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A single-cell 3D dynamic volume control system for chondrocytes. 软骨细胞单细胞三维动态体积控制系统
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-10-15 DOI: 10.1080/07366205.2024.2412414
Qiang Zhang, Yiyao Wang, Yanjun Zhang, Xiaochun Wei, Weiyi Chen, Quanyou Zhang

In articular cartilage, zone-specific cellular morphology is a typical characteristic of cartilage tissue, which is related with chondrocyte function, inflammation and osteoarthritis (OA). Chondrocyte hypertrophic phenotype is a criticle physiological process which indicates a hallmark of chondrocyte terminal differentiation and bone formation. Thus, developing a in vitro cell culture system for dynamic regulation of single chondrocyte volume at a three-dimensional (3D) level is particularly necessary for understanding how physical cues of matrix microenvironment regulate chondrocyte fate and the degeneration of articular cartilage. Here, based on the soft lithography techniques, we have constructed well-defined single-cell 3D dynamic volume control system to recapitulate the physiological matrix microenvironment of single chondrocyte niche. The results of finite element analysis indicated that the stress and strain distribution in the cell culture region is homogeneous during the stretching process. Additionally, 3D dynamic volume expansion and compression of single cells in physiological or hyperphysiological can be realized in this cell culture system. Our device for single-cell 3D dynamic culture provides a microphysiological culture system for chondrocytes to explore the mechanisms of cartilage hypertrophy, as well as develops a new paradigm for functional cartilage tissue engineering and regenerative medicine.

在关节软骨中,区域特异性细胞形态是软骨组织的典型特征,与软骨细胞功能、炎症和骨关节炎(OA)有关。软骨细胞肥大表型是一个关键的生理过程,是软骨细胞末端分化和骨形成的标志。因此,开发一种可在三维(3D)水平上动态调节单个软骨细胞体积的体外细胞培养系统,对于了解基质微环境的物理线索如何调控软骨细胞的命运和关节软骨的退化尤为必要。在此,我们基于软光刻技术构建了定义明确的单细胞三维动态体积控制系统,以再现单个软骨细胞龛的生理基质微环境。有限元分析结果表明,在拉伸过程中,细胞培养区域的应力和应变分布是均匀的。此外,该细胞培养系统还能实现单细胞在生理或超生理状态下的三维动态体积膨胀和压缩。我们的单细胞三维动态培养装置为软骨细胞提供了一个微生理学培养系统,用于探索软骨肥大的机制,并为功能性软骨组织工程和再生医学开发了一种新的范例。
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引用次数: 0
Comparison of commercially available DNA and RNA extraction kits for wildlife feces collected from the environment. 针对从环境中收集的野生动物粪便的市售 DNA 和 RNA 提取试剂盒比较。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-13 DOI: 10.1080/07366205.2024.2397284
James D Feller,Leah Colton
Wildlife fecal samples were collected across two Air Force installations to evaluate the effectiveness of commercially available DNA and RNA extraction kits. Four DNA kits, two DNA/RNA kits and one RNA only kit were used. Sample extracts were evaluated on nucleic acid concentration, TapeStation DNA or RNA Integrity Number values and presence of PCR inhibitors. For the DNA kits, PFP produced higher concentrations compared with PLM and RPM, while MWFM gave higher DNA Integrity Number values when compared with RPM. No PCR inhibition was detected. For the RNA kits, RPM gave higher concentrations compared with MWTV and no differences were seen in RNA Integrity Number values. PCR inhibition was observed in all RNA samples, with MWTV exhibiting higher inhibition compared with RPM.
在两个空军设施内收集了野生动物粪便样本,以评估市售 DNA 和 RNA 提取试剂盒的有效性。使用了四种 DNA 提取试剂盒、两种 DNA/RNA 提取试剂盒和一种仅提取 RNA 的试剂盒。对样本提取物的核酸浓度、TapeStation DNA 或 RNA 完整性数值以及是否存在 PCR 抑制剂进行了评估。就 DNA 试剂盒而言,PFP 产生的浓度高于 PLM 和 RPM,而 MWFM 产生的 DNA 完整性数值高于 RPM。没有检测到 PCR 抑制剂。在 RNA 试剂盒中,RPM 的浓度高于 MWTV,但 RNA 完整性数值没有差异。在所有 RNA 样品中都发现了 PCR 抑制现象,其中 MWTV 的抑制率高于 RPM。
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引用次数: 0
A HABA dye-based colorimetric assay to detect unoccupied biotin binding sites in an avidin-containing fusion protein. 基于 HABA 染料的比色测定法,用于检测含阿维丁融合蛋白中未被占用的生物素结合位点。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-13 DOI: 10.1080/07366205.2024.2397288
Sonia Mukherjee,Pierre Leblanc,Mark C Poznansky,Ann E Sluder
Avidin-biotin binding, the most robust non-covalent protein-ligand interaction occurring in nature, has wide-ranging applications in biotechnology. A frequent challenge in these applications is accurately determining the number of unoccupied biotin binding sites in avidin-containing fusion proteins. We delineate a novel assay protocol in miniaturized format to quantify available biotin binding sites based on the affinity of the anionic dye 4'-hydroxyazobenzene-2-carboxylic acid for biotin binding sites within avidin. We apply this assay as a quality control assay to evaluate the number of available biotin binding sites in different fusion protein production batches. This method offers a streamlined alternative to fluorescence-based assays commonly employed to assess biotin binding, is less time-consuming than other methods and is applicable to diverse fusion proteins.
阿维丁-生物素结合是自然界中最强大的非共价蛋白质-配体相互作用,在生物技术领域有着广泛的应用。这些应用中经常遇到的一个难题是如何准确确定含阿维丁融合蛋白中未被占用的生物素结合位点的数量。我们根据阴离子染料 4'-hydroxyazobenzene-2-carboxylic acid 与阿维丁内生物素结合位点的亲和力,制定了一种微型化的新型检测方案,以量化可用的生物素结合位点。我们将这种检测方法用作质量控制检测,以评估不同融合蛋白生产批次中可用生物素结合位点的数量。与常用的基于荧光的检测方法相比,这种方法可简化生物素结合的评估,比其他方法耗时更少,而且适用于各种融合蛋白。
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引用次数: 0
An automatic classification method of testicular histopathology based on SC-YOLO framework. 基于 SC-YOLO 框架的睾丸组织病理学自动分类方法。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2393544
Jinggen Wu,Yao Sun,Yangbo Jiang,Yangcheng Bu,Chong Chen,Jingping Li,Lejun Li,Weikang Chen,Keren Cheng,Jian Xu
The pathological diagnosis and treatment of azoospermia depend on precise identification of spermatogenic cells. Traditional methods are time-consuming and highly subjective due to complexity of Johnsen score, posing challenges for accurately diagnosing azoospermia. Here, we introduce a novel SC-YOLO framework for automating the classification of spermatogenic cells that integrates S3Ghost module, CoordAtt module and DCNv2 module, effectively capturing texture and shape features of spermatogenic cells while reducing model parameters. Furthermore, we propose a simplified Johnsen score criteria to expedite the diagnostic process. Our SC-YOLO framework presents the higher efficiency and accuracy of deep learning technology in spermatogenic cell recognition. Future research endeavors will focus on optimizing the model's performance and exploring its potential for clinical applications.
无精子症的病理诊断和治疗取决于对生精细胞的精确鉴定。传统方法耗时长,而且由于约翰森评分的复杂性,主观性很强,给无精子症的准确诊断带来了挑战。在此,我们介绍了一种用于自动分类生精细胞的新型 SC-YOLO 框架,该框架集成了 S3Ghost 模块、CoordAtt 模块和 DCNv2 模块,可有效捕捉生精细胞的纹理和形状特征,同时减少模型参数。此外,我们还提出了简化的约翰森评分标准,以加快诊断过程。我们的 SC-YOLO 框架展示了深度学习技术在生精细胞识别中的更高效率和准确性。未来的研究工作将侧重于优化模型的性能,并探索其在临床应用中的潜力。
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引用次数: 0
When is an SNP not an SNP? 什么时候 SNP 不是 SNP?
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2387993
Shapour Jalilzadeh,Valerie Walker,Gary P Leggatt,Eli Hatchwell
Genomic duplications are important sources of structural change and gene innovation. In humans, the most recent and highly identical sequences (>90% homology, >1 kb long) are known as segmental duplications (SDs). Single-nucleotide variants or single-nucleotide polymorphisms within SDs have not been systematically assessed due to limitations around mapping short-read sequencing data. Single-nucleotide variant rs62486260 was flagged in a study of familial renal stone disease but it was unclear whether it was real or an artifact resulting from the presence of a SD. We describe in silico and wet-lab approaches to investigate this, using segment-specific long-PCR assays, followed by short PCR for Sanger sequencing. Our conclusion was that rs62486260 is an artifact. Our approach can be generalized to deal with other such situations.
基因组复制是结构变化和基因创新的重要来源。在人类中,最新和高度相同的序列(同源性大于 90%,长度大于 1 kb)被称为片段重复(SD)。由于短线程测序数据映射的局限性,SDs 内的单核苷酸变异或单核苷酸多态性尚未得到系统评估。在一项关于家族性肾结石病的研究中,单核苷酸变异体 rs62486260 被标记出来,但尚不清楚它是真实的还是因 SD 的存在而产生的假象。我们介绍了利用分段特异性长 PCR 检测和用于 Sanger 测序的短 PCR 进行研究的硅学和湿实验室方法。我们的结论是,rs62486260 是一个假象。我们的方法可用于处理其他此类情况。
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引用次数: 0
Sampling and analysis methods of air-borne microorganisms in hospital air: a review. 医院空气中气载微生物的采样和分析方法:综述。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-12 DOI: 10.1080/07366205.2024.2372939
Xinyan Wei,Xuezheng Ma,Feng Tian,Zhaohui Wei,Liping Zhang,Kongxin Hu
Pathogenic microorganisms can spread in the air as bioaerosols. When the human body is exposed to different bioaerosols, various infectious diseases may occur. As indoor diagnosis and treatment environments, hospitals are relatively closed and have a large flow rate of people. This indoor environment contains complex aerosol components; therefore, effective sampling and detection of microbial elements are essential in airborne pathogen monitoring. This article reviews the sampling and detection of different kinds of microorganisms in bioaerosols from indoor diagnostic and therapeutic settings, with a particular focus on microbial activity. This provides deeper insights into bioaerosols in diagnostic and therapeutic settings.
病原微生物会以生物气溶胶的形式在空气中传播。当人体接触到不同的生物气溶胶时,可能会引发各种传染病。医院作为室内诊疗环境,相对封闭,人流量大。这种室内环境含有复杂的气溶胶成分,因此,有效采样和检测微生物元素对空气中病原体的监测至关重要。本文回顾了对室内诊断和治疗环境生物气溶胶中不同种类微生物的采样和检测,尤其关注微生物的活性。这有助于深入了解诊断和治疗环境中的生物气溶胶。
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引用次数: 0
Mito-kaede photoactivation and chase experiment for mitophagy: optimizing flux measurement via fluid exchange system. 有丝分裂的光激活和追逐实验:通过流体交换系统优化通量测量。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-11 DOI: 10.1080/07366205.2024.2372955
Hiroyuki Morinaga,Yoh Sugawara,Yoshinori Kitagawa,Jingyuan Chen,Nobuo Yasuda,Hiroki Ogata,Yoshihiro Yamaguchi,Masao Kaneki,Joseph A Jeevendra Martyn,Shingo Yasuhara
Modulating autophagy and mitophagy, vital cellular quality control systems, offer therapeutic potential for critical illnesses. However, limited drug screening options hinder progress. We present a novel assay using the photoswitchable fluorescent reporter, mito-Kaede, to quantify mitophagy flux. Mito-Kaede's superior UV-induced photoconversion and brightness post-conversion make it ideal for prolonged mitochondrial dynamics tracking. Its specificity in responding to mitophagy, confirmed by parkin-knockout cells, adds value. When coupled with a custom fluid exchange system, enabling efficient medium changes, precise mitophagy observations become feasible. This mitophagy assay, alongside our methodological insights, can decipher mitophagy's role in pathology and supports drug screening efforts.
自噬和有丝分裂是重要的细胞质量控制系统,调节这两个系统可为危重疾病提供治疗潜力。然而,有限的药物筛选方案阻碍了研究的进展。我们介绍了一种利用光开关荧光报告物 mito-Kaede 来量化有丝分裂通量的新型检测方法。Mito-Kaede 具有优异的紫外线诱导光电转换能力和转换后的亮度,因此非常适合用于长时间的线粒体动态跟踪。经 Parkin 基因敲除细胞证实,它对有丝分裂反应的特异性增加了其价值。如果与定制的液体交换系统配合使用,就能有效地更换培养基,从而实现对有丝分裂的精确观察。这种有丝分裂检测方法与我们的方法论见解相结合,可以破译有丝分裂在病理学中的作用,并为药物筛选工作提供支持。
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引用次数: 0
Using Longitudinal Variance Components Models to Assess Hyper-connectivity in Severe Traumatic Brain Injury Patients. 利用纵向变异成分模型评估严重脑损伤患者的超连接性。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-07-01 DOI: 10.32598/bcn.2022.3796.1
Keyvan Olazadeh, Nasrin Borumandnia, Mahin Habibi, Hamid Alavi Majd

Introduction: Traumatic brain injury (TBI) is one of the leading causes of death globally and one of the most important diseases indicated by the World Health Organization (WHO). Several studies have concluded that brain damage can dramatically increase functional connectivity (FC) in the brain. The effects of this hyper-connectivity are not yet fully understood and are being studied by neuroscientists. Accordingly, this study identifies areas of the brain where, after brain injury, an acute increase in FC in such areas is observed.

Methods: The data used in this study were downloaded from the accessible open functional magnetic resonance imaging (fMRI) site. The data included fMRI of 14 patients with severe TBI and 12 healthy individuals. The longitudinal model of variance components investigated the difference between FC in the baseline effect and the longitudinal trend between the TBI and control groups.

Results: After fitting the longitudinal model of variance components, no difference was observed between the FC of the two groups due to the baseline effect. However, in the longitudinal trend of FC, there was a statistically significant difference between the three pairs of cerebellum left, cerebellum right, superior frontal gyrus left, superior frontal gyrus right, thalamus left, and thalamus right in the TBI group compared to the control group.

Conclusion: The results showed that FC was sharply increased in 3 pairs of areas in people with TBI. This hyper-connectivity can affect individuals' cognitive functions, including motor and sensory functions. The exact extent of this effect is unclear and requires further investigation by neuroscientists.

导言:创伤性脑损伤(TBI)是导致全球死亡的主要原因之一,也是世界卫生组织(WHO)指出的最重要的疾病之一。一些研究认为,脑损伤会显著增加大脑的功能连接性(FC)。这种超连接性的影响尚未完全明了,神经科学家正在对其进行研究。因此,本研究确定了大脑中哪些区域在脑损伤后功能连通性会急剧增加:本研究使用的数据是从可访问的开放式功能磁共振成像(fMRI)网站下载的。数据包括 14 名严重创伤性脑损伤患者和 12 名健康人的 fMRI。方差成分纵向模型研究了创伤性脑损伤组和对照组之间基线效应和纵向趋势中FC的差异:结果:在拟合了方差分量纵向模型后,没有观察到基线效应导致的两组 FC 之间的差异。然而,在 FC 的纵向趋势中,创伤性脑损伤组的小脑左侧、小脑右侧、额上回左侧、额上回右侧、丘脑左侧和丘脑右侧三对之间的差异与对照组相比具有统计学意义:结论:研究结果表明,创伤性脑损伤患者的三对区域的FC急剧增加。结论:研究结果表明,创伤性脑损伤患者 3 对区域的 FC 均急剧增加,这种超连接性会影响患者的认知功能,包括运动和感觉功能。这种影响的确切程度尚不清楚,需要神经科学家进一步研究。
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引用次数: 0
Phylobook: a tool for display, clade annotation and extraction of sequences from molecular phylogenies. Phylobook:从分子系统进化论中显示、注释和提取序列的工具。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-03 DOI: 10.2144/btn-2023-0056
Jeffrey C Furlong, Peter D Darley, Wenjie Deng, James I Mullins, Roger E Bumgarner
As the volume of sequence data from variable pathogens increases, means of analyzing, annotating and extracting specific taxa for study becomes more difficult. To meet these challenges for datasets with hundreds to thousands of taxa, 'Phylobook' was developed. Starting with a sequence alignment file, Phylobook generates and displays phylogenetic trees adjacent to highlighter plots showing the position of mutations, and allows the user to identify lineages and recombinants, annotate and export selected subsets of sequences for downstream analysis. Accurate lineage assignment, which is difficult to automate, is aided using annotations created by different clustering methods. Phylobook provides web-based display combined with automated clustering and manual editing to allow for expert assessment and correction of lineage assignments and extraction for downstream analysis.
随着来自不同病原体的序列数据量的增加,分析、注释和提取特定类群进行研究的手段变得更加困难。为了应对这些挑战,"Phylobook "应运而生。从序列比对文件开始,Phylobook 生成并显示系统发生树,旁边的荧光笔图显示突变的位置,并允许用户识别世系和重组体,注释和导出选定的序列子集进行下游分析。利用不同聚类方法创建的注释,可以帮助进行难以自动化的准确系谱分配。Phylobook 提供基于网络的显示,结合自动聚类和手动编辑,允许专家评估和校正谱系分配,并提取用于下游分析。
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引用次数: 0
Comparing robotic and manual injection methods in zebrafish embryos for high-throughput RNA silencing using CRISPR-RfxCas13d. 比较使用 CRISPR-RfxCas13d 在斑马鱼胚胎中进行高通量 RNA 沉默的机器人和人工注射方法。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.2144/btn-2023-0062
Joaquin Abugattas-Nuñez Del Prado, Yi Ding, Jan de Sonneville, Kees-Jan van der Kolk, Miguel A Moreno-Mateos, Edward Málaga-Trillo, Herman P Spaink

In this study, the authors compared the efficiency of automated robotic and manual injection methods for the CRISPR-RfxCas13d (CasRx) system for mRNA knockdown and Cas9-mediated DNA targeting in zebrafish embryos. They targeted the no tail (TBXTA) gene as a proof-of-principle, evaluating the induced embryonic phenotypes. Both Cas9 and CasRx systems caused loss of function phenotypes for TBXTA. Cas9 protein exhibited a higher percentage of severe phenotypes compared with mRNA, while CasRx protein and mRNA showed similar efficiency. Both robotic and manual injections demonstrated comparable phenotype percentages and mortality rates. The findings highlight the potential of RNA-targeting CRISPR effectors for precise gene knockdown and endorse automated microinjection at a speed of 1.0 s per embryo as a high-throughput alternative to manual methods.

在这项研究中,作者比较了CRISPR-RfxCas13d(CasRx)系统在斑马鱼胚胎中进行mRNA敲除和Cas9介导的DNA靶向的自动机器人和人工注射方法的效率。他们以无尾(TBXTA)基因为靶标,评估了诱导的胚胎表型,并进行了原理验证。Cas9 和 CasRx 系统都导致了 TBXTA 的功能缺失表型。与 mRNA 相比,Cas9 蛋白表现出更高比例的严重表型,而 CasRx 蛋白和 mRNA 表现出相似的效率。机器人注射和人工注射的表型比例和死亡率相当。研究结果凸显了 RNA 靶向 CRISPR 效应器在精确基因敲除方面的潜力,并支持以每个胚胎 1.0 秒的速度进行自动显微注射,作为人工方法的高通量替代方法。
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引用次数: 0
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BioTechniques
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