KDM3A Ablation Activates Endogenous Retrovirus Expression to Stimulate Antitumor Immunity in Gastric Cancer.

The success of immunotherapy for cancer treatment is limited by the presence of an immunosuppressive tumor microenvironment (TME); Therefore, identifying novel targets to that can reverse this immunosuppressive TME and enhance immunotherapy efficacy is essential. In this study, enrichment analysis based on publicly available single-cell and bulk RNA sequencing data from gastric cancer patients are conducted, and found that tumor-intrinsic interferon (IFN) plays a central role in TME regulation. The results shows that KDM3A over-expression suppresses the tumor-intrinsic IFN response and inhibits KDM3A, either genomically or pharmacologically, which effectively promotes IFN responses by activating endogenous retroviruses (ERVs). KDM3A ablation reconfigures the dsRNA-MAVS-IFN axis by modulating H3K4me2, enhancing the infiltration and function of CD8 T cells, and simultaneously reducing the presence of regulatory T cells, resulting in a reshaped TME in vivo. In addition, combining anti-PD1 therapy with KDM3A inhibition effectively inhibited tumor growth. In conclusions, this study highlights KDM3A as a potential target for TME remodeling and the enhancement of antitumor immunity in gastric cancer through the regulation of the ERV-MAVS-IFN axis.

Quality characteristics of goat milk powder produced by freeze drying followed by UV-C radiation sterilization.

Goat milk was directly freeze-dried into milk powder after freezing and then sterilized using UV-C radiation to produce low-dose, medium-dose and high-dose UV-C radiation sterilized freeze-dried goat milk powder (LGP, MGP and HGP). UV-C sterilization effectively reduced the total bacteria count and coliform bacteria in the goat milk powder while preserving the active proteins, and maintaining the color unchanged. Additionally, LGP, MGP, and HGP all exhibited a moisture content below 5 g/100 g and water activity below 0.5. Upon reconstitution, the milk powder formed uniform and stable emulsion. During accelerated storage tests, the increased Aw did not compromise the microbial quality of milk powder, and there were no significant changes in active proteins as confirmed via SDS-PAGE results. Furthermore, the color parameters (a*, b* and ΔE) showed a strong correlation with hydroxymethyl furfural levels.

A Two-color Single-molecule Sequencing Platform and Its Clinical Applications.

DNA sequencers have become increasingly important research and diagnostic tools over the past 20 years. In this study, we developed a single-molecule desktop sequencer, GenoCare 1600 (GenoCare), which utilizes amplification-free library preparation and two-color sequencing-by-synthesis chemistry, making it more user-friendly compared with previous single-molecule sequencing platforms for clinical use. Using the GenoCare platform, we sequenced an Escherichia coli standard sample and achieved a consensus accuracy exceeding 99.99%. We also evaluated the sequencing performance of this platform in microbial mixtures and coronavirus disease 2019 (COVID-19) samples from throat swabs. Our findings indicate that the GenoCare platform allows for microbial quantitation, sensitive identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and accurate detection of virus mutations, as confirmed by Sanger sequencing, demonstrating its remarkable potential in clinical application.

Ecophysiological responses of Phragmites australis populations to a tidal flat gradient in the Yangtze River Estuary, China.

Phragmites australis is a prevalent species in the Chongming Dongtan wetland and is capable of thriving in various tidal flat environments, including high salinity habitats. P. australis population displays inconsistent ecological performances, highlighting the need to uncover their survival strategies and mechanisms in tidal flats with diverse soil salinities. Upon comparing functional traits of P. australis at multiple tidal flats (low, middle, and high) and their responses to soil physicochemical properties, this study aimed to clarify the salt-tolerant strategy of P. australis and the corresponding mechanisms. These results showed that leaf characteristics, such as specific leaf area and leaf dry matter content, demonstrated more robust stability to soil salinity than shoot height and dry weight. Furthermore, as salt stress intensified, the activities of superoxide dismutase (SOD), catalase (CAT) and peroxisome (POD) in P. australis leaves at low tidal flat exhibited an increased upward trend compared to those at other tidal flats. The molecular mechanism of salt tolerance in Phragmites australis across various habitats was investigated using transcriptome sequencing. Weighted correlation network analysis (WGCNA) combined with differentially expressed genes (DEGs) screened out 3 modules closely related to high salt tolerance and identified 105 core genes crucial for high salt tolerance. Further research was carried out on the few degraded populations at low tidal flat, and 25 core genes were identified by combining WGCNA and DEGs. A decrease in the activity of ferroptosis marker gonyautoxin-4 and an increase in the content of Fe3+ in the degenerated group were observed, indicating that ferroptosis might participate in degradation. Furthermore, correlation analysis indicated a possible regulatory network between salt tolerance and ferroptosis. In short, this study provided new insights into the salt tolerance mechanism of P. australis population along tidal flats.

Cu-N Synergism Regulation to Enhance Anionic Redox Reversibility and Activity of Li- and Mn-Rich Layered Oxides Cathode.

Anionic redox chemistry enables extraordinary capacity for Li- and Mn-rich layered oxides (LMROs) cathodes. Unfortunately, irreversible surface oxygen evolution evokes the pernicious phase transition, structural deterioration, and severe electrode-electrolyte interface side reaction with element dissolution, resulting in fast capacity and voltage fading of LMROs during cycling and hindering its commercialization. Herein, a redox couple strategy is proposed by utilizing copper phthalocyanine (CuPc) to address the irreversibility of anionic redox. The Cu-N synergistic effect of CuPc could not only inhibit surface oxygen evolution by reducing the peroxide ion O2 2- back to lattice oxygen O2-, but also enhance the reaction activity and reversibility of anionic redox in bulk to achieve a higher capacity and cycling stability. Moreover, the CuPc strategy suppresses the interface side reaction and induces the forming of a uniform and robust LiF-rich cathode electrolyte, interphase (CEI) to significantly eliminate transition metal dissolution. As a result, the CuPc-enhanced LMRO cathode shows superb cycling performance with a capacity retention of 95.0% after 500 long-term cycles. This study sheds light on the great effect of N-based redox couple to regulate anionic redox behavior and promote the development of high energy density and high stability LMROs cathode.

The complete chloroplast genome sequence of leibnitzia anandria (linnaeus) turczaninow.

Leibnitzia anandria is a perennial herbaceous plant with medicinal properties, and the entire plant can be used in traditional medicine. Leibnitzia anandria was once classified under the genus Gerbera Cass., but was reclassified under Leibnitzia Cass. recently. In this study, using the GeneLab M sequencing technology of the Genemind platform, we have sequenced, assembled, and analyzed the complete chloroplast genome of Leibnitzia anandria for the first time. The genome is 154168 bp in length, consisting of a large single-copy region(LSC, 80166 bp), a small single-copy region(SSC, 18202 bp), and a pair of inverted repeat sequences(IR, 27900 bp). We have predicted and annotated a total of 133 genes, including 88 protein-coding genes, 37 tRNA-coding genes, and 8 rRNA-coding genes. The results of the phylogenetic analysis indicate that Leibnitzia anandria and Leibnitzia nepalensis, as well as the closely related Gerbera plant, clustered into a separate clade, rather than grouping together with the other plants belonging to the tribe Mutisieae. This study provides new information for the phylogeny research of Leibnitzia anandria, contributing to a better understanding of its taxonomy and evolution.

Metallic Ru─Ru Interaction in Ruthenium Oxide Enabling Durable Proton Exchange Membrane Water Electrolysis.

Developing efficient and robust electrocatalysts toward the oxygen evolution reaction (OER) is critical for proton exchange membrane water electrolysis (PEMWE). RuO2 possesses intrinsically high OER activity, but the concurrent electrochemical dissolution leads to rapid deactivation. Here a unique RuO2 catalyst containing metallic Ru─Ru interactions (m-RuO2) is reported, which maintains stability in practical PEMWE for 100 h at 60 °C and 1 A cm-2. Experimental and theoretical investigations suggest that the presence of Ru─Ru interactions significantly increases the energy barrier for the formation of RuO2(OH)2, which is a key intermediate for Ru dissolution, and hence substantially mitigates the electrochemical corrosion of m-RuO2. Meanwhile, the Ru4d band center downshifts, accordingly, ensuring the high OER activity, and the participation of lattice oxygen in the OER is also suppressed at the Ru─Ru sites, further contributing to the enhanced durability. Interestingly, such enhanced stability is also dependent on the size of metallic Ru─Ru cluster, where the energy barrier is further increased for Ru3, but is decreased for Ru5. These results highlight the significance of local coordination structure modulation on the electrochemical stability of RuO2 and open a feasible avenue toward the development of robust OER electrocatalysts for high-performance PEMWE.

Unraveling the Unique Strong Metal-Support Interaction in Titanium Dioxide Supported Platinum Clusters for the Hydrogen Evolution Reaction.

Strong metal-support interaction (SMSI) is crucial to modulating the nature of metal species, yet the SMSI behaviors of sub-nanometer metal clusters remain unknown due to the difficulties in constructing SMSI at cluster scale. Herein, we achieve the successful construction of the SMSI between Pt clusters and amorphous TiO2 nanosheets by vacuum annealing, which requires a relatively low temperature that avoids the aggregation of small clusters. In situ scanning transmission electron microscopy observation is employed to explore the SMSI behaviors, and the results reveal the dynamic rearrangement of Pt atoms upon annealing for the first time. The originally disordered Pt atoms become ordered as the crystallizing of the amorphous TiO2 support, forming an epitaxial interface between Pt and TiO2. Such a SMSI state can remain stable in oxidation environment even at 400 °C. Further investigations prove that the electron transfer from TiO2 to Pt occupies the Pt 5d orbitals, which is responsible for the disappeared CO adsorption ability of Pt/TiO2 after forming SMSI. This work not only opens a new avenue for constructing SMSI at cluster scale but also provides in-depth understanding on the unique SMSI behavior, which would stimulate the development of supported metal clusters for catalysis applications.

Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation.

Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.

Energy stress promotes P-bodies formation via lysine-63-linked polyubiquitination of HAX1.

Energy stress, characterized by the reduction of intracellular ATP, has been implicated in various diseases, including cancer. Here, we show that energy stress promotes the formation of P-bodies in a ubiquitin-dependent manner. Upon ATP depletion, the E3 ubiquitin ligase TRIM23 catalyzes lysine-63 (K63)-linked polyubiquitination of HCLS1-associated protein X-1 (HAX1). HAX1 ubiquitination triggers its liquid‒liquid phase separation (LLPS) and contributes to P-bodies assembly induced by energy stress. Ubiquitinated HAX1 also interacts with the essential P-body proteins, DDX6 and LSM14A, promoting their condensation. Moreover, we find that this TRIM23/HAX1 pathway is critical for the inhibition of global protein synthesis under energy stress conditions. Furthermore, high HAX1 ubiquitination, and increased cytoplasmic localization of TRIM23 along with elevated HAX1 levels, promotes colorectal cancer (CRC)-cell proliferation and correlates with poor prognosis in CRC patients. Our data not only elucidate a ubiquitination-dependent LLPS mechanism in RNP granules induced by energy stress but also propose a promising target for CRC therapy.

Research advances in the identification of regulatory mechanisms of surfactin production by Bacillus: a review.

Surfactin is a cyclic hexalipopeptide compound, nonribosomal synthesized by representatives of the Bacillus subtilis species complex which includes B. subtilis group and its closely related species, such as B. subtilis subsp subtilis, B. subtilis subsp spizizenii, B. subtilis subsp inaquosorum, B. atrophaeus, B. amyloliquefaciens, B. velezensis (Steinke mSystems 6: e00057, 2021) It functions as a biosurfactant and signaling molecule and has antibacterial, antiviral, antitumor, and plant disease resistance properties. The Bacillus lipopeptides play an important role in agriculture, oil recovery, cosmetics, food processing and pharmaceuticals, but the natural yield of surfactin synthesized by Bacillus is low. This paper reviews the regulatory pathways and mechanisms that affect surfactin synthesis and release, highlighting the regulatory genes involved in the transcription of the srfAA-AD operon. The several ways to enhance surfactin production, such as governing expression of the genes involved in synthesis and regulation of surfactin synthesis and transport, removal of competitive pathways, optimization of media, and fermentation conditions were commented. This review will provide a theoretical platform for the systematic genetic modification of high-yielding strains of surfactin.

Removal of Nanoplastics from Copollutant Systems Using Seaweed Cellulose Nanofibers.

Nanoplastic pollution poses a significant global concern for public health due to the potential toxicity it induces in the human body through food and water intake. Consequently, the urgent task of removing nanoplastics, especially from water resources, is paramount for enhancing food safety, and developing eco-friendly materials capable of efficiently removing nanoplastics is crucial. In this context, we propose the use of biodegradable anionic seaweed cellulose nanofibers (TEMPO-mediated seaweed cellulose nanofibers, TCNFs) and cationic seaweed cellulose nanofibers (quaternized seaweed cellulose nanofibers, QCNFs) for nanoplastic removal in both single- and copollutant systems. In our experiments under simulated practical conditions, we revealed that TCNFs and QCNFs achieved an average removal efficiency of 98.71% against nanoplastic particles. Moreover, TCNFs and QCNFs exhibited higher adsorption capacities compared to those of existing materials, potentially offering a cost-effective advantage. Toxicity assessments conducted with mammalian cells further confirmed the biosafety of TCNFs and QCNFs. This study contributes to the scientific and theoretical understanding of using edible seaweed as well as offers promising solutions for food safety control in an efficient, cost-effective, and eco-friendly manner.

A rapid, equipment-free method for detecting avirulence genes of Pyricularia oryzae using a lateral flow strip-based RPA assay.

Rice blast, caused by Pyricularia oryzae, is one of the most destructive rice diseases worldwide. Using resistant rice varieties is the most cost-effective way to control rice blast. Consequently, it is critical to monitor the distribution frequency of avirulence genes in rice planting field to facilitate the breedings of resistant rice varieties. In this study, we established a rapid RPA-LFD detection system for the identification of AvrPik, Avr-Piz-t and Avr-Pi9. The optimized reaction temperature and duration were 37°C and 20 min, indicating that the reaction system could be initiated by body temperature without relying on any precision instruments. Specificity analysis showed that the primer and probe combinations targeting three Avr genes exhibited a remarkable specificity for at genus-level detection. Under the optimized condition, the lower detected thresholds of AvrPik, Avr-Piz-t and Avr-Pi9 were 10 fg/µl, 100 fg/µl and 10 pg/µl, respectively. Notably, the detection sensitivity of three Avr genes was much higher than that of PCR. In addition, we also successfully detected the presence of AvrPik, Avr-Piz-t and Avr-Pi9 in the leaf and panicle blast lesions with the RPA-LFD detection system. In particular, the genomic DNA was extracted using the simpler PEG-NaOH rapid extraction method. In summary, we developed the RPA detection system for AvrPik, Avr-Pi9 and Avr-Piz-t, combined with the PEG-NaOH rapid DNA extraction method. The innovative approach achieved rapid, real-time and accurate detection of three Avr genes in the field, which is helpful to understand the distribution frequency of the three Avr genes in the field and provide theoretical reference for the scientific layout of rice resistant varieties.

Insights into the antibacterial effectiveness of linalool against Shigella flexneri on pork surface: Changes in bacterial growth and pork quality.

Shigella flexneri has the ability to contaminate pork and cause foodborne diseases. This study aimed to examine the effectiveness of linalool (a natural preservative) against S. flexneri and explore its potential application in contaminated pork. The results showed that linalool was capable of damaging the cell membrane and binding to the DNA of S. flexneri, and inhibiting biofilm formation and disrupting mature biofilms. The antibacterial effectiveness of linalool on the surface of pork was further demonstrated by analyzing the physicochemical properties of the pork (i.e., weight loss rate, pH value, color index, and TVB-N value) and its protein profiles. Linalool did not completely kill S. flexneri in pork at minimum bactericidal concentration (MBC) concentration and its antibacterial effect of linalool was stronger during the initial stage of storage. During storage, linalool influenced the abundance of specific proteins in the pork, particularly those involved in pathways related to fat metabolism. These findings offer novel insights into the antibacterial efficacy of linalool and its underlying mechanism in pork.

Gelatin/agar pH-indicator film based on cranberry extract loaded with linalool nanoparticle: Survey on physical, antimicrobial, and antioxidant properties.

In this study, linalool-nanoparticles (L-NPs) were prepared (encapsulation efficiency was 68.54 %) and introduced pH-indicator film based on cranberry-extract (CEF) to develop multifunctional smart films. XRD analysis and FTIR spectroscopy indicated that cranberry-extract (CE) and L-NPs were uniformly distributed in the gelatin/agar matrix and could change the intermolecular structure of the film. Color change of smart films showed that CE endowed the film with pH-sensitive property. As CE and L-NPs were added to the film, the water contact angle (WCA) was increased from 57.03° to 117.73°, the elongation at break (EAB) was increased from 12.30 % to 34.60 %. Additionally, the introduction of L-NPs enhanced the antioxidant activity (DPPH free radical scavenging rate increased from 26.80 % to 36.35 %) and antibacterial activity (against S. aureus and E. coli) of the smart film, which were verified by its retarding effect on pork spoilage.

Bitter taste receptor activation by cholesterol and an intracellular tastant.

Bitter taste sensing is mediated by type 2 taste receptors (TAS2Rs (also known as T2Rs)), which represent a distinct class of G-protein-coupled receptors1. Among the 26 members of the TAS2Rs, TAS2R14 is highly expressed in extraoral tissues and mediates the responses to more than 100 structurally diverse tastants2-6, although the molecular mechanisms for recognizing diverse chemicals and initiating cellular signalling are still poorly understood. Here we report two cryo-electron microscopy structures for TAS2R14 complexed with Ggust (also known as gustducin) and Gi1. Both structures have an orthosteric binding pocket occupied by endogenous cholesterol as well as an intracellular allosteric site bound by the bitter tastant cmpd28.1, including a direct interaction with the α5 helix of Ggust and Gi1. Computational and biochemical studies validate both ligand interactions. Our functional analysis identified cholesterol as an orthosteric agonist and the bitter tastant cmpd28.1 as a positive allosteric modulator with direct agonist activity at TAS2R14. Moreover, the orthosteric pocket is connected to the allosteric site via an elongated cavity, which has a hydrophobic core rich in aromatic residues. Our findings provide insights into the ligand recognition of bitter taste receptors and suggest activities of TAS2R14 beyond bitter taste perception via intracellular allosteric tastants.

Comparison of Non-Covalent and Covalent Interactions between Lactoferrin and Chlorogenic Acid.

Adding polyphenols to improve the absorption of functional proteins has become a hot topic. Chlorogenic acid is a natural plant polyphenol with anti-inflammatory, antioxidant, and anticancer properties. Bovine lactoferrin is known for its immunomodulatory, anticancer, antibacterial, and iron-chelating properties. Therefore, the non-covalent binding of chlorogenic acid (CA) and bovine lactoferrin (BLF) with different concentrations under neutral conditions was studied. CA was grafted onto lactoferrin molecules by laccase catalysis, free radical grafting, and alkali treatment. The formation mechanism of non-covalent and covalent complexes of CA-BLF was analyzed by experimental test and theoretical prediction. Compared with the control BLF, the secondary structure of BLF in the non-covalent complex was rearranged and unfolded to provide more active sites, the tertiary structure of the covalent conjugate was changed, and the amino group of the protein participated in the covalent reaction. After adding CA, the covalent conjugates have better functional activity. These lactoferrin-polyphenol couplings can carry various bioactive compounds to create milk-based delivery systems for encapsulation.

Virtual Screening of a Chemically Diverse "Superscaffold" Library Enables Ligand Discovery for a Key GPCR Target.

The advent of ultra-large libraries of drug-like compounds has significantly broadened the possibilities in structure-based virtual screening, accelerating the discovery and optimization of high-quality lead chemotypes for diverse clinical targets. Compared to traditional high-throughput screening, which is constrained to libraries of approximately one million compounds, the ultra-large virtual screening approach offers substantial advantages in both cost and time efficiency. By expanding the chemical space with compounds synthesized from easily accessible and reproducible reactions and utilizing a large, diverse set of building blocks, we can enhance both the diversity and quality of the discovered lead chemotypes. In this study, we explore new chemical spaces using reactions of sulfur(VI) fluorides to create a combinatorial library consisting of several hundred million compounds. We screened this virtual library for cannabinoid type II receptor (CB2) antagonists using the high-resolution structure in conjunction with a rationally designed antagonist, AM10257. The top-predicted compounds were then synthesized and tested in vitro for CB2 binding and functional antagonism, achieving an experimentally validated hit rate of 55%. Our findings demonstrate the effectiveness of reliable reactions, such as sulfur fluoride exchange, in diversifying ultra-large chemical spaces and facilitate the discovery of new lead compounds for important biological targets.