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Cancer's sweet spot: techniques to harness saccharides in tumor biology. 癌症的甜蜜点:在肿瘤生物学中利用糖类的技术。
IF 2.7 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2023-12-04 DOI: 10.2144/btn-2023-0110
Jade Parker

All of the cells in our bodies are enveloped in sugar, this sweet coating plays a particularly interesting and crucial role in tumor biology. Here, we review the techniques being used to detect and exploit cancer's sweet spot. including click chemistry, glycoproteomic profiling and bioorthogonal chemistry.

我们体内的所有细胞都被糖包裹着,这种甜的包裹在肿瘤生物学中起着特别有趣和关键的作用。在这里,我们回顾了用于检测和利用癌症甜蜜点的技术。包括点击化学,糖蛋白组学分析和生物正交化学。
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引用次数: 0
The environmental impact of AI in the lab: a double-edged sword? 实验室人工智能对环境的影响:一把双刃剑?
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-07-31 DOI: 10.1080/07366205.2024.2376459
Annie Coulson

Computational tools, particularly AI, are becoming more ubiquitous in scientific research; but what impact do they have on the environment?[Formula: see text].

计算工具,尤其是人工智能,在科学研究中越来越无处不在;但它们对环境有什么影响?
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引用次数: 0
Transitioning from Triton X-100 to Tergitol 15-S-9: impacts on diagnostic assays using viral PCR sample solution. 从 Triton X-100 过渡到 Tergitol 15-S-9:对使用病毒 PCR 样品溶液进行诊断测定的影响。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-05-05 DOI: 10.1080/07366205.2024.2342172
Azul Zorzoli, Alasdair MacLean, Scott Nicholson, Alison Daniels, Stephen Hughes, Susan Bennet-Slater, Christine Tait-Burkard, Noha El Sakka, Rory Gunson, Kate Templeton

In 2019, the European Union banned Triton X-100, a detergent widely used in laboratory diagnostics, including the Viral PCR Sample Solution (VPSS), and urged manufacturers to find environmentally sustainable alternatives. Tergitol 15-S-9 (VPSS2) has been proposed as an alternative surfactant. This multicenter study evaluated the effectiveness of VPSS2, a Tergitol-based viral solution, as a replacement for VPSS. Our results show the equivalent performance of VPSS2 to VPSS for nucleic acid extraction and viral stability over time at different temperatures. The new VPSS formulation was also tested against external quality assurance panels and clinical samples. The results of this work support adopting this modified viral PCR sample solution to replace Triton X-100-containing viral transport solutions.

2019 年,欧盟禁用了广泛用于实验室诊断(包括病毒 PCR 样品溶液 (VPSS))的洗涤剂 Triton X-100,并敦促制造商寻找环境可持续的替代品。Tergitol 15-S-9(VPSS2)被提议作为一种替代表面活性剂。这项多中心研究评估了基于 Tergitol 的病毒溶液 VPSS2 作为 VPSS 替代品的有效性。我们的结果表明,VPSS2 与 VPSS 在不同温度下的核酸提取和病毒稳定性方面性能相当。新的 VPSS 配方还通过了外部质量保证小组和临床样本的测试。这项工作的结果支持采用这种改良的病毒 PCR 样品溶液来替代含有 Triton X-100 的病毒运输溶液。
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引用次数: 0
Adipocyte ABCA1 expression analysis using flow cytometry. 使用流式细胞仪分析脂肪细胞 ABCA1 的表达。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-07-17 DOI: 10.1080/07366205.2024.2376466
Sakshi Shukla, Ashutosh Bansal, Sandeep Aggarwal, Archna Singh

Adipocyte characterization and assessing membrane proteins using flow cytometry has been proven to be challenging as adipocytes are fragile, especially in subjects with high BMI. We overcame these challenges through a protocol optimizing tissue digestion time by reducing intermediate steps to minimize adipocyte friction and breakage. We avoided requirement for specialized instrument configuration and used a modified gating strategy to prevent inclusion of lipid droplets during analysis. Up to 90% of the cell population were available in the gating area. We checked the expression level of ABCA1, a membrane protein reaffirming adipocyte selection. In summary, this protocol requires lesser tissue sample improving feasibility and cost efficiency. Thus, our flow cytometry method is an improvement for studying adipocyte membrane characteristics.

使用流式细胞术鉴定脂肪细胞特征和评估膜蛋白已被证明具有挑战性,因为脂肪细胞很脆弱,尤其是在高体重指数的受试者中。我们通过减少中间步骤来优化组织消化时间,最大程度地减少脂肪细胞的摩擦和破损,从而克服了这些挑战。我们避免了对专业仪器配置的要求,并采用了改进的门控策略,以防止在分析过程中加入脂滴。多达 90% 的细胞群可进入选通区域。我们检测了 ABCA1 的表达水平,这是一种膜蛋白,再次证实了脂肪细胞的选择。总之,该方案所需的组织样本较少,提高了可行性和成本效益。因此,我们的流式细胞仪方法是研究脂肪细胞膜特征的一种改进。
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引用次数: 0
Dual-mode detection of glucose based on pistol-like DNAzyme-mediated exonuclease-assisted signal cycle. 基于手枪式 DNA 酶介导的外切酶辅助信号循环的葡萄糖双模式检测。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-08-05 DOI: 10.1080/07366205.2024.2381403
Huiying Lu, Xiaofeng Wang

Detecting glucose accurately and sensitively from clinical samples like tears and saliva is still difficult. We have created a sensor that can detect glucose with high sensitivity and accuracy by combining the use of glucose oxidase (GOx) to catalyze glucose, a pistol-like DNAzyme (PLDz) to transform the signal, gold nanoparticles (AuNPs) to enhance the optical properties and the exonuclease-III (Exo-III) to amplify the signal. As a result, the proposed method exhibits a low detection limit of 7.5 pM and a wide detection range covering seven orders of magnitude. The suggested dual-mode strategy provides a sensitive, precise and specific detection method for glucose. Another advantage is that the dual-mode technique significantly improves the precision and consistency of the measurements, demonstrating its immense potential for use in biomedical research and clinical diagnostics.

要从泪液和唾液等临床样本中准确而灵敏地检测葡萄糖仍然很困难。我们利用葡萄糖氧化酶(GOx)催化葡萄糖、手枪样 DNA 酶(PLDz)转换信号、金纳米粒子(AuNPs)增强光学特性以及外切酶-III(Exo-III)放大信号,创造出了一种能够高灵敏度、高准确度检测葡萄糖的传感器。因此,该方法的检测限低至 7.5 pM,检测范围广达七个数量级。建议的双模式策略提供了一种灵敏、精确和特异的葡萄糖检测方法。另一个优点是,双模式技术大大提高了测量的精确度和一致性,显示了其在生物医学研究和临床诊断中的巨大应用潜力。
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引用次数: 0
The dynamic duo: cryo-EM teams up with machine learning to visualize biomolecules in motion. 动态二重奏:低温电子显微镜与机器学习相结合,实现生物分子运动的可视化。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-06-12 DOI: 10.1080/07366205.2024.2355771
Beatrice Bowlby

Cryo-EM has been a key technique in our understanding of biomolecular structures. Now, machine learning techniques are being used to put these structures in motion, revealing dynamic interactions and processes happening on a molecular and cellular level.[Formula: see text].

低温电子显微镜一直是我们了解生物分子结构的关键技术。现在,机器学习技术正被用于使这些结构运动起来,揭示分子和细胞水平上发生的动态相互作用和过程。
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引用次数: 0
Artificial intelligence: help or hindrance in solving the reproducibility crisis? 人工智能:帮助还是阻碍解决可重复性危机?
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-06-20 DOI: 10.1080/07366205.2024.2355776
Jennifer Straiton

Science is in the midst of a reproducibility crisis and the integration of artificial intelligence into scientific research has only compounded the problem; yet could the technology hold the solution to its own problems?[Formula: see text].

科学正处于可重复性危机之中,人工智能融入科学研究只会使问题更加复杂;然而,这项技术能否解决自身的问题?
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引用次数: 0
Simple and sensitive detection of Pseudomonas aeruginosa in neonatal infection based on a both-end blocked peroxidase-mimicking DNAzyme. 基于双端阻断过氧化物酶模拟 DNA 酶对新生儿感染铜绿假单胞菌进行简单灵敏的检测。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-05-20 DOI: 10.1080/07366205.2024.2348295
Dongyun Chen, Yicong Pan, Huan Yu, Xiaoxiang Chen

Developing a simple and highly sensitive approach for Pseudomonas aeruginosa (P. aeruginosa) detection is crucial, as it is closely associated with various disorders, such as newborn infections. Nevertheless, few of techniques have the capability to accurately identify P. aeruginosa with a high level of sensitivity and significantly improved stability. The employment of the both-end blocked peroxidase-mimicking DNAzyme significantly diminished the interferences from background signals, so conferring the approach with a high degree of selectivity and reproducibility. The proposed method is demonstrated with exceptional discernment capacity in differentiating interfering microorganisms. The simplicity, elevated sensitivity and high discerning capability make the method a highly promising alternative instrument for pathogenic bacteria detection.

铜绿假单胞菌(P. aeruginosa)与新生儿感染等各种疾病密切相关,因此开发一种简单、高灵敏度的铜绿假单胞菌(P. aeruginosa)检测方法至关重要。然而,很少有技术能够准确识别铜绿假单胞菌,并具有高灵敏度和显著提高的稳定性。双端阻断过氧化物酶模拟 DNA 酶的使用大大减少了背景信号的干扰,从而使该方法具有高度的选择性和可重复性。所提出的方法在区分干扰微生物方面具有卓越的鉴别能力。该方法操作简单、灵敏度高、分辨能力强,是一种极有前途的病原菌检测替代仪器。
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引用次数: 0
Cassava for the future: embryogenic liquid cultures suitable for new biotech techniques. 未来的木薯:适合新生物技术的胚胎液体培养物。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-10-16 DOI: 10.1080/07366205.2024.2393546
Beata Dedičová, Luis Augusto Becerra Lopez-Lavalle

Cassava, a crop of importance for subsistence farming in Africa, Asia, and Latin America, has the potential to benefit from global economic integration as a versatile industrial resource. Enhancing cassava productivity is not just a matter of agricultural competitiveness but a crucial step toward ensuring many communities' food security and livelihoods. Given its high performance in marginal environments, where climate change poses threats, ensuring food security and livelihoods relies on rapidly adapting cassava. This study aimed to develop a protocol that swiftly transitions cassava embryogenic short-period liquid suspension cultures, facilitating the regeneration of genetically stable in vitro plants. The resulting protocol, with its potential to be a foundational component in future technologies employing various genome editing or genetic modification techniques, holds promise for the advancement of cassava biotechnology.

木薯是非洲、亚洲和拉丁美洲自给农作的重要作物,作为一种用途广泛的工业资源,它有可能从全球经济一体化中受益。提高木薯的生产率不仅关系到农业竞争力,也是确保许多社区粮食安全和生计的关键一步。鉴于木薯在气候变化构成威胁的边缘环境中表现优异,确保粮食安全和生计有赖于木薯的快速适应。本研究旨在开发一种可快速转化木薯胚胎的短周期液体悬浮培养物的方案,以促进基因稳定的体外植株的再生。由此产生的方案有可能成为未来采用各种基因组编辑或转基因技术的基础组成部分,为木薯生物技术的进步带来希望。
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引用次数: 0
A standardized protocol for sample preparation for scanning electron microscopy to visualize extrachromosomal DNA. 用于扫描电子显微镜观察染色体外 DNA 的样本制备标准化方案。
IF 2.2 4区 工程技术 Q3 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-01-01 Epub Date: 2024-06-19 DOI: 10.1080/07366205.2024.2346042
Jillann A Madren, Jingting Chen, William Dennis, Christina Ford, Kristen K White, Elizabeth Brunk

Extrachromosomal DNA (ecDNA) are circular DNA structures associated with cancer and drug resistance. One specific type, double minute (DM) chromosomes, has been studied since the 1960s using imaging techniques like cytogenetics and fluorescence microscopy. Specialized techniques such as atomic force microscopy (AFM) and scanning electron microscopy (SEM) offer micro to nano-scale visualization, but current sample preparation methods may not optimally preserve ecDNA structure. Our study introduces a systematic protocol using SEM for high-resolution ecDNA visualization. We have optimized the end-to-end procedure, providing a standardized approach to explore the circular architecture of ecDNA and address the urgent need for better understanding in cancer research.

染色体外 DNA(ecDNA)是与癌症和耐药性有关的环状 DNA 结构。自 20 世纪 60 年代以来,人们一直在利用细胞遗传学和荧光显微镜等成像技术研究一种特殊类型的双微粒(DM)染色体。原子力显微镜(AFM)和扫描电子显微镜(SEM)等专业技术可提供微米到纳米尺度的可视化,但目前的样品制备方法可能无法最佳地保留 ecDNA 结构。我们的研究介绍了一种利用扫描电子显微镜进行高分辨率 ecDNA 可视化的系统方案。我们优化了端到端的程序,提供了一种标准化的方法来探索 ecDNA 的环状结构,满足了癌症研究中更好地了解其结构的迫切需要。
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BioTechniques
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