encoder, BGC-Prophet captures location-dependent relationships between genes. As one of the pioneering ultrahigh-throughput tools, BGC-Prophet significantly surpasses existing methods in efficiency and fidelity, enabling comprehensive pan-phylogenetic and whole-metagenome BGC screening. Through the analysis of 85 203 genomes and 9428 metagenomes, BGC-Prophet has profiled an extensive array of sub-million BGCs. It highlights notable enrichment in phyla like Actinomycetota and the widespread distribution of polyketide, NRP, and RiPP BGCs across diverse lineages. It reveals enrichment patterns of BGCs following important geological events, suggesting environmental influences on BGC evolution. BGC-Prophet's capabilities in detection of BGCs and evolutionary patterns offer contributions to deeper understanding of microbial secondary metabolites and application in synthetic biology.

Unveiling the Neuroprotective Potential of Date Palm (Phoenix dactylifera): A Systematic Review

Background: Neurodegenerative diseases primarily afflict the elderly and are characterized by a progressive loss of neurons. Oxidative stress is intricately linked to the advancement of these conditions. This study focuses on Phoenix dactylifera (P. dactylifera; Family: Arecaceae), commonly known as "Ajwa," a globally cultivated herbal plant renowned for its potent antioxidant properties and reported neuroprotective effects in pharmacological studies. Method: This comprehensive systematic review delves into the antioxidant properties of plant extracts and their phytochemical components, with a particular emphasis on P. dactylifera and its potential neuroprotective benefits. Preferred reporting items for systemic reviews and meta-analysis (PRISMA) were employed to review the articles. Results: The study includes 269 articles published in the literature and 17 were selected after qualitative analysis. The growing body of research underscores the critical role of polyphenolic compounds found in P. dactylifera, which significantly contribute to its neuroprotective effects through antioxidant mechanisms. Despite emerging insights into the antioxidant actions of P. dactylifera, further investigation is essential to fully elucidate the specific pathways through which it confers neuroprotection. Conclusions: Like many other plant-based supplements, P. dactylifera's antioxidant effects are likely mediated by synergistic interactions among its diverse bioactive compounds, rather than by any single constituent alone. Therefore, additional preclinical and clinical studies are necessary to explore P. dactylifera's therapeutic potential comprehensively, especially in terms of its targeted antioxidant activities aimed at mitigating neurodegenerative processes. Such research holds promise for advancing our understanding and potentially harnessing the therapeutic benefits of P. dactylifera in neuroprotection.

Advances and research needs for disinfection byproducts control strategies in swimming pools

The control of disinfection byproducts (DBPs) in swimming pools is of great significance due to the non-negligible toxicity and widespread existence of DBPs. However, the management of DBPs remains challenging as the removal and regulation of DBPs is a multifactorial phenomenon in pools. This study summarized recent studies on the removal and regulation of DBPs, and further proposed some research needs. Specifically, the removal of DBPs was divided into the direct removal of the generated DBPs and the indirect removal by inhibiting DBP formation. Inhibiting DBP formation seems to be the more effective and economically practical strategy, which can be achieved mainly by reducing precursors, improving disinfection technology, and optimizing water quality parameters. Alternative disinfection technologies to chlorine disinfection have attracted increasing attention, while their applicability in pools requires further investigation. The regulation of DBPs was discussed in terms of improving the standards on DBPs and their preccursors. The development of online monitoring technology for DBPs is essential for implementing the standard. Overall, this study makes a significant contribution to the control of DBPs in pool water by updating the latest research advances and providing detailed perspectives.

Structure analysis and anti-inflammatory effect of a polysaccharide from Hippocampus mohnikei

The purpose of this study was to analyze the structure of a polysaccharide (HMP-1) from Hippocampus mohnikei, and to explore its anti-inflammatory effect. HMP-1 was obtained from Hippocampus mohnikei by ethanol sedimentation and secondary column chromatography purification. Its structural characteristics were analyzed by gel permeation chromatography (GPC), fourier transform infrared (FT-IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy and scanning electron micrograph (SEM). Results showed its molecular weight (Mw) was 7296 Da, and it mainly consisted of six residues, 1,3-β-Glcp, 1,4-α-Manp, 1,4-α-GalpA, 1,4-β-GlcpA2S, 1,4-α-Galp3S, 1,4-β-GlcNAc. HMP-1 could protect RAW246.7 cells from the cytotoxic effect induced by LPS. HMP-1 also could reduce the levels of nitric oxide and reactive oxygen species produced by LPS stimulation, suggesting that HMP-1 has anti-inflammatory activities within a certain concentration range.

Epigenetics recording varied environment and complex cell events represents the origin of cellular aging

Although a relationship between epigenetics and aging phenotypic changes has been established, a theoretical explanation of the intrinsic connection between the epigenetics and aging is lacking. In this essay, we propose that epigenetic recording of varied cell environment and complex history could be an origin of cellular aging. Through epigenetic modifications, the environment and historical events can induce the chromatin template into an activated or repressive accessible structure, thereby shaping the DNA template into a spectrum of chromatin states. The inner nature of diversity and conflicts born by the cell environment and its historical events are hence recorded into the chromatin template. This could result in a dissipated spectrum of the chromatin state and chaos in overall gene expression. An unavoidable degradation of epigenome entropy, similar to Shannon entropy, would be consequently induced. The resultant disorder in epigenome, characterized by corrosion of epigenome entropy as reflected in chromatin template, can be stably memorized and propagated through cell division. Furthermore, the hysteretic nature of epigenetics responding to the emerging environment could exacerbate the degradation of epigenome entropy. As well as stochastic errors, we propose that outside entropy (or chaos) derived from the varied environment and complex cell history, gradually input and imprinted into the chromatin via epigenetic modifications, would lead inevitably to cellular aging, the extent of which could be aggravated by hysteresis of epigenetics without error erasing and correction.

Oxygen Tension Strongly Influences Metabolic Parameters and the Release of Interleukin-6 of Human Amniotic Mesenchymal Stromal Cells In Vitro

The human amniotic membrane (hAM) has been used for tissue regeneration for over a century. In vivo (in utero), cells of the hAM are exposed to low oxygen tension (1-4% oxygen), while the hAM is usually cultured in atmospheric, meaning high, oxygen tension (20% oxygen). We tested the influence of oxygen tensions on mitochondrial and inflammatory parameters of human amniotic mesenchymal stromal cells (hAMSCs). Freshly isolated hAMSCs were incubated for 4 days at 5% and 20% oxygen. We found 20% oxygen to strongly increase mitochondrial oxidative phosphorylation, especially in placental amniotic cells. Oxygen tension did not impact levels of reactive oxygen species (ROS); however, placental amniotic cells showed lower levels of ROS, independent of oxygen tension. In contrast, the release of nitric oxide was independent of the amniotic region but dependent on oxygen tension. Furthermore, IL-6 was significantly increased at 20% oxygen. To conclude, short-time cultivation at 20% oxygen of freshly isolated hAMSCs induced significant changes in mitochondrial function and release of IL-6. Depending on the therapeutic purpose, cultivation conditions of the cells should be chosen carefully for providing the best possible quality of cell therapy.