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Issatchenkia orientalis (I. orientalis) is tolerant to various environmental stresses especially acetic acid stress in wine making. However, limited literature is available on the transcriptome profile of I. orientalis under acetic acid stress. RNA-sequence was used to investigate the metabolic changes due to underlying I. orientalis 166 (Io 166) tolerant to acetic acid. Transcriptomic analyses showed that genes involved in ergosterol biosynthesis are differentially expressed under acetic acid stress. Genes associated with ribosome function were downregulated, while energy metabolism-related genes were upregulated. Moreover, Hsp70/Hsp90 and related molecular chaperones were upregulated to recognize and degrade misfolded proteins. Compared to Saccharomyces cerevisiae, transcriptomic changes of Io 166 showed many similarities under acetic acid stress. There were significant upregulation of genes in ergosterol biosynthesis and for the application of wine production.

Characterizing the natural selection of complex traits is important for understanding human evolution and both biological and pathological mechanisms. We leveraged genome-wide summary statistics for 870 polygenic traits and attempted to quantify signals of selection on traits of different forms in European ancestry across four periods in human history and evolution. We found that 88% of these traits underwent polygenic change in the past 2,000–3,000 years. Recent selection was associated with ancient selection signals in the same trait. Traits related to pigmentation, body measurement and nutritional intake exhibited strong selection signals across different time scales. Our findings are limited by our use of exclusively European data and the use of genome-wide association study data, which identify associations between genetic variants and phenotypes that may not be causal. In sum, we provide an overview of signals of selection on human polygenic traits and their characteristics across human evolution, based on a European subset of human genetic diversity. These findings could serve as a foundation for further populational and medical genetic studies. Song et al. quantify the signal of natural selection on 870 complex traits in European individuals, finding that 88% of traits showed signals of selection in the past 3,000 years, including traits related to pigmentation, body shape and food intake.

Helicobacter pylori is a causative pathogen of many gastric and extra-gastric diseases. It has infected about half of the global population. There were no genome-wide association studies (GWAS) for H. pylori infection conducted in Chinese population, who carried different and relatively homogenous strain of H. pylori. In this work, we performed SNP (single nucleotide polymorphism)-based, gene-based and pathway-based genome-wide association analyses to investigate the genetic basis of host susceptibility to H. pylori infection in 480 Chinese individuals. We also profiled the composition and function of the gut microbiota between H. pylori infection cases and controls. We found several genes and pathways associated with H. pylori infection (P TLR1 gene region (P = 0.02). We also found that glycosaminoglycan biosynthesis related pathway was associated with both onset and progression of H. pylori infection. In the gut microbiome association study, we identified 2 species, 3 genera and several pathways had differential abundance between H. pylori infected cases and controls. This paper is the first GWAS for H. pylori infection in Chinese population, and we combined the genetic and microbial data to comprehensively discuss the basis of host susceptibility to H. pylori infection.

Four sialylated lactuloses [N-acetylneuraminic acid-α2,3-lactulose (Neu5Acα2,3lactulose), N-acetylneuraminic acid-α2,6-lactulose (Neu5Acα2,6lactulose), deaminoneuraminc acid-α2,3-lactulose (Kdnα2,3lactulose), and deaminoneuraminc acid-α-2,6-lactulose (Kdnα2,6lactulose)] were reported to modulate the immunity of mice. The influences of cytokine expression, cell immunity, humoral immunity, and nonspecific immunity were investigated in our study using several techniques. Analysis via ELISA showed that cytokine expression was induced by sialylated lactulose treatment consistently in the serum and spleen. Among the 4 tested sialylated lactuloses, Neu5Acα2,6lactulose performed the best, simultaneously and appropriately promoting the expression of proinflammatory and anti-inflammatory factors in the serum and spleen. Kdnα2,3lactulose showed the best antioxidant activity according to detection of the activity of superoxide dismutase, myeloperoxidase, peroxidase, and alkaline phosphatase. Flow cytometry revealed that only Kdnα2,3lactulose significantly boosted the CD3+ T lymphocyte ratio similarly to that of lactulose. Analysis of the hemolysin content to characterize humoral immunity revealed that Kdnα2,3lactulose notably increased hemolysin content compared with that in the control group. To evaluate the nonspecific immune effects of the 4 sialylated lactuloses, a fluorescence microsphere phagocytosis assay was used to analyze the phagocytosis of macrophages. Kdnα2,3lactulose still performed the best in enhancing the phagocytosis of macrophages, showing markedly increased phagocytic percentage and phagocytic index values compared with those in the control and lactulose groups. Comparing the differences of these 4 sialylated lactuloses in affecting immunity in mice revealed that Kdnα2,3lactulose had the best overall performance in influencing cytokine expression, cell immunity, humoral immunity, and nonspecific immunity. This study provides critical support for use of sialylated lactuloses as potential immunomodulators in foods.

IL-15 is a promising cytokine to expand NK and CD8(+) T cells for cancer immunotherapy, but its application is limited by dose-limiting, on-target off-tumor toxicity. Here, we have developed a next-generation IL-15 that is activated inside the tumor microenvironment (TME). This pro-IL-15 has the extracellular domain of IL-15Rβ fused to the N-terminus of sIL-15-Fc through a tumor-enriched Matrix Metalloproteinase (MMP) cleavable peptide linker to block its activity. Unlike sIL-15-Fc, pro-IL-15 does not activate the peripheral expansion of NK cells and T cells, thus reducing systemic toxicity, but it still preserves efficient anti-tumor abilities. In various mouse tumors, the anti-tumor effect of pro-IL-15 depends on intratumoral CD8(+) T cells and IFN-γ. Pro-IL-15 increases the stem-like TCF1(+)Tim-3(−)CD8(+) T cells within tumor tissue and helps overcome immune checkpoint blockade (ICB) resistance. Moreover, pro-IL-15 synergizes with current tyrosine kinase inhibitor (TKI) targeted-therapy in a poorly inflamed TUBO tumor model, suggesting that pro-IL-15 helps overcome targeted-therapy resistance. Our results demonstrate a next-generation IL-15 cytokine that can stimulate potent anti-tumor activity without severe toxicity.

Objective : To investigate the clinical significance of PAH c.158G>A (p.Arg53His) mutation. Methods : The blood phenylalanine (Phe) was continuously monitored in 2 unrelated newborns with suspected hyperphenylalaninimia (HPA) carrying PAH c.158G>A mutation. The cross-species conservation of the mutant amino acid was analyzed using T-Coffee. Swiss-Model software was used to construct a 3D protein structure and the impact of candidate mutations on the secondary structure of the protein product was analyzed. The population carrying rate of the p.Arg53His mutation was analyzed by literature searching. Allelic phenotype values (APV) and genotypic phenotype values (GPV) were used to predict the phenotype associated with the mutation. Results: Two mutations of PAH gene were detected in each newborn: c.611A>G(p.Tyr204Cys), c.158G>A(p.Arg53His) and c.1238G>C(p.Arg413Pro), c.158G>A(p.Arg53His). Two children tolerated normal diet and plasma Phe levels were within the normal range during follow-up. The mother of case 2 was homozygous with p.Arg53His mutation under the condition of long-term normal diet, and the blood Phe concentration and Phe/Tyr were all within the normal range. The mutant amino acids were not highly conserved among the 13 different species. The 3D structural model showed that p.Arg53His mutation reduced the hydrogen bond from 2 to 1 between the 53rd and 49th amino acids of PAH. The allele frequency of p.Arg53His was 0.015 08 in HPA patients and 0.001 621 in normal population, while the prevalence of p.Arg53His allele was highest in the East Asian normal population (0.013 73). The APV and GPV system predicted that the mutation was related to mild HPA(MHP) type. Conclusion : The different compound heterozygous mutations of p.Arg53His lead to clinical phenotype varieties. The reduction of enzyme activity caused by the mutation of p.Arg53His is not sufficient to cause symptoms of phenylketonuria, so the mutation may be “likely benign”.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global crisis, urgently necessitating the development of safe, efficacious, convenient-to-store, and low-cost vaccine options. A major challenge is that the receptor-binding domain (RBD)-only vaccine fails to trigger long-lasting protective immunity if used alone for vaccination. To enhance antigen processing and cross-presentation in draining lymph nodes (DLNs), we developed an interferon (IFN)-armed RBD dimerized by an immunoglobulin fragment (I-R-F). I-R-F efficiently directs immunity against RBD to DLNs. A low dose of I-R-F induces not only high titers of long-lasting neutralizing antibodies (NAbs) but also more comprehensive T cell responses than RBD. Notably, I-R-F provides comprehensive protection in the form of a one-dose vaccine without an adjuvant. Our study shows that the pan-epitope modified human I-R-F (I-P-R-F) vaccine provides rapid and complete protection throughout the upper and lower respiratory tracts against a high-dose SARS-CoV-2 challenge in rhesus macaques. Based on these promising results, we have initiated a randomized, placebo-controlled, phase I/II trial of the human I-P-R-F vaccine (V-01) in 180 healthy adults, and the vaccine appears safe and elicits strong antiviral immune responses. Due to its potency and safety, this engineered vaccine may become a next-generation vaccine candidate in the global effort to overcome COVID-19.

The bone is previously considered as a dominant organ involved in the processes of locomotion. However, in the past two decades, a large number of studies have suggested that the skeletal system closely coordinated with the immune system so as to result in the emerging area of ‘osteoimmunology’. In the evolution of many kinds of bone destruction-related diseases, osteoclasts could differentiate from dendritic cells, which contributed to increased expression of osteoclast-related membrane receptors and relatively higher activity of bone destruction, inducing severe bone destruction under inflammatory conditions. Numerous factors could influence the interaction between osteoclasts and dendritic cells, contributing to the pathogenesis of several bone diseases in the context of inflammation, including both immunocytes and a large number of cytokines. In addition, the products of osteoclasts released from bone destruction area serve as important signals for the differentiation and activation of immature dendritic cells. Therefore, the border between the dendritic cell-related immune response and osteoclast-related bone destruction has gradually unravelled. Dendritic cells and osteoclasts cooperate with each other to mediate bone destruction and bone remodelling under inflammatory conditions. In this review, we will pay attention to the interactions between dendritic cells and osteoclasts in physiological and pathological conditions to further understand the skeletal system and identify potential new therapeutic targets for the future by summarizing their significant roles and molecular mechanisms in bone destruction.

Aroma-active compounds in northern highbush blueberries "Bluecrop" (Vaccinium corymbosum "Bluecrop") and "Elliott" (Vaccinium corymbosum "Elliott") were isolated using solvent extraction followed by solvent-assisted flavor evaporation. The aroma-active compounds were compared by aroma extract dilution analysis (AEDA) on a polar and a chiral column and odor activity values (OAVs). The results showed that both cultivars had similar aroma-active compounds, but the flavor dilution (FD) factors and OAV values varied, responsible for the subtle aroma differences. AEDA (FD ≥ 64) suggested that the important aroma-active compounds in both cultivars could be ethyl 2-methylbutanoate, ethyl 3-methylbutanoate, (Z)-3-hexenal, 1-octen-3-one, (Z)-3-hexen-1-ol, methional, linalool, (E,Z)-2,6-nonadienal, 2-methylbutanoic acid, α-terpineol, (E,E)-2,4-nonadienal, β-damascenone, geraniol, geranyl acetone, o-cresol, eugenol, and vanillin. Different isomers can have different sensory thresholds and attributes. Enantiomer analysis revealed that although S-(+)-linalool was dominant in blueberry, R-(-)-linalool had a higher FD value and OAVs than that of the (S)-isomer. The S-(-)-α-terpineol was slightly elevated than R-(+)-α-terpineol in both cultivars.

Selective cell retention (SCR) has been widely used as a bone tissue engineering technique for the real-time fabrication of bone grafts. The greater the number of mesenchymal stem cells (MSCs) and endothelial progenitor cells (EPCs) retained in the scaffold, the better the osteoinductive and angiogenic properties of the scaffold's microenvironment. Improved bioscaffold properties in turn lead to improved bone graft survival, bone regeneration, and angiogenesis. Laminin plays a key role in cell-matrix adhesion, cell proliferation, and differentiation. We designed a collagen-binding domain (CBD) containing the core functional amino acid sequences of laminin α4 (CBD-LN peptide) to supplement the functional surface of a collagen-based decalcified bone matrix (DBM) scaffold. This scaffold promoted MSCs and EPCs early cell adhesion through up-regulating the expression of integrin α5β1 and integrin αvβ3 respectively, thus accelerated the following cell spreading, proliferation, and differentiation. Interestingly, it promoted the retention of MSCs (CD90+/CD105+ cells) and EPCs (CD31+ cells) in the scaffold following the use of clinical SCR technology. Furthermore, the DBM/CBD-LN scaffold induced the formation of type H vessels through the activation of the HIF-1α signaling pathway. The DBM/CBD-LN scaffold displayed rapid bone formation and angiogenesis in vivo, suggesting that it might be used as a new biomaterial in bone tissue engineering. STATEMENT OF SIGNIFICANCE: Selective cell retention technology (SCR) has been utilized in clinical settings to manufacture bioactive bone grafts. Specifically, demineralized bone matrix (DBM) is a widely-used SCR clinical biomaterial but it displays poor adhesion performance and angiogenic activity. In this work, we designed a collagen-binding domain (CBD) containing the core functional amino acid sequences of laminin α4 to supplement the functional surface of a collagen-based DBM scaffold. This bioscaffold promoted SCR-mediated MSCs and EPCs early cell adhesion, thus accelerated the following cell spreading, proliferation, and differentiation. Our results indicate this bioscaffold greatly induced osteogenesis and angiogenesis in vivo. In general, this bioscaffold has a good prospect for SCR application and may provide highly bioactive bone implant in clinical environment.

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are two microbial groups mediating nitrification, yet little is presently known about their abundances and community structures at the transcriptional level in wastewater treatment systems (WWTSs). This is a significant issue, as the numerical abundance of AOA or AOB at the gene level may not necessarily represent their functional role in ammonia oxidation. Using amoA genes as molecular markers, this study investigated the transcriptional abundance and community structure of active AOA and AOB in 14 WWTSs. Quantitative PCR results indicated that the transcriptional abundances of AOB amoA (averaged: 1.6 × 108 copies g−1 dry sludge) were higher than those of AOA (averaged: 3.4 × 107 copies g−1 dry sludge) in all WWTSs despite several higher abundances of AOA amoA at the gene level. Moreover, phylogenetic analysis demonstrated that Nitrosomonas europaea and unknown clusters accounted for 37.66% and 49.96% of the total AOB amoA transcripts, respectively, suggesting their dominant role in driving ammonia oxidation. Meanwhile, AOA amoA transcripts were only successfully retrieved from 3 samples, and the Nitrosospaera sister cluster dominated, accounting for 83.46%. Finally, the substrate utilization kinetics of different AOA and AOB species might play a fundamental role in shaping their niche differentiation, community composition, and functional activity. This study provides a basis for evaluating the relative contributions of ammonia-oxidizing microorganisms (AOMs) to nitrogen conversions in WWTSs.

Skeletal system has been considered a highly dynamic system, in which bone-forming osteoblasts and bone-resorbing osteoclasts go through a continuous remodeling cycle to maintain homeostasis of bone matrix. It has been well acknowledged that interferons (IFNs), acting as a subgroup of cytokines, not only have crucial effects on regulating immunology but also could modulate the dynamic balance of bone matrix. In the light of different isoforms, IFNs have been divided into three major categories in terms of amino acid sequences, recognition of specific receptors and biological activities. Currently, type I IFNs consist of a multi-gene family with several subtypes, of which IFN-α exerts pro-osteoblastogenic effects to activate osteoblast differentiation and inhibits osteoclast fusion to maintain bone matrix integrity. Meanwhile, IFN-β suppresses osteoblast-mediated bone remodeling as well as exhibits inhibitory effects on osteoclast differentiation to attenuate bone resorption. Type II IFN constitutes the only type, IFN-γ, which exerts regulatory effects on osteoclastic bone resorption and osteoblastic bone formation by biphasic ways. Interestingly, type III IFNs are regarded as new members of IFN family composed of four members, including IFN-λ1 (IL-29), IFN-λ2 (IL-28A), IFN-λ3 (IL-28B) and IFN-λ4, which have been certified to participate in bone destruction. However, the direct regulatory mechanisms underlying how type III IFNs modulate the metabolic balance of bone matrix, remains poorly elucidated. In this review, we have summarized functions of IFN family during physiological and pathological conditions and described the mechanisms by which IFNs maintain bone matrix homeostasis via affecting the osteoclast-osteoblast crosstalk. In addition, the potential therapeutic effects of IFNs on inflammatory bone destruction diseases such as rheumatoid arthritis (RA), osteoarthritis (OA) and infectious bone diseases are also well displayed, which are based on the predominant role of IFNs in modulating the dynamic equilibrium of bone matrix.

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recent years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination breakpoints using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_ AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints in the virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

Genetic abnormalities in synaptic proteins are common in individuals with autism; however, our understanding of the cellular and molecular mechanisms disrupted by these abnormalities is limited. SHANK3 is a postsynaptic scaffolding protein of excitatory synapses that has been found mutated or deleted in most patients with 22q13 deletion syndrome and about 2% of individuals with idiopathic autism and intellectual disability. Here, we generated CRISPR/Cas9-engineered human pluripotent stem cells (PSCs) with complete hemizygous SHANK3 deletion (SHANK3+/-), which is the most common genetic abnormality in patients, and investigated the synaptic and morphological properties of SHANK3-deficient PSC-derived cortical neurons engrafted in the mouse prefrontal cortex. We show that human PSC-derived neurons integrate into the mouse cortex by acquiring appropriate cortical layer identities and by receiving and sending anatomical projections from/to multiple different brain regions. We also demonstrate that SHANK3-deficient human neurons have reduced AMPA-, but not NMDA- or GABA-mediated synaptic transmission and exhibit impaired dendritic arbors and spines, as compared to isogenic control neurons co-engrafted in the same brain region. Together, this study reveals specific synaptic and morphological deficits caused by SHANK3 hemizygosity in human cortical neurons at different developmental stages under physiological conditions and validates the use of co-engrafted control and mutant human neurons as a new platform for studying connectivity deficits in genetic neurodevelopmental disorders associated with autism.

Inonotus obliquus is a rare medicinal fungus that contains several potential therapeutic ingredients. In this study, the α-glucosidase inhibitory activity of I. obliquus was examined, and a potential α-glucosidase inhibitor, (E)-4-(3,4-dihydroxyphenyl)but-3-en-2-one, was isolated from the I. obliquus extract through ultrafiltration-liquid chromatography (UF-LC). Consecutive high-speed countercurrent chromatography (HSCCC) was used for separation to obtain large quantities of the target compound. The universal quasi-chemical functional group activity coefficient (UNIFAC) model was utilized to prepare a two-phase solvent system, n-hexane/ethyl acetate/ethanol/water (4 : 4.5 : 3.5 : 5, v/v/v/v), wherein the proportions of n-hexane/ethyl acetate/ethanol/water in the stationary and mobile phases were 19.8 : 19.7 : 7.9 : 2.2 (v/v/v/v) and 1 : 16.4 : 57.5 : 136.6 (v/v/v/v), respectively. A flow rate of 2.5 mL min−1 and a column speed of 860 rpm were maintained. Consequently, 10.3 mg of the target compound (95.9% purity) was obtained from 900 mg (6 × 150 mg) of the I. obliquus extract. The use of the UNIFAC model, in combination with consecutive HSCCC separations, allows the purification of large quantities of samples over a short time. Furthermore, the volume of the organic solvent required is reduced. Thus, UF-LC is an effective technique for screening potential α-glucosidase inhibitors isolated from I. obliquus. This can ultimately aid in the discovery of bioactive compounds for the prevention and treatment of diabetes.

espanolEl presente estudio se propuso evaluar los efectos que las tecnicas de congelacion por inmersion (IF) con refrigerante y congelacion por aire (AF) empleando diferentes temperaturas de almacenamiento (-18 °C y -30 °C) tienen en la calidad de los meros tras su almacenamiento congelado. Se constato que la tasa de perdida de agua, el nitrogeno basico volatil total y el valor K se correlacionaron positivamente con el tiempo de almacenamiento. Asimismo, se comprobo que el pH primero disminuyo, para aumentar despues. Ademas, la destruccion de la estructura de las fibras musculares provoco cambios en las caracteristicas de textura del mero, como la dureza, la cohesion, la elasticidad y la masticabilidad. De esta forma, tras el almacenamiento en congelacion, las muestras de IF-30 °C fueron las que conservaron la mayor calidad, seguidas por las muestras de IF-18 °C y las de AF-18 °C. Se comprobo que la congelacion por inmersion limito la desnaturalizacion de las proteinas, disminuyo la perdida de agua y contribuyo a la formacion de cristales de hielo uniformemente distribuidos, reduciendo los danos en la microestructura. Se concluye que la congelacion por inmersion es una tecnica prometedora para preservar la calidad de los meros, y el refrigerante empleado en la inmersion (propilenglicol, oligosacaridos y sales) realizada en este estudio posee aplicaciones potenciales en la industria de procesamiento del mero. EnglishIn this study, we evaluated the effects of immersion freezing (IF) with coolant and air freezing (AF) techniques with different storage temperature (−18°C and −30°C) on the quality of groupers following frozen storage. Water loss rate, total volatile basic nitrogen, and the K-value, were positively correlated with storage time. The pH first decreased and then increased. Destruction of the muscle fiber structure led to changes in grouper texture characteristics including hardness, cohesiveness, springiness, and chewiness. IF-30°C samples retained the highest quality after frozen storage, followed by IF-18°C samples and AF-18°C samples. Immersion freezing limited protein denaturation, decreased water loss, and contributed to the formation of uniformly distributed ice crystals, decreasing microstructure damage. Immersion freezing is a promising technique for preserving the quality of groupers, and the immersion coolant (propylene glycol, oligosaccharides and salts) used in this study has potential applications in the grouper processing industry.

Introduction: A large number of unique recombinant forms have been found in China in recent years. This study aimed to report on a cluster of novel HIV-1 recombinants. Methods: We constructed phylogenetic trees using the maximum likelihood (ML) method with 1,000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: Overall, 9 near-full-length genome (NFLG) sequences were reported in this study, including 1 circulation recombinant form (CRF)01_AE NFLG sequence and 8 highly similar novel HIV-1 second-generation recombinants composed of CRF01_AE and CRF07_BC (CRF105_0107) isolated from a cluster HIV-positive male subjects infected among men who have sex with men (MSM) in Nanjing, eastern China. The phylogenetic analysis of NFLG showed 1 sequence named “nj16” to have at least 11 breakpoints inner virus and 7 other sequences to have at least 10 breakpoints inner virus. Our findings further showed as follows: first, this is the first time that a cluster of novel CRF105_0107 HIV-1 strains were identified among MSM in Nanjing, Jiangsu. Second, the Chinese “4a” cluster of CRF01_AE which mainly circulating in northern China has spread in Jiangsu for more than 15 years. Third, HIV-1 recombination events were active in Nanjing city, and novel recombinants could spread rapidly through some small-scale transmission networks. Conclusion: The continued emergence of novel recombinant HIV-1 strains in Nanjing suggests dynamics and complexity in the HIV epidemic among MSM in Jiangsu province. Further investigations and molecular epidemiological research should be taken to monitor and understand transmission networks among MSM.

The pathogenesis of osteoarthritis (OA) is still unclear. It is therefore important to identify relevant diagnostic marker genes for OA. We performed an integrated analysis with multiple microarray data cohorts to identify potential transcriptome markers of OA development. Further, to identify OA diagnostic markers, we established gene regulatory networks based on the protein-protein interaction network involved in these differentially expressed genes (DEGs). Using support vector machine (SVM) pattern recognition, a diagnostic model for OA prediction and prevention was established. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that 190 DEGs were mainly enriched in pathways like the tumor necrosis factor signaling pathway, interleukin-17 signaling pathway, mitogen-activated protein kinase signaling pathway, nuclear factor kappa-light-chain-enhancer of activated B cells signaling pathway, and osteoclast differentiation. Eight hub genes (

Seeds are complex biological systems comprising three genetically distinct tissues: embryo, endosperm, and maternal tissues (including seed coats and pericarp) nested inside one another. Cereal grains represent a special type of seeds, with the largest part formed by the endosperm, a specialized triploid tissue ensuring embryo protection and nourishment. We investigated dynamic changes in DNA content in three of the major seed tissues from the time of pollination up to the dry seed. We show that the cell cycle is under strict developmental control in different seed compartments. After an initial wave of active cell division, cells switch to endocycle and most endoreduplication events are observed in the endosperm and seed maternal tissues. Using different barley cultivars, we show that there is natural variation in the kinetics of this process. During the terminal stages of seed development, specific and selective loss of endoreduplicated nuclei occurs in the endosperm. This is accompanied by reduced stability of the nuclear genome, progressive loss of cell viability, and finally programmed cell death. In summary, our study shows that endopolyploidization and cell death are linked phenomena that frame barley grain development.

Psoriasis is a severe disease associated with the disturbance of metabolism and inflammation, but the molecular mechanisms underlying these aspects of psoriasis pathology are poorly understood. Here, we report that glutaminase 1–mediated (GLS1-mediated) glutaminolysis was aberrantly activated in patients with psoriasis and in psoriasis-like mouse models, which promoted Th17 and γδ T17 (IL-17A–producing γδ T) cell differentiation through enhancement of histone H3 acetylation of the Il17a promoter, thereby contributing to the immune imbalance and development of psoriasis. We further demonstrate that mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) protease was constitutively active in psoriatic CD4(+) and γδ T cells, thereby supporting GLS1 expression by stabilizing c-Jun, which directly binds to the GLS1 promoter region. Blocking the activity of either GLS1 or MALT1 protease resolved Th17 and γδ T17 cell differentiation and epidermal hyperplasia in the psoriasis-like mouse models. Finally, IL-17A enhanced GLS1 expression via the MALT1/cJun pathway in keratinocytes, resulting in hyperproliferation of and chemokine production by keratinocytes. Our findings identify the role of the MALT1/cJun/GLS1/glutaminolysis/H3 acetylation/T17 axis in psoriasis pathogenesis and reveal potential therapeutic targets for this disease.

Acibenzolar-S-methyl (ASM) is one of the most successfully commercialized plant activators of the systemic acquired resistance (SAR). However, its activation (hydrolysis) mechanism catalyzed by the salicylic acid binding protein 2 (SABP2) remains elusive. The fundamental catalytic mechanism of the SABP2-catalyzed hydrolysis of the ASM had been investigated by extensive computational and experimental studies, including QM/MM simulations, charge transfer analysis, small-molecule synthesis, and biochemical assays. Here we report that the promiscuous SABP2 shows different catalytic mechanisms toward different substrates. To catalyze the ASM hydrolysis, the SABP2 uses a two-proton transfer mechanism, and the key intermediate is stabilized by the charge transfer effect; to catalyze the ethyl 1,2,3-benzothiadiazole-7-carboxylate (BTM, an ASM analogue) hydrolysis, the SABP2 applies the one-proton transfer mechanism, and the classic tetrahedral intermediate is stabilized by the electrostatic effect. The HPLC analyses of the SABP2 esterase activities toward the ASM and the BTM show comparable results with our computaional results, suggesting that the obtained computational mechanism insights are reasonable. The obtained mechanism is not only an important supplement to the theory of enzymes' catalytic promiscuity, but it also contributes a possible strategy for the design of next generation plant SAR activators.

Various strains of infectious bronchitis virus (IBV) cause different forms of infectious bronchitis with different clinical signs. Here, primary chicken embryo kidney (CEK) cells and specific-pathogen-free (SPF) chickens were infected with three pathogenic IBV strains, and it was observed that the TLR7-MYD88 pathway was inhibited but the TLR3-TIRF pathway was activated. After treatment with poly(I:C)-LMW, poly (I:C)-LMW/LyoVec, and Imiquimod, the replication of IBV was significantly suppressed after 24 h. However, treatment with TLR3 pathway inhibitors such as Pepinh-TRIF, celastrol, chloroquine, and BX795 resulted in increased replication of IBV after 36 h. These results also showed that chloroquine and celastrol were most effective inhibitors of the antiviral response at 48 hpi.

A well-studied subject of epigenetics, the histone methylation located at lysine and arginine is overseen via methyltransferases and demethylases. Lysine-specific demethylase 4A (KDM4A) comprises a lysine demethylase and possesses specificity for H3K9me3 and H3K36me3, which is capable of being used in order to activate histone transcription. Our team examined the expression of KDM4A within Sprague Dawley (SD) rats and further investigated the mechanism via which this phenomena regulates osteogenic variation within the present study. The overexpression of KDM4A facilitated the process of osteoblast differentiation in bone mesenchymal stem cells (BMSC), while the knocking down differentiation via osteoblast was restrained via the suppression of the expression of Runx2, Osterix, alkaline phosphatase (ALP), and osteocalcin (OCN). Knocking down KDM4A lowered levels of the promoter expression of Runx2, osterix, and OCN, and raised levels of H3K27me3 expression. The results demonstrated that KDM4A possesses a crucial role within the differentiation of osteoblasts and furthermore regulates the expression of Runx2, Osterix, and OCN via H3K9me3. The present research may provide new insights into the treatment of bone healing.

Inflammatory osteolysis is a common osteolytic specificity that occurs during infectious orthopaedic surgery and is characterized by an imbalance in bone homeostasis due to excessive osteoclast bone resorption activity. Epothilone B (Epo B) induced α-tubulin polymerization and enhanced microtubule stability, which also played an essential role in anti-inflammatory effect on the regulation of many diseases. However, its effects on skeletal system have rarely been investigated. Our study demonstrated that Epo B inhibited osteoclastogenesis in vitro and prevented inflammatory osteolysis in vivo. Further analysis showed that Epo B also markedly induced mature osteoclasts apoptosis during osteoclastogenesis. Mechanistically, Epo B directly suppressed osteoclastogenesis by the inhibitory regulation of the phosphorylation and activation of PI3K/Akt/STAT3 signaling directly, and the suppressive regulation of the CD9/gp130/STAT3 signaling pathway indirectly. The negative regulatory effect on STAT3 signaling further restrained the translocation of NF-κB p65 and NFATc1 from the cytosol to the nuclei during RANKL stimulation. Additionally, the expression of osteoclast specific genes was also significantly attenuated during osteoclast fusion and differentiation. Taken together, these findings illustrated that Epo B protected against LPS-induced bone destruction through inhibiting osteoclastogenesis via regulating the STAT3 dependent signaling pathway.

Prevention and treatment options for hepatocellular carcinoma (HCC) are presently limited, underscoring the necessity for further elucidating molecular mechanisms underlying HCC development and identifying new prevention and therapeutic targets. Here, we demonstrate a unique protumorigenic niche in the livers of Ncoa5+/- mouse model of HCC, which is characterized by altered expression of a subset of genes including p21WAF1/CIP1 and proinflammatory cytokine genes, increased putative hepatic progenitors, and expansions of activated and tissue-resident memory (TRM) CD8+ T lymphocytes, myeloid-derived suppressor cells (MDSCs), and alternatively activated M2 macrophages. Importantly, prophylactic metformin treatment reversed these characteristics including aberrant p21WAF1/CIP1 expression and subsequently reduced HCC incidence in Ncoa5+/- male mice. Heterozygous deletion of the p21WAF1/CIP1 gene alleviated the key features associated with the protumorigenic niche in the livers of Ncoa5+/- male mice. Moreover, transcriptomic analysis reveals that preneoplastic livers of Ncoa5+/- mice are similar to the livers of nonalcoholic steatohepatitis patients as well as the adjacent noncancerous liver tissues of a subset of HCC patients with a relatively poor prognosis. Together, our results suggest that p21WAF1/CIP1 overexpression is essential in the development of protumorigenic microenvironment induced by NCOA5 deficiency and metformin prevents HCC development via alleviating p21WAF1/CIP1 overexpression and protumorigenic microenvironment.

Aroma compounds in three surimi samples, made from freshwater silver carp (Hypophthalmichthys molitrix) and saltwater Pacific whiting (Merluccius productus) and Alaska pollock (Theragra chalcogramm...

Long noncoding RNAs (lncRNAs) have been shown to play crucial roles in human cancers. However, the underlying biological functions and mechanisms of lncRNAs in cholangiocarcinoma (CCA) remain largely unknown. We aimed to characterize the transcriptional landscape of lncRNAs in CCA and identify lncRNAs that were able to serve as prognosis markers and therapeutic targets for CCA. Here, we investigated the transcriptional landscape and dysregulation of lncRNAs in CCA. LINC01714 was found to be recurrently downregulated in CCA tumor samples. Our results revealed that decreased LINC01714 expression was associated with the poor survival of CCA patients. Our observations revealed that LINC01714 suppressed the proliferation, migration, and invasion abilities of CCA cells both in vitro and in vivo. Furthermore, we found that LINC01714 physically interacted with Forkhead Box O3 (FOXO3) and increased the FOXO3 protein level. In addition, LINC01714 could decrease the phosphorylation level of FOXO3. Interestingly, LINC01714 was able to enhance the sensitivity to gemcitabine in CCA tumor cells through modulating phosphorylated FOXO3-Ser318. Our study revealed LINC01714 as a promising prognostic indictor for patients with CCA, provided insights into the molecular pathogenesis of CCA, and also showed that LINC01714 is a potential therapeutic combination for gemcitabine in CCA treatment.

Bisphosphonate-related osteonecrosis of the jaws (BRONJ) is a severe adverse reaction, which results in progressive bone destruction in the maxillofacial region of patients. To date, the pathological mechanisms remain largely unclear. Recently, we found that BRONJ patient had significantly deep periodontal pockets and severe periodontal bone defects before the exposed necrotic bone. Human periodontal ligament stem cells (hPDLSCs) play key roles in physiological maintenance and regeneration of periodontal tissues. However, the activities of hPDLSCs derived from BRONJ lesions and the role of hPDLSCs in BRONJ periodontal defect repair remain poorly understood. The aim of the present study was to elucidate the role of hPDLSCs in BRONJ. In this study, we found that the capacities of cell proliferation, adhesion, and migration of hPDLSCs derived from BRONJ lesions (BRONJ-hPDLSCs) were significantly decreased compared with control-hPDLSCs. BRONJ-hPDLSCs underwent early apoptosis compared with control-hPDLSCs. Importantly, we first demonstrated that BRONJ-hPDLSCs exhibited impaired osteogenic differentiation abilities in ectopic osteogenesis of nude mice. The above results suggested that the impaired BRONJ-hPDLSCs may be an important factor in deficient periodontal repair of BRONJ lesions and provide new insight into the underlying mechanism of BRONJ.

BackgroundAlthough approved by FDA, anti-CTLA-4 treatment has severe side effect that limits its clinical usage. Blockade of CD47, the “don't eat me” signal, has limited effects in solid tumors despite its potent anti-tumor effects in hematopoietic malignancies. Targeted delivery of immune blockers into tumor tissues are desireble.MethodsTaking advantage of the high expression of CTLA-4 on Treg cells and abundant Fc receptor+ active phagocytes inside the tumor microenvironment (TME), we design and test an anti-CTLA-4×SIRPα (CD47 ligand)-Fc heterodimer that selectively blocks CD47 on intratumoral Treg cells and increases antibody-dependent cellular phagocytosis (the “eat me” signal).ResultsAnti-CTLA-4×SIRPα preferentially depletes ICOShigh immunosuppressive Treg cells in the TME (figure 1–3) and enhances immunity against solid tumors. Mechanistically, we discovered that CD47 expression on Treg cells limits anti-CTLA-4 mediated depletion while Fc on the heterodimer enhances the depletion. Furthermore, anti-human CTLA-4×SIRPα depletes tumor Treg cells (figure 4–6) and exhibits less toxicity than anti-human CTLA-4 in a humanized mouse model.ConclusionsCollectively, these results highlight coordinatively modulating “eat me” and “don't eat me” signals for depleting Treg cells inside the TME as a unique strategy for solid tumor treatment.Abstract 800 Figure 1Anti-CTLA-4×SIRPα selectively targets intratumor Treg. (A) Expression of CTLA-4 transcripts in colorectal cancer patient tissues based on single cell sequencing online database (29). (B and C) CTLA-4 expression on Treg cells from PBMC, spleen and tumor cells in MC38 tumor-bearing mice on day 14. (D) Schematic diagram of anti-CTLA-4×SIRPα heterodimer. (E) Kinetic association (ka), dissociation (kd), and calculated affinity (KD) for binding of the indicated analyte to mouse CTLA-4 or CD47 antigen were measured by surface plasmon resonance using OpenSPR instrument. (F) Binding of SIRPα, CTLA-4 and anti-CTLA-4×SIRPα to RBC from C57BL/6 mice, n=4. (G) Anti-CTLA-4×SIRPα binding on Treg of PBMC and tumor cells from MC38 tumor-bearing mice. (H) C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells. After 13 days, 20 µg anti-CTLA-4×SIRPα was injected intraperitoneally. Five days later, mice were perfused with PBS, and tumor and other tissues were harvested and homogenized. Anti-CTLA-4×SIRPα protein abundance was determined with ELISA, n=4.Abstract 800 Figure 2Anti-CTLA-4×SIRPα preferentially depletes ICOShi Treg. (A–C) C57BL/6 mice (n=4) were inoculated with 5 × 105 MC38 tumor cells and treated with Combo or anti-CTLA-4×SIRPα on day 13. Five days later, Treg cells from tumor, spleen and draining lymph node (dLN) were analyzed. The representative flow cytometric gating was shown in (A). Treg cells frequency from different groups was shown in (B). The ratio of CD8+ T cells to Treg was shown in (C). (D–F) Foxp3-EGFP reporter mice (n=3) were inoculated with 5 × 105 MC38 tumor cells and treated with Combo or anti-CTLA-4×SIRPα on day 13. Five days later, Foxp3-EGFP+ cells from tumor, spleen and dLN were analyzed. The representative flow cytometric gating was shown in (D). Foxp3-EGFP+ cell frequency from different groups was shown in (E). The ratio of CD8+ T cells to Foxp3-EGFP+ cells was shown in (F). (G–I) Same experiment scheme as (A–F). Representative ICOS expression on Treg cells was shown in (G). (H) ICOS++ frequency among Treg cells (H) and ICOS++ frequency among YFP+ cells (I) were shown.Abstract 800 Figure 3Anti-CTLA-4×SIRPα reduces tumor in T cell dependent way. (A) C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with equal moles of anti-CTLA-4 plus SIRPα (Combo, 12 µg + 8 µg) or anti-CTLA-4×SIRPα (20 µg) on day 14. Tumor growth was measured every 3 days, n=5. (B) BALB/C mice were inoculated with 5 × 105 CT26 tumor cells and treated with Combo (30 µg+ 20 µg) or anti-CTLA-4×SIRPα (50 µg) on day 6. Tumor growth was measured every 3 days, n=5. (C) Rag1-/- mice were inoculated with 1 × 105 MC38 tumor cells and treated with Combo (12 µg+ 8 µg) or anti-CTLA-4×SIRPα (20 µg) on day 13. Tumor growth was measured every 3 days, n=5. (D) MuMT mice were inoculated with 1.5 × 106 MC38 tumor cells and treated with anti-CTLA-4×SIRPα (20 µg) on day 14. Tumor growth was measured every 3 days, n=4. (E and F) C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 13. 200 μg of anti-CD4 (E) or anti-CD8 (F) was administrated one day before treatment initiation and then twice a week for 2 weeks. Tumor growth was measured every 3 days, n=5. (G–I) C57BL/6 mice (n=4) were inoculated with 5 × 105 MC38 tumor cells and treated with Combo or anti-CTLA-4×SIRPα on day 14. Five days later, tumor-infiltrating lymphocytes (TILs) were analyzed for total CD45 in tumor (E), Ki67 expression on CD4 and CD8 T cells from different groups (F and G) after treatment.Abstract 800 Figure 4Anti-CTLA-4×SIR enhances tumor-specific T cell IFN-gamma. (A) C57BL/6 mice (n=4) were inoculated with 5 × 105 MC38 tumor cells and treated with Combo or anti-CTLA-4×SIRPα on day 13. Five days later, TILs were analyzed for tumor specific T cells. (B and C) C57BL/6 mice (n=4) were inoculated with 5 × 105 MC38 tumor cells and treated with Combo or anti-CTLA-4×SIRPα on day 13. Five days later, TILs were purified with CD45+ positive selection magnetic beads. TILs (A) and dLN (B) were re-stimulated with irradiated MC38 tumor cells or irrelevant control Lewis lung cancer (LLC) cells for 48 h. IFN-γ producing cells were determined by ELISPOT assay. (D) WT or Ifng-/- C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 13. Tumor growth was measured every 3 days, n=4. (E) C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 13. 150 μg of anti-IFN-γ was administrated one day before treatment initiation and then twice a week for 2 weeks. Tumor growth was measured every 3 days, n=5. (F and G) C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 14. Six weeks later, anti-CTLA-4×SIRPα cured mice and control naïve mice were re-challenged with 5 × 106 MC38 tumor cells on the left flank (opposite to the original injection flank) (F), and 5 × 105 LLC tumor cells were injected on the right flank (G). Tumor growth was measured every 3 days, n=5.Abstract 800 Figure 5CD47 expression on Treg cells is essential. (A) Cd47-/- tumor bearing C57BL/6 mice were treated with Combo or anti-CTLA-4×SIRPα on day 13. Tumor growth was measured every 3 days, n=5. (B) WT or Cd47-/- C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 14. Tumor growth was measured every 3 days, n=5. (C) WT or Cd47-/- T cells were purified by negative selection magnetic beads and intravenously transferred to Rag1-/- mice. 2 × 105 MC38 tumor cells were inoculated into the recipient mice the next day. Mice were treated with 40 µg anti-CTLA-4×SIRPα on day 7 and day 12. Experiment scheme was shown in upper panel and tumor growth was shown in lower panel, n=5. (D) C57BL/6 mice were inoculated with 5 × 105 MC38-cEGFR tumor cells and treated with 30 µg anti-EGFR×SIRPα or anti-CTLA-4×SIRPα on day 14. Tumor growth was measured every 3 days, n=3–4. (E) WT or Fcer1g-/- C57BL/6 mice were inoculated with 1 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα on day 13. Tumor growth was measured every 3 days, n=5. (F) WT C57BL/6 mice were inoculated with 5 × 105 MC38 tumor cells and treated with anti-CTLA-4×SIRPα or anti-CTLA-4×SIRPα with mutant Fc (Anti-CTLA-4×SIRPα-InFc) on day 14. Tumor growth was measured every 3 days, n=5. (G) Bone marrow derived macrophages from WT or Fcer1g-/-mice were mixed with CFSE labelled in vitro differentiated Treg cells from WT or Cd47-/- mice for 3 h. Phagocytosis was determined with flow cytometry. Phagocytosis index was defined as the percentage of CFSE+ macrophages among total macrophages.Abstract 800 Figure 6A human version anti-CTLA-4×SIRPα heterodimer depletes Treg. (A and B) CD47 and CTLA-4 expression level on Treg cells of PBMC and tumor from NSCLC patients. The representative flow cytometric gating was shown in (A), pooled data from different patients was show in (B). (C) Anti-hCTLA-4, SIRPα and anti-hCTLA-4×SIRPα binding on Jurkat and Jurkat-hCTLA-4 expressing cells. (D) Comparison of anti-hCTLA-4×SIRPα binding on Jurkat and Jurkat-hCTLA-4 cells based on (C). (E and F) PBMC-humanized NSG mice were inoculated with 2.5 × 106 A549 tumor cells and treated with anti-hCTLA-4 plus SIRPα (h-Combo, 18 µg +12 µg) or anti-hCTLA-4×SIRPα (30 µg) on day 12. Two days later, the frequency of tumor-infiltrating Treg cells (G) and ICOS expression level on Treg cells (F) were analyzed, n=4. (G) PBMC-humanized NSG mice were treated with 200 μg anti-hCTLA-4 or anti-hCTLA-4×SIRPα twice a week for 4 times. Mouse body weight was monitored every 3 days, n=5. Data are shown as mean ± SEM from two independent experiments. P value was determined by paired t test (B), unpaired t test (E and F) and two-way ANOVA with Geisser-Greenhouse's correction (G). The normality of data was confirmed by Shapiro-Wilk test.

Background Development of dental tissue is regulated by extensive cell crosstalk based on various signaling molecules, such as bone morphogenetic protein (BMP) and fibroblast growth factor (FGF) pathways. However, an intact network of the intercellular regulation is still lacking. Result To gain an unbiased and comprehensive view of this dental cell interactome, we applied single-cell RNA-seq on immature human tooth germ of the growing third molar, discovered refined cell subtypes, and applied multiple network analysis to identify the central signaling pathways. We found that immune cells made up over 80% of all tooth germ cells, which exhibited profound regulation on dental cells via Transforming growth factor-β, Tumor necrosis factor (TNF) and Interleukin-1. During osteoblast differentiation, expression of genes related to extracellular matrix and mineralization was continuously elevated by signals from BMP and FGF family. As for the self-renewal of apical papilla stem cell, BMP-FGFR1-MSX1 pathway directly regulated the G0-to-S cell cycle transition. We also confirmed that Colony Stimulating Factor 1 secreted from pericyte and TNF Superfamily Member 11 secreted from osteoblast regulated a large proportion of genes related to osteoclast transformation from macrophage and monocyte. Conclusions We constructed the intercellular signaling networks that regulated the essential developmental process of human tooth, which served as a foundation for future dental regeneration engineering and the understanding of oral pathology.

The coronavirus disease 2019 (COVID-19) pandemic has caused many deaths worldwide. To date, the mechanism of viral immune escape remains unclear, which is a great obstacle to developing effective clinical treatment. RNA processing mechanisms, including alternative polyadenylation (APA) and alternative splicing (AS), are crucial in the regulation of most human genes in many types of infectious diseases. Because the role of APA and AS in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unknown, we performed de novo identification of dynamic APA sites using a public dataset of human peripheral blood mononuclear cell (PBMC) RNA-Seq data in COVID-19 patients. We found that genes with APA were enriched in innate immunity -related gene ontology categories such as neutrophil activation, regulation of the MAPK cascade and cytokine production, response to interferon-gamma and the innate immune response. We also reported genome-wide AS events and enriched viral transcription-related categories upon SARS-CoV-2 infection. Interestingly, we found that APA events may give better predictions than AS in COVID-19 patients, suggesting that APA could act as a potential therapeutic target and novel biomarker in those patients. Our study is the first to annotate genes with APA and AS in COVID-19 patients and highlights the roles of APA variation in SARS-CoV-2 infection.

Cycads represent one of the most ancestral living seed plants as well as one of the most threatened plant groups in the world. South China is a major center and potential origin of Cycas, the most rapidly diversified lineage of cycads. However, genomic-wide diversity of Cycas remains poorly understood due to the challenge of generating genomic markers associated with their inherent large genomes. Here, we perform a comprehensive conservation genomic study based on restriction-site associated DNA sequencing (RADseq) data in six representative species of Cycas in South China. Consistently low genetic diversity and strong genetic differentiation were detected across species. Both phylogenetic inference and genetic structure analysis via several methods revealed generally congruent groups among the six Cycas species. The analysis with ADMIXTURE showed low mixing of genetic composition among species, while individuals of C. dolichophylla exhibited substantial genetic admixture with C. bifida, C. changjiangensis, and C. balansae. Furthermore, the results from Treemix, f4-statistic, and ABBA-BABA test were generally consistent and revealed the complex patterns of interspecific gene flow. Relatively strong signals of hybridization were detected between C. dolichophylla and C. szechuanensis, and the ancestor of C. taiwaniana and C. changjiangensis. Distinct patterns of demographic history were inferred for these species by Stairway Plot, and our results suggested that both climate fluctuation and frequent geological activities during the late Pleistocene exerted deep impacts on the population dynamics of these species in South China. Finally, we explore the practical implications of our findings for the development of conservation strategies in Cycas. The present study demonstrates the efficiency of RADseq for conservation genomic studies on non-model species with large and complex genomes. Given the great significance of cycads as a radical transition in the evolution of plant biodiversity, our study provides important insights into the mechanisms of diversification in such recently radiated living fossil taxa.

Radiation therapy is an effective method to kill cancer cells and shrink tumors using high-energy X-ray or γ-ray. Radiation pneumonitis (RP) is one of the most serious complications of radiation therapy for thoracic cancers, commonly leading to serious respiratory distress and poor prognosis. Here, we prepared curcumin-loaded mesoporous polydopamine nanoparticles (CMPN) for prevention and treatment of RP by pulmonary delivery. Mesoporous polydopamine nanoparticles (MPDA) were successfully synthesized with an emulsion-induced interface polymerization method and curcumin was loaded in MPDA via π‒π stacking and hydrogen bonding interaction. MPDA owned the uniform spherical morphology with numerous mesopores that disappeared after loading curcumin. More than 80% curcumin released from CMPN in 6 h and mesopores recovered. CMPN remarkably protected BEAS-2B cells from γ-ray radiation injury by inhibiting apoptosis. RP rat models were established after a single dose of 15 Gy 60Co γ-ray radiation was performed on the chest area. Effective therapy of RP was achieved by intratracheal administration of CMPN due to free radical scavenging and anti-oxidation ability, and reduced proinflammatory cytokines, high superoxide dismutase, decreased malondialdehyde, and alleviated lung tissue damages were observed. Inhaled CMPN paves a new avenue for the treatment of RP.

Blockade of CD47, the “do not eat me” signal, has limited effects in solid tumors despite its potent antitumor effects in hematopoietic malignancies. Taking advantage of the high expression of cytotoxic T lymphocyte–associated protein 4 (CTLA-4) on T(reg) cells and abundant Fc receptor–expressing active phagocytes inside the tumor microenvironment (TME), we designed and tested a heterodimer combining an anti–CTLA-4 antibody, which targets T(reg) cells, with the CD47 ligand, signal regulatory protein α (SIRPα), to selectively block CD47 on intratumoral T(reg) cells. We hypothesized that heterodimer treatment would increase antibody-dependent cellular phagocytosis of the targeted T(reg) cells. We found that anti–CTLA-4×SIRPα preferentially depleted ICOS(high) immunosuppressive T(reg) cells in the TME and enhanced immunity against solid tumors, including MC38 and CT26 murine colon cancers. Mechanistically, we found that CD47 expression on T(reg) cells limited anti–CTLA-4–mediated depletion and Fc on the heterodimer-enhanced depletion. Furthermore, anti-human CTLA-4×SIRPα depleted tumor T(reg) cells and exhibits less toxicity than anti-human CTLA-4 in a humanized mouse model. Collectively, these results demonstrate that simultaneously modulating both “eat me” and do not eat me signals induces T(reg) cell depletion inside the TME and may be an effective strategy for treating solid tumors.

Salmonella, an important zoonotic pathogen, causes significant morbidity and mortality in both humans and animals. Phloretin mainly isolated from strawberries and apples has the effects of treating inflammation and pathogenic bacteria, but its protective efficacy and mechanism of action against Salmonella spp. are less clear. In this study, we found that phloretin alleviated body weight loss, colon length shortening, and colonic pathological damage caused by S. Typhimurium. Phloretin also decreased S. Typhimurium translocation to the mesenteric lymph nodes (MLN) and spleen. Further mechanism studies showed that phloretin significantly inhibited inflammation and oxidative stress levels in the colonic tissue. Phloretin also prevented S. Typhimurium-mediated impairment in the colon epithelium barrier by the regulation ZO-1 and occludin levels. Interestingly, phloretin did not inhibit S. typhimurium growth in vitro, but reduced the internalization of S. Typhimurium into Caco-2 cells. Taken together, these findings indicated that phloretin may be a new dietary strategy to combat the disease.

Background: Development of dental tissue is regulated by extensive cell crosstalk based on various signaling molecules, such as BMP, FGF and SHH pathways. However, an intact network of the intercellular regulation is still lacking.Result: To gain an unbiased and comprehensive view of this dental cell interactome, we applied single-cell RNA-seq on immature human tooth germ of the third molar, discovered refined cell subtypes, and applied multiple network analysis to identify the central signaling pathways. We found that immune cells made up over 80% of all tooth germ cells, which exhibited profound regulation on dental cells via TGF-β, TNF and IL-1. During osteoblast differentiation, expression of genes related to extracellular matrix and mineralization was continuously elevated by signals from BMP and FGF family. As for the self-renewal of apical papilla stem cell, BMP-FGFR1-MSX1 pathway directly regulated the G0-to-S cell cycle transition. We also confirmed that CSF1 secreted from pericyte and TNFSF11 secreted from osteoblast regulated a large proportion of genes related to osteoclast transformation from macrophage and monocyte. Conclusion: We constructed the intercellular signaling networks that regulated the essential developmental process of human tooth, which served as a foundation for future dental regeneration engineering and the understanding of oral pathology.

Background Gallbladder cancer (GC) is a malignant disease characterized with highly cellular heterogeneity and poor prognosis. Determining the intratumoral heterogeneity and microenvironment (TME) can provide novel therapeutic strategies for GC. Methods We performed the single‐cell RNA sequencing on the primary and lymph node metastatic gallbladder tumors and the adjacent normal tissues of five patients. The transcriptomic atlas and ligand–receptor‐based intercellular communication networks of the single cells were characterized. Results The transcriptomic landscape of 24,887 single cells was obtained and characterized as 10 cellular clusters, including epithelial, neuroendocrine tumor cells, T&NK cells, B cells, RGS5+ fibroblasts, POSTN+ fibroblasts, PDGFRA+ fibroblasts, endothelial, myeloid cells, and mast cells. Different types of GC harbored distinct epithelial tumor subpopulations, and squamous cell carcinoma could be differentiated from adenocarcinoma cells. Abundant immune cells infiltrated into adenocarcinoma and squamous cell carcinoma, rather than neuroendocrine neoplasms, which showed significant enrichment of stromal cells. CD4+/FOXP3+ T‐reg and CD4+/CXCL13+ T helper cells with higher exhausting biomarkers, as well as a dynamic lineage transition of tumor‐associated macrophages from CCL20hi/CD163lo, CCL20lo/CD163hi to APOE+, were identified in GC tissues, suggesting the immunosuppressive and tumor‐promoting status of immune cells in TME. Two distinct endothelial cells (KDR+ and ACKR1+), which were involved in angiogenesis and lymphangiogenesis, showed remarkable ligand–receptor interactions with primary GC cells and macrophages in gallbladder tumors. Conclusions This study reveals a widespread reprogramming across multiple cell populations in GC progression, dissects the cellular heterogeneity and interactions in gallbladder TME, and provides potential therapeutic targets for GC., Abundant immune cells in adenocarcinoma and squamous cell carcinoma while stromal cells in neuroendocrine neoplasms were enriched.Immunosuppressive microenvironment characterized as exhausted T cells and APOE+ macrophages.Endothelial cells (KDR+ and ACKR1+) indicated that angiogenesis and lymphangiogenesis were involved in GC.There were remarkable ligand–receptor interactions between endothelial, primary GC cells, and macrophages.

The pMN domain is a restricted domain in the ventral spinal cords, defined by the expression of olig2 gene. The fate determination of pMN progenitors is highly temporally and spatially regulated, with motor neurons and oligodendrocyte progenitor cells (OPCs) developing sequentially. Insight into the heterogeneity and molecular programs of pMN progenitors is currently lacking. With the zebrafish model, we identified multiple states of neural progenitors using single-cell sequencing: proliferating progenitors, common progenitors for both motor neurons and OPCs, and restricted precursors for either motor neurons or OPCs. We found specific molecular programs for neural progenitor fate transition, and manipulations of representative genes in the motor neuron or OPC lineage confirmed their critical role in cell fate determination. The transcription factor NPAS3 is necessary for the development of the OPC lineage and can interact with many known genes associated with schizophrenia. Deciphering progenitor heterogeneity and molecular mechanisms for these transitions will elucidate the formation of complex neuron-glia networks in the central nervous system during development, and understand the basis of neurodevelopmental disorders.

Mouse models have an essential role in cancer research, yet little is known about how various models resemble human cancer at a genomic level. Here, we complete whole genome sequencing and transcriptome profiling of two widely used mouse models of breast cancer, MMTV-Neu and MMTV-PyMT. Through integrative in vitro and in vivo studies, we identify copy number alterations in key extracellular matrix proteins including collagen 1 type 1 alpha 1 (COL1A1) and chondroadherin (CHAD) that drive metastasis in these mouse models. In addition to copy number alterations, we observe a propensity of the tumors to modulate tyrosine kinase-mediated signaling through mutation of phosphatases such as PTPRH in the MMTV-PyMT mouse model. Mutation in PTPRH leads to increased phospho-EGFR levels and decreased latency. These findings underscore the importance of understanding the complete genomic landscape of a mouse model and illustrate the utility this has in understanding human cancers., Mouse models are an essential tool in breast cancer research. Here, the authors present the genomic and transcriptomic profiles of two widely used mouse models, revealing parallels with the human disease specifically with metastasis and treatment response.

Osteoporosis and cardiovascular diseases often coexist in the same elderly individuals. Does this suggest some potential correlation between the two diseases? Low bone mass and change of bone biomarker are associated with a higher risk of carotid and cardiac calcification plaques. Bone mineral density (BMD) and bone metabolism marker may contribute to the progression of carotid and cardiac arterial calcifications. The aim of this study was to investigate whether low bone mass and the change of bone biomarker are associated with the prevalence of calcified atherosclerotic plaque in elderly Chinese. We conducted a five-year prospective study. BMD was measured by dual-energy X-ray absorptiometry scanning. Carotid and cardiac computed tomography angiography (CTA) was conducted using a 64-multidetector row scanner to assess carotid and cardiac arterial plaque at baseline and during follow-up. Of 1571 community residents over 60 years of age, 184 (11.7%) subjects developed carotid calcified plaque, 510 (32.5%) subjects developed cardiac calcified plaque and 97 (6.2%) subjects developed co-existence calcified plaques in carotid and cardiac arteries. After adjustment for age and all relevant confounders, Q1, Q2 quartile of BMD, and osteoprotegerin (OPG), osteocalcin (OC), and C-terminal cross-linked telopeptide of type I collagen (CTX) were associated with increased risk of calcified plaques. This study suggested that lower BMD and change of bone metabolism biomarker were associated with a higher risk of carotid and cardiac calcified plaque development.

Through evolution, selection pressures cause both insects and the pathogens attacking them to adapt so that they will both survive and this has been called the co-evolutionary 'arms race'. Insects expand their repertoire of pattern recognition receptors (PRRs), a fundamental and core component of their immune systems, to adapt to the constantly changing and unpredictable diversity of pathogens. In this review, we discuss the diversity of PRRs based on studies conducted in recent years. The strategies associated with PRR diversity summarized here are genetic evolution, isoform diversity based on alternative splicing, 'part-time' PRRs, PRRs with opsonin function, and regulation of complex signaling pathways. Taken together, these data indicate that the function of PRRs in insect immunity is far more complex and possesses more features than originally thought.

Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) has severely decreased global tomato production. Organic amendments are widely applied to suppress Fol all over the world. However, the ways in which different amendments alter soil bulk microflora and thereby induce the suppression of Fol remain unclear. In this study, the effects of three organic amendments on the suppression of Fol in soil and the underlying mechanisms of those effects were studied. The organic amendments included in this study are rice straw, chicken manure compost, and vermicompost. High-throughput HiSeq sequencing and Real-Time PCR were used to determine the effect of the soil microbiota on the abundance of Fol. The abundance of Fol increased significantly with the duration of tomato cultivation. Vermicompost was the most effective organic fertilizer to suppress Fol in long-term continuous tomato cropping soil. Partial Least Squares Path Modeling revealed a strong positive relationship between the relative abundance of bacterial groups (including the genera Nocardioides, Ilumatobacter and Gaiella) and Fol inhibition. Soil chemical properties (pH, NH4+-N, soil organic matter and dissolved organic carbon) were positively associated with the genera Nocardioides, Ilumatobacter and Gaiella. Compared with chemical fertilizer and rice straw, vermicompost addition significantly increased soil pH, NH4+-N, soil organic matter and dissolved organic carbon concentrations in the soil with 20 years of tomato cultivation. Most importantly, the genera Nocardioides, Ilumatobacter and Gaiella were enriched in vermicompost, which may contribute to the propagation of these bacteria in the soil when vermicompost is added. This study provides a mechanistic framework that permits the exploration of specific functions at lower taxonomic levels. This may represent a novel approach in the management of crop pathogens via promotion of beneficial organisms.

Degradation of metolachlor in surface soil is extremely important to its potential mobility and overall persistence. In this study, the effects of earthworms (Eisenia fetida) on the degradation of metolachlor at two concentration levels (5 and 20 mg kg−1) in soil were investigated via the column experiment. The degradation kinetics of metolachlor indicate that addition of earthworms enhances metolachlor degradation significantly (P

Berberine, a Chinese medical herbal extract, plays a key role in antidiabetic, antiangiogenesis, anti-inflammatory, antimicrobial, anticancer, and antihypercholesterolemic. Our previous studies revealed that berberine exerted odontoprotective effect by increasing odontoblast differentiation. However, the mechanisms involved in the odontoprotective effect of berberine have not been fully explored. The Wnt/β-catenin pathway is involved in odontoblast differentiation of dental pulp stem cells (DPSCs). If β-catenin is nuclear translocation, the Wnt/β-catenin pathway is activation. In this study, DPSCs were treated with or without berberine. Then, we examined the accelerative effects of berberine on odontoblast differentiation and mineralized nodules formation by real-time polymerase chain reaction, alizarin red S staining, and alkaline phosphatase staining. In addition, while treated with berberine, β-catenin translocated to the nucleus evaluated by western blot and immunofluorescent staining. Our results revealed that berberine functions as a promoter of odontoblast differentiation by promoting Wnt/β-catenin pathway, suggesting that it may be useful in guiding therapeutic strategies for the treatment of dental caries.

In order to reveal changes in fatty acids and triglycerides during the pickling process of white-fleshed and dark-fleshed fish with high-fat, to compare the changes of triacylglycerols (TAGs) and fatty acids (FAs) in round scad (Decapterus maruadsi, dark-fleshed) and hairtail (Trichiurus lepturus, white-fleshed) during salt-dried processing, ESI-MS/MS and GC-MS techniques were used to quantify. Lipid oxidation was evaluated via peroxide values (POVs), and thiobarbituric reactive substances (TBARS). A total of 31 and 27 FAs, 45 and 44 TAGs were quantified in round scad and hairtail, respectively. DHA (C22:6n3), palmitic acid (C16:0), stearic acid (C18:0), and oleic acid (C18:1n9) were the main FAs in round scad. POO (16:0/18:1/18:1), PPO (16:0/16:0/18:1), POD (16:0/18:1/22:6), and PPaO (16:0/16:1/18:1) were dominant TAGs in both species. Salt-dried processing significantly affected (p < 0.001) 7/5 FAs and 24/29 TAGs in round scad/hairtail. MUFAs changed significantly (p < 0.05) in dark-fleshed round scad; only SFAs and PUFAs changed in white-fleshed hairtail. Both species exhibited near-identical TAG compositions with different variation trends. More significant changes were observed in FAs at the half-dried stages and in TAGs (p < 0.05) at the salted stage. This coincided with the changing stages of POV and TBARS values that also increased significantly (p < 0.05) at the salted stages but peaked at the half-dried stages of both species.

Macrophage activation determines the fate of biomaterials implantation. Though researches have shown that fibronectin (FN) is highly involved in integrin-induced macrophage activation on biomaterials, the mechanism of how nanosized structure affects macrophage behavior is still unknown. Here, titanium dioxide nanotube structures with different sizes are fabricated to investigate the effects of nanostructure on macrophage activation. Compared with larger sized nanotubes and smooth surface, 30 nm nanotubes exhibit considerable lesser pro-inflammatory properties on macrophage differentiation. Confocal protein observation and molecular dynamics simulation show that FN displays conformation changes on different nanotubes in a feature of "size-confined," which causes the hiding of Arg-Gly-Asp (RGD) domain on other surfaces. The matching size of nanotube with FN allows the maximum exposure of RGD on 30 nm nanotubes, activating integrin-mediated focal adhesion kinase (FAK)-phosphatidylinositol-3 kinase γ (PI3Kγ) pathway to inhibit nuclear factor kappa B (NF-κB) signaling. In conclusion, this study explains the mechanism of nanostructural-biological signaling transduction in protein and molecular levels, as well as proposes a promising strategy for surface modification to regulate immune responses on bioimplants.

Fermented golden pomfret (Trachinotus ovatus) is appreciated by local consumers owing to its distinct flavor. Electronic nose (E-nose) and gas chromatography-ion mobility spectrometry (GC-IMS) technologies were used to analyze the changes in volatile compounds responsible for evolution of the golden pomfret odor profile during fermentation. Forty-two ion peaks were detected using GC-IMS. Although aldehydes represented the major initial volatile compound group, their levels decreased as fermentation proceeded. Between 3 and 15 days, increased levels of esters contributed to a stable volatile organic compounds profile. After 18 days, high levels of indole and pyrazines were detected. Eleven key volatile compounds were screened based on partial least squares discriminant analysis (PLS-DA). Back propagation artificial neural network (BP-ANN) predicted the fermentation stage enabling the development of better strategies to regulate golden pomfret fermentation. This study provided a theoretical basis for real-time monitoring and quality control of Chinese fermented golden pomfet.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global crisis, urgently necessitating the development of safe, efficacious, convenient-to-store, and low-cost vaccine options. A major challenge is that the receptor-binding domain (RBD)-only vaccine fails to trigger long-lasting protective immunity if used solely for vaccination. To enhance antigen processing and cross-presentation in draining lymph nodes (DLNs), we developed an interferon (IFN)-armed RBD dimerized by immunoglobulin fragment (I-R-F). I-R-F efficiently directs immunity against RBD to DLN. A low dose of I-R-F induces not only high titer long-lasting neutralizing antibodies but also comprehensive T cell responses than RBD, and even provides comprehensive protection in one dose without adjuvant. This study shows that the I-R-F vaccine provides rapid and complete protection throughout upper and lower respiratory tracts against high dose SARS-CoV-2 challenge in rhesus macaques. Due to its potency and safety, this engineered vaccine may become one of the next-generation vaccine candidates in the global race to defeat COVID-19.

Background Microsatellite instability (MSI) and Epstein-Barr virus (EBV)-positive molecular subtypes exhibit complex immune responses in gastric cancer (GC), and PD-L1 has emerged as a prognostic biomarker associated with the cancer immune microenvironment. This study aimed to determine the prognostic value of molecular subtypes and whether the addition of PD-L1 would accurately predict the prognosis and guide postoperative chemotherapy for GC patients. Methods We performed molecular subtyping of tissue microarray slides from 226 GC patients who were treated with radical gastrectomy. The MSI status and PD-L1 expression were evaluated through immunohistochemistry (IHC) and EBV status through situ hybridization. Multiplex polymerase chain reaction (PCR) was also performed on 50 cases to validate the accuracy of IHC in defining MSI status. Differences in overall survival (OS) were assessed using the Kaplan-Meier method, log-rank test and Cox proportional hazards regression model. Results Among the 226 GC patients, 52 (23.2%) patients were classified as the MSI subtype, 11 (4.9%) were EBV+ subtype, and 161 (71.9%) were MSS (Microsatellite stable) /EBV− subtype according to TCGA analysis. Two patients were both positive for MSI and EBV infection. EBV+ cases showed higher PD-L1 positivity than MSI cases and MSS/EBV− cases (81.8% vs. 50.0% vs. 35.4%, P = 0.003). Compared with the non-MSS/EBV− (MSI or EBV+ cases) subgroup, GC patients with MSS/EBV− were associated with the worst outcomes (HR = 1.610, 95% CI [1.046–2.479], P = 0.031). MSS/EBV− GCs alone could benefit from postoperative chemotherapy (HR = 0.452, 95% CI [0.299–0.682], P P = 0.033) in this subgroup. Considering both chemotherapy efficacy and PD-L1 expression in the MSS/EBV− subgroup, chemotherapy could improve the prognosis for PD-L1-negative MSS/EBV− GCs (HR = 0.357, 95% CI [0.217–0.587], P − GCs. Conclusions Molecular subtyping combined with PD-L1 expression could serve as a potential strategy to better predict prognosis and guide postoperative chemotherapy of GC patients.