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Exogenous spike-in mouse RNAs for accurate differential gene expression analysis in barley using RT-qPCR. 利用 RT-qPCR 对大麦中的外源性尖峰小鼠 RNA 进行精确的差异基因表达分析。
IF 3.6 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-28 eCollection Date: 2023-01-01 DOI: 10.1093/biomethods/bpad034
Marcus A Vinje, David A Friedman

Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) followed by the 2-ΔΔCt method is the most common way to measure transcript levels for relative gene expression assays. The quality of an RT-qPCR assay is dependent upon the identification and validation of reference genes to normalize gene expression data. The so-called housekeeping genes are commonly used as internal reference genes because they are assumed to be ubiquitously expressed at stable levels. Commonly, researchers do not validate their reference genes but rely on historical reference genes or previously validated genes from an unrelated experiment. Using previously validated reference genes to assess gene expression changes occurring during malting resulted in extensive variability. Therefore, a new method was tested and validated to circumvent the use of internal reference genes. Total mouse RNA was chosen as the external reference RNA and a suite of primer sets to putatively stable mouse genes was created to identify stably expressed genes for use as an external reference gene. cDNA was created by co-amplifying total mouse RNA, as an RNA spike-in, and barley RNA. When using the external reference genes to normalize malting gene expression data, standard deviations were significantly reduced and significant differences in transcript abundance were observed, whereas when using the internal reference genes, standard deviations were larger with no significant differences seen. Furthermore, external reference genes were more accurate at assessing expression levels in malting and developing grains, whereas the internal reference genes overestimated abundance in developing grains and underestimated abundance in malting grains.

反转录酶定量聚合酶链反应(RT-qPCR)后的 2-ΔΔCt 法是相对基因表达检测中测量转录本水平的最常用方法。RT-qPCR 检测的质量取决于参考基因的鉴定和验证,以便对基因表达数据进行归一化。所谓的看家基因通常被用作内部参考基因,因为它们被认为以稳定的水平普遍表达。通常情况下,研究人员并不验证他们的参考基因,而是依赖于历史参考基因或先前在无关实验中验证过的基因。使用以前验证过的参考基因来评估发芽过程中发生的基因表达变化会产生很大的变异。因此,我们测试并验证了一种新方法,以避免使用内部参考基因。我们选择小鼠总 RNA 作为外部参考 RNA,并创建了一套引物组,用于鉴定小鼠基因是否稳定表达,以用作外部参考基因。使用外部参考基因对麦芽基因表达数据进行归一化处理时,标准偏差显著降低,转录本丰度也出现了显著差异;而使用内部参考基因时,标准偏差较大,且未出现显著差异。此外,外部参考基因在评估发芽谷物和发育中谷物的表达水平方面更为准确,而内部参考基因则高估了发育中谷物的丰度,低估了发芽谷物的丰度。
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引用次数: 0
Microcosmos explorers: foldscope workshop for science outreach in Mexican schools. 微型宇宙探险家:墨西哥学校科学外联折叠望远镜研讨会。
IF 3.6 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-24 eCollection Date: 2023-01-01 DOI: 10.1093/biomethods/bpad035
Samantha López Clinton

Foldscopes are ultra-low-cost paper microscopes invented by Manu Prakash and Jim Cybulski at Stanford University. They are about as light as a pencil and waterproof, all whilst offering similar optic quality to traditional microscopes. Foldscopes do not require electricity or glass slides to be used, which increases the possibilities of their use in education and outreach activities with children or people with disabilities. In 2019, thanks to a material grant of 100 foldscopes from One World Science and additional purchased foldscopes, I designed and implemented a science workshop called Exploradores del Microcosmos, or Explorers of Microcosmos in English. The aim of the workshop was to help make microscopy more accessible, in particular at underfunded schools, and stimulate active learning about ecosystems and evolution in the participants. Within this article, I describe the workshop and relay my personal insights and reflections on its execution across multiple schools and groups in Mexico.

Foldscopes 是斯坦福大学的 Manu Prakash 和 Jim Cybulski 发明的超低成本纸显微镜。它们和铅笔一样轻,而且防水,同时还具有与传统显微镜类似的光学质量。折叠显微镜的使用不需要电力或玻璃载玻片,这增加了它们在儿童或残疾人教育和外联活动中使用的可能性。2019 年,得益于 "一个世界科学 "组织提供的 100 台折叠式显微镜的物资赠款和额外购买的折叠式显微镜,我设计并实施了一个名为 "微观世界探索者"(Exploradores del Microcosmos)的科学讲习班。工作坊的目的是让更多人,尤其是资金不足的学校能够接触到显微镜,并激发参与者主动学习生态系统和进化知识。在这篇文章中,我介绍了这次研讨会,并转述了我个人对墨西哥多所学校和团体开展研讨会的见解和反思。
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引用次数: 0
Crowdsourcing Temporal Transcriptomic Coronavirus Host Infection Data: resources, guide, and novel insights 众包时间转录组冠状病毒宿主感染数据:资源,指南和新见解
Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-14 DOI: 10.1093/biomethods/bpad033
James Flynn, Mehdi M Ahmadi, Chase T McFarland, Michael D Kubal, Mark A Taylor, Zhang Cheng, Enrique C Torchia, Michael G Edwards
Abstract The emergence of SARS-CoV-2 reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of COVID-19 during the pandemic. This study coupled existing transcriptomic data from SARS-CoV-1 lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g., CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA Damage Response and Repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients that died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
SARS-CoV-2的出现再次唤醒了快速了解感染原分子病因、大流行潜力和前瞻性治疗的需求。在大流行期间,缺乏关于SARS-CoV-2的现有数据阻碍了治疗严重形式的COVID-19的早期尝试。本研究将来自SARS-CoV-1肺部感染动物研究的现有转录组学数据与众包统计方法相结合,以获得早期病毒积累和随后清除阶段宿主反应的时间元特征。无监督和有监督机器学习方法确定了顶级失调基因和潜在的生物标志物(例如,CXCL10, BEX2和ADM)。时间元特征揭示了不同的基因表达程序与一系列宿主反应的生物学意义,这些反应是持续的Cxcl10表达和Stat信号传导的基础。细胞周期从感染早期的G1/G0期基因转变为感染晚期的G2/M期基因,这与DNA损伤反应和修复基因的富集有关。新出现的RNAseq、单细胞和蛋白质组学数据显示,SARS-CoV-1元特征与人类SARS-CoV-2宿主反应非常相似,早期单核-巨噬细胞活化,随后是淋巴细胞增殖。在死于COVID-19的老年患者中,循环激素肾上腺髓质素的升高幅度最大。有可能治疗COVID-19和未来冠状病毒感染的化合物与特定阶段的相关性在一定程度上得到了24个正在进行治疗COVID-19临床试验的子集的验证。这项研究代表了利用公共领域现有数据来获得新的分子和生物学见解以及对新出现的人类病原体的潜在治疗的路线图。
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引用次数: 0
Methods for Studying Mammalian Aquaporin Biology 哺乳动物水通道蛋白生物学研究方法
Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-11 DOI: 10.1093/biomethods/bpad031
Shohini Banerjee, Ian M Smith, Autumn C Hengen, Kimberly M Stroka
Abstract Aquaporins (AQPs), transmembrane water-conducting channels, have earned a great deal of scrutiny for their critical physiological roles in healthy and disease cell states, especially in the biomedical field. Numerous methods have been implemented to elucidate the involvement of AQP-mediated water transport and downstream signaling activation in eliciting whole cell, tissue, and organ functional responses. To modulate these responses, other methods have been employed to investigate AQP druggability. This review discusses standard in vitro, in vivo, and in silico methods for studying AQPs, especially for biomedical and mammalian cell biology applications. We also propose some new techniques and approaches for future AQP research to address current gaps in methodology.
摘要水通道蛋白(Aquaporins, AQPs)是一种跨膜的水传导通道,因其在健康和疾病细胞状态中的重要生理作用而受到广泛关注,特别是在生物医学领域。许多方法已经被用于阐明aqp介导的水转运和下游信号激活在引发整个细胞、组织和器官功能反应中的作用。为了调节这些反应,研究人员采用了其他方法来研究AQP的药物作用。本文综述了aqp在体外、体内和计算机上的标准研究方法,特别是在生物医学和哺乳动物细胞生物学方面的应用。我们还为未来AQP研究提出了一些新的技术和方法,以解决目前方法上的差距。
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引用次数: 0
Getting it right: teaching undergraduate biology to undermine racial essentialism 正确的做法:教授本科生生物学以削弱种族本质论
Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-11 DOI: 10.1093/biomethods/bpad032
Elaine Guevara, Shyamalika Gopalan, Dashiell J Massey, Mayowa Adegboyega, Wen Zhou, Alma Solis, Alisha D Anaya, Steven E Churchill, Joseph Feldblum, Richard Lawler
Abstract How we teach human genetics matters for social equity. The biology curriculum appears to be a crucial locus of intervention for either reinforcing or undermining students’ racial essentialist views. The Mendelian genetic models dominating textbooks, particularly in combination with racially inflected language sometimes used when teaching about monogenic disorders, can increase middle and high school students’ racial essentialism and opposition to policies to increase equity. These findings are of particular concern given the increasing spread of racist misinformation online and misappropriation of human genomics research by white supremacists, who take advantage of low levels of genetics literacy in the general public. Encouragingly, however, teaching updated information about the geographic distribution of human genetic variation and the complex, multifactorial basis of most human traits, reduces students’ endorsement of racial essentialism. The genetics curriculum is therefore a key tool in combating misinformation and scientific racism. Here, we describe a framework and example teaching materials for teaching students key concepts in genetics, human evolutionary history, and human phenotypic variation at the undergraduate level. This framework can be flexibly applied in biology and anthropology classes and adjusted based on time availability. Our goal is to provide undergraduate-level instructors with varying levels of expertise with a set of evidence-informed tools for teaching human genetics to combat scientific racism, including an evolving set of instructional resources, as well as learning goals and pedagogical approaches instructors can apply when teaching genetics. Resources can be found at https://noto.li/YIlhZ5. Additionally, we hope to generate conversation about integrating modern genetics into the undergraduate curriculum, in light of recent findings about the risks and opportunities associated with teaching genetics.
我们如何教授人类遗传学关系到社会公平。生物课程似乎是加强或削弱学生种族本质论观点的关键干预点。孟德尔遗传模型在教科书中占主导地位,特别是在讲授单基因疾病时,有时会使用带有种族色彩的语言,这可能会增加初高中学生的种族本质主义,并反对增加公平的政策。考虑到网上种族主义错误信息的日益传播,以及白人至上主义者对人类基因组学研究的盗用,这些发现尤其令人担忧,这些白人至上主义者利用了普通公众基因知识水平较低的优势。然而,令人鼓舞的是,教授关于人类基因变异的地理分布和大多数人类特征的复杂、多因素基础的最新信息,减少了学生对种族本质主义的支持。因此,遗传学课程是打击错误信息和科学种族主义的关键工具。在这里,我们描述了一个框架和示例教材,用于在本科阶段教授学生遗传学,人类进化史和人类表型变异的关键概念。这个框架可以灵活地应用于生物学和人类学的课堂,并根据时间进行调整。我们的目标是为具有不同专业知识水平的本科水平教师提供一套基于证据的工具,用于教授人类遗传学以对抗科学种族主义,包括一套不断发展的教学资源,以及教师在教授遗传学时可以应用的学习目标和教学方法。资源可在https://noto.li/YIlhZ5上找到。此外,根据最近关于遗传学教学的风险和机会的发现,我们希望产生关于将现代遗传学纳入本科课程的对话。
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引用次数: 0
Serum starvation-based method of ovarian cancer cell dormancy induction and termination in vitro 基于血清饥饿的卵巢癌细胞体外休眠诱导与终止方法
Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-02 DOI: 10.1093/biomethods/bpad029
Szymon Rutecki, Agnieszka Leśniewska-Bocianowska, Klaudia Chmielewska, Julia Matuszewska, Eryk Naumowicz, Paweł Uruski, Artur Radziemski, Justyna Mikuła-Pietrasik, Andrzej Tykarski, Krzysztof Książek
Abstract Awakening and growth reinitiation by dormant cells may contribute to epithelial ovarian cancer (EOC) relapse. The links between these phenomena are loose because of the limited stock of compelling models of EOC dormancy. Here, we show a simple and convenient dormancy research protocol based on serum starvation. This study was conducted on established EOC cell lines A2780, OVCAR-3, and SKOV-3, as well as on primary EOC cells. Cell growth arrest and proliferation were monitored by assessing the Ki67 antigen, PKH26 fluorescence, and cell cycle distribution. In addition, cells were tested for ERK1/2/p38 MAPK activity ratio, apoptosis, and senescence. The study showed that 72-hour serum starvation induces G0/G1 growth arrest of a significant fraction of cells, accompanied by reduced Ki67 and ERK1/2/p38 MAPK activity ratio, without signs of apoptosis or cellular senescence. Moreover, providing cells with 72 hours of a medium enriched in 5% serum allows the culture to regain its proliferative potential. At the same time, we attempted to induce and terminate dormancy with Mitomycin C addition and withdrawal, which were unsuccessful. In conclusion, serum starvation is a convenient way to reliably induce dormancy in EOC cells, allowing them to be efficiently awakened for further mechanistic research in vitro.
休眠细胞的觉醒和生长重新启动可能导致上皮性卵巢癌(EOC)复发。这些现象之间的联系是松散的,因为有说服力的EOC休眠模式有限。在此,我们提出了一种基于血清饥饿的简单便捷的休眠研究方案。本研究在已建立的EOC细胞系A2780、OVCAR-3和SKOV-3以及原代EOC细胞上进行。通过评估Ki67抗原、PKH26荧光和细胞周期分布来监测细胞生长停滞和增殖。此外,检测细胞ERK1/2/p38 MAPK活性比、凋亡和衰老情况。研究表明,72小时血清饥饿诱导大量细胞G0/G1生长停滞,Ki67和ERK1/2/p38 MAPK活性比降低,无凋亡和细胞衰老迹象。此外,在含有5%血清的培养基中培养细胞72小时,可使培养物恢复其增殖潜能。同时,我们尝试加停用丝裂霉素C诱导和终止休眠,均未成功。综上所述,血清饥饿是一种方便、可靠地诱导EOC细胞休眠的方法,可以有效地唤醒EOC细胞,为进一步的体外机制研究提供依据。
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引用次数: 0
Serum Metallomics Reveals Insights into the Associations of Elements with the Progression of Preleukemic Diseases Towards Acute Leukemia 血清金属组学揭示了与白血病前期疾病向急性白血病进展相关的元素
Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-11-01 DOI: 10.1093/biomethods/bpad027
Amna Jabbar Siddiqui, Noman Khan, Kauser Fatima, Sabiha Farooq, Muhammad Ramzan, Hesham R El-Seedi, Jalal Uddin, Abdullatif Bin Muhsinah, Syed Ghulam Musharraf
Abstract Context Acute leukemia (AL) is a critical neoplasm of white blood cells with two main subtypes: acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). Objective This study is focused on understanding the association of the preleukemic disease aplastic anemia (APA) with ALL and AML at metallomic level, using healthy subject as a control. Materials and methods In this study, a validated and efficient ICP-MS/MS-based workflow was employed to profile a total of 13 metallomic features. The study encompassed 41 patients with AML, 62 patients with ALL, 46 patients with APA, and 55 age-matched healthy controls. The metallomic features consisted of 8 essential elements (Ca, Co, Cu, Fe, Mg, Mn, Se, and Zn) and 5 non-essential/toxic elements (Ag, Cd, Cr, Ni, and Pb). Results Six out of the thirteen elements were found to be substantially different (p &lt; 0.05) using absolute concentrations between serum samples of acute leukemia (ALL and AML) and preleukemia (APA) patients in comparison with healthy subjects. Elements including magnesium, calcium, iron, copper and zinc were up-regulated and only one element (chromium) was down-regulated in serum samples of disease when compared with healthy subjects. Discussion Through the utilization of both univariate tests and multivariate classification modeling, it was determined that chromium exhibited a progressive behavior among the studied elements. Specifically, chromium displayed a sequential up-regulation from healthy individuals to preleukemic disease (APA), and ultimately in patients diagnosed with ALL. Conclusion Overall, metallomic-based biomarkers may have utility to predict the association of APA with ALL.
摘要背景急性白血病(Acute leukemia, AL)是一种重要的白细胞肿瘤,主要有两种亚型:急性淋巴细胞白血病(Acute lymphoblastic leukemia, ALL)和急性髓系白血病(Acute myeloid leukemia, AML)。目的以健康受试者为对照,从金属学水平探讨白血病前再障(APA)与ALL和AML的关系。材料和方法在本研究中,采用了一种经过验证且高效的基于ICP-MS/ ms的工作流程来分析总共13个金属学特征。该研究包括41名AML患者,62名ALL患者,46名APA患者和55名年龄匹配的健康对照。金属特征包括8种必需元素(Ca、Co、Cu、Fe、Mg、Mn、Se和Zn)和5种非必需/有毒元素(Ag、Cd、Cr、Ni和Pb)。结果发现13个元素中有6个存在显著差异(p <0.05),用急性白血病(ALL和AML)和白血病前期(APA)患者血清样本的绝对浓度与健康受试者比较。与健康受试者相比,疾病血清样品中的镁、钙、铁、铜和锌元素上调,只有一种元素(铬)下调。通过单变量检验和多变量分类模型的利用,确定了铬在研究元素中表现出递进行为。具体来说,铬从健康个体到白血病前期疾病(APA),并最终在ALL患者中表现出顺序上调。结论基于金属组学的生物标志物在预测APA与ALL的相关性方面可能具有实用价值。
{"title":"Serum Metallomics Reveals Insights into the Associations of Elements with the Progression of Preleukemic Diseases Towards Acute Leukemia","authors":"Amna Jabbar Siddiqui, Noman Khan, Kauser Fatima, Sabiha Farooq, Muhammad Ramzan, Hesham R El-Seedi, Jalal Uddin, Abdullatif Bin Muhsinah, Syed Ghulam Musharraf","doi":"10.1093/biomethods/bpad027","DOIUrl":"https://doi.org/10.1093/biomethods/bpad027","url":null,"abstract":"Abstract Context Acute leukemia (AL) is a critical neoplasm of white blood cells with two main subtypes: acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). Objective This study is focused on understanding the association of the preleukemic disease aplastic anemia (APA) with ALL and AML at metallomic level, using healthy subject as a control. Materials and methods In this study, a validated and efficient ICP-MS/MS-based workflow was employed to profile a total of 13 metallomic features. The study encompassed 41 patients with AML, 62 patients with ALL, 46 patients with APA, and 55 age-matched healthy controls. The metallomic features consisted of 8 essential elements (Ca, Co, Cu, Fe, Mg, Mn, Se, and Zn) and 5 non-essential/toxic elements (Ag, Cd, Cr, Ni, and Pb). Results Six out of the thirteen elements were found to be substantially different (p &amp;lt; 0.05) using absolute concentrations between serum samples of acute leukemia (ALL and AML) and preleukemia (APA) patients in comparison with healthy subjects. Elements including magnesium, calcium, iron, copper and zinc were up-regulated and only one element (chromium) was down-regulated in serum samples of disease when compared with healthy subjects. Discussion Through the utilization of both univariate tests and multivariate classification modeling, it was determined that chromium exhibited a progressive behavior among the studied elements. Specifically, chromium displayed a sequential up-regulation from healthy individuals to preleukemic disease (APA), and ultimately in patients diagnosed with ALL. Conclusion Overall, metallomic-based biomarkers may have utility to predict the association of APA with ALL.","PeriodicalId":36528,"journal":{"name":"Biology Methods and Protocols","volume":"22 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135455894","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}
引用次数: 0
A method for measurement of human asparagine synthetase (ASNS) activity and application to ASNS protein variants associated with ASNS deficiency. 测定人天冬酰胺合成酶(ASNS)活性的方法及其在与ASNS缺陷相关的ASNS蛋白变异中的应用
IF 3.6 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-10-25 eCollection Date: 2023-01-01 DOI: 10.1093/biomethods/bpad026
Mario C Chang, Stephen J Staklinski, Matthew E Merritt, Michael S Kilberg

Human asparagine synthetase (ASNS) catalyzes the conversion of aspartate to asparagine in an ATP-dependent reaction that utilizes glutamine as a nitrogen source while generating glutamate, AMP, and pyrophosphate as additional products. Asparagine Synthetase Deficiency (ASNSD) is an inborn error of metabolism in which children present with homozygous or compound heterozygous mutations in the ASNS gene. These mutations result in ASNS variant protein expression. It is believed that these variant ASNS proteins have reduced enzymatic activity or stability resulting in a lack of sufficient asparagine production for cell function. Reduced asparagine production by ASNS appears to severely hinder fetal brain development. Although a variety of approaches for assaying ASNS activity have been reported, we present here a straightforward method for the in vitro enzymatic analysis by detection of AMP production. Our method overcomes limitations in technical feasibility, signal detection, and reproducibility experienced by prior methods like high-performance liquid chromatography, ninhydrin staining, and radioactive tracing. After purification of FLAG-tagged R49Q, G289A, and T337I ASNS variants from stably expressing HEK 293T cells, this method revealed a reduction in activity of 90, 36, and 96%, respectively. Thus, ASNS protein expression and purification, followed by enzymatic activity analysis, has provided a relatively simple protocol to evaluate structure-function relationships for ASNS variants reported for ASNSD patients.

人天冬酰胺合成酶(ASNS)在atp依赖性反应中催化天冬氨酸转化为天冬酰胺,该反应利用谷氨酰胺作为氮源,同时产生谷氨酸、AMP和焦磷酸盐作为附加产物。天冬酰胺合成酶缺乏症(ASNSD)是一种先天性代谢错误,儿童在ASNS基因中存在纯合或复合杂合突变。这些突变导致ASNS变异蛋白的表达。据信,这些变异的ASNS蛋白降低了酶活性或稳定性,导致缺乏足够的天冬酰胺生产以维持细胞功能。ASNS减少天冬酰胺的产生似乎严重阻碍胎儿大脑发育。虽然已经报道了多种测定ASNS活性的方法,但我们在这里提出了一种直接的方法,通过检测AMP的产生进行体外酶分析。我们的方法克服了高效液相色谱、茚三酮染色和放射性示踪等先前方法在技术可行性、信号检测和重现性方面的局限性。从稳定表达HEK 293T细胞中纯化flag标记的R49Q、G289A和T337I ASNS变体后,该方法显示活性分别降低了90%、36%和96%。因此,ASNS蛋白的表达和纯化,以及随后的酶活性分析,为评估ASNSD患者ASNS变异的结构-功能关系提供了一个相对简单的方案。
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引用次数: 0
The effect of the COVID-19 pandemic on life expectancy in the USA: An application of hybrid life expectancy. 新冠肺炎大流行对美国预期寿命的影响:混合预期寿命的应用。
IF 2.5 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-10-18 eCollection Date: 2023-01-01 DOI: 10.1093/biomethods/bpad025
Warren C Sanderson, Sergei Scherbov

Pandemics are, by definition, temporary intervals of substantially increased mortality rates experienced across a wide geographic area. One way of assessing the magnitude of the COVID-19 pandemic in the USA has been to compute the differences in life expectancy at birth during a pandemic year and the year before the pandemic. Such comparisons are misleading because they do not account for the duration of the pandemic. The computation of life expectancy in 2019 assumes that people spend their entire lives experiencing prepandemic mortality rates. The computation of life expectancy in 2021 assumes that people live their entire lives in a permanent pandemic. However, people do not live their entire lives experiencing the elevated mortality rates of 2021. This article introduces a method for calculating life expectancy that reflects the experience of people enduring pandemic-level mortality rates for fixed durations. We call the new quantity hybrid life expectancy because it integrates both pandemic and prepandemic mortality rates. The difference in life expectancy at birth in the USA in 2019 with and without a 3-year-long pandemic is 0.01 years. This is because mortality rates at ages 0, 1, and 2 in the pandemic were essentially unchanged from their prepandemic levels. Life expectancy at age 65 incorporating a 3-year pandemic is 0.18 years lower than life expectancy would have been without it. Reductions in life expectancy due to the COVID-19 pandemic using hybrid life expectancy are dramatically lower than differences in life expectancy that do not take the duration of the pandemic into account.

根据定义,流行病是指在广泛的地理区域内死亡率大幅上升的暂时间隔。评估美国新冠肺炎大流行规模的一种方法是计算大流行年份和大流行前一年出生时预期寿命的差异。这种比较具有误导性,因为它们没有考虑到疫情的持续时间。2019年预期寿命的计算假设人们一生都在经历大灾难前的死亡率。2021年预期寿命的计算假设人们一生都生活在一场永久性的流行病中。然而,人们并不是一辈子都在经历2021年的死亡率上升。本文介绍了一种计算预期寿命的方法,该方法反映了人们在固定时间内忍受大流行水平死亡率的经历。我们称之为新数量混合预期寿命,因为它综合了大流行和大流行前的死亡率。2019年,美国出生时的预期寿命在有和没有3年疫情的情况下相差0.01岁。这是因为疫情中0岁、1岁和2岁的死亡率与疫情前的水平基本没有变化。65岁时的预期寿命比没有3年大流行的预期寿命低0.18岁。使用混合预期寿命的新冠肺炎大流行导致的预期寿命缩短大大低于不考虑大流行持续时间的预期寿命差异。
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引用次数: 0
Robustness of quantifying mediating effects of genetically regulated expression on complex traits with mediated expression score regression. 用介导表达评分回归量化基因调控表达对复杂性状的介导作用的稳健性。
IF 3.6 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2023-10-17 eCollection Date: 2023-01-01 DOI: 10.1093/biomethods/bpad024
Chen Lin, Wei Liu, Wei Jiang, Hongyu Zhao

Genetic association signals have been mostly found in noncoding regions through genome-wide association studies (GWAS), suggesting the roles of gene expression regulation in human diseases and traits. However, there has been limited success in colocalizing expression quantitative trait locus (eQTL) with disease-associated variants. Mediated expression score regression (MESC) is a recently proposed method to quantify the proportion of trait heritability mediated by genetically regulated gene expressions (GReX). Applications of MESC to GWAS results have yielded low estimation of mediated heritability for many traits. As MESC relies on stringent independence assumptions between cis-eQTL effects, gene effects, and nonmediated SNP effects, it may fail to characterize the true relationships between those effect sizes, which leads to biased results. Here, we consider the robustness of MESC to investigate whether the low fraction of mediated heritability inferred by MESC reflects biological reality for complex traits or is an underestimation caused by model misspecifications. Our results suggest that MESC may lead to biased estimates of mediated heritability with misspecification of gene annotations leading to underestimation, whereas misspecification of SNP annotations may lead to overestimation. Furthermore, errors in eQTL effect estimates may lead to underestimation of mediated heritability.

通过全基因组关联研究(GWAS),遗传关联信号大多在非编码区发现,表明基因表达调控在人类疾病和性状中的作用。然而,将表达数量性状基因座(eQTL)与疾病相关变异共定位的成功率有限。介导表达得分回归(MESC)是最近提出的一种量化由遗传调控基因表达介导的性状遗传力比例的方法。将MESC应用于GWAS结果,对许多性状的介导遗传力估计较低。由于MESC依赖于顺式eQTL效应、基因效应和非介导SNP效应之间的严格独立性假设,它可能无法表征这些效应大小之间的真实关系,从而导致有偏差的结果。在这里,我们考虑了MESC的稳健性,以研究由MESC推断的介导遗传力的低部分是否反映了复杂性状的生物学现实,或者是由模型错误指定引起的低估。我们的结果表明,MESC可能导致介导遗传力的估计有偏差,基因注释的错误指定导致低估,而SNP注释的错误标记可能导致高估。此外,eQTL效应估计的错误可能导致对介导遗传力的低估。
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引用次数: 0
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