Metabolic regulation of epigenetic remodeling in immune cells.
Abstract Immune cells are capable of sensing various signals in the microenvironment and turning on specific immune functions in response. The appropriate transition of immune cells into diverse functional states, which is crucial for immunity, involves complex and well-regulated changes in transcriptional program. Accumulating evidence shows that epigenetic remodeling plays a central role in mediating the transcriptional program for immune cell activation and immunological memory. Concurrently, immune cells undergo significant metabolic reprogramming during immune response. Here we review recent studies that demo...
Source: Current Opinion in Biotechnology - January 15, 2020 Category: Biotechnology Authors: Britt EC, John SV, Locasale JW, Fan J Tags: Curr Opin Biotechnol Source Type: research

Flavonoids and gut health.
Abstract Flavonoids are dietary non-nutrient bioactives with antioxidant and anti-inflammatory properties. Fruits, vegetables, nuts, legumes, and tea are rich in flavonoids. After consumption, flavonoids are extensively metabolized by the gut microbiota and host tissues. Flavonoid metabolism exhibits extensive variation between individuals. It is plausible that inter-individual differences in flavonoid metabolism impact the immune system. Pre-clinical studies have characterized direct and indirect mechanisms by which flavonoids modulate intestinal immune function. This includes modulation of T cell differentiation...
Source: Current Opinion in Biotechnology - January 15, 2020 Category: Biotechnology Authors: Pei R, Liu X, Bolling B Tags: Curr Opin Biotechnol Source Type: research

Phenotypic variation in spatially structured microbial communities: ecological origins and consequences.
Abstract Microbial cells in nature live within dense multispecies conglomerates, forming a self-organizing ecosystem. In such assemblies, genotypes interact with each other in a myriad of ways, driving community dynamics and functionalities. The role of interactions between genotypes and their consequences for spatial structure and functional outcomes are being increasingly studied to understand the ecology and evolution of microbial communities. An increasing body of work with simple microbial populations has elucidated that phenotypic variation, that is, differences within isogenic cells can have important conse...
Source: Current Opinion in Biotechnology - January 15, 2020 Category: Biotechnology Authors: D'Souza GG Tags: Curr Opin Biotechnol Source Type: research

Harnessing ecological and evolutionary principles to guide the design of microbial production consortia.
Abstract Bacteria are widely used for commercially producing biomolecules. However, attempts to rationally design production strains and optimize cultivation conditions are frequently counteracted by the emergence of mutants with reduced production characteristics that decrease overall process yield. The reason why these mutants arise is likely because of a mismatch between the ecological conditions under which bacteria evolved in nature and the situation they experience in an industrial setting. Thus, there is a great potential for improving biotechnological production processes by implementing eco-evolutionary k...
Source: Current Opinion in Biotechnology - January 15, 2020 Category: Biotechnology Authors: Giri S, Shitut S, Kost C Tags: Curr Opin Biotechnol Source Type: research

Caenorhabditis elegans as a model system for human diseases.
This article considers the potential of C. elegans as a versatile platform for systematic dissection of the molecular basis of human disease, focusing on neurodegenerative disorders. PMID: 31951916 [PubMed - as supplied by publisher] (Source: Current Opinion in Biotechnology)
Source: Current Opinion in Biotechnology - January 14, 2020 Category: Biotechnology Authors: Markaki M, Tavernarakis N Tags: Curr Opin Biotechnol Source Type: research

Harnessing the metabolic potential of Streptococcus thermophilus for new biotechnological applications.
Abstract Streptococcus thermophilus is a microorganism extensively used in cheese and yogurt fermentation. Its economic value, combined with an increasing demand for novel starter cultures with improved functionality, foster numerous research efforts to unravel key aspects of S. thermophilus physiology. Several phenotypic traits are linked to industrial applications. These include sugar metabolism, proteolysis and the production of important metabolites such as acetaldehyde, exopolysaccharides, and vitamins, which affect the organoleptic properties of fermented foods and protocooperation with Lactobacillus delbrue...
Source: Current Opinion in Biotechnology - January 13, 2020 Category: Biotechnology Authors: Markakiou S, Gaspar P, Johansen E, Zeidan AA, Neves AR Tags: Curr Opin Biotechnol Source Type: research

RNA and protein-based nanodevices for mammalian post-transcriptional circuits.
Abstract Mammalian synthetic gene circuits have promise in biological and medical research due to their capability of controlling cellular functions. Especially, post-transcriptional circuits are growing in interest because of features that include compatibility and superior safety. RNA-based molecular nanodevices are often a core component in these circuits. RNA nanodevices that act as translational controllers should be suitable for designing genetic circuits that execute complex functions. In this review, we introduce recent progress in designing synthetic RNA-based circuitry and building mammalian post-transcr...
Source: Current Opinion in Biotechnology - January 11, 2020 Category: Biotechnology Authors: Kawasaki S, Ono H, Hirosawa M, Saito H Tags: Curr Opin Biotechnol Source Type: research

Network inference in systems biology: recent developments, challenges, and applications.
Abstract One of the most interesting, difficult, and potentially useful topics in computational biology is the inference of gene regulatory networks (GRNs) from expression data. Although researchers have been working on this topic for more than a decade and much progress has been made, it remains an unsolved problem and even the most sophisticated inference algorithms are far from perfect. In this paper, we review the latest developments in network inference, including state-of-the-art algorithms like PIDC, Phixer, and more. We also discuss unsolved computational challenges, including the optimal combination of al...
Source: Current Opinion in Biotechnology - January 9, 2020 Category: Biotechnology Authors: Saint-Antoine MM, Singh A Tags: Curr Opin Biotechnol Source Type: research

Making brilliant colors by microorganisms.
Abstract Anthocyanins, the colorful molecules found in plants, have positive health effects in humans, and are used as food colorants and nutraceuticals. Currently, the industrial supply of anthocyanins largely depends on extraction from plants, a method that lacks robustness and is potentially unsustainable. A promising alternative is biosynthesis by metabolically engineered microbes, which has achieved considerable success. Here, we review recent progress on anthocyanin biosynthesis in engineered microorganisms and the engineering approaches for enhancing anthocyanin production. The de novo anthocyanin productio...
Source: Current Opinion in Biotechnology - January 9, 2020 Category: Biotechnology Authors: Zha J, Wu X, Koffas MA Tags: Curr Opin Biotechnol Source Type: research

Systems and synthetic biology tools for advanced bioproduction hosts.
Abstract The genomic revolution ushered in an era of discovery and characterization of enzymes from novel organisms that fueled engineering of microbes to produce commodity and high-value compounds. Over the past decade advances in synthetic biology tools in recent years contributed to significant progress in metabolic engineering efforts to produce both biofuels and bioproducts resulting in several such related items being brought to market. These successes represent a burgeoning bio-economy; however, significant resources and time are still necessary to progress a system from proof-of-concept to market. In order...
Source: Current Opinion in Biotechnology - January 8, 2020 Category: Biotechnology Authors: Chen Y, Banerjee D, Mukhopadhyay A, Petzold CJ Tags: Curr Opin Biotechnol Source Type: research

Organs-on-a-chip as model systems for multifactorial musculoskeletal diseases.
Abstract Multifactorial diseases affecting musculoskeletal tissues are characterized by the interactions between multiple tissues, such as muscle and nerves in neuromuscular diseases, or multiple cellular components in a tissue, as in the case of bone tumors, interacting with bone cells. For these diseases also the influence of different biophysical and biochemical stimuli, such as mechanical overload and inflammatory molecules in osteoarthritis, play a key role. To investigate these complex phenomena, organ-on-a-chip systems have been developed, taking into account specific disease characteristics such as being d...
Source: Current Opinion in Biotechnology - January 8, 2020 Category: Biotechnology Authors: Arrigoni C, Lopa S, Candrian C, Moretti M Tags: Curr Opin Biotechnol Source Type: research

Biotechnologies to tackle the challenge of neoantigen identification.
Abstract Among immune correlates of clinical responses, tumor-specific neoantigens took the spotlight as relevant targets for cancer immunotherapy. The implementation of pipelines for personalized cancer therapy remains challenging due to the privacy, that is patient-specificity, of neoantigens and the low-frequency of neoantigen-specific T cells in blood and tumor samples. To overcome these obstacles, recent developments in the field of biotechnology have allowed the multiplexed identification of neoepitope-specific T cells. This review addresses the pros and cons of conventional neoantigen screening methodologie...
Source: Current Opinion in Biotechnology - January 8, 2020 Category: Biotechnology Authors: Arnaud M, Duchamp M, Bobisse S, Renaud P, Coukos G, Harari A Tags: Curr Opin Biotechnol Source Type: research

Cellular agriculture - industrial biotechnology for food and materials.
Abstract Fundamental changes of agriculture and food production are inevitable. Providing food for an increasing population will be a great challenge that coincides with the pressure to reduce negative environmental impacts of conventional agriculture. Biotechnological manufacturing of acellular products for food and materials has already been piloted but the full profit of cellular agriculture is just beginning to emerge. Cultured meat is a promising technology for animal-based proteins but still needs further development. The concept of plant cells as food offers a very attractive alternative to obtain healthy, ...
Source: Current Opinion in Biotechnology - January 8, 2020 Category: Biotechnology Authors: Rischer H, Szilvay GR, Oksman-Caldentey KM Tags: Curr Opin Biotechnol Source Type: research

The emergence and promise of single-cell temporal-omics approaches.
Abstract Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes during embryonic development, disease progression and in response to stimuli. Likewise, new methods have extended the possibilities of single-cell analysis by measuring the transcriptome while simultaneously capturing information on lineage or past molecular events. These emerging approaches have the common strategy of querying a static snapshot for inf...
Source: Current Opinion in Biotechnology - January 6, 2020 Category: Biotechnology Authors: Lederer AR, La Manno G Tags: Curr Opin Biotechnol Source Type: research

Nutritional enhancement in plants - green and greener.
Abstract The global challenges of ensuring sufficient safe and nutritious food for all are enshrined within the Sustainable Development Goals. As our planet's population continues to grow, and as the impacts of climate change and environmental pollution become more visible to all, new solutions continue to be sought as to how best address these. Transgenic crops specifically focussed on delivering health-beneficial compounds will likely play a role in this, and this review will consider several areas where good progress has been made. In particular, the transition from basic research to commercial product is a jou...
Source: Current Opinion in Biotechnology - January 3, 2020 Category: Biotechnology Authors: Napier JA, Sayanova O Tags: Curr Opin Biotechnol Source Type: research

Yeast systems biology in understanding principles of physiology underlying complex human diseases.
Abstract Complex human diseases commonly arise from deregulation of cell growth, metabolism, and/or gene expression. Yeast is a eukaryal model organism that is widely used to study these processes. Yeast systems biology benefits from the ability to exert fine experimental control over the cell growth rate and nutrient composition, which allows orthogonal experimental design and generation of multi-omics data at high resolution. This has led to several insights on the principles of cellular physiology, including many cellular processes associated with complex human diseases. Here we review these biological insights...
Source: Current Opinion in Biotechnology - December 31, 2019 Category: Biotechnology Authors: Yu R, Nielsen J Tags: Curr Opin Biotechnol Source Type: research

Biobanks for life sciences and personalized medicine: importance of standardization, biosafety, biosecurity, and data management.
l K Abstract Biological samples such as tissues, blood and other body fluids, plants or seeds, prokaryotic and eukaryotic cells or isolated biomolecules as well as associated data are the essential raw material for research and development in medicine, biotechnology and agriculture. The collection, processing, preservation, and storage of these resources, in addition to provision of access, are key activities of biobanks or biological resource centres. Biobanks have to ensure proper quality of samples and data, ethical and legal compliance as well as transparent and efficient access procedures. In this context the...
Source: Current Opinion in Biotechnology - December 30, 2019 Category: Biotechnology Authors: Müller H, Dagher G, Loibner M, Stumptner C, Kungl P, Zatloukal K Tags: Curr Opin Biotechnol Source Type: research

Cross-linking/mass spectrometry to get a closer view on protein interaction networks.
z A Abstract Just recently, chemical cross-linking combined with mass spectrometry (XL-MS) has emerged as valuable tool to study protein interaction networks on the system-wide level. The current challenges in XL-MS are to develop robust workflows enabling a comprehensive capture of dynamic biological assemblies in their native environment in a routine manner. In this review, we will highlight both the latest technological developments as well as selected applications of XL-MS for investigating protein networks in cells, organisms, and tissue. In addition, different bioinformatics tools for data analysis will be p...
Source: Current Opinion in Biotechnology - December 28, 2019 Category: Biotechnology Authors: Iacobucci C, Götze M, Sinz A Tags: Curr Opin Biotechnol Source Type: research

Current status of pan-genome analysis for pathogenic bacteria.
Abstract Biological knowledge accumulated over the decades and advances in computational methods have facilitated the implementation of pan-genome analysis that aims at better understanding of genotype-phenotype associations of a specific group of organisms. Pan-genome analysis has been shown to be an effective approach to better understand a clade of pathogenic bacteria because it helps developing various and tailored therapeutic strategies on the basis of their biological similarities and differences. Here, we review recent progress in the pan-genome analysis of pathogenic bacteria. In particular, we focus on co...
Source: Current Opinion in Biotechnology - December 28, 2019 Category: Biotechnology Authors: Kim Y, Gu C, Kim HU, Lee SY Tags: Curr Opin Biotechnol Source Type: research

Microfluidic systems for cancer diagnostics.
Abstract Although not employed in the clinic as of yet, microfluidic systems are likely to become a key technology for cancer diagnostics and prognosis. Microfluidic devices have been developed for the analysis of various biomarkers including circulating tumor cells, cell-free DNA, exosomes, and proteins, primarily in liquid biopsies such as serum, plasma, and whole blood, avoiding the need for tumor tissue biopsies. Here, we summarize microfluidic technological advances that are used in cancer diagnosis, prognosis, and to monitor its progression and recurrence, that will likely lead to personalized therapies. In ...
Source: Current Opinion in Biotechnology - December 28, 2019 Category: Biotechnology Authors: Garcia-Cordero JL, Maerkl SJ Tags: Curr Opin Biotechnol Source Type: research

Biotechnological upcycling of plastic waste and other non-conventional feedstocks in a circular economy.
Abstract The envisaged circular economy requires absolute carbon efficiency and in the long run abstinence from fossil feedstocks, and integration of industrial production with end-of-life waste management. Non-conventional feedstocks arising from industrial production and societal consumption such as CO2 and plastic waste may soon enable manufacture of multiple products from simple bulk chemicals to pharmaceuticals using biotechnology. The change to these feedstocks could be faster than expected by many, especially if the true cost, including the carbon footprint of products, is considered. The efficiency of biot...
Source: Current Opinion in Biotechnology - December 24, 2019 Category: Biotechnology Authors: Blank LM, Narancic T, Mampel J, Tiso T, O'Connor K Tags: Curr Opin Biotechnol Source Type: research

Modular Analysis and Design of Biological Circuits.
Abstract Modularity has been the subject of intense investigation in systems biology for more than two decades. Whether modularity holds in biological networks is a question that has attracted renewed attention in recent years with the advent of synthetic biology, mostly as a convenient property to perform bottom-up design of complex systems. A number of studies have appeared, which fundamentally challenge modularity as a property of engineered biological circuits. Here, we summarize some of these studies and potential engineering solutions that have been proposed to enable modular composition of biological circui...
Source: Current Opinion in Biotechnology - December 23, 2019 Category: Biotechnology Authors: Grunberg TW, Del Vecchio D Tags: Curr Opin Biotechnol Source Type: research

Environmental drivers of metabolic heterogeneity in clonal microbial populations.
Abstract Microorganisms perform multiple metabolic functions that shape the global cycling of elements, health and disease of their host organisms, and biotechnological processes. The rates, at which different metabolic activities are performed by individual cells, can vary between genetically identical cells within clonal populations. While the molecular mechanisms that result in such metabolic heterogeneity have attracted considerable interest, the environmental conditions that shape heterogeneity and its consequences have received attention only in recent years. Here, we review the environmental drivers that le...
Source: Current Opinion in Biotechnology - December 21, 2019 Category: Biotechnology Authors: Schreiber F, Ackermann M Tags: Curr Opin Biotechnol Source Type: research

Design and application of oncolytic viruses for cancer immunotherapy.
rullo V Abstract The approval of the first oncolytic virus (OV) for the treatment of metastatic melanoma and the recent discovery that the use of oncolytic viruses may enhance cancer immunotherapies targeted against various immune checkpoint proteins have attracted great interest in the field of cancer virotherapy. OVs are designed to target and kill cancer cells leaving normal cell unharmed. OV infection and concomitant cancer cell killing stimulate anti-tumour immunity and modulates tumour microenvironment towards less immunosuppressive phenotype. The intrinsic capacity of OVs to turn immunologically cold tumour...
Source: Current Opinion in Biotechnology - December 21, 2019 Category: Biotechnology Authors: Ylösmäki E, Cerullo V Tags: Curr Opin Biotechnol Source Type: research

Tracing metabolic flux through time and space with isotope labeling experiments.
Abstract Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require ...
Source: Current Opinion in Biotechnology - December 18, 2019 Category: Biotechnology Authors: Allen DK, Young JD Tags: Curr Opin Biotechnol Source Type: research

Engineered bacteriophages as programmable biocontrol agents.
Abstract Bacteriophages (or 'phages') can be potent biocontrol agents but their potential has not been fully realized due to inherent limitations of natural phages. By leveraging new tools in synthetic biology, natural phages can be engineered to overcome these limitations to markedly improve their efficacy and programmability. Engineered phages can be used for targeted detection and removal of pathogens, in situ microbiome editing, gene delivery and programmable control of phage-bacterial interactions. In this mini review we examine different ways natural phages can be engineered as effective biocontrol agents th...
Source: Current Opinion in Biotechnology - December 17, 2019 Category: Biotechnology Authors: Huss P, Raman S Tags: Curr Opin Biotechnol Source Type: research

Beyond the semi-synthetic artemisinin: metabolic engineering of plant-derived anti-cancer drugs.
Abstract The discovery and supply of plant-derived anti-cancer compounds remain challenging given their low bioavailability and structural complexity. Reconstituting the pathways of these compounds in heterologous hosts is a promising solution; however, requires the complete elucidation of the biosynthetic genes involved and extensive metabolic engineering to optimise enzyme activity and metabolic flux. This review describes the current strategies and recent advancements in the production of these valuable therapeutic compounds, and highlights plant-derived immunomodulators as an emerging class of anti-cancer agen...
Source: Current Opinion in Biotechnology - December 13, 2019 Category: Biotechnology Authors: Carqueijeiro I, Langley C, Grzech D, Koudounas K, Papon N, O'Connor SE, Courdavault V Tags: Curr Opin Biotechnol Source Type: research

Bispecific antibodies in cancer immunotherapy.
Abstract Among antibody-based cancer therapies, bispecific antibodies (biAbs) have gained momentum in preclinical and clinical investigations following the regulatory approvals of the trailblazing T-cell engaging biAb (T-biAb) blinatumomab. Discussed herein are recent strategies that aim at boosting the potency and mitigating the toxicity of T-biAbs, broadening their therapeutic utility from hematologic to solid malignancies, and generating T-biAbs in situ. In cancer immunotherapy, T-biAbs are facing fierce competition with chimeric antigen receptor T cells (CAR-Ts), a battle for clinical and commercial viability ...
Source: Current Opinion in Biotechnology - December 13, 2019 Category: Biotechnology Authors: Rader C Tags: Curr Opin Biotechnol Source Type: research

Downstream of the bioreactor: advancements in recovering fuels and commodity chemicals.
Abstract Downstream processing aims at recovering the target product at the required specifications from the bioreactor effluent. Research and development in this field relies on experimental and mathematical tools at the levels of chemical components, unit operations and processes. Recently, advances have been made in addressing the broth mixture complexity early on, in incorporating high-throughput experimentation for data generation and mechanistic understanding of the separation processes, in improving the materials and scalability of specific unit operations, as well as establishing the potential of process i...
Source: Current Opinion in Biotechnology - December 13, 2019 Category: Biotechnology Authors: Cuellar MC, Straathof AJ Tags: Curr Opin Biotechnol Source Type: research

Defining and engineering bioenergy plant feedstock ideotypes.
Abstract Ideotypes are theoretical archetypes of crops which serve as a practical framework for plant breeders to critically evaluate what traits they should be targeting for specific applications. With advances in plant biotechnology and a growing urgency to adopt more sustainable practices across our economy, new uses for crops as bioenergy feedstocks may pivot our definition of an ideal crop that is engineered for biomass and bioenergy production, in contrast to food production. Although there is a plethora of specific applications to which plant engineering efforts can contribute, here we highlight recent adva...
Source: Current Opinion in Biotechnology - December 13, 2019 Category: Biotechnology Authors: Markel K, Belcher MS, Shih PM Tags: Curr Opin Biotechnol Source Type: research

Synthetic 3D scaffolds for cancer immunotherapy.
Abstract Recent clinical success of systemic cancer immunotherapy has paved the way for the next-generation therapeutics. Nevertheless, cancer immunotherapies, in particular combination therapies, are associated in some cases with severe side effects and low response rates. Synthetic scaffolds have emerged as a promising platform to deliver immunotherapeutic agents locally. Placed at strategic locations of the body, scaffolds can reduce side effects while increasing the concentration of the agent at the site of interest. Moreover, scaffolds can mimic the context, in which biochemical cues are presented in vivo to ...
Source: Current Opinion in Biotechnology - December 12, 2019 Category: Biotechnology Authors: Kurum A, Gao M, Tang L Tags: Curr Opin Biotechnol Source Type: research

Innovation in plant-based transient protein expression for infectious disease prevention and preparedness.
Abstract Addressing new challenges in global health and biosecurity requires responsive and accessible platforms for the manufacture of preventative or therapeutic interventions. Transient protein expression in plants has evolved into a technology that offers a unique combination of rapid expression, inherent scalability, and flexibility in gene stacking with the capability to produce complex proteins and protein assemblies. Technical developments that have driven the progress of transient expression in plants include advanced expression systems, protein engineering and synthetic biology approaches to transiently,...
Source: Current Opinion in Biotechnology - December 6, 2019 Category: Biotechnology Authors: Sainsbury F Tags: Curr Opin Biotechnol Source Type: research

The impact of synthetic biology for future agriculture and nutrition.
Abstract Global food production needs to be increased by 70% to meet demands by 2050. Current agricultural practices cannot cope with this pace and furthermore are not ecologically sustainable. Innovative solutions are required to increase productivity and nutritional quality. The interdisciplinary field of synthetic biology implements engineering principles into biological systems and currently revolutionizes fundamental and applied research. We review the diverse spectrum of synthetic biology applications that started impacting plant growth and quality. We focus on latest advances for synthetic carbon-conserving...
Source: Current Opinion in Biotechnology - December 5, 2019 Category: Biotechnology Authors: Roell MS, Zurbriggen MD Tags: Curr Opin Biotechnol Source Type: research

Recent advances on constraint-based models by integrating machine learning.
Abstract Research that meaningfully integrates constraint-based modeling with machine learning is at its infancy but holds much promise. Here, we consider where machine learning has been implemented within the constraint-based modeling reconstruction framework and highlight the need to develop approaches that can identify meaningful features from large-scale data and connect them to biological mechanisms to establish causality to connect genotype to phenotype. We motivate the construction of iterative integrative schemes where machine learning can fine-tune the input constraints in a constraint-based model or cont...
Source: Current Opinion in Biotechnology - December 5, 2019 Category: Biotechnology Authors: Rana P, Berry C, Ghosh P, Fong SS Tags: Curr Opin Biotechnol Source Type: research

Aptamers in RNA-based switches of gene expression.
JS Abstract The ability to control gene expression via small molecule effectors is important in basic research as well as in future gene therapy applications. Although transcription factor-based systems are widely used, they are not well suited for certain applications due to a lack of functionality, limited available coding space, and potential immunogenicity of the regulatory proteins. RNA-based switches fill this gap since they can be designed to respond to effector compounds utilizing ligand-sensing aptamers. These systems are very modular since the aptamer can be combined with a variety of different expressi...
Source: Current Opinion in Biotechnology - December 4, 2019 Category: Biotechnology Authors: Spöring M, Finke M, Hartig JS Tags: Curr Opin Biotechnol Source Type: research

Modeling ligand docking to RNA in the design of RNA-based nanostructures.
Abstract RNA has grown in biological importance as the discovery of its many functional roles in the cellular machinery has revealed the potential for targeting it to disrupt cancer pathways. RNA structure underlies its functionality and suitability as a nanoparticle building material. Advances in modelling methods have been achieved by the recognition of common structural motifs in natural RNA molecules that can be employed in the prediction of new structures based on sequence information and in design of functional nanostructures. Ligand docking prediction programs and RNA dynamics adds an important and non-triv...
Source: Current Opinion in Biotechnology - December 3, 2019 Category: Biotechnology Authors: Kasprzak WK, Ahmed NA, Shapiro BA Tags: Curr Opin Biotechnol Source Type: research

Microfluidic single-cell analysis in biotechnology: from monitoring towards understanding.
r A Abstract Our understanding of the microbial cell is based on averaged values from bulks. Microfluidic single-cell analysis holds the promise of understanding cellular processes from a single cell perspective. But what is needed to measure single-cell physiology and to disclose the consequences of individuality for biotechnology? Current single-cell research is not yet able to provide all the necessary insights, but innovative approaches now emerge that propel the field towards a better understanding of cellular processes via quantitative physiology. Here, we critically review novel single-cell technologies tha...
Source: Current Opinion in Biotechnology - December 3, 2019 Category: Biotechnology Authors: Dusny C, Grünberger A Tags: Curr Opin Biotechnol Source Type: research

Simplified monomeric VHH-Fc antibodies provide new opportunities for passive immunization.
Abstract Simplified monomeric monoclonal antibodies consisting of a single-domain VHH, derived from camelid heavy-chain only antibodies, fused with the Fc domain of either IgG (VHH-IgG) or IgA (VHH-IgA) antibodies, are promising therapeutic proteins. These simplified single-gene encoded antibodies are much easier to manufacture and can be produced in plants and in yeast for bulk applications. These merits enable novel passive immunization applications, such as in-feed oral delivery of VHH-IgAs, which have successfully provided protection against a gastrointestinal infection in the piglet model. PMID: 31810049...
Source: Current Opinion in Biotechnology - December 3, 2019 Category: Biotechnology Authors: De Greve H, Virdi V, Bakshi S, Depicker A Tags: Curr Opin Biotechnol Source Type: research

Harnessing atmospheric nitrogen for cereal crop production.
Abstract While synthetic nitrogen fuels modern agriculture, its production is energy-intensive, and its application leads to aquatic pollution and greenhouse gas emissions. Sustainable intensification of agriculture to provide both food for humans and feedstocks for bio-based fuels and materials requires alternative options for nitrogen management. For nearly fifty years, nitrogen fixation in cereal crops has been pursued to address this challenge. Efforts to engineer plants for nitrogen fixation have made strides through eukaryotic nitrogenase expression and a deepened understanding of root nodulation pathways, b...
Source: Current Opinion in Biotechnology - November 29, 2019 Category: Biotechnology Authors: Bloch SE, Ryu MH, Ozaydin B, Broglie R Tags: Curr Opin Biotechnol Source Type: research

Molecular farming for therapies and vaccines in Africa.
Abstract Local manufacturing of protein-based vaccines and therapies in Africa is limited and contributes to a trade deficit, security of supply concerns and poor access to biopharmaceuticals by the poor. Plant molecular farming is a potential technology solution that has received growing adoption by African scientists attracted by the potential for the competitive cost of goods, safety and efficacy. Plant-made pharmaceutical technologies for veterinary and human vaccination and treatment of non-communicable and infectious diseases are available at different stages of development in Africa. There is also growth in...
Source: Current Opinion in Biotechnology - November 28, 2019 Category: Biotechnology Authors: Tsekoa TL, Singh AA, Buthelezi SG Tags: Curr Opin Biotechnol Source Type: research

Cancer biologics made in plants.
Abstract Plants are routinely utilized as efficient production platforms for the development of anti-cancer biologics leading to novel anti-cancer vaccines, immunotherapies, and drug-delivery modalities. Various biosimilar/biobetter antibodies and immunogens based on tumor-associated antigens have been produced and optimized for plant expression. Plant virus nanoparticles, including those derived from cowpea mosaic virus or tobacco mosaic virus in particular have shown promise as immunotherapies stimulating tumor-associated immune cells and as drug carriers delivering conjugated chemotherapeutics effectively to tu...
Source: Current Opinion in Biotechnology - November 27, 2019 Category: Biotechnology Authors: Dent M, Matoba N Tags: Curr Opin Biotechnol Source Type: research

Innate immune responses triggered by nucleic acids inspire the design of immunomodulatory nucleic acid nanoparticles (NANPs).
Abstract The unknown immune stimulation by nucleic acid nanoparticles (NANPs) has become one of the major impediments to a broad spectrum of clinical developments of this novel technology. Having evolved to defend against bacterial and viral nucleic acids, mammalian cells have established patterns of recognition that are also the pathways through which NANPs can be processed. Explorations into the immune stimulation brought about by a vast diversity of known NANPs have shown that variations in design correlate with variations in immune response. Therefore, as the mechanisms of stimulation are further elucidated, t...
Source: Current Opinion in Biotechnology - November 25, 2019 Category: Biotechnology Authors: Chandler M, Johnson MB, Panigaj M, Afonin KA Tags: Curr Opin Biotechnol Source Type: research

Microdroplet screening and selection for improved microbial production of extracellular compounds.
Abstract Microorganisms produce extracellular compounds that affect the final product quality in fermentation processes. Selection of overproducing mutants requires coupling of the extracellular product to the producer genotype, which can be achieved by single-cell compartmentalization. Emulsions contain up to billions of microdroplets/mL which significantly increases the screening throughput compared to microtiter-plate-based selections. Factors affecting the success of screening in microdroplets include the nature of the producing organism (robust, no invasive growth), the product (not soluble in oil) and the pr...
Source: Current Opinion in Biotechnology - November 23, 2019 Category: Biotechnology Authors: van Tatenhove-Pel RJ, Hernandez-Valdes JA, Teusink B, Kuipers OP, Fischlechner M, Bachmann H Tags: Curr Opin Biotechnol Source Type: research

Proteases of Nicotiana benthamiana: an emerging battle for molecular farming.
Abstract Molecular farming increasingly uses the tobacco relative Nicotiana benthamiana for production of recombinant proteins through transient expression. Several proteins are produced efficiently with this expression platform, but yields for other proteins are often very low. These low yields are frequently due to endogenous proteases. The latest genome annotations indicate that N. benthamiana encodes for at least 1243 putative proteases that probably act redundantly and consecutively on substrates in different subcellular compartments. Here, we discuss the N. benthamiana protease repertoire that may affect rec...
Source: Current Opinion in Biotechnology - November 22, 2019 Category: Biotechnology Authors: Jutras PV, Dodds I, van der Hoorn RA Tags: Curr Opin Biotechnol Source Type: research

Resistant starch: impact on the gut microbiome and health.
Abstract Resistant starch has received a lot of attention for its potential to exert a healthy impact on the gut and certain members of its resident microbiota, particularly through enhanced butyrate production. However, resistant starch is a broad category that encompasses several structurally different starches. While all resist digestion by human enzymes, they differ in their effects on the microbiota. Individual variation in microbiota composition also has a substantial influence on butyrate production. Research on this interaction between resistant starch and the microbiota is using in vitro fermentations, cr...
Source: Current Opinion in Biotechnology - November 22, 2019 Category: Biotechnology Authors: DeMartino P, Cockburn DW Tags: Curr Opin Biotechnol Source Type: research

Sensing the unreachable: challenges and opportunities in biofilm detection.
Abstract Bacteria can attach to essentially all materials and form multicellular biofilms with high-level tolerance to antimicrobials. Detrimental biofilms are responsible for a variety of problems ranging from food and water contamination, bio-corrosion, to drug resistant infections. Besides the challenges in control, biofilms are also difficult to detect due to the lack of biofilm-specific biomarkers and methods for non-destructive imaging. In this article, we present a concise review of recent advancements in this field, with a focus on medical device-associated infections. We also discuss the technologies that...
Source: Current Opinion in Biotechnology - November 22, 2019 Category: Biotechnology Authors: Xu Y, Dhaouadi Y, Stoodley P, Ren D Tags: Curr Opin Biotechnol Source Type: research

Reprint of: Non Canonical Genetic Material.
Abstract To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applic...
Source: Current Opinion in Biotechnology - November 20, 2019 Category: Biotechnology Authors: Eremeeva E, Herdewijn P Tags: Curr Opin Biotechnol Source Type: research

Molecular Pharming for low and middle income countries.
Abstract Interest in applications and benefits that Molecular Pharming might offer to Low and Middle Income Countries has always been a potent driver for the research discipline, and a major reason why many scientists entered the field. Although enthusiasm remains high, the reality is that such a game-changing innovation would always take longer than traditional uptake of new technology in developed countries, and be complicated by external factors beyond technical feasibility. Excitingly, signs of increasing interest by LMICS in Molecular Pharming are now emerging. Here, three case studies from Thailand, South Af...
Source: Current Opinion in Biotechnology - November 18, 2019 Category: Biotechnology Authors: Murad S, Fuller S, Menary J, Moore C, Pinneh E, Szeto T, Hitzeroth I, Freire M, Taychakhoonavudh S, Phoolcharoen W, Ma JK Tags: Curr Opin Biotechnol Source Type: research

Applications of plant-based fermented foods and their microbes.
Abstract Plant-based fermentations and their microbes provide an underexplored source for novel biotechnological applications. Recent advances in DNA sequencing technologies and analyses of sequencing data highlight that a diverse array of lactic acid bacteria (LAB) frequently dominate these plant fermentations. Because of the long history of safe LAB use in fermented foods, we argue here that various novel probiotic, synbiotic and a range of other industrial applications can be produced based on new insights in the functional and genetic potential of these LAB. To aid in this quest, comparative genomics tools are...
Source: Current Opinion in Biotechnology - November 13, 2019 Category: Biotechnology Authors: Wuyts S, Van Beeck W, Allonsius CN, van den Broek MF, Lebeer S Tags: Curr Opin Biotechnol Source Type: research

Renewable methanol and formate as microbial feedstocks.
Abstract Methanol and formate are attractive microbial feedstocks as they can be sustainably produced from CO2 and renewable energy, are completely miscible, and are easy to store and transport. Here, we provide a biochemical perspective on microbial growth and bioproduction using these compounds. We show that anaerobic growth of acetogens on methanol and formate is more efficient than on H2/CO2 or CO. We analyze the aerobic C1 assimilation pathways and suggest that new-to-nature routes could outperform their natural counterparts. We further discuss practical bioprocessing aspects related to growth on methanol and...
Source: Current Opinion in Biotechnology - November 13, 2019 Category: Biotechnology Authors: Cotton CA, Claassens NJ, Benito-Vaquerizo S, Bar-Even A Tags: Curr Opin Biotechnol Source Type: research