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The metabolic mechanism of growth inhibition by co-culture of Bacteroides xylanisolvens Y-11 and Bifidobacterium longum y37 溶木拟杆菌Y-11与长双歧杆菌y37共培养抑制生长的代谢机制
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-04-01 DOI: 10.2478/ebtj-2023-0008
Lei Tian, D. Luo, Rui Li, Pengrui Jiao, Zhiwei Zhou, Robert S Marks, Qun Sun
Abstract Bacteroides xylanisolvens Y-11 and Bifidobacterium longum y37 isolated from human gut were found to inhibit each other's growth after co-culturing in previous studies. To further reveal the potential mechanism of mutual inhibition between them, ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to investigate the metabolic changes of the strains after monoculture and co-culture, and the key differential metabolites were subject to the validation. The results showed that the types and amounts of metabolites were significantly changed during co-culture, with hydrocarbons and their derivatives, organic acids and esters being the main differential metabolites, which posed a greater influence on the metabolism of B. xylanisolvens Y-11 than on B. longumy y37. Further studies suggest that cycloserine and succinic acid may be the main metabolites that inhibit the growth of both strains, and the decrease of pH may be the main reason for succinic acid to inhibit the growth of the two strains. Moreover, B. longum y37 played a dominant role in the co-culture and its metabolites influenced the growth of B. xylanisolvens Y-11 to a greater extent. This study provides a new perspective for further understanding of the interaction between intestinal microbes and the influence of intestinal microecology on the occurrence and development of diseases.
摘要从人肠道分离得到的木聚糖溶性拟杆菌Y-11和长双歧杆菌y37在共同培养后发现相互抑制生长。为了进一步揭示它们之间相互抑制的潜在机制,使用超高效液相色谱-串联质谱法(UPLC-MS/MS)研究了菌株单培养和共培养后的代谢变化,并对关键的差异代谢产物进行了验证。结果表明,在共培养过程中,代谢产物的类型和数量发生了显著变化,其中碳氢化合物及其衍生物、有机酸和酯是主要的差异代谢产物,这对木聚糖酶Y-11的代谢影响大于对长木聚糖酶y37的影响。进一步的研究表明,环丝氨酸和琥珀酸可能是抑制两株菌株生长的主要代谢产物,pH值的降低可能是琥珀酸抑制两株生长的主要原因。此外,B.longum y37在共培养中起主导作用,其代谢产物在更大程度上影响了B.xylonisolvens Y-11的生长。这项研究为进一步了解肠道微生物之间的相互作用以及肠道微生态对疾病发生和发展的影响提供了新的视角。
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引用次数: 0
Insilico Screening for Identification of Hits against SARS-Cov-2 Variant of Concern B.1.617 and NSP12 Mutants by Molecular Docking and Simulation Studies 关注B.1.617和NSP12突变体对SARS-Cov-2变体的分子对接和模拟研究
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-04-01 DOI: 10.2478/ebtj-2023-0009
Vinuthna Vani Madishetti, Sudhakar Reddy, S. Kalagara, Ashish Garg, Sreenivas Enaganti, Sardar Hussain
Abstract Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV), also known as SARS-CoV-2, have caused global epidemics with high morbidity and mortality. Active research on finding effective drugs against 2019-nCoV/SARS-CoV-2 is going on. In silico screening represents the best approach for hits identification and could shorten the time and reduce cost compared to de novo drug discovery. Recently, CoV2 mutations have been a big concern in India, particularly on non-structural proteins (NSPs) and Spike Protein (B.1.617) which are the key targets that play a pivotal role in mediating viral replication and transcription. Herein, this study analyzed the NSPs and spike’s structural aspects of mutant strains of SARS-CoV-2. The three-dimensional structures of NSPs and S Spike proteins were retrieved from the protein data bank or modeled. And a dataset of an antiviral compound library containing 490,000 drug-like ligands and structurally diverse biologically active scaffolds was used for our studies. Initially, the molecular alignment was performed for library compounds with the reference drug molecule to find targets that match the field points. Antiviral compounds having a similarity score >0.6; were selected for further docking studies with wild and mutant NSPs and S Spike protein of SARS-CoV-2 variant B.1.617. The docking studies identified a potent analog MA-11, which exhibited the highest binding affinity towards wild and mutant proteins. Further, molecular dynamics simulation studies of selected compounds confirmed their perfect fitting into NSP12 and spike active sites and offer direction for further lead optimization and rational drug design.
摘要人类冠状病毒(HCoV),包括严重急性呼吸综合征冠状病毒(SARS-CoV)和2019年新型冠状病毒(2019-nCoV)(也称为SARS-CoV-2),已导致全球高发病率和高死亡率流行病。正在积极研究寻找对抗2019-nCoV/SARS-CoV-2的有效药物。电子筛查是识别命中率的最佳方法,与从头发现药物相比,可以缩短时间并降低成本。最近,CoV2突变在印度引起了很大的关注,特别是在非结构蛋白(NSPs)和刺突蛋白(B.1.617)上,它们是在介导病毒复制和转录中发挥关键作用的关键靶点。在此,本研究分析了严重急性呼吸系统综合征冠状病毒2型变异株的NSPs和刺突的结构方面。从蛋白质数据库中检索或建模NSPs和S刺突蛋白的三维结构。我们的研究使用了一个抗病毒化合物库的数据集,该库包含49万个类药物配体和结构多样的生物活性支架。最初,对文库化合物与参考药物分子进行分子比对,以找到与场点匹配的靶标。相似性得分大于0.6的抗病毒化合物;被选择用于与野生和突变NSP以及严重急性呼吸系统综合征冠状病毒2变种B.1.617的S刺突蛋白进行进一步对接研究。对接研究确定了一种有效的类似物MA-11,它对野生和突变蛋白表现出最高的结合亲和力。此外,对所选化合物的分子动力学模拟研究证实了它们与NSP12和刺突活性位点的完美匹配,并为进一步的先导优化和合理的药物设计提供了方向。
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引用次数: 0
Biotechnological Approaches to Generate Biogenic Solvents and Energy Carriers from Renewable Resources 从可再生资源生产生物溶剂和能源载体的生物技术方法
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-04-01 DOI: 10.2478/ebtj-2023-0007
M. Koller
Abstract Background: Current threats connected to the ongoing depletion of fossil resources and elevated levels of greenhouse gases accelerating climate change and global warming provoke a renaissance of biotechnological production of various organic bulk chemicals, which, particularly during the second half of the 20th century, were almost exclusively produced from fossil resources via chemosynthetic processes. Scope: Besides the manufacture of bioethanol, a product obtained by microbial fermentation, biogenic production of solvents and energy carriers like acetone, isopropanol, 2,3-butanediol, or 1-butanol, hence, processes known since the beginning of the last century, experiences now a substantial revival. Summary of new synthesis and conclusions reached in the review: The review illustrates how to produce these products by resorting to fossil raw materials instead of petrochemical production processes, and how this can be accomplished by the cultivation of anaerobic organisms, namely facultatively anaerobic yeasts and bacteria (production of ethanol or 2,3-butanediol), and strictly anaerobic Clostridia (1-butanol, acetone, or isopropanol) on renewable resources. Moreover, novel methods for producing biodiesel-like methyl-esters of aerobically produced bacterial polyhydroxyalkanoate biopolyester building blocks combine the synthesis of microbial biopolyesters from wastewater with the progress of innovative renewable energy carriers. The biochemical background, the current state of research and development, and the status of industrialization of these processes are reviewed. Conclusion: Challenges to make these bioprocesses, based on inexpensive renewable resources, competitive with or even superior to petrochemical production routes in terms of sustainability, scalability, and economic feasibility still exist: however, they can be overcome by the concerted action of various scientific disciplines.
背景:当前化石资源的持续枯竭和温室气体水平的升高加速了气候变化和全球变暖,这些威胁引发了生物技术生产各种有机散装化学品的复兴,特别是在20世纪下半叶,这些化学品几乎完全是通过化学合成过程从化石资源中生产的。经营范围:除微生物发酵生产生物乙醇外,生物生产溶剂和能量载体,如丙酮、异丙醇、2,3-丁二醇或1-丁醇,因此,自上世纪初以来已知的工艺,现在经历了实质性的复兴。新合成综述及结论:综述阐述了如何利用化石原料代替石油化工生产工艺来生产这些产品,以及如何通过培养厌氧生物,即兼性厌氧酵母和细菌(生产乙醇或2,3-丁二醇)和严格厌氧梭菌(生产1-丁醇、丙酮或异丙醇)来实现这一目标。此外,好氧产生的细菌聚羟基烷酸酯生物聚酯构件生产生物柴油类甲酯的新方法将从废水中合成微生物生物聚酯与创新可再生能源载体的进展相结合。综述了这些工艺的生物化学背景、研究与发展现状以及产业化现状。结论:使这些基于廉价可再生资源的生物工艺在可持续性,可扩展性和经济可行性方面与石化生产路线竞争甚至优于石化生产路线的挑战仍然存在:然而,通过各科学学科的协调行动可以克服这些挑战。
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引用次数: 0
European Biotechnology Congress 2022 - Oral Presentation Abstracts 2022年欧洲生物技术大会-口头演讲摘要
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-01-01 DOI: 10.2478/ebtj-2023-0003
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引用次数: 0
European Biotechnology Congress 2022 - Poster Presentation Abstracts 欧洲生物技术大会2022 -海报介绍摘要
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-01-01 DOI: 10.2478/ebtj-2023-0004
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引用次数: 0
European Biotechnology Congress 2022 - Invited Speaker Abstracts 2022年欧洲生物技术大会-特邀演讲人摘要
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-01-01 DOI: 10.2478/ebtj-2023-0002
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引用次数: 0
Structure of PAP-IgM FcK fusion protein with J-chain expressed in transgenic plant J链PAP-IgM-FcK融合蛋白在转基因植物中表达的结构
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-01-01 DOI: 10.2478/ebtj-2023-0006
Y. Kang, Deuk‐Su Kim, Kibum Kim, S. Myung, Y. J. Oh, Sungsu Park, P. Hinterdorfer, K. Ko
Abstract Transgenic plants expressing immunoglobulin (Ig) M Fc-fused Prostate acid phosphatase (PAP) antigenic proteins (PAP-IgM FcK) and J-chain proteins were generated by Agrobacterium-mediated transformation. The Fc region was tagged with the ER retention motif (KDEL) to make PAP-IgM FcK. Two transgenic plants were crossed together to generate F1 expressing both PAP-IgM FcK and J-chain proteins (PAP-IgM FcK × J-chain). PCR and RT-PCR analyses confirmed the transgene insertion and mRNA transcription of PAP-IgM FcK and J-chain in leaf tissue of PAP-IgM FcK × J-chain F1 plant. Western blot confirmed the expression of PAP-IgM FcK × J-chain protein. Size exclusion (SEC)-high performance liquid chromatography (HPLC) and Bio-transmission electron microscope (TEM) analyses were performed to show the size and shape of the PAP- IgM FcK × J-chain fusion proteins. These results suggest that PAP-IgM FcK with J-chain can be produced in plant expression system with plant crossing.
摘要通过农杆菌介导的转化,获得了表达免疫球蛋白(Ig)M-Fc融合的前列腺酸性磷酸酶(PAP)抗原蛋白(PAP-IgM-FcK)和J链蛋白的转基因植物。Fc区域用ER保留基序(KDEL)标记以制备PAP-IgM-FcK。将两个转基因植物杂交在一起以产生表达PAP-IgM-FcK和J链蛋白的F1(PAP-IgM-FcK×J链)。PCR和RT-PCR分析证实了PAP-IgM-FcK和J链在F1植株叶片组织中的转基因插入和mRNA转录。蛋白质印迹证实PAP-IgM-FcK×J链蛋白的表达。通过大小排阻(SEC)-高效液相色谱(HPLC)和生物透射电子显微镜(TEM)分析显示了PAP-IgM-FcK×J链融合蛋白的大小和形状。这些结果表明,具有J链的PAP-IgM-FcK可以在具有植物杂交的植物表达系统中产生。
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引用次数: 2
Silk Fibroin Hybrids for Biological Scaffolds with Adhesive Surface and Adaptability to the Target Tissue Change 具有粘附表面和对目标组织变化适应性的生物支架用丝素蛋白杂交种
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2023-01-01 DOI: 10.2478/ebtj-2023-0005
S. Ciabattini, V. Raggi, L. Valentini, A. Morabito
Abstract Background Regenerative Medicine (RM) is a branch of medicine that aims to regenerate tissues and organs to overcome the problems transplants entail (poor availability, risk of rejection and intense immunosuppression). To do this, RM makes use of tissue engineering (TE). This fundamental branch deals with creating biological scaffolds capable of performing the role that physiologically belongs to the extracellular matrix (ECM). In this review, we report how specific characteristics of the scaffolds (bio-compatibility, biodegradability and mechanical and conformal properties) can be obtained using 3D printing, which facilitates the emulation of physiological tissues and organs. Purpose and scope This review reports recent advances in the fabrication method of bioactive scaffolds that can be used clinically, providing support for cell seeding and proliferation. To this end, silk fibroin, tannin and graphene were used to improve the scaffold’s electro-bio-mechanical properties. These materials in different compositions are studied to demonstrate their potential use as bio-ink in bioadhesives and cellularized and implantable 3D-printed scaffolds. Summary of new synthesis and conclusions reached in the review Silk fibroin is a natural biopolymer; tannin, on the other hand, is a biological polyphenol, highly reactive with other molecules by nature and with promising antioxidant capabilities. Finally, graphene is nothing more than a monolayer of graphite that has been shown to implement the mechanics and electrical conductivity of the compounds in which it is inserted; it also has excellent biocompatibility and surface area, qualities that promote cell adhesion and growth. Conclusion Polyphenols and graphene have been shown to work in synergy in improving the electro-mechanical properties of silk fibroin scaffolds. We reported optimal and potentially market-competitive bioadhesives, but above all, the proliferation of neuronal precursor cells in vitro was successfully demonstrated.
再生医学(RM)是医学的一个分支,旨在再生组织和器官,以克服移植所带来的问题(可获得性差,排斥风险和强烈的免疫抑制)。为了做到这一点,RM利用组织工程(TE)。这一基本分支涉及创造能够发挥生理上属于细胞外基质(ECM)作用的生物支架。在这篇综述中,我们报告了如何使用3D打印获得支架的特定特性(生物相容性,生物降解性以及机械和保形性能),从而促进生理组织和器官的模拟。目的与范围本文综述了近年来临床应用的生物活性支架的制备方法,为细胞的播种和增殖提供支持。为此,使用丝素、单宁和石墨烯来改善支架的电-生物力学性能。研究人员对这些不同成分的材料进行了研究,以证明它们在生物粘合剂和细胞化和可植入的3d打印支架中作为生物墨水的潜在用途。丝素蛋白是一种天然的生物高聚物。另一方面,单宁是一种生物多酚,与其他分子具有高度活性,具有良好的抗氧化能力。最后,石墨烯只不过是一层石墨,已经被证明可以实现它所插入的化合物的力学和导电性;它还具有良好的生物相容性和表面积,促进细胞粘附和生长的品质。结论多酚和石墨烯在改善丝素蛋白支架的机电性能方面具有协同作用。我们报告了最佳的和具有潜在市场竞争力的生物粘合剂,但最重要的是,神经前体细胞的体外增殖被成功证明。
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引用次数: 1
Ocular Biocompatibility of a Nitinol Capsular Tension Ring (CTR) 镍钛诺胶囊张力环(CTR)的眼生物相容性
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2022-10-01 DOI: 10.2478/ebtj-2022-0016
Javier S Martinez de Aragon, J. Villada, J. Ruiz-Moreno
Abstract Introduction: The biocompatibility of nitinol in the human body has extensively been demonstrated. Although nitinol is already being used for intraocular surgeries such as lens fragmentation and foreign body extraction, little is known about its intracapsular, long-term behavior. The purpose of this study is to evaluate the long-term uveal and capsular biocompatibility of a nitinol CTR placed in the capsular bag after cataract surgery in an animal model. Method: After approval of the study by the Institutional Animal Care and the Ethics Committee, bilateral phacoemulsification was performed in 6 rabbits; 1 eye received a nitinol CTR and the other a control polymethylmethacrylate (PMMA) open-ended ring. Ophthalmic evaluation for the presence of infections in all 12 eyes was performed after 7 days, 4 weeks, 3 months, and 6 months follow-up period. After a follow-up period of 6 months, the eyes were enucleated, and a histopathologic evaluation was performed. Results: Neither of the groups showed any clinical signs of posterior capsule opacification (PCO) or inflammation. The nitinol group showed slightly less inflammation during histopathologic examination compared to the PMMA group. No biocompatibility issues have been observed in this animal study. Conclusions: There were no histological differences between eyes implanted with nitinol and eyes implanted with PMMA rings. Nitinol has proven to show high biocompatibility when implanted in the capsular bag of the rabbit eye.
摘要简介:镍钛诺在人体内的生物相容性已得到广泛证明。尽管镍钛诺已经被用于眼内手术,如晶状体破碎和异物提取,但人们对其在囊内的长期行为知之甚少。本研究的目的是在动物模型中评估白内障手术后放置在囊袋中的镍钛诺CTR的长期葡萄膜和囊的生物相容性。方法:在动物护理机构和伦理委员会批准该研究后,对6只兔子进行双侧超声乳化;1只眼睛接受镍钛诺CTR,另一只眼睛接受对照聚甲基丙烯酸甲酯(PMMA)开口环。在7天、4周、3个月和6个月的随访期后,对所有12只眼睛是否存在感染进行眼科评估。随访6个月后,摘除眼球,并进行组织病理学评估。结果:两组均未出现任何后囊混浊(PCO)或炎症的临床症状。与PMMA组相比,镍钛诺组在组织病理学检查中显示出轻微的炎症。在这项动物研究中没有观察到生物相容性问题。结论:镍钛诺植入眼与PMMA环植入眼在组织学上无差异。镍钛诺已被证明在植入兔眼的囊袋中时显示出高度的生物相容性。
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引用次数: 0
The Microbially Extended Phenotype of Plants, a Keystone against Abiotic Stress 植物的微生物扩展表型是抵御非生物胁迫的关键
IF 1.7 Q3 MULTIDISCIPLINARY SCIENCES Pub Date : 2022-10-01 DOI: 10.2478/ebtj-2022-0017
Mario X. Ruiz-González, Ó. Vicente
Abstract Background: Climate change affects every region across the globe with heterogeneous effects on local temperatures and precipitation patterns. In plants, sessile organisms, climate change imposes more drastic effects leading to loss of yield or even death. However, plants establish mutualistic interactions with microorganisms that boost plant tolerance against abiotic stresses or strengthen the plant immune system against pathogens, thus, enhancing their survival and fitness. Moreover, in the wild, microbial endophytes provide important ecosystem services. Purpose and scope: Little we know about the mechanisms of response against the adverse effects of climate change on natural populations of wild plants and even less about the potential role played by microbial biostimulants. In this article, we review the effects of biostimulants on plant responses against abiotic stresses, with a particular focus on the role of mycorrhizas and leaf endophytes. Results: We have reviewed the effects of the main abiotic stresses in plants, the mechanisms that plants use to face these abiotic challenges, and the interaction plant-biostimulant-abiotic stress, highlighting the primary responses and parameters to evaluate different plant responses. Conclusion: Abiotic stresses can check the phenotypic plasticity of plants and also trigger a complex and heterogeneous array of responses to face different abiotic stresses, and beneficial microorganisms do play an essential role in enhancing such responses. Our laboratory has initiated a project to characterise microbial populations associated with plants from wild areas and analyse their potential role in aiding the plants to cope with abiotic stresses.
摘要背景:气候变化影响着全球每个地区,对当地温度和降水模式产生了异质性影响。在植物这种固着生物中,气候变化会产生更剧烈的影响,导致产量损失甚至死亡。然而,植物与微生物建立了互惠的相互作用,提高了植物对非生物胁迫的耐受性,或增强了植物对病原体的免疫系统,从而提高了它们的生存和适应性。此外,在野外,微生物内生菌提供重要的生态系统服务。目的和范围:我们对应对气候变化对野生植物自然种群不利影响的机制知之甚少,对微生物生物刺激剂发挥的潜在作用知之甚少。在这篇文章中,我们综述了生物刺激剂对植物对非生物胁迫反应的影响,特别关注菌根和叶片内生菌的作用。结果:我们综述了植物中主要非生物胁迫的影响,植物面对这些非生物挑战的机制,以及植物生物刺激性非生物胁迫之间的相互作用,强调了评估不同植物反应的主要反应和参数。结论:非生物胁迫可以检测植物的表型可塑性,并引发一系列复杂而异质的反应来面对不同的非生物胁迫,而有益微生物在增强这种反应中确实发挥着重要作用。我们的实验室启动了一个项目,以表征与野生地区植物相关的微生物种群,并分析它们在帮助植物应对非生物胁迫方面的潜在作用。
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引用次数: 1
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The EuroBiotech Journal
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