1
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Aguiar-Cervera J, Visinoni F, Zhang P, Hollywood K, Vrhovsek U, Severn O, Delneri D. Effect of Hanseniaspora vineae and Saccharomyces cerevisiae co-fermentations on aroma compound production in beer. Food Microbiol 2024; 123:104585. [PMID: 39038891 DOI: 10.1016/j.fm.2024.104585] [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: 03/09/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 07/24/2024]
Abstract
In recent years, the boom of the craft beer industry refocused the biotech interest from ethanol production to diversification of beer aroma profiles. This study analyses the fermentative phenotype of a collection of non-conventional yeasts and examines their role in creating new flavours, particularly through co-fermentation with industrial Saccharomyces cerevisiae. High-throughput solid and liquid media fitness screening compared the ability of eight Saccharomyces and four non-Saccharomyces yeast strains to grow in wort. We determined the volatile profile of these yeast strains and found that Hanseniaspora vineae displayed a particularly high production of the desirable aroma compounds ethyl acetate and 2-phenethyl acetate. Given that H. vineae on its own can't ferment maltose and maltotriose, we carried out mixed wort co-fermentations with a S. cerevisiae brewing strain at different ratios. The two yeast strains were able to co-exist throughout the experiment, regardless of their initial inoculum, and the increase in the production of the esters observed in the H. vineae monoculture was maintained, alongside with a high ethanol production. Moreover, different inoculum ratios yielded different aroma profiles: the 50/50 S. cerevisiae/H. vineae ratio produced a more balanced profile, while the 10/90 ratio generated stronger floral aromas. Our findings show the potential of using different yeasts and different inoculum combinations to tailor the final aroma, thus offering new possibilities for a broader range of beer flavours and styles.
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Affiliation(s)
- Jose Aguiar-Cervera
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom; Singer Instruments Co. Ltd, Somerset, United Kingdom
| | - Federico Visinoni
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Penghan Zhang
- Foundation Edmund Mach, San Michele all' Adige, Trento, Italy
| | - Katherine Hollywood
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Urska Vrhovsek
- Foundation Edmund Mach, San Michele all' Adige, Trento, Italy
| | - Oliver Severn
- Singer Instruments Co. Ltd, Somerset, United Kingdom
| | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.
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2
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Saha R, Chauhan A, Rastogi Verma S. Machine learning: an advancement in biochemical engineering. Biotechnol Lett 2024; 46:497-519. [PMID: 38902585 DOI: 10.1007/s10529-024-03499-8] [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: 11/17/2023] [Revised: 02/24/2024] [Accepted: 05/18/2024] [Indexed: 06/22/2024]
Abstract
One of the most remarkable techniques recently introduced into the field of bioprocess engineering is machine learning. Bioprocess engineering has drawn much attention due to its vast application in different domains like biopharmaceuticals, fossil fuel alternatives, environmental remediation, and food and beverage industry, etc. However, due to their unpredictable mechanisms, they are very often challenging to optimize. Furthermore, biological systems are extremely complicated; hence, machine learning algorithms could potentially be utilized to improve and build new biotechnological processes. Gaining insight into the fundamental mathematical understanding of commonly used machine learning algorithms, including Support Vector Machine, Principal Component Analysis, Partial Least Squares and Reinforcement Learning, the present study aims to discuss various case studies related to the application of machine learning in bioprocess engineering. Recent advancements as well as challenges posed in this area along with their potential solutions are also presented.
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Affiliation(s)
- Ritika Saha
- Department of Biotechnology, Delhi Technological University, New Delhi, 110042, India
| | - Ashutosh Chauhan
- Department of Biotechnology, Delhi Technological University, New Delhi, 110042, India
| | - Smita Rastogi Verma
- Department of Biotechnology, Delhi Technological University, New Delhi, 110042, India.
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3
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Ferreira-Filipe DA, Oliveira L, Paço A, Fernandes AJS, Costa FM, Duarte AC, Rocha-Santos T, Patrício Silva AL. Biodegradation of e-waste microplastics by Penicillium brevicompactum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173334. [PMID: 38763191 DOI: 10.1016/j.scitotenv.2024.173334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/21/2024]
Abstract
Electronic and electric waste (e-waste) management strategies often fall short in dealing with the plastic constituents of printed circuit boards (PCB). Some plastic materials from PCB, such as epoxy resins, may release contaminants, but neither potential environmental impact has been assessed nor mitigation strategies have been put forward. This study assessed the biodegradation of microplastics (1-2 mm in size) from PCB by the fungus Penicillium brevicompactum over 28 days, thus contributing to the discussion of mitigation strategies for decreasing the environmental impact of such plastics in the environment. The capacity of P. brevicompactum to induce microplastic fragmentation and degradation has been determined by the increased the number of smaller-sized particles and microplastic mass reduction (up to 75 % within 14 days), respectively. The occurrence of chain scission and oxidation of microplastics exposed to P. brevicompactum when compared with the control conditions (which occurred only after 28 days of exposure) can be observed. Furthermore, Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy performed in dried biomass put in evidence an increase in the absorption intensities in regions that could be attributed to functional groups associated with carbohydrates. The results underline the potential role of the genus Penicillium, particularly P. brevicompactum, in the biodegradation of microplastics from PCB, thus providing the basis for further exploration of its potential for e-waste bioremediation and research on the underlying mechanisms for sustainable approaches to mitigate e-waste pollution.
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Affiliation(s)
- Diogo A Ferreira-Filipe
- Centre for Environmental and Marine Studies (CESAM) & Department of Chemistry, University of Aveiro, Portugal.
| | | | - Ana Paço
- Centre for Environmental and Marine Studies (CESAM) & Department of Chemistry, University of Aveiro, Portugal
| | | | | | - Armando C Duarte
- Centre for Environmental and Marine Studies (CESAM) & Department of Chemistry, University of Aveiro, Portugal
| | - Teresa Rocha-Santos
- Centre for Environmental and Marine Studies (CESAM) & Department of Chemistry, University of Aveiro, Portugal
| | - Ana L Patrício Silva
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, Portugal
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4
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Ye L, Bogicevic B, Bolten CJ, Wittmann C. Single-cell protein: overcoming technological and biological challenges towards improved industrialization. Curr Opin Biotechnol 2024; 88:103171. [PMID: 39024923 DOI: 10.1016/j.copbio.2024.103171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/23/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024]
Abstract
The commercialization of single-cell protein (SCP) obtained from microbial fermentation in large-scale bioreactors emerged almost 50 years ago, with Pruteen marketed as animal feed in the 1970s and Quorn®, released for human nutrition in 1985. SCP holds great promises to feed the meanwhile doubled world population in a sustainable way, but its application is still limited by price and availability on scale. There is a need to optimize the underlying manufacturing processes with enhanced affordability and productivity. From the industrial perspective, it is crucial to identify key process components and prioritize innovations that best promote cost efficiency and large-scale production. Here, we present the state-of-art in SCP manufacturing and provide a comprehensive insight into recent techno-economic analyses and life-cycle assessments of different production scenarios. Thereby, we identified the most influential technical hotspots and challenges for each of the main production scenarios and evaluated the technological opportunities to overcome them.
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Affiliation(s)
- Lijuan Ye
- Nestlé Research, Lausanne, Switzerland.
| | | | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
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5
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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024. [PMID: 39008623 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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6
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Manning L. Responsible innovation: Mitigating the food safety aspects of cultured meat production. J Food Sci 2024. [PMID: 38980973 DOI: 10.1111/1750-3841.17228] [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: 01/14/2024] [Revised: 05/30/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
There is much interest in cultured (cultivated) meat as a potential solution to concerns over the ecological and environmental footprint of food production, especially from animal-derived food products. The aim of this critical review is to undertake a structured analysis of existing literature to (i) identify the range of materials that could be used within the cultured meat process; (ii) explore the potential biological and chemical food safety issues that arise; (iii) identify the known and also novel aspects of the food safety hazard portfolio that will inform hazard analysis and risk assessment approaches, and (iv) position a responsible innovation framework that can be utilized to mitigate food safety concerns with specific emphasis on cultured meat. Although a number of potential food safety hazards are identified that need to be considered within a food safety plan, further research is required to validate and verify that these food safety hazards have been suitably controlled and, where possible, eliminated. The responsible innovation framework developed herein, which extends beyond hazard analysis and traditional risk assessment approaches, can be applied in multiple contexts, including this use case of cultured meat production.
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Affiliation(s)
- Louise Manning
- Lincoln Institute for Agri-Food Technology, University of Lincoln, Lincoln, UK
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7
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Kumar V, Pellis A, Wimmer R, Popok V, Christiansen JDC, Varrone C. Efficient Depolymerization of Poly(ethylene 2,5-furanoate) Using Polyester Hydrolases. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2024; 12:9658-9668. [PMID: 38966237 PMCID: PMC11220789 DOI: 10.1021/acssuschemeng.4c00915] [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: 01/31/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 07/06/2024]
Abstract
Poly(ethylene 2,5-furanoate) (PEF) is considered to be the next-generation green polyester and is hailed as a rising star among novel plastics. It is biobased, is nontoxic, and has comparable or improved properties compared to polyethylene terephthalate (PET). Biobased PEF offers lower life-cycle greenhouse gas emissions than PET. However, with its industrial production starting soon, relatively little is known about its actual recyclability. This work reports on the near complete depolymerization of PEF using two efficient PET hydrolases, FastPETase and leaf compost-cutinase (LCC), at loadings 4.5-17 times lower than previously reported. FastPETase and LCC exhibited maximum depolymerization of PEF, measured by weight loss and 2,5-furandicarboxylic acid (FDCA) production, using potassium phosphate-NaOH buffer at 50 and 65 °C, respectively. The 98% depolymerization of 13 g L-1 PEF film was achieved by three additions of the LCC in 72 h, while 78% weight loss was obtained using FastPETase in controlled conditions. Nonetheless, 92% weight loss was obtained with FastPETase when using only 6 g L-1 PEF. The main reaction products were identified as FDCA, ethylene glycol, and mono(2-hydroxyethyl)-furanoate. LCC performed better than FastPETase, in terms of both FDCA release and weight loss. The effect of crystallinity was evident on the enzymes' performance, as only 4% to 7% weight loss of crystalline PEF (32%) was recorded. Microscopy studies of the treated PEF films provided information on the surface erosion processes and revealed higher resistance of the crystalline phase, explaining the low level of depolymerization. The study presents important insights into the enzymatic hydrolysis of biobased PEF material and paves the path toward more viable applications within biopolymer waste recycling.
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Affiliation(s)
- Virender Kumar
- Department
of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Alessandro Pellis
- Dipartimento
di Chimica e Chimica Industriale, Universitá
degli Studi di Genova, Via Dodecaneso 31, Genova 16146, Italy
| | - Reinhard Wimmer
- Department
of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Vladimir Popok
- Department
of Materials and Production, Aalborg University, Fibigerstræde 16, 9220 Aalborg, Denmark
| | | | - Cristiano Varrone
- Department
of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
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8
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Chua JS, Rajasabhai R, Teo WZ, Xue B, Yew WS. Engineering a Metal Reductase for the Bioremediation of Anthropogenic Electronic Wastes: From Hg(II) to Au(III) and Ag(I) Enzymatic Reduction. JACS AU 2024; 4:2335-2342. [PMID: 38938813 PMCID: PMC11200239 DOI: 10.1021/jacsau.4c00297] [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: 04/03/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/29/2024]
Abstract
Recovering precious metals from electronic waste (e-waste) using microbes presents a sustainable methodology that can contribute toward the maintenance of planetary health. To better realize the potential of bioremediation using engineered microbes, enzymes that mediate the reduction of Au(III) to Au(0) have been the subject of intense research. In this study, we report the successful engineering of a metal reductase, MerA, whose cognate substrate is mercury(II), toward other precious metals such as Au(III) and Ag(I). The engineered variant, G415I, exhibited a 15-fold increase in catalytic efficiency (k cat/K M) in Au(III) reduction to Au(0) and a 200-fold increase in catalytic efficiency in Ag(I) reduction to Ag(0) with respect to the wild-type enzyme. The apparent shift in preference toward noncognate metal ions may be attributed to the energetics of valency preference. The improved Au(III) reductase has an apparent increased preference toward monovalent cations such as Au(I) and Ag(I), with respect to divalent cations such as Hg(II), the cognate substrate of the progenitor MerA (an increase in K M of 5.0-fold for Hg(II), compared to a decrease in K M of 5.8-fold for Au(III) and 1.8-fold for Ag(I), respectively). This study further extends the mechanistic understanding of Au(III) bioreduction that could proceed through the stabilization of Au(I) en route to Au(0) and suggests that the biosynthesis of Au nanoparticles with high efficiency can be realized through the engineering of promiscuous metal reductases for precious metal recovery from e-wastes.
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Affiliation(s)
- Jasmine
Puay Suan Chua
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Rashmi Rajasabhai
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456, Singapore
| | - Wei Zhe Teo
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Wen Shan Yew
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
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9
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Tica J, Chen H, Luo S, Chen M, Isalan M. Engineering Tunable, Low Latency Spatial Computation with Dual Input Quorum Sensing Promoters. ACS Synth Biol 2024; 13:1750-1761. [PMID: 38781598 PMCID: PMC11197083 DOI: 10.1021/acssynbio.4c00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/10/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Quorum sensing signals have evolved for population-level signaling in bacterial communities and are versatile tools for engineering cell-cell signaling in synthetic biology projects. Here, we characterize the spatial diffusion of a palette of quorum sensing signals and find that their diffusion in agar can be predicted from their molecular weight with a simple power law. We also engineer novel dual- and multi-input promoters that respond to quorum-sensing diffusive signals for use in engineered genetic systems. We engineer a promoter scaffold that can be adapted for activation and repression by multiple diffusers simultaneously. Lastly, we combine the knowledge on diffusion dynamics with the novel genetic components to build a new generation of spatial, stripe-forming systems with a simplified design, improved robustness, tuneability, and response time.
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Affiliation(s)
- Jure Tica
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Haobin Chen
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Shulei Luo
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Manman Chen
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
| | - Mark Isalan
- Department
of Life Sciences, Imperial College London, London SW7 2AZ, U.K.
- Imperial
College Centre for Synthetic Biology, Imperial
College London, London SW7 2AZ, U.K.
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10
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Hoang-Phou S, Pal S, Slepenkin A, Abisoye-Ogunniyun A, Zhang Y, Gilmore SF, Shelby M, Bourguet F, Mohagheghi M, Noy A, Rasley A, de la Maza LM, Coleman MA. Evaluation in mice of cell-free produced CT584 as a Chlamydia vaccine antigen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597210. [PMID: 38895407 PMCID: PMC11185655 DOI: 10.1101/2024.06.04.597210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Chlamydia trachomatis is the most prevalent bacterial sexually transmitted pathogen worldwide. Since chlamydial infection is largely asymptomatic with the potential for serious complications, a preventative vaccine is likely the most viable long-term answer to this public health threat. Cell-free protein synthesis (CFPS) utilizes the cellular protein manufacturing machinery decoupled from the requirement for maintaining cellular viability, offering the potential for flexible, rapid, and de-centralized production of recombinant protein vaccine antigens. Here, we use CFPS to produce the putative chlamydial type three secretion system (T3SS) needle-tip protein, CT584, for use as a vaccine antigen in mouse models. High-speed atomic force microscopy (HS-AFM) imaging and computer simulations confirm that CFPS-produced CT584 retains a native-like structure prior to immunization. Female mice were primed with CT584 adjuvanted with CpG-1826 intranasally (i.n.) or CpG-1826 + Montanide ISA 720 intramuscularly (i.m.), followed four-weeks later by an i.m. boost before respiratory challenge with 104 inclusion forming units (IFU) of Chlamydia muridarum. Immunization with CT584 generated robust antibody responses but weak cell mediated immunity and failed to protect against i.n. challenge as demonstrated by body weight loss, increased lungs' weights and the presence of high numbers of IFUs in the lungs. While CT584 alone may not be the ideal vaccine candidate, the speed and flexibility with which CFPS can be used to produce other potential chlamydial antigens makes it an attractive technique for antigen production.
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Affiliation(s)
- Steven Hoang-Phou
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Sukumar Pal
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Anatoli Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Abisola Abisoye-Ogunniyun
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Yuliang Zhang
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Sean F Gilmore
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Megan Shelby
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Feliza Bourguet
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Mariam Mohagheghi
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Aleksandr Noy
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Amy Rasley
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
| | - Luis M de la Maza
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Matthew A Coleman
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551, USA
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11
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Ledesma AV, Van Eenennaam AL. Global status of gene edited animals for agricultural applications. Vet J 2024; 305:106142. [PMID: 38788996 DOI: 10.1016/j.tvjl.2024.106142] [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: 01/09/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Gene editing (GnEd) involves using a site-directed nuclease to introduce a double-strand break (DSB) at a targeted location in the genome. A literature search was performed on the use of GnEd in animals for agricultural applications. Data was extracted from 212 peer-reviewed articles that described the production of at least one living animal employing GnEd technologies for agricultural purposes. The most common GnEd system reported was CRISPR/Cas9, and the most frequent type of edit was the unguided insertion or deletion resulting from the repair of the targeted DSB leading to a knock-out (KO) mutation. Animal groups included in the reviewed papers were ruminants (cattle, sheep, goats, n=63); monogastrics (pigs and rabbits, n=60); avian (chicken, duck, quail, n=17); aquatic (many species, n=65), and insects (honeybee, silkworm, n=7). Yield (32%), followed by reproduction (21%) and disease resistance (17%) were the most commonly targeted traits. Over half of the reviewed papers had Chinese first-authorship. Several countries, including Argentina, Australia, Brazil, Colombia and Japan, have adopted a regulatory policy that considers KO mutations introduced following GnEd DSB repair as akin to natural genetic variation, and therefore treat these GnEd animals analogously to those produced using conventional breeding. This approach has resulted in a non-GMO determination for a small number of GnEd food animal applications, including three species of GnEd KO fast-growing fish, (red sea bream, olive flounder and tiger pufferfish in Japan), KO fish and cattle in Argentina and Brazil, and porcine reproductive and respiratory syndrome (PRRS) virus disease-resistant KO pigs in Colombia.
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Affiliation(s)
- Alba V Ledesma
- Department of Animal Science, University of California, Davis, CA 95616, USA
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12
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Elzein B. Nano Revolution: "Tiny tech, big impact: How nanotechnology is driving SDGs progress". Heliyon 2024; 10:e31393. [PMID: 38818162 PMCID: PMC11137564 DOI: 10.1016/j.heliyon.2024.e31393] [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: 09/05/2023] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Nanotechnology has emerged as a powerful tool in addressing global challenges and advancing sustainable development. By manipulating materials at the nanoscale, researchers have unlocked new possibilities in various fields, including energy, healthcare, agriculture, construction, transportation, and environmental conservation. This paper explores the potential of nanotechnology and nanostructures in contributing to the achievement of the United Nations (UN) Sustainable Development Goals (SDGs) by improving energy efficiency and energy conversion, leading to a more sustainable and clean energy future, improving water purification processes, enabling access to clean drinking water for communities, enabling targeted drug delivery systems, early disease detection, and personalized medicine, thus revolutionizing healthcare, improving crop yields, efficient nutrient delivery systems, pest control mechanisms, and many other areas, therefore addressing food security issues. It also highlights the potential of nanomaterials in environmental remediation and pollution control. Therefore, by understanding and harnessing nanotechnology's potential, policymakers, researchers, and stakeholders can work together toward a more sustainable future by achieving the 17 UN SDGs.
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Affiliation(s)
- Basma Elzein
- Electrical Engineering Department, College of Engineering, University of Business and Technology, Jeddah, 21451, Saudi Arabia
- Sustainable Development Department, Global Council for Tolerance and Peace, Valetta, Malta
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13
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Klinzing K, Aabrandt Søndergaard I, Chirom T, Whitwell J, Bisini L, Marabottini C, Nesslany F, Tervasmäki P, Pitkänen JP. In vitro genotoxicological evaluation of protein-rich powder derived from Xanthobacter sp. SoF1. J Appl Toxicol 2024. [PMID: 38730487 DOI: 10.1002/jat.4621] [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: 02/05/2024] [Revised: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024]
Abstract
One way of limiting the environmental impact of food production and improving food security is to replace part of the animal- or plant-based protein in the human diet with protein sourced from microorganisms. The recently discovered bacterium Xanthobacter sp. SoF1 (VTT-E-193585) grows autotrophically using carbon dioxide gas as the only carbon source, yielding protein-rich biomass that can be processed further into a powder and incorporated into various food products. Since the safety of this microbial protein powder for human consumption had not been previously assessed, its genotoxic potential was evaluated employing three internationally recognized and standardized studies: a bacterial reverse mutation test, an in vitro chromosomal aberration assay in human lymphocytes, and an in vitro micronucleus test in human lymphocytes. No biologically relevant evidence of genotoxicity or mutagenicity was found.
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Affiliation(s)
| | | | | | | | - Laura Bisini
- European Research Biology Center S.r.l. (ERBC), Rome, Italy
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14
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Rahmati F, Sethi D, Shu W, Asgari Lajayer B, Mosaferi M, Thomson A, Price GW. Advances in microbial exoenzymes bioengineering for improvement of bioplastics degradation. CHEMOSPHERE 2024; 355:141749. [PMID: 38521099 DOI: 10.1016/j.chemosphere.2024.141749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/06/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Plastic pollution has become a major global concern, posing numerous challenges for the environment and wildlife. Most conventional ways of plastics degradation are inefficient and cause great damage to ecosystems. The development of biodegradable plastics offers a promising solution for waste management. These plastics are designed to break down under various conditions, opening up new possibilities to mitigate the negative impact of traditional plastics. Microbes, including bacteria and fungi, play a crucial role in the degradation of bioplastics by producing and secreting extracellular enzymes, such as cutinase, lipases, and proteases. However, these microbial enzymes are sensitive to extreme environmental conditions, such as temperature and acidity, affecting their functions and stability. To address these challenges, scientists have employed protein engineering and immobilization techniques to enhance enzyme stability and predict protein structures. Strategies such as improving enzyme and substrate interaction, increasing enzyme thermostability, reinforcing the bonding between the active site of the enzyme and substrate, and refining enzyme activity are being utilized to boost enzyme immobilization and functionality. Recently, bioengineering through gene cloning and expression in potential microorganisms, has revolutionized the biodegradation of bioplastics. This review aimed to discuss the most recent protein engineering strategies for modifying bioplastic-degrading enzymes in terms of stability and functionality, including enzyme thermostability enhancement, reinforcing the substrate binding to the enzyme active site, refining with other enzymes, and improvement of enzyme surface and substrate action. Additionally, discovered bioplastic-degrading exoenzymes by metagenomics techniques were emphasized.
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Affiliation(s)
- Farzad Rahmati
- Department of Microbiology, Faculty of Science, Qom Branch, Islamic Azad University (IAU), Qom 37185364, Iran
| | - Debadatta Sethi
- Sugarcane Research Station, Odisha University of Agriculture and Technology, Nayagarh, India
| | - Weixi Shu
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | | | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Allan Thomson
- Perennia Food and Agriculture Corporation., 173 Dr. Bernie MacDonald Dr., Bible Hill, Truro, NS, B6L 2H5, Canada
| | - G W Price
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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15
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Hassan S, Bhadwal SS, Khan M, Sabreena, Nissa KU, Shah RA, Bhat HM, Bhat SA, Lone IM, Ganai BA. Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches. CHEMOSPHERE 2024; 356:141889. [PMID: 38583533 DOI: 10.1016/j.chemosphere.2024.141889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/27/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Siloni Singh Bhadwal
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Misba Khan
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Khair-Ul Nissa
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Rameez Ahmad Shah
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Haneef Mohammad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shabir Ahmad Bhat
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Ishfaq Maqbool Lone
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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16
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Joshi J, Hanson AD. A pilot oral history of plant synthetic biology. PLANT PHYSIOLOGY 2024; 195:36-47. [PMID: 38163646 PMCID: PMC11060686 DOI: 10.1093/plphys/kiad585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/15/2023] [Indexed: 01/03/2024]
Abstract
The whole field of synthetic biology (SynBio) is only about 20 years old, and plant SynBio is younger still. Nevertheless, within that short time, SynBio in general has drawn more scientific, philosophical, government, and private-sector interest than anything in biology since the recombinant DNA revolution. Plant SynBio, in particular, is now drawing more and more interest in relation to plants' potential to help solve planetary problems such as carbon capture and storage and replacing fossil fuels and feedstocks. As plant SynBio is so young and so fast-developing, we felt it was too soon to try to analyze its history. Instead, we set out to capture the essence of plant SynBio's origins and early development through interviews with 8 of the field's founders, representing 5 countries and 3 continents. We then distilled these founders' personal recollections and reflections into this review, centering the narrative on timelines for pivotal events, articles, funding programs, and quoting from interviews. We have archived the interview recordings and documented timeline entries. This work provides a resource for future historical scholarship.
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Affiliation(s)
- Jaya Joshi
- Department of Wood Science, University of British Columbia, 2424 Main Mall, Vancouver, BC V6T 1Z4, Canada
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
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17
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Lee SJ, Kim DM. Cell-Free Synthesis: Expediting Biomanufacturing of Chemical and Biological Molecules. Molecules 2024; 29:1878. [PMID: 38675698 PMCID: PMC11054211 DOI: 10.3390/molecules29081878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The increasing demand for sustainable alternatives underscores the critical need for a shift away from traditional hydrocarbon-dependent processes. In this landscape, biomanufacturing emerges as a compelling solution, offering a pathway to produce essential chemical materials with significantly reduced environmental impacts. By utilizing engineered microorganisms and biomass as raw materials, biomanufacturing seeks to achieve a carbon-neutral footprint, effectively counteracting the carbon dioxide emissions associated with fossil fuel use. The efficiency and specificity of biocatalysts further contribute to lowering energy consumption and enhancing the sustainability of the production process. Within this context, cell-free synthesis emerges as a promising approach to accelerate the shift towards biomanufacturing. Operating with cellular machinery in a controlled environment, cell-free synthesis offers multiple advantages: it enables the rapid evaluation of biosynthetic pathways and optimization of the conditions for the synthesis of specific chemicals. It also holds potential as an on-demand platform for the production of personalized and specialized products. This review explores recent progress in cell-free synthesis, highlighting its potential to expedite the transformation of chemical processes into more sustainable biomanufacturing practices. We discuss how cell-free techniques not only accelerate the development of new bioproducts but also broaden the horizons for sustainable chemical production. Additionally, we address the challenges of scaling these technologies for commercial use and ensuring their affordability, which are critical for cell-free systems to meet the future demands of industries and fully realize their potential.
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Affiliation(s)
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-Ro, Daejeon 34134, Republic of Korea;
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18
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Emilia N, Pia SV, Tiina HP, Antti N, Anniina V, Anneli R, Michael L, Natalia RS. In vitro protein digestion and carbohydrate colon fermentation of microbial biomass samples from bacterial, filamentous fungus and yeast sources. Food Res Int 2024; 182:114146. [PMID: 38519176 DOI: 10.1016/j.foodres.2024.114146] [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: 12/08/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/24/2024]
Abstract
This study evaluated the nutritional quality of different microbial biomass samples by assessing their protein digestibility and carbohydrate fermentability in the colon using in vitro methods. Four microbial samples were produced: one hydrogen-oxidizing bacterial strain (Nocardioides nitrophenolicus KGS-27), two strains of filamentous fungi (Rhizopus oligosporus and Paecilomyces variotii), and one yeast strain (Rhodotorula babjevae). The microorganisms were grown in bioreactors, harvested and dried before analysis. The commercial fungal product Quorn was used as a reference. The protein digestibility of the microbial samples was analysed using the INFOGEST in vitro model, followed by quantification of N-terminal amine groups. An in vitro faecal fermentation experiment was also performed to evaluate the degradation of carbohydrates in microbial biomass samples and formation of short-chain fatty acids (SCFA). The fungal biomass samples had higher protein hydrolysis (60-75 %) than the bacterial sample (12 %) and Quorn (45 %), while the yeast biomass had the highest protein digestibility (85 %). Heat-treatment of the biomass significantly reduced its protein digestibility. Total dietary fibre (DF) content of fungal biomass was 31 - 43 %(DW), mostly insoluble, whereas the bacterial biomass contained mainly soluble DF (total DF: 25.7 %, of which 23.5 % were soluble and 2.2 % insoluble). After 24 h of colonic in vitro fermentation, SCFA production from the biomass of Paecilomyces, Quorn and Rhodotorula was similar to that of wheat bran, while 17 % and 32 % less SCFA were produced from the biomass of Rhizopus and the bacterial strain, respectively. Further studies are needed to clarify the reasons for the observed differences in protein digestibility and DF fermentability, especially regarding the cell wall structures and role of post-processing.
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Affiliation(s)
- Nordlund Emilia
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland.
| | | | | | - Nyyssölä Antti
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
| | - Valtonen Anniina
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland; Nordic Umami Company Ltd., Karamalmintie 2, 02630 Espoo, Finland(1)
| | - Ritala Anneli
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
| | - Lienemann Michael
- VTT Technical Research Centre of Finland, Ltd, P.O. Box 1000, FI-02044, Finland
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19
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Li Q, Wang F, Zhang Y, Shi M, Zhang Y, Yu H, Liu S, Li J, Tan SC, Chen W. Biopolymers for Hygroscopic Material Development. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2209479. [PMID: 36652538 DOI: 10.1002/adma.202209479] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Indexed: 06/17/2023]
Abstract
The effective management of atmospheric water will create huge value for mankind. Diversified and sustainable biopolymers that are derived from organisms provide rich building blocks for various hygroscopic materials. Here, a comprehensive review of recent advances in developing biopolymers for hygroscopic materials is provided. It is begun with a brief introduction of species diversity and the processes of obtaining various biopolymer materials from organisms. The fabrication of hygroscopic materials is then illustrated, with a specific focus on the use of biopolymer-derived materials as substrates to produce composites and the use of biopolymers as building blocks to fabricate composite gels. Next, the representative applications of biopolymer-derived hygroscopic materials for dehumidification, atmospheric water harvesting, and power generation are systematically presented. An outlook on future challenges and key issues worthy of attention are finally provided.
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Affiliation(s)
- Qing Li
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Fei Wang
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Yaoxin Zhang
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering drive 1, Singapore, 117574, Singapore
| | - Mengjiao Shi
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Yingying Zhang
- Key Laboratory of Organic Optoelectronics and Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Haipeng Yu
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Shouxin Liu
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Jian Li
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Swee Ching Tan
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering drive 1, Singapore, 117574, Singapore
| | - Wenshuai Chen
- Key Laboratory of Bio-based Material Science and Technology, Ministry of Education, Northeast Forestry University, Harbin, 150040, P. R. China
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20
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Liao L, Lou Y, Tang X, Deng Z, Gao J. Intellectual property and funding: fueling Chinese synbio. Trends Biotechnol 2024; 42:258-260. [PMID: 37980185 DOI: 10.1016/j.tibtech.2023.10.012] [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: 08/27/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023]
Abstract
As China emerges as a synthetic biology (synbio) global leader, it faces distinct science-society challenges. Our series offers a snapshot of China's synbio state, emphasizing the intersection and its policy implications. The debut piece elucidates the intellectual property rights (IPR)-funding interplay in China's expanding synbio territory, underlining its key role in driving innovation and commercialization.
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Affiliation(s)
- Lijuan Liao
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yi Lou
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xianming Tang
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jiangtao Gao
- Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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21
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Flight MH, Tait J, Chronopoulos T, Betancor M, Wischhusen P, Burton E, O'Neill HM, van der Heul K, Hays J, Rowe P. Analysing responsible innovation along a value chain-A single-cell protein case study. ENGINEERING BIOLOGY 2024; 8:16-29. [PMID: 38525249 PMCID: PMC10959755 DOI: 10.1049/enb2.12031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/14/2024] [Accepted: 03/03/2024] [Indexed: 03/26/2024] Open
Abstract
The British Standards Institution's Publicly Available Specification 440 (PAS 440) provides a Responsible Innovation Framework (RIF) that companies can use to continuously monitor the societal, environmental and health benefits and risks of their innovations, as well as relevant changes to the supply chain and regulations. PAS 440 is intended to help companies achieve the benefits of innovation in a timely manner and avoid any potential harm or unintended misuse of a new product, process or service. Here, the authors have applied the PAS 440 RIF to a novel single-cell protein (SCP) animal feed ingredient taking into consideration the perspectives of the value chain partners (VCPs), companies and laboratories involved in an Innovate UK research project. The authors' findings show how VCPs can use PAS440 to demonstrate that they are innovating responsibly. Using this approach to responsible innovation along the value chain-from manufacturing scale-up, through regulatory approval, to incorporation in animal feed and from there to food on supermarket shelves-can support the development of innovations that contribute to the economic and environmental sustainability of the animal feed sector. The authors conclude that the PAS 440 Guide can facilitate the progress of a new product throughout a value chain and contribute to coordinating responsible behaviour among companies involved in the value chain.
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Affiliation(s)
| | - Joyce Tait
- Innogen InstituteThe University of EdinburghHigh School YardsEdinburghUK
| | | | | | | | - Emily Burton
- Nottingham Trent University Poultry Research UnitSouthwellUK
| | | | | | - John Hays
- Deep Branch Biotechnology LtdNottinghamUK
| | - Peter Rowe
- Deep Branch Biotechnology LtdNottinghamUK
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22
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Park S, Lee SJ, Noh W, Kim YJ, Kim JH, Back SM, Ryu BG, Nam SW, Park SH, Kim J. Production of safe cyanobacterial biomass for animal feed using wastewater and drinking water treatment residuals. Heliyon 2024; 10:e25136. [PMID: 38322884 PMCID: PMC10844260 DOI: 10.1016/j.heliyon.2024.e25136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
The growing interest in microalgae and cyanobacteria biomass as an alternative to traditional animal feed is hindered by high production costs. Using wastewater (WW) as a cultivation medium could offer a solution, but this approach risks introducing harmful substances into the biomass, leading to significant safety concerns. In this study, we addressed these challenges by selectively extracting nitrates and phosphates from WW using drinking water treatment residuals (DWTR) and chitosan. This method achieved peak adsorption capacities of 4.4 mg/g for nitrate and 6.1 mg/g for phosphate with a 2.5 wt% chitosan blend combined with DWTR-nitrogen. Subsequently, these extracted nutrients were employed to cultivate Spirulina platensis, yielding a biomass productivity rate of 0.15 g/L/d, which is comparable to rates achieved with commercial nutrients. By substituting commercial nutrients with nitrate and phosphate from WW, we can achieve a 18 % reduction in the culture medium cost. While the cultivated biomass was initially nitrogen-deficient due to low nitrate levels, it proved to be protein-rich, accounting for 50 % of its dry weight, and contained a high concentration of free amino acids (1260 mg/g), encompassing all essential amino acids. Both in vitro and in vivo toxicity tests affirmed the biomass's safety for use as an animal feed component. Future research should aim to enhance the economic feasibility of this alternative feed source by developing efficient adsorbents, utilizing cost-effective reagents, and implementing nutrient reuse strategies in spent mediums.
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Affiliation(s)
- Seonghwan Park
- Biomass Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
- Environmental Safety-Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Sang-Jun Lee
- Biomass Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
- Environmental Safety-Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Won Noh
- Biomass Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
- Environmental Safety-Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Yeong Jin Kim
- Environmental Safety-Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Je-Hein Kim
- Human Risk Assessment Center, Jeonbuk Branch Institute, Korea Institute of Toxicology, Jeongeup, 56212, Republic of Korea
| | - Seng-Min Back
- Genetic & Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Byung-Gon Ryu
- Microbial Research Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Seung Won Nam
- Bioresources Collection & Bioinformation Department, Nakdonggang National Institute of Biological Resources, Sangju, 37242, Republic of Korea
| | - Seong-Hoon Park
- Genetic & Epigenetic Toxicology Research Group, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Jungmin Kim
- Biomass Research Group, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
- Environmental Exposure & Toxicology Research Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
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23
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Wang L, Liu H. Microbial electrosynthesis of single cell protein and methane by coupling fast-growing Methanococcus maripaludis with microbial electrolysis cells. BIORESOURCE TECHNOLOGY 2024; 393:130025. [PMID: 37972904 DOI: 10.1016/j.biortech.2023.130025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/13/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Single cell protein (SCP) is a promising alternative protein source, as its production bypasses the disadvantages of animal protein production in industrial agriculture. Coupling a fast-growing hydrogen consuming organism with microbial electrolysis cells (MECs) could be a viable method for SCP production. In this study, a fast-growing and protein-rich methanogen, Methanococcus maripaludis was selected as the primary SCP source. The inoculation of M. maripaludis in MECs triggered cell synthesis with methane production. The doubling time measured was 11.2 h and the specific growth rate was 0.062 1/h. The highest SCP production rate was 13.7 mg/L/h. In the dried biomass, the weight of protein was over 60 %. Amino acid profiling of the harvested biomass demonstrated high abundance of essential amino acids. The electron flux analysis indicated that 31.3 % electrons in the electrochemical systems were directed into SCP synthesis. These results illustrated the potential for SCP production by coupling a fast-growing methanogen with MECs.
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Affiliation(s)
- Luguang Wang
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, United States; Department of Biological Engineering, Utah State University, Logan, UT 84322, United States
| | - Hong Liu
- Department of Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, United States.
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24
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Amalia L, Chang CY, Wang SSS, Yeh YC, Tsai SL. Recent advances in the biological depolymerization and upcycling of polyethylene terephthalate. Curr Opin Biotechnol 2024; 85:103053. [PMID: 38128200 DOI: 10.1016/j.copbio.2023.103053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/16/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Polyethylene terephthalate (PET) is favored for its exceptional properties and widespread daily use. This review highlights recent advancements that enable the development of biological tools for PET decomposition, transforming PET into valuable platform chemicals and materials in upcycling processes. Enhancing PET hydrolases' catalytic activity and efficiency through protein engineering strategies is a priority, facilitating more effective PET waste management. Efforts to create novel PET hydrolases for large-scale PET depolymerization continue, but cost-effectiveness remains challenging. Hydrolyzed monomers must add additional value to make PET recycling economically attractive. Valorization of hydrolysis products through the upcycling process is expected to produce new compounds with different values and qualities from the initial polymer, making the decomposed monomers more appealing. Advances in synthetic biology and enzyme engineering hold promise for PET upcycling. While biological depolymerization offers environmental benefits, further research is needed to make PET upcycling sustainable and economically feasible.
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Affiliation(s)
- Lita Amalia
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Chia-Yu Chang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Steven S-S Wang
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chun Yeh
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
| | - Shen-Long Tsai
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan.
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25
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Schloßhauer JL, Dondapati SK, Kubick S, Zemella A. A Cost-Effective Pichia pastoris Cell-Free System Driven by Glycolytic Intermediates Enables the Production of Complex Eukaryotic Proteins. Bioengineering (Basel) 2024; 11:92. [PMID: 38247969 PMCID: PMC10813726 DOI: 10.3390/bioengineering11010092] [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: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Cell-free systems are particularly attractive for screening applications and the production of difficult-to-express proteins. However, the production of cell lysates is difficult to implement on a larger scale due to large time requirements, cultivation costs, and the supplementation of cell-free reactions with energy regeneration systems. Consequently, the methylotrophic yeast Pichia pastoris, which is widely used in recombinant protein production, was utilized in the present study to realize cell-free synthesis in a cost-effective manner. Sensitive disruption conditions were evaluated, and appropriate signal sequences for translocation into ER vesicles were identified. An alternative energy regeneration system based on fructose-1,6-bisphosphate was developed and a ~2-fold increase in protein production was observed. Using a statistical experiment design, the optimal composition of the cell-free reaction milieu was determined. Moreover, functional ion channels could be produced, and a G-protein-coupled receptor was site-specifically modified using the novel cell-free system. Finally, the established P. pastoris cell-free protein production system can economically produce complex proteins for biotechnological applications in a short time.
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Affiliation(s)
- Jeffrey L. Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Located at the Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| | - Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 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, 14469 Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg, 14476 Potsdam, Germany (S.K.)
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Anhel AM, Alejaldre L, Goñi-Moreno Á. The Laboratory Automation Protocol (LAP) Format and Repository: A Platform for Enhancing Workflow Efficiency in Synthetic Biology. ACS Synth Biol 2023; 12:3514-3520. [PMID: 37982688 PMCID: PMC7615385 DOI: 10.1021/acssynbio.3c00397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/21/2023]
Abstract
Laboratory automation deals with eliminating manual tasks in high-throughput protocols. It therefore plays a crucial role in allowing fast and reliable synthetic biology. However, implementing open-source automation solutions often demands experimental scientists to possess scripting skills, and even when they do, there is no standardized toolkit available for their use. To address this, we present the Laboratory Automation Protocol (LAP) Format and Repository. LAPs adhere to a standardized script-based format, enhancing end-user implementation and simplifying further development. With a modular design, LAPs can be seamlessly combined to create customized, target-specific workflows. Furthermore, all LAPs undergo experimental validation, ensuring their reliability. Detailed information is provided within each repository entry, allowing users to validate the LAPs in their own laboratory settings. We advocate for the adoption of the LAP Format and Repository as a community resource, which will continue to expand, improving the reliability and reproducibility of the automation processes.
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Affiliation(s)
- Ana-Mariya Anhel
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación
y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
| | - Lorea Alejaldre
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación
y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
| | - Ángel Goñi-Moreno
- Centro
de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación
y Tecnología Agraria y Alimentaria (INIA/CSIC), 28223, Madrid, Spain
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27
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Soong YHV, Abid U, Chang AC, Ayafor C, Patel A, Qin J, Xu J, Lawton C, Wong HW, Sobkowicz MJ, Xie D. Enzyme selection, optimization, and production toward biodegradation of post-consumer poly(ethylene terephthalate) at scale. Biotechnol J 2023; 18:e2300119. [PMID: 37594123 DOI: 10.1002/biot.202300119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023]
Abstract
Poly(ethylene terephthalate) (PET) is one of the world's most widely used polyester plastics. Due to its chemical stability, PET is extremely difficult to hydrolyze in a natural environment. Recent discoveries in new polyester hydrolases and breakthroughs in enzyme engineering strategies have inspired enormous research on biorecycling of PET. This study summarizes our research efforts toward large-scale, efficient, and economical biodegradation of post-consumer waste PET, including PET hydrolase selection and optimization, high-yield enzyme production, and high-capacity enzymatic degradation of post-consumer waste PET. First, genes encoding PETase and MHETase from Ideonella sakaiensis and the ICCG variant of leaf-branch compost cutinase (LCCICCG ) were codon-optimized and expressed in Escherichia coli BL21(DE3) for high-yield production. To further lower the enzyme production cost, a pelB leader sequence was fused to LCCICCG so that the enzyme can be secreted into the medium to facilitate recovery. To help bind the enzyme on the hydrophobic surface of PET, a substrate-binding module in a polyhydroxyalkanoate depolymerase from Alcaligenes faecalis (PBM) was fused to the C-terminus of LCCICCG . The resulting four different LCCICCG variants (LCC, PelB-LCC, LCC-PBM, and PelB-LCC-PBM), together with PETase and MHETase, were compared for PET degradation efficiency. A fed-batch fermentation process was developed to produce the target enzymes up to 1.2 g L-1 . Finally, the best enzyme, PelB-LCC, was selected and used for the efficient degradation of 200 g L-1 recycled PET in a well-controlled, stirred-tank reactor. The results will help develop an economical and scalable biorecycling process toward a circular PET economy.
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Affiliation(s)
- Ya-Hue Valerie Soong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Umer Abid
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Allen C Chang
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Christian Ayafor
- Energy Engineering Program, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Akanksha Patel
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Jin Xu
- Department of Chemistry, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Carl Lawton
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Hsi-Wu Wong
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Margaret J Sobkowicz
- Department of Plastics Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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28
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Woern C, Grossmann L. Microbial gas fermentation technology for sustainable food protein production. Biotechnol Adv 2023; 69:108240. [PMID: 37647973 DOI: 10.1016/j.biotechadv.2023.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.
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Affiliation(s)
- Carlos Woern
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
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29
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Chakraborty M, Sharma B, Ghosh A, Sah D, Rai JPN. Elicitation of E-waste (acrylonitrile-butadiene styrene) enriched soil bioremediation and detoxification using Priestia aryabhattai MGP1. ENVIRONMENTAL RESEARCH 2023; 238:117126. [PMID: 37716383 DOI: 10.1016/j.envres.2023.117126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023]
Abstract
Given the rise in both usage and disposal of dangerous electronics, there is a catastrophic rise in assemblage of electronic waste (e-waste). E-waste including various plastic resins are among the most frequently discarded materials in electronic gadgets. In current digital era, managing e-waste has become universal concern. From the viewpoint of persisting lacuna of e-waste managing methods, the current study is designed to fabricate an eco-friendly e-waste treatment with native soil bacteria employing an enrichment culture method. In the presence of e-waste, indigenous soil microbes were stimulated to degrade e-waste. Microbial cultures were isolated using enrichment medium containing acrylonitrile-butadiene styrene (ABS) as the primary carbon source. Priestia aryabhattai MGP1 was found to be the most dominant e-polymer degrading bacterial isolate, as it was reported to degrade ABS plastic in disposed-off television casings. Furthermore, to increase degradation potential of MGP1, Response Surface Methodology (RSM) was adopted which resulted in optimized conditions (pH 7, shaking-speed 120 rpm, and temperature 30 °C), for maximum degradation (18.88%) after 2 months. The structural changes induced by microbial treatment were demonstrated by comparing the findings of Field emission scanning electron microscopy (FESEM) images and Fourier Transform Infrared (FTIR) spectra confirming the disappearance of ≡ C─H peaks along with C-H, C=C and C ≡N bond destabilization following degradation. Energy-dispersive X-ray (EDX) analyzers of the native and decomposed e-polymer samples revealed a considerable loss in elemental weight % of oxygen by 8.4% and silica by 0.5%. Magnesium, aluminium and chlorine which were previously present in the untreated sample, were also removed after treatment by the bacterial action. When seeds of Vigna radiata were screened using treated soil in the presence of both e-waste and the chosen potent bacterial strain, it was also discovered that there was reduced toxicity in terms of improved germination and growth metrics as a phytotoxicity criterion.
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Affiliation(s)
- Moumita Chakraborty
- Department of Environmental Sciences, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Barkha Sharma
- Department of Microbiology, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Ankita Ghosh
- Department of Environmental Sciences, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - Diksha Sah
- Department of Environmental Sciences, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India
| | - J P N Rai
- Department of Environmental Sciences, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, Uttarakhand, India.
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30
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Zhu Q, Li X, Nie Z, Wang Y, Dang T, Papadakis VG, Goula MA, Wang W, Yang Z. In-situ microbial protein production by using nitrogen extracted from multifunctional bio-electrochemical system. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119050. [PMID: 37751664 DOI: 10.1016/j.jenvman.2023.119050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
Upgrading of waste nitrogen sources is considered as an important approach to promote sustainable development. In this study, a multifunctional bio-electrochemical system with three chambers was established, innovatively achieving 2.02 g/L in-situ microbial protein (MP) production via hydrogen-oxidizing bacteria (HOB) in the protein chamber (middle chamber), along with over 2.9 L CO2/(L·d) consumption rate. Also, 69% chemical oxygen demand was degraded by electrogenic bacteria in the anode chamber, resulting in the 394.67 J/L electricity generation. Focusing on the NH4+-N migration in the system, the current intensity contributed 4%-9% in the anode and protein chamber, whereas, the negative effect of -6.69% on contribution was shown in the cathode chamber. On the view of kinetics, NH4+-N migration in anode and cathode chambers was fitted well with Levenberg-Marquardt equation (R2 > 0.92), along with the well-matched results of HOB growth in the protein chamber based on Gompertz model (R2 > 0.99). Further evaluating MPs produced by HOB, 0.45 g/L essential amino acids was detected, showing the better amino acid profile than fish and soybean. Multifunctional bio-electrochemical system revealed the economic potential of producing 6.69 €/m3 wastewater according to a simplified economic evaluation.
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Affiliation(s)
- Qile Zhu
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xiaoyue Li
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zhenchuan Nie
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yiwen Wang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Tianqi Dang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Vagelis G Papadakis
- Department of Civil Engineering, University of Patras, 26500, Rio, Patras, Greece
| | - Maria A Goula
- Laboratory of Alternative Fuels and Environmental Catalysis, Department of Chemical Engineering, University of Western Macedonia, GR-50100, Greece
| | - Wen Wang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Ziyi Yang
- Biomass Energy and Environmental Engineering Research Center, Beijing University of Chemical Technology, Beijing, 100029, China; College of Chemical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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31
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Tiong E, Koo YS, Bi J, Koduru L, Koh W, Lim YH, Wong FT. Expression and engineering of PET-degrading enzymes from Microbispora, Nonomuraea, and Micromonospora. Appl Environ Microbiol 2023; 89:e0063223. [PMID: 37943056 PMCID: PMC10686063 DOI: 10.1128/aem.00632-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Mismanagement of PET plastic waste significantly threatens human and environmental health. Together with the relentless increase in plastic production, plastic pollution is an issue of rising concern. In response to this challenge, scientists are investigating eco-friendly approaches, such as bioprocessing and microbial factories, to sustainably manage the growing quantity of plastic waste in our ecosystem. Industrial applicability of enzymes capable of degrading PET is limited by numerous factors, including their scarcity in nature. The objective of this study is to enhance our understanding of this group of enzymes by identifying and characterizing novel enzymes that can facilitate the breakdown of PET waste. This data will expand the enzymatic repertoire and provide valuable insights into the prerequisites for successful PET degradation.
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Grants
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917006 Agency for Science, Technology, and Research (A*STAR)
- C211917003 Agency for Science, Technology, and Research (A*STAR)
- A*STAR Graduate Academy Agency for Science, Technology, and Research (A*STAR)
- C233017006 Agency for Science, Technology, and Research (A*STAR)
- C233017004 Agency for Science, Technology, and Research (A*STAR)
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Affiliation(s)
- Elaine Tiong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Ying Sin Koo
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Jiawu Bi
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Lokanand Koduru
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
| | - Winston Koh
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Yee Hwee Lim
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
- Synthetic Biology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Fong Tian Wong
- Molecular Engineering Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore
- Chemical Biotechnology and Biocatalysis, Institute of Sustainability for Chemicals, Energy, and Environment (ISCE), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
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32
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Meier F, Dixon T, Williams T, Paulsen I. Navigating the Frontier of Synthetic Biology: An AI-Driven Analytics Platform for Exploring Research Trends and Relationships. ACS Synth Biol 2023; 12:3229-3241. [PMID: 37648657 DOI: 10.1021/acssynbio.3c00192] [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] [Indexed: 09/01/2023]
Abstract
The field of synthetic biology has experienced rapid growth in recent years, leading to an overwhelming amount of literature that can make it difficult to comprehend the scope and trends of the discipline. In this study, we employ topic modeling to comprehensively map research topics within synthetic biology, revealing subtopics and their relationships, as well as trends over time. We utilize metadata to identify the most significant journals and countries in the field and discuss potential policy impact on the research output. In addition, we investigate co-authorship networks to analyze collaborations among authors, institutions, and countries. We believe that our findings could serve as a valuable resource for gaining a deeper understanding of synthetic biology and provide a foundation for analyzing other disciplines.
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Affiliation(s)
- Felix Meier
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, New South Wales 2109, Australia
| | - Thom Dixon
- ARC Centre of Excellence in Synthetic Biology, Sydney, New South Wales 2109, Australia
- School of Social Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Tom Williams
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, New South Wales 2109, Australia
| | - Ian Paulsen
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Sydney, New South Wales 2109, Australia
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33
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Stephenson A, Lastra L, Nguyen B, Chen YJ, Nivala J, Ceze L, Strauss K. Physical Laboratory Automation in Synthetic Biology. ACS Synth Biol 2023; 12:3156-3169. [PMID: 37935025 DOI: 10.1021/acssynbio.3c00345] [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] [Indexed: 11/09/2023]
Abstract
Synthetic Biology has overcome many of the early challenges facing the field and is entering a systems era characterized by adoption of Design-Build-Test-Learn (DBTL) approaches. The need for automation and standardization to enable reproducible, scalable, and translatable research has become increasingly accepted in recent years, and many of the hardware and software tools needed to address these challenges are now in place or under development. However, the lack of connectivity between DBTL modules and barriers to access and adoption remain significant challenges to realizing the full potential of lab automation. In this review, we characterize and classify the state of automation in synthetic biology with a focus on the physical automation of experimental workflows. Though fully autonomous scientific discovery is likely a long way off, impressive progress has been made toward automating critical elements of experimentation by combining intelligent hardware and software tools. It is worth questioning whether total automation that removes humans entirely from the loop should be the ultimate goal, and considerations for appropriate automation versus total automation are discussed in this light while emphasizing areas where further development is needed in both contexts.
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Affiliation(s)
- Ashley Stephenson
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Microsoft Research, Redmond, Washington 98052, United States
| | - Lauren Lastra
- Microsoft Research, Redmond, Washington 98052, United States
| | - Bichlien Nguyen
- Microsoft Research, Redmond, Washington 98052, United States
| | - Yuan-Jyue Chen
- Microsoft Research, Redmond, Washington 98052, United States
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Luis Ceze
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Karin Strauss
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
- Microsoft Research, Redmond, Washington 98052, United States
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34
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Lopes Dos Santos R, Malo M, Campillo C. Spatial Control of Arp2/3-Induced Actin Polymerization on Phase-Separated Giant Unilamellar Vesicles. ACS Synth Biol 2023; 12:3267-3274. [PMID: 37909673 DOI: 10.1021/acssynbio.3c00268] [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] [Indexed: 11/03/2023]
Abstract
Deciphering the physical mechanisms underlying cell shape changes, while avoiding the cellular interior's complexity, involves the development of controlled basic biomimetic systems that imitate cell functions. In particular, the reconstruction of cytoskeletal dynamics on cell-sized giant unilamellar vesicles (GUVs) has allowed for the reconstituting of some cell-like processes in vitro. In fact, such a bottom-up strategy could be the basis for forming protocells able to reorganize or even move autonomously. However, reconstituting the subtle and controlled dynamics of the cytoskeleton-membrane interface in vitro remains an experimental challenge. Taking advantage of the lipid-induced segregation of an actin polymerization activator, we present a system that targets actin polymerization in specific domains of phase-separated GUVs. We observe actin networks localized on Lo, Ld, or on both types of domains and the actin-induced deformation or reorganization of these domains. These results suggest that the system we have developed here could pave the way for future experiments further detailing the interplay between actin dynamics and membrane heterogeneities.
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Affiliation(s)
- Rogério Lopes Dos Santos
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
| | - Michel Malo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
| | - Clément Campillo
- Université Paris-Saclay, Univ Evry, CY Cergy Paris Université, CNRS, LAMBE, 91025 Evry, Courcouronnes, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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35
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Parthiban S, Vijeesh T, Gayathri T, Shanmugaraj B, Sharma A, Sathishkumar R. Artificial intelligence-driven systems engineering for next-generation plant-derived biopharmaceuticals. FRONTIERS IN PLANT SCIENCE 2023; 14:1252166. [PMID: 38034587 PMCID: PMC10684705 DOI: 10.3389/fpls.2023.1252166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Recombinant biopharmaceuticals including antigens, antibodies, hormones, cytokines, single-chain variable fragments, and peptides have been used as vaccines, diagnostics and therapeutics. Plant molecular pharming is a robust platform that uses plants as an expression system to produce simple and complex recombinant biopharmaceuticals on a large scale. Plant system has several advantages over other host systems such as humanized expression, glycosylation, scalability, reduced risk of human or animal pathogenic contaminants, rapid and cost-effective production. Despite many advantages, the expression of recombinant proteins in plant system is hindered by some factors such as non-human post-translational modifications, protein misfolding, conformation changes and instability. Artificial intelligence (AI) plays a vital role in various fields of biotechnology and in the aspect of plant molecular pharming, a significant increase in yield and stability can be achieved with the intervention of AI-based multi-approach to overcome the hindrance factors. Current limitations of plant-based recombinant biopharmaceutical production can be circumvented with the aid of synthetic biology tools and AI algorithms in plant-based glycan engineering for protein folding, stability, viability, catalytic activity and organelle targeting. The AI models, including but not limited to, neural network, support vector machines, linear regression, Gaussian process and regressor ensemble, work by predicting the training and experimental data sets to design and validate the protein structures thereby optimizing properties such as thermostability, catalytic activity, antibody affinity, and protein folding. This review focuses on, integrating systems engineering approaches and AI-based machine learning and deep learning algorithms in protein engineering and host engineering to augment protein production in plant systems to meet the ever-expanding therapeutics market.
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Affiliation(s)
- Subramanian Parthiban
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Thandarvalli Vijeesh
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Thashanamoorthi Gayathri
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Balamurugan Shanmugaraj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Centre of Bioengineering, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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36
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Silkwood K, Dollinger E, Gervin J, Atwood S, Nie Q, Lander AD. Leveraging gene correlations in single cell transcriptomic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532643. [PMID: 36993765 PMCID: PMC10055147 DOI: 10.1101/2023.03.14.532643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many approaches have been developed to overcome technical noise in single cell RNA-sequencing (scRNAseq). As researchers dig deeper into data-looking for rare cell types, subtleties of cell states, and details of gene regulatory networks-there is a growing need for algorithms with controllable accuracy and fewer ad hoc parameters and thresholds. Impeding this goal is the fact that an appropriate null distribution for scRNAseq cannot simply be extracted from data when ground truth about biological variation is unknown (i.e., usually). RESULTS We approach this problem analytically, assuming that scRNAseq data reflect only cell heterogeneity (what we seek to characterize), transcriptional noise (temporal fluctuations randomly distributed across cells), and sampling error (i.e., Poisson noise). We analyze scRNAseq data without normalization-a step that skews distributions, particularly for sparse data-and calculate p-values associated with key statistics. We develop an improved method for selecting features for cell clustering and identifying gene-gene correlations, both positive and negative. Using simulated data, we show that this method, which we call BigSur (Basic Informatics and Gene Statistics from Unnormalized Reads), captures even weak yet significant correlation structures in scRNAseq data. Applying BigSur to data from a clonal human melanoma cell line, we identify thousands of correlations that, when clustered without supervision into gene communities, align with known cellular components and biological processes, and highlight potentially novel cell biological relationships. CONCLUSIONS New insights into functionally relevant gene regulatory networks can be obtained using a statistically grounded approach to the identification of gene-gene correlations.
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Affiliation(s)
- Kai Silkwood
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Emmanuel Dollinger
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
- Department of Mathematics, University of California, Irvine, Irvine CA
| | - Josh Gervin
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Scott Atwood
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
| | - Qing Nie
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
- Department of Mathematics, University of California, Irvine, Irvine CA
| | - Arthur D. Lander
- Center for Complex Biological Systems, University of California, Irvine, Irvine CA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine CA
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37
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Jung JK, 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. ACS Synth Biol 2023; 12:2909-2921. [PMID: 37699423 DOI: 10.1021/acssynbio.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
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 simply adding water and DNA to freeze-dried crude extracts of non-pathogenic 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. This work promises to catalyze access to interactive synthetic biology education opportunities.
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Affiliation(s)
- Jaeyoung K Jung
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam D Silverman
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | | | - Robert Kuhn
- Centennial High School, Roswell, Georgia 30076, United States
- Innovation Academy STEM High School, Alpharetta, Georgia 30009, United States
| | - Teresa Granito
- Evanston Township High School, Evanston, Illinois 60201, United States
| | - Holly M Ekas
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Brenda M Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Center for Water Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
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38
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Su Y, Liu B, Huang Z, Teng Z, Yang L, Zhu J, Huo S, Liu A. Virus-like particles nanoreactors: from catalysis towards bio-applications. J Mater Chem B 2023; 11:9084-9098. [PMID: 37697810 DOI: 10.1039/d3tb01112g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Virus-like particles (VLPs) are self-assembled supramolecular structures found in nature, often used for compartmentalization. Exploiting their inherent properties, including precise nanoscale structures, monodispersity, and high stability, these architectures have been widely used as nanocarriers to protect or enrich catalysts, facilitating catalytic reactions and avoiding interference from the bulk solutions. In this review, we summarize the current progress of virus-like particles (VLPs)-based nanoreactors. First, we briefly introduce the physicochemical properties of the most commonly used virus particles to understand their roles in catalytic reactions beyond the confined space. Next, we summarize the self-assembly of nanoreactors forming higher-order hierarchical structures, highlighting the emerging field of nanoreactors as artificial organelles and their potential biomedical applications. Finally, we discuss the current findings and future perspectives of VLPs-based nanoreactors.
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Affiliation(s)
- Yuqing Su
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Beibei Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zhenkun Huang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Zihao Teng
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Liulin Yang
- State Key Laboratory of Physical Chemistry of Solid Surface, Key Laboratory of Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jie Zhu
- National-Local Joint Engineering Research and High-Quality Utilization, Changzhou University, Changzhou 213164, China
| | - Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
| | - Aijie Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China.
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Shepherd MJ, Pierce AP, Taylor TB. Evolutionary innovation through transcription factor rewiring in microbes is shaped by levels of transcription factor activity, expression, and existing connectivity. PLoS Biol 2023; 21:e3002348. [PMID: 37871011 PMCID: PMC10621929 DOI: 10.1371/journal.pbio.3002348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/02/2023] [Accepted: 09/25/2023] [Indexed: 10/25/2023] Open
Abstract
The survival of a population during environmental shifts depends on whether the rate of phenotypic adaptation keeps up with the rate of changing conditions. A common way to achieve this is via change to gene regulatory network (GRN) connections-known as rewiring-that facilitate novel interactions and innovation of transcription factors. To understand the success of rapidly adapting organisms, we therefore need to determine the rules that create and constrain opportunities for GRN rewiring. Here, using an experimental microbial model system with the soil bacterium Pseudomonas fluorescens, we reveal a hierarchy among transcription factors that are rewired to rescue lost function, with alternative rewiring pathways only unmasked after the preferred pathway is eliminated. We identify 3 key properties-high activation, high expression, and preexisting low-level affinity for novel target genes-that facilitate transcription factor innovation. Ease of acquiring these properties is constrained by preexisting GRN architecture, which was overcome in our experimental system by both targeted and global network alterations. This work reveals the key properties that determine transcription factor evolvability, and as such, the evolution of GRNs.
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Affiliation(s)
- Matthew J. Shepherd
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Aidan P. Pierce
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Tiffany B. Taylor
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
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40
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Dixon TA, Walker RSK, Pretorius IS. Visioning synthetic futures for yeast research within the context of current global techno-political trends. Yeast 2023; 40:443-456. [PMID: 37653687 DOI: 10.1002/yea.3897] [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: 06/22/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.
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Affiliation(s)
- Thomas A Dixon
- School of Social Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Roy S K Walker
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales, Australia
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41
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Fábrega MJ, Knödlseder N, Nevot G, Sanvicente M, Toloza L, Santos-Moreno J, Güell M. Establishing a Cell-Free Transcription-Translation Platform for Cutibacterium acnes to Prototype Engineered Metabolic and Synthetic Biology. ACS Biomater Sci Eng 2023; 9:5101-5110. [PMID: 34971313 PMCID: PMC10498419 DOI: 10.1021/acsbiomaterials.1c00894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In the past few years, new bacterial-cell-free transcription-translation systems have emerged as potent and quick platforms for protein production as well as for prototyping of DNA regulatory elements, genetic circuits, and metabolic pathways. The Gram-positive commensal Cutibacterium acnes is one of the most abundant bacteria present in the human skin microbiome. However, it has recently been reported that some C. acnes phylotypes can be associated with common inflammatory skin conditions, such as acne vulgaris, whereas others seem to play a protective role, acting as possible "skin probiotics". This fact has made C. acnes become a bacterial model of interest for the cosmetic industry. In the present study we report for the first time the development and optimization of a C. acnes-based cell-free system (CFS) that is able to produce 85 μg/mL firefly luciferase. We highlight the importance of harvesting the bacterial pellet in mid log phase and maintaining CFS reactions at 30 °C and physiological pH to obtain the optimal yield. Additionally, a C. acnes promoter library was engineered to compare coupled in vitro TX-TL activities, and a temperature biosensor was tested, demonstrating the wide range of applications of this toolkit in the synthetic biology field.
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Affiliation(s)
- María-José Fábrega
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Nastassia Knödlseder
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Guillermo Nevot
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Marta Sanvicente
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Lorena Toloza
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Javier Santos-Moreno
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
| | - Marc Güell
- Department of Experimental
and Health Sciences, Pompeu Fabra University, Carrer del Dr. Aiguader 88, 00803 Barcelona, Spain
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42
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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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43
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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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44
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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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45
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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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46
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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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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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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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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: 0] [Impact Index Per Article: 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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