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This review presents advances in the implementation of high - throughput se quencing and its application to the knowledge of medicinal plants. We conducted a bibliographic search of papers published in PubMed, Science Direct, Google Scholar, Scopus, and Web of Science databases and analyzed the obtained data using VOSviewer (versi on 1.6.19). Given that medicinal plants are a source of specialized metabolites with immense therapeutic values and important pharmacological properties, plant researchers around the world have turned their attention toward them and have begun to examine t hem widely. Recent advances in sequencing technologies have reduced cost and time demands and accelerated medicinal plant research. Such research leverages full genome sequencing, as well as RNA (ribonucleic acid) sequencing and the analysis of the transcr iptome, to identify molecular markers of species and functional genes that control key biological traits, as well as to understand the biosynthetic pathways of bioactive metabolites and regulatory mechanisms of environmental responses. As such, the omics ( e.g., transcriptomics, metabolomics, proteomics, and genomics, among others) have been widely applied within the study of medicinal plants, although their usage in Colombia is still few and, in some areas, scarce. (185)
El extracto de cloroformo (CE) y las fracciones obtenidas de las raíces de Aldama arenaria se evaluaron para determinar su actividad antiproliferativa in vitro contra 10 líneas ce lulares tumorales humanas [leucemia (K - 562), mama (MCF - 7), ovario que expresa un fenotipo resistente a múltiples fármacos (NCI/ADR - RES), melanoma (UACC - 62), pulmón (NCI - H460), próstata (PC - 3), colon (HT29), ovario (OVCAR - 3), glioma (U251) y riñón (786 - 0)]. CE presentó actividad antiproliferativa débil a moderada (log GI 50 medio 1.07), mientras que las fracciones 3 y 4, enriquecidas con diterpenos de tipo pimarane [ent - pimara - 8 (14), ácido 15 - dien - 19 - oico y ent - 8(14),15 - pimaradien - 3 ß - ol], presentaron activid ad moderada a potente para la mayoría de las líneas celulares, con un log GI 50 medio de 0.62 y 0.59, respectivamente. Los resultados mostraron una acción antiproliferativa in vitro prometedora de las muestras obtenidas de A. arenaria , con los mejores resul tados para NCI/ADR - RES, HT29 y OVCAR - 3, y valores de TGI que van desde 5.95 a 28.71 µg.mL - 1, demostrando que los compuestos de esta clase pueden ser prototipos potenciales para el descubrimiento de nuevos agentes terapéuticos
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Plantas Medicinais , Sequenciamento de Nucleotídeos em Larga Escala , Multiômica , Medicina Tradicional , ColômbiaRESUMO
Objective To evaluate the value of high-throughput sequencing(HTS)data reanalysis that does not include ERBB2 copy number variation(CNV)analysis,in identifying ERBB2 amplification in patients with colorectal cancer.Methods The HTS data of 252 cases of colorectal cancer diagnosed by pathological biopsy who received peripheral blood cfDNA HTS detection samples were retrospectively analyzed.According to the HTS data of ERBB2 non-amplified samples judged by immunohistochemistry(IHC)and/or fluorescence in situ hybridization(FISH),the number of chromosome 17(Chr17)reads in the total number of reads was calculated the range of the ratio was initially determined as the threshold for prompting ERBB2 amplification.Suspected positive samples were screened according to thresholds and verified by digital PCR,IHC and FISH.Results The proportion of the number of Chr17 reads accounts for the number of total reads in the 89 cases of ERBB2 non-amplified samples determined by IHC and/or FISH ranged from 0.188 to 0.299(0.239±0.192).Using 0.298(1.25 times the mean)as the threshold indicating ERBB2 amplification,the data of 163 samples were analyzed,of which 7 cases were suspected to be positive,and the ratio ranged from 0.302 to 0.853.Among them,5 cases were determined to be positive by IHC and/or FISH,and 6 cases were confirmed to be positive by digital PCR.The ratio of the number of Chr17 reads to the number of total reads was positively correlated with the ratio of ERBB2/EIF2C1,and the correlation was good(r2=0.909).Conclusion The high-throughput sequencing data that does not cover the ERBB2 CNV analysis has a certain hint value for ERBB2 amplification in patients with colorectal cancer.
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Objective To construct a canine model of vocal cord scar by low-termperature plasma ablation and screen the target genes closely related to the formation of vocal cord scar.Methods Four Chinese rural canines were treated with plasma ablation under the support of laryngoscope and endoscope,and the left vocal cords were injured to the muscle layer.The contralateral sides were left untreated.The gross morphology of vocal cord was observed before operation,immediately after operation,3 weeks after operation and 12 weeks after operation.The pathologi-cal structure of vocal cords was observed by HE stainning,and the ultrastructure of vocal cords was observed by transmission electron microscopy.In addition,high-throughput sequencing was used to analyze the differences in gene expression between the bilateral vocal cords,and the target genes with significantly different expression were screened out.Results In general morphology,the normal vocal cords were banded and well closed.At 3 weeks af-ter operation,the vocal cords were congested and swollen,with uneven edges and red granulation tissues were seen.At 12 weeks after operation,the vocal cord wound was localized contracture and depression,and scar was formed.HE staining showed obvious thickening of the squamous epithelium of the scarred vocal cords,thickening and disor-dered arrangement of the fiber layer,local clumping or bundle aggregation,and scattered fiber bundles were also seen in the muscle layer.Transmission electron microscopy showed interstitial thickening,uneven density,cell swelling,unclear intercellular boundary,proliferation of nuclei and mitochondria,and cells in an active state.High-throughput sequencing analysis revealed that many gene families were involved in the process of vocal cord scar re-pair,including IL family,CCL and CXCL family,MMPs family and its inhibitor TIMPs family,Wnt family,HSP family,MAPK family and TGF-β family.Conclusion We successfully constructed the canine model of vocal cord scar by low-temperature plasma ablation and screened out the target genes closely related to the formation of vocal cord scar by high-throughput sequencing,which provides certain reference value for exploring the mechanism of vo-cal cord scar.
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ObjectiveTo explore the interaction between bruceoside B and gut microbiota and the inhibitory activity of its metabolites on human lung cancer A549 cells， and to explore the value of bruceoside B in the treatment of non-small cell lung cancer（NSCLC）. MethodBruceoside B was co-incubated with the human gut microbiota under anoxic conditions in vitro， and ultra high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry（UPLC-Q-TOF-MS） was used to analyze the metabolic transformation products. Cell counting kit-8（CCK-8） assay was performed to determine the effects of bruceoside B and its metabolites on the proliferation of human lung cancer A549 cells and the half inhibitory concentration（IC50） was calculated. Five healthy male rats were gavaged with bruceoside B（2 mg·kg-1） for 7 days after adaptive feeding. The feces of rats were collected before and after administration. 16S rRNA sequencing was used to assess gut microbiota. ResultBruceoside B was mainly metabolized to brusatol by human gut microbiota， the IC50 of bruceoside B and the conversion product to A549 cells were 1 755.50， 19.57 μmol·L-1， respectively， and the conversion product had a better activity at inhibiting A549 cells proliferation than bruceoside B. Additionally， The results of intestinal flora analysis showed no significant differences in α diversity and β diversity of gut microbiota after administration. In terms of species abundance， at the phylum level， bruceoside B decreased the relative abundance of Actinobacteriota and Proteobacteria， increased the relative abundance of Firmicutes， Patescibacteria and Cyanobacteria. At the genus level， bruceoside B decreased the relative abundance of Staphylococcus， Aerococcus and Psychrobacter， increased the relative abundance of Romboutsia， Lactobacillus， Clostridium sensu stricto 1， Norank-f-norank-o-Clostridia-UCG-014， Turicibacter， Allobaculum and Candidatus Saccharimonas. The results of functional prediction showed that the gut microbiota functional compositions were relatively stable. ConclusionBruceoside B can be deglycosylated by intestinal flora and converted into brusatol， with a significant increase in antitumor activity. The administration of bruceoside B will not cause significant changes in the structure and function of the intestinal flora， resulting in intestinal microecological balance disorders， and the administration appears to be beneficial to the intestinal flora of NSCLC patients.
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Objective To investigating the microbial communities and physicochemical properties of soil and distribution of Oncomelania hupensis snails in marshlands along the Yangtze River basin at different types of land use, and to examine the effects of soil microorganisms and physicochemical properties on snail distribution, so as to provide insights into snail control and schistosomiasis prevention in marshland along the Yangtze River basin. Methods Marshlands with four types of land use were selected along the Yangtze River basin on April 2021, including poplar forest-crops integrated planting, reed areas, agricultural cultivation lands and ditches. The distribution of snails and physicochemical properties of soil were investigated in marshlands with different types of land use, and the V3 to V4 regions of the bacterial 16S ribosomal RNA (16S rRNA) gene, fungal internal transcribed spacer-1 (ITS1) gene and algal ribulose-bisphosphate carboxylase (rbcL) gene in soils were subjected to high-throughput sequencing. The occurrence of frames with living snails and density of living snails were compared in marshland with different types of land use. The associations of soil microorganisms and physicochemical properties with the density of living snails were examined using Pearson correlation analysis, and the contributions of soil microorganisms and physicochemical properties to the density of living snails were evaluated using variance partitioning analysis. Results In marshlands with four types of land use, the greatest occurrence of frames with living snails [(4.94 ± 2.14)%] and density of living snails [(0.070 ± 0.026) snails/0.1 m2] were seen in ditches, and the lowest were found in [(1.23 ± 1.23)%] agricultural cultivation lands [(0.016 ± 0.019) snails/0.1 m2]. A total of 2 phyla, 5 classes, 8 orders, 9 families and 11 genera of algae were detected in soils at four types of land use, with Chlorophyta as the dominant phylum and Pseudoneochloris as the dominant genus. A total of 44 phyla, 134 classes, 281 orders, 338 families and 516 genera of bacteria were detected in soils at four types of land use, with Proteobacteria and Acidobacteriota as the dominant phyla and uncultured Acidobacterium, MND1, Mitrospira, Haliangium and Sphingomonas as dominant genera. A total of 11 phyla, 41 classes, 108 orders, 223 families and 408 genera of fungi were detected in soils at four types of land use, with phyla Ascomycota, Basidiomycota and Mortierellomycota presenting high relative abundances and genera Cladorrhinum, Mortierella and Humicola presenting high relative abundances. Pearson correlation analysis revealed that the density of living snails correlated negatively with the relative abundance of Proteobacteria (r = −0.965, P < 0.05) and soil electronic conductivity (r = −0.962, P < 0.05) and positively with soil moisture (r = 0.951, P < 0.05). Variance partitioning analysis demonstrated that the physicochemical properties and microorganisms of soil contributed 69% and 10% to the density of living snails, respectively. Conclusion The diversity of microbial communities varies in soils at different types of land use in marshland along the Yangtze River basin, and the physicochemical properties and microorganisms of soils may affect the distribution of O. hupensis snails.
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Objective @# To explore the role of long non-coding RNA XR_378418 (LncRNA XR_378418) in the bi- ological behavior of hepatic stellate cells line JS-1 and to probe the potential molecular mechanism of LncRNA XR _378418 involved in liver fibrosis based on transcriptome sequencing．@*Methods @#In this study，the recombinant plasmid of pcDNA-LncRNA XR_378418 and control plasmid pcDNA-NC were constructed and transfected into JS-1 cells respectively．Then，the expression level of LncRNA XR_378418 was analyzed by quantitative real-time PCR (RT-qPCR) ．The effect of overexpression of LncRNA XR_378418 on proliferation and migration of JS-1 cells were detected by cell counting kit-8 assay ( CCK-8 ) and scratch assay，respectively． Finally，by high-throughput se- quencing analysis，the effect of XR_378418 on the transcriptomics of JS-1 cells was analyzed. @*Results @#T-qPCR results showed that the expression level of LncRNA XR_378418 in the overexpression group was significantly higher than that in the control group (P＜0. 05) ．The results of CCK-8 and scratch experiment suggested that the prolifer- ation and migration in the pcDNA-LncRNA XR _ 378418 group significantly increased． Furthermore ，the high- throughput sequencing analysis showed that a total of 248 genes were screened by gene differential analysis ，of which 127 were up-regulated ，and 117 were down-regulated． Gene Ontology ( GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that LncRNA XR_378418 could regulate cell adhesion，autophagy and Ca2 + signaling，etc．@*Conclusion @#LncRNA XR_378418 promotes the proliferation and migration of JS-1 cells and affects the expression of genes related to cell adhesion and calcium signaling in JS-1 cells.
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Background Hexavalent chromium [Cr(VI)] exposure can cause structural disruption of intestinal flora and functional impairment. Vitamin C (VC) is one of the essential micronutrients, which plays an important role in promoting the growth of intestinal probiotics, improving the intestinal barrier, and maintaining the homeostasis of intestinal flora. However, the regulatory effect of VC on the intestinal flora disorders caused by Cr(VI) exposure remains to be investigated. Objective To investigate the effect of VC on intestinal flora disruption in mice due to Cr(VI) exposure. Methods Thirty-two SPF-grade C57BL/6 mice were acclimatized and fed for 3 d and randomly divided into control (Con), VC, potassium dichromate [K2Cr2O7, Cr(VI)], and VC+K2Cr2O7 [VC+Cr(VI)] groups. At 8:00 a.m. on day 4, the Con group (double-distilled water given by gavage and injected intraperitoneally), the VC group (VC given by gavage and double-distilled water injected intraperitoneally), the Cr(VI) group (double-distilled water given by gavage and K2Cr2O7 solution injected intraperitoneally), and the VC+Cr(VI) group (VC given by gavage and K2Cr2O7 solution injected intraperitoneally) were treated. The dose of VC was 200 mg·kg−1, and the dose of K2Cr2O7 was 1.25 mg·kg−1. The mice were treated for 45 consecutive days and then executed, the contents of the colon were sampled in sterile freezing tubes, and three replicates were collected from each group. After labeling, the samples were immediately put into liquid nitrogen for rapid freezing. After all the samples were collected, they were transferred to a -80 ℃ ultra-low temperature refrigerator for storage. Samples of colon contents were analyzed for intestinal flora structure by high-throughput sequencing and bioinformatics software. Results The Cr(VI) exposure resulted in reduced body weight gain values in mice compared to the Con group. Pathological changes occurred in the ileal tissue of mice, with significant inflammatory cell infiltration in the Cr(VI) group and reduced inflammatory cell infiltration in the VC+Cr(VI) group. The number of operational taxonomic units (OTUs) of intestinal flora was altered in the Cr(VI) group of mice. In the α diversity analysis, the mean Sobs index in the Cr(VI) group was 240.333±67.796, the Chao index was 258.173±64.813, and the Ace index was 259.481±66.891, which were significantly lower than those in the Con group (P<0.05), the PD whole tree index in the Cr(VI) group was 27.863±2.399, which was significantly higher than that in the Con group (P<0.05), and the VC intervention significantly reversed the changes of the above indexes due to Cr(VI) exposure (P<0.05). In the β diversity analysis, the principal coordinates analysis (PCoA) results showed a significant separation between the Cr(VI) group and the Con group, and after the VC intervention, there was a retraction of the separation trend and the difference was reduced. The multi-sample similarity dendrogram results showed that the control and the VC groups clustered together first, then with the VC+Cr(VI) group, and finally with the Cr(VI) group. The abundances of Bacteroidetes, Saccharibacteria, and Tenericutes in the intestine of mice in the Cr(VI) group were decreased, and the abundance of Firmicutes was increased; the abundances of Lactobacillus, Alistipes, Bacteroides, and Ruminiclostridium were also increased. Included among these, Bacteroides showed a significantly higher abundance compared to the control mice (P<0.05). Changes in the abundances of phyla and genera of the above mentioned gut microorganisms were reversed after the VC intervention. Conclusion Cr(VI) exposure can lead to intestinal damage and disorganization of the intestinal flora structure in mice, while VC intervention can ameliorate the above changes to a certain extent and normalize the intestinal flora structure.
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Objective:To study the changes of intestinal flora before and after dietary intervention in pregnant women with gestational diabetes mellitus (GDM) and explore its correlation with the results of oral glucose tolerance test (OGTT), using third generation high-throughput sequencing of full-length 16S rDNA.Methods:Thirty pregnant women who received regular antenatal care in the First Affiliated Hospital of Xinjiang Medical University between July 2022 and March 2023 were selected. Demographic data and laboratory examination results of these pregnant women were collected. The pregnant women with GDM (the GDM group) were given individualized dietary intervention, while the control group were given routine dietary guidance, for a total of 2 weeks. The stool was collected before and after the intervention in both groups, and a total of 60 stool samples were collected. Through the PacBio Sequencing platform, the third generation sequencing of full-length 16S rDNA was utilized to investigate the intestinal microbiome diversity. The composition, abundance and diversity of intestinal flora were compared between groups, both before and after the intervention.Results:There were 74 species showing significant differences in abundance between the two groups of pregnant women, 54 of which were enriched in the GDM group. The correlation analysis of blood glucose levels tested by OGTT as an environmental factor showed that Lachnospirales ( P=0.002) and unclassified Bacteria ( P=0.035) were positively correlated with OGTT-0h blood glucose ( P<0.05), while Christensenellales ( P=0.018)and Oscillospirales ( P=0.045) negatively. Lachnospirales ( P=0.027)and unclassified Bacteria ( P=0.028) were positively correlated with OGTT-1 h blood glucose ( P<0.05), while Oscillospirales ( P=0.025) negatively. There was a positive correlation between Lachnospirales ( P=0.027) and OGTT-2h blood glucose ( P<0.05). Conclusions:After the individualized diet intervention, the dominant bacteria of the intestinal flora changed and the fasting blood glucose of declined in pregnant women with GDM. It's a reasonable presumption that individualized diet intervention can contribute to the regulation of the disordered intestinal flora in pregnant women with GDM, which implies a role of dietary intervention in the treatment of GDM.
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Objective To explore the effects of different types of drinking water on the growth and fecal flora of mice.Methods Specific pathogen-free NIH mice were randomly divided into five groups,32 mice each group,with half males and half females in each group.The group were given either purified water(control group),acidified water,alkalized water,weakly acidic water or solid water.Diet and body weight were monitored continuously for 20 days.After the experiment,animal fecal samples were collected,and the V3-V4 region was amplified with bacterial 16S rDNA universal primers.An Illumina Miseq high-throughput sequencing platform was used for high-throughput sequencing,and microbial community,α diversity and β diversity were analyzed by bioinformatics method.Results The body weight of female mice given different pH values of weakly acidic water was higher,while the weight of the other groups was lower,than that of the control group(P＞0.05).The body weight of male mice in the acidified water group was higher,while that of other groups was lower,than that of control group,but there was no statistical difference between the groups(P＞0.05).The body weights of male and female mice in the solid water group were lower than those in the control group(P＜0.05).The food and water intake of the female animals in the alkaline water group and the water intake of female animals in the solid water group were lower than those of the other groups.OTU clustering analysis showed that the data volume of the sequencing was reasonable,and the fecal flora species of NIH mice were divided into five phyla,among which Bacteroides and Firmicutes were dominant.Unclassified Pseudopurpuromonas,Lactobacillus and Alistipes were the main genera.There were differences in fecal flora abundance and diversity among the mice given the five drinking water types.α analysis showed that the acidified water group had the highest flora abundance and diversity,while the solid water group had the lowest flora diversity.β analysis showed that the fecal flora composition in the solid water group was the closest to that of the control group,followed by the alkalized water group,acidified water group and weakly acidic water group.Conclusions Through an exploration of the effects of consuming different forms of water,this study revealed that solid water consumption had the greatest effects on body weight,feed intake,water consumption,and fecal flora of mice.The abundance and diversity of fecal flora in mice were affected by different pH values of drinking water,especially acidified water.
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Objective To analyze the composition of microbial community in gut of elderly male Nycticebus bengalensis, aiming to explore the health impact factors associated with artificial captivity.Methods Fecal samples of 4 adult male Nycticebus bengalensis were collected and the V4 region was amplified using bacterial 16S rDNA universal primers. Illumina NovaSeq sequencing platform was used for microbial sequencing analysis. The complexity and similarity of the samples were analyzed using the QIIME software analysis tool. The species structure and abundance of the intestinal flora were analyzed at the phylum and genus levels based on validated data. The PICRUSt software was applied to predict the metabolic function of the flora.Results The results showed that the diversity index (Shannon index) of the flora in the youngest Nycticebus bengalensis was higher than that of the others. PCoA analysis showed that the bacterial community compositions of the four samples had a certain degree of similarity. Bacteria identified in the Nycticebus bengalensis feces included 12 phyla, 18 classes, 28 orders, 49 families, 93 genera, and 59 species. Among them, the dominant phyla were Bacteroidetes and Firmicutes with average relative abundances of 46% and 28%, respectively; The genera Bacteroides, Bifidobacterium, and Fusobacterium had higher abundances, with relative abundances of 33%, 6%, and 6%, respectively; The beneficial genus Bifidobacterium was found in all samples, with the highest relative abundance found in the younger Nycticebus bengalensis. PICRUSt function prediction analysis showed that the abundance of the functional genes related to amino acid transport and metabolism, carbohydrate transport and metabolism,was relatively high.Conclusion The use of Illumina NovaSeq high-throughput sequencing technology can comprehensively detect the fecal microbial community of the Nycticebus bengalensis. The bacterial composition of Nycticebus bengalensis has rich diversity. Many bacteria are not identified and have higher relative abundance, which need further study.
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@#Objective To investigate the diagnostic value of Xpert MTB/RIF combined with metagenic high-throughput sequencing in bacterial negative tuberculosis.Methods Retrospective analysis of 70 patients diagnosed with bacterial negative pulmonary tuberculosis from December 2019 to May 2022 enrolled in the study.Xpert MTB/RIF testing,high-throughput metagenomic sequencing,and a combination of the two were performed,respectively.Solid culture and proportional methods were used to diagnose biochemical pathogens and analyze diagnostic efficacy.The receiver operating characteristic curve was drawn with the predicted value.Results The positive rate of Xpert MTB/RIF diagnosis was 75.57%,and the negative rate was 21.43%.The positive rate of high-throughput sequencing for metagenomics was 78.57%,while the negative rate was 21.43%;The positive rate of combined diagnosis was 88.57%,and the negative rate was 11.43%.The detection sensitivity of Xpert MTB/RIF was 77.55%,the specificity was 59.86%,and the area under the curve(AUC)was 0.827.The sensitivity of high-throughput sequencing for metagenomes was 77.47%,the specificity was 61.02%,and the AUC was 0.808.The sensitivity of the combined detection was 89.75%,the specificity was 89.57%,and the AUC was 0.925.The results showed that the diagnostic sensitivity and specificity of Xpert MTB/RIF combined with high-throughput metagenomic sequencing in bacterial negative pulmonary tuberculosis were higher than those of single detection(P<0.05).Conclusion Xpert MTB/RIF combined with metagenic high-throughput sequencing has good application value in the diagnosis of bacterial negative pulmonary tuberculosis,and is worthy of clinical application.
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Objective@#To analyse the expression of differential mRNA in the plasma exosomes in patients with latent tuberculosis infection (LTBI) and active tuberculosis (ATB) using high-throughput sequencing, so as to provide insights into differential diagnosis of LTBI and ATB.@*Methods@#The plasma samples were collected from the patients treated at The Affiliated Hospital of Hangzhou Normal University, including 16 cases of LTBI and 21 cases of ATB. The exosomes were extracted by Invitrogen extracellular extracts purification kit, and the size and morphology of exosomes were observed by transmission electron microscope (TEM). The exosomes were identified by Western blotting. Total RNA was extracted from plasma exosomes using high-throughput sequencing, differential expression mRNA was identified, and gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Two differential mRNAs with the highest differential expression fold were selected, and five patients with ATB and three patients with LTBI were recruited for verification using real-time quantitative PCR.@*Results@#The sequencing results of plasma exosomes showed that compared with ATB patients, 2 875 differentially expressed mRNAs were detected in exosomes of LTBI patients, of which 1 002 mRNAs were up-regulated and 1 873 mRNAs were down-regulated. The most significant differentially expressed downregulated and upregulated mRNA were M6PR and RGPD5, respectively. GO analysis and KEGG pathway analysis showed that differential mRNAs were enriched in protein serine kinase activity, rRNA binding molecular function, human cytomegalovirus infection, pancreatic cancer, endometrial cancer, insulin signaling pathway and FoxO signaling pathway. The real-time quantitative PCR showed that the expression of differential mRNA was consistent with sequencing. Compared with ATB patients, the relative expression level of M6PR in plasma exosomes in LTBI patients (0.954±0.212) was downregulated compared with that of ATB patients (2.168±0.226), while the relative expression level of RGPD5 (2.126±0.200) was upregulated compared with that of ATB patients (0.588±0.129) (both P<0.05).@*Conclusions@#There is a difference in mRNA expression of plasma exosomes between patients with LTBI and ATB. M6PR and RGPD5 may become markers for distinguishing plasma exosomes between LTBI and ATB.
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ObjectiveTo explore the distribution of pharyngeal microbiota in coal miners exposed to dust. Methods Eight coal miners who had been engaged in occupational dust exposure for more than 20 years were selected as the dust-exposed group, and four coal miners who were not exposed to dust at work were selected as the control group using the judgment sampling method. Pharyngeal secretions of the coal miners were collected with throat swabs, and its pharyngeal microbiota was analyzed. The diversity, abundance and evenness of the microbiota were analyzed by gene sequencing using the 16sRNA gene high-throughput sequencing technology. Results A total of 254 operational taxonomic units of pharyngeal microbiota were detected in the coal miners in the control group, which was 210 more than that in the dust-exposed group. The Chao1 index, Shannon index, PD-tree index and Pielou index of pharyngeal microbiota in the dust-exposed group decreased compared with the control group (all P<0.01). The abundance of Bacteroidetes and Clostridum, at the phylum level, in the pharynx of coal miners in the dust-exposed group was higher than that in the control group (all P<0.05). The abundance of Prevotella, Neisseria, and Monas, at the genus level, in the pharynx of coal miners in the dust-exposed group was higher than that in the control group(all P<0.05), while the abundance of Lactobacillus decreased (P<0.05). The analysis results of the receiver operating characteristic curve showed that Lactobacillus, Fusobacterium and Rothia may play a role for pharyngeal microbiota imbalance prediction in dust-exposed workers, and the area under the curves were all 1.00±0.00. Conclusion The species diversity and evenness of pharyngeal microbiota in coal miners exposed to dust are decreased, which may be related to the continuous inhalation of coal dust that disrupts the microbial environment of the throat.
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The UV cross-linking immunoprecipitation (CLIP) technique was first established in 2003. Sequences of target RNAs and binding sites of specific RNA-binding proteins (RBPs) were identified within the entire transcriptome by UV cross-linking, immunoprecipitation, reverse transcription, and subsequent high-throughput sequencing. Over the last 20 years, CLIP has been continuously modified and improved. Advanced operability and accuracy have extended its application category. Currently, the widely used CLIP technologies include high-throughput sequencing with crosslinking-immunoprecipitation (HITS-CLIP), photoactivatable-ribonucleoside-enhanced CLIP (PAR-CLIP), individual nucleotide resolution CLIP (iCLIP), enhanced CLIP (eCLIP), infrared-CLIP (irCLIP), etc. HITS-CLIP combines high-throughput sequencing with UV cross-linking immunoprecipitation. The 254 nm UV cross-linking and RNAase digestion steps allow the technology to capture transient intracellular RBP-RNA interactions. However, there are limitations in the efficiency of UV cross-linking, with low resolution and high intrinsic background noise. For PAR-CLIP, photoactivatable ribonucleoside was incorporated into RNA molecules, and RBP cross-linked with RNA by 365 nm UV light to improve cross-linking efficiency and resolution. Cross-linking mediated single-base mutations provide more accurate binding site information and reduce interference from background sequences. Long-term alternative nucleotide incorporation, on the other hand, can be cytotoxic and may skew experimental results. iCLIP can identify RBP-RNA cross-linking sites at the single nucleotide level through cDNA circularization and subsequent re-linearization steps, but it has more experimental procedures, and partial cDNAs lost in the circularization step are inevitable. eCLIP discards the radioisotope labeling procedure and reduces RNA loss by ligating adaptors in two separate steps, greatly improving the library-building efficiency, and reducing bias associated with PCR amplification; however, the efficiency of immunoprecipitation cannot be visually assessed at the early stage of the experiment. The irCLIP technique replaces radioisotopes with infrared dyes and greatly reduces the initial number of cells required for the experiment; however, an infrared imaging scanner is essential for the irCLIP application. To address more particular scientific issues, derivative CLIP-related techniques such as PAPERCLIP, cTag-PAPERCLIP, hiCLIP, and tiCLIP have also been developed in recent years. In practice, the aforementioned CLIP approaches have their advantages and disadvantages. When deciding on a technical strategy, we should take into account our experimental objectives and conditions, such as whether we need to precisely define the RNA site for binding to RBP; whether we have the necessary experimental conditions for working with radioisotopes or performing infrared imaging; the amount of initial sample size, and so on. In addition, the CLIP technique has a relatively large number of procedures and can be divided into several successive experimental modules. We can try to combine modules from different mainstream CLIP technologies to meet our experimental requirements, which also gives us more opportunities to improve and refine them and to build more targeted derivative CLIP technologies according to our research objectives.
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italic>Cynanchum wallichii and Cynanchum otophyllum belong to the genus Cynanchum in the family Apocynaceae, and are important medicinal plants. In this study, we sequenced and assembled the chloroplast genomes of C. wallichii and C. otophyllum, and performed a phylogenetic analysis of the structural characteristics of their chloroplast genomes and their phylogenetic positions. The results showed that the chloroplast genomes of both C. wallichii and C. otophyllum had a typical tetrad structure, with 133 genes annotated, and the total GC contents of both were similar. Codon preference analysis showed that the relative synonymous codon usage in the chloroplast genomes of C. wallichii and C. otophyllum differed slightly, but the differences were not significant, and there was a strong A or U preference at the third codon position. In both chloroplast genomes, 91 and 103 simple sequence repeats were detected respectively, and the largest proportion of A/T type repeats. Nucleotide polymorphism analysis showed that the nucleotide diversity of the intergenic sequences in the chloroplast genome of genus Cynanchum were generally higher than those of the common gene sequences. A pair of primers was designed based on the high variation region of the chloroplast genome to identify C. wallichii and C. otophyllum. The phylogenetic analysis showed that the C. wallichii and Cynanchum thesioides were the closest relatives, while the C. otophyllum, Cynanchum bungei and Cynanchum wilfordii formed a stable monophyletic clade within the genus Cynanchum, and the three species were closely related. The comparative analysis of the chloroplast genomic characteristics and phylogeny of C. wallichii and C. otophyllum will provide a theoretical basis for the species identification of the two plants and for the study of genetic diversity and phylogeny of the genus Cynanchum.
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AIM: To investigate the correlation between xanthelasma palpebrarum(XP)and the genetic factor of hypercholesterolemia and provide a basis for the elucidation of the pathogenesis of xanthelasma palpebrarum.METHODS: A total of 29 patients with XP who treated in the ophthalmology department of Foshan Sanshui District People's Hospital from November 2019 to January 2021 were selected. Peripheral blood was drawn, and the Next Generation Sequencing(NGS)technology was used to detect the genetic mutations of patients, while blood lipids of XP patients were analyzed.RESULTS: Gene mutations were detected in 21 patients with XP, among which 13 cases had hypercholesterolemia and 8 cases had normal cholesterol levels. Genes including STAP1, APOB, LDLRAP1, LDLR, PCSK9 and APOE mutated, and the types of gene mutation included 3-UTR mutation, in-frame deletion, missense mutation, 5-UTR mutation, synonymous mutation, intronic mutation, alternative splice variant, non coding transcript exon variant, and non coding transcript variant.CONCLUSION: There is a correlation between genetic factors of hypercholesterolemia and XP.
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@#Abstract: Objective To investigate the composition and diversity of midgut microbial community of Haemaphysalis longicornis infected with severe fever with thrombocytopenia syndrome virus (SFTSV)． Methods The midgut DNA of three group Haemaphysalis longicornis infected with SFTSV was extracted, and the 16S rDNA gene of the sample was sequenced by HiSeq platform. The composition and diversity of endosymbiotic microbial community were clarified by OTU cluster analysis and alpha diversity analysis. Results The midgut microbial clusters of the three groups infected with SFTSV were 143, 113, 163 OTUs respectively; the sparsity curve and abundance grade curve showed that the data had sufficient sequencing depth, and the midgut of Haemaphysalis longicornis infected with SFTSV was rich in microbial composition, but the species distribution was uneven. The analysis of microbial community composition showed that Proteobacteria, Firmicutes and Actinobacteria were the main dominant bacteria at the phyla level. At the class level, Gammaproteobacteria, Bacilli, Betaproteobacteria and Actinomycetia were the main dominant bacteria. At the order level, Legionellales, Bacillales, Burkholderiales and Actinomycetales were the main dominant orders. At the family level, Coxiellaceae, Bacillaceae, Moraxellaceae and Rhodococcaceae were the main dominant families. At the genus level, the relative abundance of Coxiella was the highest, followed by Aeribaillus and Azonexus. Alpha diversity analysis showed that the average Shannon index was 139.67, the average Simpson index was 0.48, the average Chao index was 145.06, and the average ACE index was 147.11. Conclusions The species diversity of intestinal microorganisms in Haemaphysalis longicornis infected with SFTSV is rich. The results provide a basis for further exploring the interaction between intestinal microbes of Haemaphysalis longicornis and SFTSV and developing new ideas for the prevention and control of ticks and tick-borne diseases.
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OBJECTIVES@#This study aimed to analyze the bacteria in dental caries and establish an optimized dental-ca-ries diagnosis model based on 16S ribosomal RNA (rRNA) data of oral flora.@*METHODS@#We searched the public databa-ses of microbiomes including NCBI, MG-RAST, EMBL-EBI, and QIITA and collected data involved in the relevant research on human oral microbiomes worldwide. The samples in the caries dataset (1 703) were compared with healthy ones (20 540) by using the microbial search engine (MSE) to obtain the microbiome novelty score (MNS) and construct a caries diagnosis model based on this index. Nonparametric multivariate ANOVA was used to analyze and compare the impact of different host factors on the oral flora MNS, and the model was optimized by controlling related factors. Finally, the effect of the model was evaluated by receiver operating characteristic (ROC) curve analysis.@*RESULTS@#1) The oral microbiota distribution obviously differed among people with various oral-health statuses, and the species richness and species diversity index decreased. 2) ROC curve was used to evaluate the caries data set, and the area under ROC curve was AUC=0.67. 3) Among the five hosts' factors including caries status, country, age, decayed missing filled tooth (DMFT) indices, and sampling site displayed the strongest effect on MNS of samples (P=0.001). 4) The AUC of the model was 0.87, 0.74, 0.74, and 0.75 in high caries, medium caries, low caries samples in Chinese children, and mixed dental plaque samples after controlling host factors, respectively.@*CONCLUSIONS@#The model based on the analysis of 16S rRNA data of oral flora had good diagnostic efficiency.
Assuntos
Humanos , Criança , Bactérias/genética , Cárie Dentária/microbiologia , Suscetibilidade à Cárie Dentária , Microbiota/genética , RNA Ribossômico 16SRESUMO
ObjectiveTo explore the effects of Wumeisan on gut lactase activity and microflora diversity of mice with dysbacteriosis diarrhea. MethodThe mice were randomly divided into 4 groups， namely， the normal group， the model group， and the low-dose and high-dose Wumeisan groups， with 8 mice in each group. The mouse model was made by gavage of mixed antibiotics for 7 d， and the low-dose and high-dose Wumeisan groups （5.98， 11.96 g·kg-1） were given gavage for 7 d continuously. The normal group and the model group were given the same volume of sterile water. The changes in the body weight， food intake， and diarrhea of mice were recorded. Feces were collected after the last administration， and the lactase activity was detected by the colorimetric method. The gut microbiota changes were detected by the 16S rRNA high-throughput sequencing technology. ResultCompared with those in the normal group， the mice in the model group had dilute and soft stools， reduced body mass， reduced food intake， reduced lactase activity， significantly reduced intestinal flora diversity， and significant changes in the relative abundance phylum and genus levels of flora. Compared with the model group， Wumeisan reduced the diarrhea rate of mice， promoted the rapid recovery of body weight and food intake， increased the lactase activity decreased by antibiotic， improved the community abundance and diversity of mice with dysbacteriosis， and made the species composition closer to that in the normal group. The abundance of three phyla （Bacteroidota， Proteobacteria， Verrucomicrobiota） and nine genera （Odoribacter， Enterococcus， Clostridium innocuum group， etc.） of mice with diarrhea were regulated by Wumeisan. Among them， norank f Muribaculaceae， norank f norank o Clostridia UCG-014， Lachnospiraceae NK4A136 group， and Odoribacter showed significant positive correlation with the body weight and lactase activity， and Escherichia-Shigella， Enterobacter， Enterococcus， and Clostridium innocuum group showed significant positive correlation with the diarrhea rate. Function prediction showed that the high-dose Wumeisan significantly reseted 6 functional levels of metabolism， genetic information processing， and human diseases， and had positive effects on endocrine and metabolic diseases， immune diseases， infectious disease， and parasitic infectious diseases. ConclusionWumeisan can relieve the symptoms of dysbacteriological diarrhea by increasing the lactase activity and regulating the gut microbiota composition.
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In order to determine the changes of bacterial community structure and function in the early, middle and late stage of aerobic composting of chicken manure, high-throughput sequencing and bioinformatics methods were used to determine and analyze the 16S rRNA sequence of samples at different stages of composting. Wayne analysis showed that most of the bacterial OTUs in the three composting stages were the same, and only about 10% of the operational taxonomic units (OTUs) showed stage specificity. The diversity indexes including Ace, Chao1 and Simpson showed a trend of increasing at first, followed by decreasing. However, there was no significant difference among different composting stages (P < 0.05). The dominant bacteria groups in three composting stages were analyzed at the phylum and genus levels. The dominant bacteria phyla at three composting stages were the same, but the abundances were different. LEfSe (line discriminant analysis (LDA) effect size) method was used to analyze the bacterial biological markers with statistical differences among three stages of composting. From the phylum to genus level, there were 49 markers with significant differences among different groups. The markers included 12 species, 13 genera, 12 families, 8 orders, 1 boundary, and 1 phylum. The most biomarkers were detected at early stage while the least biomarkers were detected at late stage. The microbial diversity was analyzed at the functional pathway level. The function diversity was the highest in the early stage of composting. Following the composting, the microbial function was enriched relatively while the diversity decreased. This study provides theoretical support and technical guidance for the regulation of livestock manure aerobic composting process.