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Biotechnology Notes

Pub Date : 2025-01-01

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Biotechnology Notes

Pub Date : 2025-01-01

引用次数: 0

Biotechnology Notes

Pub Date : 2025-01-01

引用次数: 0

Tackling carbapenem-resistant Acinetobacter baumannii (CRAB) and their virulence factors using biosynthesized silver nanoparticles combined with imipenem 生物合成纳米银与亚胺培南联合处理耐碳青霉烯鲍曼不动杆菌及其毒力因子

Biotechnology Notes

Pub Date : 2025-01-01 DOI: 10.1016/j.biotno.2025.07.002

Mohamed Shawky, Mohamed H. Kalaba, Gamal M. El-Sherbiny

Carbapenem-resistant Acinetobacter baumannii is an extremely hazardous microorganism due to its high level of resistance to a wide array of antibiotics, making it a significant public health concern. Herein, this study aimed to biofabricate silver nanoparticles using a cell-free filter derived from Streptomyces sp., with a focus on characterizing their physicochemical properties, and use them to combat CRAB and their virulence factors. The biofabricated Ag-NPs were predominantly spherical with an average size 50 nm, confirmed through TEM analyses, while DLS measurements showed an average hydrodynamic diameter of approximately 36.78 nm. UV–Vis spectroscopy displayed a characteristic surface plasmon resonance peak in the range of 420 nm, indicative of nanoparticle formation. XRD confirmed the crystalline structure, presenting peaks corresponding to face-centered cubic silver. FTIR spectroscopy revealed active participation of metabolite compounds derived from the Streptomyces cell-free filter in both reduction and stabilization processes. Eight clinical bacterial isolates were identified as CRAB using the Vitek-2 system, and biofilm formation with 100 % was assessed through Congo red and microplate assays. The MIC for Ag-NPs and imipenem (IMP) were found to be between 4 and 5 μg/mL and 13 and 15 μg/mL, respectively. Additionally, the fractional inhibitory concentration index (FICI) for the synergistic combinations of Ag-NPs and IMP ranged from 0.5 to 0.375, indicating a notable decrease in the MIC values for both IMP and Ag-NPs from 14 and 5 μg/mL to 1.75 and 1.25 μg/mL, respectively. The qRT-PCR demonstrated a significant reduction in the expression levels of the Bap and ompA genes by up to 4.0-fold (p ≤ 0.001). The time-killing assay confirmed that the bacterial strain was effectively eliminated through the synergistic action of Ag-NPs and IMP. Moreover, the cytotoxicity assessment of Ag-NPs and their combination with IMP revealed low toxicity of the combination of Ag-NPs and IMP, with an IC₅₀ of 26.13 ± 0.24 and 45.33 ± 0.21 μg/mL, respectively (p < 0.0019), indicating good biosafety, while the hemolysis rates were recorded at 0.4 and 0.7 at 12 and 24 h, respectively. We concluded that the combination of Ag-NPs with IMP could serve as a promising alternative strategy for treating CRAB.

耐碳青霉烯鲍曼不动杆菌是一种极其危险的微生物，因为它对多种抗生素具有高度耐药性，使其成为一个重大的公共卫生问题。本研究旨在利用链霉菌（Streptomyces sp.）衍生的无细胞过滤器生物制备纳米银，重点研究其物理化学性质，并利用其对抗螃蟹及其毒力因子。通过TEM分析证实，生物制备的Ag-NPs主要为球形，平均尺寸为50 nm，而DLS测量显示其平均水动力直径约为36.78 nm。紫外可见光谱显示，表面等离子体共振峰在420 nm范围内，表明纳米颗粒形成。XRD证实其晶体结构为面心立方银。FTIR光谱显示，链霉菌无细胞过滤器衍生的代谢物化合物积极参与还原和稳定过程。使用Vitek-2系统鉴定8株临床分离细菌为CRAB，通过刚果红和微孔板检测100%的生物膜形成情况。Ag-NPs和亚胺培南（IMP）的MIC分别为4 ~ 5 μg/mL和13 ~ 15 μg/mL。此外，Ag-NPs和IMP协同组合的分数抑制浓度指数（FICI）在0.5 ~ 0.375之间，表明IMP和Ag-NPs的MIC值分别从14和5 μg/mL显著降低到1.75和1.25 μg/mL。qRT-PCR结果显示，Bap和ompA基因的表达水平显著降低了4.0倍（p≤0.001）。时间杀伤实验证实，Ag-NPs与IMP的协同作用可有效杀灭该菌株，细胞毒性评价显示Ag-NPs与IMP联用毒性较低，IC50分别为26.13±0.24和45.33±0.21 μg/mL (p <；0.0019)，生物安全性较好，12 h和24 h溶血率分别为0.4和0.7。我们的结论是Ag-NPs与IMP的联合治疗可能是一种有希望的治疗螃蟹的替代策略。

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引用次数: 0

Modeling and simulation of soft bio-mimetic fingers with a novel soft thumb design for bionic hand applications using ANN 基于人工神经网络的柔性仿生手指建模与仿真研究

Biotechnology Notes

Pub Date : 2025-01-01 DOI: 10.1016/j.biotno.2025.05.002

Eman R.A. Soliman , Ayman Nada , Hiroyuki Ishii , Ahmed M.R. Fathelbeb

The paper presents a novel design for a soft bio-mimetic finger and soft thumb structure for bionic hand applications. It introduces an anthropomorphic pneumatic flexible finger system using a PneuNets framework to enhance flexibility and maneuverability. The research investigates the influence of geometric variations (wall thickness, chamber number, and spacing) on finger deformation, demonstrating that reduced wall thickness and augmented chambers substantially improve flexibility. A key innovation is the soft thumb design that accurately replicates the complex movements of the Carpometacarpal (CMC) joint, enabling natural opposition and dexterity. Eight models were developed for four fingers and two models for the thumb. Simulation results indicate that models with thinner walls (2 mm) achieve bending angles exceeding 80° at 120 KPa, whereas 3 mm models remain below 50°. Moreover, increasing the number of chambers enhances deformation, with each added chamber contributing approximately 41 % more flexibility. For the thumb models, we successfully mapped the motion ranges and accurately mimicked the base joint, enabling natural opposition and dexterity. Furthermore, the paper also integrates Artificial Neural Networks (ANNs) to model forward kinematics, improving the estimation of bending angles and end-tip positions, which enhances the overall adaptability and control of the system.

本文提出了一种适用于仿生手的柔性仿生手指和柔性拇指结构设计。采用PneuNets框架设计了一种拟人气动柔性手指系统，提高了系统的灵活性和可操作性。该研究调查了几何变化（壁厚、室数和间距）对手指变形的影响，表明减少壁厚和增加室可大大提高灵活性。一个关键的创新是柔软的拇指设计，准确地复制了复杂的腕掌骨（CMC）关节的运动，使自然对立和灵巧。为四个手指开发了八个模型，为拇指开发了两个模型。仿真结果表明，在120 KPa下，壁较薄（2 mm）的模型的弯曲角超过80°，而3 mm的模型的弯曲角低于50°。此外，增加腔室的数量可以增强变形，每增加一个腔室，可使弹性提高约41%。对于拇指模型，我们成功地绘制了运动范围，并准确地模拟了基础关节，实现了自然的对立和灵巧性。此外，本文还将人工神经网络（ann）集成到机器人的正运动学建模中，改进了机器人弯曲角度和端尖位置的估计，增强了系统的整体适应性和控制能力。

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引用次数: 0

Cell-free protein synthesis platforms for accelerating drug discovery 加速药物发现的无细胞蛋白质合成平台

Biotechnology Notes

Pub Date : 2025-01-01 DOI: 10.1016/j.biotno.2025.02.001

Filippo Caschera

Cell-free protein synthesis is a platform for streamlined production of macromolecules. Recently, several proteins with pharmaceutical relevance were synthesised and characterised. Off-the-shelf reagents and parallelised experimentation have enabled the exploration of many different conditions for in vitro protein synthesis and engineering. Herein is described how machine learning algorithms were applied for protein yield maximisation as well as for protein engineering and de novo design. Cell-free protein synthesis provides the biotechnological platform to unlock the power and benefit of AI/ML for drug discovery and improve human health.

无细胞蛋白质合成是大分子流线型生产的平台。最近，几种与药物相关的蛋白质被合成和表征。现成的试剂和并行实验使得探索体外蛋白质合成和工程的许多不同条件成为可能。本文描述了机器学习算法如何应用于蛋白质产量最大化以及蛋白质工程和从头设计。无细胞蛋白合成提供了生物技术平台，以释放AI/ML的力量和益处，用于药物发现和改善人类健康。

引用次数: 0

Biotechnology Notes

Pub Date : 2025-01-01

引用次数: 0

Biotechnology Notes

Pub Date : 2025-01-01

引用次数: 0

Biotechnology Notes

Pub Date : 2025-01-01

引用次数: 0

Mevalonate secretion is not mediated by a singular non-essential transporter in Saccharomyces cerevisiae 麦角酵母中的甲羟戊酸分泌不是由单一的非必要转运体介导的

Biotechnology Notes

Pub Date : 2024-01-01 DOI: 10.1016/j.biotno.2024.10.001

Scott A. Wegner , José L. Avalos

Isoprenoids are highly valued targets for microbial chemical production, allowing the creation of fragrances, biofuels, and pharmaceuticals from renewable carbon feedstocks. To increase isoprenoid production, previous efforts have manipulated pyruvate dehydrogenase (PDH) bypass pathway flux to increase cytosolic acetyl-coA; however, this results in mevalonate secretion and does not necessarily translate into higher isoprenoid production. Identification and disruption of the transporter mediating mevalonate secretion would allow us to determine whether increasing PDH bypass activity in the absence of secretion improves conversion of mevalonate into downstream isoprenoids. Attempted identification of the mevalonate transporter was accomplished using a pooled CRISPR library targeting all nonessential transporters and two different screening methods. Using a high throughput screen, based on growth of a mevalonate auxotrophic Escherichia coli strain, it was found that ZRT3 disruption largely abolished accumulation of extracellular mevalonate. However, disruption of ZRT3 was found to lower overall mevalonate pathway activity, rather than prevent secretion, indicating a previously unreported interaction between zinc availability and the mevalonate pathway. In a second screen, significant differences in PDR5/15 and QDR1/2 library representation were found between wild-type and mevalonate secreting Saccharomyces cerevisiae strains. However, no single deletion (or selected pair of double deletions) abolishes mevalonate secretion, indicating that this process appears to be mediated through multiple redundant transporters.

异戊烯类化合物是微生物化学生产的重要目标，可利用可再生碳原料生产香料、生物燃料和药物。为了提高异戊烯类化合物的产量，以前的研究曾通过操纵丙酮酸脱氢酶（PDH）旁路通量来增加细胞膜乙酰-coA；但这会导致甲羟戊酸的分泌，并不一定会转化为更高的异戊烯类化合物产量。鉴定和破坏介导甲羟戊酸分泌的转运体将使我们能够确定，在没有甲羟戊酸分泌的情况下，增加 PDH 旁路活性是否会改善甲羟戊酸向下游异丙烯酸的转化。我们尝试使用针对所有非必要转运体的 CRISPR 文库和两种不同的筛选方法来鉴定甲羟戊酸转运体。通过高通量筛选，在甲羟戊酸辅助营养大肠杆菌菌株生长的基础上发现，ZRT3 的破坏在很大程度上抑制了细胞外甲羟戊酸的积累。然而，研究发现破坏 ZRT3 会降低甲羟戊酸通路的整体活性，而不是阻止分泌，这表明锌的可用性与甲羟戊酸通路之间存在一种以前未报道过的相互作用。在第二个筛选中，发现野生型和分泌甲羟戊酸的酿酒酵母菌株之间的 PDR5/15 和 QDR1/2 文库代表性存在显著差异。然而，没有任何单个缺失（或选定的一对双缺失）会取消甲羟戊酸的分泌，这表明这一过程似乎是通过多个冗余转运体介导的。

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