Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.

In this study, we investigated the codon bias of twelve mitochondrial core protein coding genes (PCGs) in eight Pleurotus strains, two of which are from the same species. The results revealed that the codons of all Pleurotus strains had a preference for ending in A/T. Furthermore, the correlation between codon base compositions and codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) indices was also detected, implying the influence of base composition on codon bias. The two P. ostreatus species were found to have differences in various base bias indicators. The average effective number of codons (ENC) of mitochondrial core PCGs of Pleurotus was found to be less than 35, indicating strong codon preference of mitochondrial core PCGs of Pleurotus. The neutrality plot analysis and PR2-Bias plot analysis further suggested that natural selection plays an important role in Pleurotus codon bias. Additionally, six to ten optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified in eight Pleurotus strains, with UGU and ACU being the most widely used optimal codons in Pleurotus. Finally, based on the combined mitochondrial sequence and RSCU value, the genetic relationship between different Pleurotus strains was deduced, showing large variations between them. This research has improved our understanding of synonymous codon usage characteristics and evolution of this important fungal group.

Decoding Biomechanical Cues Based on DNA Sensors.

Biological systems perceive and respond to mechanical forces, generating mechanical cues to regulate life processes. Analyzing biomechanical forces has profound significance for understanding biological functions. Therefore, a series of molecular mechanical techniques have been developed, mainly including single-molecule force spectroscopy, traction force microscopy, and molecular tension sensor systems, which provide indispensable tools for advancing the field of mechanobiology. DNA molecules with a programmable structure and well-defined mechanical characteristics have attached much attention to molecular tension sensors as sensing elements, and are designed for the study of biomechanical forces to present biomechanical information with high sensitivity and resolution. In this work, a comprehensive overview of molecular mechanical technology is presented, with a particular focus on molecular tension sensor systems, specifically those based on DNA. Finally, the future development and challenges of DNA-based molecular tension sensor systems are looked upon.

Adjusting Catalytic Activity of ß-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site.

ß-Amyrin synthase (bAS) is a representative plant oxidosqualene cyclase (OSC), and previous studies have identified many functional residues and mutants that can alter its catalytic activity. However, the regulatory mechanism of the active site architecture for adjusting the catalytic activity remains unclear. In this study, we investigate the function of key residues and their regulatory effects on the catalytic activity of Glycyrrhiza glabra ß-amyrin synthase (GgbAS) through molecular dynamics simulations and site-directed mutagenesis experiments. We identified the plasticity residues located in two active site regions and explored the interactions between these residues and tetracyclic/pentacyclic intermediates. Based on computational and experimental results, we further categorize these plasticity residues into three types: effector, adjuster, and supporter residues, according to their functions in the catalytic process. This study provides valuable insights into the catalytic mechanism and active site plasticity of GgbAS, offering important references for the rational enzyme engineering of other OSC enzyme.

Peptides Used for Heavy Metal Remediation: A Promising Approach.

In recent years, heavy metal pollution has become increasingly prominent, severely damaging ecosystems and biodiversity, and posing a serious threat to human health. However, the results of current methods for heavy metal restoration are not satisfactory, so it is urgent to find a new and effective method. Peptides are the units that make up proteins, with small molecular weights and strong biological activities. They can effectively repair proteins by forming complexes, reducing heavy metal ions, activating the plant's antioxidant defense system, and promoting the growth and metabolism of microorganisms. Peptides show great potential for the remediation of heavy metal contamination due to their special structure and properties. This paper reviews the research progress in recent years on the use of peptides to remediate heavy metal pollution, describes the mechanisms and applications of remediation, and provides references for the remediation of heavy metal pollution.

An investigation of the effects of meteorological factors on the incidence of tuberculosis.

To explore the influence of meteorological factors on the incidence of tuberculosis (TB) in Yingjisha County, Kashgar Region, Xinjiang, and to provide a scientific basis for the prevention and control of TB. The Spearman correlation analysis and distribution lag nonlinear model analysis were conducted on the number of daily reported cases of TB from 2016 to 2023 to study the association effect of various meteorological factors and the daily incidence number of TB in Yingjisha County. A total of 13,288 TB cases were reported from January 2016 to June 2023, and June to October is the peak period of annual TB incidence. Spearman correlation analysis revealed that average daily temperature (AT) and average daily wind speed (WS) were positively correlated with TB incidence (rAT = 0.110, rWS = 0.090); and average daily relative humidity (RH) and TB incidence was negatively correlated (rRH = - 0.093). When AT was - 15 °C, the RR reached a maximum of 2.20 (95% CI: 0.77-6.29) at a lag of 21 days. When RH was 92%, the RR reached a maximum of 1.05 (95% CI: 0.92-1.19) at a lag of 6 days. When WS was 5.2 m/s, the RR reached a maximum of 1.30 (95% CI: 0.78-2.16) at a lag of 16 days. There is a non-linearity and a certain lag between meteorological factors and the occurrence and prevalence of TB in the population, which is mainly manifested in the fact that the risk of incidence of TB decreases with the increase of the daily AT, has a hazardous effect within a certain range of humidity as the average daily RH rises, and gradually increases with the increase of the average daily WS. Local residents are advised to pay attention to climate change so as to take appropriate preventive measures, especially women and middle and old age group should pay close attention to climate change and add more clothes in time, minimise travelling in hazy weather and windy and sandy weather, maintain good nutrition, adequate sleep and moderate exercise in daily life to enhance their immunity, wash hands frequently and ventilate the air, and try to avoid staying in humid and confined spaces in order to reduce the risk of latent TB patients developing the disease.

Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico.

Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains to affect cell proliferation, apoptosis, and differentiation. In this work, 43 selective benzoazepinone BRD4-BD1 inhibitors were studied using molecular simulations and three-dimensional quantitative conformation relationships (3D-QSAR). A reliable 3D-QSAR model was established based on COMFA (Q2 = 0.532, R2 = 0.981) and COMSIA (S + E + H (Q2 = 0.536, R2 = 0.979) two different analysis methods. Through 3D-QSAR model prediction and quantum chemical analysis, 15 small molecules with stronger inhibitory activity than the template compounds were constructed, and 5 new compounds with higher predictive activity and binding affinity were screened by molecular docking and ADMET methods. According to the molecular dynamics simulation, the key residues that can interact with BRD4-BD1 protein and molecular docking results are consistent, including ASN140, MET132, GLN85, MET105, ASN135 and TYR97. From the MD trajectory, we calculated and analyzed RMSD, RMSF, free binding energy, FECM, DCCM and PCA, the loop region formed by amino acids VAL45∼PRO62 showed α-helix, ß-folding and clustering towards the active center with the extension of simulation time. Further optimization of the structure of active candidate compounds A6, A11, A14, and A15 will provide the necessary theoretical basis for the synthesis and activity evaluation of novel BRD4-BD1 inhibitors.Communicated by Ramaswamy H. Sarma.

Engineering novel scaffolds for specific HDAC11 inhibitors against metabolic diseases exploiting deep learning, virtual screening, and molecular dynamics simulations.

The prevalence of metabolic diseases is increasing at a frightening rate year by year. The burgeoning development of deep learning enables drug design to be more efficient, selective, and structurally novel. The critical relevance of Histone deacetylase 11 (HDAC11) to the pathogenesis of several metabolic diseases makes it a promising drug target for curbing metabolic disorders. The present study aims to design new specific HDAC11 inhibitors for the treatment of metabolic diseases. Deep learning was performed to learn the properties of existing HDAC11 inhibitors and yield a novel compound library containing 23,122 molecules. Subsequently, the compound library was screened by ADMET properties, Lipinski & Veber rules, traditional machine classification models, and molecular docking, and 10 compounds were screened as candidate HDAC11 inhibitors. The stability of the 10 new molecules was further evaluated by deploying RMSD, RMSF, MM/GBSA, free energy landscape mapping, and PCA analysis in molecular dynamics simulations. As a result, ten compounds, Cpd_17556, Cpd_2184, Cpd_8907, Cpd_7771, Cpd_14959, Cpd_7108, Cpd_12383, Cpd_13153, Cpd_14500and Cpd_21811, were characterized as good HDAC11 inhibitors and are expected to be promising drug candidates for metabolic disorders, and further in vitro, in vivo and clinical trials to demonstrate in the future.

Addressing pollution challenges for enterprises under diverse extreme climate conditions: artificial intelligence-driven experience and policy support of top Chinese enterprises.

Introduction: This study investigates the experiences of leading Chinese companies in environmental conservation under varying extreme climate conditions, focusing on the role of artificial intelligence (AI) and governmental assistance. Methods: A survey was conducted involving 200 participants to assess recognition and endorsement of AI's role in environmental protection and to explore the adoption of AI technologies by firms for enhancing environmental management practices. Results: The survey revealed widespread recognition of Tencent's green initiatives and strong support for AI's role in environmental protection. Many firms are considering adopting AI technologies to optimize energy management, deploy intelligent HVAC systems, and improve the operations of data centers and smart lighting systems. Discussion: The findings highlight a strong belief in AI's potential to advance environmental protection efforts, with a call for increased governmental support to foster this development. The study underscores the importance of a partnership between businesses and governments to leverage AI for environmental sustainability, contributing significantly to conservation efforts.

Anti-inflammatory activity of Boletus aereus polysaccharides: Involvement of digestion and gut microbiota fermentation.

Boletus aereus, an edible mushroom, has gained popularity as a medicinal and functional food. This study aimed to investigate the digestive characteristics of B. aereus polysaccharide (BAP) and its effects on gut microbiota. In vitro digestion results indicated partial degradation of BAP. Furthermore, the digested BAP displayed significantly enhanced antioxidant ability. The 16S rRNA sequencing data revealed that BAP positively influenced the abundance of Phascolarctobacterium, Prevotella, and Bifidobacterium in the gut microbiota. Additionally, BAP promoted the production of short-chain fatty acids (SCFAs). Metabolites of BAP utilized by the gut microbiota effectively reduced the concentration of TNF-α, IL-1ß, and NO in an LPS-stimulated RAW 264.7 cell inflammation model. Mantel tests demonstrated a strong correlation among fermentation indicators, gut microbiome composition, SCFAs, and inflammatory cytokines. Overall, this research revealed the underlying digestive and fermentation mechanisms of BAP and provided new insights into the usage of edible mushroom polysaccharides in functional food.

Application of Strain Selection Technology in Alcoholic Beverages: A Review.

The diversity of alcohol beverage microorganisms is of great significance for improving the brewing process and the quality of alcohol beverage products. During the process of making alcoholic beverages, a group of microorganisms, represented by yeast and lactic acid bacteria, conducts fermentation. These microorganisms have complex synergistic or competitive relationships, and the participation of different microorganisms has a major impact on the fermentation process and the flavor and aroma of the product. Strain selection is one of the key steps. Utilizing scientific breeding technology, the relationship between strains can be managed, the composition of the alcoholic beverage microbial community can be improved, and the quality and flavor of the alcoholic beverage products can be increased. Currently, research on the microbial diversity of alcohol beverages has received extensive attention. However, the selection technology for dominant bacteria in alcohol beverages has not yet been systematically summarized. To breed better-quality alcohol beverage strains and improve the quality and characteristics of wine, this paper introduces the microbial diversity characteristics of the world's three major brewing alcohols: beer, wine, and yellow wine, as well as the breeding technologies of related strains. The application of culture selection technology in the study of microbial diversity of brewed wine was reviewed and analyzed. The strain selection technology and alcohol beverage process should be combined to explore the potential application of a diverse array of alcohol beverage strains, thereby boosting the quality and flavor of the alcohol beverage and driving the sustainable development of the alcoholic beverage industry.

Soil Microplastic Pollution and Microbial Breeding Techniques for Green Degradation: A Review.

Microplastics (MPs), found in many places around the world, are thought to be more detrimental than other forms of plastics. At present, physical, chemical, and biological methods are being used to break down MPs. Compared with physical and chemical methods, biodegradation methods have been extensively studied by scholars because of their advantages of greenness and sustainability. There have been numerous reports in recent years summarizing the microorganisms capable of degrading MPs. However, there is a noticeable absence of a systematic summary on the technology for breeding strains that can degrade MPs. This paper summarizes the strain-breeding technology of MP-degrading strains for the first time in a systematic way, which provides a new idea for the breeding of efficient MP-degrading strains. Meanwhile, potential techniques for breeding bacteria that can degrade MPs are proposed, providing a new direction for selecting and breeding MP-degrading bacteria in the future. In addition, this paper reviews the sources and pollution status of soil MPs, discusses the current challenges related to the biodegradation of MPs, and emphasizes the safety of MP biodegradation.

Small-Molecule Inhibitors of TIPE3 Protein Identified through Deep Learning Suppress Cancer Cell Growth In Vitro.

Tumor necrosis factor-α-induced protein 8-like 3 (TNFAIP8L3 or TIPE3) functions as a transfer protein for lipid second messengers. TIPE3 is highly upregulated in several human cancers and has been established to significantly promote tumor cell proliferation, migration, and invasion and inhibit the apoptosis of cancer cells. Thus, inhibiting the function of TIPE3 is expected to be an effective strategy against cancer. The advancement of artificial intelligence (AI)-driven drug development has recently invigorated research in anti-cancer drug development. In this work, we incorporated DFCNN, Autodock Vina docking, DeepBindBC, MD, and metadynamics to efficiently identify inhibitors of TIPE3 from a ZINC compound dataset. Six potential candidates were selected for further experimental study to validate their anti-tumor activity. Among these, three small-molecule compounds (K784-8160, E745-0011, and 7238-1516) showed significant anti-tumor activity in vitro, leading to reduced tumor cell viability, proliferation, and migration and enhanced apoptotic tumor cell death. Notably, E745-0011 and 7238-1516 exhibited selective cytotoxicity toward tumor cells with high TIPE3 expression while having little or no effect on normal human cells or tumor cells with low TIPE3 expression. A molecular docking analysis further supported their interactions with TIPE3, highlighting hydrophobic interactions and their shared interaction residues and offering insights for designing more effective inhibitors. Taken together, this work demonstrates the feasibility of incorporating deep learning and MD simulations in virtual drug screening and provides inhibitors with significant potential for anti-cancer drug development against TIPE3-.

Effects of uranium mining on the rhizospheric bacterial communities of three local plants on the Qinghai-Tibet Plateau.

In this study, we used 16S high-throughput sequencing to investigate the effects of uranium mining on the rhizospheric bacterial communities and functions of three local plant species, namely, Artemisia frigida, Acorus tatarionwii Schott., and Salix oritrepha Schneid. The results showed that uranium mining significantly reduced the diversity of rhizospheric bacteria in the three local plant species, including the Shannon index and Simpson index (P < 0.05). Interestingly, we found that Sphingomonas and Pseudotrichobacter were enriched in the rhizosphere soil of the three local plants from uranium mining areas, indicating their important ecological role. The three plants were enriched in various dominant rhizospheric bacterial populations in the uranium mining area, including Vicinamidobacteriaceae, Nocardioides, and Gaiella, which may be related to the unique microecological environment of the plant rhizosphere. The rhizospheric bacterial community of A. tatarionwii plants from tailings and open-pit mines also showed a certain degree of differentiation, indicating that uranium mining is the main factor driving the differentiation of plant rhizosphere soil communities on the plateau. Functional prediction revealed that rhizospheric bacteria from different plants have developed different functions to cope with stress caused by uranium mining activities, including enhancing the translational antagonist Rof, the translation initiation factor 2B subunit, etc. This study explores for the first time the impact of plateau uranium mining activities on the rhizosphere microecology of local plants, promoting the establishment of effective soil microecological health monitoring indicators, and providing a reference for further soil pollution remediation in plateau uranium mining areas.

Lactiplantibacillus plantarum exerts strain-specific effects on malolactic fermentation, antioxidant activity, and aroma profile of apple cider.

This study aimed to investigate the impact of different strains of Lactiplantibacillus plantarum on malolactic fermentation (MLF), antioxidant activity, and aroma of ciders. A commercial strain of Saccharomyces cerevisiae and six indigenous L. plantarum strains were co-inoculated into apple juice to induce simultaneous alcoholic fermentation (AF) and MLF. The findings indicated that despite belonging to the same species, the different L. plantarum strains significantly differed (p < 0.05) in terms of antioxidant activity and aroma compounds in the ciders. MLF induced by L. plantarum resulted in the substantial consumption of malic acid and increased levels of lactic acid in the ciders, with strain-specific effects observed, particularly with L. plantarum SCFF284. In addition, ciders produced from mixed fermentations exhibited higher levels of antioxidant activity than those from pure S. cerevisiae fermentation (p < 0.05), especially for LAM284. Furthermore, ciders produced from mixed fermentations exhibited higher levels of aroma compounds, such as ethyl acetate and isoamyl alcohol, and also received higher sensory scores compared to ciders produced through pure S. cerevisiae fermentation (p < 0.05). These results highlight the effectiveness of MLF induced by L. plantarum in enhancing the antioxidant activity and aroma profile of ciders.

Effect of a New Fermentation Strain Combination on the Fermentation Process and Quality of Highland Barley Yellow Wine.

Yellow wine fermented from highland barley is an alcoholic beverage with high nutritional value. However, the industrialization of barley yellow wine has been constrained to a certain extent due to the lack of a systematic starter culture. Therefore, the present study aims to simulate barley yellow wine fermentation using a starter culture consisting of Rhizopus arrhizus, Saccharomyces cerevisiae, Pichia kudriavzevii, and Lacticaseibacillus rhamnosus. In this study, changes in enzyme activity, fermentation characteristics, volatile substance production, and amino acid content during the fermentation of highland barley yellow wine brewed with different starter cultures were evaluated. The results of this study show that regulating the proportion of mixed starter bacteria can effectively control the various stages of the fermentation process and improve the organoleptic characteristics and quality of yellow wine to varying degrees. Additionally, we found that the addition of probiotics could effectively improve the palatability of yellow wine. To the best of our knowledge, we have validated for the first time the use of the above multispecies starter culture, consisting of R. arrhizus, S. cerevisiae, P. kudriavzevii, and L. rhamnosus, in the production of highland barley yellow wine. The obtained findings provided reference data for optimizing highland barley yellow wine fermentation.

Structural changes of rice starch-anthocyanins complexes (V-type) and its impact on gut microbiotas and potential metabolic pathways during in vitro fermentation.

This study explored the differences in the in vitro fermentation properties of rice starch (RS) and rice starch-anthocyanins complexes (RS-A). Structural characterization suggested that RS and RS-A complexes showed a V-type crystalline structure. The degree of order (DO) and degree of double helix (DD) values of RS and RS-A complexes were enhanced after fermentation. Moreover, the RS-A complexes could improve the relative abundance of Bacteroidetes, Ruminococcaceae, and up-regulate gut microbiota diversity to maintain gut homeostasis. Relative abundance of potential metabolic pathways, such as energy metabolism, digestion system, and carbohydrate degradation overexpressed in the presence of RS-A complexes. The results demonstrated that the RS-A complexes had slower fermentation rates contributing to the transport of the formed short-chain fatty acid (SCFA) to the end of the colon and that the crystallinity might be a factor influencing the utilization of the starch matrix by the gut microbiota for SCFA formation.

The Diversity and Community Composition of Three Plants' Rhizosphere Fungi in Kaolin Mining Areas.

Mining activities in the kaolin mining area have led to the disruption of the ecological health of the mining area and nearby soils, but the effects on the fungal communities in the rhizosphere soils of the plants are not clear. Three common plants (Conyza bonariensis, Artemisia annua, and Dodonaea viscosa) in kaolin mining areas were selected and analyzed their rhizosphere soil fungal communities using ITS sequencing. The alpha diversity indices (Chao1, Shannon, Simpson, observed-species, pielou-e) of the fungal communities decreased to different extents in different plants compared to the non-kauri mining area. The ß-diversity (PCoA, NMDS) analysis showed that the rhizosphere soil fungal communities of the three plants in the kaolin mine area were significantly differentiated from those of the control plants grown in the non-kaolin mine area, and the extent of this differentiation varied among the plants. The analysis of fungal community composition showed that the dominant fungi in the rhizosphere fungi of C. bonariensis and A. annua changed, with an increase in the proportion of Mycosphaerella (genus) by about 20% in C. bonariensis and A. annua. An increase in the proportion of Didymella (genus) by 40% in D. viscosa was observed. At the same time, three plant rhizosphere soils were affected by kaolin mining activities with the appearance of new fungal genera Ochrocladosporium and Plenodomus. Predictive functional potential analysis of the samples revealed that a significant decrease in the potential of functions such as biosynthesis and glycolysis occurred in the rhizosphere fungal communities of kaolin-mined plants compared to non-kaolin-mined areas. The results show that heavy metals and plant species are the key factors influencing these changes, which suggests that selecting plants that can bring more abundant fungi can adapt to heavy metal contamination to restore soil ecology in the kaolin mining area.

Polysaccharide from Boletus aereus ameliorates DSS-induced colitis in mice by regulating the MANF/MUC2 signaling and gut microbiota.

Inflammatory bowel diseases (IBD) are chronic inflammatory conditions characterized by disruptions in the colonic mucus barrier and gut microbiota. In this study, a novel soluble polysaccharide obtained from Boletus aereus (BAP) through water extraction was examined for its structure. The protective effects of BAP on colitis were investigated using a DSS-induced mice model. BAP was found to promote the expression of intestinal mucosal and tight junction proteins, restore the compromised mucus barrier, and suppress the activation of inflammatory signaling. Moreover, BAP reshape the gut microbiota and had a positive impact on the composition of the gut microbiota by reducing inflammation-related microbes. Additionally, BAP decreased cytokine levels through the MANF-BATF2 signaling pathway. Correlation analysis revealed that MANF was negatively correlated with the DAI and the level of cytokines. Furthermore, the depletion of gut microbiota using antibiotic partially inhabited the effect of BAP on the activation of MANF and Muc2, indicating the role of gut microbiota in its protective effect against colitis. In conclusion, BAP had an obvious activation on MANF under gut inflammation. This provides new insights into the prospective use of BAP as a functional food to enhance intestinal health.

Topological Magneto-optical Effect from Skyrmions in Two-Dimensional Ferromagnets.

Skyrmions in two-dimensional (2D) magnetic materials are considered as ideal candidates for information carriers in next-generation spintronic devices. However, conventional methods for elucidating the physical properties of skyrmions have limited the development of skyrmions in diverse 2D magnetic material systems due to their requirements for electrical conductivity. To overcome this limitation, we propose to utilize an optical method (magneto-optical Kerr technique) to detect the skyrmions in 2D magnetic materials. Herein, the graphene/Fe3GeTe2/graphene vertical van der Waals (vdW) heterostructure devices are fabricated to generate stabilized skyrmions by applying out-of-plane current. In combination with magnetic circular dichroism measurements, we observe topological-reflective magnetic circular dichroism (T-RMCD) effects in Fe3GeTe2 flakes and attribute the peak-shaped component in T-RMCD to the annihilation of skyrmion magnetic domains. Notably, the T-RMCD signal can maintain up to a temperature as high as the Curie temperature of Fe3GeTe2 flakes (∼200 K). Our work provides a universal, contactless, and nondestructive approach for studying the physical properties of skyrmions in 2D vdW magnetic materials while adding another degree of freedom to the modulation of skyrmions.

The Easily Overlooked Effect of Global Warming: Diffusion of Heavy Metals.

Since industrialization, global temperatures have continued to rise. Human activities have resulted in heavy metals being freed from their original, fixed locations. Because of global warming, glaciers are melting, carbon dioxide concentrations are increasing, weather patterns are shifting, and various environmental forces are at play, resulting in the movement of heavy metals and alteration of their forms. In this general context, the impact of heavy metals on ecosystems and organisms has changed accordingly. For most ecosystems, the levels of heavy metals are on the rise, and this rise can have a negative impact on the ecosystem as a whole. Numerous studies have been conducted to analyze the combined impacts of climate change and heavy metals. However, the summary of the current studies is not perfect. Therefore, this review discusses how heavy metals affect ecosystems during the process of climate change from multiple perspectives, providing some references for addressing the impact of climate warming on environmental heavy metals.