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Gizewski J, V D Sande L, Holtmann D. Contribution of electrobiotechnology to sustainable development goals. Trends Biotechnol 2023; 41:1106-1108. [PMID: 36959083 DOI: 10.1016/j.tibtech.2023.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
The UN Sustainable Development Goals (SDGs) are 17 interlinked goals designed to be a 'shared blueprint for peace and prosperity for people and the planet, now and into the future'. Therefore, global efforts should focus on achieving these. Herein, we discuss the contribution of electrobiotechnology to the realization of the SDGs.
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Affiliation(s)
- Jakub Gizewski
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Lisa V D Sande
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany.
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52
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Trump BD, Cummings CL, Loschin N, Keisler JM, Wells EM, Linkov I. The worsening divergence of biotechnology: the importance of risk culture. Front Bioeng Biotechnol 2023; 11:1250298. [PMID: 37711457 PMCID: PMC10499176 DOI: 10.3389/fbioe.2023.1250298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023] Open
Abstract
In the last 20 years, the field of biotechnology has made significant progress and attracted substantial investments, leading to different paths of technological modernization among nations. As a result, there is now an international divide in the commercial and intellectual capabilities of biotechnology, and the implications of this divergence are not well understood. This raises important questions about why global actors are motivated to participate in biotechnology modernization, the challenges they face in achieving their goals, and the possible future direction of global biotechnology development. Using the framework of prospect theory, this paper explores the role of risk culture as a fundamental factor contributing to this divergence. It aims to assess the risks and benefits associated with the early adoption of biotechnology and the regulatory frameworks that shape the development and acceptance of biotechnological innovations. By doing so, it provides valuable insights into the future of biotechnology development and its potential impact on the global landscape.
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Affiliation(s)
- Benjamin D. Trump
- United States Army Corps of Engineers, Washington, DC, United States
| | - Christopher L. Cummings
- United States Army Corps of Engineers, Washington, DC, United States
- Department of Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, United States
- Department of Sociology, Iowa State University, Ames, IA, United States
| | - Nicholas Loschin
- Department of Genetic Engineering and Society Center, North Carolina State University, Raleigh, NC, United States
| | - Jeffrey M. Keisler
- Department of Management Science & Info Sys, University of Massachusetts Boston, Boston, MA, United States
| | - Emily M. Wells
- United States Army Corps of Engineers, Washington, DC, United States
| | - Igor Linkov
- United States Army Corps of Engineers, Washington, DC, United States
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53
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Choi S, Yang JW, Kim JE, Jeon H, Shin S, Wui D, Kim LS, Kim BJ, Son H, Min K. Infectivity and stress tolerance traits affect community assembly of plant pathogenic fungi. Front Microbiol 2023; 14:1234724. [PMID: 37692392 PMCID: PMC10486888 DOI: 10.3389/fmicb.2023.1234724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/26/2023] [Indexed: 09/12/2023] Open
Abstract
Understanding how ecological communities assemble is an urgent research priority. In this study, we used a community ecology approach to examine how ecological and evolutionary processes shape biodiversity patterns of plant pathogenic fungi, Fusarium graminearum and F. asiaticum. High-throughput screening revealed that the isolates had a wide range of phenotypic variation in stress tolerance traits. Net Relatedness Index (NRI) and Nearest Taxon Index (NTI) values were computed based on stress-tolerant distance matrices. Certain local regions exhibited positive values of NRI and NTI, indicating phenotypic clustering within the fungal communities. Competition assays of the pooled strains were conducted to investigate the cause of clustering. During stress conditions and wheat colonization, only a few strains dominated the fungal communities, resulting in reduced diversity. Overall, our findings support the modern coexistence theory that abiotic stress and competition lead to phenotypic similarities among coexisting organisms by excluding large, low-competitive clades. We suggest that agricultural environments and competition for host infection lead to locally clustered communities of plant pathogenic fungi in the field.
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Affiliation(s)
- Soyoung Choi
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Jung Wook Yang
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jung-Eun Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Hosung Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Soobin Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Dayoun Wui
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Lee Seul Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Byung Joo Kim
- Crop Cultivation and Environment Research Division, National Institute of Crop Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyunghun Min
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
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54
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Trossmann VT, Lentz S, Scheibel T. Factors Influencing Properties of Spider Silk Coatings and Their Interactions within a Biological Environment. J Funct Biomater 2023; 14:434. [PMID: 37623678 PMCID: PMC10455157 DOI: 10.3390/jfb14080434] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Biomaterials are an indispensable part of biomedical research. However, although many materials display suitable application-specific properties, they provide only poor biocompatibility when implanted into a human/animal body leading to inflammation and rejection reactions. Coatings made of spider silk proteins are promising alternatives for various applications since they are biocompatible, non-toxic and anti-inflammatory. Nevertheless, the biological response toward a spider silk coating cannot be generalized. The properties of spider silk coatings are influenced by many factors, including silk source, solvent, the substrate to be coated, pre- and post-treatments and the processing technique. All these factors consequently affect the biological response of the environment and the putative application of the appropriate silk coating. Here, we summarize recently identified factors to be considered before spider silk processing as well as physicochemical characterization methods. Furthermore, we highlight important results of biological evaluations to emphasize the importance of adjustability and adaption to a specific application. Finally, we provide an experimental matrix of parameters to be considered for a specific application and a guided biological response as exemplarily tested with two different fibroblast cell lines.
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Affiliation(s)
- Vanessa T. Trossmann
- Chair of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann-Straße 1, 95447 Bayreuth, Germany; (V.T.T.); (S.L.)
| | - Sarah Lentz
- Chair of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann-Straße 1, 95447 Bayreuth, Germany; (V.T.T.); (S.L.)
| | - Thomas Scheibel
- Chair of Biomaterials, Faculty of Engineering Science, University of Bayreuth, Prof.-Rüdiger-Bormann-Straße 1, 95447 Bayreuth, Germany; (V.T.T.); (S.L.)
- Bayreuth Center for Colloids and Interfaces (BZKG), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bavarian Polymer Institute (BPI), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bayreuth Center for Molecular Biosciences (BZMB), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Bayreuth Materials Center (BayMAT), University of Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany
- Faculty of Medicine, University of Würzburg, Pleicherwall 2, 97070 Würzburg, Germany
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55
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Sloan WT, Gómez-Borraz TL. Engineering biology in the face of uncertainty. Interface Focus 2023; 13:20230001. [PMID: 37303745 PMCID: PMC10251114 DOI: 10.1098/rsfs.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/24/2023] [Indexed: 06/13/2023] Open
Abstract
Combining engineering and biology surely must be a route to delivering solutions to the world's most pressing problems in depleting resources, energy and the environment. Engineers and biologists have long recognized the power in coupling their disciplines and have evolved a healthy variety of approaches to realizing technologies. Yet recently, there has been a movement to narrow the remit of engineering biology. Its definition as 'the application of engineering principles to the design of biological systems' ought to encompass a broad church. However, the emphasis is firmly on construction '…of novel biological devices and systems from standardized artificial parts' within cells. Thus, engineering biology has become synonymous with synthetic biology, despite the many longstanding technologies that use natural microbial communities. The focus on the nuts and bolts of synthetic organisms may be deflecting attention from the significant challenge of delivering solutions at scale, which cuts across all engineering biology, synthetic and natural. Understanding, let alone controlling, every component of an engineered system is an unrealistic goal. To realize workable solutions in a timely manner we must develop systematic ways of engineering biology in the face of the uncertainties that are inherent in biological systems and that arise through lack of knowledge.
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Affiliation(s)
- William T. Sloan
- James Watt School of Engineering, University of Glasgow, Glasgow, UK
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56
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Deng C, Li S, Liu Y, Bao W, Xu C, Zheng W, Wang M, Ma X. Split-Cas9-based targeted gene editing and nanobody-mediated proteolysis-targeting chimeras optogenetically coordinated regulation of Survivin to control the fate of cancer cells. Clin Transl Med 2023; 13:e1382. [PMID: 37620295 PMCID: PMC10449816 DOI: 10.1002/ctm2.1382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Precise regulation of partial critical proteins in cancer cells, such as anti-apoptotic proteins, is one of the crucial strategies for treating cancer and discovering related molecular mechanisms. Still, it is also challenging in actual research and practice. The widely used CRISPR/Cas9-based gene editing technology and proteolysis-targeting chimeras (PROTACs) have played an essential role in regulating gene expression and protein function in cells. However, the accuracy and controllability of their targeting remain necessary. METHODS Construction of UMUC-3-EGFP stable transgenic cell lines using the Sleeping Beauty system, Flow cytometry, quantitative real-time PCR, western blot, fluorescence microplate reader and fluorescence inverted microscope analysis of EGFP intensity. Characterization of Survivin inhibition was done by using Annexin V-FITC/PI apoptosis, calcein/PI/DAPI cell viability/cytotoxicity assay, cloning formation assay and scratch assay. The cell-derived xenograft (CDX) model was constructed to assess the in vivo effects of reducing Survivin expression. RESULTS Herein, we established a synergistic control platform that coordinated photoactivatable split-Cas9 targeted gene editing and light-induced protein degradation, on which the Survivin gene in the nucleus was controllably edited by blue light irradiation (named paCas9-Survivin) and simultaneously the Survivin protein in the cytoplasm was degraded precisely by a nanobody-mediated target (named paProtacL-Survivin). Meanwhile, in vitro experiments demonstrated that reducing Survivin expression could effectively promote apoptosis and decrease the proliferation and migration of bladder cancerous cells. Furthermore, the CDX model was constructed using UMUC-3 cell lines, results from animal studies indicated that both the paCas9-Survivin system and paProtacL-Survivin significantly inhibited tumour growth, with higher inhibition rates when combined. CONCLUSIONS In short, the coordinated regulatory strategies and combinable technology platforms offer clear advantages in controllability and targeting, as well as an excellent reference value and universal applicability in controlling the fate of cancer cells through multi-level regulation of key intracellular factors.
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Affiliation(s)
- Changping Deng
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Shihui Li
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
| | - Yuping Liu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wen Bao
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Chengnan Xu
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Wenyun Zheng
- Shanghai Key Laboratory of New Drug DesignSchool of PharmacyEast China University of Science and TechnologyShanghaiP. R. China
| | - Meiyan Wang
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory BiologyInstitute of BiomedicalSciences and School of Life SciencesEast China Normal UniversityShanghaiP. R. China
| | - Xingyuan Ma
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiP. R. China
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57
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Thakur P, Kumar S. Exploring bioleaching potential of indigenous Bacillus sporothermodurans ISO1 for metals recovery from PCBs through sequential leaching process. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2023; 41:1255-1266. [PMID: 37293749 DOI: 10.1177/0734242x231155102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The low efficiency and selectivity limitations of biohydrometallurgy technique compel the researchers to explore novel microbial strains acclimated to metal existence site with higher toxicity tolerance and bioleaching capability in order to improve the role of bioleaching process for e-waste management. The current study aimed to explore bioleaching potential of indigenous Bacillus sporothermodurans ISO1; isolated from metal habituated site. The statistical approach was utilized to optimize a variety of culture variables including temperature, pH, glycine concentration and pulp density that impact bio-cyanide production and leaching efficiency. The highest dissolution of Cu and Ag, 78% and 37% respectively, was obtained at 40 °C, pH 8, glycine concentration 5 g L-1, and pulp density 10 g L-1 through One Factor at a Time (OFAT), which was further increased up to 95% Cu and 44% Ag recovery through the interactive effect of key factors in the Response Surface Methodology (RSM) approach. Furthermore, Chemo-biohydrometallurgy approach was utilized to overwhelm the specificity limitation; as higher concentration of Cu in computer printed circuit boards (CPCBs) causes interference to recover other metals. The sequential leaching through ferric chloride (FeCl3), recovered Cu prior to bio-cyanidation by B. sporothermodurans ISO1 and resulted in the improved leaching of Ag (57%), Au (67%), Pt (60%), etc. The current work reports on B. sporothermodurans ISO1, a new Bacillus strain that exhibits highest toxicity tolerance (EC50 = 425 g L-1) than earlier reported stains and has higher leaching potential that can be implemented to large-scale biometallurgical process for e-waste treatment to achieve the agenda of sustainable development goal (SDG) under the strategies of urban mining.
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Affiliation(s)
- Pooja Thakur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Sudhir Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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58
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Lefin N, Miranda J, Beltrán JF, Belén LH, Effer B, Pessoa A, Farias JG, Zamorano M. Current state of molecular and metabolic strategies for the improvement of L-asparaginase expression in heterologous systems. Front Pharmacol 2023; 14:1208277. [PMID: 37426818 PMCID: PMC10323146 DOI: 10.3389/fphar.2023.1208277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023] Open
Abstract
Heterologous expression of L-asparaginase (L-ASNase) has become an important area of research due to its clinical and food industry applications. This review provides a comprehensive overview of the molecular and metabolic strategies that can be used to optimize the expression of L-ASNase in heterologous systems. This article describes various approaches that have been employed to increase enzyme production, including the use of molecular tools, strain engineering, and in silico optimization. The review article highlights the critical role that rational design plays in achieving successful heterologous expression and underscores the challenges of large-scale production of L-ASNase, such as inadequate protein folding and the metabolic burden on host cells. Improved gene expression is shown to be achievable through the optimization of codon usage, synthetic promoters, transcription and translation regulation, and host strain improvement, among others. Additionally, this review provides a deep understanding of the enzymatic properties of L-ASNase and how this knowledge has been employed to enhance its properties and production. Finally, future trends in L-ASNase production, including the integration of CRISPR and machine learning tools are discussed. This work serves as a valuable resource for researchers looking to design effective heterologous expression systems for L-ASNase production as well as for enzymes production in general.
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Affiliation(s)
- Nicolás Lefin
- Department of Chemical Engineering, Science and Engineering Faculty, Universidad de La Frontera, Temuco, Chile
| | - Javiera Miranda
- Department of Chemical Engineering, Science and Engineering Faculty, Universidad de La Frontera, Temuco, Chile
| | - Jorge F. Beltrán
- Department of Chemical Engineering, Science and Engineering Faculty, Universidad de La Frontera, Temuco, Chile
| | - Lisandra Herrera Belén
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Santiago, Chile
| | - Brian Effer
- Center of Excellence in Translational Medicine and Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jorge G. Farias
- Department of Chemical Engineering, Science and Engineering Faculty, Universidad de La Frontera, Temuco, Chile
| | - Mauricio Zamorano
- Department of Chemical Engineering, Science and Engineering Faculty, Universidad de La Frontera, Temuco, Chile
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Hartmann FSF, Weiß T, Kastberg LLB, Workman CT, Seibold GM. Precise and versatile microplate reader-based analyses of biosensor signals from arrayed microbial colonies. Front Microbiol 2023; 14:1187228. [PMID: 37389345 PMCID: PMC10303141 DOI: 10.3389/fmicb.2023.1187228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in Corynebacterium glutamicum, or promoter activity using GFP as reporter in Saccharomyces cerevisiae, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in Escherichia coli colonies. Applicability of this novel technique was further demonstrated by assessing redox states in C. glutamicum colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
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Dixit R, Kumar S, Pandey G. Biological approaches for E-waste management: A green-go to boost circular economy. CHEMOSPHERE 2023:139177. [PMID: 37307925 DOI: 10.1016/j.chemosphere.2023.139177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
E-waste is a pressing situation on human due to its complex composition. Although E-waste on one hand has some toxic components but at the same time, it would be a promising business sector. Recycling of E-waste to mine-out valuable metals and other components has opened a chance of business and hence a way towards transformation of linear economy to circular one. Chemical, physical and traditional technologies are holding the position in E-waste recycling sector but sustainability with respect to cost and environmental issues is a major concern associated with these technologies. In order to overcome these gaps, lucrative, environment friendly and sustainable technologies need to be implied. Biological approaches could be a green and clean approach to handle E-waste through sustainable and cost-effective means by considering socio-economic and environmental aspects. This review elaborates biological approaches for E-waste management and advancements in expanse. The novelty covers the environmental and socio-economic impacts of E-waste, solution and further scope of biological approaches, further research and development need in this contour to come up with sustainable recycling process.
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Affiliation(s)
- Rashmi Dixit
- CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagp, 440 020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201 002, India; CSIR- TMD, 3rd Floor, 14, NISCAIR Building, Satsang Vihar Marg, Block A, Qutab Institutional Area, New Delhi, Delhi, 110 016, India
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagp, 440 020, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201 002, India.
| | - Govind Pandey
- Madan Mohan Malaviya University of Technology, Gorakhpur, 273 010, India
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Huang WH, Ding SL, Zhao XY, Li K, Guo HT, Zhang MZ, Gu Q. Collagen for neural tissue engineering: Materials, strategies, and challenges. Mater Today Bio 2023; 20:100639. [PMID: 37197743 PMCID: PMC10183670 DOI: 10.1016/j.mtbio.2023.100639] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
Neural tissue engineering (NTE) has made remarkable strides in recent years and holds great promise for treating several devastating neurological disorders. Selecting optimal scaffolding material is crucial for NET design strategies that enable neural and non-neural cell differentiation and axonal growth. Collagen is extensively employed in NTE applications due to the inherent resistance of the nervous system against regeneration, functionalized with neurotrophic factors, antagonists of neural growth inhibitors, and other neural growth-promoting agents. Recent advancements in integrating collagen with manufacturing strategies, such as scaffolding, electrospinning, and 3D bioprinting, provide localized trophic support, guide cell alignment, and protect neural cells from immune activity. This review categorises and analyses collagen-based processing techniques investigated for neural-specific applications, highlighting their strengths and weaknesses in repair, regeneration, and recovery. We also evaluate the potential prospects and challenges of using collagen-based biomaterials in NTE. Overall, this review offers a comprehensive and systematic framework for the rational evaluation and applications of collagen in NTE.
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Affiliation(s)
- Wen-Hui Huang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Huairou District, Beijing, 101499, PR China
| | - Sheng-Long Ding
- Department of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, PR China
| | - Xi-Yuan Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Huairou District, Beijing, 101499, PR China
| | - Kai Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, PR China
| | - Hai-Tao Guo
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Huairou District, Beijing, 101499, PR China
| | - Ming-Zhu Zhang
- Department of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, PR China
- Corresponding author.
| | - Qi Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Chaoyang District, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Huairou District, Beijing, 101499, PR China
- Corresponding author. Institute of Zoology, Chinese Academy of Sciences, No. 5 of Courtyard 1, Beichen West Road, Chaoyang District, Beijing 100101, PR China.
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Demeester W, De Baets J, Duchi D, De Mey M, De Paepe B. MoBioS: Modular Platform Technology for High-Throughput Construction and Characterization of Tunable Transcriptional Biological Sensors. BIOSENSORS 2023; 13:590. [PMID: 37366955 DOI: 10.3390/bios13060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
All living organisms have evolved and fine-tuned specialized mechanisms to precisely monitor a vast array of different types of molecules. These natural mechanisms can be sourced by researchers to build Biological Sensors (BioS) by combining them with an easily measurable output, such as fluorescence. Because they are genetically encoded, BioS are cheap, fast, sustainable, portable, self-generating and highly sensitive and specific. Therefore, BioS hold the potential to become key enabling tools that stimulate innovation and scientific exploration in various disciplines. However, the main bottleneck in unlocking the full potential of BioS is the fact that there is no standardized, efficient and tunable platform available for the high-throughput construction and characterization of biosensors. Therefore, a modular, Golden Gate-based construction platform, called MoBioS, is introduced in this article. It allows for the fast and easy creation of transcription factor-based biosensor plasmids. As a proof of concept, its potential is demonstrated by creating eight different, functional and standardized biosensors that detect eight diverse molecules of industrial interest. In addition, the platform contains novel built-in features to facilitate fast and efficient biosensor engineering and response curve tuning.
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Affiliation(s)
- Wouter Demeester
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Jasmine De Baets
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Dries Duchi
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
| | - Brecht De Paepe
- Centre for Synthetic Biology (CSB), Ghent University, 9000 Ghent, Belgium
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Lioi M, Tengattini S, Bagatin F, Galliani S, Daly S, Massolini G, Temporini C. Development of a rapid, efficient, and reusable magnetic bead-based immunocapture system for recombinant human procollagen type II isolation from yeast fermentation broth. Anal Bioanal Chem 2023:10.1007/s00216-023-04752-1. [PMID: 37246979 DOI: 10.1007/s00216-023-04752-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
Recombinant collagen production, especially using yeasts as expression systems, could represent a promising alternative over traditional extractive methods from animal sources, offering controllable, scalable, and high-quality products. Monitoring the efficiency and efficacy of procollagen/collagen expression, especially in the initial fermentation phases, can be difficult and time consuming, as biological matrices necessitate purification and commonly used analytical methods are only partially informative. We propose a straightforward, efficient, and reusable immunocapture system able to specifically isolate human procollagen type II from fermentation broths and to release it in few experimental steps. A recovered sample allows for a detailed characterization providing information on structural identity and integrity, which can strongly support the monitoring of fermentation processes. The immunocapture system relies on the use of protein A-coated magnetic beads which have been functionalized and cross-linked with a human anti-procollagen II antibody (average immobilization yield of 97.7%) to create a stable and reusable support for the specific procollagen fishing. We set up the binding and release conditions ensuring specific and reproducible binding with a synthetic procollagen antigen. The absence of non-specific interaction with the support and binding specificity was demonstrated, and the latter was also confirmed by a peptide mapping epitope study in reversed-phase liquid chromatography high-resolution mass spectrometry (RP-LC-HRMS). The bio-activated support proved to be reusable and stable over 21 days from the initial use. Finally, the system was successfully tested on a raw yeast fermentation sample to provide a proof of concept of the applicability within recombinant collagen production.
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Affiliation(s)
- Martina Lioi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Sara Tengattini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Francesca Bagatin
- Gnosis By Lesaffre, Via Lavoratori Autobianchi 1, 20832, Desio, Italy
| | - Stefano Galliani
- Gnosis By Lesaffre, Via Lavoratori Autobianchi 1, 20832, Desio, Italy
| | - Simona Daly
- Gnosis By Lesaffre, Via Lavoratori Autobianchi 1, 20832, Desio, Italy
| | - Gabriella Massolini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Caterina Temporini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy.
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64
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Puiman L, Almeida Benalcázar E, Picioreanu C, Noorman HJ, Haringa C. Downscaling Industrial-Scale Syngas Fermentation to Simulate Frequent and Irregular Dissolved Gas Concentration Shocks. Bioengineering (Basel) 2023; 10:bioengineering10050518. [PMID: 37237589 DOI: 10.3390/bioengineering10050518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023] Open
Abstract
In large-scale syngas fermentation, strong gradients in dissolved gas (CO, H2) concentrations are very likely to occur due to locally varying mass transfer and convection rates. Using Euler-Lagrangian CFD simulations, we analyzed these gradients in an industrial-scale external-loop gas-lift reactor (EL-GLR) for a wide range of biomass concentrations, considering CO inhibition for both CO and H2 uptake. Lifeline analyses showed that micro-organisms are likely to experience frequent (5 to 30 s) oscillations in dissolved gas concentrations with one order of magnitude. From the lifeline analyses, we developed a conceptual scale-down simulator (stirred-tank reactor with varying stirrer speed) to replicate industrial-scale environmental fluctuations at bench scale. The configuration of the scale-down simulator can be adjusted to match a broad range of environmental fluctuations. Our results suggest a preference for industrial operation at high biomass concentrations, as this would strongly reduce inhibitory effects, provide operational flexibility and enhance the product yield. The peaks in dissolved gas concentration were hypothesized to increase the syngas-to-ethanol yield due to the fast uptake mechanisms in C. autoethanogenum. The proposed scale-down simulator can be used to validate such results and to obtain data for parametrizing lumped kinetic metabolic models that describe such short-term responses.
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Affiliation(s)
- Lars Puiman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Eduardo Almeida Benalcázar
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
| | - Cristian Picioreanu
- Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Henk J Noorman
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
- Royal DSM, Alexander Fleminglaan 1, 2613 Delft, The Netherlands
| | - Cees Haringa
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 Delft, The Netherlands
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65
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Caringella G, Bandiera L, Menolascina F. Recent advances, opportunities and challenges in cybergenetic identification and control of biomolecular networks. Curr Opin Biotechnol 2023; 80:102893. [PMID: 36706519 DOI: 10.1016/j.copbio.2023.102893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Cybergenetics is a new area of research aimed at developing digital and biological controllers for living systems. Synthetic biologists have begun exploiting cybergenetic tools and platforms to both accelerate the development of mathematical models and develop control strategies for complex biological phenomena. Here, we review the state of the art in cybergenetic identification and control. Our aim is to lower the entry barrier to this field and foster the adoption of methods and technologies that will accelerate the pace at which Synthetic Biology progresses toward applications.
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Affiliation(s)
- Gianpio Caringella
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Lucia Bandiera
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EH9 3DW, UK; Centre for Engineering Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK.
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66
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Zurier HS, Goddard JM. A high-throughput expression and screening platform for applications-driven PETase engineering. Biotechnol Bioeng 2023; 120:1000-1014. [PMID: 36575047 DOI: 10.1002/bit.28319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Abstract
The environmental consequences of plastic waste have impacted all kingdoms of life in terrestrial and aquatic ecosystems. However, as the burden of plastic pollution has increased, microbes have evolved to utilize anthropogenic polymers as nutrient sources. Of depolymerase enzymes, the best characterized is PETase, which hydrolyzes aromatic polyesters. PETase engineering has made impressive progress in recent years; however, further optimization of engineered PETase toward industrial application has been limited by lower throughput techniques used in protein purification and activity detection. Here, we address these deficiencies through development of a higher-throughput PETase engineering platform. Secretory expression via YebF tagging eliminates lysis and purification steps, facilitating production of large mutant libraries. Fluorescent detection of degradation products permits rapid screening of depolymerase activity in microplates as opposed to serial chromatographic methods. This approach enabled development of more stable PETase, semi-rational (SR) PETase variant containing previously unpublished mutations. SR-PETase releases 1.9-fold more degradation products and has up to 7.4-fold higher activity than wild-type PETase over 10 days at 40°C. These methods can be adapted to a variety of chemical environments, enabling screening of PETase mutants in applications-relevant conditions. Overall, this work promises to facilitate advancements in PETase engineering toward industrial depolymerization of plastic waste.
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Affiliation(s)
- Hannah S Zurier
- Department of Food Science and Technology, Cornell University, Ithaca, New York, USA
| | - Julie M Goddard
- Department of Food Science and Technology, Cornell University, Ithaca, New York, USA
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67
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Philp J. Bioeconomy and net-zero carbon: lessons from Trends in Biotechnology, volume 1, issue 1. Trends Biotechnol 2023; 41:307-322. [PMID: 36272819 DOI: 10.1016/j.tibtech.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Many biotechnology applications tend to be for low production volumes and relatively high-value products such as insulin and vaccines. More difficult to perfect at scale are bioprocesses for high-volume products with lower value, especially if the target product is a reduced chemical such as a solvent or a plastic. Historically, industrial microbiology succeeded under special circumstances when fossil feedstocks were either unavailable or expensive. Inevitably, as these circumstances relaxed, bioprocesses struggled to compete with petrochemistry. Why try to compete? Fossil resources will be phased out in the coming decades in the struggle with climate change. To reach net-zero carbon by 2050 will require all sectors to transition, not only energy and transportation. This may herald a new opportunity for industrial bioprocesses with much better tools.
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Affiliation(s)
- Jim Philp
- Organization for Economic Cooperation and Development (OECD), Paris, France.
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68
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Dupuis JH, Cheung LKY, Newman L, Dee DR, Yada RY. Precision cellular agriculture: The future role of recombinantly expressed protein as food. Compr Rev Food Sci Food Saf 2023; 22:882-912. [PMID: 36546356 DOI: 10.1111/1541-4337.13094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Cellular agriculture is a rapidly emerging field, within which cultured meat has attracted the majority of media attention in recent years. An equally promising area of cellular agriculture, and one that has produced far more actual food ingredients that have been incorporated into commercially available products, is the use of cellular hosts to produce soluble proteins, herein referred to as precision cellular agriculture (PCAg). In PCAg, specific animal- or plant-sourced proteins are expressed recombinantly in unicellular hosts-the majority of which are yeast-and harvested for food use. The numerous advantages of PCAg over traditional agriculture, including a smaller carbon footprint and more consistent products, have led to extensive research on its utility. This review is the first to survey proteins currently being expressed using PCAg for food purposes. A growing number of viable expression hosts and recent advances for increased protein yields and process optimization have led to its application for producing milk, egg, and muscle proteins; plant hemoglobin; sweet-tasting plant proteins; and ice-binding proteins. Current knowledge gaps present research opportunities for optimizing expression hosts, tailoring posttranslational modifications, and expanding the scope of proteins produced. Considerations for the expansion of PCAg and its implications on food regulation, society, ethics, and the environment are also discussed. Considering the current trajectory of PCAg, food proteins from any biological source can likely be expressed recombinantly and used as purified food ingredients to create novel and tailored food products.
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Affiliation(s)
- John H Dupuis
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lennie K Y Cheung
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lenore Newman
- Food and Agriculture Institute, University of the Fraser Valley, Abbotsford, British Columbia, Canada
| | - Derek R Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rickey Y Yada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
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69
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Microbial Enzyme Biotechnology to Reach Plastic Waste Circularity: Current Status, Problems and Perspectives. Int J Mol Sci 2023; 24:ijms24043877. [PMID: 36835289 PMCID: PMC9967032 DOI: 10.3390/ijms24043877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The accumulation of synthetic plastic waste in the environment has become a global concern. Microbial enzymes (purified or as whole-cell biocatalysts) represent emerging biotechnological tools for waste circularity; they can depolymerize materials into reusable building blocks, but their contribution must be considered within the context of present waste management practices. This review reports on the prospective of biotechnological tools for plastic bio-recycling within the framework of plastic waste management in Europe. Available biotechnology tools can support polyethylene terephthalate (PET) recycling. However, PET represents only ≈7% of unrecycled plastic waste. Polyurethanes, the principal unrecycled waste fraction, together with other thermosets and more recalcitrant thermoplastics (e.g., polyolefins) are the next plausible target for enzyme-based depolymerization, even if this process is currently effective only on ideal polyester-based polymers. To extend the contribution of biotechnology to plastic circularity, optimization of collection and sorting systems should be considered to feed chemoenzymatic technologies for the treatment of more recalcitrant and mixed polymers. In addition, new bio-based technologies with a lower environmental impact in comparison with the present approaches should be developed to depolymerize (available or new) plastic materials, that should be designed for the required durability and for being susceptible to the action of enzymes.
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70
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Stocker JE, Nozari E, van Vugt M, Jansen A, Jamalabadi H. Network controllability measures of subnetworks: implications for neurosciences. J Neural Eng 2023; 20. [PMID: 36633267 DOI: 10.1088/1741-2552/acb256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Objective:Recent progress in network sciences has made it possible to apply key findings from control theory to the study of networks. Referred to as network control theory, this framework describes how the interactions between interconnected system elements and external energy sources, potentially constrained by different optimality criteria, result in complex network behavior. A typical example is the quantification of the functional role certain brain regions or symptoms play in shaping the temporal dynamics of brain activity or the clinical course of a disease, a property that is quantified in terms of the so-called controllability metrics. Critically though, contrary to the engineering context in which control theory was originally developed, a mathematical understanding of the network nodes and connections in neurosciences cannot be assumed. For instance, in the case of psychological systems such as those studied to understand psychiatric disorders, a potentially large set of related variables are unknown. As such, while the measures offered by network control theory would be mathematically correct, in that they can be calculated with high precision, they could have little translational values with respect to their putative role suggested by controllability metrics. It is therefore critical to understand if and how the controllability metrics estimated over subnetworks would deviate, if access to the complete set of variables, as is common in neurosciences, cannot be taken for granted.Approach:In this paper, we use a host of simulations based on synthetic as well as structural magnetic resonance imaging (MRI) data to study the potential deviation of controllability metrics in sub- compared to the full networks. Specifically, we estimate average- and modal-controllability, two of the most widely used controllability measures in neurosciences, in a large number of settings where we systematically vary network type, network size, and edge density.Main results:We find out, across all network types we test, that average and modal controllability are systematically, over- or underestimated depending on the number of nodes in the sub- and full network and the edge density.Significance:Finally, we provide formal theoretical proof that our observations generalize to any network type and discuss the ramifications of this systematic bias and potential solutions to alleviate the problem.
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Affiliation(s)
- Julia Elina Stocker
- Department of Psychiatry and Psychotherapy, Philipps University of Marburg, Marburg, Germany
| | - Erfan Nozari
- Department of Mechanical Engineering, University of California, Riverside, United States of America.,Department of Electrical and Computer Engineering, University of California, Riverside, United States of America.,Department of Bioengineering, University of California, Riverside, United States of America
| | - Marieke van Vugt
- Bernoulli Institute of Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Groningen, The Netherlands
| | - Andreas Jansen
- Department of Psychiatry and Psychotherapy, Philipps University of Marburg, Marburg, Germany.,Core-Facility Brainimaging, Faculty of Medicine, University of Marburg, Marburg, Germany
| | - Hamidreza Jamalabadi
- Department of Psychiatry and Psychotherapy, Philipps University of Marburg, Marburg, Germany
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71
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The Fashion Industry Needs Microbiology: Opportunities and Challenges. mSphere 2023; 8:e0068122. [PMID: 36744949 PMCID: PMC10117041 DOI: 10.1128/msphere.00681-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The fashion industry is the second most polluting industry in the world, representing a 2 trillion dollars and growing valuation. Fashion design practices have been perpetuating an industrial-focused approach, which relies mostly in the economic improvement through fast cycles of product development. Additionally, the fashion industry has also been closed to either multidisciplinary or transdisciplinary initiatives outside the scope of the artistic disciplines. Therefore, innovative approaches are needed to solve fashion industrial challenges. One of the most promising fields to tackle current environmental and technological problems in the fashion industry is microbiology. Through the emergent field of synthetic biology, the number of tools and approaches available is increasing and they can already be seen in niche applications. Despite the current advances and urgent need for change, there is still a long way until a more sustainable fashion industry is achieved.
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72
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Gravity-driven microfluidic device placed on a slow-tilting table enables constant unidirectional perfusion culture of human induced pluripotent stem cells. J Biosci Bioeng 2023; 135:151-159. [PMID: 36586792 DOI: 10.1016/j.jbiosc.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022]
Abstract
Gravity-driven microfluidics, which utilizes gravity force to drive liquid flow, offers portability and multi-condition setting flexibility because they do not require pumps or connection tubes to drive the flow. However, because the flow rate decreases with time in gravity-driven microfluidics, it is not suitable for stem cell experiments, which require long-term (at least a day) stability. In this study, gravity-driven microfluidics and a slow-tilting table were developed to culture cells under constant unidirectional perfusion. The microfluidic device was placed on a slow-tilting table, which tilts unidirectionally at a rate of approximately 7° per day to compensate for the reduction in the flow rate. Computational simulations showed that the pulsation of the flow arising from the stepwise movement of the table was less than 0.2%, and the flow was laminar. Hydrophilization of the tanks increased the flow rate, which is consistent with the theoretical values. We showed that vitronectin is better than laminin 511 fragments as a coating material for adhering human induced pluripotent stem cells on a microchamber made of polydimethylsiloxane, and succeeded in culturing the cells for 3 days. It is believed that the system offers easy-to-use cell culture tools, such as conventional multiwell culture vessels, and enables the control of the cell microenvironment.
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73
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Cell-free protein synthesis systems for vaccine design and production. Curr Opin Biotechnol 2023; 79:102888. [PMID: 36641905 DOI: 10.1016/j.copbio.2022.102888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Vaccines are vital for protection against existing and emergent diseases. Current vaccine production strategies are limited by long production times, risky viral material, weak immunogenicity, and poor stability, ultimately restricting the safe or rapid production of vaccines for widespread utilization. Cell-free protein synthesis (CFPS) systems, which use extracted transcriptional and translational machinery from cells, are promising tools for vaccine production because they can rapidly produce proteins without the constraints of living cells, have a highly optimizable open system, and can be used for on-demand biomanufacturing. Here, we review how CFPS systems have been explored for the production of subunit, conjugate, virus-like particle (VLP), and membrane-augmented vaccines and as a tool in vaccine design. We also discuss efforts to address potential limitations with CFPS such as the presence of endotoxins, poor protein folding, reaction stability, and glycosylation to enable promising future vaccine design and production.
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74
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Jung KJ, Rasor BJ, Rybnicky GA, Silverman AD, Standeven J, Kuhn R, Granito T, Ekas HM, Wang BM, Karim AS, Lucks JB, Jewett MC. At-home, cell-free synthetic biology education modules for transcriptional regulation and environmental water quality monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523248. [PMID: 36711593 PMCID: PMC9881948 DOI: 10.1101/2023.01.09.523248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
As the field of synthetic biology expands, the need to grow and train science, technology, engineering, and math (STEM) practitioners is essential. However, the lack of access to hands-on demonstrations has led to inequalities of opportunity and practice. In addition, there is a gap in providing content that enables students to make their own bioengineered systems. To address these challenges, we develop four shelf-stable cell-free biosensing educational modules that work by just-adding-water and DNA to freeze-dried crude extracts of Escherichia coli . We introduce activities and supporting curricula to teach the structure and function of the lac operon, dose-responsive behavior, considerations for biosensor outputs, and a 'build-your-own' activity for monitoring environmental contaminants in water. We piloted these modules with K-12 teachers and 130 high school students in their classrooms - and at home - without professional laboratory equipment or researcher oversight. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Kirsten J. Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Blake J. Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Grant A. Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Adam D. Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | | | - Robert Kuhn
- Centennial High School, Roswell, GA 30076, USA
- Fulton County Schools Innovation Academy, Alpharetta, GA 30009, USA
| | | | - Holly M. Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Brenda M. Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ashty S. Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Center for Water Research, Northwestern University, Evanston, IL 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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75
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Trentesaux C, Yamada T, Klein OD, Lim WA. Harnessing synthetic biology to engineer organoids and tissues. Cell Stem Cell 2023; 30:10-19. [PMID: 36608674 DOI: 10.1016/j.stem.2022.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023]
Abstract
The development of an organism depends on intrinsic genetic programs of progenitor cells and their spatiotemporally complex extrinsic environment. Ex vivo generation of organoids from progenitor cells provides a platform for recapitulating and exploring development. Current approaches rely largely on soluble morphogens or engineered biomaterials to manipulate the physical environment, but the emerging field of synthetic biology provides a powerful toolbox to genetically manipulate cell communication, adhesion, and even cell fate. Applying these modular tools to organoids should lead to a deeper understanding of developmental principles, improved organoid models, and an enhanced capability to design tissues for regenerative purposes.
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Affiliation(s)
- Coralie Trentesaux
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Toshimichi Yamada
- Cell Design Institute, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ophir D Klein
- Department of Orofacial Sciences and Program in Craniofacial Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
| | - Wendell A Lim
- Cell Design Institute, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.
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76
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Greene D, Palmer MJ, Relman DA. Motivating Proactive Biorisk Management. Health Secur 2023; 21:46-60. [PMID: 36633603 PMCID: PMC9940813 DOI: 10.1089/hs.2022.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/29/2022] [Accepted: 11/03/2022] [Indexed: 01/13/2023] Open
Abstract
Scholars and practitioners of biosafety and biosecurity (collectively, biorisk management or BRM) have argued that life scientists should play a more proactive role in monitoring their work for potential risks, mitigating harm, and seeking help as necessary. However, most efforts to promote proactive BRM have focused on training life scientists in technical skills and have largely ignored the extent to which life scientists wish to use them (ie, their motivation). In this article, we argue that efforts to promote proactive BRM would benefit from a greater focus on life scientists' motivation. We review relevant literature on life scientists' motivation to practice BRM, offer examples of successful interventions from adjacent fields, and outline ideas for possible interventions to promote proactive BRM, along with strategies for iterative development, testing, and scaling.
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Affiliation(s)
- Daniel Greene
- Daniel Greene, PhD, is a Senior Analyst, Biosafety, Biosecurity & Emerging Technologies, Gryphon Scientific, Takoma Park, MD. Daniel Greene is also a Postdoctoral Fellow, Center for International Security and Cooperation; Stanford University, Stanford, CA
| | - Megan J. Palmer
- Megan J. Palmer, PhD, is Executive Director, Bio Policy & Leadership Initiatives, and an Adjunct Professor, Department of Bioengineering; Stanford University, Stanford, CA
| | - David A. Relman
- David A. Relman, MD, is a Senior Fellow, Center for International Security and Cooperation; Stanford University, Stanford, CA. David A. Relman is also the Thomas C. and Joan M. Merigan Professor, Departments of Medicine, and of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA
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Abstract
Future applications of synthetic biology will rely on deploying engineered cells outside of lab environments for long periods of time. Currently, a significant roadblock to this application is the potential for deactivating mutations in engineered genes. A recently developed method to protect engineered coding sequences from mutation is called Constraining Adaptive Mutations using Engineered Overlapping Sequences (CAMEOS). In this chapter we provide a workflow for utilizing CAMEOS to create synthetic overlaps between two genes, one essential (infA) and one non-essential (aroB), to protect the non-essential gene from mutation and loss of protein function. In this workflow we detail the methods to collect large numbers of related protein sequences, produce multiple sequence alignments (MSAs), use the MSAs to generate hidden Markov models and Markov random field models, and finally generate a library of overlapping coding sequences through CAMEOS scripts. To assist practitioners with basic coding skills to try out the CAMEOS method, we have created a virtual machine containing all the required packages already installed that can be downloaded and run locally.
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Affiliation(s)
- Dominic Y Logel
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Paul R Jaschke
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia.
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.
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78
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Abstract
Synthetic DNA is of increasing demand across many sectors of research and commercial activities. Engineering biology, therapy, data storage and nanotechnology are set for rapid developments if DNA can be provided at scale and low cost. Stimulated by successes in next generation sequencing and gene editing technologies, DNA synthesis is already a burgeoning industry. However, the synthesis of >200 bp sequences remains unaffordable. To overcome these limitations and start writing DNA as effectively as it is read, alternative technologies have been developed including molecular assembly and cloning methods, template-independent enzymatic synthesis, microarray and rolling circle amplification techniques. Here, we review the progress in developing and commercializing these technologies, which are exemplified by innovations from leading companies. We discuss pros and cons of each technology, the need for oversight and regulatory policies for DNA synthesis as a whole and give an overview of DNA synthesis business models.
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79
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Chung SC, Park JS, Jha RK, Kim J, Kim J, Kim M, Choi J, Kim H, Park DH, Gogurla N, Lee TY, Jeon H, Park JY, Choi J, Kim G, Kim S. Engineering Silk Protein to Modulate Polymorphic Transitions for Green Lithography Resists. ACS APPLIED MATERIALS & INTERFACES 2022; 14:56623-56634. [PMID: 36524808 DOI: 10.1021/acsami.2c17843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Silk protein is being increasingly introduced as a prospective material for biomedical devices. However, a limited locus to intervene in nature-oriented silk protein makes it challenging to implement on-demand functions to silk. Here, we report how polymorphic transitions are related with molecular structures of artificially synthesized silk protein and design principles to construct a green-lithographic and high-performative protein resist. The repetition number and ratio of two major building blocks in synthesized silk protein are essential to determine the size and content of β-sheet crystallites, and radicals resulting from tyrosine cleavages by the 193 nm laser irradiation induce the β-sheet to α-helix transition. Synthesized silk is designed to exclusively comprise homogeneous building blocks and exhibit high crystallization and tyrosine-richness, thus constituting an excellent basis for developing a high-performance deep-UV photoresist. Additionally, our findings can be conjugated to design an electron-beam resist governed by the different irradiation-protein interaction mechanisms. All synthesis and lithography processes are fully water-based, promising green lithography. Using the engineered silk, a nanopatterned planar color filter showing the reduced angle dependence can be obtained. Our study provides insights into the industrial scale production of silk protein with on-demand functions.
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Affiliation(s)
- Soon-Chun Chung
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Joon-Song Park
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Rakesh Kumar Jha
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Jieun Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Jinha Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Muyoung Kim
- Department of Plasma Engineering, Korea Institute of Machinery and Materials, Daejeon 34103, Korea
| | - Juwan Choi
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
| | - Hongdeok Kim
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan 15588, Korea
| | - Da-Hye Park
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Narendar Gogurla
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Tae-Yun Lee
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Heonsu Jeon
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Ji-Yong Park
- Department of Energy Systems Research, Ajou University, Suwon 16499, Korea
| | - Joonmyung Choi
- Department of Mechanical Engineering, BK21 FOUR ERICA-ACE Center, Hanyang University, Ansan 15588, Korea
| | - Ginam Kim
- Material Research Center, Samsung Advanced Institute of Technology, Samsung Electronics Co., Ltd., Suwon 16678, Korea
| | - Sunghwan Kim
- Department of Electronic Engineering, Hanyang University, Seoul 04763, Korea
- Department of Biomedical Engineering, Hanyang University, Seoul 04763, Korea
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80
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Bismuth Vanadate (BiVO4) Nanostructures: Eco-Friendly Synthesis and Their Photocatalytic Applications. Catalysts 2022. [DOI: 10.3390/catal13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Green nanotechnology plays an important role in designing environmentally-benign and sustainable synthesis techniques to provide safer products for human health and environments. In this context, the synthesis of bismuth vanadate (BiVO4) nanoparticles (NPs) based on green chemistry principles with the advantages of eco-friendliness, cost-effectiveness, and simplicity has been explored by researchers. Despite the advantages of these synthesis techniques, crucial aspects regarding their repeatability and large-scale production still need to be comprehensively explored. BiVO4 NPs have shown excellent potential in the pharmaceutical industry, cancer therapy, and photocatalysis. BiVO4 particles with monoclinic scheelite structures have been widely investigated for their environmental applications owing to their fascinating optical and electrical properties as well as their high stability and unique crystal structure properties. These NPs with good photostability and resistance to photocorrosion can be considered as promising nanophotocatalysts for degradation of pollutants including organic dyes and pharmaceutical wastes. However, additional explorations should be moved toward the optimization of reaction/synthesis conditions and associated photocatalytic mechanisms. Herein, recent developments regarding the environmentally-benign fabrication of BiVO4 NPs and their photocatalytic degradation of pollutants are deliberated, with a focus on challenges and future directions.
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81
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Mosquera-Romero S, Anaya-Garzon J, Garcia-Timermans C, Van Dorpe J, Hoorens A, Commenges-Bernole N, Verbeken K, Rabaey K, Varia J. Combined Gold Recovery and Nanoparticle Synthesis in Microbial Systems Using Fractional Factorial Design. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 13:83. [PMID: 36615993 PMCID: PMC9824045 DOI: 10.3390/nano13010083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Green synthesis of gold nanoparticles (AuNPs) using microorganisms has been generally studied aiming for high-yield production and morphologies appropriated for various applications, such as bioremediation, (bio)sensors, and (bio)catalysis. Numerous approaches showed the individual effect of factors influencing the synthesis of AuNPs with limited analysis of the governing factors enhancing the production and desired quality of the precipitates. This study proposes a fractional-factorial design to investigate the simultaneous influence of seven environmental factors (cell concentration, temperature, anoxic/oxic conditions, pH, gold concentration, electron donor type, and bacterial species) on the recovery yield and synthesis of targeted AuNPs. Various sizes and morphologies of the AuNPs were obtained by varying the environmental factors studied. The factors with significant effects (i.e., 0.2 mM Au and pH 5) were selected according to statistical analysis for optimal removal of 88.2 ± 3.5% of gold and with the production of valuable 50 nm AuNPs, which are known for their enhanced sensitivity. Implications of the cytochrome-C on the bacterial mechanisms and the provision of electron donors via an electrochemical system are further discussed. This study helps develop gold recovery and nanoparticle synthesis methods, focusing on the determining factor(s) for efficient, low-cost, green synthesis of valuable materials.
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Affiliation(s)
- Suanny Mosquera-Romero
- Center for Microbial Ecology & Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
- ESPOL Polytechnic University, Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias Naturales y Matemáticas, Campus Gustavo Galindo km. 30.5 Vía Perimetral, Guayaquil P.O. Box 09-01-5863, Ecuador
| | - Juan Anaya-Garzon
- Center for Microbial Ecology & Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, Grenoble INP (Institute of Engineering and Management University Grenoble Alpes), LEPMI, 38000 Grenoble, France
| | - Cristina Garcia-Timermans
- Center for Microbial Ecology & Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Anne Hoorens
- Department of Pathology, Ghent University Hospital, Entrance 23, Corneel Heymanslaan 10, B-9000 Ghent, Belgium
| | - Nadine Commenges-Bernole
- University Grenoble Alpes, University Savoie Mont Blanc, CNRS, Grenoble INP (Institute of Engineering and Management University Grenoble Alpes), LEPMI, 38000 Grenoble, France
| | - Kim Verbeken
- Department of Materials, Textiles and Chemical Engineering, Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Gent, Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology & Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
- Centre for Advanced Process Technology for Urban Resource Recovery (CAPTURE), Frieda Saeysstraat 1, B-9000 Ghent, Belgium
| | - Jeet Varia
- Center for Microbial Ecology & Technology (CMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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82
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Przybyłek M, Bełdowski P, Wieland F, Cysewski P, Sionkowska A. Collagen Type II-Chitosan Interactions as Dependent on Hydroxylation and Acetylation Inferred from Molecular Dynamics Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010154. [PMID: 36615345 PMCID: PMC9821911 DOI: 10.3390/molecules28010154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
Chitosan-collagen blends have been widely applied in tissue engineering, joints diseases treatment, and many other biomedical fields. Understanding the affinity between chitosan and collagen type II is particularly relevant in the context of mechanical properties modulation, which is closely associated with designing biomaterials suitable for cartilage and synovial fluid regeneration. However, many structural features influence chitosan's affinity for collagen. One of the most important ones is the deacetylation degree (DD) in chitosan and the hydroxylation degree (HD) of proline (PRO) moieties in collagen. In this paper, combinations of both factors were analyzed using a very efficient molecular dynamics approach. It was found that DD and HD modifications significantly affect the structural features of the complex related to considered types of interactions, namely hydrogen bonds, hydrophobic, and ionic contacts. In the case of hydrogen bonds both direct and indirect (water bridges) contacts were examined. In case of the most collagen analogues, a very good correlation between binding free energy and DD was observed.
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Affiliation(s)
- Maciej Przybyłek
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
- Correspondence: (M.P.); (A.S.)
| | - Piotr Bełdowski
- Institute of Mathematics and Physics, Bydgoszcz University of Science and Technology, al. Kaliskiego 7, 85-796 Bydgoszcz, Poland
- Helmholtz-Zentrum Hereon, Institute for Metallic Biomaterials, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - Florian Wieland
- Helmholtz-Zentrum Hereon, Institute for Metallic Biomaterials, Max-Planck-Straße 1, 21502 Geesthacht, Germany
| | - Piotr Cysewski
- Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
| | - Alina Sionkowska
- Department of Biomaterials and Cosmetics Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarin 7, 87-100 Toruń, Poland
- Correspondence: (M.P.); (A.S.)
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83
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Genome-Wide Analysis of Gene Expression Noise Brought About by Transcriptional Regulation in Pseudomonas aeruginosa. mSystems 2022; 7:e0096322. [PMID: 36377899 PMCID: PMC9765613 DOI: 10.1128/msystems.00963-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The part of expression noise that is brought about by transcriptional regulation (represented here as NTR) is an important criterion for estimating the regulatory mode of a gene. However, characterization of NTR is an under-explored area, and there is little knowledge regarding the genome-wide NTR in the model pathogen Pseudomonas aeruginosa. Here, with a library of dual-color transcriptional reporters, we estimated the NTR for over 90% of the promoters in P. aeruginosa. Most promoters exhibit low NTR, while 42 and 115 promoters with high NTR were screened out in the exponential and the stationary growth phases, respectively. Specifically, a rearrangement of NTR was found in promoters involved in amino acid metabolism when bacteria enter the exponential phase. In addition, during the stationary phase, high NTR was found in a wide range of iron-related promoters involving siderophore synthesis and heme uptake, ExsA-regulated promoters involving bacterial virulence, and FleQ-regulated promoters involving biofilm development. We also found a large-scale negative dependence of transcriptional regulation between high-NTR promoters belonging to different functional categories. Our findings offer a global view of transcriptional heterogeneity in P. aeruginosa. IMPORTANCE The phenotypic diversity of Pseudomonas aeruginosa is frequently observed in research, suggesting that bacteria adopt strategies such as bet-hedging to survive ever-changing environments. Gene expression noise (GEN) is the major source of phenotypic diversity. Large GEN from transcriptional regulation (represented as NTR) represent an evolutionary necessity to maintain the copy number diversity of certain proteins in the population. Here, we provide a system-wide view of NTR in P. aeruginosa under nutrient-rich and stressed conditions. High NTR was found in genes involved in flagella biosynthesis and amino acid metabolism under both conditions. Specially, iron acquisition genes exhibited high NTR in the stressed condition, suggesting a great diversity of iron physiology in P. aeruginosa. We further revealed a global negative dependence of transcriptional regulation between those high-NTR genes under the stressed condition, suggesting a mutually exclusive relationship between different bacterial survival strategies.
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84
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Wang X, Blumenfeld R, Feng XQ, Weitz DA. 'Phase transitions' in bacteria - From structural transitions in free living bacteria to phenotypic transitions in bacteria within biofilms. Phys Life Rev 2022; 43:98-138. [PMID: 36252408 DOI: 10.1016/j.plrev.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
Phase transitions are common in inanimate systems and have been studied extensively in natural sciences. Less explored are the rich transitions that take place at the micro- and nano-scales in biological systems. In conventional phase transitions, large-scale properties of the media change discontinuously in response to continuous changes in external conditions. Such changes play a significant role in the dynamic behaviours of organisms. In this review, we focus on some transitions in both free-living and biofilms of bacteria. Particular attention is paid to the transitions in the flagellar motors and filaments of free-living bacteria, in cellular gene expression during the biofilm growth, in the biofilm morphology transitions during biofilm expansion, and in the cell motion pattern transitions during the biofilm formation. We analyse the dynamic characteristics and biophysical mechanisms of these phase transition phenomena and point out the parallels between these transitions and conventional phase transitions. We also discuss the applications of some theoretical and numerical methods, established for conventional phase transitions in inanimate systems, in bacterial biofilms.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China; John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA.
| | - Raphael Blumenfeld
- Gonville & Caius College, University of Cambridge, Trinity St., Cambridge CB2 1TA, UK
| | - Xi-Qiao Feng
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA; Department of Physics, Harvard University, 9 Oxford St, Cambridge, MA, 02138, USA
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85
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Goncalves AG, Hartzell EJ, Sullivan MO, Chen W. Recombinant protein polymer-antibody conjugates for applications in nanotechnology and biomedicine. Adv Drug Deliv Rev 2022; 191:114570. [PMID: 36228897 DOI: 10.1016/j.addr.2022.114570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/03/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
Currently, there are over 100 antibody-based therapeutics on the market for the treatment of various diseases. The increasing importance of antibody treatment is further highlighted by the recent FDA emergency use authorization of certain antibody therapies for COVID-19 treatment. Protein-based materials have gained momentum for antibody delivery due to their biocompatibility, tunable chemistry, monodispersity, and straightforward synthesis and purification. In this review, we discuss progress in engineering the molecular features of protein-based biomaterials, in particular recombinant protein polymers, for introducing novel functionalities and enhancing the delivery properties of antibodies and related binding protein domains.
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Affiliation(s)
- Antonio G Goncalves
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Emily J Hartzell
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, Newark, DE 19716, United States.
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86
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Angenent SC, Schuttinga JH, van Efferen MFH, Kuizenga B, van Bree B, van der Krieken RO, Verhoeven TJ, Wijffels RH. Hydrogen Oxidizing Bacteria as Novel Protein Source for Human Consumption: An Overview. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2207270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The increasing threat of climate change combined with the prospected growth in the world population puts an enormous pressure on the future demand for sustainable protein sources for human consumption. In this review, hydrogen oxidizing bacteria (HOB) are presented as a novel protein source that could play a role in fulfilling this future demand. HOB are species of bacteria that merely require an inflow of the gasses hydrogen, oxygen, carbon dioxide, and a nitrogen source to grow in a conventional bioreactor. Cupriavidus necator is proposed as HOB for industrial cultivation due to its remarkably high protein content (up to 70% of mass), suitability for cultivation in a bioreactor, and the vast amount of available background information. A broad overview of the unique aspects of the bacteria will be provided, from the production process, amino acid composition, and source of the required gasses to the future acceptance of HOB into the market.
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87
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Zhu J, Li Z, Zou Y, Lu G, Ronca A, D’Amora U, Liang J, Fan Y, Zhang X, Sun Y. Advanced application of collagen-based biomaterials in tissue repair and restoration. JOURNAL OF LEATHER SCIENCE AND ENGINEERING 2022. [DOI: 10.1186/s42825-022-00102-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractIn tissue engineering, bioactive materials play an important role, providing structural support, cell regulation and establishing a suitable microenvironment to promote tissue regeneration. As the main component of extracellular matrix, collagen is an important natural bioactive material and it has been widely used in scientific research and clinical applications. Collagen is available from a wide range of animal origin, it can be produced by synthesis or through recombinant protein production systems. The use of pure collagen has inherent disadvantages in terms of physico-chemical properties. For this reason, a processed collagen in different ways can better match the specific requirements as biomaterial for tissue repair. Here, collagen may be used in bone/cartilage regeneration, skin regeneration, cardiovascular repair and other fields, by following different processing methods, including cross-linked collagen, complex, structured collagen, mineralized collagen, carrier and other forms, promoting the development of tissue engineering. This review summarizes a wide range of applications of collagen-based biomaterials and their recent progress in several tissue regeneration fields. Furthermore, the application prospect of bioactive materials based on collagen was outlooked, aiming at inspiring more new progress and advancements in tissue engineering research.
Graphical Abstract
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88
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Gueta O, Amiram M. Expanding the chemical repertoire of protein-based polymers for drug-delivery applications. Adv Drug Deliv Rev 2022; 190:114460. [PMID: 36030987 DOI: 10.1016/j.addr.2022.114460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 01/24/2023]
Abstract
Expanding the chemical repertoire of natural and artificial protein-based polymers (PBPs) can enable the production of sequence-defined, yet chemically diverse, biopolymers with customized or new properties that cannot be accessed in PBPs composed of only natural amino acids. Various approaches can enable the expansion of the chemical repertoire of PBPs, including chemical and enzymatic treatments or the incorporation of unnatural amino acids. These techniques are employed to install a wide variety of chemical groups-such as bio-orthogonally reactive, cross-linkable, post-translation modifications, and environmentally responsive groups-which, in turn, can facilitate the design of customized PBP-based drug-delivery systems with modified, fine-tuned, or entirely new properties and functions. Here, we detail the existing and emerging technologies for expanding the chemical repertoire of PBPs and review several chemical groups that either demonstrate or are anticipated to show potential in the design of PBP-based drug delivery systems. Finally, we provide our perspective on the remaining challenges and future directions in this field.
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Affiliation(s)
- Osher Gueta
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel
| | - Miriam Amiram
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
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89
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Gajbhiye S, Wairkar S. Collagen fabricated delivery systems for wound healing: A new roadmap. BIOMATERIALS ADVANCES 2022; 142:213152. [PMID: 36270159 DOI: 10.1016/j.bioadv.2022.213152] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Collagen is a biopolymer found in the animal body. It is one of the most abundant proteins in the extracellular matrix that provides strength to the skin, joints, and bones in the human body. It is an important source of elasticity and strength in the extracellular matrix and contributes to the structural and physiological integrity of tissues. Collagen plays an important role in regulating the wound healing process. It helps in wound healing by attracting fibroblasts and encouraging new collagen formation in the wound bed. Therefore, it can be used as a supplementary aid for wound treatment to accelerate the healing process. A prominent benefit of incorporating collagen in wound dressings is its ability to enhance the healing process for critical wounds. Not only collagen but various collagen-containing systems are being prepared to boost its efficacy in wound healing. Different strategies like nanoscale reductions, biopolymers, and incorporating anti-inflammatory and antimicrobial drugs with collagen have been reported. This review article emphasizes the use of collagen for wound healing and various collagen fabricated delivery systems such as nanofibres, nanoparticles, hydrogels, films, and sponges that aid in the healing of wounds.
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Affiliation(s)
- Shruti Gajbhiye
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai, Maharashtra 400056, India
| | - Sarika Wairkar
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKMs NMIMS, V.L. Mehta Road, Vile Parle (W), Mumbai, Maharashtra 400056, India.
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90
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Walter RM, Zemella A, Schramm M, Kiebist J, Kubick S. Vesicle-based cell-free synthesis of short and long unspecific peroxygenases. Front Bioeng Biotechnol 2022; 10:964396. [PMID: 36394036 PMCID: PMC9663805 DOI: 10.3389/fbioe.2022.964396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Unspecific peroxygenases (UPOs, EC 1.11.2.1) are fungal enzymes that catalyze the oxyfunctionalization of non-activated hydrocarbons, making them valuable biocatalysts. Despite the increasing interest in UPOs that has led to the identification of thousands of putative UPO genes, only a few of these have been successfully expressed and characterized. There is currently no universal expression system in place to explore their full potential. Cell-free protein synthesis has proven to be a sophisticated technique for the synthesis of difficult-to-express proteins. In this work, we aimed to establish an insect-based cell-free protein synthesis (CFPS) platform to produce UPOs. CFPS relies on translationally active cell lysates rather than living cells. The system parameters can thus be directly manipulated without having to account for cell viability, thereby making it highly adaptable. The insect-based lysate contains translocationally active, ER-derived vesicles, called microsomes. These microsomes have been shown to allow efficient translocation of proteins into their lumen, promoting post-translational modifications such as disulfide bridge formation and N-glycosylations. In this study the ability of a redox optimized, vesicle-based, eukaryotic CFPS system to synthesize functional UPOs was explored. The influence of different reaction parameters as well as the influence of translocation on enzyme activity was evaluated for a short UPO from Marasmius rotula and a long UPO from Agrocybe aegerita. The capability of the CFPS system described here was demonstrated by the successful synthesis of a novel UPO from Podospora anserina, thus qualifying CFPS as a promising tool for the identification and evaluation of novel UPOs and variants thereof.
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Affiliation(s)
- Ruben Magnus Walter
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
| | - Marina Schramm
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Jan Kiebist
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Potsdam, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry – Biochemistry, Berlin, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus – Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- *Correspondence: Stefan Kubick,
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91
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Pien N, Bray F, Gheysens T, Tytgat L, Rolando C, Mantovani D, Dubruel P, Vlierberghe SV. Proteomics as a tool to gain next level insights into photo-crosslinkable biopolymer modifications. Bioact Mater 2022; 17:204-220. [PMID: 35386456 PMCID: PMC8965084 DOI: 10.1016/j.bioactmat.2022.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/16/2022] [Indexed: 12/25/2022] Open
Abstract
The distribution of photo-crosslinkable moieties onto a protein backbone can affect a biomaterial's crosslinking behavior, and therefore also its mechanical and biological properties. A profound insight in this respect is essential for biomaterials exploited in tissue engineering and regenerative medicine. In the present work, photo-crosslinkable moieties have been introduced on the primary amine groups of: (i) a recombinant collagen peptide (RCPhC1) with a known amino acid (AA) sequence, and (ii) bovine skin collagen (COL BS) with an unknown AA sequence. The degree of substitution (DS) was quantified with two conventional techniques: an ortho-phthalic dialdehyde (OPA) assay and 1H NMR spectroscopy. However, neither of both provides information on the exact type and location of the modified AAs. Therefore, for the first time, proteomic analysis was evaluated herein as a tool to identify functionalized AAs as well as the exact position of photo-crosslinkable moieties along the AA sequence, thereby enabling an in-depth, unprecedented characterization of functionalized photo-crosslinkable biopolymers. Moreover, our strategy enabled to visualize the spatial distribution of the modifications within the overall structure of the protein. Proteomics has proven to provide unprecedented insight in the distribution of photo-crosslinkable moieties along the protein backbone, undoubtedly contributing to superior functional biomaterial design to serve regenerative medicine.
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Affiliation(s)
- Nele Pien
- Ghent University, Polymer Chemistry and Biomaterials Research Group, Centre of Macromolecular Chemistry (CMaC), Krijgslaan 281 S4bis, 9000 Gent, Belgium
- Laval University, Laboratory for Biomaterials and Bioengineering, CRC-I, Pavillon Pouliot, Québec G1V 0A6, Canada
| | - Fabrice Bray
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique, F-59 000, Lille, France
| | - Tom Gheysens
- Ghent University, Polymer Chemistry and Biomaterials Research Group, Centre of Macromolecular Chemistry (CMaC), Krijgslaan 281 S4bis, 9000 Gent, Belgium
| | - Liesbeth Tytgat
- Ghent University, Polymer Chemistry and Biomaterials Research Group, Centre of Macromolecular Chemistry (CMaC), Krijgslaan 281 S4bis, 9000 Gent, Belgium
| | - Christian Rolando
- Univ. Lille, CNRS, USR 3290, MSAP, Miniaturisation pour la Synthèse l'Analyse et la Protéomique, F-59 000, Lille, France
| | - Diego Mantovani
- Laval University, Laboratory for Biomaterials and Bioengineering, CRC-I, Pavillon Pouliot, Québec G1V 0A6, Canada
| | - Peter Dubruel
- Ghent University, Polymer Chemistry and Biomaterials Research Group, Centre of Macromolecular Chemistry (CMaC), Krijgslaan 281 S4bis, 9000 Gent, Belgium
| | - Sandra Van Vlierberghe
- Ghent University, Polymer Chemistry and Biomaterials Research Group, Centre of Macromolecular Chemistry (CMaC), Krijgslaan 281 S4bis, 9000 Gent, Belgium
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92
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Mother–Fetus Immune Cross-Talk Coordinates “Extrinsic”/“Intrinsic” Embryo Gene Expression Noise and Growth Stability. Int J Mol Sci 2022; 23:ijms232012467. [PMID: 36293324 PMCID: PMC9604428 DOI: 10.3390/ijms232012467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/15/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022] Open
Abstract
Developmental instability (DI) is thought to be inversely related to a capacity of an organism to buffer its development against random genetic and environmental perturbations. DI is represented by a trait’s inter- and intra-individual variabilities. The inter-individual variability (inversely referred to as canalization) indicates the capability of organisms to reproduce a trait from individual to individual. The intra-individual variability reflects an organism’s capability to stabilize a trait internally under the same conditions, and, for symmetric traits, it is expressed as fluctuating asymmetry (FA). When representing a trait as a random variable conditioned on environmental fluctuations, it is clear that, in statistical terms, the DI partitions into “extrinsic” (canalization) and “intrinsic” (FA) components of a trait’s variance/noise. We established a simple statistical framework to dissect both parts of a symmetric trait variance/noise using a PCA (principal component analysis) projection of the left/right measurements on eigenvectors followed by GAMLSS (generalized additive models for location scale and shape) modeling of eigenvalues. The first eigenvalue represents “extrinsic” and the second—“intrinsic” DI components. We applied this framework to investigate the impact of mother–fetus major histocompatibility complex (MHC)-mediated immune cross-talk on gene expression noise and developmental stability. We showed that “intrinsic” gene noise for the entire transcriptional landscape could be estimated from a small subset of randomly selected genes. Using a diagnostic set of genes, we found that allogeneic MHC combinations tended to decrease “extrinsic” and “intrinsic” gene noise in C57BL/6J embryos developing in the surrogate NOD-SCID and BALB/c mothers. The “intrinsic” gene noise was negatively correlated with growth (embryonic mass) and the levels of placental growth factor (PLGF), but not vascular endothelial growth factor (VEGF). However, it was positively associated with phenotypic growth instability and noise in PLGF. In mammals, the mother–fetus MHC interaction plays a significant role in development, contributing to the fitness of the offspring. Our results demonstrate that a positive impact of distant MHC combinations on embryonic growth could be mediated by the reduction of “intrinsic” gene noise followed by the developmental stabilization of growth.
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93
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Plekhanova YV, Reshetilov AN. Nanomaterials for Controlled Adjustment of the Parameters of Electrochemical Biosensors and Biofuel Cells. BIOL BULL+ 2022. [DOI: 10.1134/s1062359022040124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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94
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Clements-Brod N, Holmes L, Rawlins EL. Exploring the challenges and opportunities of public engagement with fundamental biology. Development 2022; 149:276538. [DOI: 10.1242/dev.201170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The Human Developmental Biology Initiative (HDBI) is a Wellcome-funded research consortium involving scientists based in institutions across the UK and Europe. It aims to pioneer new technologies and techniques to answer fundamental questions about human development and could, therefore, eventually improve treatments for fertility, birth defects and developmental diseases, as well as aiding regenerative medicine. HDBI research relies on human fetal and embryonic tissues donated following pregnancy terminations or fertility treatment. The situations in which these tissues are donated, their use in research and the potential healthcare impacts of this work all present complex ethical and moral questions that are of interest not only to scientists but also to the public. As such, HDBI's public engagement programme ‘What makes us human?’ aspires to test new ways of engaging the public with fundamental biology. In this brief Perspective, we provide an overview of this public engagement approach, exploring its challenges and opportunities, and outline our longer-term plans. We hope that by sharing our experiences we will encourage and enable others to organise similarly experimental public engagement, even if their research is very fundamental or potentially controversial.
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Affiliation(s)
- Naomi Clements-Brod
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge 1 , Tennis Court Road, Cambridge CB2 1QN , UK
| | - Leah Holmes
- Vocal, Manchester University NHS Foundation Trust, Nowgen Centre 2 , 29 Grafton Street, Manchester M13 9WU , UK
| | - Emma L. Rawlins
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge 1 , Tennis Court Road, Cambridge CB2 1QN , UK
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95
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Abpeikar Z, Alizadeh AA, Ahmadyousefi Y, Najafi AA, Safaei M. Engineered cells along with smart scaffolds: critical factors for improving tissue engineering approaches. Regen Med 2022; 17:855-876. [PMID: 36065834 DOI: 10.2217/rme-2022-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this review, gene delivery and its applications are discussed in tissue engineering (TE); also, new techniques such as the CRISPR-Cas9 system, synthetics biology and molecular dynamics simulation to improve the efficiency of the scaffolds have been studied. CRISPR-Cas9 is expected to make significant advances in TE in the future. The fundamentals of synthetic biology have developed powerful and flexible methods for programming cells via artificial genetic circuits. The combination of regenerative medicine and artificial biology allows the engineering of cells and organisms for use in TE, biomaterials, bioprocessing and scaffold development. The dynamics of protein adsorption at the scaffold surface at the atomic level can provide valuable guidelines for the future design of TE scaffolds /implants.
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Affiliation(s)
- Zahra Abpeikar
- Department of Tissue Engineering & Applied Cell Sciences, School of Advance Medical Science & Technology, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Ali Akbar Alizadeh
- Department of Tissue Engineering & Applied Cell Sciences, School of Advance Medical Science & Technology, Shiraz University of Medical Sciences, Shiraz, 7133654361, Iran
| | - Yaghoub Ahmadyousefi
- Research Center for Molecular Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, 6517838687, Iran
| | - Ali Akbar Najafi
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7919693116, Iran
| | - Mohsen Safaei
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, 8815713471, Iran
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96
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Aristi Capetillo A, Bauer F, Chaminade C. Emerging Technologies Supporting the Transition to a Circular Economy in the Plastic Materials Value Chain. CIRCULAR ECONOMY AND SUSTAINABILITY 2022; 3:1-30. [PMID: 36065416 PMCID: PMC9434076 DOI: 10.1007/s43615-022-00209-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/21/2022] [Indexed: 11/24/2022]
Abstract
Plastic waste has come to the forefront of academic and political debates as a global problem that demands an urgent solution. Promoted by policymakers, academia, and corporations alike, the circular economy model presents a viable path to reach more sustainable levels of development. Emerging and disruptive technologies can catalyse the transition to a circular economy, but their application to the transition of the plastic materials realm is not fully understood. Based on a systematic review of the literature, this paper aims to understand the role of key emerging technologies in the transition towards a circular economy in the plastic materials value chain, their potential impact, as well as the barriers of adoption and diffusion. Employing the ReSOLVE framework, the analysis reveals that rather than individual technologies, four technology sets associated with Industry 4.0, distributed economies, bio-based systems, and chemical recycling stand as major enablers of this transition. The complementarity of technologies and the change needed from a systemic perspective are discussed along with a proposal for governance and practical implementation pathway to overcome barriers and resistance to the transition.
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Affiliation(s)
| | - Fredric Bauer
- Environmental and Energy Systems Studies, Lund University, Lund, Sweden
- CIRCLE – Centre for Innovation Research, Lund University, Lund, Sweden
| | - Cristina Chaminade
- CIRCLE – Centre for Innovation Research, Lund University, Lund, Sweden
- Department of Economic History, Lund University, Lund, Sweden
- Department of Business and Management, Aalborg University, Aalborg, Denmark
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97
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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98
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Corrigendum: Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. ENGINEERING BIOLOGY 2022; 6:69. [PMID: 36972189 PMCID: PMC9996692 DOI: 10.1049/enb2.12023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1049/enb2.12020.].
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99
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Guthrie J, Charlebois D. Non-genetic resistance facilitates survival while hindering the evolution of drug resistance due to intraspecific competition. Phys Biol 2022; 19. [PMID: 35998624 DOI: 10.1088/1478-3975/ac8c17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022]
Abstract
Rising rates of resistance to antimicrobial drugs threaten the effective treatment of infections across the globe. Drug resistance has been established to emerge from non-genetic mechanisms as well as from genetic mechanisms. However, it is still unclear how non-genetic resistance affects the evolution of genetic drug resistance. We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. We find that non-genetic resistance facilitates the survival of cell populations during drug treatment while hindering the development of genetic resistance due to competition between the non-genetically and genetically resistant subpopulations. Non-genetic resistance in the presence of subpopulation competition increases the fixation times of drug resistance mutations, while increasing the probability of mutation before population extinction during cidal drug treatment. Intense intraspecific competition during drug treatment leads to extinction of susceptible and non-genetically resistant subpopulations. Alternating between drug and no drug conditions results in oscillatory population dynamics, increased resistance mutation fixation timescales, and reduced population survival. These findings advance our fundamental understanding of the evolution of resistance and may guide novel treatment strategies for patients with drug-resistant infections.
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Affiliation(s)
- Joshua Guthrie
- Department of Physics, University of Alberta, 11455 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2E1, CANADA
| | - Daniel Charlebois
- Departments of Physics and Biological Sciences, University of Alberta, 11455 Saskatchewan Drive NW, Edmonton, Alberta, T6G 2E1, CANADA
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100
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Ziółkowska N, Lewczuk B. Profiles of Rho, Opn4, c-Fos, and Birc5 mRNA expression in Wistar rat retinas exposed to white or monochromatic light. Front Neuroanat 2022; 16:956000. [PMID: 36059433 PMCID: PMC9434339 DOI: 10.3389/fnana.2022.956000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022] Open
Abstract
Despite concern over potential retinal damage linked to exposure to light-emitting-diode (LED) light (particularly blue light), it remains unknown how exposure to low-intensity monochromatic LED light affects the expression of rhodopsin (Rho, a photopigment that mediates light-induced retinal degeneration), melanopsin (Opn4, a blue-light sensitive photopigment), c-Fos (associated with retinal damage/degeneration), and Birc5 (anti-apoptotic). This study investigated the mRNA expression profiles of these genes under exposure to white and monochromatic light (blue, red, green) in the retinas of albino rats under a cycle of 12 h of light and 12 h of darkness. In each group, 32 Wistar rats were exposed to one type of monochromatic-LED or white-fluorescent light for 7 day (150 lx). Retinal samples were taken for qPCR analysis and light and electron microscopy. Blue and green light exposure markedly decreased expression of Rho and Opn4 mRNA and increased expression of Birc5 and c-Fos mRNA (P < 0.05). In retinas from the blue-light group, loss and vesiculation of photoreceptor outer segments were visible, but not in retinas from the red-light and control group. Measurements of the photoreceptor inner and outer segments length revealed, that this length was significantly decreased in the blue- and green-light exposure groups (P < 0.02), but not in the red-light exposure group. Increased expression of Birc5 and decreased expression of Rho and Opn4 after exposure to blue and green light may be early responses that help to reduce light-induced retinal damage.
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Affiliation(s)
- Natalia Ziółkowska
- Department of Histology and Embryology, Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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