Systematic discovery of DNA-binding tandem repeat proteins.

Tandem repeat proteins (TRPs) are widely distributed and bind to a wide variety of ligands. DNA-binding TRPs such as zinc finger (ZNF) and transcription activator-like effector (TALE) play important roles in biology and biotechnology. In this study, we first conducted an extensive analysis of TRPs in public databases, and found that the enormous diversity of TRPs is largely unexplored. We then focused our efforts on identifying novel TRPs possessing DNA-binding capabilities. We established a protein language model for DNA-binding protein prediction (PLM-DBPPred), and predicted a large number of DNA-binding TRPs. A subset was then selected for experimental screening, leading to the identification of 11 novel DNA-binding TRPs, with six showing sequence specificity. Notably, members of the STAR (Short TALE-like Repeat proteins) family can be programmed to target specific 9 bp DNA sequences with high affinity. Leveraging this property, we generated artificial transcription factors using reprogrammed STAR proteins and achieved targeted activation of endogenous gene sets. Furthermore, the members of novel families such as MOON (Marine Organism-Originated DNA binding protein) and pTERF (prokaryotic mTERF-like protein) exhibit unique features and distinct DNA-binding characteristics, revealing interesting biological clues. Our study expands the diversity of DNA-binding TRPs, and demonstrates that a systematic approach greatly enhances the discovery of new biological insights and tools.

PLM_Sol: predicting protein solubility by benchmarking multiple protein language models with the updated Escherichia coli protein solubility dataset.

Protein solubility plays a crucial role in various biotechnological, industrial, and biomedical applications. With the reduction in sequencing and gene synthesis costs, the adoption of high-throughput experimental screening coupled with tailored bioinformatic prediction has witnessed a rapidly growing trend for the development of novel functional enzymes of interest (EOI). High protein solubility rates are essential in this process and accurate prediction of solubility is a challenging task. As deep learning technology continues to evolve, attention-based protein language models (PLMs) can extract intrinsic information from protein sequences to a greater extent. Leveraging these models along with the increasing availability of protein solubility data inferred from structural database like the Protein Data Bank holds great potential to enhance the prediction of protein solubility. In this study, we curated an Updated Escherichia coli protein Solubility DataSet (UESolDS) and employed a combination of multiple PLMs and classification layers to predict protein solubility. The resulting best-performing model, named Protein Language Model-based protein Solubility prediction model (PLM_Sol), demonstrated significant improvements over previous reported models, achieving a notable 6.4% increase in accuracy, 9.0% increase in F1_score, and 11.1% increase in Matthews correlation coefficient score on the independent test set. Moreover, additional evaluation utilizing our in-house synthesized protein resource as test data, encompassing diverse types of enzymes, also showcased the good performance of PLM_Sol. Overall, PLM_Sol exhibited consistent and promising performance across both independent test set and experimental set, thereby making it well suited for facilitating large-scale EOI studies. PLM_Sol is available as a standalone program and as an easy-to-use model at https://zenodo.org/doi/10.5281/zenodo.10675340.

Heterologous survey of 130 DNA transposons in human cells highlights their functional divergence and expands the genome engineering toolbox.

Experimental studies on DNA transposable elements (TEs) have been limited in scale, leading to a lack of understanding of the factors influencing transposition activity, evolutionary dynamics, and application potential as genome engineering tools. We predicted 130 active DNA TEs from 102 metazoan genomes and evaluated their activity in human cells. We identified 40 active (integration-competent) TEs, surpassing the cumulative number (20) of TEs found previously. With this unified comparative data, we found that the Tc1/mariner superfamily exhibits elevated activity, potentially explaining their pervasive horizontal transfers. Further functional characterization of TEs revealed additional divergence in features such as insertion bias. Remarkably, in CAR-T therapy for hematological and solid tumors, Mariner2_AG (MAG), the most active DNA TE identified, largely outperformed two widely used vectors, the lentiviral vector and the TE-based vector SB100X. Overall, this study highlights the varied transposition features and evolutionary dynamics of DNA TEs and increases the TE toolbox diversity.

Estrogen Induces LCAT to Maintain Cholesterol Homeostasis and Suppress Hepatocellular Carcinoma Development.

Hepatocellular carcinoma (HCC) is an aggressive disease that occurs predominantly in men. Estrogen elicits protective effects against HCC development. Elucidation of the estrogen-regulated biological processes that suppress HCC could lead to improved prevention and treatment strategies. Here, we performed transcriptomic analyses on mouse and human liver cancer and identified lecithin cholesterol acyltransferase (LCAT) as the most highly estrogen-upregulated gene and a biomarker of favorable prognosis. LCAT upregulation inhibited HCC in vitro and in vivo and mediated estrogen-induced suppression of HCC in an ESR1-dependent manner. LCAT facilitated high-density lipoprotein cholesterol production and uptake via the LDLR and SCARB1 pathways. Consistently, high HDL-C levels corresponded to a favorable prognosis in HCC patients. The enhanced HDL-C absorption induced by LCAT impaired SREBP2 maturation, which ultimately suppressed cholesterol biosynthesis and dampened HCC cell proliferation. HDL-C alone inhibited HCC growth comparably to the cholesterol-lowering drug lovastatin, and SREBF2 overexpression abolished the inhibitory activity of LCAT. Clinical observations and cross-analyses of multiple databases confirmed the correlation of elevated LCAT and HDL-C levels to reduced cholesterol synthesis and improved HCC patient prognosis. Furthermore, LCAT deficiency mimicked whereas LCAT overexpression abrogated the tumor growth-promoting effects of ovariectomy in HCC-bearing female mice. Most importantly, HDL-C and LCAT delayed the development of subcutaneous tumors in nude mice, and HDL-C synergized with lenvatinib to eradicate orthotopic liver tumors. Collectively, this study reveals that estrogen upregulates LCAT to maintain cholesterol homeostasis and to dampen hepatocarcinogenesis. LCAT and HDL-C represent potential prognostic and therapeutic biomarkers for targeting cholesterol homeostasis as a strategy for treating HCC. Significance: Estrogen mediates the sex differences in hepatocellular carcinoma development by reducing cholesterol biosynthesis through activation of an LCAT/HDL-C axis, providing strategies for improving liver cancer prevention, prognosis, and treatment.

Nuclear RNA homeostasis promotes systems-level coordination of cell fate and senescence.

Understanding cellular coordination remains a challenge despite knowledge of individual pathways. The RNA exosome, targeting a wide range of RNA substrates, is often downregulated in cellular senescence. Utilizing an auxin-inducible system, we observed that RNA exosome depletion in embryonic stem cells significantly affects the transcriptome and proteome, causing pluripotency loss and pre-senescence onset. Mechanistically, exosome depletion triggers acute nuclear RNA aggregation, disrupting nuclear RNA-protein equilibrium. This disturbance limits nuclear protein availability and hinders polymerase initiation and engagement, reducing gene transcription. Concurrently, it promptly disrupts nucleolar transcription, ribosomal processes, and nuclear exporting, resulting in a translational shutdown. Prolonged exosome depletion induces nuclear structural changes resembling senescent cells, including aberrant chromatin compaction, chromocenter disassembly, and intensified heterochromatic foci. These effects suggest that the dynamic turnover of nuclear RNA orchestrates crosstalk between essential processes to optimize cellular function. Disruptions in nuclear RNA homeostasis result in systemic functional decline, altering the cell state and promoting senescence.

Impact of the COVID-19 pandemic on the prevalence of respiratory viral pathogens in patients with acute respiratory infection in Shanghai, China.

Objective: This study aimed to evaluate the impact of nonpharmaceutical interventions (NPIs) taken to combat COVID-19 on the prevalence of respiratory viruses (RVs) of acute respiratory infections (ARIs) in Shanghai. Methods: Samples from ARI patients were collected and screened for 17 respiratory viral pathogens using TagMan low density microfluidic chip technology in Shanghai from January 2019 to December 2020. Pathogen data were analyzed to assess changes in acute respiratory infections between 2019 and 2020. Results: A total of 2,744 patients were enrolled, including 1,710 and 1,034 in 2019 and 2020, respectively. The total detection rate of RVs decreased by 149.74% in 2020. However, detection rates for human respiratory syncytial virus B (RSVB), human coronavirus 229E (HCoV229E), human coronavirus NL63 (HCoVNL63), and human parainfluenza virus 3 (HPIV3) increased by 91.89, 58.33, 44.68 and 24.29%, in 2020. The increased positive rates of RSVB, HPIV3, resulted in more outpatients in 2020 than in 2019. IFV detection rates declined dramatically across gender, age groups, and seasons in 2020. Conclusion: NPIs taken to eliminate COVID-19 had an impact on the prevalence of respiratory viral pathogens, especially the IFVs in the early phases of the pandemic. Partial respiratory viruses resurged with the lifting of NPIs, leading to an increase in ARIs infection.

Corrigendum: From function to metabolome: metabolomic analysis reveals the effect of probiotic fermentation on the chemical compositions and biological activities of Perilla frutescens leaves.

[This corrects the article DOI: 10.3389/fnut.2022.933193.].

The Impact of AAPH-Induced Oxidation on the Functional and Structural Properties, and Proteomics of Arachin.

The aim of this study was to investigate the effect of 2,2'-azobis (2-amidinopropane) dihydrochloride (AAPH)-induced oxidation on the functional, structural properties and proteomic information of arachin. The results showed that moderate oxidation improved the water/oil holding capacity of proteins and increased the emulsifying stability, while excessive oxidation increased the carbonyl content, reduced the thiol content, altered the structure and thermal stability, and reduced most of the physicochemical properties. Through LC-QE-MS analysis, it was observed that oxidation leads to various modifications in arachin, including carbamylation, oxidation, and reduction, among others. In addition, 15 differentially expressed proteins were identified. Through gene ontology (GO) analysis, these proteins primarily affected the cellular and metabolic processes in the biological process category. Further Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed that the "proteasome; protein processing in the endoplasmic reticulum (PPER)" pathway was the most significantly enriched signaling pathway during the oxidation process of arachin. In conclusion, this study demonstrated that AAPH-induced oxidation can alter the conformation and proteome of arachin, thereby affecting its corresponding functional properties. The findings of this study can potentially serve as a theoretical basis and foundational reference for the management of peanut processing and storage.

Establishing an emission inventory for ammonia, a key driver of haze formation in the southern North China plain during the COVID-19 pandemic.

Despite the significant reduction in atmospheric pollutant levels during the COVID-19 lockdown, the presence of haze in the North China Plain remained a frequent occurrence owing to the enhanced formation of secondary inorganic aerosols under ammonia-rich conditions. Quantifying the increase or decrease in atmospheric ammonia (NH3) emissions is a key step in exploring the causes of the COVID-19 haze. Historic activity levels of anthropogenic NH3 emissions were collected through various yearbooks and studies, an anthropogenic NH3 emission inventory for Henan Province for 2020 was established, and the variations in NH3 emissions from different sources between COVID-19 and non-COVID-19 years were investigated. The validity of the NH3 emission inventory was further evaluated through comparison with previous studies and uncertainty analysis from Monte Carlo simulations. Results showed that the total NH3 emissions gradually increased from north-west to south-east, totalling 751.80 kt in 2020. Compared to the non-COVID-19 year of 2019, the total NH3 emissions were reduced by approximately 4 %, with traffic sources, waste disposal and biomass burning serving as the sources with the top three largest reductions, approximately 33 %, 9.97 % and 6.19 %, respectively. Emissions from humans and fuel combustion slightly increased. Meanwhile, livestock waste emissions decreased by only 3.72 %, and other agricultural emissions experienced insignificant change. Non-agricultural sources were more severely influenced by the COVID-19 lockdown than agricultural sources; nevertheless, agricultural activities contributed 84.35 % of the total NH3 emissions in 2020. These results show that haze treatment should be focused on reducing NH3, particularly controlling agricultural NH3 emissions.

Characterization and sources of water-soluble inorganic ions during sulfate-driven and nitrate-driven haze on the largest loess accumulation plateau.

With the rapid reduction of anthropogenic SO2 emissions, the critical driver of haze in China has shifted from being dominated by sulfate to alternating sulfate and nitrate. Haze induced by different driver species may differ in the chemical forms of water-soluble inorganic ions (WSIIs). The unique topography and high-emission industrial agglomeration of the Loess Plateau determine its severe local PM2.5 pollution and influence global weather patterns through the outward export of pollutants. PM2.5 samples were conducted in Pingyao, on the eastern Loess Plateau of China, in autumn and winter. The average mass of PM2.5 was 88.82 ± 57.37 µg/m3; sulfate, nitrate, and ammonium were the dominant component. The chemical form of the ion was dominated by (NH4)2SO4, NH4NO3, NaNO3 and KNO3 during the nitrate-driven (ND) haze, while (NH4)2SO4, NH4HSO4, NH4NO3, NaNO3 and KNO3 were predominant species during the sulfate-driven (SD) haze. Heterogeneous oxidation reactions dominated the mechanism of sulfate formation. Primary sulfate emissions or other generation pathways contributed to sulfate formation during the SD haze. The gas-phase homogeneous reaction of NO2 and NH3 dominates the nitrate generation during the ND haze. The heterogeneous reactions also played an essential role during the SD haze. Nitrate aerosol (42.30%) and coal and biomass combustion (23.23%) were the dominant sources of WSIIs during the ND haze. In comparison, nitrate aerosol (31.80%) and sulfate aerosol (25.08%) were considered the primary control direction during the SD haze. The chemical characteristics and sources of aerosols under various types of haze differ significantly, and knowledge gained from this investigation provides insight into the causes of heavy haze.

Chemical Constituents, Antioxidant, and α-Glucosidase Inhibitory Activities of Different Fermented Gynostemma Pentaphyllum Leaves and Untargeted Metabolomic Measurement of the Metabolite Variation.

To assess the effects of microbial fermentation on Gynostemma pentaphyllum leaves (GPL), four probiotics were used to ferment GPL (FGPL) for 7 days. At different stages of fermentation, changes in the active components and biological activities of FGPL were determined. The findings suggest that short-term fermentation with probiotics can enhance both the content and bioactivity of active components in GPL. However, prolonged fermentation may lead to a decline in these aspects. Among them, the best effect was observed with SWFU D16 fermentation for 2 days. This significantly improved the total phenolic and total flavonoid content, antioxidant capacity, and inhibitory ability against α-glucosidase activity with an increase of 28%, 114.82%, 7.42%, and 31.8%, respectively. The high-performance liquid chromatography (HPLC) analysis results also supported this trend. Untargeted metabolomics analysis revealed metabolite changes between GPL and FGPL and the key metabolites associated with these functional activities. These key metabolites are mainly organic acids, flavonoids, carbohydrates, terpenoids, and other substances. KEGG analysis demonstrated that microbial metabolism in diverse environments and carbon metabolism were the most significantly enriched pathways. Among them, 3-(3-hydroxyphenyl) propanoic acid, d-glucose, gallic acid, gluconic acid, l-lactic acid, and l-malic acid were mostly involved in the microbial metabolism of diverse environmental pathways. In contrast, D-glucose, gluconic acid, and l-malic acid were mainly related to the carbon metabolism pathway. This study revealed the positive effect of probiotic fermentation on GPL and its potential metabolism mechanism, which could provide supporting data for further research.

Decreased propionyl-CoA metabolism facilitates metabolic reprogramming and promotes hepatocellular carcinoma.

BACKGROUND & AIMS: Alterations of multiple metabolites characterize distinct features of metabolic reprograming in hepatocellular carcinoma (HCC). However, the role of most metabolites, including propionyl-CoA (Pro-CoA), in metabolic reprogramming and hepatocarcinogenesis remains elusive. In this study, we aimed to dissect how Pro-CoA metabolism affects these processes. METHODS: TCGA data and HCC samples were used to analyze ALDH6A1-mediated Pro-CoA metabolism and its correlation with HCC. Multiple metabolites were assayed by targeted mass spectrometry. The role of ALDH6A1-generated Pro-CoA in HCC was evaluated in HCC cell lines as well as xenograft nude mouse models and primary liver cancer mouse models. Non-targeted metabolomic and targeted energy metabolomic analyses, as well as multiple biochemical assays, were performed. RESULTS: Decreases in Pro-CoA and its derivative propionyl-L-carnitine due to ALDH6A1 downregulation were tightly associated with HCC. Functionally, ALDH6A1-mediated Pro-CoA metabolism suppressed HCC proliferation in vitro and impaired hepatocarcinogenesis in mice. The aldehyde dehydrogenase activity was indispensable for this function of ALDH6A1, while Pro-CoA carboxylases antagonized ALDH6A1 function by eliminating Pro-CoA. Mechanistically, ALDH6A1 caused a signature enrichment of central carbon metabolism in cancer and impaired energy metabolism: ALDH6A1-generated Pro-CoA suppressed citrate synthase activity, which subsequently reduced tricarboxylic acid cycle flux, impaired mitochondrial respiration and membrane potential, and decreased ATP production. Moreover, Pro-CoA metabolism generated 2-methylcitric acid, which mimicked the inhibitory effect of Pro-CoA on citrate synthase and dampened mitochondrial respiration and HCC proliferation. CONCLUSIONS: The decline of ALDH6A1-mediated Pro-CoA metabolism contributes to metabolic remodeling and facilitates hepatocarcinogenesis. Pro-CoA, propionyl-L-carnitine and 2-methylcitric acid may serve as novel metabolic biomarkers for the diagnosis and treatment of HCC. Pro-CoA metabolism may provide potential targets for development of novel strategies against HCC. IMPACT AND IMPLICATIONS: Our study presents new insights on the role of propionyl-CoA metabolism in metabolic reprogramming and hepatocarcinogenesis. This work has uncovered potential diagnostic and predictive biomarkers, which could be used by physicians to improve clinical practice and may also serve as targets for the development of therapeutic strategies against HCC.

Prediction of ground-level ozone by SOM-NARX hybrid neural network based on the correlation of predictors.

Current approaches to ozone prediction using hybrid neural networks are numerous but not perfect. Decomposition algorithms ignore the correlation between predictors and ozone, and feature extraction methods rarely select appropriate predictors in terms of correlation, especially for VOCs. Therefore, this study proposes a hybrid neural network model SOM-NARX based on the correlation of predictors. The model is based on MIC to filter predictors, using SOM to make predictors as feature sequences and using NARX networks to make predictions. Data from the JCDZURI site were used for training, testing, and validation. The results show that the correlation of the predictors, classification numbers of SOM, neuron numbers, and delay steps can affect prediction accuracy. Model comparison shows that the SOM-NARX model has 13.82, 10.60, 6.58% and 12.05, 9.44, 68.14% RMSE, MAE, and MAEP in winter and summer, which is smaller than CNN-LSTM, CNN-BiLSTM, CNN-GRU, SOM-LSTM, SOM-BiLSTM, and SOM-GRU.

DNASE1L3 inhibits hepatocellular carcinoma by delaying cell cycle progression through CDK2.

PURPOSE: Dysregulated cell cycle targeting is a well-established therapeutic strategy against hepatocellular carcinoma (HCC). Dissecting the underlying mechanism may improve the efficacy of HCC therapy. METHODS: HCC data from TCGA and new clinical samples were used for DNASE1L3 expression analysis and for assessing its correlation with HCC development. The in vitro function of DNASE1L3 in HCC cell proliferation, colony formation, migration and invasion was assessed using RTCA, CCK-8 and transwell assays and the in vivo function in subcutaneous tumor formation in a xenograft nude mouse model. The role of DNASE1L3 in HCC tumorigenesis was further verified in AKT/NRASV12-induced and DEN/CCl4-induced primary liver cancers in wildtype and Dnase1l3-/- mice. Finally, RNA-Seq analysis followed by biochemical methods including cell cycle, immunofluorescence, co-immunoprecipitation and Western blotting assays were employed to reveal the underlying mechanism. RESULTS: We found that DNASE1L3 was significantly downregulated and served as a favorable prognostic factor in HCC. DNASE1L3 dramatically attenuated HCC cell proliferation, colony formation, migration and invasion in vitro and reduced subcutaneous tumor formation in nude mice in vivo. Furthermore, DNASE1L3 overexpression dampened AKT/NRASV12-induced mouse liver cancer in wildtype mice and DNASE1L3 deficiency worsened DEN/CCl4-induced liver cancer in Dnase1l3-/- mice. Systemic analysis revealed that DNASE1L3 impaired HCC cell cycle progression by interacting with CDK2 and inhibiting CDK2-stimulated E2F1 activity. C-terminal deletion (DNASE1L3ΔCT) diminished the interaction with CDK2 and abrogated the inhibitory function against HCC. CONCLUSION: Our study unveils DNASE1L3 as a novel HCC cell cycle regulator and tumor suppressor. DNASE1L3 impairs HCC tumorigenesis by delaying cell cycle progression possibly through disrupting the positive E2F1-CDK2 regulatory loop. DNASE1L3 may serve as a target for the development of novel therapeutic strategies against HCC.

Genome-wide characterization of the chitinase gene family in wild apple (Malus sieversii) and domesticated apple (Malus domestica) reveals its role in resistance to Valsa mali.

Chitinases are responsible for catalyzing the hydrolysis of chitin and contribute to plant defense against fungal pathogens by degrading fungal chitin. In this study, genome-wide identification of the chitinase gene family of wild apple (Malus sieversii) and domesticated apple (Malus domestica) was conducted, and the expression profile was analyzed in response to Valsa mali infection. A total of 36 and 47 chitinase genes belonging to the glycosyl hydrolase 18 (GH18) and 19 (GH19) families were identified in the genomes of M. sieversii and M. domestica, respectively. These genes were classified into five classes based on their phylogenetic relationships and conserved catalytic domains. The genes were randomly distributed on the chromosomes and exhibited expansion by tandem and segmental duplication. Eight of the 36 MsChi genes and 17 of the 47 MdChi genes were differentially expressed in response to V. mali inoculation. In particular, MsChi35 and its ortholog MdChi41, a class IV chitinase, were constitutively expressed at high levels in M. sieversii and domesticated apple, respectively, and may play a crucial role in the defense response against V. mali. These results improve knowledge of the chitinase gene family in apple species and provide a foundation for further studies of fungal disease prevention in apple.

A preliminary study of the chemical composition and bioactivity of Bombax ceiba L. flower and its potential mechanism in treating type 2 diabetes mellitus using ultra-performance liquid chromatography quadrupole-time-flight mass spectrometry and network pharmacology analysis.

This study aimed to preliminary investigate the phytochemistry, bioactivity, hypoglycemic potential, and mechanism of action of Bombax ceiba L. flower (BCF), a wild edible and food plant in China. By using methanol extraction and liquid-liquid extraction, the crude extract (CE) of BCF and its petroleum ether (PE), dichloromethane (DCM), ethyl acetate (EtOAc), n-butanol (n-BuOH), and aqueous (AQ) fractions were obtained, and their chemical components and biological activities were evaluated. Further high-performance liquid chromatography (HPLC) analysis was carried out to identify and quantify the active constituents of BFC and its five fractions, and the phytochemical composition of the best-performing fraction was then analyzed by ultra-performance liquid chromatography quadrupole-time-flight mass spectrometry (UPLC/Q-TOF-MS). Finally, a network pharmacology strategy based on the chemical profile of this fraction was applied to speculate its main hypoglycemic mechanism. Results revealed the excellent biological activities of BCF, especially the EtOAc fraction. In addition to the highest total flavonoid content (TFC) (367.72 µg RE/mg E) and total phenolics content (TPC) (47.97 µg GAE/mg E), EtOAc showed the strongest DPPH⋅ scavenging ability (IC50 value = 29.56 µg/mL), ABTS⋅+ scavenging ability (IC50 value = 84.60 µg/mL), and ferric reducing antioxidant power (FRAP) (889.62 µg FeSO4/mg E), which were stronger than the positive control BHT. EtOAc also exhibited the second-best α-glucosidase inhibitory capacity and second-best acetylcholinesterase (AChE) inhibitory capacity with the IC50 values of 2.85 and 3.27 mg/mL, respectively. Also, EtOAc inhibited HepG2, MCF-7, Raw264.7, and A549 cell with IC50 values of 1.08, 1.62, 0.77, and 0.87 mg/mL, which were the second or third strongest in all fractions. Additionally, HPLC analysis revealed significant differences in the compounds' abundance between different fractions. Among them, EtOAc had the most detected compounds and the highest content. According to the results of UPLC/Q-TOF-MS, 38 compounds were identified in EtOAc, including 24 phenolic acids and 6 flavonoids. Network pharmacological analysis further confirmed 41 potential targets of EtOAc in the treatment of type 2 diabetes, and intracellular receptor signaling pathways, unsaturated fatty acid, and DNA transcription pathways were the most possible mechanisms. These findings suggested that BCF was worthwhile to be developed as an antioxidant and anti-diabetic food/drug.

Obesity caused by an OVOL2 mutation reveals dual roles of OVOL2 in promoting thermogenesis and limiting white adipogenesis.

Using random germline mutagenesis in mice, we identified a viable hypomorphic allele (boh) of the transcription-factor-encoding gene Ovol2 that resulted in obesity, which initially developed with normal food intake and physical activity but decreased energy expenditure. Fat weight was dramatically increased, while lean weight was reduced in 12-week-old boh homozygous mice, culminating by 24 weeks in massive obesity, hepatosteatosis, insulin resistance, and diabetes. The Ovol2boh/boh genotype augmented obesity in Lepob/ob mice, and pair-feeding failed to normalize obesity in Ovol2boh/boh mice. OVOL2-deficient mice were extremely cold intolerant. OVOL2 is essential for brown/beige adipose tissue-mediated thermogenesis. In white adipose tissues, OVOL2 limited adipogenesis by blocking C/EBPα engagement of its transcriptional targets. Overexpression of OVOL2 in adipocytes of mice fed with a high-fat diet reduced total body and liver fat and improved insulin sensitivity. Our data reveal that OVOL2 plays dual functions in thermogenesis and adipogenesis to maintain energy balance.

Probiotic fermentation improves the bioactivities and bioaccessibility of polyphenols in Dendrobium officinale under in vitro simulated gastrointestinal digestion and fecal fermentation.

The objective of the research was to investigate and compare the bioactivities and bioaccessibility of the polyphenols (PPs) from Dendrobium officinale (DO) and probiotic fermented Dendrobium officinale (FDO), by using in vitro simulated digestion model under oral, gastric and intestinal phases as well as colonic fermentation. The results indicated that FDO possessed significantly higher total phenolic contents (TPC) and total flavonoid contents (TFC) than DO, and they were released most in the intestinal digestion phase with 6.96 ± 0.99 mg GAE/g DE and 10.70 ± 1.31 mg RE/g DE, respectively. Using high-performance liquid chromatography (HPLC), a total of six phenolic acids and four flavonoids were detected. In the intestinal phase, syringaldehyde and ferulic acid were major released by DO, whereas they were p-hydroxybenzoic acid, vanillic acid, and syringic acid for FDO. However, apigenin and scutellarin were sustained throughout the digestion whether DO or FDO. As the digestive process progressed, their antioxidant ability, α-amylase and α-glucosidase inhibitory activities were increased, and FDO was overall substantially stronger in these activities than that of DO. Both DO and FDO could reduce pH values in the colonic fermentation system, and enhance the contents of short-chain fatty acids, but there were no significantly different between them. The results of the 16S rRNA gene sequence analysis showed that both DO and FDO could alter intestinal microbial diversity during in vitro colonic fermentation. In particular, after colonic fermentation for 24 h, FDO could significantly improve the ratio of Firmicutes to Bacteroidetes, and enrich the abundancy of Enterococcus and Bifidobacterium (p < 0.05), which was most likely through the carbohydrate metabolism signal pathway. Taken together, the PPs from DO and FDO had good potential for antioxidant and modulation of gut bacterial flora during the digestive processes, and FDO had better bioactivities and bioaccessibility. This study could provide scientific data and novel insights for Dendrobium officinale to be developed as functional foods.

A comparative study of nutrient composition, bioactive properties and phytochemical characteristics of Stauntonia obovatifoliola flesh and pericarp.

A comparative study was conducted among the flesh (SOF) and pericarp (SOP) of Stauntonia obovatifoliola, a wild edible fruit in China. The nutrient composition of both these tissues was firstly quantified, and liquid-liquid extraction was then used to separate their methanolic extracts to get petroleum ether, chloroform, ethyl acetate, n-butanol, and residual aqueous fractions, which were evaluated for their total phenol content (TPC), total flavonoid content (TFC), antioxidant capacities, and α-glucosidase and acetylcholinesterase inhibition abilities. Finally, high-performance liquid chromatography (HPLC) was used to analyze their phytochemical composition. The results revealed the excellent nutritional properties of both SOF and SOP, especially SOP (total dietary fiber, 15.50 g/100 g; total amino acids, 0.80 g/100 g; vitamin C, 18.00 mg/100 g; Ca, 272.00 mg/kg; K, 402.00 mg/100 g). For both tissues, their ethyl acetate fractions showed the highest TPC (355.12 and 390.99 mg GAE/g DE) and TFC (306.58 and 298.48 mg RE/g DE). Surprisingly, the ethyl acetate fraction of SOP exhibited the strongest DPPH and ABTS radical scavenging capacity with 1046.94 and 1298.64 mg Trolox/g, respectively, which were higher than that of controls Vc and BHT. In contrast, their chloroform fractions exhibited the strongest ferric reducing antioxidant power (1903.05 and 1407.11 mg FeSO4/g DE) and oxygen radical absorbance capacity (951.12 and 1510.21 mg Trolox/g DE). In addition, the ethyl acetate fraction of SOF displayed superior α-glucosidase inhibition ability with the IC50 value of 0.19 mg/mL, which was comparable to control acarbose. In comparison, the ethyl acetate fraction of SOP had the best acetylcholinesterase inhibition ability with the IC50 value of 0.47 mg/mL. The HPLC analysis results demonstrated that the ethyl acetate fraction of SOP showed significantly higher phenolic content, particularly for phenolic acids (p-hydroxybenzoic acid, 8.00 ± 0.65 mg/g) and flavonoids (epicatechin, 28.63 ± 1.26 mg/g), as compared to other samples. The above results suggest that Stauntonia obovatifoliola, especially its pericarp, had excellent nutrient compositions, bioactive properties and phytochemical characteristics, and had the potential to be developed as natural functional food.

The influence of in vitro gastrointestinal digestion and fecal fermentation on the flowers of Juglans regia: Changes in the active compounds and bioactivities.

The objective of the research was to investigate the digestion and fecal fermentation characteristics of the flowers of Juglans regia (FJR), by using in vitro simulated digestion model (oral, gastric, and intestine) as well as colonic fermentation. As a result, the contents of most active substances and functional activities of FJR were decreased as the digestion proceeded, and showed a trend of first increasing and then decreasing in the fecal fermentation phase. In the oral digestion phase, the total phenolic and total flavonoid contents were released most with the values of 11.43 and 9.41 µg/mg, respectively. While in the gastric digestion phase, the antioxidant abilities, α-glucosidase and α-amylase inhibitory abilities were the weakest. By using high-performance liquid chromatography, 13 phenolic acids and 3 flavonoids were detected. Of these, the highest number of identified compounds were found in the undigested and the oral digestion stages, which were mainly salicylic acid, epicatechin, 3,5-dihydroxybenoic acid, vanillic acid, and protocatechuic acid. However, great losses were observed during the gastric and intestinal digestion stages, only epicatechin, salicylic acid, and protocatechuic acid were found. Surprisingly, fecal fermentation released more abundant phenolic substances compared to gastric and intestinal digestion. Additionally, FJR reduced the pH values in the colonic fermentation system, significantly promoted the production of short-chain fatty acids, and regulated the microbe community structure by improving the community richness of beneficial microbiota. This indicated that FJR had the benefit to improve the microorganismal environment in the intestine. Further Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that FJR could suppress the metabolic pathways related to diseases, such as infectious diseases, metabolic diseases and neurodegenerative diseases. In conclusion, although the bioactivities of FJR decreased significantly after in vitro gastrointestinal digestion and fecal fermentation, it still maintained certain antioxidant and hypoglycemic ability in vitro. This study described the detailed changes in the active compounds and bioactivities of FJR during in vitro gastrointestinal digestion and fecal fermentation, and its effects on microbiota composition and SCFAs levels in feces. Our results revealed the potential health benefits of FJR, and could provide a reference for its further research and development.