Identification of Scolopendra Dispensing Granules by Allele-specific PCR / 中国实验方剂学杂志

ObjectiveTo establish an allele-specific polymerase chain reaction （PCR） method for identifying Scolopendra dispensing granules， so as to ensure the quality and therapeutic effects of Scolopendra and its preparations. MethodThe primer interval suitable for the PCR was selected based on the cytochrome c oxidase subunit 3（COX-3） gene sequence of Scolopendra， and the single nucleotide polymorphism （SNP） loci of Scolopendra and its adulterants were mined from the interval for the design of specific primers. The samples of Scolopendra and its adulterants were collected. The PCR system was established and optimized regarding the annealing temperature， cycles， Taq enzymes， DNA template amount， PCR instruments， and primer concentrations， and the specificity and applicability of this method were evaluated. ResultThe PCR system was composed of 12.5 μL 2×M5 PCR Mix， 0.4 μL forward primer （10 μmol·L-1）， 0.4 μL reverse primer （10 μmol·L-1）， 2.5 μL DNA template， and 9.2 μL sterile double distilled water. PCR parameters： Pre-denaturation at 94 ℃ for 3 min， 30 cycles （94 ℃ for 20 s， 62 ℃ for 20 s， 72 ℃ for 45 s）， and extension at 72 ℃ for 5 min. After PCR amplification with the system and parameters above， the electrophoresis revealed a bright band at about 135 bp for Scolopendra and no band for the adulterants. ConclusionThe established allele-specific PCR method can accurately identify the medicinal materials， decoction pieces， and standard decoction freeze-dried powder of Scolopendra， as well as the intermediates and final products of Scolopendra dispensing granules， which is of great significance for ensuring the quality and clinical efficacy of Scolopendra and its preparations.

Application of metagenomic next-generation sequencing in prevention and control of infection in solid organ transplantation / 器官移植

Organ transplantation has become an effective treatment for multiple end-stage diseases. However, the recipients of organ transplantation need to take immunosuppressive drugs for a long time after operation, which leads to low immune function and relatively high incidence of bacterial, viral and fungal infections. Traditional microbial detection methods, such as pathogen culture, immunological detection and polymerase chain reaction, have been widely applied in infection detection, whereas these methods may cause problems, such as long detection time and presumed pathogens. Metagenomic next-generation sequencing has been widely adopted in infection prevention and control in organ transplantation in recent years due to high detection rate and comprehensive detection of pathogen spectrum. In this article, the application of metagenomic next-generation sequencing in the prevention and control of infection in solid organ transplantation was reviewed, aiming to provide reference for the diagnosis and treatment of transplantation-related infection.

Performance of the tetra-primer PCR technique compared to PCR-RFLP in the search for rs12979860 (C/T) and rs8099917 (T/G) single nucleotide polymorphisms (SNPs) in the IFNL4 gene / Desempenho da técnica tetra-primer PCR em relação a PCR-RFLP na pesquisa de polimorfismos de nucleotídeos únicos (SNPs) rs12979860 (C/T) e rs8099917 (T/G) no gene IFNL4

Single nucleotide polymorphisms (SNPs, rs12979860 e rs8099917) in the Interferon Lambda 4 gene (IFNL4, formerly IFNL3and/or IL28B) has been associated with failure in the innate immune response, sustained virological response in hepatitis C, and HTLV-1-associated myelopathy (HAM) development. To search for these polymorphisms several methodologies can be employed, such as sequencing, real-time or quantitative polymerase chain reaction (qPCR), restriction fragment length polymorphism analysis in PCR products (PCR-RFLP), and tetra-primer PCR. The present study compared the performance of the tetra-primer PCR in relation to the PCR-RFLP, both optimized in the Research HTLV Laboratory of the Center of Immunology of Instituto Adolfo Lutz in São Paulo. One hundred DNA samples obtained from patients of STD/Aids Reference Centre in São Paulo, previously analyzed for IL28B SNPs by PCR-RFLP were selected for analysis, after confirming that they represent all IL28B SNPs patterns described in the literature. The results obtained showed concordance between the PCR-RFLP and the tetra-primer PCR SNPs results, and because of the low cost, easy to perform, and minor employment of biological specimen and reagents, the tetra-primer PCR is of choice to be used in routine. (AU)

Polimorfismos de nucleotídeos únicos (single nucleotide polymorphisms, SNPs rs12979860 e rs8099917) no gene que codifica o Interferon Lambda 4 (IFNL4, antigamente IFNL3 e/ou IL28B) têm sido associados às falhas na resposta imune inata e resposta virológica sustentada na hepatite C, e a mielopatia associada ao HTLV-1 (HTLV-1-associated myelopathy, HAM). A pesquisa destes polimorfismos pode empregar diversas metodologias: sequenciamento, reação em cadeia da polimerase em tempo real ou quantitativa (quantitative polymerase chain reaction, qPCR), análise de fragmentos de restrição enzimática em produtos de PCR (restriction fragment length polymorphism in PCR products, PCR-RFLP) e a tetra-primer PCR. Este estudo comparou o desempenho da tetra-primer PCR em relação a PCR-RFLP, ambas otimizadas no Laboratório de Pesquisa em HTLV do Centro de Imunologia do Instituto Adolfo Lutz de São Paulo. Foram selecionadas 100 amostras de DNA obtidas de pacientes do Centro de Referência e Treinamento em DST/Aids de São Paulo cujos SNPs na IL28B foram anteriormente determinados por PCR-RFLP e representaram todos os perfis descritos em literatura. Os resultados obtidos mostraram concordância entre elas, e pelo fato da tetra-primer PCR ter menor custo, ser de fácil execução, empregar menos tempo, insumos e material biológico, é a técnica de escolha para uso em rotina. (AU)

Molecular detection of oral Trichomonas tenax in periodontal disease patients by polymerase chain reaction -based 18S rRNA gene

@#Trichomonas tenax, an oral flagellated protozoon found in humans, potentially associated with the inflammation of periodontal tissues and decreased immunity that causes the tissue damage and tooth loss from chronic infection. Currently, there is a lack of data regarding the prevalence of T. tenax infection in Thailand. Therefore, this study aimed to measure prevalence of T. tenax in periodontal disease patients by using polymerase chain reaction (PCR) to amplify the 18S ribosomal RNA (18S rRNA) gene and to determine the factors associated with the presence of this protozoan. A cross-sectional descriptive study was conducted among 230 patients with periodontal disease, who visited the oral health center of Suranaree University of Technology Hospital, Thailand from 2021 to 2022. Dental plaque specimens were collected and examined to identify the presence of T. tenax using the PCR-based 18S rRNA gene. The occurrence of factors associated with T. tenax infection was analyzed by the chi-square test and binary logistic regression. The prevalence of T. tenax infection was 13.48% (31/230), in patients, including 96.77% (30/31) and 3.23% (1/31) in periodontitis and gingivitis patients, respectively. The presence of T. tenax was associated with periodontal disease (p<0.001) and the Periodontal Screening and Record (PSR) index (p=0.001). The significant risk factors for T. tenax infection were periodontitis (ORadj=239.89, 95% CI=23.801-2417.746), no-underlying disease (ORadj=0.31, 95% CI=0.099–0.942), and male sex (ORadj=0.25, 95% CI=0.062-0.981). Dentists should be concerned about this oral protozoan in periodontitis patients. Furthermore, epidemiologic studies of T. tenax are still needed to investigate the mechanism of pathogenesis from T. tenax infection.

Oral parasitic protozoan Entamoeba gingivalis in periodontal disease patients, northeastern Thailand

@#Entamoeba gingivalis is present in the oral cavity of humans and is associated with periodontal disease. Consequently, this study aimed to comprehensively investigate the E. gingivalis infection and the associated risk factors among individuals suffering from periodontal conditions. A cross-sectional descriptive study was carried out within a cohort of periodontal patients. Dental plaque specimens were meticulously collected and subsequently subjected to thorough examination using the polymerase chain reaction (PCR)-based technique targeting the small subunit ribosomal RNA (SrRNA) gene of the organism. The occurrence of risk factors for E. gingivalis infection was analyzed by the chi-square test and binary logistic regression. Out of the 230 participants, 60 were clinically diagnosed with periodontitis, while 170 were afflicted with gingivitis. Out of the 230 patients, 25 (10.9%) tested positive for E. gingivalis infections. An in-depth analysis unveiled that a significant majority of infections were recorded within subgroups characterized by a marital status (15.45%), manifestation of periodontitis (25.00%), and concomitant presence of underlying disease (20.83%). Furthermore, the high risk factor associated with E. gingivalis infection was the female (ORadj = 13.65, 95% CI = 1.08-173.21), followed by periodontitis (ORadj = 3.30, 95% CI = 1.21-9.00), respectively. The study employs a molecular diagnostic approach to screen for E. gingivalis enrichment within a subset of periodontal patients with advancing disease. The findings emphasize the necessity for further research to elucidate the pathogenesis of E. gingivalis and advocate for vigilant surveillance within a substantial population of periodontal patients.

Comparison of Effect of Euodiae Fructus Processed with Different Proportions of Glycyrrhizae Radix et Rhizoma on Oxidative Stress and Autophagy in Mouse Liver Under Toxic Dose / 中国实验方剂学杂志

ObjectiveTo investigate the principle and scientific connotation of Euodiae Fructus（EF） processed with Glycyrrhizae Radix et Rhizoma（Gly） by comparing the effects of unprocessed products of EF（UEF） and processed products of EF with the different proportions of Gly（GEFs） at toxic doses on oxidative stress and autophagy in the liver of mice. MethodSeventy mice were randomly divided into 7 groups， namely the control group， the UEF group， the group of the processed products of EF without Gly（PEF） and 4 groups of GEFs（the mass ratios of EF to Gly were 100∶3， 100∶6， 100∶12 and 100∶24， respectively， hereinafter referred to as the processed products of EF with the mass ratios of 100∶3， 100∶6， 100∶12 and 100∶24 of Gly）. The mice were given purified water， the decoction of UEF， PEF and GEFs by gavage at a dose of 30 g·kg-1. PEF and GEFs were prepared according to the method under EF in the 2020 edition of Chinese Pharmacopoeia. Levels of alanine aminotransferase（ALT） and aspartate aminotransferase（AST） were determined by ultraviolet-visible spectrophotometry， hematoxylin-eosin（HE） staining was used to evaluate the pathological changes of liver tissue， the level of reactive oxygen species（ROS） was detected by fluorescence method， the mRNA expression of heme oxygenase-1（HO-1）， quinone oxidoreductase-1（NQO1）， glutathione-S-transferase 1（GSTA1）， Kelch-like epichlorohydrin-associated protein 1（Keap1） and p62 were measured by Real-time fluorescence quantitative polymerase chain reaction（Real-time PCR）， western blot was used to detect the protein expression of phosphorylated mammal target of rapamycin（p-mTOR）， phosphorylated ribosomal p70 S6 protein kinase（p-p70S6K）， p62， microtubule-associated protein 1 light chain 3Ⅰ（LC3Ⅰ） and LC3Ⅱ. ResultCompared with the control group， after 7 d of administration， the increase in body mass of mice in the UEF group began to slow down and the difference gradually increased， and the liver body index significantly increased（P<0.01）， pathomorphological observation showed that the structure of hepatic lobules was disordered， and local hepatic sinuses were narrowed or disappeared， and there were inflammatory infiltration and local bleeding， the levels of ALT and AST in serum and ROS in liver tissue were significantly increased（P<0.01）， and the expressions of Keap1， HO-1， NQO1， GSTA1， p62 mRNA and p-mTOR， p-p70S6K， p62 protein in liver tissue were significantly decreased（P<0.01）， and LC3Ⅱ/LC3Ⅰ was significantly increased（P<0.01）. Compared with the UEF group， the body mass of mice increased， and the liver body index， the levels of ALT and AST in serum， and the level of ROS in liver tissue all decreased in the groups of PEF and GEFs. Among these groups， only the liver lobules in GEF（100∶6） group were intact， and the size of liver sinuses was close to that in the control group. The mRNA expressions of Keap1， HO-1， NQO1， GSTA1 and p62 in liver tissue showed an overall upward trend in the groups of PEF and GEFs. Among these groups， only the ones of the above mRNA in the GEF（100∶6） group had a significant increase（P<0.05， P<0.01）. The protein expressions of p-mTOR， p-p70S6K， p62 and LC3Ⅱ/LC3Ⅰ had a callback in the groups of PEF and GEFs， of which the protein expressions of p-mTOR， p-p70S6K and LC3Ⅱ/LC3Ⅰ in the GEF（100∶6） group and the expression of p62 protein in the GEF（100∶24） group had the largest callback. Except for p-mTOR protein， other protein expressions were statistically significant（P<0.05， P<0.01）. ConclusionThe hepatotoxicity of EF is closely related to its ability to induce oxidative stress， which leads to pathological autophagy and hepatocyte damage. This ability can be reduced by the processing with different proportions of Gly， especially the ratio of 100∶6.

Evolution of the newest diagnostic methods for COVID-19: a Chinese perspective / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Coronavirus disease 2019 (COVID-19) has continued to spread globally since late 2019, representing a formidable challenge to the world's healthcare systems, wreaking havoc, and spreading rapidly through human contact. With fever, fatigue, and a persistent dry cough being the hallmark symptoms, this disease threatened to destabilize the delicate balance of our global community. Rapid and accurate diagnosis of COVID-19 is a prerequisite for understanding the number of confirmed cases in the world or a region, and an important factor in epidemic assessment and the development of control measures. It also plays a crucial role in ensuring that patients receive the appropriate medical treatment, leading to optimal patient care. Reverse transcription-polymerase chain reaction (RT-PCR) technology is currently the most mature method for detecting viral nucleic acids, but it has many drawbacks. Meanwhile, a variety of COVID-19 detection methods, including molecular biological diagnostic, immunodiagnostic, imaging, and artificial intelligence methods have been developed and applied in clinical practice to meet diverse scenarios and needs. These methods can help clinicians diagnose and treat COVID-19 patients. This review describes the variety of such methods used in China, providing an important reference in the field of the clinical diagnosis of COVID-19.

Differential expression of sigma factor of Mycobacterium tuberculosis under in vivo infection and in vitro culture conditions / 公共卫生与预防医学

Objective To investigate the gene expression of sigma factors in vivo, and to explore the sigma factors that may be closely related to the virulence of pathogenic Mycobacterium tuberculosis Methods Tuberculosis (TB) patients diagnosed in the outpatient department of Tianjin Tuberculosis Control Center from January to December 2018 were selected, and 20 sputum-positive specimens were randomly selected from TB patients confirmed with Xpert-positive for the present study. Two immediate sputum specimens were collected from each case of pulmonary tuberculosis before treatment, one for RNA extraction and one for in vitro culture. In vitro cultured strains in the logarithmic phase of growth were harvested for RNA extraction. The specific primers for 13 sigma factors were designed. The differential expression of the 13 sigma factors between sputum isolates and in vitro cultured strains was analyzed by fluorescence quantitative PCR. Taking ribosomal 16s as the reference gene, the transcription level of sigma factors was analyzed by 2ΔCt. Using the stably expressed sigA as the control reference, the expression differences of other sigma factors were analyzed by one-way ANOVA. Results Within 0 days, stress-associated sigma factors have a different expression profile in clinical isolate strains vs H37Rv or in vitro. All the sigma factors induced up regulation in sputum ,while no difference transcription between clinical isolate strains vs H37Rv（P＞0.05）. When compared to in vitro culture ,only sigM transcript highest in sputum(P＜0.05). Conclusion SigM plays an important role in the initial stages of bacterial infection, but its exact role is unclear.We assumed it could have a role in the interplay between the host immune defenses and the bacterial escape mechanisms.

Analysis on Changes of Aquaporin and Intestinal Flora in a Rat Model with Spleen-Yin Deficiency Syndrome / 中国实验方剂学杂志

ObjectiveTo investigate the effects of spleen-Yin deficiency on gastrointestinal absorption， water metabolism and intestinal flora in rats with spleen-Yin deficiency syndrome. MethodA rat model of spleen-Yin deficiency syndrome was established by using the composite factors， including irregular meat and vegetable diet， weight-bearing fatigue swimming and gavage with warm-heat injury-Yin drugs. The changes of body weight， food intake， water intake and duration of swimming in the blank and model groups were observed. Hematoxylin-eosin（HE） staining was used to observe the histopathological damage of the stomach and colon. Urinary excretion rate of D-xylose was determined by phloroglucinol method. The content of gastrin（GAS） in serum was determined by enzyme-linked immunosorbent assay（ELISA）. The relative expression levels of vasoactive intestinal peptide（VIP）， aquaporin 3（AQP3） and AQP4 in gastric tissues were detected by Western blot. The relative mRNA expression levels of VIP， AQP3 and AQP4 in gastric tissues were detected by Real-time fluorescence quantitative polymerase chain reaction（Real-time PCR）， and the changes of intestinal flora were analyzed by 16S rDNA sequencing. ResultCompared with the blank group， the results of general physical signs showed that the body weight and food intake of rats in the model group were significantly decreased， the water intake was significantly increased（P<0.05， P<0.01）， and the duration of swimming was significantly decreased（P<0.01）. Pathological examination results showed that in the mucosa of gastric tissues of rats in the model group appeared to be misaligned， the mucosa of colonic tissues could be seen to be obviously thinned or mutilated， and the epithelial cells appeared to be necrotic or even exfoliated. Compared with the blank group， the urinary D-xylose excretion rate of rats in the model group was significantly decreased（P<0.01）， and the serum GAS content was significantly decreased（P<0.05）. Compared with the blank group， Western blot results showed that the relative expression level of VIP protein in gastric tissues of rats in the model group was significantly decreased， while the relative expression levels of AQP4 and AQP3 proteins were significantly increased（P<0.01）. Compared with the blank group， Real-time PCR results showed that the relative expression level of VIP mRNA in gastric tissues of rats in the model group was significantly decreased（P<0.01）， and the relative mRNA expression levels of AQP3 and AQP4 were significantly increased（P<0.05， P<0.01）. Compared with the blank group， the results of intestinal flora analysis showed that the number of operational taxonomic units（OTUs） and α-diversity increased and β-diversity decreased significantly in the model group， the abundance of Porphyromonadaceae was increased significantly， and the abundance of Oscillibacter_ruminantium was decreased significantly（P<0.05）. Spearman correlation analysis showed that Porphyromonadaceae was significantly positively correlated with AQP4 protein level， while Oscillibacter_ruminantium was significantly positively correlated with VIP protein level， and negatively correlated with AQP3 and AQP4 protein levels（P<0.05）. Linear discriminant analysis effect size（LEfSe） analysis results showed that there were significant differences in a variety of intestinal bacteria between groups， and the intestinal bacteria of the model group were significantly enriched in the phylum/order/family/genus of Elusimicrobia， Betaproteobacteria， Burkholderiales， Sutterellaceae and Parasutterella（P<0.05）. ConclusionSpleen-Yin deficiency syndrome can weaken the digestion and absorption capacity of gastrointestinal tract， and cause the disturbance of water metabolism and intestinal flora. AQP4， AQP3 and VIP protein levels of gastric mucosa are closely related to Porphyromonadaceae and Oscillibacter_ruminantium. And AQP4， AQP3 and VIP may be involved in the regulation of intestinal flora in order to affect the physiological function of spleen governing transportation and transformation.

Organ transplantation and parasitic infection / 器官移植

Parasitic infection is manifested with the characteristics of both endemic and infectious diseases, and the onset of parasitic infection is regional and infectious. The incidence of parasitic infection after organ transplantation is relatively low, primarily occurring in single case or case series in developing countries and regions. With the development of social economy and a gradual increasing number of organ transplantation, the risk of parasitic exposure is increased when the recipients travel among different countries or regions. In addition, immunosuppression is the risk factor of parasitic infection. Consequently, the risk of parasitic infection in organ transplant recipients cannot be ignored. In this article, epidemiological characteristics, clinical manifestations, diagnosis, treatment and prevention of parasitic infection after organ transplantation were classified and summarized according to literature review, aiming to provide reference for the prevention and treatment of parasitic infection in organ transplant recipients.

Specific PCR Identification of Hibisci Cortex and Its Adulterants Based on DNA Signature Sequence Tags / 中国实验方剂学杂志

ObjectiveUncommon medicinal herbs are valuable medicinal resources， but their identification is a difficult problem in Chinese medicine due to their particularity and complexity. It is， therefore， urgent to establish a method for the identification of uncommon medicinal herbs. In this study， DNA signature sequence （DSS） tags were used to establish a specific polymerase chain reaction （PCR） identification method for Hibisci Cortex， the origin plant of Hibisci Cortex， and its adulterants. MethodThe candidate DSS tags were obtained from the chloroplast genome sequence analysis， and the DSS tags were verified by DNA sequencing. The specific identification primers for H. syriacus were designed based on the obtained reliable DSS tags. The PCR reaction conditions were optimized， and the tolerance and feasibility were investigated. ResultA DSS tag for identification of H. syriacus was obtained from the comparison of sequencing results of the amplified products with DSS， which revealed the distinguishing characteristics of Hibisci Cortex and its adulterants. A pair of specific primers for H. syriacus was designed according to the DSS tag. After PCR amplification and gel electrophoresis with the primers， a single bright band of about 270 bp was observed from H. syriacus， which did not appear in the four adulterants. ConclusionA DSS tag obtained in this study can be used to identify H. syriacus. The specific primers designed based on this DSS tag can accurately and simply identify the original plant of Hibisci Cortex and its adulterants， which provides a new method and idea for the molecular identification of genuine and counterfeit products of Hibisci Cortex.

Identification of Pheretima （Pheretima aspergillum） Formula Granule by Allele-specific PCR / 中国实验方剂学杂志

ObjectiveIn order to ensure the safety and effectiveness of clinical drug use ， the identification method of mixed and adulterated specific polymerase chain reaction （PCR） identification of Pheretima aspergillum and its processed products was established. MethodBased on the cytochrome C oxidase subunit I sequence of P. aspergillum， primers were designed to cover the whole sequences， and the stable DNA ranges suitable for the identification of Pheretima （P. aspergillum） formula granule were screened out. Specific primers were designed according to the specific single nucleotide polymorphisms （SNP） of P. aspergillum in the stable DNA range. The P. aspergillum and its mixture were collected respectively， the PCR reaction system was established and optimized， and PCR reaction system and procedure were optimized， and the tolerance and applicability were investigated. ResultWhen the annealing temperature was 62 ℃ and the cycle number was 36， both P. aspergillum formula granule and its formula particles could amplify a single specific identification band of about 170 bp， and the other 20 adulterants and negative controls had no band. ConclusionThe allele-specific PCR identification method established in this study can quickly and accurately identify the P. aspergillum formula granule. The orgin of Chinese herbal medicine and decoction pieces and P. aspergillum were accurately identified. It can also provide a reference for other studies on the quality standard research of other Chinese herbal formula granule.

Identification of Murrayae Folium et Cacumen by Multiplex Allele-Specific PCR / 中国实验方剂学杂志

ObjectiveTo establish a polymerase chain reaction（PCR） method to accurately discriminate the crude materials of Murrayae Folium et Cacumen， Murraya exotica and M. paniculata. MethodBased on the difference in chloroplast genome sequences of M. exotica and M. paniculata， species-specific identification primers P03 and P04 of M. exotica and M. paniculata were designed according to single nucleotide polymorphism （SNP） on the chloroplast genome. A multiplex allele-specific PCR identification method was established for the identification of M. exotica and M. paniculata following the optimization of annealing temperature， number of cycles， and primer concentration ratio. The established PCR method for identification was explored and verified in terms of tolerance and feasibility by investigating the type of Taq polymerases and PCR system model. ResultIn this multiplex allele-specific PCR identification method， about 330 and 230 bp of specific fragments were amplified from DNA templates of M. exotica and M. paniculata， respectively， under the following conditions：cycle number of 31， annealing temperature of 60 ℃， and primer concentration ratio of P03 and P04 of 1∶2. Consistent results were obtained for samples from different sources. ConclusionThe multiplex allele-specific PCR identification method established in this study can accurately identify the origin of Murrayae Folium et Cacumen， which can be used for the simultaneous identification of M. exotica and M. paniculata by the length of fragments in a single identification assay.

Phylogenetic and Mutation Points Analysis of Sophora japonica cv. jinhuai Based on DNA Barcoding Sequences / 中国实验方剂学杂志

ObjectiveTo conduct phylogenetic analysis of internal transcribed spacer 2 （ITS2） and chloroplast gene segments including psbA-trnH， rbcL， and matK of Sophora japonica cv. jinhuai resource samples from different geographical sources， and to explore the genetic diversity of S. japonica cv. jinhuai. MethodPolymerase chain reaction （PCR） method was used to amplify the nucleic acid sequences of ITS2， psbA-trnH， rbcL， and matK of S. japonica cv. jinhuai. Neighbor joining （NJ） method was used to construct phylogenetic trees， and Kimura 2-Parameter （K2P） model was used to calculate the genetic distance of different samples. MEGA and BIOEDIT softwares were applied for mutiple alignment and analysis of ITS2， psbA-trnH， rbcL， and matK sequences of S. japonica cv. jinhuai. ResultThe lengths of ITS2 sequence were 278-279 bp. The lengths of psbA-trnH were 289 bp. The lengths of rbcL sequence were 673 bp. The lengths of matK sequences were 786-792 bp. There were 3 mutation points in ITS2 and psbA-trnH， no mutation point in rbcL， and 13 mutation points in matK. The samples of S. japonica cv. jinhuai were clustered into two groups based on the phylogenetic tree constructed by ITS2 sequences. The sample of seedling tree in Baibao was clustered into one group， while the other 25 samples were clustered into another group. For the psbA-trnH sequence， the success rate of PCR amplification of 28 samples of S. japonica cv. jinhuai was 100%. The 28 samples of S. japonica cv. jinhuai were clustered into three groups based on the clustering results of psbA-trnH sequence. The sample of seedling tree in Shaoshui was clustered into one group. The five samples of grafting tree and seedling tree in Miaotou， grafting trees in Jiantang， Wenqiao， and Daxu， and seeding tree in Xianshui were clustered into one group. The other 21 samples were clustered into another group. The 26 samples of S. japonica cv. jinhuai were clustered into two groups based on the phylogenetic tree constructed by matK sequences. The sample of seedling tree in Xianshui was clustered into one group， while the other 25 samples were clustered into another group. The clustering results of the rbcL sequence of S. japonica cv. jinhuai could not distinguish 28 resource samples. The phylogenetic tree constructed by the combined sequence of ITS2+psbA-trnH+rbcL+matK divided S. japonica cv. jinhuai resource samples into 4 groups. The 13 samples of seedling trees in Qiyang， Daoxian， Miaotou， Shaoshui， Shitang， Xianshui， Jiantang， and Xiangli， and grafting trees in Qiyang， Miaotou， Yongsui， Wenqiao， and Yangtang were clustered into one group. The sample of seedling tree in Wenqiao was clustered into one group. The sample of seedling tree in Daxu was clustered into one group. The remaining samples were clustered into another group. ConclusionPhylogenetic and mutation analysis provide the theoretic foundation to investigate the evolution of the resources of S. japonica cv. jinhuai， and evaluate their genuineness. The results of mutation points can be used to identify the related S. japonica cv. jinhuai resources. The findings of this study show that the combination of different gene sequences has an optimal effect on plant identification.

Mechanism of Aconiti Kusnezoffii Radix Processed with Chebulae Fructus Against H9c2 Cardiomyocyte Toxicity Based on TRPV1 Channel / 中国实验方剂学杂志

ObjectiveTo explore the role of transient receptor potential vanilloid 1 （TRPV1） channel in reducing cardiomyocyte toxicity of Aconiti Kusnezoffii Radix processed with Chebulae Fructus. MethodH9c2 cardiomyocytes cultured in vitro were used as a model to assess cell viability by methyl thiazolyl tetrazolium （MTT） assay， the expression of TRPV1 mRNA was detected by real-time fluorescence quantitative polymerase chain reaction （Real-time PCR）， and the leakage rate of lactate dehydrogenase （LDH）， the changes of nucleus， reactive oxygen species （ROS）， mitochondrial membrane potential and Ca2+ contents were detected by enzyme linked immunosorbent assay （ELISA）. ResultCompared with the blank group， when the concentration was ≥0.5 g·L-1， the cell viability was significantly decreased （P<0.01）， the leakage rate of LDH， the release of ROS and Ca2+ were increased， the mitochondrial membrane potential was decreased， and the nucleus was pyknosis or even broken in raw Aconiti Kusnezoffii Radix and Aconiti Kusnezoffii Radix processed with Chebulae Fructus groups. When the concentration was ≥0.5 g·L-1， compared with the same mass concentration of raw Aconiti Kusnezoffii Radix group， the cell viability increased significantly （P<0.01）， the leakage rate of LDH， the release of ROS and Ca2+ decreased， the mitochondrial membrane potential increased， and the nuclear morphology improved in Aconiti Kusnezoffii Radix processed with Chebulae Fructus group. Application of the same mass concentration of raw Aconiti Kusnezoffii Radix to H9c2 cardiomyocytes pretreated with the TRPV1 inhibitor BCTC significantly increased cell viability， decreased leakage rate of LDH， ROS and Ca2+ release， increased mitochondrial membrane potential and improved nuclear pyknosis compared with untreated H9c2 cardiomyocytes. Application of the same mass concentration of Aconiti Kusnezoffii Radix processed with Chebulae Fructus to H9c2 cardiomyocytes pretreated with BCTC decreased cell viability， increased LDH leakage rate， ROS and Ca2+ release， reduced mitochondrial membrane potential compared with untreated H9c2 cardiomyocytes. Real-time PCR results showed that both raw Aconiti Kusnezoffii Radix and Chebulae Fructus decoction could increase the expression of TRPV1 mRNA in cardiomyocytes in a concentration dependent manner. ConclusionRaw Aconiti Kusnezoffii Radix can induce cardiomyocyte apoptosis and cardiotoxicity by activating TRPV1 channel， while Aconiti Kusnezoffii Radix processed with Chebulae Fructus can attenuate the toxicity through TRPV1 channel， which may be related to the synergistic effect of acid components in Chebulae Fructus and alkaloids in Aconiti Kusnezoffii Radix on TRPV1 channel.

Diagnosis of neurosyphilis with cerebrospinal fluid pcr: a systematic review

ABSTRACT Background Neurosyphilis is difficult to be diagnosed. CSF VDRL is the gold standard, but its sensitivity is low. Cerebrospinal fluid (CSF) PCR for the detection of Treponema pallidum DNA has been evaluated; however, its diagnostic value is still poorly understood. Methods Here we performed a systematic review including articles that assessed the diagnostic sensitivity of CSF PCR in patients with syphilis and neurosyphilis. The CSF PCR sensitivity and specificity of different PCR assays was assessed in patients with neurosyphilis with or without HIV coinfection and in patients with syphilis with no central nervous system (CNS) manifestations. Results Eighteen studies evaluating 703 patients were included. The PCR sensitivity for neurosyphilis was 73.9% among HIV negative and 37.5% among HIV infected patients, having varied from 62.2% to 100% with different PCR assays. The sensitivity of CSF VDRL CSF was 68% in the same population. The specificity of CSF PCR was 93%. CSFPCR was positive in16.4% of the patients with primary and secondary syphilisand 28.9% of patients with latent syphilis. None of the syphilis cases without neurological manifestations were positive with CSF VDRL. Conclusion CSF PCR seems to be at least as sensitive as CSF VDRL, with good specificity. In addition, CSF PCR may potentially reveal early neuroinvasion in patients withsyphilis with no CNS symptoms. Future studies are still needed to assess the potential clinical value of detecting T. pallidum DNA in CSF in syphilis cases prior to the development of CNS symptoms.

Analysis of Salivary Bacterial Community by Direct PCR and High Resolution Melting Curve and Its Forensic Applications / 法医学杂志

OBJECTIVES@#To develop a rapid test for salivary bacterial community based on direct PCR (dPCR) and high resolution melting (HRM) curve analysis, to evaluate its application value in forensic medicine.@*METHODS@#The salivary bacteria were collected by centrifugation and then resuspended in Tris-EDTA (TE) buffer, and directly used as the template for amplification and HRM curve analysis (dPCR-HRM) of the 16S rDNA V4 region. The genotype confidence percentage (GCP) of the HRM profiles compared with the reference profile was calculated. The template DNA was extracted by traditional kit and then PCR-HRM (namely kPCR-HRM) was used as reference to validate the feasibility of dPCR-HRM. The gradient dilution templates, population samples and simulated salivary stains were analyzed by dPCR-HRM to evaluate its sensitivity, typing ability and adaptability.@*RESULTS@#Using dPCR-HRM method, the HRM profiles of salivary bacterial community were obtained within 90 minutes. The GCP between dPCR-HRM and kPCR-HRM was greater than 95.85%. For general individuals, the HRM type of bacterial community could be determined with 0.29 nL saliva by dPCR-HRM. The 61 saliva samples could be divided into 10 types. The typing of salivary stains deposited within 8 h was the same as those of fresh saliva (GCP>90.83%).@*CONCLUSIONS@#dPCR-HRM technology can be used for rapid typing of salivary bacterial community, and has the advantage of low cost and simple operation.

ROLE OF REAL TIME PCR (RT-PCR) IN CLINICAL DIAGNOSIS FOR COVID-19 REVIEW

The pandemic of Coronavirus Disease 2019 (COVID19) has compelled scientists to create highly reliable diagnostic tools quickly in order to successfully and properly diagnose this pathology and thereby prevent infection transmission. Even though structural and molecular properties of the severe acute respiratory syndrome coronavirus 2 (SARSCoV2) were previously unknown, private research institutes and biomedical firms quickly developed numerous diagnostic procedures beneficial for making a correct detection of COVID19. Rapid antigen or antibody testing, immunoenzymatic serological tests, and RT-PCR based molecular assays are the most frequently used and validated procedures now available. The PCR has grown in popularity in molecular diagnostics to the point where it is still considered the gold standard for finding nucleotides from a variety of sources becoming an indispensable tool in the research lab. Because of its improved speed, sensitivity, reproducibility, and lower likelihood of carry-over contamination, real-time PCR has gained greater popularity. Currently, five different chemistries are employed to detect PCR product during real-time PCR. The self- fluorescing amplicons, DNA binding fluorophores, 5? endonuclease, neighbouring linear and hairpin oligoprobes, and self-fluorescing amplicons are all detailed in depth. We also go through the problems that have hampered the development of multiplex real-time PCR and the importance of real-time PCR in nucleic acid quantification.

Identification of Armeniacae Semen Amarum Adulterated in Persicae Semen by Allele-specific Polymerase Chain Reaction / 中国实验方剂学杂志

Objective:Due to the limitation of traditional identification methods of Chinese medicinal materials， the study established a rapid method to identify Persicae Semen mixed with Armeniacae Semen Amarum by allele-specific polymerase chain reaction （PCR）. Method:By comparing the ribosomal DNA internal transcribed spacer （ITS） gene sequences of Persicae Semen and Armeniacae Semen Amarum， single nucleotide polymorphism （SNP） sites were searched and specific primers were designed. Different Persicae Semen and Armeniacae Semen Amarum samples were amplified by PCR， the effects of annealing temperature， primer concentration and cycle number on the PCR reaction system were optimized， and the specificity and detection limit of this method were investigated. In addition， the established PCR method was used to detect the samples of Persicae Semen mixed with different proportion of Armeniacae Semen Amarum from different sources and producing areas. Result:A specific PCR method for identifying Persicae Semen mixed with Armeniacae Semen Amarum was established. When the annealing temperature was 63 ℃ and the number of primer cycles was 30， only Armeniacae Semen Amarum could be amplified with 432 bp specific band， while Persicae Semen samples did not have this band. The minimum detection limit of this method for Armeniacae Semen Amarum was 0.2 ng， and the detection limit for Armeniacae Semen Amarum adulterated in Persicae Semen was 1%. Conclusion:The established allele-specific PCR method can accurately detect whether there is Armeniacae Semen Amarum in Persicae Semen， which can provide experimental basis for the quality control of Persicae Semen and guarantee the safety of its clinical use.

Cloning，Bioinformatics and Expression Analysis of UGDH1 Gene in Glycyrrhiza uralensis / 中国实验方剂学杂志

Objective:To clone uridine diphosphate （UDP）-glucose dehydrogenase （<italic>UGDH</italic>） gene of <italic>Glycyrrhiza uralensis</italic> and analyze its bioinformatics and expression. Method:Total RNA was extracted from roots， stems， and leaves of 6-week-old seedlings of <italic>G. uralensis</italic>， the complementary deoxyribonucleic acid （cDNA） sequence of <italic>GuUGDH</italic>1 gene （Gu was short for <italic>G. uralensis</italic>） was cloned by reverse transcription polymerase chain reaction （RT-PCR）， then sequencing and bioinformatic analysis were performed， and the specificity of the tissue was analyzed by real-time fluorescence quantitative PCR （Real-time PCR）. Result:The open reading frame（ORF）of <italic>GuUGDH</italic>1 gene was 1 443 bp in length and encoded 480 amino acid residues （GenBank accession number of MT968993）. Bioinformatics analysis showed that GuUGDH1 was a stable acidic hydrophilic protein with a relative molecular weight of 53.056 kDa， an isoelectric point of 5.89， no signal peptide and no transmembrane helix， and all of them were outside the membrane. There were three typical conserved domains， which belonged to the UDP-glucose/guanosine diphosphate （GDP）-mannose dehydrogenase family. Phylogenetic analysis showed that the <italic>GuUGDH</italic>1 gene was closely related to <italic>Glycine max</italic> and <italic>Spatholobus suberectus</italic>. The results of Real-time PCR showed that the expression of <italic>GuUGDH</italic>1 gene could be detected in the roots， stems， and leaves of 6-week-old seedlings of <italic>G. uralensis</italic>， and the expression level in the roots was significantly higher than that in the stems and leaves. Conclusion:In this study， the <italic>UGDH</italic>1 gene of <italic>G. uralensis</italic> was cloned and its protein sequence characteristics were systematically analyzed， which can provide theoretical basis for further research on the catalytic function of UGDH1 protein.