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《医学前沿(英文)》 2022年 第16卷 第2期 页码 251-262 doi: 10.1007/s11684-021-0915-9
关键词: scRNA-seq intracellular pathogen microbe COVID-19 SARS-CoV-2
《医学前沿(英文)》 doi: 10.1007/s11684-023-1017-7
关键词: single-cell RNA-seq glioma radial glia primitive oligodendrocyte precursor cell immune escape
Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in
《医学前沿(英文)》 页码 939-956 doi: 10.1007/s11684-023-0987-9
关键词: mononuclear diploid cardiomyocytes cell–cell communication cardiac fibroblast single-cell RNA sequencing cardiac regeneration
Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao
《医学前沿(英文)》 2021年 第15卷 第1期 页码 144-154 doi: 10.1007/s11684-020-0792-7
关键词: human metaphase II oocyte vitrification cryostorage duration single-cell RNA-Seq lncRNA
Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han
《医学前沿(英文)》 页码 185-192 doi: 10.1007/s11684-020-0754-0
It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV and originated from Wuhan (China), invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.
A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation
Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang
《化学科学与工程前沿(英文)》 2021年 第15卷 第2期 页码 410-420 doi: 10.1007/s11705-020-1950-9
信息科学应引领未来的生物医学研究 Perspective
Kenta Nakai
《工程(英文)》 2019年 第5卷 第6期 页码 1155-1158 doi: 10.1016/j.eng.2019.07.023
笔者从长期回顾的角度阐述了对人工智能(AI)/数据科学与生物医学之间关系的看法。随着新技术的不断出现,现代生物医学的发展持续加速。由于所有生命系统基本上都受其自身DNA中信息的支配,因此信息科学对生物医学的研究具有特别重要的意义。与物理学不同,在生物学中没有发现(或很少有)主导定律。因此,在生物学中,“数据到知识”方法很重要。人工智能在历史上一直应用于生物医学,最近的新闻表明,基于人工智能的方法在国际蛋白质结构预测竞争中获得了最佳性能,这可能被视为该领域的另一个里程碑。类似的方法可能有助于解决基因组序列解释中的问题,如确定患者基因组中的癌症驱动突变。最近,新一代测序(NGS)的爆炸性发展已产生大量数据,并且这种趋势将加速。NGS不仅用于“读取”DNA序列,而且还用于在单细胞水平上获得各种类型的信息。这些数据可以视为气候模拟中的网格数据点。数据科学和人工智能对于这些数据的综合解释/模拟都将变得至关重要,并将在未来的精密医学中起主导作用。
徐健, 马波, 苏晓泉, 黄适, 徐欣, 周学东, 黄巍, Rob Knight
《工程(英文)》 2017年 第3卷 第1期 页码 66-70 doi: 10.1016/J.ENG.2017.01.020
方法学创新一直是微生物组学研究的核心驱动力。我们认为在未来五到十年,微生物组的方法学体系在研究理念与技术平台方面将发生三大变革:①从监测菌群“结构”变化向监测菌群“功能/状态”变化的变革;②从细胞“群体”分析精度向细胞“个体”分析精度的转变;③从“数据分析”向“数据科学”的跨越。在这里我们针对实现上述三大方法学变革需要克服的关键科学或技术挑战,重点介绍了部分中国微生物组分析方法学研究团队及其国际合作伙伴的最新工作进展。我们相信中国微生物组计划应把握住当前这一重要机遇,通过在微生物组分析方法学前沿开展富有雄心、远见、创意与竞争力的交叉合作研究,为国际微生物组计划贡献一系列“中国制造”的新方法、新工具和新仪器。
《农业科学与工程前沿(英文)》 2021年 第8卷 第2期
Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F1 bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The Pm024074(PmUGT72B3) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T66(upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. Pm024074 had exceptionally high expression in buds and stems of weeping P. mume. Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in P. mume, and indicates potential applications for the manipulation of tree architecture.
关键词: BSR-seq / PmUGT72B3 / Prunus mume / UDP-glycosyltransferase / weeping shoots / WGCNA
单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article
张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟
《工程(英文)》 2022年 第17卷 第10期 页码 161-169 doi: 10.1016/j.eng.2021.05.009
了解重症新型冠状病毒肺炎(COVID-19)患者单核细胞的免疫学特征(包括与纤维化相关的特征)对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者(包括3名重症/危重症患者和4名普通型患者)和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本,包括重症/危重症时期血样3例,轻症时期血样4例,康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期,单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加,多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群:Mono 0和Mono 5。这两个亚群表达amphiregulin(AREG)、epiregulin(EREG)和细胞因子基因IL-18,KEGG分析显示富集的ErbB信号通路,这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变,包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群,可作为重症COVID-19的潜在预测因子和治疗靶点。
Effect on proliferation and apoptosis of T24 cell lines via silencing DNMT1 with RNA interference
ZHANG Shilong, ZENG Fuqing, PENG Shibo, WANG Liang
《医学前沿(英文)》 2008年 第2卷 第4期 页码 374-379 doi: 10.1007/s11684-008-0072-4
Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom
Wen Zhang,Jack W. Szostak,Zhen Huang
《化学科学与工程前沿(英文)》 2016年 第10卷 第2期 页码 196-202 doi: 10.1007/s11705-016-1565-3
Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG
《农业科学与工程前沿(英文)》 页码 196-214 doi: 10.15302/J-FASE-2020379
关键词: BSR-seq PmUGT72B3 Prunus mume UDP-glycosyltransferase weeping shoots WGCNA
Jing Ma, Shiyu Chen, Lili Hao, Wei Sheng, Weicheng Chen, Xiaojing Ma, Bowen Zhang, Duan Ma, Guoying Huang
《医学前沿(英文)》 2021年 第15卷 第1期 页码 91-100 doi: 10.1007/s11684-020-0778-5
关键词: congenital heart disease Gene Expression Omnibus lncRNA SAP30-2:1 cell proliferation RNA immunoprecipitation HAND2
null
《医学前沿(英文)》 2015年 第9卷 第4期 页码 468-477 doi: 10.1007/s11684-015-0419-6
Mature T-cell lymphoid malignancies comprise a group of heterogeneous diseases that vary in clinicopathological features, biological behavior, treatment response, and prognosis. Bone marrow (BM) infiltration is more commonly present in mature T-cell lymphoid malignancies compared with their B-cell counterparts and hence important for differential diagnosis. In this study, clinical characteristics and prognostic factors were analyzed in 225 patients with mature T-cell lymphoid malignancies treated in a single institution. These included 29 cases of T-cell lymphoproliferative disorders (T-LPD, all with BM infiltration) and 196 cases of T-/natural-killer-cell lymphoma (T/NKCL, 56 with BM infiltration and 140 without BM infiltration). The estimated 5-year overall survival (OS) rates of T-LPD and T/NKCL were 96.6% and 37.3%, respectively. T-LPD patients were less likely to exhibit poor performance status, advanced disease stage, presence of B symptoms, or abnormal level of serum β-2 microglobulin. With similar pathological characteristics, T/NKCL patients with BM infiltration showed significantly lower response rates and shorter OS than those without BM infiltration (P = 0.0264 and P<0.0001, respectively). Multivariate analysis indicated that poor performance status, advanced disease stage, elevated serum lactate dehydrogenase level, and BM involvement were independent unfavorable prognostic factors. The Glasgow Prognostic Score may be more efficient than the International Prognostic Index in predicting disease outcome in T/NKCL. In conclusion, clinical characteristics may be useful in more effectively stratifying patients with mature T-cell lymphoid malignancies.
关键词: mature T-cell lymphoid malignancies clonal T-cell population bone marrow infiltration prognostic factors
标题 作者 时间 类型 操作
PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing
期刊论文
Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis
期刊论文
Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in
期刊论文
Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed
Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao
期刊论文
Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different
Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han
期刊论文
A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation
Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang
期刊论文
BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN
期刊论文
Effect on proliferation and apoptosis of T24 cell lines via silencing DNMT1 with RNA interference
ZHANG Shilong, ZENG Fuqing, PENG Shibo, WANG Liang
期刊论文
Nucleic acid crystallization and X-ray crystallography facilitated by single selenium atom
Wen Zhang,Jack W. Szostak,Zhen Huang
期刊论文
BULKED SEGREGANT RNA SEQUENCING (BSR-SEQ) IDENTIFIES A NOVEL ALLELE ASSOCIATED WITH WEEPING TRAITS IN
Xiaokang ZHUO, Tangchun ZHENG, Zhiyong ZHANG, Suzhen LI, Yichi ZHANG, Lidan SUN, Weiru YANG, Jia WANG, Tangren CHENG, Qixiang ZHANG
期刊论文
Long non-coding RNA SAP30-2:1 is downregulated in congenital heart disease and regulates cell proliferation
Jing Ma, Shiyu Chen, Lili Hao, Wei Sheng, Weicheng Chen, Xiaojing Ma, Bowen Zhang, Duan Ma, Guoying Huang
期刊论文