Effect of circadian rhythm change on gut microbiota and the development of nonalcoholic fatty liver disease in mice.

BACKGROUND: This study was to investigate the effect and possible mechanism of circadian rhythm change on the development of nonalcoholic fatty liver disease (NAFLD) in mice. METHODS: A total of 80 male SPF-grade 4-week C57BL/6J mice were randomly divided into normal diet normal light/dark cycle (ND-LD) and high-fat diet all dark (HFD-DD) groups. Weight measurements were taken weekly, and after 24 weeks of intervention, 24 mice from both groups were randomly selected and analyzed. Additionally, the remaining mice in the HFD-DD group were divided into two groups: one group continued the high-fat all-dark treatment (HFD-DD-DD), and the other group was restored to normal light/dark cycle treatment (HFD-DD-LD). Mice were euthanized after a total of 48 weeks of intervention. Measurements were taken for each mouse including liver function serum indicators, liver tissue pathological sections, rhythm-related proteins, and determination of the gut microbiota community. RESULTS: The HFD induced NAFLD in mice, exhibiting symptoms such as obesity, lipid and glucose metabolism disorders, elevated liver enzymes, and decreased gut microbiota diversity. The composition of the gut microbiota was significantly different from that of the normal diet group, with a significant increase in the ratio of Firmicutes to Bacteroides. Restoration of normal light/dark cycles exacerbated the disorder of lipid metabolism, liver steatosis, and the expression of BMAL1 in mice and significantly reduced the diversity of gut microbiota. CONCLUSIONS: Circadian rhythm changes aggravate the development of NAFLD induced by a high-fat diet by affecting glucose metabolism, liver steatosis, and gut microbiota diversity. Restoration of normal circadian rhythm did not improve NAFLD. Our findings open up new avenues for the prevention, diagnosis, and treatment of NAFLD.

Polyethylene fibers containing directional microchannels for passive radiative cooling.

Passive radiative cooling (PRC) that realizes thermal management without consuming any energy has attracted increasing attention. Unfortunately, polymer fibers with radiative cooling function fabricated via a facile, continuous, large-scale and eco-friendly method have been scarcely reported. Herein, polyethylene fibers containing directional microchannels (PFCDM) are facilely fabricated via melt extrusion and water leaching. Interestingly, fabric based on such hydrophobic PFCDM shows high sunlight reflectivity (93.6%), and mid-infrared emissivity (93.9%), endowing it with remarkable PRC performance. Compared with other reported examples, the as-prepared PFDCM fabric has the highest cooling power (i.e., 104.285 W m-2) and temperature drop (i.e., 27.71 °C). Furthermore, decent self-cleaning performance can keep the PFCDM fabric away from contamination and enable it to retain an excellent radiative cooling effect. The method proposed to fabricate PFCDM in this paper will widen the potential application of thermoplastic polyolefins in the field of radiative cooling.

MCAFNet: multiscale cross-layer attention fusion network for honeycomb lung lesion segmentation.

Accurate segmentation of honeycomb lung lesions from lung CT images plays a crucial role in the diagnosis and treatment of various lung diseases. However, the availability of algorithms for automatic segmentation of honeycomb lung lesions remains limited. In this study, we propose a novel multi-scale cross-layer attention fusion network (MCAFNet) specifically designed for the segmentation of honeycomb lung lesions, taking into account their shape specificity and similarity to surrounding vascular shadows. The MCAFNet incorporates several key modules to enhance the segmentation performance. Firstly, a multiscale aggregation (MIA) module is introduced in the input part to preserve spatial information during downsampling. Secondly, a cross-layer attention fusion (CAF) module is proposed to capture multiscale features by integrating channel information and spatial information from different layers of the feature maps. Lastly, a bidirectional attention gate (BAG) module is constructed within the skip connection to enhance the model's ability to filter out background information and focus on the segmentation target. Experimental results demonstrate the effectiveness of the proposed MCAFNet. On the honeycomb lung segmentation dataset, the network achieves an Intersection over Union (IoU) of 0.895, mean IoU (mIoU) of 0.921, and mean Dice coefficient (mDice) of 0.949, outperforming existing medical image segmentation algorithms. Furthermore, experiments conducted on additional datasets confirm the generalizability and robustness of the proposed model. The contribution of this study lies in the development of the MCAFNet, which addresses the lack of automated segmentation algorithms for honeycomb lung lesions. The proposed network demonstrates superior performance in accurately segmenting honeycomb lung lesions, thereby facilitating the diagnosis and treatment of lung diseases. This work contributes to the existing literature by presenting a novel approach that effectively combines multi-scale features and attention mechanisms for lung lesion segmentation. The code is available at https://github.com/Oran9er/MCAFNet .

Managing genomic diversity in conservation programs of Chinese domestic chickens.

BACKGROUND: Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations. RESULTS: Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (FST), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation. CONCLUSIONS: Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.

Therapeutic effect of fenofibrate for non-alcoholic steatohepatitis in mouse models is dependent on regime design.

Background: Non-alcoholic fatty liver disease (NAFLD) is the leading cause of chronic liver diseases. In most cases, NAFLD progresses from benign steatosis to steatohepatitis (NASH), and then to cirrhosis. No treatment is currently approved for NAFLD/NASH in the clinic. Fenofibrate (FENO) has been clinically used to treat dyslipidemia for more than a half century, but its effects on NASH are not established. FENO's half-life is quite different between rodent and human. The aim of this study was to investigate the potential of pharmacokinetic-based FENO regime for NASH treatment and the underlying mechanisms. Methods: Two typical mouse NASH models, methionine-choline deficient (MCD) diet-fed mice and choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD)-fed mice, were used. MCD model was designed as therapeutic evaluation in experiment 1 and CDAHFD model was designed as preventive in experiment 2. Three doses of FENO (5, 25, 125 mg/kg), two times a day (BID), were administered to the above models. Serum markers of liver injury, cholestasis, and the histology of liver tissues were investigated. Normal mice were used as a model in experiment 3 for toxicity evaluation, Quantitative-PCR and Western Blot assays were used to investigate the inflammatory responses, bile acid synthesis as well as lipid catabolism. Results: Mice on the MCD and CDAHFD diets developed steatohepatitis as expected. Treatment with FENO (25 mg/kg·BID) significantly decreased hepatic steatosis, inflammation and fibrosis in both therapeutic and preventive models. In the MCD model, the therapeutic action of FENO (25 mg/kg·BID) and 125 mg/kg·BID on histopathology and the expression of inflammatory cytokines were comparable. In reducing macrophage infiltration and bile acid load, FENO (25 mg/kg·BID) was superior to 125 mg/kg·BID. In all the aspects mentioned above, FENO (25 mg/kg·BID) was the best among the 3 doses in the CDAHFD model. In a third experiment, the effects of FENO (25 mg/kg·BID) and 125 mg/kg·BID on lipid catabolism were comparable, but 125 mg/kg·BID increased the expression of inflammatory factors and bile acid load. In both models, FENO (5 mg/kg·BID) showed little effect in hepatic steatosis and inflammation, neither the adverse effects. FENO (125 mg/kg·BID) aggravated liver inflammation, increased bile acid synthesis, and promoted the potential of liver proliferation. In toxicity risk assay, FENO (25 mg/kg·BID) treatment showed low potential to trigger bile acid synthesis, inflammation and hepatocyte proliferation. Conclusion: A new regime, FENO (25 mg/kg·BID) is potentially a therapeutic strategy for the NASH treatment. Translational medicine is warranted to prove its effectiveness in the clinic.

Identification of disease-related genes and construction of a gene co-expression database in non-alcoholic fatty liver disease.

Background: The mechanism of NAFLD progression remains incompletely understood. Current gene-centric analysis methods lack reproducibility in transcriptomic studies. Methods: A compendium of NAFLD tissue transcriptome datasets was analyzed. Gene co-expression modules were identified in the RNA-seq dataset GSE135251. Module genes were analyzed in the R gProfiler package for functional annotation. Module stability was assessed by sampling. Module reproducibility was analyzed by the ModulePreservation function in the WGCNA package. Analysis of variance (ANOVA) and Student's t-test was used to identify differential modules. The receiver operating characteristic (ROC) curve was used to illustrate the classification performance of modules. Connectivity Map was used to mine potential drugs for NAFLD treatment. Results: Sixteen gene co-expression modules were identified in NAFLD. These modules were associated with multiple functions such as nucleus, translation, transcription factors, vesicle, immune response, mitochondrion, collagen, and sterol biosynthesis. These modules were stable and reproducible in the other 10 datasets. Two modules were positively associated with steatosis and fibrosis and were differentially expressed between non-alcoholic steatohepatitis (NASH) and non-alcoholic fatty liver (NAFL). Three modules can efficiently separate control and NAFL. Four modules can separate NAFL and NASH. Two endoplasmic reticulum related modules were both upregulated in NAFL and NASH compared to normal control. Proportions of fibroblasts and M1 macrophages are positively correlated with fibrosis. Two hub genes Aebp1 and Fdft1 may play important roles in fibrosis and steatosis. m6A genes were strongly correlated with the expression of modules. Eight candidate drugs for NAFLD treatment were proposed. Finally, an easy-to-use NAFLD gene co-expression database was developed (available at https://nafld.shinyapps.io/shiny/). Conclusion: Two gene modules show good performance in stratifying NAFLD patients. The modules and hub genes may provide targets for disease treatment.

Oral vaccination with recombinant Lactobacillus casei with surface displayed OmpK fused to CTB as an adjuvant against Vibrio mimicus infection in Carassius auratus.

Vibrio mimicus (V. mimicus) is a pathogenic bacterium that causes diseases in humans and various aquatic animals. A particularly efficient way to provide protection against V. mimicus is through vaccination. However, there are few commercial vaccines against V. mimics, especially oral vaccines. In our study, two surface-display recombinant Lactobacillus casei (L. casei) Lc-pPG-OmpK and Lc-pPG-OmpK-CTB were constructed using L. casei ATCC393 as an antigen delivery vector, outer membrane protein K (OmpK) of V. mimicus as an antigen, and cholera toxin B subunit (CTB) as a molecular adjuvant; furthermore, the immunological effects of recombinant L.casei in Carassius auratus (C. auratus) were assessed. The results indicated that oral recombinant L.casei Lc-pPG-OmpK and Lc-pPG-OmpK-CTB stimulated higher levels of serum-specific immunoglobulin M (IgM) and increased the activity of acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase (SOD), lysozyme (LYS), lectin, C3, and C4 in C. auratus, compared with control groups (Lc-pPG group and PBS group). Furthermore, the expression of interleukin-1ß (IL-1ß), interleukin-10 (IL-10), tumor necrosis factor-α (TNF-α), and transforming growth factor-ß (TGF-ß) in the liver, spleen, head kidney, hind intestine and gills of C. auratus was significantly increased, compared with that in the controls. These results demonstrated that the two recombinant L. casei strains could effectively trigger humoral and cellular immunity in C. auratus. In addition, two recombinant L.casei strains were able to survive and colonize the intestine of C. auratus. Importantly, after being challenged with V. mimicus, C. auratus fed Lc-pPG-OmpK and Lc-pPG-OmpK-CTB exhibited greater survival rates than the controls (52.08% and 58.33%, respectively). The data showed that recombinant L. casei could elicit a protective immunological response in C. auratus. The effect of the Lc-pPG-OmpK-CTB group was better than that of the Lc-pPG-OmpK group, and Lc-pPG-OmpK-CTB was found to be an effective candidate for oral vaccination.

Natural Foods for the Treatment of Nonalcoholic Fatty Liver Disease.

Nonalcoholic fatty liver disease (NAFLD) is one of the most common chronic liver diseases worldwide. The etiology of NAFLD is highly heterogeneous, which occurs and develops under the joint action of metabolism, inflammation, genetics, environment, and gut microbiota. At present, the principal therapeutic modalities targeting NAFLD are lifestyle interventions such as weight loss through diet and exercise. At present, there is no established therapy for the treatment of NAFLD, and many therapies are associated with a variety of side effects. A great number of in vitro and in vivo experiments have indicated that there are many natural foods that have therapeutic potential for NAFLD. This review summarizes the natural foods and their mechanisms that were found in recent years, furthermore, provides further information relevant to the treatment of NAFLD.

Rational Design and Synthesis of D-galactosyl Lysophospholipids as Selective Substrates and non-ATP-competitive Inhibitors of Phosphatidylinositol Phosphate Kinases.

Phosphatidylinositol phosphate kinases (PIPKs) produce lipid signaling molecules and have been attracting increasing attention as drug targets for cancer, neurodegenerative diseases, and viral infection. Given the potential cross-inhibition of kinases and other ATP-utilizing enzymes by ATP-competitive inhibitors, targeting the unique lipid substrate binding site represents a superior strategy for PIPK inhibition. Here, by taking advantage of the nearly identical stereochemistry between myo-inositol and D-galactose, we designed and synthesized a panel of D-galactosyl lysophospholipids, one of which was found to be a selective substrate of phosphatidylinositol 4-phosphate 5-kinase. Derivatization of this compound led to the discovery of a human PIKfyve inhibitor with an apparent IC50 of 6.2 µM, which significantly potentiated the inhibitory effect of Apilimod, an ATP-competitive PIKfyve inhibitor under clinical trials against SARS-CoV-2 infection and amyotrophic lateral sclerosis. Our results provide the proof of concept that D-galactose-based phosphoinositide mimetics can be developed into artificial substrates and new inhibitors of PIPKs.

Effects of Different Preparation Methods on Microbiota Composition of Fecal Suspension.

Fecal microbiota transplantation is an emerging disease-modifying therapy. The viability of the microbiome in feces and its successful transfer depends on the preparation of fecal microbiota suspension. However, currently, no standard operation procedure is proposed for fecal suspension preparation. This study aims to compare the effect of different preparation methods on the composition of fecal microbiota composition in the rat. Four methods were used to collect the fecal suspension from fresh rat fecal (Group A), including stirring with normal saline (Group B), stirring with normal saline and then standing (Group C), stirring with normal saline and filtered with gauze (Group D), and stirring with normal saline and centrifuged (Group E). 16S ribosomal RNA gene (16S rDNA) sequencing technology was used to analyze the microbiota diversity and composition of each group of samples. Compared with fresh feces, the bacterial richness of the fecal suspension obtained by the four methods was significantly decreased (P < 0.05). The structural similarity with fresh fecal microbiota from high to low is groups B, D, C, and E. All four methods changed the microbiota structure to varying degrees, thus may affect the effect of FMT. In conclusion, choosing different methods to prepare fecal suspensions may help to better optimize the application of FMT.

Gene Network Analysis of Hepatocellular Carcinoma Identifies Modules Associated with Disease Progression, Survival, and Chemo Drug Resistance.

BACKGROUND: Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality worldwide. HCC transcriptome has been extensively studied; however, the progress in disease mechanisms, prognosis, and treatment is still slow. METHODS: A rank-based module-centric workflow was introduced to analyze important modules associated with HCC development, prognosis, and drug resistance. The currently largest HCC cell line RNA-Seq dataset from the LIMORE database was used to construct the reference modules by weighted gene co-expression network analysis. RESULTS: Thirteen reference modules were identified with validated reproducibility. These modules were all associated with specific biological functions. Differentially expressed module analysis revealed the crucial modules during HCC development. Modules and hub genes are indicative of patient survival. Modules can differentiate patients in different HCC stages. Furthermore, drug resistance was revealed by drug-module association analysis. Based on differentially expressed modules and hub genes, six candidate drugs were screened. The hub genes of those modules merit further investigation. CONCLUSION: We proposed a reference module-based analysis of the HCC transcriptome. The identified modules are associated with HCC development, survival, and drug resistance. M3 and M6 may play important roles during HCV to HCC development. M1, M3, M5, and M7 are associated with HCC survival. High M4, high M9, low M1, and low M3 may be associated with dasatinib, doxorubicin, CD532, and simvastatin resistance. Our analysis provides useful information for HCC diagnosis and treatment.

Optimization of nitrogen and carbon removal with simultaneous partial nitrification, anammox and denitrification in membrane bioreactor.

In this study, a membrane bioreactor (MBR) was used to achieve both nitrogen and carbon removal by a simultaneous partial nitrification, anammox and denitrification (SNAD) process. During the entire experiment, the intermittent aeration (non-aerobic time : aeration time, min min-1) cycle was controlled by a time-controlled switch, and the aeration rate was controlled by a gas flowmeter, and the optimal operating parameters as determined by response surface methodology (RSM) were a C/N value of 1.16, a DO value of 0.84 mg l-1 and an aerobic time (T ae) of 15.75 min. Under these conditions, the SNAD process achieved efficient and stable nitrogen and carbon removal; the total inorganic nitrogen removal efficiency and chemical oxygen demand removal efficiency were 92.31% and 95.67%, respectively. With the formation of granular sludge, the membrane fouling rate decreased significantly from 35.0 Pa h-1 at SNAD start-up to 19.9 Pa h-1 during stable operation. Fluorescence in situ hybrid analyses confirmed the structural characteristics and the relative ratio of aerobic ammonia-oxidizing bacteria, anaerobic ammonia-oxidizing bacteria and denitrifying bacteria in the SNAD system.

Preparation and characterization of nano amitriptyline hydrochloride particles by spray freeze drying.

Aim: To investigate the enhancement of bioavailability by the usage of drug nanoparticles for increasing the efficacy of antidepressant therapeutic value. Materials & methods: Nano-amitriptyline HCI (AMT·HCl) particles were successfully prepared via a simple spray freeze drying (SFD) method. Results: The as-prepared nanoparticles are amorphous instead of crystalline. The mean size of AMT·HCl nanoparticles is 90 nm. In in vitro evaluation, AMT·HCl nanoparticles have greatly improved the dissolution compared with pure bulk materials, which have potential for enhancing human bioavailability and diminishing toxic effect. A nanoparticle formation mechanism was also proposed. Conclusion: These findings promote the development of antidepressant therapeutic evaluation based on the usage of AMT·HCl nanoparticles by SFD method and indicate that SFD is an alternative for a range of nanoparticle preparation in industrial pharmacy.

Gene Expression Analysis of Pak Choi in Response to Vernalization.

Pak choi is a seed vernalization-type plant whose vernalization mechanism is currently unclear. Therefore, it is critical to discover genes related to vernalization and research its functions during vernalization in pak choi. Here, the gene expression profiles in the shoot apex were analyzed after low temperature treatment using high-throughput RNA sequencing technology. The results showed that there are 1,664 and 1,192 differentially expressed genes (DEGs) in pak choi in cold treatment ending and before flower bud differentiation, respectively, including 42 genes that exhibited similar expression trend at both stages. Detailed annotation revealed that the proteins encoded by the DEGs are located in the extracellular region, cell junction and extracellular matrix. These proteins exhibit activity such as antioxidant activity and binding protein/transcription factor activity, and they are involved in signal transduction and the immune system/biological processes. Among the DEGs, Bra014527 was up-regulated in low temperature treatment ending, Bra024097 was up-regulated before flower bud differentiation and Bra035940 was down-regulated at both stages in low temperature-treated shoot apices. Homologues of these genes in A. thaliana, AT3G59790, AT4G30200 and AT5G61150, are involved in flowering and vernalization, suggesting that they take part in the vernalization process in pak choi. Further pathway enrichment analysis revealed that most genes were enriched in the tryptophan metabolism and glucosinolate biosynthesis pathways. However, the functions of tryptophan and glucosinolate in vernalization are not yet clear and require further analysis.

Influence of chlorine coordination number on the catalytic mechanism of ruthenium chloride catalysts in the acetylene hydrochlorination reaction: a DFT study.

The catalytic mechanism of Ru-based catalysts in the acetylene hydrochlorination reaction has been investigated via the density functional theory (DFT) method. To study the effect of the chlorine coordination number on the catalytic mechanism, Ru3Cl9, Ru3Cl7, Ru5Cl7, Ru3Cl3 and Ru3 clusters were chosen as the catalytic models. Our results show that the energy barrier for acetylene hydrochlorination on Ru3Cl9 was as high as 1.51 eV at 458 K. When the chlorine coordination number decreased, the energy barriers on Ru3Cl7, Ru5Cl7, Ru3Cl3 and Ru3 were 1.29, 0.89, 1.01 and 1.42 eV, respectively. On Ru3Cl9, the H and Cl atoms of HCl were simultaneously added to C2H2 to form C2H3Cl, while the reaction was divided into two steps on Ru3Cl7, Ru3Cl3 and Ru3 clusters. The first step was the addition of H atom of HCl to C2H2 to form C2H3˙, and the second step was the addition of Cl atom to C2H3˙ to form C2H3Cl. The step involving the addition of Cl was the rate-controlling step during the whole reaction. On Ru5Cl7 cluster, there was an additional step before the steps involving the addition of H and Cl: the transfer of H atom from HCl to Ru atom. This step was the rate-controlling step during the reaction of acetylene hydrochlorination on Ru5Cl7 and its energy barrier was the lowest among all the above-mentioned catalytic models. Therefore, the Ru5Cl7 cluster played the most predominant role in acetylene hydrochlorination with the largest reaction rate constant kTST of 10(3).