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Trends in Biotechnology
Journal Prestige (SJR): 3.524
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ISSN (Print) 0167-7799
Published by Elsevier Homepage  [3184 journals]
  • Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing
    • Abstract: Publication date: Available online 13 September 2019Source: Trends in BiotechnologyAuthor(s): Kutubuddin A. Molla, Yinong YangSpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of mutations, and the predictability of editing outcomes using machine learning models.
       
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    • Abstract: Publication date: October 2019Source: Trends in Biotechnology, Volume 37, Issue 10Author(s):
       
  • Editorial Bioard
    • Abstract: Publication date: October 2019Source: Trends in Biotechnology, Volume 37, Issue 10Author(s):
       
  • CRISPR-Based Directed Evolution for Crop Improvement
    • Abstract: Publication date: Available online 30 August 2019Source: Trends in BiotechnologyAuthor(s): Haroon Butt, Syed Shan-e-Ali Zaidi, Norhan Hassan, Magdy MahfouzDirected evolution involves generating diverse sequence variants of a gene of interest to produce a desirable trait under selective pressure. CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated protein 9) systems can be programmed to target any genomic locus and perform targeted directed evolution. Here, we discuss the opportunities and challenges of this emerging platform for targeted crop improvement.
       
  • Biological Applications and Toxicity Minimization of Semiconductor Quantum
           Dots
    • Abstract: Publication date: Available online 28 August 2019Source: Trends in BiotechnologyAuthor(s): Samira Filali, Fabrice Pirot, Pierre MiossecThe extraordinary potential of semiconductor quantum dots (QDs) has resulted in their widespread application in various fields, from engineering technology and the development of laboratory techniques to biomedical imaging and therapeutic strategies. However, the toxicity of QDs remains a concern and has limited their applications in human health. Better understanding of the behavior of QDs as it relates to their composition will enable the exploration of their limitations and development of a strategy to control their toxicity for potential therapeutic applications. Here, we describe approaches to minimize their toxicities according to the specific cell type, organ, or animal species, summarizing recent promising research at the cellular, organ, and whole-organism level.
       
  • Dynamic Metabolomics for Engineering Biology: Accelerating Learning Cycles
           for Bioproduction
    • Abstract: Publication date: Available online 28 August 2019Source: Trends in BiotechnologyAuthor(s): Christopher J. Vavricka, Tomohisa Hasunuma, Akihiko KondoMetabolomics is a powerful tool to rationally guide the metabolic engineering of synthetic bioproduction pathways. Current reports indicate great potential to further develop metabolomics-directed synthetic bioproduction. Advanced mass metabolomics methods including isotope flux analysis, untargeted metabolomics, and system-wide approaches are assisting the characterization of metabolic pathways and enabling the biosynthesis of more complex products. More importantly, a design, build, test, and learn (DBTL) cycle is accelerating synthetic biology research and is highly compatible with metabolomics data to further expand bioproduction capability. However, learning processes are currently the weakest link in this workflow. Therefore, guidelines for the development of metabolic learning processes are proposed based on bioproduction examples. Linking dynamic mass spectrometry (MS) methodologies together with automated learning workflows is encouraged.
       
  • Dunaliella Microalgae for Nutritional Protein: An Undervalued
           Asset
    • Abstract: Publication date: Available online 23 August 2019Source: Trends in BiotechnologyAuthor(s): Yixing Sui, Siegfried E. Vlaeminckβ-carotene production using Dunaliella microalgae is established, yet their potential as a source of protein for food and feed applications appears to be overlooked. The rich protein content and nutritional tunability of Dunaliella make these algae intriguing sources of sustainable protein. Thus, it is of societal interest to exploit these promising proteinaceous Dunaliella traits.
       
  • Multienzymatic Nanoassemblies: Recent Progress and Applications
    • Abstract: Publication date: Available online 22 August 2019Source: Trends in BiotechnologyAuthor(s): Archontoula Giannakopoulou, Elena Gkantzou, Αngeliki Polydera, Haralambos StamatisBiotechnological research has turned to multienzymatic nanoassemblies as a promising concept to host multiple applications. Here, we consider important aspects around the development and optimization of such biocatalytic systems and present current advances in utilizing bi- and multienzymatic cascade reactions in diverse fields, including ultrasensitive biosensing, development of pharmaceuticals, and conversion of natural biopolymers to valuable products, highlighting their future potential in the chemical, biotechnological, and pharmaceutical industries. Diverse co-immobilization techniques and different parameters affecting the performance of multienzymatic cascade reactions are discussed. Continuous flow processes incorporating multienzymatic nanoassemblies in different reactor configurations are also presented. This technology provides an arsenal of tools for the development of innovative and effective multienzymatic systems offering new possibilities for biocatalysts applications.
       
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    • Abstract: Publication date: September 2019Source: Trends in Biotechnology, Volume 37, Issue 9Author(s):
       
  • Editors, Contents, Cover details
    • Abstract: Publication date: September 2019Source: Trends in Biotechnology, Volume 37, Issue 9Author(s):
       
  • Using Remote Fields for Complex Tissue Engineering
    • Abstract: Publication date: Available online 20 August 2019Source: Trends in BiotechnologyAuthor(s): James P.K. Armstrong, Molly M. StevensGreat strides have been taken towards the in vitro engineering of clinically relevant tissue constructs using the classic triad of cells, materials, and biochemical factors. In this perspective, we highlight ways in which these elements can be manipulated or stimulated using a fourth component: the application of remote fields. This arena has gained great momentum over the last few years, with a recent surge of interest in using magnetic, optical, and acoustic fields to guide the organization of cells, materials, and biochemical factors. We summarize recent developments and trends in this arena and then lay out a series of challenges that we believe, if met, could enable the widespread adoption of remote fields in mainstream tissue engineering.
       
  • Designing Eukaryotic Gene Expression Regulation Using Machine Learning
    • Abstract: Publication date: Available online 17 August 2019Source: Trends in BiotechnologyAuthor(s): Ronald P.H. de Jongh, Aalt D.J. van Dijk, Mattijs K. Julsing, Peter J. Schaap, Dick de RidderControlling the expression of genes is one of the key challenges of synthetic biology. Until recently fine-tuned control has been out of reach, particularly in eukaryotes owing to their complexity of gene regulation. With advances in machine learning (ML) and in particular with increasing dataset sizes, models predicting gene expression levels from regulatory sequences can now be successfully constructed. Such models form the cornerstone of algorithms that allow users to design regulatory regions to achieve a specific gene expression level. In this review we discuss strategies for data collection, data encoding, ML practices, design algorithm choices, and finally model interpretation. Ultimately, these developments will provide synthetic biologists with highly specific genetic building blocks to rationally engineer complex pathways and circuits.
       
  • Resources to Discover and Use Short Linear Motifs in Viral Proteins
    • Abstract: Publication date: Available online 16 August 2019Source: Trends in BiotechnologyAuthor(s): Peter Hraber, Paul E. O’Maille, Andrew Silberfarb, Katie Davis-Anderson, Nicholas Generous, Benjamin H. McMahon, Jeanne M. FairViral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.
       
  • Reinventing the Wheel: Synthetic Circular RNAs for Mammalian Cell
           Engineering
    • Abstract: Publication date: Available online 14 August 2019Source: Trends in BiotechnologyAuthor(s): Alan Costello, Nga T. Lao, Niall Barron, Martin ClynesThe circular RNA renaissance is upon us. Recent reports demonstrate applications of synthetic circular RNA molecules as gene therapies and in the production of biologics from cell-based expression systems. Circular RNAs are covalently closed loop RNA species that are formed naturally through noncolinear splicing of pre-mRNA. Although once thought to be noncoding artefacts from splicing errors, it is now accepted that circular RNAs are abundant and have diverse functions in gene regulation and protein coding in eukaryotes. Numerous reports have investigated circular RNAs in various diseases, but the promise of synthetic circular RNAs in the production of recombinant proteins and as RNA-based therapies is only now coming into focus. This review highlights reported uses of synthetic circular RNAs and describes methods for generating these molecules.
       
  • Bringing Microscopy-By-Sequencing into View
    • Abstract: Publication date: Available online 12 August 2019Source: Trends in BiotechnologyAuthor(s): Alexander A. Boulgakov, Andrew D. Ellington, Edward M. MarcotteThe spatial distribution of molecules and cells is fundamental to understanding biological systems. Traditionally, microscopies based on electromagnetic waves such as visible light have been used to localize cellular components by direct visualization. However, these techniques suffer from limitations of transmissibility and throughput. Complementary to optical approaches, biochemical techniques such as crosslinking can colocalize molecules without suffering the same limitations. However, biochemical approaches are often unable to combine individual colocalizations into a map across entire cells or tissues. Microscopy-by-sequencing techniques aim to biochemically colocalize DNA-barcoded molecules and, by tracking their thus unique identities, reconcile all colocalizations into a global spatial map. Here, we review this new field and discuss its enormous potential to answer a broad spectrum of questions.
       
  • Industrial Biotechnology: To What Extent Is Responsible Innovation on the
           Agenda'
    • Abstract: Publication date: Available online 6 August 2019Source: Trends in BiotechnologyAuthor(s): Achim Rosemann, Susan Molyneux-HodgsonThe UK Industrial Biotechnology (IB) Strategy presents a consistent plan to develop the IB sector but fails to endorse an innovation process that allows for input from multiple publics. This could be disadvantageous for the bioeconomy: there are notable cases where negligence to address societal dimensions has caused innovation failure.
       
  • Detecting Harmful Algal Blooms with Isothermal Molecular Strategies
    • Abstract: Publication date: Available online 6 August 2019Source: Trends in BiotechnologyAuthor(s): Anna Toldrà, Ciara K. O’Sullivan, Mònica CampàsThe use of isothermal nucleic acid amplification strategies to detect harmful algal blooms (HABs) is in its infancy. We describe recent advances in these systems and highlight the challenges for the achievement of simple, low-cost, compact, and portable devices for field applications.
       
  • The Microbiome: A Life Science Opportunity for Our Society and Our Planet
    • Abstract: Publication date: Available online 22 July 2019Source: Trends in BiotechnologyAuthor(s): Aleksandra Małyska, Marios Nektarios Markakis, Carina F. Pereira, Marc CornelissenMicrobiome research and innovation (R&I) promises solutions to a broad range of business and societal challenges. To bridge the gap between today’s potential and the moment at which concrete applications start generating societal impact, critical-scale efforts offering visible progress on topics of public interest will be essential.
       
  • Integrating Organs-on-Chips: Multiplexing, Scaling, Vascularization, and
           Innervation
    • Abstract: Publication date: Available online 22 July 2019Source: Trends in BiotechnologyAuthor(s): DoYeun Park, Jaeseo Lee, Justin J. Chung, Youngmee Jung, Soo Hyun KimOrgans-on-chips (OoCs) have attracted significant attention because they can be designed to mimic in vivo environments. Beyond constructing a single OoC, recent efforts have tried to integrate multiple OoCs to broaden potential applications such as disease modeling and drug discoveries. However, various challenges remain for integrating OoCs towards in vivo-like operation, such as incorporating various connections for integrating multiple OoCs. We review multiplexed OoCs and challenges they face: scaling, vascularization, and innervation. In our opinion, future OoCs will be constructed to have increased predictive power for in vivo phenomena and will ultimately become a mainstream tool for high quality biomedical and pharmaceutical research.
       
  • Production and Quality Requirements of Human Platelet Lysate: A Position
           Statement from the Working Party on Cellular Therapies of the
           International Society of Blood Transfusion
    • Abstract: Publication date: Available online 17 July 2019Source: Trends in BiotechnologyAuthor(s): Katharina Schallmoser, Reinhard Henschler, Christian Gabriel, Mickey B.C. Koh, Thierry BurnoufHuman platelet lysate (HPL), rich in growth factors, is an efficient alternative supplement to fetal bovine serum (FBS) for ex vivo propagation of stromal cell-based medicinal products. Since 2014, HPL has been a focus of the Working Party for Cellular Therapies of the International Society of Blood Transfusion (ISBT). Currently, as several Good Manufacturing Practice (GMP)-compliant manufacturing protocols exist, an international consensus defining the optimal modes of industrial production, product specification, pathogen safety, and release criteria of this ancillary material (AM) is needed. This opinion article by the ISBT Working Party summarizes the current knowledge on HPL production and proposes recommendations on manufacturing and quality management in line with current technological innovations and regulations of biological products and advanced therapy medicinal products.
       
  • Hands-On Introduction to Synthetic Biology for Security Professionals
    • Abstract: Publication date: Available online 15 July 2019Source: Trends in BiotechnologyAuthor(s): Neil R. Adames, Jenna E. Gallegos, Sonia Y. Hunt, William K. So, Jean PeccoudThe rapid pace of life sciences innovations and a growing list of nontraditional actors engaging in biological research make it challenging to develop appropriate policies to protect sensitive infrastructures. To address this challenge, we developed a five-day awareness program for security professionals, including laboratory work, site visits, and lectures.
       
  • The Regulation of Wearable Medical Devices
    • Abstract: Publication date: Available online 15 July 2019Source: Trends in BiotechnologyAuthor(s): Nan Jiang, Julia E. Mück, Ali K. YetisenThis article provides a guideline for the design, manufacture, regulatory approval, and post-market surveillance (PMS) of wearable medical devices (WMDs). The integration of regulatory considerations can accelerate wearable device (WD) development from laboratory to market while mitigating device failure risks. The implementation of stringent clinical evaluations will transcend WDs beyond consumer products.
       
  • A Physiology-Inspired Multifactorial Toolbox in Soft-to-Hard
           Musculoskeletal Interface Tissue Engineering
    • Abstract: Publication date: Available online 15 July 2019Source: Trends in BiotechnologyAuthor(s): Isabel Calejo, Raquel Costa-Almeida, Rui L. Reis, Manuela E. GomesMusculoskeletal diseases are increasing the prevalence of physical disability worldwide. Within the body, musculoskeletal soft and hard tissues integrate through specific multitissue transitions, allowing for body movements. Owing to their unique compositional and structural gradients, injuries challenge the native interfaces and tissue regeneration is unlikely to occur. Tissue engineering strategies are emerging to emulate the physiological environment of soft-to-hard tissue interfaces. Advances in biomaterial design enable control over biophysical parameters, but biomaterials alone are not sufficient to provide adequate support and guide transplanted cells. Therefore, biological, biophysical, and biochemical tools can be integrated into a multifactorial toolbox, steering prospective advances toward engineering clinically relevant soft-to-hard tissue interfaces.
       
  • Synthesis of Recoded Bacterial Genomes toward Bespoke Biocatalysis
    • Abstract: Publication date: Available online 13 July 2019Source: Trends in BiotechnologyAuthor(s): Pablo I. NikelOngoing efforts in synthetic biology aim at constructing (micro)organisms with (pre)defined properties. A recent breakthrough is the chemical synthesis of a recoded Escherichia coli genome by Fredens et al. (Nature, 2019). Besides the conceptual and technological tour de force, the consequences of this unprecedented effort for whole-cell biocatalysis are multifold.
       
  • Will Following the Regulatory Script for GMOs Promote Public Acceptance of
           Gene-Edited Crops'
    • Abstract: Publication date: Available online 13 July 2019Source: Trends in BiotechnologyAuthor(s): Rod A. Herman, Maria Fedorova, Nicholas P. StorerRisk-disproportionate regulation of gene-edited crops has been proposed to gain public acceptance for this breeding technique. However, confounding safety regulations with advocacy for an underlying technology risks weakening achievement of both objectives. Dedicated factual communication and education from trusted sources is likely to better support public acceptance of gene-edited crops.
       
  • A Makerspace for Life Support Systems in Space
    • Abstract: Publication date: Available online 11 July 2019Source: Trends in BiotechnologyAuthor(s): Jessica E. Snyder, David Walsh, Peter A. Carr, Lynn J. RothschildHuman space exploration and settlement will require leaps forward in life support for environmental management and healthcare. Life support systems must efficiently use nonrenewable resources packed from Earth while increasingly relying on resources available locally in space. On-demand production of components and materials (e.g., 3D printing and synthetic biology) holds promise to satisfy the evolving set of supplies necessary to outfit human missions to space. We consider here life support systems for missions planned in the 2020s, and discuss how the maker and 'do-it-yourself' (DIY) biology communities can develop rapid, on-demand manufacturing techniques and platforms to address these needs. This Opinion invites the diverse maker community into building the next generation of flight hardware for near-term space exploration.
       
  • Improving CRISPR Technology to Sustain Animal Welfare: Response to Bailey
    • Abstract: Publication date: Available online 1 July 2019Source: Trends in BiotechnologyAuthor(s): Do Yon Kim, Su Bin Moon, Yong-Sam Kim
       
  • Synthetic Biology and the United Nations
    • Abstract: Publication date: Available online 27 June 2019Source: Trends in BiotechnologyAuthor(s): Hung-En Lai, Caoimhe Canavan, Loren Cameron, Simon Moore, Monika Danchenko, Todd Kuiken, Zuzana Sekeyová, Paul S. FreemontSynthetic biology is a rapidly emerging interdisciplinary field of science and engineering that aims to redesign living systems through reprogramming genetic information. The field has catalysed global debate among policymakers and publics. Here we describe how synthetic biology relates to these international deliberations, particularly the Convention on Biological Diversity (CBD).
       
  • New Horizons in Acetogenic Conversion of One-Carbon Substrates and
           Biological Hydrogen Storage
    • Abstract: Publication date: Available online 27 June 2019Source: Trends in BiotechnologyAuthor(s): Volker MüllerStrictly anaerobic, acetogenic (acetate-forming) bacteria are characterized by a reductive pathway in which two mol of CO2 are reduced to one mol of acetyl coenzyme A (acetyl-CoA) and then further to acetate, ethanol, or butyrate. Therefore, they have come into focus for an alternative, CO2-based bioeconomy. Other one-carbon (C1) substrates, such as formic acid or methanol, are promising feedstocks for an alternative bioeconomy using acetogens as biocatalysts that have been somewhat overlooked. In addition, acetogens, such as Acetobacterium woodii and Thermoanaerobacter kivui, have a unique enzyme system capable of reducing CO2 to formate with H2 as reductant that is superior over any chemical catalyst for CO2-based hydrogen storage. Therefore, acetogens are also promising candidates in the hydrogen economy as potential catalysts for hydrogen storage or production.
       
  • Accelerating Climate Resilient Plant Breeding by Applying Next-Generation
           Artificial Intelligence
    • Abstract: Publication date: Available online 21 June 2019Source: Trends in BiotechnologyAuthor(s): Antoine L. Harfouche, Daniel A. Jacobson, David Kainer, Jonathon C. Romero, Antoine H. Harfouche, Giuseppe Scarascia Mugnozza, Menachem Moshelion, Gerald A. Tuskan, Joost J.B. Keurentjes, Arie AltmanBreeding crops for high yield and superior adaptability to new and variable climates is imperative to ensure continued food security, biomass production, and ecosystem services. Advances in genomics and phenomics are delivering insights into the complex biological mechanisms that underlie plant functions in response to environmental perturbations. However, linking genotype to phenotype remains a huge challenge and is hampering the optimal application of high-throughput genomics and phenomics to advanced breeding. Critical to success is the need to assimilate large amounts of data into biologically meaningful interpretations. Here, we present the current state of genomics and field phenomics, explore emerging approaches and challenges for multiomics big data integration by means of next-generation (Next-Gen) artificial intelligence (AI), and propose a workable path to improvement.
       
  • Optogenetics in the Era of Cerebral Organoids
    • Abstract: Publication date: Available online 18 June 2019Source: Trends in BiotechnologyAuthor(s): Zahra Shiri, Susan Simorgh, Somayeh Naderi, Hossein BaharvandThe human brain has been deemed the most complex organ and has captivated neuroscientists for decades. Most studies of this organ have relied on reductionist model systems. Although all model systems are essentially wrong, cerebral organoids so far represent the closest recapitulation of human brain development and disease both in terms of cell diversity and organization. The optogenetic technique can be used in this context to study the functional neuroanatomy of the brain, to examine the neural circuits, and to determine the etiology of neurological disorders. In this opinion article, we suggest ways in which optogenetics can be combined with cerebral organoids to allow unprecedented precision and accuracy in studying normal and aberrant neurodevelopmental processes and, as well, neurodegenerative diseases.
       
  • New Frontiers for Biofabrication and Bioreactor Design in
           Microphysiological System Development
    • Abstract: Publication date: Available online 12 June 2019Source: Trends in BiotechnologyAuthor(s): Jonathon Parrish, Khoon Lim, Boyang Zhang, Milica Radisic, Tim B.F. WoodfieldMicrophysiological systems (MPSs) have been proposed as an improved tool to recreate the complex biological features of the native niche with the goal of improving in vitro–in vivo extrapolation. In just over a decade, MPS technologies have progressed from single-tissue chips to multitissue plates with integrated pumps for perfusion. Concurrently, techniques for biofabrication of complex 3D constructs for regenerative medicine and 3D in vitro models have evolved into a diverse toolbox for micrometer-scale deposition of cells and cell-laden bioinks. However, as the complexity of biological models increases, experimental throughput is often compromised. This review discusses the existing disparity between MPS complexity and throughput, then examines an MPS-terminated biofabrication line to identify the hurdles and potential approaches to overcoming this disparity.
       
  • CRISPR-Mediated Gene Editing: Scientific and Ethical Issues
    • Abstract: Publication date: Available online 7 June 2019Source: Trends in BiotechnologyAuthor(s): Jarrod BaileyThere remains substantial evidence to warrant great concern over the poor efficiency and specificity of clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genetic modification (GM), despite relatively minor improvements compared to other GM methods. These issues cause persistent, adverse, ethical, and scientific consequences for GM animals, which may never be sufficiently resolvable.
       
  • New Prospects for Modified Algae in Heavy Metal Adsorption
    • Abstract: Publication date: Available online 4 June 2019Source: Trends in BiotechnologyAuthor(s): Sze Yin Cheng, Pau-Loke Show, Beng Fye Lau, Jo-Shu Chang, Tau Chuan LingHeavy metal pollution is one of the most pervasive environmental problems globally. Novel finely tuned algae have been proposed as a means to improve the efficacy and selectivity of heavy metal biosorption. This article reviews current research on selective algal heavy metal adsorption and critically discusses the performance of novel biosorbents. We emphasize emerging state-of-the-art techniques that customize algae for enhanced performance and selectivity, particularly molecular and chemical extraction techniques as well as nanoparticle (NP) synthesis approaches. The mechanisms and processes for developing novel algal biosorbents are also presented. Finally, we discuss the applications, challenges, and future prospects for modified algae in heavy metal biosorption.
       
  • Paradigm Shift in Algal H2 Production: Bypassing Competitive
           Processes
    • Abstract: Publication date: Available online 4 June 2019Source: Trends in BiotechnologyAuthor(s): Szilvia Z. Tóth, Iftach YacobyHydrogen is a promising energy carrier, but producing it sustainably remains a challenge. Green algae can produce hydrogen photosynthetically using their efficient but oxygen-sensitive hydrogenases. Recent strategies aiming to bypass competing processes provide a promising route for scaling up algal hydrogen production.
       
  • Antimicrobial Inks: The Anti-Infective Applications of Bioprinted
           Bacterial Polysaccharides
    • Abstract: Publication date: Available online 3 June 2019Source: Trends in BiotechnologyAuthor(s): Ronan R. McCarthy, Muhammad Wajid Ullah, Eujin Pei, Guang YangBioprinting is a rapidly emerging technology with the potential to transform the biomedical sector. Here, we discuss how a range of bacterial polysaccharides with antibiofilm and antibacterial activity could be used to augment current bioink formulations to improve their biocompatibility and tackle the spread of antibiotic-resistant infections.
       
  • Thermodynamic Activity-Based Solvent Design for Bioreactions
    • Abstract: Publication date: Available online 31 May 2019Source: Trends in BiotechnologyAuthor(s): Anton Wangler, Christoph Held, Gabriele SadowskiTo improve the kinetics of enzyme-catalyzed reactions, cosolvents are commonly added to reaction mixtures. The search for a good cosolvent is still empirical and experimentally based. We discuss a thermodynamic activity-based approach that improves biocatalytic processes by predicting cosolvent influences on Michaelis constants, ultimately reducing time and cost.
       
  • Translating Biofabrication to the Market
    • Abstract: Publication date: Available online 29 May 2019Source: Trends in BiotechnologyAuthor(s): Pedro F. CostaBiofabrication holds great potential to revolutionize important industries in the health, food, and textile sectors, but its translation to market is still challenging. I analyze the current state of innovation and commercialization in biofabrication and try to assess its limitations, strengths, and future progress.
       
  • Designing Biobased Recyclable Polymers for Plastics
    • Abstract: Publication date: Available online 28 May 2019Source: Trends in BiotechnologyAuthor(s): Rajni Hatti-Kaul, Lars J. Nilsson, Baozhong Zhang, Nicola Rehnberg, Stefan LundmarkSeveral concurrent developments are shaping the future of plastics. A transition to a sustainable plastics system requires not only a shift to fossil-free feedstock and energy to produce the carbon-neutral building blocks for polymers used in plastics, but also a rational design of the polymers with both desired material properties for functionality and features facilitating their recyclability. Biotechnology has an important role in producing polymer building blocks from renewable feedstocks, and also shows potential for recycling of polymers. Here, we present strategies for improving the performance and recyclability of the polymers, for enhancing degradability to monomers, and for improving chemical recyclability by designing polymers with different chemical functionalities.
       
  • Plant–Bacterial Degradation of Polyaromatic Hydrocarbons in the
           Rhizosphere
    • Abstract: Publication date: Available online 23 May 2019Source: Trends in BiotechnologyAuthor(s): Olga Turkovskaya, Anna MuratovaStudies of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria and plant root exudate enzymes from contaminated rhizospheres suggest that pollutant rhizodegradation involves the joint work of bacteria and plants. Plant–microbial associations with coupled metabolic capabilities that completely degrade PAHs while avoiding the formation of dangerous intermediates are biotechnologically promising.
       
  • Advances in Microfluidic Blood–Brain Barrier (BBB) Models
    • Abstract: Publication date: Available online 23 May 2019Source: Trends in BiotechnologyAuthor(s): Arianna Oddo, Bo Peng, Ziqiu Tong, Yingkai Wei, Wing Yin Tong, Helmut Thissen, Nicolas Hans VoelckerTherapeutic options for neurological disorders currently remain limited. The intrinsic complexity of the brain architecture prevents potential therapeutics from reaching their cerebral target, thus limiting their efficacy. Recent advances in microfluidic technology and organ-on-chip systems have enabled the development of a new generation of in vitro platforms that can recapitulate complex in vivo microenvironments and physiological responses. In this context, microfluidic-based in vitro models of the blood–brain barrier (BBB) are of particular interest as they provide an innovative approach for conducting research related to the brain, including modeling of neurodegenerative diseases and high-throughput drug screening. Here, we present the most recent advances in BBB-on-chip devices and examine validation steps that will strengthen their future applications.
       
  • Oligonucleotide Analogs and Mimics for Sensing Macromolecular Biocompounds
    • Abstract: Publication date: Available online 17 May 2019Source: Trends in BiotechnologyAuthor(s): Katarzyna Bartold, Agnieszka Pietrzyk-Le, Francis D’Souza, Wlodzimierz KutnerLiving organisms create life-sustaining macromolecular biocompounds including biopolymers. Artificial polymers can selectively recognize biocompounds and are more resistant to harsh physical, chemical, and physiological conditions than biopolymers are. Due to recognition at a molecular level, molecularly imprinted polymers (MIPs) provide powerful tools to correlate structure with biological functionality and are often used to build next-generation chemosensors. We envision an increasing emergence of nucleic acid analogs (NAAs) or biorelevant monomers built into nature-mimicking polymers. For example, if nucleobases bearing monomers arranged by a complementary template are polymerized to form NAAs, the resulting MIPs will open up novel perspectives for synthesizing NAAs. Despite their usefulness, it is still challenging to use MIPs to devise adaptive biomaterials and to implement them in point-of-care testing.
       
  • Recent Advances in Biosensors for Detecting Cancer-Derived Exosomes
    • Abstract: Publication date: Available online 16 May 2019Source: Trends in BiotechnologyAuthor(s): Nan Cheng, Dan Du, Xinxian Wang, Dong Liu, Wentao Xu, Yunbo Luo, Yuehe LinEarly detection and effective treatments are two of the greatest challenges in the fight against cancer. Cancer-derived exosomes are attractive biomarkers for the early diagnosis and therapeutic response evaluation of cancer. Here, we review recent advances in biosensors for the detection of cancer-derived exosomes. We discuss the potential exosomal biomarkers of various cancers, which can be applied as indicative targets in the design of biosensors. We further describe the fabrication of exosome detection biosensors with respect to biological recognition strategies and signal transduction techniques, which involve integrated scientific and technological aspects of analytical chemistry and nanotechnology. Furthermore, future research directions and challenges in using cancer-derived exosomes for point-of-care (POC) testing are presented.
       
  • Microchannels in Development, Survival, and Vascularisation of Tissue
           Analogues for Regenerative Medicine
    • Abstract: Publication date: Available online 7 May 2019Source: Trends in BiotechnologyAuthor(s): Khoon S. Lim, Marissa Baptista, Shahana Moon, Tim B.F. Woodfield, Jelena Rnjak-KovacinaMicrochannels are simple, perfusable architectural features engineered into biomaterials to promote mass transport of solutes to cells, effective cell seeding and compartmentalisation for tissue engineering applications, control over spatiotemporal distribution of molecules and ligands, and survival, integration, and vascularisation of engineered tissue analogues in vivo. Advances in biofabrication have led to better control over microchannel fabrication in 3D scaffolds, enabling sophisticated designs that drive the development of complex tissue structures. This review addresses the importance of microchannel structures in biomaterial design and regenerative medicine, and discusses their function, fabrication methods, and proposed mechanisms underlying their effects.
       
  • Wearable Devices for Single-Cell Sensing and Transfection
    • Abstract: Publication date: Available online 6 May 2019Source: Trends in BiotechnologyAuthor(s): Lingqian Chang, Yu-Chieh Wang, Faheem Ershad, Ruiguo Yang, Cunjiang Yu, Yubo FanWearable healthcare devices are mainly used for biosensing and transdermal delivery. Recent advances in wearable biosensors allow for long-term and real-time monitoring of physiological conditions at a cellular resolution. Transdermal drug delivery systems have been further scaled down, enabling wide selections of cargo, from natural molecules (e.g., insulin and glucose) to bioengineered molecules (e.g., nanoparticles). Some emerging nanopatches show promise for precise single-cell gene transfection in vivo and have advantages over conventional tools in terms of delivery efficiency, safety, and controllability of delivered dose. In this review, we discuss recent technical advances in wearable micro/nano devices with unique capabilities or potential for single-cell biosensing and transfection in the skin or other organs, and suggest future directions for these fields.
       
  • Grand Research Challenges for Sustainable Industrial Biotechnology
    • Abstract: Publication date: Available online 1 May 2019Source: Trends in BiotechnologyAuthor(s): Adrie J.J. Straathof, S. Aljoscha Wahl, Kirsten R. Benjamin, Ralf Takors, Nick Wierckx, Henk J. NoormanFuture manufacturing will focus on new, improved products as well as on new and enhanced production methods. Recent biotechnological and scientific advances, such as CRISPR/Cas and various omic technologies, pave the way to exciting novel biotechnological research, development, and commercialization of new sustainable products. Rigorous mathematical descriptions of microbial cells and consortia thereof will enable deeper biological understanding and lead to powerful in silico cellular models. Biological engineering, namely model-based design together with synthetic biology, will accelerate the construction of robust and high-performing microorganisms. Using these organisms, and ambitions towards zero-concepts with respect to emissions and excess resources in bioprocess engineering, industrial biotechnology is expected to become highly integrated into sustainable generations of technology systems.
       
  • Pick a Tag and Explore the Functions of Your Pet Protein
    • Abstract: Publication date: Available online 27 April 2019Source: Trends in BiotechnologyAuthor(s): Giel Vandemoortele, Sven Eyckerman, Kris GevaertProtein tags have been essential for advancing our knowledge of the function of proteins, their localization, and the mapping of their interaction partners. Expressing epitope-tagged proteins has become a standard practice in every life science laboratory and, thus, continues to enable new studies. In recent years, several new tagging moieties have entered the limelight, many of them bringing new functionalities, such as targeted protein degradation, accurate quantification, and proximity labeling. Other novel tags aim at tackling research questions in challenging niches. In this review, we elaborate on recently introduced tags and the opportunities they provide for future research endeavors. In addition, we highlight how the genome-engineering revolution may boost the field of protein tags.
       
  • Enabling the Advanced Bioeconomy through Public Policy Supporting
           Biofoundries and Engineering Biology
    • Abstract: Publication date: Available online 26 April 2019Source: Trends in BiotechnologyAuthor(s): Richard Kitney, Michael Adeogun, Yoshiyuki Fujishima, Ángel Goñi-Moreno, Richard Johnson, Mary Maxon, Scott Steedman, Sean Ward, David Winickoff, Jim PhilpThe bioeconomy concept is proliferating globally. However, the enabling roles of biotechnology may be getting sidelined in the strategies of some countries. A goal for engineering biology is alignment with the engineering design cycle to enable more rapid commercialization. This paper considers several policy options to remove critical technical barriers to commercialization.
       
  • Bioprocessing Butanol into More Valuable Butyl Butyrate
    • Abstract: Publication date: Available online 23 April 2019Source: Trends in BiotechnologyAuthor(s): Fengxue Xin, Wenming Zhang, Min JiangThe toxicity of butanol to microbial cells makes it difficult to scale-up the acetone–butanol–ethanol (ABE) fermentation process. Bioconversion of butanol into more valuable and nontoxic short-chain esters, such as butyl butyrate which is widely used in the food, beverage, and biofuel sectors, offers a promising alternative.
       
  • Production and Biomedical Application of Flavivirus-like
           Particles
    • Abstract: Publication date: Available online 16 April 2019Source: Trends in BiotechnologyAuthor(s): Ewelina Krol, Gabriela Brzuska, Boguslaw SzewczykMany viruses belonging to the Flaviviridae family are transmitted by invertebrate vectors. Among those transmitted by mosquitos, there are many human pathogens of great medical importance, such as Japanese encephalitis virus, West Nile virus, dengue virus, Zika virus, or yellow fever virus. Millions of people contract mosquito-borne diseases each year, leading to thousands of deaths. Co-circulation of genetically similar flaviviruses in the same areas result in the generation of crossreactive antibodies, which is of serious concern for the development of effective vaccines and diagnostic tests. This review provides comprehensive insight into the potential use of virus-like particles as safe and effective antigens in both diagnostics tests, as well as in the development of vaccines against several mosquito-borne flaviviruses.
       
  • Engineering Polymerases for New Functions
    • Abstract: Publication date: Available online 16 April 2019Source: Trends in BiotechnologyAuthor(s): Timothy A. Coulther, Hannah R. Stern, Penny J. BeuningDNA polymerases are critical tools in biotechnology, enabling efficient and accurate amplification of DNA templates, yet many desired functions are not readily available in natural DNA polymerases. New or improved functions can be engineered in DNA polymerases by mutagenesis or through the creation of protein chimeras. Engineering often necessitates the development of new techniques, such as selections in water-in-oil emulsions that connect genotype to phenotype and allow more flexibility in engineering than phage display. Engineering efforts have led to DNA polymerases that can withstand extreme conditions or the presence of inhibitors, as well as polymerases with the ability to copy modified DNA templates. In this review we discuss polymerases for biotechnology that have been reported along with tools to enable further development.
       
  • Deep Eutectic Solvents as Efficient Solvents in Biocatalysis
    • Abstract: Publication date: Available online 16 April 2019Source: Trends in BiotechnologyAuthor(s): Magdalena Pätzold, Sascha Siebenhaller, Selin Kara, Andreas Liese, Christoph Syldatk, Dirk Holtmann‘Ideal’ solvents in biocatalysis have to fulfill a large number of requirements, such as high substrate solubility, high enzyme activity and stability, and positive effects on reaction equilibrium. In the past decades, many enzymatic synthesis routes in water-based and nonaqueous (organic solvents, ionic or supercritical fluids) reaction media have been developed. However, no solvent meets every demand for different reaction types at the same time, and there is still a need for novel solvents suited for different reaction types and applications. Deep eutectic solvents (DESs) have recently been evaluated as solvents in different biocatalytic reactions. They can improve substrate supply, conversion, and stability. The best results were obtained when the DES is formed by the substrates of an enzymatic reaction.
       
  • Mimicking the Articular Joint with In Vitro Models
    • Abstract: Publication date: Available online 16 April 2019Source: Trends in BiotechnologyAuthor(s): Susanna Piluso, Yang Li, Florencia Abinzano, Riccardo Levato, Liliana Moreira Teixeira, Marcel Karperien, Jeroen Leijten, René van Weeren, Jos MaldaTreating joint diseases remains a significant clinical challenge. Conventional in vitro cultures and animal models have been helpful, but suffer from limited predictive power for the human response. Advanced models are therefore required to mimic the complex biological interactions within the human joint. However, the intricate structure of the joint microenvironment and the complex nature of joint diseases have challenged the development of in vitro models that can faithfully mimic the in vivo physiological and pathological environments. In this review, we discuss the current in vitro models of the joint and the progress achieved in the development of novel and potentially more predictive models, and highlight the application of new technologies to accurately emulate the articular joint.
       
  • CRISPR/Cas-Mediated Base Editing: Technical Considerations and Practical
           Applications
    • Abstract: Publication date: Available online 14 April 2019Source: Trends in BiotechnologyAuthor(s): Kutubuddin A. Molla, Yinong YangGenome editing with CRISPR/Cas has rapidly gained popularity. Base editing, a new CRISPR/Cas-based approach, can precisely convert one nucleotide to another in DNA or RNA without inducing a double-strand DNA break (DSB). A combination of catalytically impaired nuclease variants with different deaminases has yielded diverse base-editing platforms that aim to address the key limitations such as specificity, protospacer adjacent motif (PAM) compatibility, editing window length, bystander editing, and sequence context preference. Because new base editors significantly reduce unintended editing in the genome, they hold great promise for treating genetic diseases and for developing superior agricultural crops. We review here the development of various base editors, assess their technical advantages and limitations, and discuss their broad applications in basic research, medicine, and agriculture.
       
  • Integrated Printed Microfluidic Biosensors
    • Abstract: Publication date: Available online 13 April 2019Source: Trends in BiotechnologyAuthor(s): Jacky F.C. Loo, Aaron H.P. Ho, Anthony P.F. Turner, Wing Cheung MakIntegrated printed microfluidic biosensors are one of the most recent point-of-care (POC) sensor developments. Fast turnaround time for production and ease of customization, enabled by the integration of recognition elements and transducers, are key for on-site biosensing for both healthcare and industry and for speeding up translation to real-life applications. Here, we provide an overview of recent progress in printed microfluidics, from the 2D to the 4D level, accompanied by novel sensing element integration. We also explore the latest trends in integrated printed microfluidics for healthcare, especially POC diagnostics, and food safety applications.
       
  • Newest Methods for Detecting Structural Variations
    • Abstract: Publication date: Available online 19 March 2019Source: Trends in BiotechnologyAuthor(s): Wouter De Coster, Christine Van BroeckhovenA substantial amount of structural variation in the human genome remains uninvestigated due to the limitations of existing technologies, the presence of repetitive sequences, and the complexity of a diploid genome. New technologies have been developed, increasing resolution and appreciation of structural variation and how it affects human diversity and disease. The genetic etiology of most patients with complex disorders such as neurodegenerative brain diseases is not yet elucidated, complicating disease diagnosis, genetic counseling, and understanding of underlying pathological mechanisms needed to develop therapeutic interventions. Here, we focus on innovative progress and opportunities provided by the newest methods such as linked read sequencing, strand-specific sequencing, and long-read sequencing. Finally, we describe a strategy for generating a comprehensive catalog of structural variations across populations.
       
  • Microparticles in Contact with Cells: From Carriers to Multifunctional
           Tissue Modulators
    • Abstract: Publication date: Available online 19 March 2019Source: Trends in BiotechnologyAuthor(s): Mafalda D. Neto, Mariana B. Oliveira, João F. ManoFor several decades microparticles have been exclusively and extensively explored as spherical drug delivery vehicles and large-scale cell expansion carriers. More recently, microparticulate structures gained interest in broader bioengineering fields, integrating myriad strategies that include bottom-up tissue engineering, 3D bioprinting, and the development of tissue/disease models. The concept of bulk spherical micrometric particles as adequate supports for cell cultivation has been challenged, and systems with finely tuned geometric designs and (bio)chemical/physical features are current key players in impacting technologies. Herein, we critically review the state of the art and future trends of biomaterial microparticles in contact with cells and tissues, excluding internalization studies, and with emphasis on innovative particle design and applications.
       
  • Mitigating Clonal Variation in Recombinant Mammalian Cell Lines
    • Abstract: Publication date: Available online 18 March 2019Source: Trends in BiotechnologyAuthor(s): Jae Seong Lee, Helene Faustrup Kildegaard, Nathan E. Lewis, Gyun Min LeeMammalian expression platforms are primary production systems for therapeutic proteins that require complex post-translational modifications. Current processes used for developing recombinant mammalian cell lines generate clonal cell lines with high phenotypic heterogeneity, which has puzzled researchers that use mammalian cell culture systems for a long time. Advances in mammalian genome-editing technologies and systems biotechnology have shed light on clonal variation and enabled rational cell engineering in a targeted manner. We propose a new approach for a next-generation cell line development platform that can minimize clonal variation. Combined with the knowledge-based selection of ideal integration sites and engineering targets, targeted integration-based cell line development will allow tailored control of recombinant gene expression with predicted phenotypes.
       
  • Towards Self-Transfecting Nucleic Acid Nanostructures for Gene Regulation
    • Abstract: Publication date: Available online 14 March 2019Source: Trends in BiotechnologyAuthor(s): Saketh Gudipati, Ke Zhang, Jessica L. RougeNanoscale structures of therapeutic nucleic acids have shown enormous potential to help clinicians realize the promise of personaliz ed medicine using gene-specific treatments. With the advent of better sequencing through bioinformatic approaches and advancements in nucleic acid stabilization chemistries, the field of synthetic nucleic acid nanomaterials has advanced tremendously. This review focuses on an emerging strategy geared at gene silencing without the use of traditional polycation-based transfection agents and discusses how such nanostructures are being chemically tailored to navigate biological systems to improve their circulation time and biodistribution. We also address important challenges moving forward, including quantification of delivery and the multiplexing of sequences for regulating gene networks – a goal well suited for this unique class of materials.
       
  • Engineering Zymomonas mobilis for Robust Cellulosic Ethanol
           Production
    • Abstract: Publication date: Available online 13 March 2019Source: Trends in BiotechnologyAuthor(s): Juan Xia, Yongfu Yang, Chen-Guang Liu, Shihui Yang, Feng-Wu BaiGreat effort has been devoted to engineering Saccharomyces cerevisiae with pentose metabolism through the oxido-reductase pathway for cellulosic ethanol production, but intrinsic cofactor imbalance is observed, which substantially compromises ethanol yield. Zymomonas mobilis not only can be engineered for pentose metabolism through the isomerase pathway without cofactor imbalance but also metabolizes sugar through the Entner–Doudoroff pathway with less ATP and biomass produced for more sugar to be used for ethanol production. Moreover, the availabilities of genome sequence information for multiple Z. mobilis strains and advanced genetics tools have laid a solid foundation for engineering this species, and the self-flocculation of the bacterial cells also presents significant advantages for bioprocess engineering. Here, we highlight some of recent advances in these aspects.
       
  • Multifunctional Magnetic Gold Nanomaterials for Cancer
    • Abstract: Publication date: Available online 9 March 2019Source: Trends in BiotechnologyAuthor(s): Pradip Das, Parisa Fatehbasharzad, Miriam Colombo, Luisa Fiandra, Davide ProsperiThe integration of multiple imaging and therapeutic agents into a customizable nanoplatform for accurate identification and rapid prevention of cancer is attracting great attention. Among the available theranostic nanosystems, magnetic gold nanoparticles are particularly promising as they exhibit unique physicochemical properties that can support multiple functions, including cancer diagnosis by magnetic resonance imaging, X-ray computed tomography, Raman and photoacoustic imaging, drug delivery, and plasmonic photothermal and photodynamic therapies. This review gives an overview of recent advances in the fabrication of multifunctional gold nanohybrids with magnetic and optical properties and their successful demonstration in multimodal imaging and therapy of cancer. Concerns around toxicity of these nanomaterials are also discussed in view of an imminent transition to clinical practice.
       
 
 
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