1.Establishment and evaluation of a high throughput sequencing technology for detection of Salmonella in laboratory animals
Yixiang HU ; Huanhuan ZHANG ; Chenhuan YU ; Xiaoyin JIN ; Huazhong YING
Chinese Journal of Comparative Medicine 2016;26(10):72-78
Objective To establish a detection method of Salmonella in laboratory animals based on a high-throughput sequencing technology, and to apply it in detection of Salmonella in laboratory animals.Methods DNA samples were extracted from mouse feces.Universal primers for 16S rDNA, 23S rDNA, 16S-23S rDNA, 23S-5S rDNA region, gyrB preferred area were designed, respectively.Each primer was tested and analyzed to determine the best amplification conditions and build a database.Forty-two samples of Salmonella were assayed by Illumina high-throughput sequencing technology and evaluated the specificity and stability of this method.Results The species preferred region of Salmonella was gyrB gene region.The primers for gyrB gene were FP5 ’-AACCACCGCAATCAGACCTT3‘ and FP5 ’-AGCCACGAAACCTTCACYA-3’.The primers were optimized and determined, through a high-throughput sequencing, and the sequence analysis detected very small amount of Salmonella in the 42 samples, indicating that this detection method is stable, highly sensitive, and the limit of detection reached to 0-102 CFU.Conclusions We have established a complete detection system for detection of Salmonella in laboratory animals based on a high-throughput sequencing technology, This system can detect trace amounts of Salmonella in laboratory animals, and this detection method is stable and highly sensitive, which can be also used in detection of other kinds of pathogenic microorganism in laboratory animals.
2.Effect of mitochondrial cytochrome c on hepatocyte apoptosis in non-alcoholic fatty liver disease in rabbits
Fang WU ; Chenhuan YU ; Huanhuan ZHANG ; Yue MA ; Bing YU ; Huazhong YING
Chinese Journal of Comparative Medicine 2016;26(4):7-13,23
Objective To investigate the role of mitochondrial cytochrome c on hepatocyte apoptosis in non-alcoholic fatty liver disease in rabbits and its pathogenesis.Methods Forty Japanese white rabbits were randomly assigned to control group and model group.The model group was divided into three subgroups: 4-week, 6-week, and 8-week groups, with 10 rabbits in each group.The model groups were subcutaneously injected with peanut oil (1.2 mL/kg), twice a week for 4 weeks, 6 weeks or 8 weeks.The rabbits of all groups were killed at the right time.Serum samples were collected to detect the serum biochemical index levels.Liver tissue samples were taken for pathological observation using HE staining.The hepatocyte apoptosis index ( AI ) was measured by flow cytometry, and mitochondrial permeability transition pore ( MPTP) was evaluated by ultraviolet spectrophotometry.Immunohistochemistry was employed to detect the hepatic expressions of Bcl-2, Bax, CYT C and caspase-3.Western blot was performed to detect the changes of CYT C and caspase-3 protein expressions.Results The model groups showed hepatic injury and high level of TC, TG, CRP, IL-6 and TNF-αbeginning from 4 weeks.With the NAFLD process, the hepatocyte apoptosis index was significantly increased at 4-8 weeks and the MPTP was gradually increased.In the model group, hepatic Bcl-2, Bax, CYT C and caspase-3 expressions were increased steadily with the time passing.Conclusions NAFLD-induced liver damage is associated with apoptosis, and the mitochondrial cytochrome c-mediated apoptotic pathway plays a role in the occurrence of NAFLD.
3. Reversal effects and mechanisms of Flavonoids from Tetrastigma hemsleyanum on drug resistance in gefitinib-resistant lung cancer cells
Jiaqi HE ; Juanjuan LI ; Xiaoai LV ; Huanhuan ZHANG ; Chenhuan YU ; Chenhuan YU
Chinese Journal of Clinical Pharmacology and Therapeutics 2021;26(4):368-375
AIM: To investigate the sensitization of flavonoids from Tetrastigma hemsleyanum (FTH) on gefitinib (GEF)-resistant lung adenocarcinoma cells. METHODS: The viabilities of A549 and A549/GR cells treated with FTH and GEF were detected by MTT method. The apoptotic rates and cell cycles of A549/GR cells treated with FTH and GEF were detected by Flow cytometry. The anti-tumor effects of flavonoids from FTH and GEF were assayed in A549/GR tumor-bearing mice. The expressions of proteins (PTEN, PI3K, p-PI3K, AKT, p-AKT) were detected by Western blot analysis. RESULTS: Compared with GEF group, FTH significantly enhanced the inhibition of GEF on the proliferation of A549/GR cells (P< 0.05). Combination with FTH and GEF significantly increased the apoptosis of A549/GR cells which were arrested at the G
4.Evaluation of polysaccharide hemostatic system for arterial hemorrhage of upper digestive tract
Yibin SUN ; Chen CHEN ; Yujia XIONG ; Chenhuan TAN ; Yiting LIU ; Ji FENG ; Yifan MA ; Dongtao SHI ; Deqing ZHANG ; Ling LI ; Rui LI
Chinese Journal of Digestive Endoscopy 2022;39(7):559-563
Objective:To study the efficacy and safety of EndoClot polysaccharide hemostatic system (EndoClot PHS) for heparinized arterial hemorrhage of upper digestive tract (Forrest Ⅰa) in animal model.Methods:Twelve experimental pigs were randomly divided into the test group ( n=6) and the control group ( n=6) by simple random grouping method. Gastric arterial hemorrhage models were established. Endoclot PHS and Hemospray were used to spray on the wound to stop bleeding in the test group and the control group respectively. The time of effective hemostasis, the amount of hemostatic particles used, and the blockage of the powder feeding tube and its replacement were compared between the two groups. The survival and complications of experimental pigs were observed after the operation. In 10 days after the operation, the experimental pigs were euthanized for pathological dissection. Results:Spurting or pulsatile bleeding was achieved in all experimental pigs. There were significant differences in the time of effective hemostasis (8.75±0.84 min VS 9.83±0.62 min, t=-2.53, P=0.030) and the amount of hemostatic particles used to achieve effective hemostasis (6.71±0.39 g VS 14.10±1.62 g, t=-10.86, P<0.001) between the test group and the control group. There was no significant difference in the occurence of clogging or the replacement of powder feeding pipes between the two groups (0.64±0.02 times VS 0.67±0.04 times, t=-1.64, P=0.131). In addition, the gas source of the test group was stable, and the visual field under the endoscope was clear. Neither the test group nor the control group had gastric lesions, perforation, or embolism. The blood glucose, blood routine, and liver and kidney functions were normal, and no thrombosis or embolism of the main organs occurred in either group. Conclusion:EndoClot PHS is safe and effective for heparinized upper gastrointestinal arterial hemorrhage (Forrest Ⅰa) in animal models.
5.Analysis and forecast of the disease burden of schistosomiasis in China from 1992 to 2030
Kai LIN ; Chenhuan ZHANG ; Zhendong XU ; Xuemei LI ; Renzhan HUANG ; Yawen LIU ; Haihang YU ; Lisi GU
Chinese Journal of Schistosomiasis Control 2025;37(1):24-34
Objective To analyze the trends in the disease burden of schistosomiasis in China from 1992 to 2021, and to project the disease burden of schistosomiasis in China from 2022 to 2030, so as to provide insights into the elimination of schistosomiasis in China. Methods The prevalence, age-standardized prevalence, disability-adjusted life year (DALYs) rate and age-standardized DALYs rate of schistosomiasis, as well as the years lost due to disability (YLDs) rate and age-standardized YLDs rate of anemia attributable to Schistosoma infections in China, the world and different socio-demographic index (SDI) regions were captured from the Global Burden of Disease Study 2021 (GBD 2021) data resources, and the trends in the disease burden due to schistosomiasis were evaluated with estimated annual percentage change (EAPC) and its 95% confidence interval (CI). In addition, the age, period and cohort effects on the prevalence of schistosomiasis were examined in China using an age-period-cohort (APC) model, and the disease burden of schistosomiasis was predicted in China from 2022 to 2030 using a Bayesian age-period-cohort (BAPC) model. Results The age-standardized prevalence and DALYs rate of schistosomiasis, and the age-standardized YLDs rate of anemia attributable to Schistosoma infections were 761.32/105, 5.55/105 and 0.38/105 in China in 2021. These rates were all lower than the global levels (1 914.30/105, 21.90/105 and 3.36/105, respectively), as well as those in the medium SDI regions (1 413.61/105, 12.10/105 and 1.93/105, respectively), low-medium SDI regions (2 461.03/105, 26.81/105 and 4.48/105, respectively), and low SDI regions (5 832.77/105, 94.48/105 and 10.65/105, respectively), but higher than those in the high SDI regions (59.47/105, 0.49/105 and 0.05/105, respectively) and high-medium SDI regions (123.11/105, 1.20/105 and 0.12/105, respectively). The prevalence and DALYs rate of schistosomiasis were higher among men (820.79/105 and 5.86/105, respectively) than among women (697.96/105 and 5.23/105, respectively) in China in 2021, while the YLDs rate of anemia attributable to Schistosoma infections was higher among women (0.66/105) than among men (0.12/105). The prevalence of schistosomiasis peaked at ages of 30 to 34 years among both men and women, while the DALYs rate of schistosomiasis peaked among men at ages of 15 to 19 years and among women at ages of 20 to 24 years. The age-standardized prevalence of schistosomiasis showed a moderate decline in China from 1992 to 2021 relative to different SDI regions [EAPC = -1.51%, 95% CI: (-1.65%, -1.38%)], while the age-standardized DALYs rate [EAPC = -3.61%, 95% CI: (-3.90%, -3.33%)] and age-standardized YLDs rate of anemia attributable to Schistosoma infections [EAPC = -4.16%, 95% CI: (-4.38%, -3.94%)] appeared the fastest decline in China from1992 to 2021 relative to different SDI regions. APC modeling showed age, period, and cohort effects on the trends in the prevalence of schistosomiasis in China from 1992 to 2021, and the prevalence of schistosomiasis appeared a rise followed by decline with age, and reduced with period and cohort. BAPC modeling revealed that the age-standardized prevalence and age-standardized DALYs rate of schistosomiasis, and age-standardized YLDs rate of anemia attributable to Schistosoma infections all appeared a tendency towards a decline in China from 2022 to 2030, which reduced to 722.72/105 [95% CI: (538.74/105, 906.68/105)], 5.19/105 [95% CI: (3.54/105, 6.84/105)] and 0.30/105 [95% CI: (0.21/105, 0.39/105)] in 2030, respectively. Conclusions The disease burden of schistosomiasis appeared a tendency towards a decline in China from 1992 to 2021, and is projected to appear a tendency towards a decline from 2022 to 2030. There are age, period and cohort effects on the prevalence of schistosomiasis in China. Precision schistosomiasis control is required with adaptations to current prevalence and elimination needs.
6.DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery
Zhu TIANSHENG ; Zhu YI ; Xuan YUE ; Gao HUANHUAN ; Cai XUE ; Piersma R. SANDER ; Pham V. THANG ; Schelfhorst TIM ; Haas R.G.D. RICHARD ; Bijnsdorp V. IRENE ; Sun RUI ; Yue LIANG ; Ruan GUAN ; Zhang QIUSHI ; Hu MO ; Zhou YUE ; Winan J. Van Houdt ; Tessa Y.S. Le Large ; Cloos JACQUELINE ; Wojtuszkiewicz ANNA ; Koppers-Lalic DANIJELA ; B(o)ttger FRANZISKA ; Scheepbouwer CHANTAL ; Brakenhoff H. RUUD ; Geert J.L.H. van Leenders ; Ijzermans N.M. JAN ; Martens W.M. JOHN ; Steenbergen D.M. RENSKE ; Grieken C. NICOLE ; Selvarajan SATHIYAMOORTHY ; Mantoo SANGEETA ; Lee S. SZE ; Yeow J.Y. SERENE ; Alkaff M.F. SYED ; Xiang NAN ; Sun YAOTING ; Yi XIAO ; Dai SHAOZHENG ; Liu WEI ; Lu TIAN ; Wu ZHICHENG ; Liang XIAO ; Wang MAN ; Shao YINGKUAN ; Zheng XI ; Xu KAILUN ; Yang QIN ; Meng YIFAN ; Lu CONG ; Zhu JIANG ; Zheng JIN'E ; Wang BO ; Lou SAI ; Dai YIBEI ; Xu CHAO ; Yu CHENHUAN ; Ying HUAZHONG ; Lim K. TONY ; Wu JIANMIN ; Gao XIAOFEI ; Luan ZHONGZHI ; Teng XIAODONG ; Wu PENG ; Huang SHI'ANG ; Tao ZHIHUA ; Iyer G. NARAYANAN ; Zhou SHUIGENG ; Shao WENGUANG ; Lam HENRY ; Ma DING ; Ji JIAFU ; Kon L. OI ; Zheng SHU ; Aebersold RUEDI ; Jimenez R. CONNIE ; Guo TIANNAN
Genomics, Proteomics & Bioinformatics 2020;18(2):104-119
To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipe-line and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to gen-erate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.