Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulv...Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulvar lichen sclerosus.Methods:Nine patients with vulvar lichen sclerosus diagnosed pathologically were selected as the study object,and the Baiban ointment was applied locally for 3 months.Gene chip technology was used to detect the vulva skin tissue in the same area before and after treatment,and the peripheral normal skin was used as the normal control group to analyze the change of gene expression profile.FC and P values were used as research indicators,and the standard of differential expression was FC value≥1.5,P value<0.05.The differentially expressed genes were screened,and GO analysis and KEGG database gene pathway analysis were carried out.Results:Compared with the normal control group,there were 22 differentially expressed genes in Group A before treatment,of which 21 were up-regulated and 1 was down regulated;compared with Group B before treatment,there were 23 differentially expressed genes,all of which were up regulated.The differentially expressed genes related to Baiban ointment treatment included TBK1、STAT1、ITGAM、VCAN、PRKACB、PROM1、PLAT、SERPINA1.Go analysis showed that the up-regulated differential genes were mainly concentrated in the extracellular exosome,cytosol,extracellular space,Golgi apparatus and other cellular component,using the biological process such as positive regulation of cell metabolism,signal transduction regulation,cell adhesion,etc.,to play a role in protein binding,enzyme activity regulation and other molecular functions.KEGG signaling pathway showed that the differentially expressed genes were significantly enriched in Toll like receptor signaling pathway,Nod like receptor signaling pathway and Fc RI signaling pathway,all of which were up-regulated signaling pathways.Among them,Toll like receptor signaling pathway and Nod like receptor signaling pathway are most closely related to the disease.Conclusion:Baiban ointment may play a role in regulating metabolism,inflammation and immune response by regulating the expression of related genes,affecting the signal transduction such as Toll like receptor signal pathway.The pathway and the genes screened in this study will provide a direction for the future study of this disease.展开更多
Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the...Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.展开更多
Targeted genotyping is an extremely powerful approach for the detection of known genetic variations that are biologically or clinically important.However,for non-model organisms,large-scale target geno-typing in a cos...Targeted genotyping is an extremely powerful approach for the detection of known genetic variations that are biologically or clinically important.However,for non-model organisms,large-scale target geno-typing in a cost-effective manner remains a major challenge.To address this issue,we present an ultrahigh-multiplex,in-solution probe array-based high-throughput diverse marker genotyping(HD-Marker)approach that is capable of targeted genotyping of up to 86000 loci,with coverage of the whole gene repertoire,in what is a 27-fold and six-fold multiplex increase in comparison with the conventional Illumina GoldenGate and original HD-Marker assays,respectively.We perform extensive analyses of var-ious ultrahigh-multiplex levels of HD-Marker(30 k-plex,56 k-plex,and 86 k-plex)and show the power and excellent performance of the proposed method with an extremely high capture rate(about 96%)and genotyping accuracy(about 96%).With great advantages in terms of cost(as low as 0.0006 USD per geno-type)and high technical flexibility,HD-Marker is a highly efficient and powerful tool with broad appli-cation potential for genetic,ecological,and evolutionary studies of non-model organisms.展开更多
BACKGROUND： Natural cerebrolysin （NC）, a Chinese herbal drug for the treatment of Alzheimer＇s disease （AD）, induces mesenchymal stem cell （MSC） differentiation into neuron-like cells, with low toxicity. But th...BACKGROUND： Natural cerebrolysin （NC）, a Chinese herbal drug for the treatment of Alzheimer＇s disease （AD）, induces mesenchymal stem cell （MSC） differentiation into neuron-like cells, with low toxicity. But the mechanisms involved in NC effects on MSCs remain poorly understood. OBJECTIVE： We used a whole genome microarray technique to further investigate the molecular, genetic, and pharmacodynamic mechanisms of NC on MSC gene expression profiles. DESIGN, TIME AND SETTING： A parallel, controlled, in vitro experiment was performed at the First Affiliated Hospital of Shenzhen University, Shenzhen Institute of Integrated Chinese and Western Medicine, China, between September 2006 and October 2008. MATERIALS： NC was provided by Shenzhen Institute of Integrated Chinese and Western Medicine China. It was predominantly composed of Renshen （Radix Ginseng）, Tianma （Rhizoma Gastrodiae） and Yinxingye （Ginkgo Leaf） and prepared by conventional water extractJon technology. Twelve adult, male, New Zealand rabbits were included, six of which underwent intragastric administration of NC extract for 1 month to create NC-containing serum. METHODS： Bone marrow was collected from the tibia and femur of Sprague Dawley rats, aged 6 8 months old. Rat MSCs were isolated and purified by the whole bone marrow adherence method. After in vitro culture, MSCs from passage 4 were treated with NC-containing serum for 48 hours, and total RNA was extracted. Gene expression in MSCs was analyzed using Affymetrix whole genome microarray analysis. MAIN OUTCOME MEASURES： Differentially expressed genes in NC serum-treated MSCs. RESULTS： NC treated MSCs displayed 46 differentially expressed genes, 22 with upregulated expression （fold change 〉 2） and 24 with downregulated expression （fold change 〈 -2）. Differentially expressed genes participated in neuronal growth, differentiation, and function, cell growth, differentiation, proliferation, apoptosis, signal transduction, substance/energy metabolism, ion transport, and immune responses. NC treatment changed levels of transforming growth factor β/ bone morphogenetic proteins, Hedgehog, Bmp, and Wntsignaling pathways, which regulate nerve cell differentiation, development and function, as well as learning and memory; Ras, G protein- coupled receptor signal pathways that are related to cell growth, proliferation, and apoptosis; and mitogen-activated protein kinase kinase kinase signaling cascades. CONCLUSION： NC can regulate gene expression for many signal transduction pathways related to nerve cell differentiation, development and function, learning and memory function, as well as regulation of cell growth, differentiation, proliferation, or apoptosis to mediate the genetic effects of NC treatment on AD.展开更多
目的对我国NIPBL基因突变的德朗热综合征(Cornelia de Lange syndrome,CdLS)1型患儿进行基因型和表现型分析。方法以知网、万方、PubMed数据库为文献来源,检索建库至2022年9月发表的相关文献。本研究共纳入41例CdLS1型患者,其中1例来自...目的对我国NIPBL基因突变的德朗热综合征(Cornelia de Lange syndrome,CdLS)1型患儿进行基因型和表现型分析。方法以知网、万方、PubMed数据库为文献来源,检索建库至2022年9月发表的相关文献。本研究共纳入41例CdLS1型患者,其中1例来自四川省妇幼保健院儿科个案报道,其余40例均来自文献综述。回顾性分析这41例CdLS1型患者的基因型与表现型特征。结果我国CdLS1型患者临床表现主要为特殊颅面畸形100.0%(41/41)、肢体畸形100.0%(41/41)、智力障碍100.0%(21/21)、矮小症97.1%(33/34),偶有先天性心脏病(5例)、肾囊肿(3例)、隐睾(2例)、腭裂(2例)、癫痫(2例)等表现,尚无合并先天性膈疝病例报道。诊断年龄为生后胎儿期至12岁,产前诊断6.1%(2/33),新生儿期诊断30.3%(10/33)。本研究CdLS1型患儿中移码突变26.8%(11/41)、剪切突变24.4%(10/41)、错义突变22.0%(9/41)、无义突变22.0%(9/41),CdLS1患者基因型与表现型比较结果差异无统计学意义(H=3.005,P=0.391)。结论本研究CdLS1型患者中,经典型80.5%,非经典型14.6%,疑似4.9%,尚未发现基因型与表型相关。总结并分析CdLS1型患者的临床特点和基因分型,可为临床上早期识别和诊断提供参考。展开更多
基金Harbin Science and technology plan project(NO.2016RAXJ060)
文摘Objective:To study the effect of Baiban Ointment on gene expression profile of vulvar lichen sclerosus before and after treatment,and to provide theoretical basis for the early diagnosis and clinical treatment of vulvar lichen sclerosus.Methods:Nine patients with vulvar lichen sclerosus diagnosed pathologically were selected as the study object,and the Baiban ointment was applied locally for 3 months.Gene chip technology was used to detect the vulva skin tissue in the same area before and after treatment,and the peripheral normal skin was used as the normal control group to analyze the change of gene expression profile.FC and P values were used as research indicators,and the standard of differential expression was FC value≥1.5,P value<0.05.The differentially expressed genes were screened,and GO analysis and KEGG database gene pathway analysis were carried out.Results:Compared with the normal control group,there were 22 differentially expressed genes in Group A before treatment,of which 21 were up-regulated and 1 was down regulated;compared with Group B before treatment,there were 23 differentially expressed genes,all of which were up regulated.The differentially expressed genes related to Baiban ointment treatment included TBK1、STAT1、ITGAM、VCAN、PRKACB、PROM1、PLAT、SERPINA1.Go analysis showed that the up-regulated differential genes were mainly concentrated in the extracellular exosome,cytosol,extracellular space,Golgi apparatus and other cellular component,using the biological process such as positive regulation of cell metabolism,signal transduction regulation,cell adhesion,etc.,to play a role in protein binding,enzyme activity regulation and other molecular functions.KEGG signaling pathway showed that the differentially expressed genes were significantly enriched in Toll like receptor signaling pathway,Nod like receptor signaling pathway and Fc RI signaling pathway,all of which were up-regulated signaling pathways.Among them,Toll like receptor signaling pathway and Nod like receptor signaling pathway are most closely related to the disease.Conclusion:Baiban ointment may play a role in regulating metabolism,inflammation and immune response by regulating the expression of related genes,affecting the signal transduction such as Toll like receptor signal pathway.The pathway and the genes screened in this study will provide a direction for the future study of this disease.
文摘Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.
基金the grant support from National Natural Science Foundation of China (32130107, 32002446 and 32102778)Project of Sanya Yazhouwan Science and Technology City Management Foundation (SKJC-KJ-2019KY01)+1 种基金China Agriculture Research System of MOF and MARATaishan Scholar Project Fund of Shandong Province of China
文摘Targeted genotyping is an extremely powerful approach for the detection of known genetic variations that are biologically or clinically important.However,for non-model organisms,large-scale target geno-typing in a cost-effective manner remains a major challenge.To address this issue,we present an ultrahigh-multiplex,in-solution probe array-based high-throughput diverse marker genotyping(HD-Marker)approach that is capable of targeted genotyping of up to 86000 loci,with coverage of the whole gene repertoire,in what is a 27-fold and six-fold multiplex increase in comparison with the conventional Illumina GoldenGate and original HD-Marker assays,respectively.We perform extensive analyses of var-ious ultrahigh-multiplex levels of HD-Marker(30 k-plex,56 k-plex,and 86 k-plex)and show the power and excellent performance of the proposed method with an extremely high capture rate(about 96%)and genotyping accuracy(about 96%).With great advantages in terms of cost(as low as 0.0006 USD per geno-type)and high technical flexibility,HD-Marker is a highly efficient and powerful tool with broad appli-cation potential for genetic,ecological,and evolutionary studies of non-model organisms.
基金Scientific and Technological Foundation of the National Administration of Traditional Chinese Medicine of China,No.02-03LP41the Scientific and Techno-logical Key Project of Guangdong Province,No.2006B35630007
文摘BACKGROUND： Natural cerebrolysin （NC）, a Chinese herbal drug for the treatment of Alzheimer＇s disease （AD）, induces mesenchymal stem cell （MSC） differentiation into neuron-like cells, with low toxicity. But the mechanisms involved in NC effects on MSCs remain poorly understood. OBJECTIVE： We used a whole genome microarray technique to further investigate the molecular, genetic, and pharmacodynamic mechanisms of NC on MSC gene expression profiles. DESIGN, TIME AND SETTING： A parallel, controlled, in vitro experiment was performed at the First Affiliated Hospital of Shenzhen University, Shenzhen Institute of Integrated Chinese and Western Medicine, China, between September 2006 and October 2008. MATERIALS： NC was provided by Shenzhen Institute of Integrated Chinese and Western Medicine China. It was predominantly composed of Renshen （Radix Ginseng）, Tianma （Rhizoma Gastrodiae） and Yinxingye （Ginkgo Leaf） and prepared by conventional water extractJon technology. Twelve adult, male, New Zealand rabbits were included, six of which underwent intragastric administration of NC extract for 1 month to create NC-containing serum. METHODS： Bone marrow was collected from the tibia and femur of Sprague Dawley rats, aged 6 8 months old. Rat MSCs were isolated and purified by the whole bone marrow adherence method. After in vitro culture, MSCs from passage 4 were treated with NC-containing serum for 48 hours, and total RNA was extracted. Gene expression in MSCs was analyzed using Affymetrix whole genome microarray analysis. MAIN OUTCOME MEASURES： Differentially expressed genes in NC serum-treated MSCs. RESULTS： NC treated MSCs displayed 46 differentially expressed genes, 22 with upregulated expression （fold change 〉 2） and 24 with downregulated expression （fold change 〈 -2）. Differentially expressed genes participated in neuronal growth, differentiation, and function, cell growth, differentiation, proliferation, apoptosis, signal transduction, substance/energy metabolism, ion transport, and immune responses. NC treatment changed levels of transforming growth factor β/ bone morphogenetic proteins, Hedgehog, Bmp, and Wntsignaling pathways, which regulate nerve cell differentiation, development and function, as well as learning and memory; Ras, G protein- coupled receptor signal pathways that are related to cell growth, proliferation, and apoptosis; and mitogen-activated protein kinase kinase kinase signaling cascades. CONCLUSION： NC can regulate gene expression for many signal transduction pathways related to nerve cell differentiation, development and function, learning and memory function, as well as regulation of cell growth, differentiation, proliferation, or apoptosis to mediate the genetic effects of NC treatment on AD.
文摘目的对我国NIPBL基因突变的德朗热综合征(Cornelia de Lange syndrome,CdLS)1型患儿进行基因型和表现型分析。方法以知网、万方、PubMed数据库为文献来源,检索建库至2022年9月发表的相关文献。本研究共纳入41例CdLS1型患者,其中1例来自四川省妇幼保健院儿科个案报道,其余40例均来自文献综述。回顾性分析这41例CdLS1型患者的基因型与表现型特征。结果我国CdLS1型患者临床表现主要为特殊颅面畸形100.0%(41/41)、肢体畸形100.0%(41/41)、智力障碍100.0%(21/21)、矮小症97.1%(33/34),偶有先天性心脏病(5例)、肾囊肿(3例)、隐睾(2例)、腭裂(2例)、癫痫(2例)等表现,尚无合并先天性膈疝病例报道。诊断年龄为生后胎儿期至12岁,产前诊断6.1%(2/33),新生儿期诊断30.3%(10/33)。本研究CdLS1型患儿中移码突变26.8%(11/41)、剪切突变24.4%(10/41)、错义突变22.0%(9/41)、无义突变22.0%(9/41),CdLS1患者基因型与表现型比较结果差异无统计学意义(H=3.005,P=0.391)。结论本研究CdLS1型患者中,经典型80.5%,非经典型14.6%,疑似4.9%,尚未发现基因型与表型相关。总结并分析CdLS1型患者的临床特点和基因分型,可为临床上早期识别和诊断提供参考。
