sequencing

摘要： BACKGROUND Osteonecrosis of the femoral head(ONFH)is a frequent and refractory disease whose pathogenesis has not yet been elucidated.Infection and other factors that reduce the local blood supply can lead to bone necrosis.AIM To aim of this study was to assess the relationship of ONFH with bone infection by use of metagenomic sequencing.METHODS Twelve patients with idiopathic ONFH and 12 comparable controls who were undergoing hip arthroplasty were followed up in parallel.Necrotic femoral head specimens were collected for bacterial and fungal cultures using standard methods.Bone specimens were subjected to preliminary processing,and metagenomics sequencing of microorganisms was performed.A one-way analysis of variance was used to compare bacterial species in the two groups.RESULTS Bacterial and fungal cultures exhibited no evidence of microbial growth in all isolated necrotic femoral head tissues.We thus performed metagenomic sequencing and classified the species as suspected pathogens or suspected background microorganisms based on known bacterial pathogenicity.There was no evidence of viruses,fungi,parasites,M.tuberculosis complex,or mycoplasma/chlamydia.There were also no significant differences in suspected pathogens or suspected background microorganisms(P>0.05).CONCLUSION Although we found no pathogens specific for ONFH in necrotic femoral head tissue,our research provides a foundation for future research on the metagenomics of bone pathogens.

摘要： BACKGROUND The gut microbiota(GM)has been proven to play a role in the regulation of host lipid metabolism,which provides a new theory about the pathogenesis of dyslipidemia.However,the associations of GM with dyslipidemia based on sex differences remain unclear and warrant elucidation.AIM To investigate the associations of GM features with serum lipid profiles based on sex differences in a Chinese population.METHODS This study ultimately recruited 142 participants(73 females and 69 males)at Honghui Hospital,Xi’an Jiaotong University.The anthropometric and blood metabolic parameters of all participants were measured.According to their serum lipid levels,female and male participants were classified into a high triglyceride(H_TG)group,a high total cholesterol(H_CHO)group,a low high-density lipoprotein cholesterol(L_HDL-C)group,and a control(CON)group with normal serum lipid levels.Fresh fecal samples were collected for 16S rRNA gene sequencing.UPARSE software,QIIME software,the RDP classifier and the FAPROTAX database were used for sequencing analyses.RESULTS The GM composition at the phylum level included Firmicutes and Bacteroidetes as the core GM.Different GM features were identified between females and males,and the associations between GM and serum lipid profiles were different in females and males.The GM features in different dyslipidemia subgroups changed in both female patients and male patients.Proteobacteria,Lactobacillaceae,Lactobacillus and Lactobacillus_salivarius were enriched in H_CHO females compared with CON females,while Coriobacteriia were enriched in L_HDL-C females.In the comparison among the three dyslipidemia subgroups in females,Lactobacillus_salivarius were enriched in H_CHO females,and Prevotellaceae were enriched in L_HDL-C females.Compared with CON or H_TG males,Prevotellaceae,unidentified_Ruminococcaceae,Roseburia and Roseburia_inulinivorans were decreased in L_HDL-C males(P value<0.05),and linear discriminant analysis effect size analysis indicated an enrichment of the above GM taxa in H_TG males compared with other male subgroups.Additionally,Roseburia_inulinivorans abundance was positively correlated with serum TG and total cholesterol levels,and Roseburia were positively correlated with serum TG level.Furthermore,Proteobacteria(0.724,95%CI:0.567-0.849),Lactobacillaceae(0.703,95%CI:0.544-0.832),Lactobacillus(0.705,95%CI:0.547-0.834)and Lactobacillus_salivarius(0.706,95%CI:0.548-0.835)could distinguish H_CHO females from CON females,while Coriobacteriia(0.710,95%CI:0.547-0.841),Coriobacteriales(0.710,95%CI:0.547-0.841),Prevotellaceae(0.697,95%CI:0.534-0.830),Roseburia(0.697,95%CI:0.534-0.830)and Roseburia_inulinivorans(0.684,95%CI:0.520-0.820)could discriminate H_TG males from CON males.Based on the predictions of GM metabolic capabilities with the FAPROTAX database,a total of 51 functional assignments were obtained in females,while 38 were obtained in males.This functional prediction suggested that cellulolysis increased in L_HDL-C females compared with CON females,but decreased in L_HDL-C males compared with CON males.CONCLUSION This study indicates associations of GM with serum lipid profiles,supporting the notion that GM dysbiosis may participate in the pathogenesis of dyslipidemia,and sex differences should be considered.

摘要： The diagnosis of bacterial or fungal infections requires the identification of the pathogen etiology in the shortest time possible. Although some biomarkers are used as indicators of bacterial infections, their specificity and sensitivity are highly variable, and there is no direct relationship between the level increase of these biomarkers for mycosis. It is common to obtain negative microbiological cultures in patients infected by non-culturable, intracellular bacteria or mycosis, even though there is a high clinical suspicion of infection. This study identifies the pathogen present in critically infected patients through 16S and 18S/eEF1 genes detection by polymerase chain reaction (PCR) coupled with Sanger sequencing. Thirty clinical samples were evaluated by PCR, of which 40% were positive for fungi, 23.33% for bacteria, 26.7% for fungi and bacteria, and 10% for no pathogen. The PCRs outcomes period for bacteria or fungi was one day compared to seven and up to 14 days (on average) of microbiological culture for bacteria and fungi. Then, we assessed the relationship with the most used biomarkers (procalcitonin, C-reactive protein, globular sedimentation velocity, and the neutrophil-lymphocyte index). This combination of molecular techniques has been shown as helpful in identifying intracellular bacteria and fungi that are difficult to culture by conventional methods. Screening with genomic markers 16S and 18S/eEF1 by PCR allowed us to optimize the time to obtain the result of the infection caused by bacteria or fungi. Also, identifying the specific etiological microorganism by Sanger sequencing was very helpful in avoiding the progression of the disease and setting targeted treatment with better clinical outcomes.

摘要： Objective:To identity the variation of sand flies in the Gampaha and Kurunegala districts of Sri Lanka and to assess DNA barcoding as a complementing method for morphological identification.Methods:A total of 38441 sand flies were collected from selected localities in Gampaha and Kurunegala districts using standard entomological techniques from May 2017 to December 2018.Specimens were identified using morphological features and compared with mitochondrial cytochrome C oxidase subunitⅠgene-based DNA barcoding as an alternative tool.Results:Morphological and molecular identification confirmed the presence of four species under two genera(Phlebotomus and Sergentomyia).Phlebotomus argentipes was the predominant species,followed by Sergentomyia(S.)punjabensis,S.babu insularis,and an unidentified Sergentomyia sp.Phlebotomus argentipes showed a clear genetic differentiation from other species.S.babu insularis and S.punjabensis showed a higher genetic affinity to each other than the unidentified species.The unidentified Sergentomyia species is morphologically similar to S.zeylanica,but differs only in clavate gonostyle.Conclusions:DNA barcoding is an effective technique for the identification of sand flies.Further studies using molecular techniques will improve the knowledge of the cryptic diversity of Sri Lankan sand fly fauna.Establishing a reliable and standardized identification system for sand fly species in Sri Lanka is recommended.

摘要： BACKGROUND Gut microbiota dysbiosis is reportedly actively involved in autoimmune diseases such as type 1 diabetes mellitus(T1DM).However,the alterations in the gut microbiota and their correlation with fasting blood glucose(FBG)in Chinese children with T1DM remain unclear.AIM To investigate alterations in the gut microbiota in Chinese children with T1DM and their associations with clinical indicators.METHODS Samples from 51 children with T1DM and 47 age-matched and gender-matched healthy controls were obtained,to explore the structural and functional alterations in the fecal microbiota.The V3-V4 regions of the 16S rRNA gene were sequenced on a MiSeq instrument,and the association with FBG were analyzed.RESULTS We found that the bacterial diversity was significantly increased in the T1DMassociated fecal microbiota,and changes in the microbial composition were observed at different taxonomic levels.The T1DM-reduced differential taxa,such as Bacteroides vulgatus ATCC8482,Bacteroides ovatus,Bacteroides xylanisolvens,and Flavonifractor plautii,were negatively correlated with FBG,while the T1DMenriched taxa,such as Blautia,Eubacterium hallii group,Anaerostipes hadrus,and Dorea longicatena,were positively correlated with FBG.Bacteroides vulgatus ATCC8482,Bacteroides ovatus,the Eubacterium hallii group,and Anaerostipes hadrus,either alone or in combination,could be used as noninvasive diagnostic biomarkers to discriminate children with T1DM from healthy controls.In addition,the functional changes in the T1DM-associated fecal microbiota also suggest that these fecal microbes were associated with altered functions and metabolic activities,such as glycan biosynthesis and metabolism and lipid metabolism,which might play vital roles in the pathogenesis and development of T1DM.CONCLUSION Our present comprehensive investigation of the T1DM-associated fecal microbiota provides novel insights into the pathogenesis of the disease and sheds light on the diagnosis and treatment of T1DM.

摘要： The microbiome has been identified as a causing factor for many cancers.Helicobacter pylori contributes to the development of gastric cancer(GC)and impacts disease treatments.The rapid development of sequencing technology is increasingly producing large-scale and complex big data.However,there are many obstacles in the analysis of these data by humans,which limit clinicians from making rapid decisions.Recently,the emergence of artificial intelligence(AI),including machine learning and deep learning,has greatly assisted clinicians in processing and interpreting large microbiome data.This paper reviews the application of AI in the study of the microbiome and discusses its potential in the diagnosis and therapy of GC.We also exemplify strategies for implementing microbiome-based precision medicines for patients with GC.

摘要： During the last decades,further knowledge of hepatocellular carcinoma(HCC)molecular mechanisms has led to development of effective systemic treatments including tyrosine kinase inhibitors(TKIs)and immunotherapy.In this review,we describe first and second line systemic treatment options for advanced HCC.Several trials have evaluated new drugs for the treatment of HCC patients:In first line,lenvatinib resulted non-inferior to sorafenib and it can be used as alternative,even in the lack of evidence for sequential treatment options in second line after lenvatinib.Recently,atezolizumab plus bevacizumab have shown superiority over sorafenib in first-line.Sorafenib-regorafenib sequential administration in selected patients has opened a new paradigm of treatment in advanced HCC with a life expectancy exceeding two years.Other TKIs for second line treatment include cabozantinib and ramucirumab(specifically for patients with Alpha-fetoprotein values≥400 ng/mL).The combination of TKIs with immunotherapy may represent a big step forward for these patients in the near future.

摘要： BACKGROUND Peutz-Jeghers syndrome(PJS)is a rare disease with clinical manifestations of pigmented spots on the lips,mucous membranes and extremities,scattered gastrointestinal polyps,and susceptibility to tumors.The clinical heterogeneity of PJS is obvious,and the relationship between clinical phenotype and genotype is still unclear.AIM To investigate the mutation status of hereditary colorectal tumor-associated genes in hamartoma polyp tissue of PJS patients and discuss its relationship with the clinicopathological data of PJS.METHODS Twenty patients with PJS were randomly selected for this study and were treated in the Air Force Medical Center(former Air Force General Hospital)PLA between 2008 and 2017.Their hamartoma polyp tissues were used for APC,AXIN2,BMPR1A,EPCAM,MLH1,MLH3,MSH2,MSH6,MUTYH,PMS1,PMS2,PTEN,SMAD4,and LKB1/STK11 gene sequencing using next-generation sequencing technology.The correlations between the sequencing results and clinical pathological data of PJS were analyzed.RESULTS Fourteen types of LKB1/STK11 mutations were detected in 16 cases(80.0%),of which 8 new mutations were found(3 types of frameshift deletion mutations:c.243delG,c.363_364delGA,and c.722delC;2 types of frameshift insertions:c.144_145insGCAAG,and c.454_455insC;3 types of splice site mutations:c.464+1G>T,c.464+1G>A,and c.598-1G>A);9 cases(45.0%)were found to have 18 types of heterozygous mutations in the remaining 13 genes except LKB1/STK11.Of these,MSH2:c.792+1G>A,MSH6:c.3689C>G,c.4001+13C>CTTAC,PMS1:c.46C>t,and c.922G>A were new mutations.CONCLUSION The genetic mutations in hamartoma polyp tissue of PJS are complex and diverse.Moreover,other gene mutations in PJS hamartoma polyp tissue were observed,with the exception of LKB1/STK11 gene,especially the DNA mismatch repair gene(MMR).Colorectal hamartoma polyps with LKB1/STK11 mutations were larger in diameter than those with other gene mutations.

摘要： Annona squamosa is a multipurpose fruit tree employed in nutritional,medicinal,and industrial fields.Its fruit is significantly enriched in sugars,making it an excellent species to study sugar accumulation in fruit.However,the scarcity of genomic resources hinders genetic studies in this species.This study aimed at generating large-scale genomic resources in A.squamosa and deciphering the molecular basis of its high sugar content.Herein,we sequenced and characterized the full-length transcriptome of A.squamosa fruit using PacBio Iso-seq.In addition,we analyzed the changes in sugar content over five fruit growth and ripening stages,and we applied RNA-sequencing technology to investigate the changes in gene expression related to sugar accumulation.A total of 783,647 circular consensus sequences were generated,from which we obtained 48,209 high-quality,full-length transcripts.Additionally,1,838 transcription factors and 1,768 long non-coding RNAs were detected.Furthermore,we identified 10,400 alternative splicing events from 2,541 unigenes having on average 2–4 isoforms.A total of 15,061 simple sequence repeat(SSR)motifs were discovered and up to three primer pairs were designed for each SSR locus.Sugars mainly accumulate during the ripening stage in A.squamosa.Most of the genes involved in sugar transport and metabolism in the fruit were progressively repressed overgrowth and ripening stages.However,sucrose phosphate synthase involved in sucrose synthesis and more importantly,isoamylase,alpha-amylase,beta-amylase,4-alphaglucanotransferase genes involved in starch degradation displayed positive correlations with sugar accumulation in fruit.Overall,we provide here a high-quality,full-length transcriptome assembly which will facilitate gene discovery and molecular breeding of A.squamosa.We found that starch degradation during fruit ripening was the main channel for sugar accumulation in A.squamosa fruit,and the key genes positively linked to sugar accumulation could be further studied to identify targets for controlling sugar content in A.squamosa fruit.

摘要： BACKGROUND There is growing evidence proving that many human carcinomas, including colon cancer, can overexpress immunoglobulin(Ig); the non B cancer cell-derived Ig usually displayed unique V(D)J rearrangement pattern that are distinct from B cell-derived Ig. Especially, the cancer-derived Ig plays important roles in cancer initiation, progression, and metastasis. However, it still remains unclear if the colon cancer-derived Ig can display unique V(D)J pattern and sequencing, which can be used as novel target for colon cancer therapy.AIM To investigate the Ig repertoire features expressed in human colon cancer cells.METHODS Seven cancerous tissue samples of colon adenocarcinoma and corresponding noncancerous tissue samples were sorted by fluorescence-activated cell sorting using epithelial cell adhesion molecule as a marker for epithelial cells. Ig repertoire sequencing was used to analyze the expression profiles of all 5 classes of Ig heavy chains(IgH) and the Ig repertoire in colon cancer cells and corresponding normal epithelial cells.RESULTS We found that all 5 IgH classes can be expressed in both colon cancer cells and normal epithelial cells. Surprisingly, unlike the normal colonic epithelial cells that expressed 5 Ig classes, our results suggested that cancer cells most prominently express IgG. Next, we found that the usage of Ig in cancer cells caused the expression of some unique Ig repertoires compared to normal cells. Some VH segments, such as VH3-7, have been used in cancer cells, and VH3-74 was frequently present in normal epithelial cells. Moreover, compared to the normal cell-derived Ig, most cancer cell-derived Ig showed unique VHDJH patterns.Importantly, even if the same VHDJH pattern was seen in cancer cells and normal cells, cancer cell-derived IgH always displayed distinct hypermutation hot points.CONCLUSION We found that colon cancer cells could frequently express IgG and unique IgH repertoires, which may be involved in carcinogenesis of colon cancer. The unique IgH repertoire has the potential to be used as a novel target in immune therapy for colon cancer.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.

摘要： Lines maintenance is one of the important measures to assure the power of running reliably. Today a power management mainly depends on experiences to draw maintenance plan. But there are many kinds of factors and their complex relation in the power lines maintenance, which leads to a difficult problem. Analytic hierarchy process is an effective method that can solve a multiple criteria and multiple objective decision-making problem. We import analytic hierarchy process to the power lines maintenance problem. An AHP model was firstly built up and an example was then given to appear how the analytic hierarchy process to apply in the power lines maintenance. By this way we try to contribute a scientific and objective maintenance scheduling to the power lines maintenance.