Genetic diversity analysis and fingerprinting of 175 Chimonanthus praecox germplasm based on SSR molecular marker / 生物工程学报

The elucidation of resources pertaining to the Chimonanthus praecox varieties and the establishment of a fingerprint serve as crucial underpinnings for advancing scientific inquiry and industrial progress in relation to C. praecox. Employing the SSR molecular marker technology, an exploration of the genetic diversity of 175 C. praecox varieties (lines) in the Yanling region was conducted, and an analysis of the genetic diversity among these varieties was carried out using the UPDM clustering method in NTSYSpc 2.1 software. We analyzed the genetic structure of 175 germplasm using Structure v2.3.3 software based on a Bayesian model. General linear model (GLM) association was utilized to analyze traits and markers. The genetic diversity analysis revealed a mean number of alleles (Na) of 6.857, a mean expected heterozygosity (He) of 0.496 3, a mean observed heterozygosity (Ho) of 0.503 7, a mean genetic diversity index of Nei՚s of 0.494 9, and a mean Shannon information index of 0.995 8. These results suggest that the C. praecox population in Yanling exhibits a rich genetic diversity. Additionally, the population structure and the UPDM clustering were examined. In the GLM model, a total of fifteen marker loci exhibited significant (P < 0.05) association with eight phenotypic traits, with the explained phenotypic variation ranging from 14.90% to 36.03%. The construction of fingerprints for C. praecox varieties (lines) was accomplished by utilizing eleven primer pairs with the highest polymorphic information content, resulting in the analysis of 175 SSR markers. The present study offers a thorough examination of the genetic diversity and SSR molecular markers of C. praecox in Yanling, and establishes a fundamental germplasm repository of C. praecox, thereby furnishing theoretical underpinnings for the selection and cultivation of novel and superior C. praecox varieties, varietal identification, and resource preservation and exploitation.

Identification and expression analysis of the YABBY gene family in strawberry / 生物工程学报

YABBY proteins are important transcription factors that regulate morphogenesis and organ development in plants. In order to study the YABBY of strawberry, bioinformatic technique were used to identify the YABBY gene families in Fragaria vesca (diploid) and Fragaria×ananassa (octoploid), and then analyze the sequence characters, phylogeny and collinearity of the family members. The RNA-seq data and the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) technique were used to assay the expression patterns of the family members. A green fluorescent protein (GFP) was fused with FvYABBYs and transiently expressed in tobacco leaf cells for the subcellular localization. As the results, six FvYABBY genes and 26 FxaYABBY genes were identified from F. vesca and F.×ananassa, respectively. The FvYABBY genes were grouped into five clades, and five family members were orthologous with AtYABBY genes of Arabidopsis. In F. vesca, all of the FvYABBYs were basically not expressed not expressed in root and receptacle, while FvYABBY1, FvYABBY2, FvYABBY5 and FvYABBY6 were highly expressed in leaf, shoot, flower and achene. In F.×ananassa, FxaYABBY1, FxaYABBY2, FxaYABBY5 and FxaYABBY6 were expressed in achene, and all FxaYABBY were poorly or not expressed in receptacle. Additionally, under the abiotic stresses of low temperature, high salt and drought, the expression of FvYABBY1, FvYABBY3, FvYABBY4 and FvYABBY6 were down-regulated, FvYABBY5 was up-regulated, and FvYABBY2 was up-regulated and then down-regulated. In tobacco leaf cells, the subcellular localization of FvYABBY proteins were in the nucleus. These results provides a foundation for the functional researches of YABBY gene in strawberry.

Progress of Microsatellite (GT/CA)n Repeat Polymorphisms in Non-small Cell Lung Cancer / 肿瘤防治研究

Non-small cell lung cancer (NSCLC) is the most important histological type of lung cancer. This disease affects a large number of patients, and the prognosis of advanced patients is poor. Although great progress has been achieved for existing treatment methods, challenges still exist. Cancer is a genetic disease, and its occurrence is accompanied by substantial genomic-sequence instability. (GT/CA)n repeat sequence is a common microsatellite sequence serving as transcriptional function-related regions, DNA-methylation modification sites, and other functional sites. Its polymorphism is closely related to the expression of EGFR, HO-1, and HIF-1α in NSCLC patients. (GT/CA)n repeat sequence is the breakthrough point to explore the molecular mechanism of NSCLC occurrence and development, develop molecular markers for diagnosis and prognosis and epigenetics research. This paper summarizes the studies on (GT/CA)n repeat polymorphisms in NSCLC with the aim of providing references for relevant NSCLC research.

Isolation and identification of Coxsackievirus A16 strains in Kunming,Yunnan Province in 2019 and analysis of genetic characteristics of VP1 gene / 中国生物制品学杂志

@#Objective To analyze the genetic characteristics of the entire VP1 gene of Coxsackievirus A16(CVA16) strains isolated from the feces of patients with hand,foot and mouth disease(HFMD) in Yunnan Province in 2019.Methods The virus was isolated from human embryonic lung diploid fibroblast(KMB-17) cells and African green monkey kidney(Vero)cells,and the primers for the complete VP1 gene sequence of CVA16 were designed.The target fragment was amplified by RT-PCR and sequenced;the complete VP1 sequence was analyzed by softwares such as MEGA 7.0 and Geneious 9.0.2.Results A total of 26 CVA16 strains were isolated,including eight KMB-17 isolates and 18 Vero isolates.Twenty CVA16isolates were randomly selected for analysis,and three isolates were found to have Bla and 17 B1b genotypes;the nucleotide and amino acid homology of 17 CVA16 B1b isolates were 93.8%—100% and 98.3%—100%,and the nucleotide and amino acid homology with other domestic isolates was 91.1 %—99.2% and 97.3%—99.0%,respectively;the nucleotide and amino acid homology of the three Bla isolates was 98.0%—98.1% and 99.3%,and those with other domestic Bla isolates was 88.7%—98.1% and 98.3%—99.7%,respectively;17 B1b isolates and other three Bla isolates showed the nucleotide and amino acid homology of 87.4%—88.4% and 97.3%—98.7%.Conclusion The CVA16 prevalent in Kunming in 2019 belonged to Bla and B1b genotypes,with B1b as the main strain,and all of them were prevalent strains in the mainland of China.

Effect of Spatial Contiguity on Learning Sequences of Positions / Efecto de la contigüidad espacial sobre el aprendizaje de secuencias de posiciones

Abstract Four conditions of spatial contiguity of positions were used to assess sequence learning. Two sequences of 16 and 25 positions presented in two matrices of 4x4 and 5x5 respectively were used. Within each matrix, 4 (in the 4x4 matrix) or 6 positions (in the 5x5 matrix) presented spatial contiguity. The place at the sequence in which contiguous positions occurred varied across groups. In this way, spatial contiguity of the 4 or 6 positions was presented at the beginning of the sequence (Group 1), in the middle part (Group 2), at the end of the sequence (Group 3) or it was presented a sequence in which all positions occurred without spatial contiguity (Group 4). 28 undergraduate students participated. Results showed no differences among groups in the number of trials required to reproduce the sequence correctly. Number of errors was lower when contiguous positions were presented at the beginning of the sequence. These findings are explained as a possible effect of accentuation of primacy given by the occurrence of contiguous positions at the beginning of the sequence.

Resumen Cuatro condiciones de contigüidad espacial de posiciones fueron empleadas para evaluar el aprendizaje de secuencias. Se emplearon dos secuencias de 16 y 25 posiciones presentadas en dos matrices de 4x4 y 5x5, respectivamente. Dentro de cada matriz, 4 (en la matriz de 4x4) o 6 posiciones (en la matriz de 5x5) presentaron contigüidad espacial. Entre grupos, se varió el punto de la secuencia en el que se presentaron las posiciones contiguas. De este modo, la contigüidad espacial de las 4 o 6 posiciones se presentó al inicio de la secuencia (Grupo 1), en la parte media (Grupo 2), al final de la secuencia (Grupo 3), o bien, se presentó una secuencia en la que todas las posiciones ocurrieron sin contigüidad espacial (Grupo 4). Participaron 28 estudiantes de licenciatura. Los resultados no mostraron diferencias entre grupos en cuanto al número de ensayos requeridos para reproducir la secuencia correctamente. El número de errores fue menor cuando las posiciones contiguas se presentaron al inicio de la secuencia. Los hallazgos se explican a partir de un posible efecto de acentuación de la primacía, dado por la ocurrencia de posiciones contiguas al inicio de la secuencia.

Review on Applicability of Bioinformatics in Current Research and Database Management

A generation of new science has evolved with the development of bioinformatics and computational biology, which have molecular biology as an integrated part. In the past decade, technological advances have promoted a prominent development in expertise and knowledge in the molecular basis of phenotypes. In Bioinformatics, biological data is evaluated by computational science and processed in a more statistical and meaningful way. It includes the collection classification storage and evaluation of biochemical and organic statistics using computers in particular as implemented in molecular genetics and genomics. Computational Biology and Bioinformatics are emerging branches of science and include the use of techniques and concepts from informatics statistics, mathematics, chemistry, biochemistry, physics and linguistics. Therefore, bioinformatics and computational biology have sought to triumph over many challenges of which a few are listed in this overview. This evaluation intends to provide insight into numerous bioinformatics databases and their uses in the analysis of biological records exploring approaches emerging methodologies strategies tools that can provide scientific meaning to the information generated.

Differential gene expression analysis in germinating and dormant teliospores of Tilletia indica using RNA seq approach

Karnal bunt of wheat is an important quarantine disease that interrupts India’s wheat trade in the international market. The whole transcriptome of germinating and dormant teliospores of Tilletia indica was performed using the RNA Seq approach to identify germination-related genes. Approximately 63 million reads were generated using the RNA sequencing by the Illumina NextSeq500 platform. The high-quality reads were deposited in NCBI SRA database (accession: PRJNA522347). The unigenes from the pooled teliospores were 16,575 having unigenes length of 28,998,753 bases. The high-quality reads of germinating teliospores mapped on to 21,505 predicted CDSs. 9,680 CDSs were common between dormant and germinating teliospores of T. indica. 11,825 CDSs were found to be in germinating teliospores while only 91 were unique in dormant spores of pathogen. The pathway analysis showed the highest number of pathways was found in germinating spores than dormant spores. The highest numbers of CDSs were found to be associated with translation (431 in number), transport and catabolism (340), signal transduction (326), and carbohydrate metabolism (283). The differential expression analysis (DESeq) of germinating and dormant teliospores showed that 686 CDS were up-regulated and 114 CDS were down-regulated in the germinating teliospores. Significant germination-related genes in the spores were validated using qPCR analysis. Ten genes viz. Ti3931, Ti6828, Ti7098, Ti7462, Ti7522, Ti 9289, Ti 8670, Ti 7959, Ti 7809,and Ti10095 were highly up-regulated in germinated teliospores which may have role in germination of spores.Further, these differentially expressed genes provide insights into the molecular events. This first study of transcriptome will be helpful to devise better management strategies to manage Karnal bunt disease.

CONTEXTUAL LEARNING APPROACH FOR SYNDROME DISEASE NAMED ENTITY RECOGNITION

The groundwork for extracting a significant amount of biomedical information from unstructured texts into structured formats is the difficult research area of biological entity recognition from medical documents. The existing work implemented the named entity recognition for diseases using the sequence labelling framework. The performance of this strategy, however, is not always adequate, and it frequently cannot fully exploit the semantic information in the dataset. The Syndrome Diseases Named Entity problem is presented in this work as a sequence labelling with multi-context learning. By using well-designed text/queries, this formulation may incorporate more previous information and to decode it using decoding techniques such conditional random fields (CRF). We performed experiments on three biomedical datasets, and the outcomes show how effective our methodology is on the BC5CDR-Disease, JNLPBA and NCBI-Disease, compared with other techniques our methodology performs with accuracy levels of 96.70%,98.65 and 96.72% respectively.

Perfusão arterial reversa gemelar: revisão da literatura / Twin reverse arterial perfusion: literature review

A perfusão arterial reversa gemelar é uma anormalidade rara que pode ocorrer em gestações gemelares monocoriônicas. Consiste em uma alteração na circulação fetoplacentária, com desvio de sangue de um dos gemelares para o outro, por meio de anastomoses arterioarteriais e venovenosas na superfície placentária e anastomoses arteriovenosas em áreas de circulação placentária compartilhada. O feto bombeador pode desenvolver insuficiência cardíaca devido ao aumento do débito cardíaco, e o feto receptor, perfundido por sangue pobre em oxigênio por meio do fluxo reverso, é severamente malformado, incompatível com a vida extrauterina. Este artigo apresenta o caso de uma gestação gemelar monocoriônica diamniótica, com manejo clínico conservador. O objetivo é relatar um caso de complicação rara de gestações monozigóticas e revisar condutas para diagnóstico e manejo adequado.(AU)

Twin reverse arterial perfusion is a rare abnormality that can occur in monochorionic twin pregnancies. It consists of an alteration in the fetal-placental circulation, with blood diversion from one of the twins to the other, through arterio-arterial and veno- venous anastomosis on the placental surface and arterio-venous anastomosis in areas of shared placental circulation. The pumping fetus may develop heart failure due to increased cardiac output, and the recipient fetus, perfused by oxygen-poor blood through reverse flow, is severely malformed, incompatible with extrauterine life. This article presents the case of a monochorionic diamniotic twin pregnancy, with conservative clinical management. The objective is to report a case of rare complication of monozygotic pregnancies and review procedures for diagnosis and adequate management.(AU)

Molecular epidemiology and antifungal susceptibilities of Aspergillus species isolated from patients with invasive aspergillosis

SUMMARY OBJECTIVE: The aim of this study was to evaluate the demographic data, molecular epidemiology, and in vitro antifungal susceptibility results of patients with Aspergillus isolated from various clinical specimens. METHODS: A total of 44 Aspergillus strains were studied. The definition of invasive aspergillosis in patients was made according to European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) criteria. Strains were phenotypically and molecularly identified. Demographic characteristics of patients and genotypes of strains were evaluated. Phylogenetic analysis was done by the The Unweighted Pair-Group Method with Arithmetic Mean (UPGMA). Antifungal susceptibility of strains was determined according to The Clinical and Laboratory Standards Institute (CLSI)-M61-Ed2 and The European Committee on Antimicrobial Susceptibility Testing (EUCAST). RESULTS: A total of 11 patients were classified as proven and 33 as probable invasive aspergillosis. There was a statistically significant difference in age groups, subdisease, neutropenic, and receiving chemotherapy between groups. A total of 23 strains were identified as Aspergillus fumigatus, 12 as Aspergillus niger, 6 as Aspergillus flavus, and 3 as Aspergillus terreus. Phylogenetic analysis revealed five different genotypes. No statistical difference was found in the comparisons between patients groups and genotype groups. There was a statistically significant difference between genotype groups and voriconazole, posaconazole, and itraconazole Minimum Inhibition Concentration (MIC). CONCLUSION: Accurate identification of strains and antifungal susceptibility studies should be performed due to azole and amphotericin B resistance. Genotyping studies are important in infection control due to identifying sources of infection and transmission routes.

Antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby isolates from clinical patients and food sources in Hangzhou / 中华微生物学和免疫学杂志

Objective:To analyze the antimicrobial resistance and genomic characteristics of Salmonella enterica serovar Derby strains isolated from human and food sources in Hangzhou. Methods:A total of 60 Salmonella enterica serovar Derby strains isolated in Hangzhou during the period from 2015 to 2020 were subjected to antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE) typing and whole-genome sequencing. Multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST) and the identification of antimicrobial resistance genes were performed using the sequencing data. Phylogenetic tree based on the single nucleotide polymorphism (SNP) sites in the 60 genomes from Hangzhou and 379 genomes from public databases was constructed. Results:No significant difference was observed in the drug resistance rates between the clinical strains and food strains in Hangzhou. The multidrug resistance (MDR) rate was 76.7% (46/60). All of the 60 Salmonella Derby strains were positive for the antimicrobial resistance genes aac(6′)- Iaa and fosA7. The 60 strains were subtyped into 46 molecular types by PFGE and 53 molecular types by cgMLST(HC2). Except for one strain belonging to ST3220, the other Salmonella Derby strains were ST40. The phylogenetic analysis showed that some strains isolated in Hangzhou were close to the strains in Southeast Asia, suggesting the possibility of cross-border transmission of ST40 strains, with the main food sources being pork and fish; other strains were close to those circulating in Beijing, Guangzhou, Hubei, Chongqing and other provinces, suggesting the possibility of cross-province transmission of the strains, with the main food sources being pork, beef and chicken. Conclusions:The epidemic of Salmonella Derby in Hangzhou was mainly caused by the spread of ST40 strains and MDR was common. Clinical infections might be closely related to the consumption of pork, beef, chicken and fish. There was the possibility of cross-border transmission of Salmonella Derby between Hangzhou and Southeast Asia and cross-province transmission in China.

Risk factors for first weaning failure following mandibular distraction osteogenesis in pediatric patients with Pierre Robin sequence: a nested case-control study / 中华麻醉学杂志

Objective:To identify the risk factors for the first weaning failure following mandibular distraction osteogenesis in pediatric patients with Pierre Robin sequence (PRS).Methods:Clinical data of pediatric patients with PRS who underwent mandibular distraction osteogenesis from January 2018 to February 2023 were collected, including sex, age, premature birth, birth weight, surgical weight, cleft palate, syndrome type PRS, laryngeal/tracheobronchial malacia, simple congenital heart disease, complex congenital heart disease, preoperative mechanical ventilation, preoperative pulmonary infection, blood albumin concentration, difficulty in tracheal intubation under a visual laryngoscope, surgical duration, postoperative ventilator-associated pneumonia, duration of mechanical ventilation at first weaning, and traction length at first weaning. Children in whom the first postoperative machine withdrawal failed were included in observation group and matched to control cases(control group) in a 1∶4 ratio. The risk factors of which P values were less than 0.05 would enter the logistic regression analysis to stratify the risk factors for postoperative weaning failure. Results:There were significant differences in birth weight, cleft palate, duration of mechanical ventilation and traction length at first weaning, rate of combined cleft palate, preoperative pulmonary infection rate, rate of preoperative mechanical ventilation, and rate of postoperative ventilator-associated pneumonia between the two groups ( P<0.05). Binary logistic stepwise regression analysis showed that the preoperative mechanical ventilation ( OR=18.154, 95% CI 3.971-82.990, P<0.001) and postoperative ventilator-associated pneumonia ( OR=36.942, 95% CI 1.307-1043.985, P=0.034) were independent risk factors for first weaning failure after mandibular distraction osteogenesis, while birth weight gain ( OR=0.225, 95% CI 0.076-0.668, P=0.007) was a protective factor for first weaning failure ( P<0.05). Conclusions:Preoperative mechanical ventilation and postoperative ventilator-associated pneumonia are independent risk factors and birth weight gain is a protective factor for first weaning failure following mandibular distraction osteogenesis in pediatric patients with PRS.

Postoperative infection after anterior cruciate ligament reconstruction caused by Finegoldia magna: a case report / 中华骨科杂志

One case of knee infection after anterior cruciate ligament reconstruction caused by the gram-positive anaerobic bacterium Finegoldia magna was reported. The patient was admitted to hospital due to fever and knee joint swelling and pain after anterior cruciate ligament reconstruction. Through medical history, physical examination, imaging examination and next-generation sequencing, it was confirmed that the infection was caused by Finegoldia magna. Through literature review, 37 literatures on infectious diseases caused by Finegoldia magna was retrieved and analyzed, and the identification points of anaerobic bacteria, the application of second-generation sequencing technology and the treatment status of infection after anterior cruciate ligament reconstruction were reviewed. The incidence of infection after arthroscopic anterior cruciate ligament reconstruction is low, while anaerobic infection is even more rare and difficult to culture. The next-generation sequencing can be used to assist the diagnosis. On the basis of giving priority to the preservation of the reconstructed ligament, the combined use of arthroscopic debridement, irrigation and sensitive antibiotics is the main treatment method.

Transcriptomic comparative study on mouse liver injury caused by ultra-high dose rate irradiation and conventional irradiation / 中华放射医学与防护杂志

Objective:To study the effects of FLASH irradiation (FLASH-RT) and conventional irradiation (CONV-RT) on gene expression profile in mouse liver, in order to provide theoretical basis of the potential mechanism of FLASH-RT.Methods:A total of 11 C57BL/6J male mice were divided into healthy control group (Ctrl group), CONV-RT group and FLASH-RT group according to random number table method. Mouse abdomen was treated with 12 Gy CONV-RT or FLASH-RT. Then the mice were killed by neck removal, and the liver tissues were collected to extract total RNA for transcriptome sequencing (RNA-Seq) that was then analyzed by bio-informatics analysis to investigate the changes of gene expression profiles. The mRNA expression levels of Stat1, Irf9 and Rela were verified by quantitative real-time PCR assay.Results:1 762 differentially expressed genes (DEGs) were identified in group FLASH-RT vs. CONV-RT. Among them, 660 genes were up-regulated and 1 102 genes were down-regulated. 1 918 DEGs were identified in groups FLASH-RT vs. Ctrl. Among them, 728 genes were up-regulated and 1 190 genes were down-regulated. 1 569 DEGs were identified in group CONV-RT vs. Ctrl. Among them, 1 046 genes were up-regulated and 523 genes were down-regulated. According to Gene Ontology (GO) analysis, these DEGs from groups FLASH-RT vs. CONV-RT were involved in various functions including defense response to virus, other organisms in cell components, adenylyltransferase activity in molecular function activity. These DEGs from group FLASH-RT vs. Ctrl were involved in various functions including defense response to other oranisms, endoplasmic reticulum chaperone complex, double-stranded RNA binding and so on. These DEGs from group FLASH-RT vs. CONV-RT were involved in several Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including influenza A, Herpes simplex infection and so on. These DEGs from group FLASH-RT vs. Ctrl were involved in several KEGG pathways including influenza A, NOD-like receptor signaling pathway. Stat1 was likely to be activated by FLASH radiation. The quantitative real-time PCR assay showed that FLASH-RT obviously increased the mRNA expressions of Stat1, Irf9 and Rela ( t=6.62, 2.11, 1.67, P<0.05). Conclusions:FLASH-RT and CONV-RT could alter gene expression profiles in mouse liver tissues, and these DEGs are involved in multiple radiobiological functional pathways. In comparison with CONV-RT, FLASH-RT induces a low level of liver injury, which may due to hypoxia radiation resistance.

Genetic variation characteristics of HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019 / 中国基层医药

Objective:To analyze the genetic variation characteristics of the HA gene of influenza A virus (H3N2) in Guizhou province from 2017 to 2019. Methods:Twenty strains of influenza A virus (H3N2) were randomly selected from 10 network laboratories in Guizhou province for RNA extraction. Reverse transcriptase-polymerase chain reaction and sequencing were performed. The products were analyzed using bioinformatics software.Results:The nucleotide homology of the HA gene of the 20 strains was 97.7%-100%, which was highly homologous to the vaccine strains A/Hong-Kong/4801/2014 recommended by WHO in 2017 and A/Singapore-INFIMH/16-0019/2016 recommended by WHO in 2018, but they were significantly different from the vaccine strain A/Kansas/14/2017 recommended by WHO in 2019. Genetic analysis showed that the 20 strains were divided into two branches, and the strains that were prevalent in 2019 were located in different branches, with marked genetic differences. Key site analysis showed mutations in antigenic determinants A, B, C, and E and mutations in the anterior and posterior walls of receptor binding sites. Key site analysis also showed that there was an increase in the number of glycosylation sites compared with the vaccine strains prevalent in the same year. Genetic distance, antigen sites, and glycosylation sites were slightly different between virus strains prevalent in 2017-2018 and virus strains prevalent in 2019. Conclusion:The HA gene of the influenza A virus subtype H3N2 in Guizhou province from 2017 to 2019 showed heterogeneity and gene mutation, especially in 2019. Therefore, close monitoring of the genetic evolution of the influenza A virus subtype H3N2 is necessary.

Genetic characteristics of multi-locus sequence typing of Brucella isolates in Guizhou Province from 2017 to 2021 / 中华地方病学杂志

Objective:To study the multi-locus sequence typing (MLST) gene characteristics of Brucella isolates in Guizhou Province. Methods:Brucella strains, which were isolated from 2017 to 2021 in Guizhou Province (preserved in the Bacterial and Viral Seed Bank of Guizhou Center for Disease Control and Prevention) were identified Brucella and species/types by BCSP31-PCR and AMOS-PCR methods, respectively. MLST method was used for genotyping, and Biometrics 8.0 software was used for cluster analysis of the typing results. Results:A total of 32 strains of Brucella were isolated in Guizhou Province and identified as Brucella melitensis ( B.melitensis) by BCSP31-PCR and AMOS-PCR methods. These strains were classified into 2 ST types (ST8 and ST39) by MLST method, with 28 strains of ST8 type(87.5%) and 4 strains of ST39 type (12.5%). The 28 strains of ST8 type were distributed in 7 cities (prefectures) of Guizhou Province, while the 4 strains of ST39 type were only found in Qianxinan Buyi and Miao Autonomous Prefecture. The cluster analysis results showed that ST8 and ST39 types strains were clustered in a group with the reference strain of B.melitensis, and there was only one nucleotide site difference between ST39 and ST8 types in the glk gene, indicating a close genetic relationship. Conclusions:B.melitensis is the main pathogen of the brucellosis epidemic in Guizhou Province in recent years. ST8 is the dominant MLST genotype in Guizhou Province.

Multi-locus sequence typing of human Brucella isolated in Sichuan Province from 2014 to 2020 / 中华地方病学杂志

Objective:To learn about the genotyping of human Brucella isolated from Sichuan Province. Methods:BCSP31-PCR and AMOS-PCR were used to identify the genus and biotype of the 66 strains isolated from confirmed human brucellosis cases in Sichuan Province from 2014 to 2020, respectively. The isolated strains were genotyped by multi-locus sequence typing (MLST)-9. The sequence type (ST) was compared trough the online MLST database. A minimum spanning tree (MST) was constructed to cluster the newly discovered and known ST using the BioNumerics software version 7.6.Results:The 66 strains isolated from human cases of brucellosis in Sichuan Province from 2014 to 2020 were Brucella, and 65 of them were Brucella melitensis while one strain was Brucella abortus. The MLST method identified three known STs (ST-8, ST-39 and ST-2) and one newly type (ST-101). Among them, ST-8 was the main ST in Sichuan Province (90.91%, 60/66), another 4 strains of Brucella melitensis were ST-39, and 1 strain of Brucella abortus was ST-2. The newly type ST-101 was isolated from Leshan City in 2019, belonging to the Brucella melitensis and closely related to the evolution of ST-8. Conclusion:Brucella melitensis is the main epidemic Brucella strain in Sichuan Province, ST-8 is predominant genotype, with a small amount of ST-39, ST-101 and ST-2.

Multilocus sequence typing, clinical characteristic, and drug resistance of Salmonella typhimurium in 93 children / 中华实用儿科临床杂志

Objective:To investigate the multilocus sequence typing (MLST), clinical manifestations, and drug resistance of Salmonella typhimurium in children, thus providing references for the diagnosis, treatment, and prevention of pediatric Salmonella typhimurium infection.Methods:The clinical data of patients with Salmonella typhimurium serotypes confirmed by stool or blood culture between November 2017 and October 2020 were retrospectively collected from Fujian Maternity and Child Health Hospital.MSLT and drug susceptibility test were performed on Salmonella typhimurium isolated from the samples. Kruskal- Wallis test, Chi- square test, and Fisher′ s exact probability method were employed for data analyses. Results:Salmonella typhimurium was cultured from clinical samples of 96 children, of which, 93 samples were effective, including 92 stool samples and 1 blood sample from 53 boys(56.99%) and 40 girls(43.01%). The median age of disease onset occurred at 12.0 (8.5-22.0) months, with peak months of onset ranging from July to October.According to MLST classification, 93 children were divided into ST34 classification( n=58), ST19 classification( n=22) and other classification( n=13). Respiratory symptoms were significant different among MLST classification, and ST34 type Salmonella typhimurium enteritis was more commonly accompanied by respiratory symptoms ( χ2=17.657, P<0.001; Cramer V=0.421, P<0.001). There were significant differences in the drug sensitivity to Ampicillin ( χ2=8.774, P=0.033), Piperacillin tazobactam ( χ2=6.713, P=0.022), Ciprofloxacin ( χ2=20.780, P<0.001), Sulfamethoxazole ( χ2=15.364, P=0.001), Ampicillin sulbactam ( χ2=17.626, P=0.001) and Levofloxacin ( χ2=25.648, P<0.001) among 3 groups.No significant difference was found in the sensitivity to Ceftriaxone ( χ2=1.027, P=0.621), Ceftazidime ( χ2=7.637, P=0.059), Cefepime ( χ2=6.099, P=0.116) and Cefoperazone/Sulbactam ( χ2=2.405, P=0.649). All MLST types were sensitive to Imipenem and Meropenem. Conclusions:Salmonella typhimurium infection mainly affects infants, with the peak months of onset ranging from July to October.MLST34 is the main serotype, accompanied respiratory symptoms.Antibiotics should be selected according to drug sensitivity, and third-generation cephalosporins can be selected empirically without drug susceptibility test results.

Analysis of circRNA in esophageal squamous cell carcinoma based on high-throughput sequencing data / 国际肿瘤学杂志

Objective:To analyze circRNAs specifically differentially expressed in esophageal squamous cell carcinoma (ESCC) based on high-throughput sequencing data.Methods:Six patients with pathologically confirmed ESCC in Tangdu Hospital of Air Force Medical University from March 2018 to March 2019 were selected as the research subjects, among which 3 were stage Ⅰ ESCC and 3 were stage Ⅲ ESCC. High-throughput sequencing technology was used to analyze the difference in the expression of circRNA in cancer tissues and adjacent tissues of patients. GO enrichment analysis, KEGG enrichment analysis and Venn analysis were performed on differentially expressed genes. The circRNA-miRNA-mRNA network was constructed using Cytoscape software. The most significantly differentially expressed genes in cancer tissues were verified in cells and tissues, and the relationships between circRNAs and clinical pathological indicators of patients were analyzed.Results:A total of 553 differentially expressed circRNAs were screened in paracancerous tissues and cancer tissues of 3 stage Ⅰ ESCC patients, of which 413 were up-regulated and 140 were down-regulated in cancer tissues; A total of 425 differentially expressed circRNAs were screened in paracancerous tissues and cancer tissues of 3 stage Ⅲ ESCC patients, of which 276 were up-regulated and 149 were down-regulated in cancer tissues. GO enrichment analysis showed that the host genes of differential circRNAs in patients with stage Ⅰ ESCC were mainly enriched in cell cycle-related biological processes such as mitotic G 2/M transition. The host genes of differential circRNAs in patients with stage Ⅲ ESCC were mainly enriched in biological processes related to cell division and tumor development, such as mitotic spindle checkpoint and cell matrix adhesion. KEGG enrichment analysis showed that the differential circRNAs in cancer tissues of stage Ⅰ and stage Ⅲ ESCC patients were mainly enriched in cancer-related biological pathways such as cell adhesion. The results of Venn analysis showed that in stage Ⅰ ESCC patients and stage Ⅲ ESCC patients, 2 and 8 circRNAs that were only specifically expressed in paracancerous tissues and had significant differences were screened out respectively, and were only specifically expressed in cancer tissues with significant differences were 11 and 14 respectively. The circRNA-miRNA-mRNA network showed that the cancer tissue-related circRNA-miRNA-mRNA network in stage Ⅰ ESCC patients consisted of 7 circRNA nodes, 10 miRNA nodes and 28 mRNA nodes, and the cancer tissue-related circRNA-miRNA-mRNA network in stage Ⅲ ESCC patients consisted of 7 circRNA nodes, 9 miRNA nodes and 49 mRNA nodes. The most significantly differentially expressed hsa-circ-0060927 and hsa-circ-0109301 in cancer tissues of patients with stage Ⅰ ESCC and stage Ⅲ ESCC were selected for cytological and histological verification. The results showed that the relative expression levels of hsa-circ-0060927 in ESCC cell lines TE1, TE13, KYSE30, KYSE170, and human normal esophageal epithelial cell line HEEC were 7.82±1.96, 12.69±2.68, 12.78±2.74, 7.53±1.75, and 2.43±0.17, respectively, with a statistically significant difference ( F=4.68, P=0.004). The relative expression levels of hsa-circ-0060927 in ESCC cell lines TE1, TE13, KYSE30, and KYSE170 were higher than that in human normal esophageal epithelial cell line HEEC, with statistically significant differences ( P=0.009; P=0.003; P=0.003; P=0.007). The relative expression levels of hsa-circ-0109301 in ESCC cell lines TE1, TE13, KYSE30, KYSE170, and human normal esophageal epithelial cell line HEEC were 5.16±1.32, 6.28±1.57, 4.89±1.13, 8.92±2.12, and 22.56±4.13, respectively, with a statistically significant difference ( F=4.31, P=0.022). The relative expression levels of hsa-circ-0109301 in ESCC cell lines TE1, TE13, KYSE30, and KYSE170 were lower than that in human normal esophageal epithelial cell line HEEC, with statistically significant differences ( P=0.027; P=0.015; P=0.024; P=0.008). The expression level of hsa-circ-0060927 in cancer tissues of 13 early ESCC patients was 12.89±2.67, significantly higher than 5.73±1.18 in paracancerous tissue, and there was a statistically significant difference ( t=15.02, P<0.001) ; the expression level of hsa-circ-0109301 in cancer tissues of 19 patients with advanced ESCC was 7.78±2.17, significantly lower than 16.32±3.15 in paracancerous tissue, and there was a statistically significant difference ( t=9.73, P<0.001). The expression of hsa-circ-0109301 was related to the degree of tumor differentiation in advanced ESCC patients ( P=0.023) . Conclusion:One circRNA (hsa-circ-0060927 and hsa-circ-0109301) with the most significanty differential expression is selected in early and advanced ESCC patients respectively, in which hsa-circ-0060927 is highly expressed in ESCC cancer tissues and hsa-circ-0109301 is lowly expressed in ESCC cancer tissues, and the expression of hsa-circ-0109301 is correlated with the degree of tumor differentiation.

Application of targeted capture high depth sequencing and transcriptome sequencing in childhood B-cell acute lymphoblastic leukemia / 白血病·淋巴瘤

Objective:To investigate the differences among targeted capture high depth sequencing (Panel-seq), transcriptome sequencing (RNA-seq) and traditional detection methods in cytogenetic and molecular genetic typing of childhood B-cell acute lymphoblastic leukemia (B-ALL) and their significances.Methods:The clinical data of 152 newly diagnosed childhood B-ALL cases in Guangzhou Women and Children's Medical Center from September 2020 to December 2021 were retrospectively analyzed. Along with traditional cytogenetic and molecular detection methods including karyotyping, fluorescence in situ hybridization (FISH) and 43 kinds of fusion gene quantitative screening for traditional cells and molecular genetic detection, both Panel-seq and RNA-seq were also performed. Panel-seq covered more than 600 genes with common mutations in hematological tumors, from which fusion genes and gene mutations were both analyzed. RNA-seq was used to analyze fusion genes, gene mutations, gene expression, and copy number variation at the chromosome level. High hyperdiploid karyotype was estimated by using gene expression profile clustering and copy number variations. The cytogenetic typing results of all detection methods were also analyzed.Results:Among 152 patients, 93 cases were males and 59 cases were females, with the median age of 4.0 years (0.8-13.0 years). The median blast cell ratio was 0.855 (0.215-0.965). The traditional detection methods could identify 4 cases (2.6%) with BCR-ABL1, 2 cases (1.3%) with CRLF2 gene-related fusion, 27 cases (17.8%) with ETV6-RUNX1, 1 case (0.7%) with iAMP21, 5 cases (3.3%) with MLL rearrangement, 8 cases (5.3%) with TCF3-PBX1 and 22 cases (14.5%) with high hyperdiploid karyotype. Panel-seq could identify 4 cases (2.6%) with BCR-ABL1, 2 cases (1.3%) with CRLF2 gene-related fusions, 27 cases (17.8%) with ETV6-RUNX1, 3 cases (2.0%) with MEF2D gene-related fusions, 1 case (0.7%) with MEIS1-FOXO1, 5 cases (3.3%) with MLL rearrangement, 5 cases (3.3%) with PAX5 gene-related fusions, 8 cases (5.3%) with TCF3-PBX1 fusions, 4 cases (2.6%) with ZNF384 gene-related fusions, and 2 cases (1.3%) with IKZF1 N159Y mutations. Among 152 patients, 1 case with MLL rearrangement didn't receive RNA-seq detection because of sample quality; in other 151 B-ALL cases, 1 case (0.7%) with ACIN1-NUTM1, 4 cases (2.6%) with BCR-ABL1, 3 cases (2.0%) with CRLF2 gene-related fusions, 8 cases (5.3%) with DUX4 gene-related fusions, 27 cases (17.9%) with ETV6-RUNX1, 3 cases (2.0%) with MEF2D gene-related fusions, 1 case (0.7%) with MEIS1-FOXO1, 4 cases (2.6%) with MLL rearrangement, 5 cases (3.3%) with PAX5 gene-related fusions, 1 case (0.7%) with ZMIZ1-ABL1, 8 cases (5.3%) with TCF3-PBX1,4 cases (2.6%) with ZNF384 gene-related fusions, 61 cases (40.4%) with hyperdiploid karyotypes, and 2 cases (1.3%) with IKZF1 N159Y mutations were detected; RNA-seq had obvious advantage in detecting fusion gene and hyperdiploid karyotype. The cytogenetic and molecular genetic typing rates of traditional method, Panel-seq and RNA-seq were 45.4% (69/152), 40.1% (61/152) and 87.4% (132/151), respectively. The combination of the three could identify 89.5% (136/152) of childhood B-ALL patients.Conclusions:The combination of Panel-seq and RNA-seq can increase the detection rate of genetic abnormality in childhood B-ALL, which provides a more accurate molecular genetic classification for B-ALL and the basis for treatment guideline and prognosis judgement.