Future Biotechnology Research Articles

Alaskan plants and their assembled rhizosphere communities vary in their responses to soil antimony

Arctic and subarctic soils are undergoing rapid changes that influence vegetation, bacteria, and their interactions with each other and the environment. Our objective was to understand how rhizosphere bacterial communities from diverse Alaskan boreal and tundra habitats and common Alaskan plant species interact with an anthropogenic soil stressor. A variety of soil types associated with plant communities from Interior and Arctic Alaska were selected. Soils were seeded with a forb, grass, or tree, spiked with antimony (Sb) or kept as a control, and grown for 60 days under warm conditions. Plant growth and Sb uptake, rhizosphere prokaryote composition, and mycorrhizal colonization data were collected. Antimony altered rhizosphere bacterial community richness, diversity, and composition, dependent on soil type and plant identity. Of 20 rhizosphere bacterial orders, Burkholderiales proved most responsive to Sb, but the responses varied by plant species. Plant species' uptake of Sb were strongly influenced by soil biological, chemical, and physical properties. Picea glauca (white spruce) accumulated hyperaccumulator-level Sb concentrations in its roots in 2 of 6 soils. Future biotechnology applications to mitigate land degradation in this environment must acknowledge the complex interactions between vegetation, soils, microbes, and climate for successful utilization.

Tools and Methods for Investigating Synthetic Metal-Catalyzed Reactions in Living Cells.

Although abiotic catalysts are capable of promoting numerous new-to-nature reactions, only a small subset has so far been successfully integrated into living systems. Research in intracellular catalysis requires an interdisciplinary approach that takes advantage of both chemical and biological tools as well as state-of-the-art instrumentations. In this perspective, we will focus on the techniques that have made studying metal-catalyzed reactions in cells possible using representative examples from the literature. Although the lack of quantitative data in vitro and in vivo has somewhat limited progress in the catalyst development process, recent advances in characterization methods should help overcome some of these deficiencies. Given its tremendous potential, we believe that intracellular catalysis will play a more prominent role in the development of future biotechnologies and therapeutics.

Demystifying the momilactone pathway.

Re-channeling metabolic routes in Nicotiana benthamiana allows elucidation and reconstitution of the biosynthesis of the natural products momilactones A and B. Insights into how plants make these and other natural crop protection chemicals promise future biotechnologies for sustainable agriculture.

Engineering microalgae as a whole cell catalyst for PET degradation.

Plastic pollution has become a serious issue on Earth. Although efficient industrial recycling processes exist, a significant fraction of plastic waste still ends up in nature, where it can endure for centuries. Slow mechanical and chemical decay lead to the formation of micro- and nanoplastics, which are washed from land into rivers and finally end up in the oceans. As such particles cannot be efficiently removed from the environment, biological degradation mechanisms are highly desirable. Several enzymes have been described that are capable of degrading certain plastic materials such as polyethylene terephthalate (PET). Such enzymes have a huge potential for future biotechnology applications. However, they require model systems that can be efficiently adapted to very specific conditions. Here, we present detailed instructions, how to convert the model diatom Phaeodactylum into a solar-fueled microbial cell factory for PETase expression, resulting in a whole cell catalyst for PET degradation at moderate temperatures under saltwater conditions.

Driving innovation in biotechnology with Private-Public Partnerships: A Singapore perspective

Public and private sector institutions share different goals and perspectives, but they can form a formidable innovation drive when they join forces. Private-Public Partnerships (PPPs), common in biomedical and pharmaceutical research, are entities where interactions and integrated innovation can take place to serve business and societal goals. In this perspective, we examine how PPPs function in the life sciences sector, and how they differ from other models of private-public cooperation. We examine two successful examples of PPPs in the Singaporean biomedical field. Finally, we look into the role PPPs can have in the development of future biotechnology applications, as one of the ways small(er) countries can develop significant bioengineering competencies and translate scientific research into real-life applications.

Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar

Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2, which have the highest similarity (≥ 90\%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1-encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 Å, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors.

Harvesting Microalgae for Food and Energy Products

AbstractMicroalgae are promising biological factories for diverse natural products. Microalgae tout high productivity, and their biomass has value in industrial products ranging from biofuels, feedstocks, food additives, cosmetics, pharmaceuticals, and as alternatives to synthetic or animal‐derived products. However, harvesting microalgae to extract bioproducts is challenging given their small size and suspension in liquid growth media. In response, technologic developments have relied upon mechanical, chemical, thermal, and biological means to dewater microalgal suspensions and further extract bioproducts. In this review, the effectiveness and considerations were evaluated for the implementation of microalgae harvesting techniques. Nonbiological methods—filtration, chemical, electrical, and magnetic nanoparticle flocculation, centrifugation, hydrothermal liquefaction, and solvent‐based extraction, as well as biological coculture‐based methods are included. Recent advances in coculture algae‐flocculation technologies that involve bacteria and fungi are summarized. These produce a variety of natural bioproducts, which show promise in fuel and food additive applications. Furthermore, this review addresses the developments of genetic tools and resources to optimize the productivity and harvesting of microalgae or to provide new bioproducts via heterologous expression. Finally, a glimpse of future biotechnologies that will converge to produce, harvest, and process microalgae using sustainable and cost‐effective methods is offered.

Prospects of mutation breeding in grapefruit (Citrus paradisi Macf.)

Grapefruit is considered as a minor citrus crop in Pakistan and its annual production is less than 0.5% of total citrus production. Grapefruit industry is depending upon pink flesh cultivar ‘Shamber’ and need varietal diversification. Mutation breeding has played a pivotal role in grapefruit crop improvement and most of the commercial cultivars are bud sports or induced mutants which were selected and later released as new cultivars. Flesh color enhancement, seedlessness and low furanocoumarin level have been main objectives for grapefruit breeders. An overview of potential of mutation breeding in grapefruit and leading mutants produced is presented in the following sections. Though physical mutagens have been more successful, breeders’ interest is rising in more precise and targeted mutagenesis technologies including CRISPR/Cas9 which has enormous potential in genome editing and could shorten breeding and selection cycle. The available leading grapefruit cultivars were screened for horticultural traits and potential candidate varieties has been selected for diversification and selection of better parents for breeding programs. Several putative mutants have been developed using gamma irradiated plant material. The effect of irradiation on plant growth, morphology and biochemical properties has been evaluated and salient findings are discussed. The developed genetically diverse material could be useful for future biotechnology applications.

Diversity and antimicrobial activity of endophytic fungi isolated from Securinega suffruticosa in the Yellow River Delta.

Securinega suffruticosa (Pall.) Rehd is an excellent natural secondary shrub in the Shell Islands of Yellow River Delta. The roots of S. suffruticosa have high medicinal value and are used to treat diseases, such as neurasthenia and infant malnutrition. Any organism that is isolated from this species is of immense interest due to its potential novel bioactive compounds. In this research, the distribution and diversity of culturable endophytic fungi in S. suffruticosa were studied, and the endophytic fungi with antimicrobial activity were screened. A total of 420 endophytic fungi isolates were obtained from the S. suffruticosa grown in Shell Islands, from which 20 genera and 35 species were identified through morphological and internal transcribed spacer (ITS) sequence analyses. Chaetomium, Fusarium, Cladosporium, and Ceratobasidium were the dominant genera. The high species richness S (42), Margalef index D' (5.6289), Shannon-Wiener index H' (3.1000), Simpson diversity index Ds (0.9459), PIE index (0.8670), and evenness Pielou index J (0.8719) and a low dominant index λ (0.0541) indicated the high diversity of endophytic fungi in S. suffruticosa, the various species of endophytic fungi with obvious tissue specificity. The inhibition percentages of the 12 species of such endophytic fungi against Colletotrichum siamense were 3.6%-26.3%. C. globosum, Fusarium sp.3, and C. ramotenellum had a high antibacterial activity against Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. The Minimum Inhibitory Concentration (MIC) and the Minimum Bactericidal Concentration (MBC) were between 0.5 mg/mL and 2 mg/mL. Alkaloid content detection indicated that endophytic fungi had a high alkaloid content, whereas the alkaloid contents of C. globosum and Fusarium sp.3 reached 0.231% and 0.170%, respectively. Members belonging to the endophytic fungal community in the S. suffruticosa of Shell Islands that may be used as antagonists and antibacterial agents for future biotechnology applications were identified for the first time.

An alternative future of digitized genetic information and digital procreation

This research looks what happens to human reproduction when human genetic information is digitized. By employing speculative design as a transdisciplinary strategy to construct such an alternative future to open up public dialogues, it aims to stimulate audiences in an artistic way to deliberate two key questions: (1) how will biotechnology recondition and recontextualize the natural processes of genetic information (i.e. expression, replication, transmission and mutation) and our physiological processes (e.g. reproduction)? And (2) what might be the ethical, legal and social implications (ELSI) for using such biotechnology? To this end, this practice-based research introduces the ‘e-gamete Digital Procreation Service’ (2019) – a speculative design project that has been developed as an approach to invite audiences to a future scenario of network-transmitted genetic information and computer-simulated human procreation. The carefully designed future service (an ironic practice of commercialization) allows human reproduction to take place outside of the human body. Audiences are encouraged to contemplate what novel situations might occur within their own futures and to consider broader questions like how family, parenthood, marriage, etc. are redefined and what new social relationships might emerge. By employing speculative design as an artistic research tool/tactic to step outside the technical limitations and craft the future service, the project asks vital question about the future in a provocative and quasi-realistic manner. Thus, the research forms a unique entanglement of sensitive topics by dealing with future biotechnology and human reproduction.

Ecophysiological Features of Polar Soil Unicellular Microalgae1.

Due to their ecological, physiological, and molecular adaptations to low and varying temperatures, as well as varying seasonal irradiances, polar non-marine eukaryotic microalgae could be suitable for low-temperature biotechnology. Adaptations include the synthesis of compounds from different metabolic pathways that protect them against stress. Production of biological compounds and various biotechnological applications, for instance, water treatment technology, are of interest to humans. To select prospective strains for future low-temperature biotechnology in polar regions, temperature and irradiance of growth requirements (Q10 and Ea of 10 polar soil unicellular strains) were evaluated. In terms of temperature, three groups of strains were recognized: (i) cold-preferring where temperature optima ranged between 10.1 and 18.4°C, growth rate 0.252 and 0.344 · d-1 , (ii) cold- and warm-tolerating with optima above 10°C and growth rate 0.162-0.341 · d-1 , and (iii) warm-preferring temperatures above 20°C and growth rate 0.249-0.357 · d-1 . Their light requirements were low. Mean values Q10 for specific growth rate ranged from 0.7 to 3.1. The lowest Ea values were observed on cold-preferring and the highest in the warm-preferring strains. One strain from each temperature group was selected for PN and RD measurements. The PN :RD ratio of the warm-preferring strains was less affected by temperature similarly as Q10 and Ea. For future biotechnological applications, the strains with broad temperature tolerance (i.e., the group of cold- and warm-tolerating and warm-preferring strains) will be most useful.

Progress and challenges in engineering cyanobacteria as chassis for light‐driven biotechnology

SummaryCyanobacteria are prokaryotic phototrophs that, in addition to being excellent model organisms for studying photosynthesis, have tremendous potential for light‐driven synthetic biology and biotechnology. These versatile and resilient microorganisms harness the energy of sunlight to oxidise water, generating chemical energy (ATP) and reductant (NADPH) that can be used to drive sustainable synthesis of high‐value natural products in genetically modified strains. In this commentary article for the Synthetic Microbiology Caucus we discuss the great progress that has been made in engineering cyanobacterial hosts as microbial cell factories for solar‐powered biosynthesis. We focus on some of the main areas where the synthetic biology and metabolic engineering tools in cyanobacteria are not as advanced as those in more widely used heterotrophic chassis, and go on to highlight key improvements that we feel are required to unlock the full power of cyanobacteria for future green biotechnology.

Role of the malic enzyme in metabolism of the halotolerant methanotroph Methylotuvimicrobium alcaliphilum 20Z.

The bacteria utilizing methane as a growth substrate (methanotrophs) are important constituents of the biosphere. Methanotrophs mitigate the emission of anthropogenic and natural greenhouse gas methane to the environment and are the promising agents for future biotechnologies. Many aspects of CH4 bioconversion by methanotrophs require further clarification. This study was aimed at characterizing the biochemical properties of the malic enzyme (Mae) from the halotolerant obligate methanotroph Methylotuvimicrobium alcaliphilum 20Z. The His6-tagged Mae was obtained by heterologous expression in Escherichia coli BL21 (DE3) and purified by affinity metal chelating chromatography. As determined by gel filtration and non-denaturating gradient gel electrophoresis, the molecular mass of the native enzyme is 260 kDa. The homotetrameric Mae (65x4 kDa) catalyzed an irreversible NAD+-dependent reaction of L-malate decarboxylation into pyruvate with a specific activity of 32 ± 2 units mg-1 and Km value of 5.5 ± 0.8 mM for malate and 57 ± 5 μM for NAD+. The disruption of the mae gene by insertion mutagenesis resulted in a 20-fold increase in intracellular malate level in the mutant compared to the wild type strain. Based on both enzyme and mutant properties, we conclude that the malic enzyme is involved in the control of intracellular L-malate level in Mtm. alcaliphilum 20Z. Genomic analysis has revealed that Maes present in methanotrophs fall into two different clades in the amino acid-based phylogenetic tree, but no correlation of the division with taxonomic affiliations of the host bacteria was observed.

The methylation pattern of DNA and complex correlations with gene expressions during TuMV infection in Chinese cabbage

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most important economic crops. However, its yield and quality can be severely threatened by Turnip mosaic virus (TuMV). Emerging evidence indicates that epigenetic mechanisms, especially DNA methylation, play an important role in regulating gene expression. Therefore, identification of resistance genes modified by DNA methylation during the virus infection would provide a critical clue for improving disease resistance breeding programs. Here, we present detailed analysis for the correlation of DNA methylation and gene expression involved in several anti-pathogen pathways. We also found that different methylation patterns exist in different methylation sites (CG, CHG, and CHH, where H represents A, G, or T) and genomic regions. Furthermore, we identified disease-resistant genes related to the nucleotide binding site-leucine-rich repeats family, auxin, salicylic acid signaling transduction, cell wall biosynthesis, and protein degradation among the different methylated genes (DMGs) suggesting that these genes may be modified by DNA methylation and work together to activate an immune response. The identified DMGs are a valuable resource for discovering resistance genes. Our study not only provides valuable data for future biotechnology research and epigenetic studies, but also helps to explore how the epigenetic mechanisms modify antiviral pathways.

Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits.

Synthetic logic circuits have been proposed as potential solutions for theranostics of biotechnological problems. One proposed model is the engineering of bacteria cells to create logic gates, and the communication between the bacteria populations will enable the circuit operation. In this paper, we analyze the quality of bacteria-based synthetic logic circuit through molecular communications that represent communication along a bus between three gates. In the bacteria-based synthetic logic circuit, the system receives environmental signals as molecular inputs and will process this information through a cascade of synthetic logic gates and free diffusion channels. We analyze the performance of this circuit by evaluating its quality and its relationship to the channel capacity of the molecular communications links that interconnect the bacteria populations. Our results show the effect of the molecular environmental delay and molecular amplitude differences over both the channel capacity and circuit quality. Furthermore, based on these metrics, we also obtain an optimum region for the circuit operation resulting in an accuracy of 80% for specific conditions. These results show that the performance of synthetic biology circuits can be evaluated through molecular communications, and lays the groundwork for combined systems that can contribute to future biomedical and biotechnology applications.

Biotechnology, Big Data and Artificial Intelligence.

Developments in biotechnology are increasingly dependent on the extensive use of big data, generated by modern high-throughput instrumentation technologies, and stored in thousands of databases, public and private. Future developments in this area depend, critically, on the ability of biotechnology researchers to master the skills required to effectively integrate their own contributions with the large amounts of information available in these databases. This article offers a perspective of the relations that exist between the fields of big data and biotechnology, including the related technologies of artificial intelligence and machine learning and describes how data integration, data exploitation, and process optimization correspond to three essential steps in any future biotechnology project. The article also lists a number of application areas where the ability to use big data will become a key factor, including drug discovery, drug recycling, drug safety, functional and structural genomics, proteomics, pharmacogenetics, and pharmacogenomics, among others.

Filamentous phages: masters of a microbial sharing economy.

Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering andmolecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.

Future Biotechnology

Abstract The field of biotechnology is large and could be considered tritely as simply the development of technology that is based on biology. It is clear that the concepts of biotechnology can spread to cover many different fields of application and so the future developments in biotechnology will be similarly wide-ranging across many fields of applications. Here we focus onto medical biotechnology and further refine our discussion onto considering aspects of genetics and nanotechnologies that could impact on the development of future biotechnologies in the medical field. These areas that we consider in this brief article provide the basis for a panel discussion on Future Biotechnology at the European Biotechnology Congress held in Valencia, Spain in April 2019.

Cyborgology and bioprinting: The biotechnological future of maxillofacial rehabilitation

Maxillofacial prostheses now benefit from the growing advances in converging technologies, such as nanotechnologies, biotechnologies, informatics and cognitivism (NBIC). Instead of being laid and passive, prostheses can now ensure true neurophysiological interactions with their wearers through complex phenomena of hybridization and vicariance. These new devices get closer to “maxillofacial amplification prosthesesâ€, by improving the world perception through restored sensory properties and new extra-sensory properties. These technological devices also benefit from the bioengineering revolution that will soon allow the bioprinting of graft prostheses with an intimate integration to the organic maxillofacial support. In this article, the authors would like to present some major advances in cyborgology and bio-printing in maxillofacial hybridization contexts. (Int J Maxillofac Prosthetics 2019;1:20-26)

Dimond, R. and Stephen, N.Legalising Mitochondrial Donation: Enacting Ethical Futures in UK Biomedical Politics. Printforce, The Netherlands: Palgrave Macmillan. 2018. 147pp £43.99 (Hardcover) ISBN 978‐3‐319‐74644‐9 £34.99 (eBook) ISBN 978‐3‐319‐74645‐6

Rebecca Dimond and Neil Stephens’ book Legalising Mitochondrial Donation: Enacting Ethical Futures in UK Biomedical Politics documents how the UK became the first country to legalise mitochondrial donation. Mitochondrial donation is a technique developed to prevent the transmission of mitochondrial disease from mother to child using part of a donated egg to replace faulty mitochondria (Castro 2016). The book contributes to wider science and technology studies (STS) commentary on mitochondrial donation and is rich with data extracts, from both stakeholder interviews and documentary analysis. The text then employs a thematic analysis that is both ‘structural’ and ‘microsocial’ (p. 16) to demonstrate its thesis. The book argues, ‘The legalisation of mitochondrial donation is the latest iteration of a particular UK sociotechnical around human embryo research and use is rendered ethical through a permissive but highly scrutinised system’ (p. 1). The book realises this argument through rich historical examples as well as the mitochondrial donation case and, importantly, raises how this sociotechnical imaginary will impact future biotechnology debates in the UK context, for example, genome editing. Legalising Mitochondrial Donation: Enacting Ethical Futures in UK Biomedical Politics draws upon a theoretical base from within STS and sociology, particularly Jasanoff and Kim's recent work on sociotechnical imaginaries (Jasanoff and Kim 2015). Dimond and Stephens complete an effective unpacking of the sociotechnical imaginary and its relevance for the mitochondrial donation debate. Dimond and Stephens ground their claim of the UK's significant as a case study by citing its historical reputation as a permissive regulator of biomedical technologies. In providing this historical overview, the authors cite numerous examples from both interviews and documentary analyses that hone in on imaginaries and performances in debates in quangos, governmental bodies and parliamentary committees. After setting up these organisations as integral to the process of legalising biomedical technologies, the book examines how consensus-building activities and public gauging tools were used by these organisations to implement the legalisation of mitochondrial donation in the UK. The book's establishment of the lens of ‘for’ clusters and ‘against’ clusters represents a novel contribution to STS methodological approaches and assists in generating a new understanding of the mitochondrial donation debate. This approach allows the reader to visualise the networks and cements the authors’ claim that links forged by the ‘for’ group allowed them to establish a collective narrative surrounding mitochondrial donation techniques that was eventually integral to their success in legalising these technologies (p. 27). Dimond and Stephens also identify political strategies used by the ‘for’ cluster to achieve its goal. Examples of these strategies include the establishment of Doug Turnbull as a ‘promissory agent’ (p. 27) and collective action by the ‘for’ cluster to enact an ethical future which aligned with the established sociotechnical imaginary of embryo research in the UK (p. 27). Legalising Mitochondrial Donation: Enacting Ethical Futures in UK Biomedical Politics is of relevance to those interested in social constructivist approaches to new and emerging biomedical and, or, assisted reproductive technologies. As such, it is likely to appeal to STS scholars, medical anthropologists and sociologists. Scholars reading this book will benefit from the strong empirical and conceptual investigations of this text. Through examining the sociotechnical imaginaries, the book aims to explore the ‘operation of power’ (p. 131). However, the text could be more explicit about what this operation of power refers to, and the ways in which these operations of power were performed successfully by the ‘for’ cluster and unsuccessfully by the ‘against’ cluster. If this were achieved the reader could have a better understanding of the role of power dynamics within the particular sociotechnical imaginary set out by Dimond and Stephens. Dimond and Stephens’ book sits within a small but very well-established epoch of literature that employs critical approaches to the mitochondrial debate through interdisciplinary approaches. An example of such literature is the special issue of the journal Bioethics (Volume 31, Issue 1) that focused on issues raised by mitochondrial replacement techniques. Furthermore, Dimond and Stephens’ book builds upon critical perspectives on mitochondrial donation arising from bioethics, STS and social science disciplines, filling gaps in the academic discussion before building upon their own thesis using empirical data and conceptual approaches in this far longer text. The book highlights an emerging area of study where the authors look forward to the relationship between mitochondrial donation and the next ‘potential iteration of this imaginary’ (p. 137) which relates to the contestation of the genome-editing debate. Legalising Mitochondrial Donation gives a clear and concise historical account of the debate and Dimond and Stephens demonstrate their thesis, concerning the role that sociotechnical imaginaries play in the legalisation of new and emerging biomedical technologies in the UK.