1.Research on The Genealogical Inference Efficiency of High-density SNPs
Jing LI ; Yi-Jie SUN ; Wen-Ting ZHAO ; Zi-Chen TANG ; Jing LIU ; Cai-Xia LI
Progress in Biochemistry and Biophysics 2026;53(3):740-753
ObjectiveThis study aims to explore the potential of different orders of magnitude single-nucleotide polymorphism (SNP) locus combinations for predicting distant kinship relationships. A high-density SNP locus set was constructed, and a comprehensive assessment of its inference capability was conducted. MethodsFirstly, we selected three commercial chip panels, CGA (Chinese genotyping array, Illumina), GSA (Global screening array, Illumina), Affy (23MF_V2 high-density SNP array, Affymetrix) and merged them after quality control, forming a high-density SNP locus panel(1 180 k). Secondly, we selected 161 samples and collected their peripheral blood samples by using whole-genome sequencing technology. Within this sample population, the levels of kinship relationships fully covered the range from level 1 to level 9, and the number of kinship pairs at each level was consistently maintained at over 50 pairs. From 161 samples data of whole-genome sequencing, the 1 180 k locus set was extracted, which is referred to as the high-density SNP locus set in the following text. The kinship inference was conducted using the identity-by-descent (IBD) algorithm with the selected optimal parameters. To comprehensively evaluate the performance of the high-density SNP locus set in kinship inference, we compared it with the three commercial chip panels, the intersection of these three chip loci, and the control sets constructed by randomly reducing the number of the high-density SNP locus set. Based on the changes in the IBD lengths, as well as the dynamic trends in prediction accuracy, we conducted a scientific assessment of the kinship inference capability of the high-density SNP locus set. ResultsAfter screening, a set of 1 184 334 autosomal SNPs was obtained. During the process of screening the optimal IBD length threshold, the result revealed that 0 cM, 1 cM, and 2 cM all demonstrated good applicability. However, to avoid the issue of a large amount of redundant information caused by setting a too low IBD length threshold, this study ultimately selected 2 cM as the optimal threshold. Compared with the average results of three chip panels, the high-density SNP locus set increased the total IBD length and the average IBD length across levels 1-9; the accuracy of the confidence interval for level 8 was 70.97%, which represented a 3.50% improvement; the average confidence interval accuracy for levels 1-8 was 91.39%, representing a 1.00% increase; and the false negative rates at levels 8 and 9 were reduced by 2.42% and 6.76%, respectively. The system efficacy of the high-density SNP locus set for kinship inference of first to eighth degree relationships reached 98.91%. Through random reduction of the high-density SNP locus set results, it is found that increasing the number of SNPs with the panel, the detection efficiency of IBD length showed a significant upward trend. At the same time, the overall trend in the accuracy of kinship relationship prediction as well as the confidence interval accuracy also indicated that both metrics steadily increased with the addition of more loci. ConclusionThe results show that the high-density SNPs panel significantly enhances the efficacy of distant kinship inference, accurately covering kinship degrees, with the average confidence interval accuracy for first to eighth degree relationships stably above 90%. The study finds that increasing the number of SNPs panel can improve the ability to predict distant kinship.
2.Zhuluan Decoction Ameliorates Premature Ovarian Insufficiency by Inhibiting Excessive Autophagy of KGN Through Regulation of PI3K/Akt/mTOR Pathway
Yao CHEN ; Sainan TIAN ; Jing ZENG ; Xingxing YI ; Wen'e LIU ; Lei LEI ; Li TANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):89-98
ObjectiveTo elucidate the underlying mechanism through which Zhuluan decoction suppresses excessive autophagy in human ovarian granulosa cells (KGN) and ameliorates premature ovarian insufficiency (POI) via the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway. MethodsThe optimal concentration of cyclophosphamide for inducing a POI model in KGN cells was identified via the cell counting kit-8 (CCK-8) assay. Subsequently, the impacts of varying concentrations of Zhuluan decoction-containing serum on the viability of the KGN cell model were assessed. After the optimal drug concentration was determined, KGN cells were categorized into the following groups: blank control (20% blank serum), model (20% blank serum + 5 μmol·L-1 cyclophosphamide), Zhuluan decoction-containing serum (20% Zhuluan decoction-containing serum + 5 μmol·L-1 cyclophosphamide), autophagy inhibitor (20% blank serum + 5 μmol·L-1 cyclophosphamide + 20 μmol·L-1 chloroquine phosphate), autophagy inhibitor + Zhuluan decoction-containing serum (20% Zhuluan decoction-containing serum + 5 μmol·L-1 cyclophosphamide + 20 μmol·L-1 chloroquine phosphate), and estradiol valerate (20% estradiol valerate-containing serum + 5 μmol·L-1 cyclophosphamide). Following 48 hours of incubation, flow cytometry was utilized to measure the apoptosis rate of KGN cells in each group. Western blotting was employed to quantify the protein levels of PI3K, phosphorylated (p)-Akt, Akt, p-mTOR, and mTOR, along with the expression levels of autophagy-related proteins such as Beclin1, autophagy-related 5 homolog (ATG5), and microtubule-associated protein 1 light chain 3 (LC3), in each group. Additionally, monodansylcadaverine (MDC) staining was performed to evaluate the extent of autophagy in each group. ResultsIncubation of KGN cells with 5 μmol·L-1 cyclophosphamide for 48 h successfully established a POI model, marked by a significant inhibition of KGN cell proliferation. Notably, the inhibitory effect of cyclophosphamide on KGN cell proliferation exhibited a positive correlation with its concentration. Zhuluan decoction-containing serum at 20% and 30% promoted cell proliferation and mitigated the inhibitory effect of cyclophosphamide on KGN cell proliferation, with comparable therapeutic efficacy observed at both concentrations. Compared with the blank control group, the model group displayed an elevated apoptosis rate (P<0.01), reduced protein levels of PI3K, p-Akt, and p-mTOR (P<0.01), increased protein levels of Beclin1, LC3, and ATG5 (P<0.01), no significant alterations in the protein levels of Akt and mTOR, and an enhanced MDC autophagy fluorescence intensity (P<0.01). In comparison to that the model group, the apoptosis rates in the blank control group, model group, Zhuluan decoction-containing serum group, autophagy inhibitor group, autophagy inhibitor + Zhuluan decoction-containing serum group, and estradiol valerate group all reduced (P<0.05, P<0.01), with the most pronounced reduction observed in the autophagy inhibitor + Zhuluan decoction-containing serum group. The protein levels of PI3K, p-Akt, and p-mTOR were higher in other groups than in the model group (P<0.05, P<0.01), being the highest in the autophagy inhibitor + Zhuluan decoctio-containing serum group (P<0.01). The protein levels of Beclin1 and ATG5 were lower in other groups than in the model group (P<0.05, P<0.01). The expression level of LC3 declined in the Zhuluan decoction-containing serum group and the estradiol valerate group (P<0.05, P<0.01), while it decreased without statistical significance in the autophagy inhibitor group and the autophagy inhibitor + Zhuluan decoction-containing serum group. ConclusionZhuluan decoction may activate the PI3K/Akt/mTOR pathway to inhibit excessive autophagy and counteract the detrimental effects of cyclophosphamide on the KGN cell model, thus managing POI.
3.Zhuluan Decoction Ameliorates Premature Ovarian Insufficiency by Inhibiting Excessive Autophagy of KGN Through Regulation of PI3K/Akt/mTOR Pathway
Yao CHEN ; Sainan TIAN ; Jing ZENG ; Xingxing YI ; Wen'e LIU ; Lei LEI ; Li TANG
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(8):89-98
ObjectiveTo elucidate the underlying mechanism through which Zhuluan decoction suppresses excessive autophagy in human ovarian granulosa cells (KGN) and ameliorates premature ovarian insufficiency (POI) via the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway. MethodsThe optimal concentration of cyclophosphamide for inducing a POI model in KGN cells was identified via the cell counting kit-8 (CCK-8) assay. Subsequently, the impacts of varying concentrations of Zhuluan decoction-containing serum on the viability of the KGN cell model were assessed. After the optimal drug concentration was determined, KGN cells were categorized into the following groups: blank control (20% blank serum), model (20% blank serum + 5 μmol·L-1 cyclophosphamide), Zhuluan decoction-containing serum (20% Zhuluan decoction-containing serum + 5 μmol·L-1 cyclophosphamide), autophagy inhibitor (20% blank serum + 5 μmol·L-1 cyclophosphamide + 20 μmol·L-1 chloroquine phosphate), autophagy inhibitor + Zhuluan decoction-containing serum (20% Zhuluan decoction-containing serum + 5 μmol·L-1 cyclophosphamide + 20 μmol·L-1 chloroquine phosphate), and estradiol valerate (20% estradiol valerate-containing serum + 5 μmol·L-1 cyclophosphamide). Following 48 hours of incubation, flow cytometry was utilized to measure the apoptosis rate of KGN cells in each group. Western blotting was employed to quantify the protein levels of PI3K, phosphorylated (p)-Akt, Akt, p-mTOR, and mTOR, along with the expression levels of autophagy-related proteins such as Beclin1, autophagy-related 5 homolog (ATG5), and microtubule-associated protein 1 light chain 3 (LC3), in each group. Additionally, monodansylcadaverine (MDC) staining was performed to evaluate the extent of autophagy in each group. ResultsIncubation of KGN cells with 5 μmol·L-1 cyclophosphamide for 48 h successfully established a POI model, marked by a significant inhibition of KGN cell proliferation. Notably, the inhibitory effect of cyclophosphamide on KGN cell proliferation exhibited a positive correlation with its concentration. Zhuluan decoction-containing serum at 20% and 30% promoted cell proliferation and mitigated the inhibitory effect of cyclophosphamide on KGN cell proliferation, with comparable therapeutic efficacy observed at both concentrations. Compared with the blank control group, the model group displayed an elevated apoptosis rate (P<0.01), reduced protein levels of PI3K, p-Akt, and p-mTOR (P<0.01), increased protein levels of Beclin1, LC3, and ATG5 (P<0.01), no significant alterations in the protein levels of Akt and mTOR, and an enhanced MDC autophagy fluorescence intensity (P<0.01). In comparison to that the model group, the apoptosis rates in the blank control group, model group, Zhuluan decoction-containing serum group, autophagy inhibitor group, autophagy inhibitor + Zhuluan decoction-containing serum group, and estradiol valerate group all reduced (P<0.05, P<0.01), with the most pronounced reduction observed in the autophagy inhibitor + Zhuluan decoction-containing serum group. The protein levels of PI3K, p-Akt, and p-mTOR were higher in other groups than in the model group (P<0.05, P<0.01), being the highest in the autophagy inhibitor + Zhuluan decoctio-containing serum group (P<0.01). The protein levels of Beclin1 and ATG5 were lower in other groups than in the model group (P<0.05, P<0.01). The expression level of LC3 declined in the Zhuluan decoction-containing serum group and the estradiol valerate group (P<0.05, P<0.01), while it decreased without statistical significance in the autophagy inhibitor group and the autophagy inhibitor + Zhuluan decoction-containing serum group. ConclusionZhuluan decoction may activate the PI3K/Akt/mTOR pathway to inhibit excessive autophagy and counteract the detrimental effects of cyclophosphamide on the KGN cell model, thus managing POI.
4.A convenient research strategy for functional verification of epigenetic regulators during spermatogenesis.
Shan LI ; Ying YUAN ; Ke-Yu ZHANG ; Yi-Dan GUO ; Lu-Tong WANG ; Xiao-Yuan ZHANG ; Shu ZHANG ; Qi YAN ; Rong ZHANG ; Jie CHEN ; Feng-Tang YANG ; Jing-Rui LI
Asian Journal of Andrology 2025;27(2):261-267
Spermatogenesis is a fundamental process that requires a tightly controlled epigenetic event in spermatogonial stem cells (SSCs). The mechanisms underlying the transition from SSCs to sperm are largely unknown. Most studies utilize gene knockout mice to explain the mechanisms. However, the production of genetically engineered mice is costly and time-consuming. In this study, we presented a convenient research strategy using an RNA interference (RNAi) and testicular transplantation approach. Histone H3 lysine 9 (H3K9) methylation was dynamically regulated during spermatogenesis. As Jumonji domain-containing protein 1A (JMJD1A) and Jumonji domain-containing protein 2C (JMJD2C) demethylases catalyze histone H3 lysine 9 dimethylation (H3K9me2), we firstly analyzed the expression profile of the two demethylases and then investigated their function. Using the convenient research strategy, we showed that normal spermatogenesis is disrupted due to the downregulated expression of both demethylases. These results suggest that this strategy might be a simple and alternative approach for analyzing spermatogenesis relative to the gene knockout mice strategy.
Spermatogenesis/physiology*
;
Animals
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Male
;
Mice
;
Epigenesis, Genetic
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Jumonji Domain-Containing Histone Demethylases/metabolism*
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Histones/metabolism*
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RNA Interference
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Testis/metabolism*
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Methylation
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Mice, Knockout
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Histone Demethylases
5.Comprehensive Review on Rhodiola crenulata: Ethnopharmacology, Phytochemistry, Pharmacological Properties and Clinical Applications.
Rui ZHU ; Cui-Fen FANG ; Shu-Jing ZHANG ; Zhu HAN ; Ge-Hui ZHU ; Shang-Zuo CAI ; Cheng ZHENG ; Yu TANG ; Yi WANG
Chinese journal of integrative medicine 2025;31(8):752-759
6.Clinical characteristics and prognosis of perioperative myocardial injury after non-cardiac surgery in intensive care unit patients
Shi-hong XIA ; Xue-li MA ; Guo-feng SHEN ; Li-jing JIANG ; Kang-yi LIU ; Wei-yi TANG ; Jin-di NI ; Xiang LI
Fudan University Journal of Medical Sciences 2025;52(3):424-428,445
Objective To retrospectively analyze the clinical risk factors and prognosis of perioperative myocardial injury(MINS)in non-cardiac surgery patients admitted to the intensive care unit(ICU).Methods A total of 478 postoperative patients admitted to the Department of Intensive Medicine,Minhang Hospital,Fudan University from Jan 2020 to Dec 2023 were selected.They were divided into MINS group(n=302)and normal group(n=176)based on whether myocardial injury occurred within 7 days after surgery.The differences in clinical characteristics between the two groups were compared,and risk factors for perioperative myocardial injury were identified.Risk factors for mortality in the MINS group were analyzed with 30-day mortality as the clinical endpoint.Results The prevalence of acute physiology and chronic health evaluation Ⅱ(Apache Ⅱ)score,coronary artery disease,and chronic kidney disease were all higher in the MINS group than those in the normal group,with statistically significant differences(P<0.05).The proportion of emergency surgeries,co-infection,and perioperative hypotension were significantly different between the MINS group and the normal group(P<0.05).Multivariate logistic regression analysis revealed that chronic kidney disease,emergency surgery,co-infection,and intraoperative and postoperative hypotension were risk factors for MINS occurrence.Prognostic analysis indicated that perioperative hypotension was a risk factor for 30-day mortality in MINS patients.Conclusion MINS is closely associated with patients'underlying conditions,timing of surgery,and perioperative hypotension status,and especially perioperative hypotension affects the final outcomes.
7.Mechanistic investigation of Fuzheng Hefu Zhiyang Formula in alleviating psoriasis inflammatory microenvironment via P38/Erk/NF-κB signaling pathway
Yi-jing LIAO ; Yan-jie LIU ; Yue LU ; Bin TANG ; Jun-hong ZHANG ; Jing-jie YU ; Hao DENG ; Ling HAN ; Chuan-jian LU ; Hai-ming CHEN
Chinese Traditional Patent Medicine 2025;47(8):2550-2558
AIM To investigate the effect of Fuzheng Hefu Zhiyang Formula(FZHFZY)on psoriasis-like skin lesions and immune regulation in mice.METHODS In the in vivo experiment,30 BALB/c mice were randomly divided into the blank group,the model group,the dexamethasone group(1.5 g/kg of compound dexamethasone acetate cream),and the low-dose(2.5 g/kg)and high-dose(5 g/kg)FZHFZY groups,with six mice in each group.The experiment groups were treated with respective FZHFZY and dexamethasone,and the other groups were given normal saline for 10 consecutive days,during which psoriatic skin lesions were induced with imiquimod cream for 7 consecutive days.The mice had their area and severity of psoriasis assessed by PASI score;their histological changes of skin lesions.observed with Hematoxylin-eosin(HE)staining;their F4/80 ratio of skin lesions observed with immunohistochemical(IHC)staining;their protein expressions of P38,p-P38,Erk,p-Erk,P65 and p-P65 detected by Western blot;and their mRNA expressions of tumor necrosis factor-α(TNF-α),IL-17,IL-23 and IL-1β detected by RT-qPCR.In the in vitro research,the cultured RAW264.7 cells were divided into the blank group,the LPS group,and the FZHFZY groups(1 200,600,300,150 μg/mL).The cells had their protein expressions of P38,p-P38,Erk,p-Erk,P65 and p-P65 detected with Western blot;and their mRNA expressions of IL-6,TNF-α,IL-23 and IL-8 detected by RT-qPCR.RESULTS The in vivo experiment showed that compared to the model group,the FZHFZY groups demonstrated decreased PASI score(P<0.01);improved epidermal thickening and parakeratosis of skin lesions as revealed by HE staining result and increased expression of F4/80 in IHC staining sections;decreased protein expression ratios of p-P38/P38,p-ERK/Erk and p-P65/P65 in skin(P<0.05,P<0.01);and reduced mRNA expressions of TNF-α,IL-17,IL-23 and IL-1β in the skin(P<0.01).FZHFZY(0~2 400 μg/mL)showed no significant cytotoxicity towards RAW264.7 cells in vitro(P>0.05).Compared to those of the LPS group,the cells exposed to FZHFZ at concentrations of 1 200 and 600 μg/mL demonstrated decreased protein expression ratios of p-P38/P38,p-ERK/Erk,and p-P65/P65(P<0.05,P<0.01);and significantly decreased mRNA expressions of TNF-α,IL-17,IL-23 and IL-1β(P<0.01).CONCLUSION FZHFZY alleviates imiquimod-induced psoriatic lesions in mice and suppresses inflammatory response in LPS-stimulated RAW264.7 cells by inhibiting P38/Erk/NF-κB signaling pathway.
8.Study on the Theory of"Any Deficiency of Spleen and Stomach Being A Disease of the Blood"
Journal of Zhejiang Chinese Medical University 2025;49(7):923-927,934
[Objective]To investigate LI Dongyuan's theory of"any deficiency of spleen and stomach is a disease of the blood"and provide reference for modern clinical practice.[Methods]Taking Discussion on Internal and External Injuries,Treatise on Spleen and Stomach,Orchid Chamber of Secrets and Invention of Medicine as references,it starts from the connotation of"any deficiency of spleen and stomach is a disease of the blood",and explores the etiology and pathogenesis of the diseases,the theoretical construction and the clinical application respectively.[Results]Taking Inner Canon of Yellow Emperor and Zhongjing's academic thought as the source,absorbing CHENGs' and ZHU Xi's ideas of science.Being inspired by his teacher ZHANG Yuansu,and driven by his own clinical practice,LI Dongyuan put forward the academic thought of"any deficiency of spleen and stomach is a disease of the blood".From the Treatise on Spleen and Stomach-Treatise on the Prosperity and Decline of Spleen and Stomach,"any deficiency of spleen and stomach is a disease of the blood",which is a pathological state caused by the deficiency of spleen and stomach Qi and the weakness of elevation due to the disorders of emotions and moods,overwork and overdose,and uncontrolled diets,there fore causes insufficient blood production and too much blood consumption,and then leads to the deficiency of blood and Yin,and the essence of which is the disordered ascending,descending,floating and sinking of the human body's Qi.In treatment,LI Dongyuan always based on regulating blood,to restore the body's Qi,and harmonize Qi and blood as the goal,with"blood replenishment must have Yang Qi,Qi and blood double tonic""rising Yang must be in response to the time of the day,and make good use of the wind herbs""relieving heat must protect the Yin and blood,moderation in attacking and destroying".[Conclusion]Exploring this theory can help to view the relationship between Qi and blood from a new perspective,better grasp LI Dongyuan's academic thinking,and provide reference for the treatment of spleen and stomach diseases and blood diseases.
9.Application of 3D printing technology in bone graft fusion surgery for cervical spondylotic myelopathy
Lei TANG ; Qi WANG ; Zhi-yong CHAI ; Jun WANG ; Jing-ying GAI ; Yi-feng LIU
Journal of Regional Anatomy and Operative Surgery 2025;34(8):702-706
Objective To explore the clinical effect of 3D-printed interbody fusion cage applied in anterior cervical decompression and bone graft fusion for the treatment of cervical spondylotic myelopathy.Methods A total of 100 patients with cervical spondylotic myelopathy who underwent anterior cervical fusion surgery in our hospital from June 2020 to June 2023 were selected as the research subjects,they were randomly divided into the 3D group and the control group according to the random number table method,with 50 cases in each group.Patients in the 3D group were implanted with a 3D-printed interbody fusion cage which was made of microporous metal materials,while patients in the control group were implanted with intervertebral fusion cage which was made of polyetheretherketone material.The surgery-related indicators,cervical imaging parameters,cervical spinal cord function,cervical axial function and surgical complications of patients between the two groups were compared.Results There was no statistically significant difference in the operation time,intraoperative blood loss or length of hospital stay of patients between the two groups(P>0.05).The height of the cervical fusion segments and the Cobb angle of the fusion segments of patients in both groups at each time point after the operation were significantly increased compared with those before the operation(P<0.05).The height of the cervical fusion segments and the Cobb angle of the fusion segments of patients 1 month,3 months,and 6 months after the operation in the 3D group were all greater than those in the control group(P>0.05).The subjective symptom score and the total score of the Japanese orthopaedic association(JOA)of patients 6 months after the operation in the 3D group were higher than those in the control group(P<0.05).The cervical axial function of patients 6 months after the operation in the 3D group was better than that in the control group(P<0.05).The incidence of surgical complications in the 3D group was lower than that in the control group(P<0.05).Conclusion The use of 3D-printed interbody fusion cage during the anterior cervical decompression and bone graft fusion for patients with cervical spondylotic myelopathy can significantly improve the clinical symptoms of patients,achieve better cervical axial function,and have fewer complications.
10.The effect of rutaecarpine on improving fatty liver and osteoporosis in MAFLD mice
Yu-hao ZHANG ; Yi-ning LI ; Xin-hai JIANG ; Wei-zhi WANG ; Shun-wang LI ; Ren SHENG ; Li-juan LEI ; Yu-yan ZHANG ; Jing-rui WANG ; Xin-wei WEI ; Yan-ni XU ; Yan LIN ; Lin TANG ; Shu-yi SI
Acta Pharmaceutica Sinica 2025;60(1):141-149
Metabolic-associated fatty liver disease (MAFLD) and osteoporosis (OP) are two very common metabolic diseases. A growing body of experimental evidence supports a pathophysiological link between MAFLD and OP. MAFLD is often associated with the development of OP. Rutaecarpine (RUT) is one of the main active components of Chinese medicine Euodiae Fructus. Our previous studies have demonstrated that RUT has lipid-lowering, anti-inflammatory and anti-atherosclerotic effects, and can improve the OP of rats. However, whether RUT can improve both fatty liver and OP symptoms of MAFLD mice at the same time remains to be investigated. In this study, we used C57BL/6 mice fed a high-fat diet (HFD) for 4 months to construct a MAFLD model, and gave the mice a low dose (5 mg·kg-1) and a high dose (15 mg·kg-1) of RUT by gavage for 4 weeks. The effects of RUT on liver steatosis and bone metabolism were then evaluated at the end of the experiment [this experiment was approved by the Experimental Animal Ethics Committee of Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences (approval number: IMB-20190124D303)]. The results showed that RUT treatment significantly reduced hepatic steatosis and lipid accumulation, and significantly reduced bone loss and promoted bone formation. In summary, this study shows that RUT has an effect of improving fatty liver and OP in MAFLD mice.

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