1.Genomic sequencing analysis of Cryptococcus neoformans var grubii strains of two genotypes with dif-ferent virulence and selection of virulence-associated genes
Taohua LIU ; Yanyan WANG ; Yuru CHEN ; Liang ZHAO ; Qian LYU ; Lili MOU ; Yingqian KANG
Chinese Journal of Microbiology and Immunology 2016;36(2):103-109
Objective To analyze the genomic sequences of Cryptococcus neoformans var grubii strains of two genotypes with different virulence and to screen out the virulence-associated genes. Methods A clinical strain (IFM56800) with the strongest virulence and an environmental strain (IFM56731) with the weakest virulence were screened out for whole genome sequencing analysis. The results of sequencing analy-sis were comprehensively analyzed by using the method of comparative genomics. Genetic variations were ex-tensively screened by using the strategies of non-synonymous single nucleotide polymorphisms ( nsSNPs), nonsense SNPs and the insertions or deletions ( InDels) causing frameshift mutations. The filtered genes were sequenced in 20 experimental strains. The whole RNAs were extracted and then the full-length cDNAs were sequenced by using the rapid amplification of 5′ and 3′ cDNA ends (RACE) method. Results By whole genome sequencing, valid data with high coverage (127 times and 111 times) was obtained in both the environmental strain IFM56731 and the clinical strain IFM56800. The data of InDels and SNPs were statisti-cally analyzed, respectively. Six genes were chosen for further analysis based on the strategies of nonsense SNPs and the InDels causing frameshift mutations. The six genes were amplified and sequenced in all of the experimental strains, three of which were further analyzed with cDNA sequencing. Ultimately, the location and structure of CNAG_01032 gene were determined. The predicted nonsense mutation locus was verified to present in the actual mRNA. Conclusion The strategies of nonsense SNPs and the InDels causing frame-shift mutations showed high-efficiency in screening potential virulence-associated genes. The CNAG_01032 gene was screened out as a novel virulence-associated gene.
2.PCR detection of the Nocardia gene SecA1 using molecular beacon probe
Yanyan WANG ; Maoning XIA ; Chunyan MING ; Jing HUANG ; Taohua LIU ; Bing ZHOU ; Yingqian KANG
Chinese Journal of Zoonoses 2017;33(6):508-512
Molecular beacon probe was designed based on a specific DNA sequence of Nocardia to PCR detection of thisbacterium.The strains of Nocardia、Gordina and Rhodococcus were inoculated in Brain Heart Infusion Agar medium separately,then the growth condition was observed,DNA was extracted as a template;the molecular beacon probe was designed based on the partial secA 1 gene sequences of Nocardia strains,and the probe was added into the reaction system of real time fluorescence quantitative PCR (RT-PCR),and the fluorescence signal was tested at the end of PCR.Showed that the amplified secA1 gene of Nocardia could produce positive fluorescence signal in RT-PCR,but those of Gordonia and Rhodococcus with control groups showed negative results because of no fluorescence signal.In conclusion as a housekeeping gene,secA1 is an ideal target molecule to identify the actinomycetes strains on the species level in the systematic evolution research,and the technique of fluorescence molecular beacon probe is accurate,rapid and sensitive for detecting the Nocardia strains with secA1 gene.
3.Cannulated screw fixation directly via the anterior approach for femoral neck fractures difficultly reducible in young and middle-aged patients
Taohua WU ; Lianyun GAO ; Zhen LIN ; Yanhua CHEN ; Kangming RUAN ; Qingping LIU
Chinese Journal of Orthopaedic Trauma 2020;22(9):765-770
Objective:To investigate the clinical outcomes of open reduction and cannulated screw fixation directly via the anterior approach for femoral neck fracture of Garden type Ⅳ which is difficultly reducible in young and middle-aged patients.Methods:Forty patients aged younger than 65 years old were treated by open reduction and cannulated screw fixation directly via the anterior approach for femoral neck fractures which were difficulty reducible at Department of Orthopaedics, Mindong Hospital from March 2015 to October 2017. They were 28 males and 12 females, aged from 22 to 62 years (mean, 49.2 years). All the fractures were type Ⅳ by the Garden classification. The time from injury to operation averaged 3.2 d (range, from 1 to 6 d). Their postoperative fracture nonunion and femoral head necrosis were recorded. The reduction quality and hip function were evaluated using Garden reduction index and Harris hip scores.Results:All the 40 patients were followed up for 11 to 44 months (mean, 22.3 months). Nonunion occurred in one patient who had to accept secondary artificial hip replacement. No avascular necrosis of the femoral head occurred in any patients. The anteroposterior Garden reduction indexes at 2 d after surgery and at the last follow-up for the 40 patients were respectively 156.97°±1.40° and 157.07°±1.47°, showing no significant difference( t=-0.302, P=0.765); so were the lateral Garden reduction indexes (171.82°±4.48° and 172.10°±4.27°) ( t=-2.333, P=0.817). The Harris hip scores at the final follow-up for the hip ranged from 77 to 98 (average, 92); 31 cases were rated as excellent, 6 as good, 2 as fair and one as poor, giving an excellent to good rate of 92.5%. Conclusion:In the treatment of femoral neck fracture of Garden type Ⅳ which is difficultly reducible in young and middle-aged patients, if closed reduction has failed, open reduction and cannulated screw fixation directly via the anterior approach can achieve satisfactory short-term outcomes because it facilitates fracture reduction and fixation under direct vision, promotes fracture union and reduces avascular necrosis of the femoral head.
4.Data Mining and Experimental Validation of Total Ginsenosides Ameliorating Alcoholic Hepatitis
Shuling CHEN ; Yitao LIU ; Xiao WU ; Duo ZHANG ; Jinhui AI ; Taohua YUAN ; Jianfei SUN
Chinese Journal of Experimental Traditional Medical Formulae 2024;30(21):95-103
ObjectiveTo explore new targets and herbal medicines of total ginsenosides in ameliorating alcoholic hepatitis (AH) by data mining and experimental validation and to provide new directions for the clinical treatment of AH. MethodGSE28619 was selected as the test set from the GEO database and GSE83148 and GSE103580 were selected as the validation sets. The limma package and weighted gene co-expression network analysis (WGCNA) were employed to identify the AH-related differentially expressed genes and modular genes, and Venny was used to extract the common genes. The protein-protein interaction (PPI) network was constructed and the enrichment analysis was carried out. The hub genes were further screened and evaluated for their diagnostic value. After validation with the datasets, new potential targets of AH and traditional Chinese medicine were predicted. Molecular docking between the targets and active ingredients of traditional Chinese medicine was performed, and the results were validated by experiments. Eight out of 48 SD rats were randomly selected into a blank group and received an equal amount of normal saline. The rest rats were subjected to modeling with ethanol by gavage and then randomized into low- (10 mg·kg-1), medium- (20 mg·kg-1), and high-dose (40 mg·kg-1) total ginsenosides, model, and positive control (metadoxine, 117 mg·kg-1) groups. After 3 weeks of gavage, serum samples were collected for the measurement of aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels, and liver samples were collected for hematoxylin-eosin (HE) staining. Western blot and Real-time PCR were employed to determine the protein and mRNA levels, respectively, of potential targets in the liver tissue. ResultData mining predicted the potential genes: Proto-oncogene FOS and collagen type Ⅰ alpha 2 (COL1A2). Experimental validation showed that the liver injury was alleviated after drug administration compared with that after modeling. The serum AST and ALT levels were reduced after drug administration. The protein and mRNA levels of FOS were significantly up-regulated, while those of COL1A2 were down-regulated after drug administration. ConclusionTotal ginsenosides ameliorate HA via FOS and COL1A2.
5.Construction of A Macro-evaluation Tool for Dampness Syndrome Animal Model in Traditional Chinese Medicine
Chuang LI ; Peng XU ; Ruimin TIAN ; Zhaorui CAO ; Mingjia LIU ; Lei ZHANG ; Zhaoyu LU ; Taohua LAN ; Xiaowan WANG ; Wei MAO
Journal of Traditional Chinese Medicine 2024;65(14):1449-1457
ObjectiveTo construct a macro-evaluation tool for dampness syndrome (DS) animal model, which will provide a basis for experimental research on dampness syndrome in traditional Chinese medicine (TCM). MethodsConceptual framework of this study was clarified through discussions within the core working group, and dimensions of the evaluation of the animal model of DS were identified according to TCM principles. We searched CNKI, Wanfang, VIP and SinoMed databases from the inception to June 30th, 2023, on experiments involving dampness syndrome animals to create a pool of items about DS animal models. The core items were selected and extracted for factor analysis and cluster analysis. An expert importance rating questionnaire was developed based on the results of the literature review, analyzing the distribution of item scores, importance averages, and coefficient of variation. Through a comprehensive analysis of literature, expert importance scoring, and specific expert opinions, items that did not meet anyone of the criteria of average importance rating ≥2.04, coefficient of variation ≤30%, or literature eva-luation frequency ≥2% were removed, thereafter, the macro-evaluation tool for DS animal model was preliminarily constructed. ResultsSpirit and body state, autonomic activity state, body surface characteristics, diet, urination and defecation, tongue manifestation, and motor behavior assessment were constructed as the seven dimensions in the evaluation of DS animal model. A total of 348 papers about animal experiments were included and analyzed, resulting in a saturated pool of 72 items, which was refined to 38 core items of DS animal models. Factor analysis obtained 16 common factors, which were further clustered into two categories, named dampness transforming from heat syndrome and dampness transforming from cold syndrome. The expert importance scoring showed that the Kendall harmony coefficient was 0.359 (P<0.05) indicating a high level of agreement, coordination and reliability among the experts. Notably, 50% or more of the experts considered the items thick and greasy tongue coating, unclean perianal area, loose stools, lethargy, unformed stools, and listless expression as very important. The median scores for all items were 2.04(1.73, 2.37), with a coefficient of variation ranging from 19.73% to 53.38%. After expert evaluation, the macro-evaluation tool for DS animal model in TCM with 33 items and corresponding criteria for assessing the formation of DS models was finally contructed. ConclusionThe Macro-evaluation tool for DS animal model in TCM is highly scientific, credible, and operable, and can be utilized in DS animal experiments after its characteristics are actually evaluated.