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  • A Comparison of Techniques to Evaluate the Effectiveness of Genome Editing
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-17
    Diego Germini, Tatiana Tsfasman, Vlada V. Zakharova, Nikolajs Sjakste, Marс Lipinski, Yegor Vassetzky

    Genome editing using engineered nucleases (meganucleases, zinc finger nucleases, transcription activator-like effector nucleases) has created many recent breakthroughs. Prescreening for efficiency and specificity is a critical step prior to using any newly designed genome editing tool for experimental purposes. The current standard screening methods of evaluation are based on DNA sequencing or use mismatch-sensitive endonucleases. They can be time-consuming and costly or lack reproducibility. Here, we review and critically compare standard techniques with those more recently developed in terms of reliability, time, cost, and ease of use.

  • CRISPR-Based Antibacterials: Transforming Bacterial Defense into Offense
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-17
    Adrienne C. Greene

    The development of antimicrobial-resistant (AMR) bacteria poses a serious worldwide health concern. CRISPR-based antibacterials are a novel and adaptable method for building an arsenal of antibacterials potentially capable of targeting any pathogenic bacteria.

  • Microfluidics for Combating Antimicrobial Resistance
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-15
    Zhengzhi Liu, Niaz Banaei, Kangning Ren

    The ever-growing threat of antimicrobial resistance (AMR) demands immediate countermeasures. With its novelty and enabling features including downscaled analysis, precisely controlled local environment, and enhanced speed, accuracy, and cost-efficiency, microfluidics has demonstrated potential in several key areas, including furthering our understanding of bacteria, developing better susceptibility testing tools, and overcoming obstacles in discovery and research of new antibiotics. While ample research results in the field of microfluidics are available, their transformation into practical application is still lagging far behind. We believe that the challenge of AMR will give microfluidics a much-needed opportunity to leap from research papers to true productivity, and gain wider acceptance as a mature technology.

  • Gravity, Tissue Engineering, and the Missing Link
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-16
    Raquel Costa-Almeida, Pedro L. Granja, Manuela E. Gomes

    The influence of microgravity and hypergravity on living systems has attracted significant attention, but the use of these tools in tissue engineering (TE) remains relatively unexplored. This Forum article highlights an emerging field of research to uncover new potential applications at the interface between altered gravity and TE.

  • Basic and Clinical Approaches for Fertility Preservation and Restoration in Cancer Patients
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-15
    Jose V Medrano, María del Mar Andrés, Sofía García, Sonia Herraiz, Teresa Vilanova-Pérez, Ellen Goossens, Antonio Pellicer

    As gonadotoxic adverse effects of antineoplastic treatments can result in infertility, gamete cryopreservation is routinely offered to patients as the strategy to preserve their fertility. However, there are many cases where gold standards cannot be applied, as is the case for prepubertal cancer patients and others unable to produce gametes or their precursors at the moment of diagnosis. With an increasing number of cancer survivors in our society, strategies using either cryopreserved gonadal tissue or stem cells have been developed to allow cancer survivors to achieve fatherhood, and recent advances in the field have increased public interest. In this review, we discuss the latest updates in fertility preservation from a basic and a clinical point of view.

  • A Plea for the Renewal of the ISBR
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-14
    Giovanni Tagliabue, Marcel Kuntz, Henry I. Miller, Klaus Ammann

    The recent meeting of the International Society for Biosafety Research (ISBR) focused on so-called genetically modified organisms. For decades, in most regulatory frameworks, recombinant DNA-modified organisms have been the wrong focus of unbalanced agri-food regulations. The ISBR should instead adopt a scientifically defensible and truly risk-based perspective, abandoning a misleading pseudo-category.

  • Biofabrication: A Guide to Technology and Terminology
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-11
    Lorenzo Moroni, Thomas Boland, Jason A. Burdick, Carmelo De Maria, Brian Derby, Gabor Forgacs, Jürgen Groll, Qing Li, Jos Malda, Vladimir A. Mironov, Carlos Mota, Makoto Nakamura, Wenmiao Shu, Shoji Takeuchi, Tim B.F. Woodfield, Tao Xu, James J. Yoo, Giovanni Vozzi

    Biofabrication holds the potential to generate constructs that more closely recapitulate the complexity and heterogeneity of tissues and organs than do currently available regenerative medicine therapies. Such constructs can be applied for tissue regeneration or as in vitro 3D models. Biofabrication is maturing and growing, and scientists with different backgrounds are joining this field, underscoring the need for unity regarding the use of terminology. We therefore believe that there is a compelling need to clarify the relationship between the different concepts, technologies, and descriptions of biofabrication that are often used interchangeably or inconsistently in the current literature. Our objective is to provide a guide to the terminology for different technologies in the field which may serve as a reference for the biofabrication community.

  • Multi-Product Microalgae Biorefineries: From Concept Towards Reality
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-10
    G.P. 't Lam, M.H. Vermuë, M.H.M. Eppink, R.H. Wijffels, C. van den Berg

    Although microalgae are a promising biobased feedstock, industrial scale production is still far off. To enhance the economic viability of large-scale microalgae processes, all biomass components need to be valorized, requiring a multi-product biorefinery. However, this concept is still too expensive. Typically, downstream processing of industrial biotechnological bulk products accounts for 20–40% of the total production costs, while for a microalgae multi-product biorefinery the costs are substantially higher (50–60%). These costs are high due to the lack of appropriate and mild technologies to access the different product fractions such as proteins, carbohydrates, and lipids. To reduce the costs, simplified processes need to be developed for the main unit operations including harvesting, cell disruption, extraction, and possibly fractionation.

  • The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-10
    Young-Kyoung Park, Jean-Marc Nicaud, Rodrigo Ledesma-Amaro

    Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.

  • Functionally-Relevant Morphological Profiling: A Tool to Assess Cellular Heterogeneity
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-07
    Ross A. Marklein, Johnny Lam, Murat Guvendiren, Kyung E. Sung, Steven R. Bauer

    Heterogeneity in cell function has presented a significant hurdle to the successful clinical translation of many cellular therapies. Current techniques for assessing cell quality and the effects of microenvironmental cues and manufacturing processes on cell behavior often inadequately address heterogeneity due to issues such as population versus single-cell measurements and the therapeutic relevance and throughput/robustness of the assay. Due to the well-established relationship between morphology and cellular function, morphological profiling has become increasingly utilized to better understand functional heterogeneity and its impact on therapeutic development. In this review, we introduce an emerging field we term functionally-relevant morphological profiling with great potential to improve our understanding of cellular heterogeneity through discovering novel quality attributes, optimizing manufacturing, and screening drugs/biomaterials.

  • Genomics-Driven Natural Product Discovery in Actinomycetes
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-07
    Guoqing Niu

    The prevalence of antimicrobial-resistant pathogens has highlighted the urgent need for new drugs. Actinomycetes have been the most prominent sources of natural products for drug discovery and development. Advances in genomics have inspired several emerging strategies to reinvigorate the field of natural product discovery, especially in actinomycete-derived natural products.

  • Potential Applications of the Escherichia coli Heat Shock Response in Synthetic Biology
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-07
    Joana L. Rodrigues, Lígia R. Rodrigues

    The Escherichia coli heat shock response (HSR) is a complex mechanism triggered by heat shock and by a variety of other growth-impairing stresses. We explore here the potential use of the E. coli HSR mechanism in synthetic biology approaches. Several components of the regulatory mechanism (such as heat shock promoters, proteins, and RNA thermosensors) can be extremely valuable in the creation of a toolbox of well-characterized biological parts to construct biosensors or microbial cell factories with applications in the environment, industry, or healthcare. In the future, these systems can be used for instance to detect a pollutant in water, to regulate and optimize the production of a compound with industrial relevance, or to administer a therapeutic agent in vivo.

  • Bioprocessing Strategies for Pluripotent Stem Cells Based on Waddington’s Epigenetic Landscape
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-06
    Mee-Hae Kim, Masahiro Kino-oka

    As increasing numbers of cell-based therapies advance through clinical trials towards approval for use in humans, the need for robust and well-characterized cell culturing strategies is becoming increasingly apparent. We discuss here novel stem cell bioprocessing strategies based on the concept of using Waddington’s epigenetic landscape to represent the process of cellular decision-making during development. Specifically, we focus on the manner in which cell behavior triggers cell signaling pathways related to the initial cell fate decision. We also consider how various biochemical engineering strategies can be used to develop these bioprocesses to further enhance their utility in research and therapy.

  • Thermodynamic Activity-Based Progress Curve Analysis in Enzyme Kinetics
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-05
    Jürgen Pleiss

    Macrokinetic Michaelis–Menten models based on thermodynamic activity provide insights into enzyme kinetics because they separate substrate–enzyme from substrate–solvent interactions. Kinetic parameters are estimated from experimental progress curves of enzyme-catalyzed reactions. Three pitfalls are discussed: deviations between thermodynamic and concentration-based models, product effects on the substrate activity coefficient, and product inhibition.

  • From Genetic Stock to Genome Editing: Gene Exploitation in Wheat
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-11-05
    Meng Wang, Shubin Wang, Zhen Liang, Weiming Shi, Caixia Gao, Guangmin Xia

    Bread wheat (Triticum aestivum) ranks as one of our most important staple crops. However, its hexaploid nature has complicated our understanding of the genetic bases underlying many of its traits. Historically, functional genetic studies in wheat have focused on identifying natural variations and have contributed to assembling and enriching its genetic stock. Recently, mold-breaking advances in whole genome sequencing, exome-capture based mutant libraries, and genome editing have revolutionized strategies for genetic research in wheat. We review new trends in wheat functional genetic studies along with germplasm conservation and innovation, including the relevance of genetic stocks, and the application of sequencing-based mutagenesis and genome editing. We also highlight the potential of multiplex genome editing toolkits in addressing species-specific challenges in wheat.

  • Emerging Biomedical Applications of Enzyme-Like Catalytic Nanomaterials
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-26
    David P. Cormode, Lizeng Gao, Hyun Koo

    Nanomaterials have been developed for many biomedical applications, including medical imaging, drug delivery, and antimicrobial coatings. Intriguingly, nanoparticles can display ‘enzyme-like’ activity and have been explored as alternatives to natural enzymes in several industrial and energy-related applications. Recently, these catalytic nanomaterials with enzyme-mimetic properties have found new biomedical applications, from biofilm disruption to protection against neurodegeneration and tumor prevention. In this review we focus on recent in vivo studies demonstrating potential therapeutic uses of catalytic nanomaterials. We also provide insights about the relationships between catalytic activity, therapeutic efficacy, and biocompatibility that are critical for clinical translatability. Finally, we discuss current challenges and future directions for the use of these nanomaterials as novel platforms for the development of sustainable, affordable, and safe therapeutics.

  • Fully Artificial Exosomes: Towards New Theranostic Biomaterials
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-23
    Pablo García-Manrique, Gemma Gutiérrez, Maria Carmen Blanco-López

    Bionanotechnology routes have been recently developed to produce fully artificial exosomes: biomimetic particles designed to overcome certain limitations in extracellular vesicle (EV) biology and applications. These particles could soon become true therapeutic biomaterials. Here, we outline their current preparation techniques, their explored and future possibilities, and their present limits.

  • Artificial Metalloenzymes on the Verge of New-to-Nature Metabolism
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-20
    Markus Jeschek, Sven Panke, Thomas R. Ward

    Residing at the interface of chemistry and biotechnology, artificial metalloenzymes (ArMs) offer an attractive technology to combine the versatile reaction repertoire of transition metal catalysts with the exquisite catalytic features of enzymes. While earlier efforts in this field predominantly comprised studies in well-defined test-tube environments, a trend towards exploiting ArMs in more complex environments has recently emerged. Integration of these artificial biocatalysts in enzymatic cascades and using them in whole-cell biotransformations and in vivo opens up entirely novel prospects for both preparative chemistry and synthetic biology. We highlight selected recent developments with a particular focus on challenges and opportunities in the in vivo application of ArMs.

  • Myths and Realities Surrounding the Mysterious Caterpillar Fungus
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-18
    Jan Martel, Yun-Fei Ko, Jian-Ching Liau, Chien-Sheng Lee, David M. Ojcius, Hsin-Chih Lai, John D. Young

    The caterpillar fungus Ophiocordyceps sinensis is a medicinal mushroom increasingly used as a dietary supplement for various health conditions, including fatigue, chronic inflammation, and male impotence. Here, we propose strategies to address the existing challenges related to the study and commercial production of this mysterious fungus.

  • Imaging Biomaterial–Tissue Interactions
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-17
    Yu Shrike Zhang, Junjie Yao

    Modern biomedical imaging has revolutionized life science by providing anatomical, functional, and molecular information of biological species with high spatial resolution, deep penetration, enhanced temporal responsiveness, and improved chemical specificity. In recent years, these imaging techniques have been increasingly tailored for characterizing biomaterials and probing their interactions with biological tissues. This in turn has spurred substantial advances in engineering material properties to accommodate different imaging modalities that was previously unattainable. Here, we review advances in engineering both imaging modalities and material properties with improved contrast, providing a timely practical guide to better assess biomaterial–tissue interactions both in vitro and in vivo.

  • Flow Bioreactors as Complementary Tools for Biocatalytic Process Intensification
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-17
    Lucia Tamborini, Pedro Fernandes, Francesca Paradisi, Francesco Molinari

    Biocatalysis has widened its scope and relevance since new molecular tools, including improved expression systems for proteins, protein and metabolic engineering, and rational techniques for immobilization, have become available. However, applications are still sometimes hampered by low productivity and difficulties in scaling up. A practical and reasonable step to improve the performances of biocatalysts (including both enzymes and whole-cell systems) is to use them in flow reactors. This review describes the state of the art on the design and use of biocatalysis in flow reactors. The encouraging successes of this enabling technology are critically discussed, highlighting new opportunities, problems to be solved and technological advances.

  • Can Microalgae Remove Pharmaceutical Contaminants from Water?
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-06
    Jiu-Qiang Xiong, Mayur B. Kurade, Byong-Hun Jeon

    The increase in worldwide water contamination with numerous pharmaceutical contaminants (PCs) has become an emerging environmental concern due to their considerable ecotoxicities and associated health issues. Microalgae-mediated bioremediation of PCs has recently gained scientific attention, as microalgal bioremediation is a solar-power driven, ecologically comprehensive, and sustainable reclamation strategy. In this review, we comprehensively describe the current research on the possible roles and applications of microalgae for removing PCs from aqueous media. We summarize several novel approaches including constructing microbial consortia, acclimation, and cometabolism for enhanced removal of PCs by microalgae, which would improve practical feasibility of these technologies. Some novel concepts for degrading PCs using integrated processes and genetic modifications to realize algal-based bioremediation technologies are also recommended.

  • The Impact of Systems Biology on Bioprocessing
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-10-04
    Kate Campbell, Jianye Xia, Jens Nielsen

    Bioprocessing offers a sustainable and green approach to the production of chemicals. However, a bottleneck in introducing bioprocesses is cell factory development, which is costly and time-consuming. A systems biology approach can expedite cell factory design by using genome-wide analyses alongside mathematical modeling to characterize and predict cellular physiology. This approach can drive cycles of design, build, test, and learn implemented by metabolic engineers to optimize the cell factory performance. Streamlining of the design phase requires a clearer understanding of metabolism and its regulation, which can be achieved using quantitative and integrated omic characterization, alongside more advanced analytical methods. We discuss here the current impact of systems biology and challenges of closing the gap between bioprocessing and more traditional methods of chemical production.

  • Challenges of the Nano–Bio Interface in Lateral Flow and Dipstick Immunoassays
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-28
    Helena de Puig, Irene Bosch, Lee Gehrke, Kimberly Hamad-Schifferli

    Lateral flow assays (LFAs) are highly attractive for point-of-care (POC) diagnostics for infectious disease, food safety, and many other medical uses. The unique optical, electronic, and chemical properties that arise from the nanostructured and material characteristics of nanoparticles provide an opportunity to increase LFA sensitivity and impart novel capabilities. However, interfacing to nanomaterials in complex biological environments is challenging and can result in undesirable side effects such as non-specific adsorption, protein denaturation, and steric hindrance. These issues are even more acute in LFAs where there are many different types of inorganic–biological interfaces, often of a complex nature. Therefore, the unique properties of nanomaterials for LFAs must be exploited in a way that addresses these interface challenges.

  • Ultra High Field MRI-Guided Deep Brain Stimulation
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-20
    Birte U. Forstmann, Bethany R. Isaacs, Yasin Temel

    Deep brain stimulation (DBS) is a neurosurgical treatment for neurological disorders often planned with 1.5-T or 3-T MRI. The clinical efficacy of DBS can be improved using ultrahigh-field (UHF) MRI for planning by increasing the level of precision required for an individualized approach.

  • Pushing Bacterial Biohybrids to In Vivo Applications
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-10
    Morgan M. Stanton, Samuel Sánchez

    Bacterial biohybrids use the energy of bacteria to manipulate synthetic materials with the goal of solving biomedical problems at the micro- and nanoscale. We explore current in vitro studies of bacterial biohybrids, the first attempts at in vivo biohybrid research, and problems to be addressed for the future.

  • Biotechnological Perspectives of Pyrolysis Oil for a Bio-Based Economy
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-06-27
    Stefanie Arnold, Karin Moss, Marius Henkel, Rudolf Hausmann

    Lignocellulosic biomass is an important feedstock for a potential future bio-based economy. Owing to its compact structure, suitable decomposition technologies will be necessary to make it accessible for biotechnological conversion. While chemical and enzymatic hydrolysis are currently established methods, a promising alternative is provided by fast pyrolysis. The main resulting product thereof, referred to as pyrolysis oil, is an energy-rich and easily transportable liquid. Many of the identified constituents of pyrolysis oil, however, have previously been reported to display adverse effects on microbial growth. In this Opinion we discuss relevant biological, biotechnological, and technological challenges that need to be addressed to establish pyrolysis oil as a reliable microbial feedstock for a bio-based economy of the future.

  • Advances in Alzheimer’s Diagnosis and Therapy: The Implications of Nanotechnology
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-06-27
    Mohammad Javad Hajipour, Michelle R. Santoso, Farhad Rezaee, Haniyeh Aghaverdi, Morteza Mahmoudi, George Perry

    Alzheimer’s disease (AD) is a type of dementia that causes major issues for patients’ memory, thinking, and behavior. Despite efforts to advance AD diagnostic and therapeutic tools, AD remains incurable due to its complex and multifactorial nature and lack of effective diagnostics/therapeutics. Nanoparticles (NPs) have demonstrated the potential to overcome the challenges and limitations associated with traditional diagnostics/therapeutics. Nanotechnology is now offering new tools and insights to advance our understanding of AD and eventually may offer new hope to AD patients. Here, we review the key roles of nanotechnologies in the recent literature, in both diagnostic and therapeutic aspects of AD, and discuss how these achievements may improve patient prognosis and quality of life.

  • Fast Science and Sluggish Policy: The Herculean Task of Regulating Biodiscovery
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-27
    Rachel Wynberg, Sarah A. Laird

    New rules for access and benefit sharing (ABS) of genetic resources and associated traditional knowledge have been established by the Nagoya Protocol but have not kept up with rapid scientific and technological advances in biodiscovery. This suggests the need for innovative, transdisciplinary approaches to regulate ABS and emerging technologies.

  • Nanoenvironmental Effects Dramatically Influence the Sensitivity of Immunoassays
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-21
    B. Mattiasson, K. Teeparuksapun, L. Lebogang, M. Hedström

    It is possible to improve the sensitivity of immunoassays by several orders of magnitude by exploiting nanoenvironmental effects. This approach can detect trace amounts of compounds and will better illuminate the presence of signal substances in biological systems. Here we describe a method for ultrasensitive immunoassays using ‘normal’ antibodies (Abs).

  • Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-21
    Amanda Randles, David H. Frakes, Jane A. Leopold

    Noninvasive engineering models are now being used for diagnosing and planning the treatment of cardiovascular disease. Techniques in computational modeling and additive manufacturing have matured concurrently, and results from simulations can inform and enable the design and optimization of therapeutic devices and treatment strategies. The emerging synergy between large-scale simulations and 3D printing is having a two-fold benefit: first, 3D printing can be used to validate the complex simulations, and second, the flow models can be used to improve treatment planning for cardiovascular disease. In this review, we summarize and discuss recent methods and findings for leveraging advances in both additive manufacturing and patient-specific computational modeling, with an emphasis on new directions in these fields and remaining open questions.

  • Improving Biopharmaceutical Safety through Verification-Based Quality Control
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-21
    Yihua Bruce Yu, Marc B. Taraban, Weizhen Wang, Katharine T. Briggs

    Biopharmaceuticals and small-molecule drugs have different approval pathways but the same quality control (QC) paradigm, where the quality of released but untested units is inferred from that of tested but destroyed units. This inference-based QC will likely miss rare prerelease defects, and defects emerging after product release. The likelihood for such defects is heightened for biopharmaceuticals due to their complexity, which makes manufacturing errors more likely, and fragility, which makes postrelease damage more likely. To improve biopharmaceutical safety, we suggest transitioning their QC from inference- to verification-based practice by developing inspection technologies that can nondestructively verify the quality of every vial from the point of release to the point of care. One candidate, water proton NMR (wNMR), is briefly discussed.

  • New Light for Phytochemicals
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-19
    Jarmo K. Holopainen, Minna Kivimäenpää, Riitta Julkunen-Tiitto

    Light-emitting diode (LED) lighting technology with narrow-bandwidth illumination helps to reduce energy consumption on covered crops. Here, we discuss how this new technology, which provides flexible modification of light spectra, will open new avenues for natural modulation of medicinal and crop plant metabolomes for better colour, flavour, fragrance, and antioxidant properties.

  • Deciphering Cell Intrinsic Properties: A Key Issue for Robust Organoid Production
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-17
    Nathalie Picollet-D’hahan, Monika E. Dolega, Delphine Freida, Donald K. Martin, Xavier Gidrol

    We highlight the disposition of various cell types to self-organize into complex organ-like structures without necessarily the support of any stromal cells, provided they are placed into permissive 3D culture conditions. The goal of generating organoids reproducibly and efficiently has been hampered by poor understanding of the exact nature of the intrinsic cell properties at the origin of organoid generation, and of the signaling pathways governing their differentiation. Using microtechnologies like microfluidics to engineer organoids would create opportunities for single-cell genomics and high-throughput functional genomics to exhaustively characterize cell intrinsic properties. A more complete understanding of the development of organoids would enhance their relevance as models to study organ morphology, function, and disease and would open new avenues in drug development and regenerative medicine.

  • Optical Imaging Paves the Way for Autophagy Research
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-12
    Yimin Wang, Yu Li, Fujing Wei, Yixiang Duan

    Autophagy is a degradation process in eukaryotic cells that recycles cellular components for nutrition supply under environmental stress and plays a double-edged role in development of major human diseases. Noninvasive optical imaging enables us to clearly visualize various classes of structures involved in autophagy at macroscopic and microscopic dynamic levels. In this review, we discuss important trends of emerging optical imaging technologies used to explore autophagy and provide insights into the mechanistic investigation and structural study of autophagy in mammalian cells. Some exciting new prospects and future research directions regarding optical imaging techniques in this field are also highlighted.

  • 3D Quantitative Chemical Imaging of Tissues by Spectromics
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-08
    Cyril Petibois

    Mid-infrared (IR), Raman, and X-ray fluorescence (XRF) spectroscopy methods, as well as mass spectrometry (MS), can be used for 3D chemical imaging. These techniques offer an invaluable opportunity to access chemical features of biological samples in a nonsupervised way. The global chemical information they provide enables the exploitation of a large array of chemical species or parameters, so-called ‘spectromics’. Extracting chemical data from spectra is critical for the high-quality chemical analysis of biosamples. Furthermore, these are the only currently available techniques that can quantitatively analyze tissue content (e.g., molecular concentrations) and substructures (e.g., cells or blood vessels). The development of chemical-derived biological metadata appears to be a new way to exploit spectral information with machine learning algorithms.

  • Genome Editing for Global Food Security
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-08
    Xingliang Ma, Martin Mau, Timothy F. Sharbel

    Global food security is increasingly challenging in light of population increase, the impact of climate change on crop production, and limited land available for agricultural expansion. Here we outline how genome editing provides excellent and timely methods to optimize crop plants, and argue the urgency for societal acceptance and support.

  • Unlocking Marine Biotechnology in the Developing World
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-07
    Cristiane C. Thompson, Ricardo H. Kruger, Fabiano L. Thompson

    Fulfilling the promise of marine biotechnology as a source for environmental and biomedical applications remains challenging. New technologies will be necessary to harness marine biodiversity, and collaboration across government, academic, and private sectors will be crucial to create mechanisms of technology transfer and promote the development of new marine biotechnology companies.

  • Wastewater Opportunities for Denitrifying Anaerobic Methane Oxidation
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-03-08
    Yali Wang, Dongbo Wang, Qi Yang, Guangming Zeng, Xiaoming Li

    Denitrifying anaerobic methane oxidation (DAMO) can concurrently reduce methane emissions and nitrogen levels in aquatic environments, but how useful is this process? We propose the use of DAMO-based technology as a tool for sustainably operating wastewater treatment plants (WWTPs).

  • Ethnophytotechnology: Harnessing the Power of Ethnobotany with Biotechnology
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-07-24
    John de la Parra, Cassandra L. Quave

    Ethnobotany (the scientific study of traditional plant knowledge) has aided the discovery of important medicines. However, as single-molecule drugs or synergistic mixtures, these remedies have faced obstacles in production and analysis. Now, advances in bioreactor technology, metabolic engineering, and analytical instrumentation are improving the production, manipulation, and scientific understanding of such remedies.

  • Carbon Concentration in Algae: Reducing CO2 From Exhaust Gas
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-26
    Atreyee Ghosh, Bala Kiran

    Algal carbon-concentrating mechanisms can be used to sequester CO2 from the atmosphere, and the resulting biomass can produce various value-added products. Mechanisms for carbon concentration in algae are complex and sometimes inefficient. We need to understand how algae successfully overcome these challenges while capturing CO2 from their nearby environment.

  • Endolichenic Fungi: A Hidden Reservoir of Next Generation Biopharmaceuticals
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-03-28
    Brahma N. Singh, Dalip K. Upreti, Vijai K. Gupta, Xiao-Feng Dai, Yueming Jiang

    Endolichenic fungi (ELF) offer an opportunity to discover emerging natural drugs. ELF are promising bioresources given their ability to produce bioactive metabolites that represent unique and diverse structural classes. Here, we assess the potential of recent technologies to provide insight into the chemical diversity of ELF for biopharmaceutical development.

  • Microbiome Tools for Forensic Science
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-03-30
    Jessica L. Metcalf, Zhenjiang Z. Xu, Amina Bouslimani, Pieter Dorrestein, David O. Carter, Rob Knight

    Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics.

  • Discovering Protein-Coding Genes from the Environment: Time for the Eukaryotes?
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-03-07
    Roland Marmeisse, Harald Kellner, Laurence Fraissinet-Tachet, Patricia Luis

    Eukaryotic microorganisms from diverse environments encompass a large number of taxa, many of them still unknown to science. One strategy to mine these organisms for genes of biotechnological relevance is to use a pool of eukaryotic mRNA directly extracted from environmental samples. Recent reports demonstrate that the resulting metatranscriptomic cDNA libraries can be screened by expression in yeast for a wide range of genes and functions from many of the different eukaryotic taxa. In combination with novel emerging high-throughput technologies, we anticipate that this approach should contribute to exploring the functional diversity of the eukaryotic microbiota.

  • Biodegradation of Carbon Nanotubes, Graphene, and Their Derivatives
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-01-05
    Ming Chen, Xiaosheng Qin, Guangming Zeng

    Carbon nanotubes (CNTs), graphene (GRA), and their derivatives are promising materials for a wide range of applications such as pollutant removal, enzyme immobilization, bioimaging, biosensors, and drug delivery and are rapidly increasing in use and increasingly mass produced. The biodegradation of carbon nanomaterials by microbes and enzymes is now of great importance for both reducing their toxicity to living organisms and removing them from the environment. Here we review recent progress in the biodegradation field from the point of view of the primary microbes and enzymes that can degrade these nanomaterials, along with experimental and molecular simulation methods for the exploration of nanomaterial degradation. Further efforts should primarily aim toward expanding the repertoire of microbes and enzymes and exploring optimal conditions for the degradation of nanomaterials.

  • Biotechnological Advances for Restoring Degraded Land for Sustainable Development
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-06-12
    Vishal Tripathi, Sheikh Adil Edrisi, Bin Chen, Vijai K. Gupta, Raivo Vilu, Nicholas Gathergood, P.C. Abhilash

    Global land resources are under severe threat due to pollution and unsustainable land use practices. Restoring degraded land is imperative for regaining ecosystem services, such as biodiversity maintenance and nutrient and water cycling, and to meet the food, feed, fuel, and fibre requirements of present and future generations. While bioremediation is acknowledged as a promising technology for restoring polluted and degraded lands, its field potential is limited for various reasons. However, recent biotechnological advancements, including producing efficient microbial consortia, applying enzymes with higher degrees of specificity, and designing plants with specific microbial partners, are opening new prospects in remediation technology. This review provides insights into such promising ways to harness biotechnology as ecofriendly methods for remediation and restoration.

  • Biotechnologies for Marine Oil Spill Cleanup: Indissoluble Ties with Microorganisms
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-13
    Francesca Mapelli, Alberto Scoma, Grégoire Michoud, Federico Aulenta, Nico Boon, Sara Borin, Nicolas Kalogerakis, Daniele Daffonchio

    The ubiquitous exploitation of petroleum hydrocarbons (HCs) has been accompanied by accidental spills and chronic pollution in marine ecosystems, including the deep ocean. Physicochemical technologies are available for oil spill cleanup, but HCs must ultimately be mineralized by microorganisms. How environmental factors drive the assembly and activity of HC-degrading microbial communities remains unknown, limiting our capacity to integrate microorganism-based cleanup strategies with current physicochemical remediation technologies. In this review, we summarize recent findings about microbial physiology, metabolism and ecology and describe how microbes can be exploited to create improved biotechnological solutions to clean up marine surface and deep waters, sediments and beaches.

  • Next-Generation Insect-Resistant Plants: RNAi-Mediated Crop Protection
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-07-19
    Jiang Zhang, Sher Afzal Khan, David G. Heckel, Ralph Bock

    Plant-mediated RNA interference (RNAi) shows great potential in crop protection. It relies on plants stably expressing double-stranded RNAs (dsRNAs) that target essential genes in pest insects. Practical application of this strategy is challenging because producing sufficient amounts of stable dsRNA in plants has proven to be difficult to achieve with conventional transgenesis. In addition, many insects do not respond to exogenously applied dsRNAs, either degrading them or failing to import them into the cytoplasm. We summarize recent progress in RNAi-mediated insect pest control and discuss factors determining its efficacy. Expressing dsRNA in chloroplasts overcomes many of the difficulties previously encountered. We also highlight remaining challenges and discuss the environmental and biosafety issues involved in the use of this technology in agriculture.

  • Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-07-20
    Michael Gatheru Waigi, Kai Sun, Yanzheng Gao

    Soil pollution has become a major concern in various terrestrial ecosystems worldwide. One in situ soil bioremediation strategy that has gained popularity recently is microbe-assisted phytoremediation, which is promising for remediating pollutants. Sphingomonads, a versatile bacteria group comprising four well-known genera, are ubiquitous in vegetation grown in contaminated soils. These Gram-negative microbes have been investigated for their ability to induce innate plant growth-promoting (PGP) traits, including the formation of phytohormones, siderophores, and chelators, in addition to their evolutionary adaptations enabling biodegradation and microbe-assisted removal of contaminants. However, their capacity for bacterial-assisted phytoremediation has to date been undervalued. Here, we highlight the specific features, roles, advantages, and challenges associated with using sphingomonads in plant–microbe interactions, from the perspective of future phytotechnologies.

  • Frugal Biotech Applications of Low-Temperature Plasma
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-09-01
    Zdenko Machala, David B. Graves

    Gas discharge low-temperature air plasma can be utilized for a variety of applications, including biomedical, at low cost. We term these applications ‘frugal plasma’ – an example of frugal innovation. We demonstrate how simple, robust, low-cost frugal plasma devices can be used to safely disinfect instruments, surfaces, and water.

  • Mechanistic Fermentation Models for Process Design, Monitoring, and Control
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-30
    Lisa Mears, Stuart M. Stocks, Mads O. Albaek, Gürkan Sin, Krist V. Gernaey

    Mechanistic models require a significant investment of time and resources, but their application to multiple stages of fermentation process development and operation can make this investment highly valuable. This Opinion article discusses how an established fermentation model may be adapted for application to different stages of fermentation process development: planning, process design, monitoring, and control. Although a longer development time is required for such modeling methods in comparison to purely data-based model techniques, the wide range of applications makes them a highly valuable tool for fermentation research and development. In addition, in a research environment, where collaboration is important, developing mechanistic models provides a platform for knowledge sharing and consolidation of existing process understanding.

  • Microbial Identification Using Electrochemical Detection of Metabolites
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-30
    Edgar D. Goluch

    Curbing antibiotic use requires the development of simple diagnostic tests that provide caregivers with reliable, immediately actionable information to identify whether there is a need to prescribe a specific antibiotic. This Forum article highlights advances in infection screening approaches that use electrochemistry to detect molecular biomarkers for distinct pathogenic infections.

  • Flashing LEDs for Microalgal Production
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-30
    Peter S.C. Schulze, Rui Guerra, Hugo Pereira, Lisa M. Schüler, João C.S. Varela

    Flashing lights are next-generation tools to mitigate light attenuation and increase the photosynthetic efficiency of microalgal cultivation systems illuminated by light-emitting diodes (LEDs). Optimal flashing light conditions depend on the reaction kinetics and properties of the linear electron transfer chain, energy dissipation, and storage mechanisms of a phototroph. In particular, extremely short and intense light flashes potentially mitigate light attenuation in photobioreactors without impairing photosynthesis. Intelligently controlling flashing light units and selecting electronic components can maximize light emission and energy efficiency. We discuss the biological, physical, and technical properties of flashing lights for algal production. We combine recent findings about photosynthetic pathways, self-shading in photobioreactors, and developments in solid-state technology towards the biotechnological application of LEDs to microalgal production.

  • Tracking the Penetration of Plasma Reactive Species in Tissue Models
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-23
    Endre J. Szili, Sung-Ha Hong, Jun-Seok Oh, Nishtha Gaur, Robert D. Short

    Electrically generated cold atmospheric plasma is being intensively researched for novel applications in biology and medicine. Significant attention is being given to reactive oxygen and nitrogen species (RONS), initially generated upon plasma–air interactions, and subsequently delivered to biological systems. Effects of plasma exposure are observed to millimeter depths within tissue. However, the exact nature of the initial plasma–tissue interactions remains unknown, including RONS speciation and delivery depth, or how plasma-derived RONS intervene in biological processes. Herein, we focus on current research using tissue and cell models to learn more about the plasma delivery of RONS into biological environments. We argue that this research is vital in underpinning the knowledge required to realize the full potential of plasma in biology and medicine.

  • Limitations in Clinical Translation of Nanoparticle-Based Gene Therapy
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-17
    Joanna K.L. Wong, Rashin Mohseni, Amir Ali Hamidieh, Robert E. MacLaren, Nagy Habib, Alexander M. Seifalian

    Organic nanoparticle-based (ONP) gene therapy is a potential strategy to cure human cancer. However, there are still many practical barriers before the promising results from in vitro and preclinical studies can be translated to clinical success. We discuss the reasons behind the hesitant uptake by the clinic.

  • Organic Nanoparticle-Based Combinatory Approaches for Gene Therapy
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-14
    Brahma N. Singh, Prateeksha, Vijai K. Gupta, Jieyin Chen, Atanas G. Atanasov

    Engineered organic nanoparticle (ONP)-mediated co-delivery of genes and therapeutic agents is emerging as a powerful tool in the treatment of several genetic and non-genetic disorders. The ONP-based combinatory approach provides a technological platform that delivers genes with chemo/radio/photo/immunotherapies for the prevention or treatment of disease progression.

  • Bioprinting and Cellular Therapies for Type 1 Diabetes
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-08-05
    Dino J. Ravnic, Ashley N. Leberfinger, Ibrahim T. Ozbolat

    Type 1 diabetes mellitus is a chronic autoimmune disease that results from the destruction of beta (β) cells in the pancreatic islets, leading to loss of insulin production and resultant hyperglycemia. Recent developments in stem cell biology have generated much excitement for β-cell replacement strategies; β cells are one of many cell types in the complex islet environment and pancreas. In this Opinion, we discuss recent successful attempts to generate β cells and how this can be coupled with bioprinting technologies in order to fabricate pancreas tissues, which holds great potential for type 1 diabetes. Possibilities of integrating vascularization and encapsulation in bioprinted tissues are expounded, and future prospects, such as pancreas-on-a-chip, are also presented.

  • Engineering ‘Posthumans’: To Be or Not to Be?
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-15
    Marianna Karamanou, Theodore G. Papaioannou, Dimitrios Soulis, Dimitrios Tousoulis

    Emerging technological innovations have transformed some science fiction ideas into reality, promising radical changes in human nature. New philosophical and intellectual movements such as ‘transhumanism’ and ‘posthumanism’ try to foretell and even direct the future of our existence while dealing with new and complex ethical, social, political issues and dilemmas.

  • Designer Probiotics: Paving the Way to Living Therapeutics
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-05
    Birbal Singh, Gorakh Mal, Francesco Marotta

    Enhancing the functional repertoire of probiotics is a promising approach to cope with the inexorable rise of antibiotic-resistant pathogens and the rather slow development of new antibiotics. Probiotics that deliver novel therapeutics efficiently and with site specificity are emerging living therapeutics that may transform existing paradigms of disease diagnosis and prevention.

  • Clusters in Industrial Biotechnology and Bioeconomy: The Roles of the Public Sector
    Trends Biotechnol. (IF 11.126) Pub Date : 2017-05-06
    Jim Philp, David E. Winickoff

    Government policies across the world seek to create clusters of companies and other stakeholders that specialise in a particular technology to build an ‘industrial ecosystem’. This article looks at some examples of clusters created specifically with industrial biotechnology in mind and examines measures for policymakers.

Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.