An alignment- and reference-free strategy using -mer present pattern for population genomic analyses.

Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-genome alignments. -mer decomposition is an alternative to graph-based pangenomes. However, how to directly use -mers for the population genetic analyses is unknown.

Effect of Deformation Mode on Grain Characteristics and Strength-Toughness of Al-Zn-Mg-Cu Alloy.

The Al-Zn-Mg-Cu alloy plate is a structural material widely used in aerospace, and its rolling process plays a crucial role in determining its performance. This study investigated the effects of different pass combinations of forward and spread rolling on the grain characteristics, strength, and fracture toughness of Al-Zn-Mg-Cu aluminum alloy plates under industrial conditions. The results show that initially using a small pass reduction followed by a larger one can improve the grain width and thickness on the Long Transverse-Short Transverse surface.

Global Analysis of Natural Products Biosynthetic Diversity Encoded in Fungal Genomes.

Fungal secondary metabolites (SMs) represent an invaluable source of therapeutic drugs. Genomics-based approaches to SM discovery have revealed a vast and largely untapped biosynthetic potential within fungal genomes. Here, we used the publicly available fungal genome sequences from the NCBI public database, as well as tools such as antiSMASH, BIG-SLiCE, etc.

Exploration on cold adaptation of Antarctic lichen via detection of positive selection genes.

Lichen as mutualistic symbiosis is the dominant organism in various extreme terrestrial environment on Earth, however, the mechanisms of their adaptation to extreme habitats have not been fully elucidated. In this study, we chose the Antarctic dominant lichen species Usnea aurantiacoatra to generate a high-quality genome, carried out phylogenetic analysis using maximum likelihood and identify genes under positive selection. We performed functional enrichment analysis on the positively selected genes (PSGs) and found that most of the PSGs focused on transmembrane transporter activity and vacuole components.

Graph-Based Pan-Genome Reveals the Pattern of Deleterious Mutations during the Domestication of .

The "cost of domestication" hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used , the world's oldest domesticated fungus, as a model to investigate the genomic characteristics of deleterious variants arising from fungal domestication.

Prenatal exposure to hexafluoropropylene oxide trimer acid (HFPO-TA) disrupts the maternal gut microbiome and fecal metabolome homeostasis.

Initially considered a "safe" substitute for perfluorooctanoic acid (PFOA), hexafluoropropylene oxide trimer acid (HFPO-TA) has been extensively used in the production of fluoropolymers for several years, leading to its environmental ubiquity and subsequent discovery of its significant bio-accumulative properties and toxicological effects. However, the specific impact of HFPO-TA on females, particularly those who are pregnant, remains unclear. In the present study, pregnant mice were exposed to 0.

Identifying genetic variants associated with amphotericin B (AMB) resistance in via merbased GWAS.

is one of the most common pathogenic fungi, which results in high morbidity and mortality in immunocompromised patients. Amphotericin B (AMB) is used as the core drug for the treatment of triazole-resistant . Following the usage of amphotericin B drugs, the number of amphotericin B-resistant isolates showed an increasing trend over the years, but the mechanism and mutations associated with amphotericin B sensitivity are not fully understood.

Using Polygenic Risk Scores Related to Complex Traits to Predict Production Performance in Cross-Breeding of Yeast.

The cultivation of hybrids with favorable complex traits is one of the important goals for animal, plant, and microbial breeding practices. A method that can closely predict the production performance of hybrids is of great significance for research and practice. In our study, polygenic risk scores (PRSs) were introduced to estimate the production performance of .

Dioxin-like polychlorinated biphenyl 126 (PCB126) disrupts gut microbiota-host metabolic dysfunction in mice via aryl hydrocarbon receptor activation.

Exposure to environmental pollutants, including dioxin-like pollutants, can cause numerous health issues. A common exposure route to pollutants is through contaminated foods, and thus the gastrointestinal system and gut microbiota are often exposed to high amounts of pollutants. Multiple studies have focused on the imbalance in intestinal microbiota composition caused by dioxin-like pollutants.

Genomic landscape of a relict fir-associated fungus reveals rapid convergent adaptation towards endophytism.

Comparative and pan-genomic analyses of the endophytic fungus Pezicula neosporulosa (Helotiales, Ascomycota) from needles of the relict fir, Abies beshanzuensis, showed expansions of carbohydrate metabolism and secondary metabolite biosynthetic genes characteristic for unrelated plant-beneficial helotialean, such as dark septate endophytes and ericoid mycorrhizal fungi. The current species within the relatively young Pliocene genus Pezicula are predominantly saprotrophic, while P. neosporulosa lacks such features.

Divergence of a genomic island leads to the evolution of melanization in a halophyte root fungus.

Understanding how organisms adapt to extreme living conditions is central to evolutionary biology. Dark septate endophytes (DSEs) constitute an important component of the root mycobiome and they are often able to alleviate host abiotic stresses. Here, we investigated the molecular mechanisms underlying the beneficial association between the DSE Laburnicola rhizohalophila and its host, the native halophyte Suaeda salsa, using population genomics.

Activity Components from for Preventing Hepatic Fibrosis and of Its Molecular Targets by Network Pharmacology Approach.

Hepatic fibrosis would develop into cirrhosis or cancer without treating. Hence, it is necessary to study the mechanism and prevention methods for hepatic fibrosis. is a traditional medicinal material with a high medicinal and health value.

Optimization of flash extraction, separation of ginsenosides, identification by HPLC-FT-ICR-MS and determination of rare ginsenosides in mountain cultivated ginseng.

In this paper, we used the flash extraction method (FEM) to extract ginsenosides from mountain cultivated ginseng (MCG), optimized the FEM process by response surface methodology (RSM), and separated 23 kinds of ginsenosides from MCG, including rare ginsenoside Rg, 20(/)-Rg, Rk, 20()-Rh, 20()-Rh, F and Rg. Among them, notoginsenoside R was isolated from MCG for the first time. Additionally, we established an HPLC-FT-ICR-MS method to accurately identify 20 ginsenosides in MCG, and quantitatively analyzed the differences in the content of rare ginsenosides in MCG and Garden-Cultivated Ginseng (CG) by HPLC-UV.

Perfluoropolyether carboxylic acids (novel alternatives to PFOA) impair zebrafish posterior swim bladder development via thyroid hormone disruption.

Perfluoropolyether carboxylic acids (PFECAs, CF(OCF)COO, n = 2-5) are novel alternatives to perfluorooctanoic acid (PFOA) and are widely used in industrial production. However, although they have been detected in surface water and human blood, their toxicities on aquatic organisms remain unknown. We used zebrafish embryos to compare the developmental toxicities of various PFECAs (e.

Accumulation, Biotransformation, and Endocrine Disruption Effects of Fluorotelomer Surfactant Mixtures on Zebrafish.

As an alternative to perfluorooctanesulfonate (PFOS), novel fluorotelomer surfactants (6:2 fluorotelomer sulfonamide alkylbetaine (6:2 FTAB) and 6:2 fluorotelomer sulfonamide alkylamine (6:2 FTAA)) are widely used in aqueous film-forming foams and are frequently found to coexist in the environment. However, their potential toxicities remain unknown. Here, we investigated the chronic toxicity of 6:2 FTAB (65%) and 6:2 FTAA (35%) coexposure on adult zebrafish at doses of 0, 5, 50, or 500 μg/L using a flow-through exposure system for 180 days.

Chronic exposure to 6:2 chlorinated polyfluorinated ether sulfonate acid (F-53B) induced hepatotoxic effects in adult zebrafish and disrupted the PPAR signaling pathway in their offspring.

As a Chinese-specific alternative to perfluorooctane sulfonate (PFOS), 6:2 chlorinated polyfluorinated ether sulfonate (commercial name: F-53B) has been used in the metal plating industry for over 40 years. This prevalence of use has resulted in its subsequent detection within the environment, wildlife, and humans. Despite this, however, its hepatotoxic effects on aquatic organisms remain unclear.

Parental exposure to 6:2 chlorinated polyfluorinated ether sulfonate (F-53B) induced transgenerational thyroid hormone disruption in zebrafish.

Although 6:2 chlorinated polyfluorinated ether sulfonate (F-53B), an alternative to perfluorooctanesulfonate (PFOS), has been regularly detected in different environmental matrices, information regarding its toxicity remains limited. To explore the transgenerational thyroid-disrupting capacity of F-53B, adult zebrafish (F0) were exposed to different concentrations of F-53B (0, 5, 50, or 500μg/L) for 180d, with their offspring (F1 and F2) subsequently reared in uncontaminated water. Thyroid disturbances were then examined in the three (F0, F1, and F2) generations.

Gypensapogenin H from hydrolyzate of total saponins induces apoptosis in human breast carcinoma cells.

Gypensapogenin H (Gyp H) is a novel dammarane-type triterpene, isolated from hydrolyzate of total saponins from . Our previous work demonstrated that Gyp H exhibited potent growth inhibitory effects on tumor cells. It significantly inhibited the growth of human breast cancer cells (MDA-MB-231), while having low toxicity to normal human breast epithelial cells, MCF-10a.

Two-generational reproductive toxicity assessment of 6:2 chlorinated polyfluorinated ether sulfonate (F-53B, a novel alternative to perfluorooctane sulfonate) in zebrafish.

As an alternative to perfluorooctane sulfonate (PFOS), 6:2 chlorinated polyfluorinated ether sulfonate (commercial name: F-53B) has been used in the Chinese chrome plating industry for over four decades. It has been increasingly detected in environmental matrices in recent years, causing great concern regarding its potential health risks to humans and wildlife. However, its adverse effects on biota remain largely unknown.

Four new dammarane-type triterpenes derivatives from hydrolyzate of total saponins and their bioactivities.

Phytochemical investigation of hydrolysate of total saponins led to the isolation of four novel triterpenes, Gypensapogenin U (), Gypensapogenin V (), Gypensapogenin W () and Gypensapogenin X (). The structures of these compounds were identified by 1D, 2D-NMR and HR-ESI-MS evidences. Additionally, the protective activity of these new compounds against cardiomyocytes injury induced by HO and their cytotoxic activity against t-HSC/Cl-6 cells were evaluated.

6:2 fluorotelomer sulfonamide alkylbetaine (6:2 FTAB), a novel perfluorooctane sulfonate alternative, induced developmental toxicity in zebrafish embryos.

6:2 fluorotelomer sulfonamide alkylbetaine (6:2 FTAB) is a major component of Forafac1157, a novel perfluorooctane sulfonate (PFOS) alternative used globally in aqueous film forming foams (AFFFs). Although 6:2 FTAB has been recently detected in the aquatic environment, its toxic effects on aquatic organisms remain unclear. Here, zebrafish embryos were exposed to various concentrations of 6:2 FTAB (0, 5, 10, 20, 40, 60, 80, and 100 mg/L) from 6 to 120 h post-fertilization (hpf) to investigate its developmental toxicity and possible mechanism of action.

Triterpenes derived from hydrolyzate of total Gynostemma pentaphyllum saponins with anti-hepatic fibrosis and protective activity against HO-induced injury.

Gynostemma pentaphyllum is a popular functional food, and it is also used as a traditional medicine in Asia. In this study, five previously undescribed triterpenes, gypensapogenin M, gypensapogenin N, gypensapogenin O, gypensapogenin P, and gypensapogenin Q, together with five known compounds were isolated from the hydrolyzate of total G. pentaphyllum saponins.

6:2 fluorotelomer carboxylic acid (6:2 FTCA) exposure induces developmental toxicity and inhibits the formation of erythrocytes during zebrafish embryogenesis.

Saturated fluorotelomer carboxylic acids (FTCAs) are intermediates in the degradation of fluorotelomer alcohols (FTOHs) to perfluorinated carboxylic acids (PFCAs). Recent studies have detected FTCAs in precipitation, surface waters, and wildlife, but few studies have focused on their toxicity. In this study, zebrafish embryos were exposed to different concentrations of 6:2 FTCA (0, 4, 8, and 12mg/L) from 6 to 120h post-fertilization (hpf) to investigate its developmental toxicity.