Pub Date : 2021-09-01DOI: 10.1097/JBR.0000000000000105
Han Zhu, Xin Lin, Yarui Diao
Abstract Skeletal muscle plays an essential role in generating the mechanical force necessary to support the movement of our body and daily exercise. Compared with cardiac and smooth muscle, in mammals, skeletal muscle exhibits remarkable regenerative capacity in response to damage. Muscle stem cells, also known as satellite cells, directly contribute to regeneration. Here, we review primary and secondary myogenesis processes with a focus on muscle stem cells, as well as the function and regulation of muscle stem cells in adult muscle regeneration in mammals.
{"title":"Function and regulation of muscle stem cells in skeletal muscle development and regeneration: a narrative review","authors":"Han Zhu, Xin Lin, Yarui Diao","doi":"10.1097/JBR.0000000000000105","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000105","url":null,"abstract":"Abstract Skeletal muscle plays an essential role in generating the mechanical force necessary to support the movement of our body and daily exercise. Compared with cardiac and smooth muscle, in mammals, skeletal muscle exhibits remarkable regenerative capacity in response to damage. Muscle stem cells, also known as satellite cells, directly contribute to regeneration. Here, we review primary and secondary myogenesis processes with a focus on muscle stem cells, as well as the function and regulation of muscle stem cells in adult muscle regeneration in mammals.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116536595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-26DOI: 10.1097/JBR.0000000000000109
Yifan Chen, J. Pu
Abstract The coronavirus disease 2019 (COVID-19) pandemic has been an unmitigated disaster for society and the economy worldwide. However, much remains unknown about the pathogenesis of, treatment methods for, and preventive measures against COVID-19. Single-cell sequencing is a novel sequencing technology whose use has recently become prevalent in various life-science fields. This high-resolution technology is being used to analyze the COVID-19 pandemic at a single-cell level. In this review, we summarize the application of single-cell sequencing technology to the field of COVID-19-related research, including the biology of severe acute respiratory syndrome coronavirus 2, clinical concerns associated with COVID-19, neutralizing antibody screening, and vaccine development. We also address challenges to, and improvements in, existing single-cell research related to COVID-19.
{"title":"Exploring COVID-19 at the single-cell level: a narrative review","authors":"Yifan Chen, J. Pu","doi":"10.1097/JBR.0000000000000109","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000109","url":null,"abstract":"Abstract The coronavirus disease 2019 (COVID-19) pandemic has been an unmitigated disaster for society and the economy worldwide. However, much remains unknown about the pathogenesis of, treatment methods for, and preventive measures against COVID-19. Single-cell sequencing is a novel sequencing technology whose use has recently become prevalent in various life-science fields. This high-resolution technology is being used to analyze the COVID-19 pandemic at a single-cell level. In this review, we summarize the application of single-cell sequencing technology to the field of COVID-19-related research, including the biology of severe acute respiratory syndrome coronavirus 2, clinical concerns associated with COVID-19, neutralizing antibody screening, and vaccine development. We also address challenges to, and improvements in, existing single-cell research related to COVID-19.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123692818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-26DOI: 10.1097/JBR.0000000000000108
Honglan Zheng, Wanning Cui, Zhiqiang Yan
Abstract Sensorineural hearing loss is the most common sensory deficit in humans, with an estimated prevalence of 1 in 500 newborns. Approximately half of childhood hearing loss is attributed to genetic factors and can be classified as syndromic or non-syndromic based on the inheritance pattern. The ion channel genes KCNQ1, KCNE1, KCNQ4, P2RX2, TMC1, KCNJ10, and CACNA1D have frequently been associated with genetic hearing loss. Because of the important roles these genes play in cochlear hair cell function and the auditory pathways, mutations in these genes that result in impaired ion channel function can lead to hereditary hearing loss. The main purpose of this review was to examine the latest research progress on the functional roles, inheritance pattern, gene expression, protein structure, clinical phenotypes, mouse models, and possible treatments of the most commonly studied ion channels associated with inherited deafness. A comprehensive summary could help highlight ion channels that should be investigated as potential drug targets for the treatment of inherited deafness.
{"title":"Ion channel-related hereditary hearing loss: a narrative review","authors":"Honglan Zheng, Wanning Cui, Zhiqiang Yan","doi":"10.1097/JBR.0000000000000108","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000108","url":null,"abstract":"Abstract Sensorineural hearing loss is the most common sensory deficit in humans, with an estimated prevalence of 1 in 500 newborns. Approximately half of childhood hearing loss is attributed to genetic factors and can be classified as syndromic or non-syndromic based on the inheritance pattern. The ion channel genes KCNQ1, KCNE1, KCNQ4, P2RX2, TMC1, KCNJ10, and CACNA1D have frequently been associated with genetic hearing loss. Because of the important roles these genes play in cochlear hair cell function and the auditory pathways, mutations in these genes that result in impaired ion channel function can lead to hereditary hearing loss. The main purpose of this review was to examine the latest research progress on the functional roles, inheritance pattern, gene expression, protein structure, clinical phenotypes, mouse models, and possible treatments of the most commonly studied ion channels associated with inherited deafness. A comprehensive summary could help highlight ion channels that should be investigated as potential drug targets for the treatment of inherited deafness.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121162174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-26DOI: 10.1097/JBR.0000000000000107
Pengjun Wang, Wen Lu, Yini Li, Haibo Shi, S. Yin
Abstract The vestibular system involves high-level sensory and cognitive processes, such as spatial perception, balance control, visual stability, and emotional control. Vestibular dysfunction can induce vertigo, blurred vision, postural imbalance, walking instability, and spatial discomfort, which causes serious damage to health. It has long been known that after peripheral vestibular lesion, vestibular dysfunction may spontaneously recover. This is known as vestibular compensation. However, at least 20% to 30% of patients with vestibular disorders cannot yield vestibular compensation and remain with vestibular dysfunction for the rest of their lives. The exploration of the biological characteristics and regulatory factors of the loss and reestablishment of vestibular function will establish a new understanding of the mechanism of vestibular compensation and provide new tools and strategies for promoting vestibular rehabilitation. We aim to comprehensively review the mechanism of vestibular compensation and discuss future directions in this field.
{"title":"The molecular, electrophysiological, and structural changes in the vestibular nucleus during vestibular compensation: a narrative review","authors":"Pengjun Wang, Wen Lu, Yini Li, Haibo Shi, S. Yin","doi":"10.1097/JBR.0000000000000107","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000107","url":null,"abstract":"Abstract The vestibular system involves high-level sensory and cognitive processes, such as spatial perception, balance control, visual stability, and emotional control. Vestibular dysfunction can induce vertigo, blurred vision, postural imbalance, walking instability, and spatial discomfort, which causes serious damage to health. It has long been known that after peripheral vestibular lesion, vestibular dysfunction may spontaneously recover. This is known as vestibular compensation. However, at least 20% to 30% of patients with vestibular disorders cannot yield vestibular compensation and remain with vestibular dysfunction for the rest of their lives. The exploration of the biological characteristics and regulatory factors of the loss and reestablishment of vestibular function will establish a new understanding of the mechanism of vestibular compensation and provide new tools and strategies for promoting vestibular rehabilitation. We aim to comprehensively review the mechanism of vestibular compensation and discuss future directions in this field.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114062999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-25DOI: 10.1097/JBR.0000000000000104
Aamir Fahira, Zijia Zhu, Zhiqiang Li, Yongyong Shi
Abstract Objective: Observational studies have reported malnutrition and vitamin deficiency in patients with schizophrenia (SZ), which can lead to serious metabolic syndromes and decrease anti-psychiatric drug outcomes. Whereas, vitamin intake along with psychiatric medication can enhance the medication outcomes. However, it is still unknown if SZ induces vitamin deficiency. Herein, we conduct the Mendelian randomization analysis to explore the causal relationship between schizophrenia and vitamins supplementation. Methods: We retrieved the genome-wide summary statistical data for schizophrenia from recent SZ GWAS data (43,175 cases and 65,166 controls) and vitamins supplementation GWAS data from Neale's GWAS datasets (more than 337,000 samples from the European population) and performed a two-sample Mendelian randomization analysis to determine the causal association of SZ with vitamin supplementation, in addition, we conduct the sensitivity analysis to obtain reliable results and remove confounding bias. Results: SZ have causal relationships with vitamins A, B, C, D, and E (SZ/vitamin A: β = 0.002, se = 0.001, 95% confidence interval (CI): 0.001 to 0.004, P = 1.41E-05, heterogeneity P = 0.4486; SZ/vitamin B: β = 0.004, se = 0.001, 95% CI: 0.002-0.005, P = 7.0E-05, heterogeneity P = 0.2217; SZ/vitamin C: β = 0.004, se = 0.001, 95% CI: 0.002-0.007, P = 0.001, heterogeneity P = 0.1349; SZ/vitamin D: β = 0.003, se = 0.001, 95% CI: 0.002-0.005, P = 0.001, heterogeneity P = 0.433; SZ/vitamin E: β = 0.003, se = 0.001, 95% CI: 0.002-0.005, P = 5.0E-05, heterogeneity P = 0.1382). Conclusion: Our findings suggest that vitamin levels and supplementation should be carefully controlled in patients with SZ, which in turn may enhance the therapeutic effects of antipsychotic drug treatments.
摘要目的:观察性研究报道了精神分裂症(SZ)患者营养不良和维生素缺乏，这可能导致严重的代谢综合征和降低抗精神药物疗效。然而，在服用精神药物的同时摄入维生素可以提高治疗效果。然而，尚不清楚SZ是否会导致维生素缺乏。在此，我们通过孟德尔随机化分析来探讨精神分裂症与维生素补充之间的因果关系。方法:我们从最近的SZ GWAS数据(43,175例和65,166例对照)和Neale的GWAS数据集(来自欧洲人群的超过337,000个样本)中检索精神分裂症的全基因组汇总统计数据，并进行双样本孟德尔随机化分析以确定SZ与维生素补充的因果关系，此外，我们进行敏感性分析以获得可靠的结果并消除混杂偏倚。结果:SZ与维生素A、B、C、D、E之间存在因果关系(SZ/维生素A: β = 0.002, se = 0.001, 95%置信区间(CI): 0.001 ~ 0.004, P = 1.41E-05，异质性P = 0.4486;SZ/维生素B: β = 0.004, se = 0.001, 95% CI: 0.002 ~ 0.005, P = 7.0E-05，异质性P = 0.2217;SZ/维生素C: β = 0.004, se = 0.001, 95% CI: 0.002 ~ 0.007, P = 0.001，异质性P = 0.1349;SZ/维生素D: β = 0.003, se = 0.001, 95% CI: 0.002 ~ 0.005, P = 0.001，异质性P = 0.433;SZ/维生素E: β = 0.003, se = 0.001, 95% CI: 0.002 ~ 0.005, P = 5.0e ~ 05，异质性P = 0.1382)。结论:我们的研究结果表明，SZ患者应仔细控制维生素水平和补充，这反过来可能会提高抗精神病药物治疗的效果。
{"title":"Scrutinizing the causal relationship between schizophrenia and vitamin supplementation: a Mendelian randomization study","authors":"Aamir Fahira, Zijia Zhu, Zhiqiang Li, Yongyong Shi","doi":"10.1097/JBR.0000000000000104","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000104","url":null,"abstract":"Abstract Objective: Observational studies have reported malnutrition and vitamin deficiency in patients with schizophrenia (SZ), which can lead to serious metabolic syndromes and decrease anti-psychiatric drug outcomes. Whereas, vitamin intake along with psychiatric medication can enhance the medication outcomes. However, it is still unknown if SZ induces vitamin deficiency. Herein, we conduct the Mendelian randomization analysis to explore the causal relationship between schizophrenia and vitamins supplementation. Methods: We retrieved the genome-wide summary statistical data for schizophrenia from recent SZ GWAS data (43,175 cases and 65,166 controls) and vitamins supplementation GWAS data from Neale's GWAS datasets (more than 337,000 samples from the European population) and performed a two-sample Mendelian randomization analysis to determine the causal association of SZ with vitamin supplementation, in addition, we conduct the sensitivity analysis to obtain reliable results and remove confounding bias. Results: SZ have causal relationships with vitamins A, B, C, D, and E (SZ/vitamin A: β = 0.002, se = 0.001, 95% confidence interval (CI): 0.001 to 0.004, P = 1.41E-05, heterogeneity P = 0.4486; SZ/vitamin B: β = 0.004, se = 0.001, 95% CI: 0.002-0.005, P = 7.0E-05, heterogeneity P = 0.2217; SZ/vitamin C: β = 0.004, se = 0.001, 95% CI: 0.002-0.007, P = 0.001, heterogeneity P = 0.1349; SZ/vitamin D: β = 0.003, se = 0.001, 95% CI: 0.002-0.005, P = 0.001, heterogeneity P = 0.433; SZ/vitamin E: β = 0.003, se = 0.001, 95% CI: 0.002-0.005, P = 5.0E-05, heterogeneity P = 0.1382). Conclusion: Our findings suggest that vitamin levels and supplementation should be carefully controlled in patients with SZ, which in turn may enhance the therapeutic effects of antipsychotic drug treatments.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114340565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-23DOI: 10.1097/JBR.0000000000000101
Hengbo Jia, Shaofen Wang, Lujun Shen, J. You, Fan Yang, Masanobu Abe, Yingying Xu, L. Zong
Abstract Objective: Chinese rhubarb is a promising Chinese medicine for the promotion of gastrointestinal function. This study was conducted to investigate the safety and efficacy of Chinese rhubarb administered via ultrasound delivery in promoting the early recovery of gastrointestinal function after gastrectomy. Methods: In this prospective randomized controlled study, 100 patients who were scheduled to undergo total or subtotal gastrectomy in Changzhi People's Hospital or Subei People's Hospital from August 2017 to January 2018 were recruited. These patients were randomly assigned into two equal groups before surgery: 50 in the experimental (Chinese rhubarb) group, and 50 in the control (routine nursing) group. After surgery, time to flatus, bowel movement, clear liquid diet, and removal of nasogastric tube were recorded and analyzed. In addition, postoperative pain, postoperative bowel movement-related complications, and postoperative hospital stay duration were also recorded and analyzed. The study was approved by The protocol was approved by the Institutional Review Board of Changzhi People's Hospital and Subei People's Hospital on July 1, 2017 and registered with the Chinese Clinical Trial Registry on December 17, 2018 (registration number: ChiCTR1800020143). Results: Time to flatus (control group 85.68 ± 22.00 hours vs experimental group 73.06 ± 23.42 hours; P = 0.007), bowel movement (5.52 ± 1.56 vs 4.40 ± 1.21 days; P < 0.001), clear liquid diet (6.72 ± 1.16 vs 6.22 ± 1.28 days; P = 0.044), and removal of nasogastric tube (6.30 ± 1.52 vs 5.65 ± 1.58 days; P = 0.044) were significantly shorter in the experimental group compared with the control group, as was the postoperative hospital stay duration (14.30 ± 3.46 vs 12.86 ± 1.36 days; P = 0.006). In addition, better pain relief (P = 0.003) and a lower incidence of postoperative bowel movement-related complications (6 vs 21; P = 0.001) were noted in the experimental group. Conclusion: Ultrasound delivery of Chinese rhubarb is useful to promote the early recovery of gastrointestinal function after gastrectomy.
【摘要】目的:大黄是一种很有前景的促进胃肠功能的中药。本研究旨在探讨超声给药大黄促进胃切除术后胃肠功能早期恢复的安全性和有效性。方法:本前瞻性随机对照研究招募2017年8月至2018年1月在长治市人民医院或苏北人民医院行胃全切除术或次全切除术的患者100例。术前将患者随机分为两组，实验组(大黄)50例，对照组(常规护理)50例。术后记录并分析排气时间、排便时间、清食时间和鼻胃管拔除时间。此外，还记录和分析了术后疼痛、术后排便相关并发症和术后住院时间。该方案于2017年7月1日由长治市人民医院和苏北人民医院机构审查委员会批准，并于2018年12月17日在中国临床试验注册中心注册(注册号:ChiCTR1800020143)。结果:排气时间(对照组85.68±22.00 h vs实验组73.06±23.42 h);P = 0.007),排便(5.52±1.56 vs 4.40±1.21天;P < 0.001)，透明液体日粮(6.72±1.16 vs 6.22±1.28);P = 0.044)，鼻胃管拔除(6.30±1.52 vs 5.65±1.58;P = 0.044)，术后住院时间(14.30±3.46天vs 12.86±1.36天;p = 0.006)。此外，更好的疼痛缓解(P = 0.003)和更低的术后排便相关并发症发生率(6 vs 21;P = 0.001)。结论:超声给予大黄可促进胃切除术后胃肠功能的早期恢复。
{"title":"Ultrasound delivery of Chinese rhubarb promotes early recovery of gastrointestinal function after gastrectomy: a prospective randomized controlled study","authors":"Hengbo Jia, Shaofen Wang, Lujun Shen, J. You, Fan Yang, Masanobu Abe, Yingying Xu, L. Zong","doi":"10.1097/JBR.0000000000000101","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000101","url":null,"abstract":"Abstract Objective: Chinese rhubarb is a promising Chinese medicine for the promotion of gastrointestinal function. This study was conducted to investigate the safety and efficacy of Chinese rhubarb administered via ultrasound delivery in promoting the early recovery of gastrointestinal function after gastrectomy. Methods: In this prospective randomized controlled study, 100 patients who were scheduled to undergo total or subtotal gastrectomy in Changzhi People's Hospital or Subei People's Hospital from August 2017 to January 2018 were recruited. These patients were randomly assigned into two equal groups before surgery: 50 in the experimental (Chinese rhubarb) group, and 50 in the control (routine nursing) group. After surgery, time to flatus, bowel movement, clear liquid diet, and removal of nasogastric tube were recorded and analyzed. In addition, postoperative pain, postoperative bowel movement-related complications, and postoperative hospital stay duration were also recorded and analyzed. The study was approved by The protocol was approved by the Institutional Review Board of Changzhi People's Hospital and Subei People's Hospital on July 1, 2017 and registered with the Chinese Clinical Trial Registry on December 17, 2018 (registration number: ChiCTR1800020143). Results: Time to flatus (control group 85.68 ± 22.00 hours vs experimental group 73.06 ± 23.42 hours; P = 0.007), bowel movement (5.52 ± 1.56 vs 4.40 ± 1.21 days; P < 0.001), clear liquid diet (6.72 ± 1.16 vs 6.22 ± 1.28 days; P = 0.044), and removal of nasogastric tube (6.30 ± 1.52 vs 5.65 ± 1.58 days; P = 0.044) were significantly shorter in the experimental group compared with the control group, as was the postoperative hospital stay duration (14.30 ± 3.46 vs 12.86 ± 1.36 days; P = 0.006). In addition, better pain relief (P = 0.003) and a lower incidence of postoperative bowel movement-related complications (6 vs 21; P = 0.001) were noted in the experimental group. Conclusion: Ultrasound delivery of Chinese rhubarb is useful to promote the early recovery of gastrointestinal function after gastrectomy.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134407320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-19DOI: 10.1097/JBR.0000000000000100
Zhou Zhou, Qing Sang, Lei Wang
Abstract Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases; however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allelespecific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.
{"title":"Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review","authors":"Zhou Zhou, Qing Sang, Lei Wang","doi":"10.1097/JBR.0000000000000100","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000100","url":null,"abstract":"Abstract Targeted sequencing and whole exome sequencing are the most common approaches used to detect causative variants in Mendelian diseases; however, using DNA-based sequencing techniques, the current molecular diagnostic yield is at best 50%. In recent years, RNA sequencing has been shown to be able to provide a genetic diagnosis in patients whose conditions were previously unable to be identified by DNA analysis. RNA sequencing can reveal expression outliers, aberrant splicing events, allelespecific expression, and new pathogenic variants, and as such can complement and expand on the traditional genomic methods used to diagnose Mendelian diseases. Therefore, RNA sequencing is expected to become a routine method for genetic diagnosis in the future. This article reviews the applications and challenges of RNA sequencing in the genetic diagnosis of Mendelian diseases.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122083997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-19DOI: 10.1097/JBR.0000000000000102
Jingwen Liu, Xuchu Duan, Ming Li, Dong Liu, Xiaohui Bai
Abstract Objective: The zebrafish is an excellent model for studying gene function in auditory system development. Pou4f3 plays an important role in mouse hair cell formation. Here, we constructed a pou4f3-knockout Tg(Brn3c:GFP) zebrafish to provide an efficient fluorescence-visualized model for studying the molecular mechanisms of ear development. Methods: Cas9/single guide RNAs targeting exon 2 of pou4f3 were designed and injected into one-cell stage zebrafish embryos (G0 generation). The G0 generation were crossed with Tg(Brn3c:GFP) zebrafish to obtain pou4f3-mutant Tg(Brn3c:GFP) zebrafish. The targeting efficiency was detected by polymerase chain reaction amplification and Sanger sequencing. Zebrafish hair cells were observed by laser scanning confocal microscopy in vivo. The morphology of the otoliths and semicircular canals were analyzed. All animal experiments were approved by the Animal Care and Use Committee of Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University (approval No. 2016-KY-040) on March 3, 2016. Results: The pou4f3-mutant Tg(Brn3c:GFP) zebrafish line was successfully established. Fluorescence observation suggested that hair cell development was delayed in pou4f3-knockout zebrafish. Knockout of pou4f3 also induced defects in the otoliths and semicircular canals and impaired ear function in zebrafish. Conclusion: A CRISPR/Cas9-mediated pou4f3 mutant Tg(Brn3c:GFP) zebrafish model was established for the first time to demonstrate the essential role of pou4f3 in zebrafish ear development. Our study provides a highly efficient method for the establishment of a visualized model of gene knockout zebrafish and has the potential to allow high-throughput drug screening to explore therapeutics for related diseases.
{"title":"CRISPR/Cas9-mediated pou4f3 knockout induces defects in the development of the zebrafish inner ear","authors":"Jingwen Liu, Xuchu Duan, Ming Li, Dong Liu, Xiaohui Bai","doi":"10.1097/JBR.0000000000000102","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000102","url":null,"abstract":"Abstract Objective: The zebrafish is an excellent model for studying gene function in auditory system development. Pou4f3 plays an important role in mouse hair cell formation. Here, we constructed a pou4f3-knockout Tg(Brn3c:GFP) zebrafish to provide an efficient fluorescence-visualized model for studying the molecular mechanisms of ear development. Methods: Cas9/single guide RNAs targeting exon 2 of pou4f3 were designed and injected into one-cell stage zebrafish embryos (G0 generation). The G0 generation were crossed with Tg(Brn3c:GFP) zebrafish to obtain pou4f3-mutant Tg(Brn3c:GFP) zebrafish. The targeting efficiency was detected by polymerase chain reaction amplification and Sanger sequencing. Zebrafish hair cells were observed by laser scanning confocal microscopy in vivo. The morphology of the otoliths and semicircular canals were analyzed. All animal experiments were approved by the Animal Care and Use Committee of Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University (approval No. 2016-KY-040) on March 3, 2016. Results: The pou4f3-mutant Tg(Brn3c:GFP) zebrafish line was successfully established. Fluorescence observation suggested that hair cell development was delayed in pou4f3-knockout zebrafish. Knockout of pou4f3 also induced defects in the otoliths and semicircular canals and impaired ear function in zebrafish. Conclusion: A CRISPR/Cas9-mediated pou4f3 mutant Tg(Brn3c:GFP) zebrafish model was established for the first time to demonstrate the essential role of pou4f3 in zebrafish ear development. Our study provides a highly efficient method for the establishment of a visualized model of gene knockout zebrafish and has the potential to allow high-throughput drug screening to explore therapeutics for related diseases.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123670994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Objective: Medical data mining and sharing is an important process in E-Health applications. However, because these data consist of a large amount of personal private information of patients, there is the risk of privacy disclosure when sharing and mining. Therefore, ensuring the security of medical big data in the process of publishing, sharing, and mining has become the focus of current research. The objective of our study is to design a framework based on a differential privacy protection mechanism to ensure the secure sharing of medical data. We developed a privacy protection query language (PQL) that integrates multiple data mining methods and provides a secure sharing function. Methods: This study is mainly performed in Xuzhou Medical University, China and designs three sub-modules: a parsing module, mining module, and noising module. Each module encapsulates different computing methods, such as a composite parser and a noise theory. In the PQL framework, we apply the differential privacy theory to the results of the computing between modules to guarantee the security of various mining algorithms. These computing devices operate independently, but the mining results depend on their cooperation. In addition, PQL is encapsulated in MNSSp3 that is a data mining and security sharing platform and the data comes from public data sets, such as UCBI. The public data set (NCBI database) was used as the experimental data, and the data collection time was January 2020. Results: We designed and developed a query language that provides functions for medical data mining, sharing, and privacy preservation. We theoretically proved the performance of the PQL framework. The experimental results show that the PQL framework can ensure the security of each mining result and the availability of the output results is above 97%. Conclusion: Our framework enables medical data providers to securely share health data or treatment data and develops a usable query language, based on a differential privacy mechanism, that enables researchers to mine information securely using data mining algorithms.
{"title":"A differential privacy protection query language for medical data: a proof-of-concept system validation","authors":"Huanhuan Wang, Yongting Zhang, Hong-Li Yin, Ruirui Li, Xiang Wu","doi":"10.1097/JBR.0000000000000099","DOIUrl":"https://doi.org/10.1097/JBR.0000000000000099","url":null,"abstract":"Abstract Objective: Medical data mining and sharing is an important process in E-Health applications. However, because these data consist of a large amount of personal private information of patients, there is the risk of privacy disclosure when sharing and mining. Therefore, ensuring the security of medical big data in the process of publishing, sharing, and mining has become the focus of current research. The objective of our study is to design a framework based on a differential privacy protection mechanism to ensure the secure sharing of medical data. We developed a privacy protection query language (PQL) that integrates multiple data mining methods and provides a secure sharing function. Methods: This study is mainly performed in Xuzhou Medical University, China and designs three sub-modules: a parsing module, mining module, and noising module. Each module encapsulates different computing methods, such as a composite parser and a noise theory. In the PQL framework, we apply the differential privacy theory to the results of the computing between modules to guarantee the security of various mining algorithms. These computing devices operate independently, but the mining results depend on their cooperation. In addition, PQL is encapsulated in MNSSp3 that is a data mining and security sharing platform and the data comes from public data sets, such as UCBI. The public data set (NCBI database) was used as the experimental data, and the data collection time was January 2020. Results: We designed and developed a query language that provides functions for medical data mining, sharing, and privacy preservation. We theoretically proved the performance of the PQL framework. The experimental results show that the PQL framework can ensure the security of each mining result and the availability of the output results is above 97%. Conclusion: Our framework enables medical data providers to securely share health data or treatment data and develops a usable query language, based on a differential privacy mechanism, that enables researchers to mine information securely using data mining algorithms.","PeriodicalId":150904,"journal":{"name":"Journal of Bio-X Research","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114260535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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