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Soil microbiome characterization and its future directions with biosensing 利用生物传感技术确定土壤微生物群特征及其未来发展方向
IF 5.6 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-10 DOI: 10.1186/s13036-024-00444-1
Lexi DeFord, Jeong-Yeol Yoon
Soil microbiome characterization is typically achieved with next-generation sequencing (NGS) techniques. Metabarcoding is very common, and meta-omics is growing in popularity. These techniques have been instrumental in microbiology, but they have limitations. They require extensive time, funding, expertise, and computing power to be effective. Moreover, these techniques are restricted to controlled laboratory conditions; they are not applicable in field settings, nor can they rapidly generate data. This hinders using NGS as an environmental monitoring tool or an in-situ checking device. Biosensing technology can be applied to soil microbiome characterization to overcome these limitations and to complement NGS techniques. Biosensing has been used in biomedical applications for decades, and many successful commercial products are on the market. Given its previous success, biosensing has much to offer soil microbiome characterization. There is a great variety of biosensors and biosensing techniques, and a few in particular are better suited for soil field studies. Aptamers are more stable than enzymes or antibodies and are more ready for field-use biosensors. Given that any microbiome is complex, a multiplex sensor will be needed, and with large, complicated datasets, machine learning might benefit these analyses. If the signals from the biosensors are optical, a smartphone can be used as a portable optical reader and potential data-analyzing device. Biosensing is a rich field that couples engineering and biology, and applying its toolset to help advance soil microbiome characterization would be a boon to microbiology more broadly.
土壤微生物组的特征描述通常是通过新一代测序(NGS)技术实现的。元条码技术非常普遍,元组学技术也越来越受欢迎。这些技术在微生物学领域发挥了重要作用,但也有局限性。它们需要大量的时间、资金、专业知识和计算能力才能有效发挥作用。此外,这些技术仅限于受控的实验室条件,不适用于野外环境,也不能快速生成数据。这就阻碍了将 NGS 用作环境监测工具或现场检查设备。生物传感技术可应用于土壤微生物组表征,以克服这些局限性,并对 NGS 技术进行补充。生物传感技术在生物医学领域的应用已有几十年的历史,市场上已有许多成功的商业产品。鉴于其以往的成功经验,生物传感在土壤微生物组表征方面大有可为。生物传感器和生物传感技术种类繁多,其中有几种尤其适合土壤实地研究。与酶或抗体相比,Aptamers 更为稳定,更适于现场使用的生物传感器。鉴于任何微生物群都很复杂,因此需要一种多重传感器,而对于大型复杂的数据集,机器学习可能对这些分析有帮助。如果生物传感器发出的信号是光学信号,智能手机就可以用作便携式光学阅读器和潜在的数据分析设备。生物传感是一个结合了工程学和生物学的丰富领域,应用它的工具集来帮助推进土壤微生物组的特征描述,将为更广泛的微生物学带来福音。
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引用次数: 0
Current advances in Hepatitis C diagnostics 丙型肝炎诊断技术的最新进展
IF 5.6 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-09 DOI: 10.1186/s13036-024-00443-2
Anna S. Baber, Baviththira Suganthan, Ramaraja P. Ramasamy
Nearly 60 million people worldwide are infected with Hepatitis C Virus (HCV), a bloodborne pathogen which leads to liver cirrhosis and increases the risk of hepatocellular carcinoma. Those with limited access to healthcare resources, such as injection drug users and people in low- and middle-income countries, carry the highest burden. The current diagnostic algorithm for HCV is slow and costly, leading to a significant barrier in diagnosis and treatment for those most at risk from HCV. There remains no available vaccine for HCV, and infection is often asymptomatic until significant cirrhosis has occurred, which makes screening incredibly important to prevent liver damage and transmission. Recent investigation has sought to address these issues through improvements in various aspects of the diagnostic procedure, using methods such as isothermal amplification techniques for viral RNA amplification, the use of viral protein as an analyte, and the incorporation of streamlined, self-contained testing systems to reduce administrative skill requirements. This review provides a comprehensive overview of current commercial standards and novel improvements in HCV diagnostics, as well as a framework for future integration of these improvements to develop a one-step diagnostic that meets the needs of those most affected.
全世界有近 6000 万人感染了丙型肝炎病毒(HCV),这种血液传播的病原体会导致肝硬化并增加肝细胞癌的风险。注射毒品使用者和中低收入国家的人等医疗资源有限的人群负担最重。目前的丙型肝炎病毒(HCV)诊断算法既缓慢又昂贵,导致丙型肝炎病毒高危人群在诊断和治疗方面面临巨大障碍。目前还没有针对丙型肝炎病毒的疫苗,而且感染者在出现严重肝硬化之前往往没有症状,因此筛查对于预防肝损伤和传播极其重要。最近的研究试图通过改进诊断程序的各个方面来解决这些问题,所采用的方法包括用于病毒 RNA 扩增的等温扩增技术、使用病毒蛋白作为分析物,以及采用精简、独立的检测系统来降低对管理技能的要求。本综述全面概述了 HCV 诊断的现行商业标准和新的改进,以及未来整合这些改进的框架,以开发出一步到位的诊断方法,满足最受影响人群的需求。
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引用次数: 0
Investigation of pH-dependent Paclitaxel delivery mechanism employing Chitosan-Eudragit bioresponsive nanocarriers: a molecular dynamics simulation 利用壳聚糖-Eudragit 生物反应性纳米载体研究紫杉醇的 pH 值依赖性递送机制:分子动力学模拟
IF 5.6 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-09 DOI: 10.1186/s13036-024-00445-0
Reza Maleki, Mohammad Khedri, Sima Rezvantalab, Nima Beheshtizadeh
Before embarking on any experimental research endeavor, it is advisable to do a mathematical computation and thoroughly examine the methodology. Despite the use of polymeric nanocarriers, the regulation of bioavailability and drug release at the disease site remains insufficient. Several effective methods have been devised to address this issue, including the creation of polymeric nanocarriers that can react to stimuli such as redox potential, temperature, pH, and light. The present study has been utilized all-atom molecular dynamics (AA-MD) and coarse-grained molecular dynamics (CG-MD) methods and illustrated the drug release mechanism, which is influenced by pH, for Chitosan-Eudragit bioresponsive nanocarriers. The aim of current work is to study the molecular mechanism and atomistic interactions of PAX delivery using a Chitosan-Eudragit carrier. The ability of Eudragit polymers to dissolve in various organic solvents employed in the process of solvent evaporation is a crucial benefit in enhancing the solubility of pharmaceuticals. This study investigated the use of Chitosan-Eudragit nanocarriers for delivering an anti-tumor drug, namely Paclitaxel (PAX). Upon analyzing several significant factors affecting the stability of the drug and nanocarrier, it has been shown that the level of stability is more significant in the neutral state than the acidic state. Furthermore, the system exhibits higher stability in the neutral state. The used Chitosan-Eudragit nanocarriers exhibit a stable structure under alkaline conditions, but undergo deformation and release their payloads under acidic conditions. It was demonstrated that the in silico analysis of anti-tumor drugs and carriers’ integration could be quantified and validated by experimental results (from previous works) at an acceptable level.
在开展任何实验研究工作之前,最好先进行数学计算,并对方法论进行彻底研究。尽管使用了聚合物纳米载体,但对疾病部位的生物利用度和药物释放的调节仍然不足。为解决这一问题,人们设计了几种有效的方法,包括创造出能对氧化还原电位、温度、pH 值和光等刺激做出反应的聚合物纳米载体。本研究利用全原子分子动力学(AA-MD)和粗粒度分子动力学(CG-MD)方法,阐述了壳聚糖-Eudragit 生物响应纳米载体受 pH 值影响的药物释放机制。当前工作的目的是研究使用壳聚糖-Eudragit 载体递送 PAX 的分子机理和原子相互作用。在溶剂蒸发过程中,Eudragit 聚合物能够溶解于各种有机溶剂,这对于提高药物的溶解度至关重要。本研究调查了壳聚糖-Eudragit 纳米载体用于递送抗肿瘤药物紫杉醇(PAX)的情况。对影响药物和纳米载体稳定性的几个重要因素进行分析后发现,中性状态下的稳定性比酸性状态下的稳定性更高。此外,该系统在中性状态下表现出更高的稳定性。所使用的壳聚糖-Eudragit 纳米载体在碱性条件下结构稳定,但在酸性条件下会发生变形并释放有效载荷。实验证明,抗肿瘤药物和载体整合的硅学分析可以量化,并通过实验结果(来自以前的工作)进行验证,达到可接受的水平。
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引用次数: 0
Epithelial cell-cell interactions in an overcrowded environment: jamming or live cell extrusion. 过度拥挤环境中上皮细胞与细胞之间的相互作用:干扰还是活细胞挤压。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-05 DOI: 10.1186/s13036-024-00442-3
Ivana Pajic-Lijakovic, Milan Milivojevic, Peter V E McClintock

Epithelial tissues respond strongly to the mechanical stress caused by collective cell migration and are able to regulate it, which is important for biological processes such as morphogenesis, wound healing, and suppression of the spread of cancer. Compressive, tensional, and shear stress components are produced in cells when epithelial monolayers on substrate matrices are actively or passively wetted or de-wetted. Increased compressive stress on cells leads to enhanced cell-cell interactions by increasing the frequency of change the cell-cell distances, triggering various signalling pathways within the cells. This can ultimately lead either to cell jamming or to the extrusion of live cells. Despite extensive research in this field, it remains unclear how cells decide whether to jam, or to extrude a cell or cells, and how cells can reduce the compressive mechanical stress. Live cell extrusion from the overcrowded regions of the monolayers is associated with the presence of topological defects of cell alignment, induced by an interplay between the cell compressive and shear stress components. These topological defects stimulate cell re-alignment, as a part of the cells' tendency to re-establish an ordered trend of cell migration, by intensifying the glancing interactions in overcrowded regions. In addition to individual cell extrusion, collective cell extrusion has also been documented during monolayer active de-wetting, depending on the cell type, matrix stiffness, and boundary conditions. Cell jamming has been discussed in the context of the cells' contact inhibition of locomotion caused by cell head-on interactions. Since cell-cell interactions play a crucial role in cell rearrangement in an overcrowded environment, this review is focused on physical aspects of these interactions in order to stimulate further biological research in the field.

上皮组织对细胞集体迁移造成的机械应力反应强烈,并能对其进行调节,这对形态发生、伤口愈合和抑制癌症扩散等生物过程非常重要。当基底基质上的上皮单层被主动或被动润湿或去湿时,细胞中会产生压应力、张应力和剪切应力成分。细胞受到的压应力增加,会导致细胞-细胞间距的变化频率增加,从而增强细胞-细胞间的相互作用,触发细胞内的各种信号通路。这最终可能导致细胞堵塞或活细胞挤出。尽管在这一领域进行了广泛的研究,但目前仍不清楚细胞是如何决定是卡住还是挤出一个或多个细胞的,也不清楚细胞如何减少压缩机械应力。单层细胞拥挤区域的活细胞挤出与细胞排列的拓扑缺陷有关,这种缺陷是由细胞压应力和剪切应力相互作用引起的。这些拓扑缺陷会刺激细胞重新排列,通过加强过度拥挤区域的闪烁相互作用,使细胞重新形成有序的迁移趋势。除了单个细胞挤压外,在单层主动去湿过程中,细胞集体挤压也被记录在案,这取决于细胞类型、基质硬度和边界条件。细胞堵塞是在细胞接触抑制运动的背景下讨论的,这种运动是由细胞正面相互作用引起的。由于细胞与细胞之间的相互作用对细胞在拥挤环境中的重新排列起着至关重要的作用,因此本综述将重点放在这些相互作用的物理方面,以促进该领域的进一步生物学研究。
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引用次数: 0
Hyperactivation of crosslinked lipases in elastic hydroxyapatite microgel and their properties. 弹性羟基磷灰石微凝胶中交联脂肪酶的超活化及其特性。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-09-02 DOI: 10.1186/s13036-024-00440-5
Hyo Won Jeon, Jun Seop Lee, Chan Hee Lee, Dain Kim, Hye Sun Lee, Ee Taek Hwang

Effective enzyme stabilization through immobilization is essential for the functional usage of enzymatic reactions. We propose a new method for synthesizing elastic hydroxyapatite microgel (E-HAp-M) materials and immobilizing lipase using this mesoporous mineral via the ship-in-a-bottle-neck strategy. The physicochemical parameters of E-HAp-M were thoroughly studied, revealing that E-HAp-M provides efficient space for enzyme immobilization. As a model enzyme, lipase (LP) was entrapped and then cross-linked enzyme structure, preventing leaching from mesopores, resulting in highly active and stable LP/E-HAp-M composites. By comparing LP activity under different temperature and pH conditions, it was observed that the cross-linked LP exhibited improved thermal stability and pH resistance compared to the free enzyme. In addition, they demonstrated a 156% increase in catalytic activity compared with free LP in hydrolysis reactions at room temperature. The immobilized LP maintained 45% of its initial activity after 10 cycles of recycling and remained stable for over 160 days. This report presents the first demonstration of a stabilized cross-linked LP in E-HAp-M, suggesting its potential application in enzyme-catalyzed processes within biocatalysis technology.

通过固定化有效地稳定酶对酶促反应的功能使用至关重要。我们提出了一种合成弹性羟基磷灰石微凝胶(E-HAp-M)材料的新方法,并通过 "瓶颈船 "策略利用这种介孔矿物固定脂肪酶。对 E-HAp-M 的理化参数进行了深入研究,发现 E-HAp-M 为酶的固定化提供了有效的空间。以脂肪酶(LP)为模型酶,夹持后交联酶结构,防止从中孔沥滤,从而得到高活性、高稳定性的LP/E-HAp-M复合材料。通过比较不同温度和 pH 条件下的 LP 活性,发现与游离酶相比,交联的 LP 具有更好的热稳定性和耐 pH 性。此外,在室温下的水解反应中,它们的催化活性比游离 LP 提高了 156%。固定化 LP 在循环使用 10 次后仍能保持 45% 的初始活性,并能在 160 多天内保持稳定。本报告首次展示了 E-HAp-M 中的稳定交联 LP,表明它有可能应用于生物催化技术中的酶催化过程。
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引用次数: 0
Oxygenator assisted dynamic microphysiological culture elucidates the impact of hypoxia on valvular interstitial cell calcification. 充氧器辅助动态微生理学培养阐明了缺氧对瓣膜间质细胞钙化的影响。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-23 DOI: 10.1186/s13036-024-00441-4
Claudia Dittfeld, Florian Schmieder, Stephan Behrens, Anett Jannasch, Klaus Matschke, Frank Sonntag, Sems-Malte Tugtekin

Introduction: Microphysiological systems (MPS) offer simulation of (patho)physiological parameters. Investigation includes items which lead to fibrosis and calcification in development and progress of calcific aortic valve disease, based e.g. on culturing of isolated valvular interstitial cells (VICs). Hypoxia regulated by hypoxia inducible factors impacts pathological differentiation in aortic valve (AV) disease. This is mimicked via an MPS implemented oxygenator in combination with calcification inducing medium supplementation.

Methods: Human valvular interstitial cells were isolated and dynamically cultured in MPS at hypoxic, normoxic, arterial blood oxygen concentration and cell incubator condition. Expression profile of fibrosis and calcification markers was monitored and calcification was quantified in induction and control media with and without hypoxia and in comparison to statically cultured counterparts.

Results: Hypoxic 24-hour culture of human VICs leads to HIF1α nuclear localization and induction of EGLN1, EGLN3 and LDHA mRNA expression but does not directly impact expression of fibrosis and calcification markers. Dependent on medium formulation, induction medium induces monolayer calcification and elevates RUNX2, ACTA2 and FN1 but reduces SOX9 mRNA expression in dynamic and static MPS culture. But combining hypoxic oxygen concentration leads to higher calcification potential of human VICs in calcification and standard medium formulation dynamically cultured for 96 h.

Conclusion: In hypoxic oxygen concentration an increased human VIC calcification in 2D VIC culture in an oxygenator assisted MPS was detected. Oxygen regulation therefore can be combined with calcification induction media to monitor additional effects of pathological marker expression. Validation of oxygenator dependent VIC behavior envisions future advancement and transfer to long term aortic valve tissue culture MPS.

引言微生理学系统(MPS)可模拟(病理)生理参数。研究包括在钙化性主动脉瓣疾病的发生和发展过程中导致纤维化和钙化的项目,例如基于分离的瓣膜间质细胞(VICs)的培养。由缺氧诱导因子调节的缺氧会影响主动脉瓣(AV)疾病的病理分化。方法:分离人瓣膜间质细胞,并在缺氧、常氧、动脉血氧浓度和细胞培养箱条件下在 MPS 中进行动态培养。监测纤维化和钙化标志物的表达情况,并在有缺氧和无缺氧的诱导培养基和对照培养基中量化钙化情况,并与静态培养的对应细胞进行比较:结果:24小时缺氧培养人VICs会导致HIF1α核定位并诱导EGLN1、EGLN3和LDHA mRNA的表达,但不会直接影响纤维化和钙化标志物的表达。根据培养基配方的不同,在动态和静态 MPS 培养中,诱导培养基可诱导单层钙化并提高 RUNX2、ACTA2 和 FN1 的表达,但会降低 SOX9 mRNA 的表达。但在钙化培养基和标准培养基配方中,结合低氧浓度动态培养 96 小时后,人 VICs 的钙化潜能更高:结论:在缺氧氧气浓度下,氧气辅助 MPS 中的二维 VIC 培养可增加人 VIC 的钙化。因此,氧气调节可与钙化诱导培养基相结合,以监测病理标记表达的其他影响。氧合器依赖性 VIC 行为的验证预示着未来的进步,并将转移到长期主动脉瓣组织培养 MPS 中。
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引用次数: 0
Enhancing bioprocessing of red pigment from immobilized culture of gamma rays mutant of the endophytic fungus Monascus ruber SRZ112. 利用内生真菌 Monascus ruber SRZ112 的伽马射线突变体的固定培养物加强红色素的生物加工。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-15 DOI: 10.1186/s13036-024-00439-y
El-Sayed R El-Sayed, Shaimaa A Mousa, Tomasz Strzała, Filip Boratyński

Considerable attention has been paid to exploring the biotechnological applications of several Monascus sp. for pigment production. In this study, our focus is on enhancing the bioprocessing of red pigment (RP) derived from the endophytic fungus Monascus ruber SRZ112. To achieve this, we developed a stable mutant strain with improved productivity through gamma irradiation. This mutant was then employed in the immobilization technique using various entrapment carriers. Subsequently, we optimized the culture medium for maximal RP production using the Response Surface Methodology. Finally, these immobilized cultures were successfully utilized for RP production using a semi-continuous mode of fermentation. After eight cycles of fermentation, the highest RP yield by immobilized mycelia reached 309.17 CV mL-1, a significant increase compared to the original titer. Importantly, this study marks the first report on the successful production of Monascus RP in a semi-continuous mode using gamma rays' mutant strain, offering prospects for commercial production.

人们对探索几种用于生产色素的蒙那斯古斯菌的生物技术应用给予了极大的关注。在本研究中,我们的重点是提高从内生真菌 Monascus ruber SRZ112 中提取的红色素(RP)的生物加工能力。为此,我们开发了一种稳定的突变菌株,通过伽马射线照射提高了生产率。然后,我们使用各种夹持载体将这种突变株用于固定化技术中。随后,我们利用响应面方法优化了培养基,以获得最大的 RP 产量。最后,我们利用半连续发酵模式成功地将这些固定化培养物用于 RP 生产。经过八个周期的发酵,固定化菌丝体的最高 RP 产量达到了 309.17 CV mL-1,与原始滴度相比有了显著提高。重要的是,这项研究首次报道了利用伽马射线突变菌株在半连续模式下成功生产莫纳氏菌可溶性磷酸酯,为商业化生产提供了前景。
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引用次数: 0
Cell-cultivated aquatic food products: emerging production systems for seafood. 细胞培养的水产食品:新兴的海产品生产系统。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-08-07 DOI: 10.1186/s13036-024-00436-1
Mukunda Goswami, Reza Ovissipour, Claire Bomkamp, Nitin Nitin, Wazir Lakra, Mark Post, David L Kaplan

The demand for fish protein continues to increase and currently accounts for 17% of total animal protein consumption by humans. About 90% of marine fish stocks are fished at or above maximum sustainable levels, with aquaculture propagating as one of the fastest growing food sectors to address some of this demand. Cell-cultivated seafood production is an alternative approach to produce nutritionally-complete seafood products to meet the growing demand. This cellular aquaculture approach offers a sustainable, climate resilient and ethical biotechnological approach as an alternative to conventional fishing and fish farming. Additional benefits include reduced antibiotic use and the absence of mercury. Cell-cultivated seafood also provides options for the fortification of fish meat with healthier compositions, such as omega-3 fatty acids and other beneficial nutrients through scaffold, media or cell approaches. This review addresses the biomaterials, production processes, tissue engineering approaches, processing, quality, safety, regulatory, and social aspects of cell-cultivated seafood, encompassing where we are today, as well as the road ahead. The goal is to provide a roadmap for the science and technology required to bring cellular aquaculture forward as a mainstream food source.

对鱼类蛋白质的需求持续增长,目前占人类动物蛋白质总消费量的 17%。约 90% 的海洋鱼类种群的捕捞量已达到或超过最大可持续水平,水产养殖业作为增长最快的食品行业之一,正在满足部分需求。细胞培养海产品生产是生产营养全面的海产品以满足日益增长的需求的另一种方法。这种细胞水产养殖方法提供了一种可持续的、气候适应性强的、符合道德规范的生物技术方法,可替代传统的捕鱼和养鱼。其他好处还包括减少抗生素的使用和不含汞。细胞培养的海产品还可通过支架、培养基或细胞方法,为鱼肉添加更健康的成分,如欧米加-3 脂肪酸和其他有益营养物质。本综述探讨了细胞培养海产品的生物材料、生产工艺、组织工程方法、加工、质量、安全、监管和社会方面的问题,包括我们目前所处的阶段以及未来的发展方向。其目的是为将细胞培养作为主流食物来源所需的科学和技术提供路线图。
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引用次数: 0
Unraveling pathogenesis, biomarkers and potential therapeutic agents for endometriosis associated with disulfidptosis based on bioinformatics analysis, machine learning and experiment validation. 基于生物信息学分析、机器学习和实验验证,揭示与二硫化钼相关的子宫内膜异位症的发病机制、生物标志物和潜在治疗药物。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-07-26 DOI: 10.1186/s13036-024-00437-0
Xiaoxuan Zhao, Yang Zhao, Yuanyuan Zhang, Qingnan Fan, Huanxiao Ke, Xiaowei Chen, Linxi Jin, Hongying Tang, Yuepeng Jiang, Jing Ma
<p><strong>Background: </strong>Endometriosis (EMs) is an enigmatic disease of yet-unknown pathogenesis. Disulfidptosis, a novel identified form of programmed cell death resulting from disulfide stress, stands a chance of treating diverse ailments. However, the potential roles of disulfidptosis-related genes (DRGs) in EMs remain elusive. This study aims to thoroughly explore the key disulfidptosis genes involved in EMs, and probe novel diagnostic markers and candidate therapeutic compounds from the aspect of disulfidptosis based on bioinformatics analysis, machine learning, and animal experiments.</p><p><strong>Results: </strong>Enrichment analysis on key module genes and differentially expressed genes (DEGs) of eutopic and ectopic endometrial tissues in EMs suggested that EMs was closely related to disulfidptosis. And then, we obtained 20 and 16 disulfidptosis-related DEGs in eutopic and ectopic endometrial tissue, respectively. The protein-protein interaction (PPI) network revealed complex interactions between genes, and screened nine and ten hub genes in eutopic and ectopic endometrial tissue, respectively. Furthermore, immune infiltration analysis uncovered distinct differences in the immunocyte, human leukocyte antigen (HLA) gene set, and immune checkpoints in the eutopic and ectopic endometrial tissues when compared with health control. Besides, the hub genes mentioned above showed a close correlation with the immune microenvironment of EMs. Furthermore, four machine learning algorithms were applied to screen signature genes in eutopic and ectopic endometrial tissue, including the binary logistic regression (BLR), the least absolute shrinkage and selection operator (LASSO), the support vector machine-recursive feature elimination (SVM-RFE), and the extreme gradient boosting (XGBoost). Model training and hyperparameter tuning were implemented on 80% of the data using a ten-fold cross-validation method, and tested in the testing sets which determined the excellent diagnostic performance of these models by six indicators (Sensitivity, Specificity, Positive Predictive Value, Negative Predictive Value, Accuracy, and Area Under Curve). And seven eutopic signature genes (ACTB, GYS1, IQGAP1, MYH10, NUBPL, SLC7A11, TLN1) and five ectopic signature genes (CAPZB, CD2AP, MYH10, OXSM, PDLIM1) were finally identified based on machine learning. The independent validation dataset also showed high accuracy of the signature genes (IQGAP1, SLC7A11, CD2AP, MYH10, PDLIM1) in predicting EMs. Moreover, we screened 12 specific compounds for EMs based on ectopic signature genes and the pharmacological impact of tretinoin on signature genes was further verified in the ectopic lesion in the EMs murine model.</p><p><strong>Conclusion: </strong>This study verified a close association between disulfidptosis and EMs based on bioinformatics analysis, machine learning, and animal experiments. Further investigation on the biological mechanism of disulfidptosis in EMs is ant
背景:子宫内膜异位症(EMs)是一种发病机制尚不清楚的神秘疾病。二硫化硫是一种新发现的由二硫化物应激导致的程序性细胞死亡形式,有可能治疗多种疾病。然而,二硫化相关基因(DRGs)在电磁疾病中的潜在作用仍然难以捉摸。本研究旨在通过生物信息学分析、机器学习和动物实验,深入探讨参与EMs的关键二硫化相关基因,并从二硫化相关方面探寻新型诊断标志物和候选治疗化合物:结果:对EMs中异位和异位子宫内膜组织的关键模块基因和差异表达基因(DEGs)的富集分析表明,EMs与二硫化血症密切相关。随后,我们在异位和异位子宫内膜组织中分别获得了20个和16个与二硫化相关的DEGs。蛋白-蛋白相互作用(PPI)网络揭示了基因间复杂的相互作用,并在异位和异位子宫内膜组织中分别筛选出9个和10个枢纽基因。此外,免疫浸润分析发现,与健康对照组相比,异位和异位子宫内膜组织中的免疫细胞、人类白细胞抗原(HLA)基因组和免疫检查点存在明显差异。此外,上述枢纽基因与异位内膜的免疫微环境密切相关。此外,研究人员还应用了四种机器学习算法来筛选异位和异位子宫内膜组织中的特征基因,包括二元逻辑回归(BLR)、最小绝对收缩和选择算子(LASSO)、支持向量机-递归特征消除(SVM-RFE)和极梯度提升(XGBoost)。采用十倍交叉验证法对80%的数据进行了模型训练和超参数调整,并在测试集上进行了测试,通过六项指标(灵敏度、特异度、阳性预测值、阴性预测值、准确度和曲线下面积)确定了这些模型的卓越诊断性能。通过机器学习,最终确定了 7 个异位特征基因(ACTB、GYS1、IQGAP1、MYH10、NUBPL、SLC7A11、TLN1)和 5 个异位特征基因(CAPZB、CD2AP、MYH10、OXSM、PDLIM1)。独立验证数据集也显示,特征基因(IQGAP1、SLC7A11、CD2AP、MYH10、PDLIM1)预测EM的准确率很高。此外,我们还根据异位特征基因筛选出了12种针对EMs的特异性化合物,并在EMs鼠模型的异位病变中进一步验证了曲安奈德对特征基因的药理影响:本研究基于生物信息学分析、机器学习和动物实验,验证了二硫化硫与EMs之间的密切联系。对二硫化硫在EMs中的生物学机制的进一步研究有望为寻找EMs的潜在诊断生物标志物和革命性治疗方法带来新的进展。
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引用次数: 0
Frontier and hot topics in the application of hydrogel in the biomedical field: a bibliometric analysis based on CiteSpace. 水凝胶在生物医学领域应用的前沿和热点话题:基于 CiteSpace 的文献计量分析。
IF 5.7 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-07-23 DOI: 10.1186/s13036-024-00435-2
Weiming Sun, Wendi Wu, Xiangli Dong, Guohua Yu

Hydrogels are formed of crosslinked polymer chains arranged in three-dimensional (3D) networks. These chains have good water-containing capacity and are soft and malleable. Hydrogels have good biocompatibility due to their significant water content, flexible structure, and numerous holes. These characteristics make them analogous to biological tissues. Despite the publication of 8700 literature related to hydrogel biomedical applications in the past 52 years (1973 ~ 2024), studies on the use of hydrogels in biomedicine are few. To gain a comprehensive understanding of their current development status, research trends, and prospects in the biomedical application field, it is imperative to conduct a thorough retrospective analysis. In this study, we employ bibliometric analysis and CiteSpace software to quantitatively and visually analyze articles published in this field. Firstly, we provide a quantitative analysis of authorship and institutional publications over the past 52 years to elucidate the fundamental development status regarding hydrogel biomedical applications. Secondly, we did visual studies on terms that are high-frequency, explosive, keyword clustering, and so on, to understand the directionality and evolution of the main research hotspots during each period. Notably, our findings emphasize that fabricating hydrogels into wound healing-promoting dressings emerges as a prominent hotspot within the application field. We anticipate that this paper will inspire researchers with novel ideas for advancing hydrogel applications in biomedicine.

水凝胶由排列成三维(3D)网络的交联聚合物链组成。这些链具有良好的含水能力,柔软且可塑。由于水凝胶含有大量水分、结构柔韧、孔洞众多,因此具有良好的生物相容性。这些特性使它们类似于生物组织。尽管在过去的 52 年(1973 年至 2024 年)中发表了 8700 篇与水凝胶生物医学应用相关的文献,但有关水凝胶在生物医学中应用的研究却很少。为了全面了解水凝胶在生物医学应用领域的发展现状、研究趋势和前景,必须进行全面的回顾性分析。在本研究中,我们采用文献计量分析和 CiteSpace 软件对该领域发表的文章进行了定量和直观分析。首先,我们对过去 52 年的作者和机构发表的文章进行了定量分析,以阐明水凝胶生物医学应用的基本发展状况。其次,我们对高频词、爆炸性词、关键词聚类等进行了直观研究,以了解各个时期主要研究热点的方向性和演变情况。值得注意的是,我们的研究结果强调,将水凝胶制成促进伤口愈合的敷料成为应用领域的一个突出热点。我们希望本文能激发研究人员的新思路,推动水凝胶在生物医学中的应用。
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引用次数: 0
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Journal of Biological Engineering
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