ALBERT

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Maciek R Antoniewicz〈/p〉 〈div〉〈p〉Methanol is an attractive and broadly available substrate for large-scale bioproduction of fuels and chemicals. It contains more energy and electrons per carbon than carbohydrates and can be cheaply produced from natural gas. Synthetic methylotrophy refers to the development of non-native methylotrophs such as 〈em〉Escherichia coli〈/em〉 and 〈em〉Corynebacterium glutamicum〈/em〉 to utilize methanol as a carbon source. Here, we discuss recent advances in engineering these industrial hosts to assimilate methanol for growth and chemicals production through the introduction of the ribulose monophosphate (RuMP) cycle. In addition, we present novel strategies based on flux coupling and adaptive laboratory evolution to engineer new strains that can grow exclusively on methanol.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301599-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Connor Wiegand, Ipsita Banerjee〈/p〉 〈div〉〈p〉Pluripotent stems cells (PSCs) can be expanded indefinitely and differentiated into almost any organ-specific cell type. This has enabled the generation of disease relevant tissues from patients in scalable quantities. iPSC-derived organs and organoids are currently being evaluated both in regenerative therapy which are proceeding towards clinical trials, and for disease modeling, which are facilitating drug screening efforts for discovery of novel therapeutics. Here we will review the current efforts and advances in iPSC technology and its subsequent applications and provide a brief commentary on future outlook of this promising technology.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302106-fx1.jpg" width="226" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Josi Buerger, Luisa S. Gronenberg, Hans Jasper Genee, Morten O.A. Sommer〈/p〉 〈div〉〈p〉Microbial cell factories offer new and sustainable production routes for high-value chemicals. However, identification of high producers within a library of clones remains a challenge. When product formation is coupled to growth, millions of metabolic variants can be effectively interrogated by growth selection, dramatically increasing the throughput of strain evaluation. While growth-coupled selections for cell factories have a long history of success based on metabolite auxotrophies and toxic antimetabolites, such methods are generally restricted to molecules native to their host metabolism. New synthetic biology tools offer the opportunity to rewire cellular metabolism to depend on specific and non-native products for growth.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉 〈p〉A diverse library of producers is characterized for production variants. Suitable selection systems allow growth only above the threshold, reducing the original library to the top producers.〈/p〉 〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302155-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉 〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Mathilde Koch, Amir Pandi, Olivier Borkowski, Angelo Cardoso Batista, Jean-Loup Faulon〈/p〉 〈div〉〈p〉Transcriptional biosensors allow screening, selection, or dynamic regulation of metabolic pathways, and are, therefore, an enabling technology for faster prototyping of metabolic engineering and sustainable chemistry. Recent advances have been made, allowing for routine use of heterologous transcription factors, and new strategies such as chimeric protein design allow engineers to tap into the reservoir of metabolite-binding proteins. However, extending the sensing scope of biosensors is only the first step, and computational models can help in fine-tuning properties of biosensors for custom-made behavior. Moreover, metabolic engineering is bound to benefit from advances in cell-free expression systems, either for faster prototyping of biosensors or for whole-pathway optimization, making it both a means and an end in biosensor design.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301563-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Sonya Ardley, Paul Arnold, Jessica Younker, Jennie Rand〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉Carrot and blueberry processing wastewaters were tested to determine total suspended solids (TSS) and organics (COD and BOD〈sub〉5〈/sub〉) levels before and after wastewater treatment. Wastewater treatment by filtration through 1/8″ and 1/16″ reels provided no significant reduction in either TSS, COD or BOD〈sub〉5〈/sub〉. Blueberry wastewater was found to have TSS concentrations of 297 ± 85 mgL〈sup〉−1〈/sup〉, BOD〈sub〉5〈/sub〉 concentrations of 1013 ± 292 mgL〈sup〉−1〈/sup〉, a maximum respiration rate of 10.3 mg(L h)〈sup〉−1〈/sup〉 and COD concentrations of 1947 ± 388 mgL〈sup〉−1〈/sup〉 before discharge. The final effluent of carrot processing wastewater had TSS concentrations of 3030 ± 2975 mgL〈sup〉−1〈/sup〉, BOD〈sub〉5〈/sub〉 concentrations of 2780 ± 1848 mgL〈sup〉−1〈/sup〉, a maximum respiration rate of 65 mg(L h)〈sup〉−1〈/sup〉 and COD concentrations of 6363 ± 2760 mgL〈sup〉−1〈/sup〉. After acclimatization, extended respiration tests indicated a dramatic reduction in oxygen demand was possible in post-reel wastewater, with a 75% reduction in respiration rate over 150 h for blueberry wastewater and an 85% reduction in respiration rate over only 20 h for the more organically-rich carrot wastewater.〈/p〉 〈p〉Bench-scale treatments of preliminary settling, alum coagulation and sedimentation, and aeration were performed on the carrot processing wastewater. Preliminary settling and coagulation-sedimentation were highly effective for TSS removal, achieving 99% reduction in TSS as compared to raw wastewater, but were not effective for organics removal, however, aeration for eight hours with activated sludge achieved 73% removal of COD and 42% removal of BOD〈sub〉5〈/sub〉, indicating that biological treatment was the most promising avenue for organics removal from carrot processing wastewater.〈/p〉 〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Devin L Trudeau, Dan S Tawfik〈/p〉 〈div〉〈p〉The advent of laboratory directed evolution yielded a fruitful crosstalk between the disciplines of molecular evolution and bio-engineering. Here, we outline recent developments in both disciplines with respect to how one can identify the best starting points for directed evolution, such that highly efficient and robust tailor-made enzymes can be obtained with minimal optimization. Directed evolution studies have highlighted essential features of engineer-able enzymes: highly stable, mutationally robust enzymes with the capacity to accept a broad range of substrates. Robust, evolvable enzymes can be inferred from the natural sequence record. Broad substrate spectrum relates to conformational plasticity and can also be predicted by phylogenetic analyses and/or by computational design. Overall, an increasingly powerful toolkit is becoming available for identifying optimal starting points including network analyses of enzyme superfamilies and other bioinformatics methods.〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Oscar Gustavo Miranda Sandoval, Alma Elia Leal Orozco, Sandra Valenzuela, Gerardo Cesar Díaz Trujillo〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉A wastewater regeneration treatment was successfully designed by using modified amorphous silica as an adsorption agent, this ceramic material is generated as an industrial waste in a geothermal power plant located in the City of Mexicali, Baja California.〈/p〉 〈p〉A tertiary wastewater process for the removal of heavy metals from wastewater was designed by modifying purified amorphous silica (99.40% by weight) with low cost reagents as urea and sodium carbonate in a sol – gel reaction.〈/p〉 〈p〉The wastewater treatment with the urea modification allowed to eliminate 40% of chromium and zinc, 70% of nickel, 60% of copper and 90% of lead; while the carbonate modification allowed to remove 30% of nickel, 70 – 80% of chromium and copper and over 90% of aluminum and zinc; achieving a good effluent quality with optimal chemical-physical conditions for its re -use.〈/p〉 〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Marco Zaccaria, William Dawson, Viviana Cristiglio, Massimo Reverberi, Laura E Ratcliff, Takahito Nakajima, Luigi Genovese, Babak Momeni〈/p〉 〈div〉〈p〉Bioremediators are cells or non-living subcellular entities of biological origin employed to degrade target pollutants. Rational, mechanistic design can substantially improve the performance of bioremediators for applications, including waste treatment and food safety. We highlight how such improvements can be informed at the cellular level by theoretical observations especially in the context of phenotype plasticity, cell signaling, and community assembly. At the molecular level, we suggest enzyme design using techniques such as Small Angle Neutron Scattering and Density Functional Theory. To provide an example of how these techniques could be synergistically combined, we present the case-study of the interaction of the enzyme laccase with the food contaminant aflatoxin B〈sub〉1〈/sub〉. In designing bioremediators, we encourage interdisciplinary, mechanistic research to transition from an observation-oriented approach to a principle-based one.〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Jing Ke, Yasuo Yoshikuni〈/p〉 〈div〉〈p〉Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 20 October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology〈/p〉 〈p〉Author(s): Sven Panke, Thomas Ward〈/p〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Elvira Sgobba, Volker F Wendisch〈/p〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300801-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Sikandar Khan, Pengcheng Fu〈/p〉 〈div〉〈p〉Because of their biofuel producing capabilities, algae (including microalgae and cyanobacteria) are effective and sustainable tools to attain energy security with a growing world population and for reduction of our current reliance on fossil fuels. Algal metabolic and genetic engineering could provide substantial advancements in producing novel and promising strains for the production of alternative biofuels. In this review, we have highlighted biotechnological strategies for microalgae and cyanobacteria that target the improvement of: (1) biosynthesis of biofuel precursors (fatty acid, TAGs, and lipids etc.), (2) carbon-capture ability to accumulate more lipids, and (3) engineering hydrogenases for augmented production of biohydrogen. Other strategies for improving quality and quantity of algal biofuels are also explored.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300953-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Nick Wierckx, Gennaro Agrimi, Peter Stephensen Lübeck, Matthias G. Steiger, Nuno Pereira Mira, Peter J. Punt〈/p〉 〈div〉〈p〉Some of the oldest and most established industrial biotechnology processes involve the fungal production of organic acids. In these fungi, the transport of metabolites between cellular compartments, and their secretion, is a major factor. In this review we exemplify the importance of both mitochondrial and plasma membrane transporters in the case of itaconic acid production in two very different fungal systems, 〈em〉Aspergillus〈/em〉 and 〈em〉Ustilago.〈/em〉 Homologous and heterologous overexpression of both types of transporters, and biochemical analysis of mitochondrial transporter function, show that these two fungi produce the same compound through very different pathways. The way these fungi respond to itaconate stress, especially at low pH, also differs, although this is still an open field which clearly needs additional research.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300898-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Zhe Lyu, William B Whitman〈/p〉 〈div〉〈p〉Biological methanogenesis evolved early in Earth’s history and was likely already a major process by 3.5 Ga. Modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts. Owing to their long evolution and extensive adaptations to various habitats, methanogens possess enormous metabolic and physiological diversity. Not only does this diversity offers unique opportunities for biotechnology applications, but also reveals their direct impact on the environment, agriculture, and human and animal health. These efforts are facilitated by an advanced genetic toolbox, emerging new molecular tools, and systems-level modelling for methanogens. Further developments and convergence of these technical advancements provide new opportunities for bioengineering methanogens.〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Larissa Schocke, Christopher Bräsen, Bettina Siebers〈/p〉 〈div〉〈p〉Archaea dominate extreme habitats and possess unique cellular and metabolic properties with novel or modified metabolic pathways and unusual enzymes. Thermoacidophilic 〈em〉Sulfolobus〈/em〉 species and their thermo(acido)philic enzymes gained special attention due to their adaptation toward two extremes, high temperature (75–80°C) and low pH (pH 2–5), that matches harsh process conditions in industrial applications. For different 〈em〉Sulfolobus〈/em〉 species versatile genetic systems have been established and significant metabolic and physiological information from classical biochemistry and genetic as well as poly-omics and systems biology approaches is available. Their ease of growth under aerobic or microaerophilic conditions and established fermentation technologies gaining high cell yields promote 〈em〉Sulfolobus〈/em〉 as source for extremozymes and as valuable novel platform organism for industrial biotechnology.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉 〈p〉〈em〉Sulfolobus species〈/em〉 – thermoacidophilic Archaea – as sources for novel extremozymes and as novel platform organism for metabolic engineering and synthetic biology.〈/p〉 〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301952-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉 〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Mohammadreza Kamali, Seyedeh Azadeh Alavi-Borazjani, Zahra Khodaparast, Mohammadreza Khalaj, Akram Jahanshahi, Elisabete Costa, Isabel Capela〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In the present manuscript, novel effluent treatment processes for pulp and paper mill effluents are divided into two categories: a) those involving the use of chemical additives and b) those which are free of such chemicals. It is especially of high importance for pulp and paper industry to adopt the most efficient and cost-effective treatment methods. This paper critically reviews the recent studies on the treatment of pulp and paper mill effluents while providing suggestions for further studies on the application of various physic-chemical and biological methods for the treatment of such complex effluents containing a number of recalcitrant pollutants.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371717300707-fx1.jpg" width="500" alt="fx1" title="fx1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): David Frederic Emerson, Gregory Stephanopoulos〈/p〉 〈div〉〈p〉Carbon dioxide remediation is of vital importance in mitigating the impact of greenhouse gases on climate change. While various technologies have been presented in the literature, we argue that only by valorizing CO〈sub〉2〈/sub〉 capture can such technologies reach widespread adoption in the current geo-political disposition. One such option is CO〈sub〉2〈/sub〉 fixation by autotrophic bacteria into bio-diesel and commodity chemicals. While proof of concept technologies have been published in the literature, yet key limitations exist, including maximal yield of aerobic CO〈sub〉2〈/sub〉 fixation, and growth rates, productivities, and titers of anaerobic CO〈sub〉2〈/sub〉 fixation. Researchers are currently addressing these issues through metabolic engineering and the controlled supplementation of secondary metabolites.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301708-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Jonathan Strutz, Jacob Martin, Jennifer Greene, Linda Broadbelt, Keith Tyo〈/p〉 〈div〉〈p〉Metabolic models containing kinetic information can answer unique questions about cellular metabolism that are useful to metabolic engineering. Several kinetic modeling frameworks have recently been developed or improved. In addition, techniques for systematic identification of model structure, including regulatory interactions, have been reported. Each framework has advantages and limitations, which can make it difficult to choose the most appropriate framework. Common limitations are data availability and computational time, especially in large-scale modeling efforts. However, recently developed experimental techniques, parameter identification algorithms, as well as model reduction techniques help alleviate these computational bottlenecks. Opportunities for additional improvements may come from the rich literature in catalysis and chemical networks. In all, kinetic models are positioned to make significant impact in cellular engineering.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301551-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Fabian Tolle, Pascal Stücheli, Martin Fussenegger〈/p〉 〈div〉〈p〉Synthetic biology uses engineering principles to design and assemble biological components and systems for a variety of applications. On the basis of genetic engineering, synthetic gene switches can be interconnected to construct complex gene circuits, capable of sensing and integrating diverse input signals for precise spatiotemporal control of target gene expression in living cells. Designer cells can be equipped with advanced gene circuitry enabling them to react precisely to pre-programmed combinations of conditions, automatically triggering a specified response, such as therapeutic protein production. Such cells are promising therapeutic modalities for applications where traditional medical treatments have limitations. Herein, we highlight selected recent examples of designer cells with engineered gene circuits targeted toward applications in personalized human medicine.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301630-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): James R Crosby, Tunyaboon Laemthong, April M Lewis, Christopher T Straub, Michael WW Adams, Robert M Kelly〈/p〉 〈div〉〈p〉Going forward, industrial biotechnology must consider non-model metabolic engineering platforms if it is to have maximal impact. This will include microorganisms that natively possess strategic physiological and metabolic features but lack either molecular genetic tools or such tools are rudimentary, requiring further development. If non-model platforms are successfully deployed, new avenues for production of fuels and chemicals from renewable feedstocks or waste materials will emerge. Here, the challenges and opportunities for extreme thermophiles as metabolic engineering platforms are discussed.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301897-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Mary E Krause, Erinc Sahin〈/p〉 〈div〉〈p〉Development of a robust biologic drug product is accomplished by extensive formulation and process development screening studies; however, even in the most optimal formulation, a protein can undergo spontaneous degradation during manufacture, storage, and clinical use. Chemical changes to amino acid residues, such as oxidation of methionine or tryptophan, or changes in charge such as deamidation or carbonylation, can induce conformational changes in the overall protein structure, potentially leading to changes in physical – in addition to chemical – stability. Oxidation is often caused by light exposure or the presence of metal ions or peroxides. Asparagine deamidation is more likely to occur at higher pH and/or elevated temperature. Mechanical and interfacial stresses during manufacturing can lead to physical instabilities (i.e. various forms of aggregation). A well-defined manufacturing process and effective in-process controls are essential in minimizing chemical and physical instabilities, enabling robust production and distribution of a safe and efficacious drug product. In this work, the authors provide a review of developments in these areas over the past two years, with emphasis on manufacturability of therapeutically relevant proteins and protein-based drug products.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301381-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Chen-Yuan Kao, Eleftherios T Papoutsakis〈/p〉 〈div〉〈p〉Extracellular vesicles (EVs) are membrane vesicles, the submicron-size microparticles and the nanometer-size exosomes, that carry RNAs, proteins and lipids from their parent cells. EV generation takes place under cellular activation or stress. Cells use EVs to communicate with other cells by delivering signals through their content and surface proteins. Beyond diagnostic and discovery applications, EVs are excellent candidates for enabling safe and potent cell and gene therapies, especially those requiring strong target specificity. Here we examine EVs, their engineering and applications by dissecting mechanistic and engineering aspects of their components that endow them with their unique capabilities: their cargo and membranes proteins. Both EV cargo and membranes can be independently engineered and used for various applications. We review early efforts for their biomanufacturing.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691830140X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Han A B Wösten〈/p〉 〈div〉〈p〉Filamentous fungi have been used for more than a century as versatile and highly productive cell factories. They are used to produce enzymes and small molecule compounds such as antibiotics and organic acids. Filamentous fungi are now also being explored for the production of sustainable materials that can for instance replace plastics. Mutagenesis and genetic modification are used to improve performance of production strains. Single cell technologies and bulk sample analysis are novel strategies to identify genes that can be used for genetic modification of production strains. Such genes may for instance be involved in fungal reproduction and hyphal heterogeneity. These differentiation processes have recently been implicated to affect production of enzymes and small molecule compounds. Finally, use of mixed cultures instead of monocultures can be a strategy to improve production processes.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302283-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Victoria Armario Najera, Richard M Twyman, Paul Christou, Changfu Zhu〈/p〉 〈div〉〈p〉Multiplex genome editing involves the simultaneous targeting of multiple related or unrelated targets. The latter is most straightforward using the CRISPR/Cas9 system because multiple gRNAs can be delivered either as independent expression cassettes with their own promoters or as polycistronic transcripts processed into mature gRNAs by endogenous or introduced nucleases. Multiplex genome editing in plants initially focused on input traits such as herbicide resistance, but has recently expanded to include hormone biosynthesis and perception, metabolic engineering, plant development and molecular farming, with more than 100 simultaneous targeting events reported. Usually the coding region is targeted but recent examples also include promoter modifications to generate mutants with varying levels of gene expression.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉 〈p〉Multiplex genome editing in plants is typically carried out using the CRISPR/Cas9 system because it is more amenable to multiplexing than any other platform. A single gRNA can be used to target multiple alleles of the same gene (A1, A2) or homeoalleles from different ancestral genomes in a polyploid plant (A1, A2, B1, B2). A single gRNA can also be used to target multiple genes (X, Y, Z) if they contain a conserved region (C). Multiple gRNAs can be used to target unrelated sites in the same gene or in conserved sequences such as homeoalleles or members of the same gene family. Multiple gRNAs can also be used to target completely unrelated genes (D, E, F).〈/p〉 〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301496-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉 〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Dhanya Vijay, M Kalim Akhtar, Wolfgang R Hess〈/p〉 〈div〉〈p〉Cyanobacteria are a group of photosynthetic microorganisms with high commercial potential. They can utilize sunlight directly to convert carbon dioxide or even nitrogen into a variety of industrially relevant chemicals. However, commercial platforms for the renewable and sustainable production of chemicals have yet to be demonstrated for cyanobacteria. Diverse strategies have therefore been employed in recent years to improve the production yields and efficiency of target chemicals. These include the use of CRISPR/Cas systems for mutant selection, synthetic RNA elements for controlling transcription, metabolic network modelling for understanding pathway fluxes, enzyme engineering, improving growth rates, alleviating product toxicity and microbial consortia. More elaborate strategies for engineering cyanobacteria, however, are still very much required if we are to meet the grand challenge of employing cyanobacteria as photosynthetic workhorses for large-scale industrial applications.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301502-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Arlinda Rezhdo, Mariha Islam, Manjie Huang, James A Van Deventer〈/p〉 〈div〉〈p〉There is growing evidence that noncanonical amino acids (ncAAs) can be utilized in the creation of biological therapeutics ranging from protein conjugates to cell-based therapies. However, when does genetically encoding ncAAs yield biologics with unique properties compared to other approaches? In this review, we attempt to answer this question in the broader context of therapeutic development, emphasizing advances within the past two years. In several areas, ncAAs add valuable routes to therapeutically relevant entities, but application-specific needs ultimately determine whether ncAA-mediated or alternative solutions are preferred. Looking forward, using ncAAs to perform ‘protein medicinal chemistry,’ in which atomic-level changes to proteins dramatically enhance therapeutic properties, is a promising emerging area. Further upgrades to the performance of ncAA incorporation technologies will be essential to realizing the full potential of ncAAs in biological therapeutics.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302118-fx1.jpg" width="221" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Esteban Martínez-García, Víctor de Lorenzo〈/p〉 〈div〉〈p〉Traditional microbial biotechnology is in the midst of a profound transformation brought about not only by many conceptual and technical breakthroughs (e.g. systems and synthetic biology, the CRISPR revolution) but also by the major change of socioeconomic context generically known as the 4th Industrial Revolution. Owing to its naturally evolved properties of stress endurance, metabolic versatility, and physiological robustness the soil bacterium 〈em〉Pseudomonas putida〈/em〉 has recently received a considerable attention as the basis for developing whole-cell catalysts. The review below sketches the ongoing journey of this bacterium from being a soil-dweller, root-colonizer microbe all the way to become a programmable catalyst for executing complex biotransformations at very different scales—having in the background the contemporary developments in non-biological programmable chemistry.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300035-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Weiqi Fu, David R Nelson, Alexandra Mystikou, Sarah Daakour, Kourosh Salehi-Ashtiani〈/p〉 〈div〉〈p〉Microalgae have been investigated for the photosynthetic production of natural products with industrial and biomedical applications. Their rapid growth offers an advantage over higher plants, while their complex metabolic capacities allow for the production of various molecules. Despite their potentials, molecular techniques are underdeveloped in microalgae compared to higher plants, fungi, and bacteria. However, recent advances in genome sequencing, strain development, and genome editing technologies, are providing thrust to enhance research on microalgal species that have branched out from several focal model organisms to encompass a great diversity of species. In this review, we highlight the recent, significant advances in microalgal research, with a focus on the development of new resources that can enhance work on model and non-model species.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301666-fx1.jpg" width="252" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Matthew S Faber, Timothy A Whitehead〈/p〉 〈div〉〈p〉Protein therapeutics requires a series of properties beyond biochemical activity, including serum stability, low immunogenicity, and manufacturability. Mutations that improve one property often decrease one or more of the other essential requirements for therapeutic efficacy, making the protein engineering challenge difficult. The past decade has seen an explosion of new techniques centered around cheaply reading and writing DNA. This review highlights the recent use of such high throughput technologies for engineering protein therapeutics. Examples include the use of human antibody repertoire sequence data to pair antibody heavy and light chains, comprehensive mutational analysis for engineering antibody specificity, and the use of ancestral and inter-species sequence data to engineer simultaneous improvements in enzyme catalytic efficiency and stability. We conclude with a perspective on further ways to integrate mature protein engineering pipelines with the exponential increases in the volume of sequencing data expected in the forthcoming decade.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301587-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Laurence C Chen, Yvonne Y Chen〈/p〉 〈div〉〈p〉Adoptive T-cell therapy has shown remarkable clinical efficacy in treating refractory hematological cancers. However, challenges presented by solid tumors impede the applicability of adoptive T-cell therapy to the majority of cancers. In order to engineer effective T-cell therapies targeting solid tumors, two synergistic design criteria—T-cell therapeutic programs and anti-tumor T-cell chassis—should be taken into consideration. Recent advances in synthetic biology have enabled genetic programming of therapeutic sense-and-respond modalities in T cells. Furthermore, systems-level integration of multi-omics datum have allowed researchers to holistically profile robust anti-tumor T-cell populations. In this review, we feature novel strategies that can be incorporated into adoptive T-cell therapy design–ushering in a new paradigm of solid tumor treatment options.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301393-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Joeri Willet, Koen Wetser, Jan Vreeburg, Huub H.M. Rijnaarts〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The projected increase of industrial water demands raises the need to assess the environmental sustainability of industrial water use. Assessment methods need to use Sustainable Systems Indicators (SSIs) which relate resource use to the carrying capacity of the local environment. SSIs for water use evaluate whether water use exceeds the natural water renewal (quantity) and whether emissions remain within the assimilation capacity of ecosystems (quality). We systematically reviewed the scientific literature to show which methods are used to assess industrial water use, and of these, which methods incorporate SSIs. In total, 82 assessment methods were identified in 340 papers. The methods were assigned to five categories: Key Performance Indicators, Composite Indices, Environmental Accounting, Material and Energy Flow Analysis, and Life Cycle Analysis. In 26% of the reviewed papers, the assessment methods used SSIs. The number of papers incorporating SSIs is growing at a slower rate than the overall number of papers in the area of sustainability assessments of industrial water use. Considering the expected growth in industrial water use this poses a risk to sustainable water use. The best performing category in terms of incorporating SSIs is Material and Energy Flow Analysis (42% of papers). Papers assessing several industrial sectors in the same study incorporate SSIs more frequently (68%) than research focused on a single industry or process (20%). We discuss examples from the reviewed papers which successfully incorporate SSIs, in order to: (1) identify the elements needed to create SSIs for industrial water use, (2) aid researchers and practitioners in selecting methods which incorporate SSIs, and (3) provide a starting point for future methodological development incorporating SSIs.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371718300404-fx1.jpg" width="500" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Casey A Hooker, Kok Zhi Lee, Kevin V Solomon〈/p〉 〈div〉〈p〉Early-branching anaerobic fungi are critical for hydrolyzing untreated lignocellulose in the digestive tracts of large herbivorous animals. While these fungi were discovered more than 40 years ago, they remain understudied and underexploited. Recent advances in -omics technologies, however, have enabled studies that reveal significant biosynthetic potential within anaerobic fungal genomes for diverse biotechnological applications. Applications range from enhanced second-generation bioenergy platforms to improved animal health. However, developing gut fungi for these applications will require significant advances in genome engineering technologies for these organisms. Here, we review the biotechnological abilities of anaerobic fungi and highlight challenges that must be addressed to develop them for a range of biotechnological applications.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301484-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Ali Izadi, Morteza Hosseini, Ghasem Najafpour Darzi, Gholamreza Nabi Bidhendi, Farshid Pajoum Shariati〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Recently, new technologies regarding water and wastewater treatment have been developed and among these processes, the fixed bed biofilm reactor combined with membrane bioreactor is the recent alternative solution to conventional technologies. In this research, an integrated fixed bed membrane bioreactor (FBMBR) with a hydraulic retention time (HRT) of 36 h was developed to remove pollutants from real paper-recycling wastewater. The removal efficiencies of chemical oxygen demand (COD), ammonium, nitrite, nitrate and total nitrogen (TN) for permeate and supernatant were in the range of 92–99%, 59–97%, 78–97%, 59–98% and 68–92%, respectively. In addition, the membrane fouling was evaluated by transmembrane pressure (TMP) monitoring during experimental period at a constant flux of 12 l m〈sup〉−2〈/sup〉.h〈sup〉−1〈/sup〉, and the TMP increasing rate was 2 mbar/day. The results as a whole indicated that the FBMBR can be applied effectively to removal of pollutants from real paper-recycling wastewater.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371718301409-fx1.jpg" width="262" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 18 August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry〈/p〉 〈p〉Author(s): Kali D. Frost, Inez Hua〈/p〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371719300150-fx1.jpg" width="500" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 29 July 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry〈/p〉 〈p〉Author(s): Geethu Gopinatha Kurup, Benu Adhikari, Bogdan Zisu〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Dairy manufacturing sector generates large quantity of nutrient-rich wastewater which requires treatment before it can be released into the environment. This study aimed to use a low-cost food grade sodium lignosulphonate (Na-lignosulphonate) to recover proteins and lipids from dairy wastewater and reduce the BOD. The colloidal particles of wastewater sample were precipitated with varying the concentration of Na-lignosulphonate (0.002–0.032%, w/v) and pH of medium (1.0–3.5). Experiments were conducted at ambient (22 °C) and mildly elevated (40 °C) temperatures. At the optimum concentration (0.016%, w/v) of Na-lignosulphonate, the highest turbidity removal (98%) was achieved at pH 3.5 and at both temperatures. This method recovered 96% lipids and 46% proteins (mostly caseins) and reduced the BOD by 73% at 22 °C. Na-lignosulphonate is found to be an effective coagulant owing to its ability to readily complex with positively charged colloidal particles at acidic pH.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 22〈/p〉 〈p〉Author(s): Roya Mourad, Hadi H. Jaafar, Nuhad Daghir〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The Middle East and North Africa region (MENA) is one of the most water-scarce worldwide. Up-to-date estimates of the origin and types of water use in various industries are necessary to manage water resources and guide food and water policies. The objective of this study is to determine new estimates for the color-coded water footprint (WF). Using the Water Footprint Network approach, country-specific blue, green and grey WFs and total virtual water were calculated for 2010–2016 using recent production data. We find that animal production in MENA increased by 50% as compared to the previous decade. Virtual water consumption account for more than 80 billion m〈sup〉3〈/sup〉 annually, mostly for beef (61%), followed by broilers (20%), and sheep (17%). 40% of which is local. Almost 50% of the feed grains used in the region are produced locally, accounting for 40% of the total WF for animal production in MENA.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: Available online 3 June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology〈/p〉 〈p〉Author(s): Lutgarde Raskin, Per Halkjær Nielsen〈/p〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Timothy A Su, Kevin J Bruemmer, Christopher J Chang〈/p〉 〈div〉〈p〉Bioluminescence imaging is a powerful modality for 〈em〉in vivo〈/em〉 imaging owing to its low background and high signal-to-noise ratio. Because bioluminescent emission occurs only upon the catalytic reaction between the luciferase enzyme and its luciferin substrate, caging luciferins with analyte-reactive triggers offers a general approach for activity-based sensing of specific biochemical processes in living systems across cell, tissue, and animal models. In this review, we summarize recent efforts in the development of synthetic caged luciferins for tracking enzyme, small molecule, and metal ion activity and their contributions to physiological and pathological processes.〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Todd A Duncombe, Petra S Dittrich〈/p〉 〈div〉〈p〉Droplet microfluidics has become a powerful analytical platform in biological research for conducting high-throughput screening in millions of discrete micro-reactors per hour. While the method facilitates faster and cheaper testing than conventional microtiter plates, the mobile nature of droplets makes micro-reaction tracking a notable challenge. To address this, researchers are developing a variety of tracking methods, ranging from organizing droplets into an index or labeling droplets with a barcode. The optimal tracking approach depends on the criteria for each specific application. Considerations include the requisite assay readout, throughput, droplet library size, reagent tracking and more. In this review, we summarize different strategies for droplet micro-reaction tracking and comment on promising future approaches in droplet barcoding. Topics range from indexing droplets by sequence or in an array, labeling droplets with barcodes, and reagent barcoding to track the input conditions in parametric screens.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691830212X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Marco Santorelli, Calvin Lam, Leonardo Morsut〈/p〉 〈div〉〈p〉Synthetic biology efforts began in simple single-cell systems, which were relatively easy to manipulate genetically (Cameron 〈em〉et al.〈/em〉, 2014). The field grew exponentially in the last two decades, and one of the latest frontiers are synthetic developmental programs for multicellular mammalian systems (Black 〈em〉et al.〈/em〉, 2017; Wieland and Fussenegger, 2012) to genetically control features such as patterning or morphogenesis. These programs rely on engineered cell–cell communications, multicellular gene regulatory networks and effector genes. Here, we contextualize the first of these synthetic developmental programs, examine molecular and computational tools that can be used to generate next generation versions, and present the general logic that underpins these approaches. These advances are exciting as they represent a novel way to address both control and understanding in the field of developmental biology and tissue development (Elowitz and Lim, 2010; Velazquez 〈em〉et al.〈/em〉, 2018; White 〈em〉et al.〈/em〉, 2018; Morsut, 2017). This field is just at the beginning, and it promises to be of major interest in the upcoming years of biomedical research.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301617-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Haiyang Jia, Petra Schwille〈/p〉 〈div〉〈p〉Bottom-up reconstituting well-characterized functional molecular entities, parts and modules towards a synthetic cell will give new insights into the mechanisms and origin of life. However, a remaining central challenge is how to organize cellular processes spatiotemporally from their component parts 〈em〉in vitro〈/em〉. Here, we review cutting edge tools and technologies that can facilitate such a bottom-up reconstitution towards a synthetic cell in space and time, particularly with regard to the following aspects: (1) reliable model membrane-environment and microenvironment; (2) dynamic genetic regulation and self-sustaining transcription and translation machinery; (3) spatially organized cytoskeleton that supports the biological architecture and cellular self-reproduction in 3D.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302015-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 3 November 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology〈/p〉 〈p〉Author(s): Yvonne Y Chen, James A Van Deventer〈/p〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Charles G Starr, Peter M Tessier〈/p〉 〈div〉〈p〉Despite the recent explosion in the use of monoclonal antibodies (mAbs) as drugs, it remains a significant challenge to generate antibodies with a combination of physicochemical properties that are optimal for therapeutic applications. We argue that one of the most important and underappreciated drug-like antibody properties is high specificity — defined here as low levels of antibody non-specific and self-interactions — which is linked to low off-target binding and slow antibody clearance 〈em〉in vivo〈/em〉 and high solubility and low viscosity 〈em〉in vitro〈/em〉. Here, we review the latest advances in characterizing antibody specificity and elucidating its molecular determinants as well as using these findings to improve the selection and engineering of antibodies with extremely high, drug-like specificity.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301368-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 58〈/p〉 〈p〉Author(s): Hung X Nguyen, Nenad Bursac〈/p〉 〈div〉〈p〉Ion channels play essential roles in regulating electrical properties of excitable tissues. By leveraging various ion channel gating mechanisms, scientists have developed a versatile set of genetically encoded tools to modulate intrinsic tissue excitability under different experimental settings. In this article, we will review how ion channels activated by voltage, light, small chemicals, stretch, and temperature have been customized to enable control of tissue excitability both 〈em〉in vitro〈/em〉 and 〈em〉in vivo〈/em〉. Advantages and limitations of each of these ion channel-engineering platforms will be discussed and notable applications will be highlighted. Furthermore, we will describe recent progress on 〈em〉de novo〈/em〉 generation of excitable tissues via expression of appropriate sets of engineered voltage-gated ion channels and discuss potential therapeutic implications.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918300983-fx1.jpg" width="211" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Alice Guarneri, Willem JH van Berkel, Caroline E Paul〈/p〉 〈div〉〈p〉Coenzymes are ubiquitous in Nature, assisting in enzyme-catalysed reactions. Several coenzymes, nicotinamides and flavins, have been known for close to a century, whereas variations of those organic molecules have more recently come to light. In general, the requirement of these coenzymes imposes certain constraints for 〈em〉in vitro〈/em〉 enzyme use in biocatalytic processes. Alternative coenzymes have risen to circumvent the cost factor, tune reaction rates or obtain different chemical reactivity. This review will focus on these alternatives and their role and applications in biocatalysis.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301964-fx1.jpg" width="245" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Andrea Belluati, Ioana Craciun, Claire E Meyer, Serena Rigo, Cornelia G Palivan〈/p〉 〈div〉〈p〉One of the main features of living matter is compartmentalization, that is the temporal and spatial division of biological reactions and containment of the cellular components. Nanotechnology aims to replicate this, separating tiny environments from the exterior into nano-sized and micro-sized self-assembled compartments. Those synthetic compartments can perform reactions, be tracked and act 〈em〉in vivo〈/em〉. Here, an overview of the techniques to fabricate vesicular, polymer-based catalytic compartments and the parameters affecting their architecture is presented. How communication can be ensured across their membranes, recent developments in the enzymes that have been loaded into them and the latest advances in biological applications are discussed. This review highlights the characteristics that make polymers an enticing choice, the protection they offer, and their applications in compartmentalizing biologically relevant reactions.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691830199X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Christopher Barnes, Olivia Scheideler, David Schaffer〈/p〉 〈div〉〈p〉Gene therapy is progressively emerging as a promising and powerful therapeutic modality, and adeno-associated virus (AAV) is a major delivery vehicle for such therapies. Among the most significant challenges that limit AAV’s utility, however, is the immune response it elicits. Antibodies elicited by prior exposure to natural virus or vector can bind to an AAV vector, preventing it from entering the cell. Furthermore, even if AAV manages to infect a target cell, these cells can then be attenuated by lymphocytes. Improvements in our understanding of how the immune system responds to AAV have guided engineering of the capsid to reduce those responses, yielding capsid variants that are much stealthier and more effective. This review summarizes recent advances in understanding the immune response to AAV as well as highlights engineering methods that enhance AAV’s potential as a gene therapy vector.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301423-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Patrick J Krohl, Seth D Ludwig, Jamie B Spangler〈/p〉 〈div〉〈p〉Protein interactions communicate critical information from the environment into cells to orchestrate functional responses relevant to health and disease. Whereas the natural repertoire of protein interfaces is finite, biomolecular engineering tools provide access to an unlimited scope of potential interactions that can be custom-designed for affinity, specificity, mechanism, or other properties of interest. This review highlights recent developments in protein interface engineering that offer insight into human physiology to inform the design of new pharmaceuticals, with a particular focus on immunotherapeutics. We cover three innovative and translationally promising approaches: (1) reprogramming receptor oligomerization to manipulate signaling pathways; (2) computational protein interface design strategies; and (3) engineering bioorthogonal protein interaction networks.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301411-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Poul Erik Jensen, Lars B. Scharff〈/p〉 〈div〉〈p〉Plastids are interesting targets for metabolic engineering using the tools of synthetic biology. Plastids carry their own genome, which can be manipulated genetically in many algae and plants. Incorporating foreign genes into the plastid genome offers valuable benefits, such as high-level foreign protein expression and the absence of gene silencing. Here, we review progress in bioengineering of chloroplasts to produce valuable metabolites and proteins. Various strategies for enhancing yields of desired products, including design of operons, fusion proteins for improved translational efficiency, protein scaffolding, metabolic channeling and storage, are described. Efforts to control plastid differentiation also offer promising ways of turning plastids into controllable bio-factories, and the construction of synthetic plastids optimized for specific functions would be a major advance.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301526-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Anthony B DeNicola, Yi Tang〈/p〉 〈div〉〈p〉Mutated RNA splicing machinery drives many human diseases and is a promising therapeutic target for engineering and small molecule therapy. In the case of mutations in individual genes that cause them to be incorrectly spliced, engineered splicing factors can be introduced to correct splicing of these aberrant transcripts and reduce the effects of the disease phenotype. Mutations that occur in certain splicing factor genes themselves have been implicated in many cancers, particularly myelodysplastic syndromes. Small molecules that target splicing factors have been developed as therapies to preferentially induce apoptosis in these cancer cells. Specifically, drugs targeting the splicing factor SF3B1 have led to recent clinical trials. Here, we review the role of alternative splicing in disease, approaches to rescue incorrect splicing using engineered splicing factors, and small molecule splicing inhibitors developed to treat hematological cancers.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302350-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Amanda Y van Tilburg, Haojie Cao, Sjoerd B van der Meulen, Ana Solopova, Oscar P Kuipers〈/p〉 〈div〉〈p〉Metabolic engineering and synthetic biology approaches have prospered the field of biotechnology, in which the main focus has been on 〈em〉Escherichia coli〈/em〉 and 〈em〉Saccharomyces cerevisiae〈/em〉 as microbial workhorses. In more recent years, improving the Gram-positive bacteria 〈em〉Lactococcus lactis〈/em〉 and 〈em〉Bacillus subtilis〈/em〉 as production hosts has gained increasing attention. This review will demonstrate the different levels at which these bacteria can be engineered and their various application possibilities. For instance, engineered 〈em〉L. lactis〈/em〉 strains show great promise for biomedical applications. Moreover, we provide an overview of recent synthetic biology tools that facilitate the use of these two microorganisms even more.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301460-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Koli Basu, Evan M Green, Yifan Cheng, Charles S Craik〈/p〉 〈div〉〈p〉Antibodies (Abs) are ubiquitous reagents for biological and biochemical research and are rapidly expanding into new therapeutic areas. They are one of the most important probes for determining how proteins function under normal and pathophysiological conditions. Abs are required for the quantification of targets, detection of temporal and spatial patterns of protein expression in cells and tissues, and identification of interacting partners and their biological activities. Their remarkable specificity and unique binding properties can facilitate three-dimensional structure determination using X-ray crystallography and electron cryomicroscopy. While hybridoma technology that involves animal immunization is often productive, many antigen targets do not generate useful Abs. This is particularly true if unique states of the target or critical non-immunogenic target sequences need to be recognized by the Abs. By using the methods of recombinant antibody generation, identification, and engineering, these ‘hybridoma-refractory’ antigens can be readily targeted. Specific, reproducible, and renewable recombinant Abs are proving to be invaluable reagents in applications ranging from biological discovery to structure determination of challenging macromolecules.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301940-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Benjamin J Umlauf, Eric V Shusta〈/p〉 〈div〉〈p〉The blood–brain barrier (BBB) segregates the central nervous system from the systemic circulation. As such, the BBB not only prevents toxins and pathogens from entering the brain, but also limits the brain uptake of therapeutic molecules. However, under certain pathological conditions, the BBB is disrupted, allowing direct interaction between blood components and the diseased site. Moreover, techniques such as focused ultrasound can further disrupt the BBB in diseased regions. This review focuses on strategies that leverage such BBB disruption for delivering nanocarriers to the central nervous system (CNS). BBB disruption, as it relates to nanocarrier delivery, will be discussed in the context of acute pathologies such as stroke and traumatic brain injury, as well as chronic pathologies such as brain tumors, Alzheimer’s disease, and Parkinson’s disease. Key aspects of nanocarrier design as they relate to penetration and retention in the CNS are also highlighted.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301721-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Gwen Swinnen, Alain Goossens, Maite Colinas〈/p〉 〈div〉〈p〉Metabolic pathways are tightly regulated at the transcriptional and post-translational level, often relying on protein–protein interactions or post-translational protein modifications. Whereas these principles have been established already for a long time, the number of experimentally established cases is expected to rise exponentially in the near future as a result of recent advances in protein-based detection methods. Interactions and modifications are often dependent on only short amino-acid sequences that represent excellent targets for new gene editing technologies by which specific base pairs can be exchanged. Here, we introduce the concept of metabolic editing, which is based on identifying specific amino-acid sequences that are subsequently targeted for gene editing. The proposed workflow will serve for both applied metabolic engineering purposes and proof-of-concept studies in fundamental research.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301514-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Keiji Nakamura, Norihiro Itsubo〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Japanese pigs are farmed by giving them cereal crop feed, consequently, the Japanese pig industry increases indirect impact on the environment. Contrastingly, French pigs are farmed by feeding them an appropriate quantity of low-protein feed to decrease environmental impact of feed cereal cultivation. The proposed study aims to assess the carbon and water footprints of conventional and low-protein pig feeds in the French model and extends these findings to Japan. When essential amino acids of soybean meals were partially replaced by industrially manufactured amino acids (forming a low-protein feed), the carbon and water-consumption footprints in France were lowered by 0.41 t-CO2/t-feed and 100 m3/t-feed, respectively. The low-protein feed also incurred a 10% lower water-eutrophication footprint in comparison with the conventional feed. Based on these findings, if low-protein feed is widely used in Japan, the pig industry would reduce CO〈sub〉2〈/sub〉 emissions and water consumption by 248,000 t-CO〈sub〉2〈/sub〉/y and 68,000 km〈sup〉3〈/sup〉/y, respectively.〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Qin Zeng, Christopher M Jewell〈/p〉 〈div〉〈p〉A key challenge facing immunotherapy is poor infiltration of T cells into tumors, along with suppression of cells reaching these sites. However, macrophages make up a majority of immune cell infiltrates into tumors, creating natural targets for immunotherapies able to direct macrophages away from tumor-supportive functions and toward anti-tumor phenotypes. Recent studies demonstrate that toll-like receptors (TLRs) – pathways that quickly trigger early immune responses – play an important role in polarizing macrophages. Here, we present emerging ways in which TLR signaling is being manipulated in macrophages to create new opportunities for cancer immunotherapy. In particular, we discuss approaches to deliver TLR agonists, to leverage biomaterials in these therapies, and to couple TLR-based approaches with other frontline treatments as combination cancer therapies.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691830171X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Hussain Dahodwala, Kelvin H Lee〈/p〉 〈div〉〈p〉Chinese hamster ovary (CHO) cell-based bioproduction of recombinant proteins can now routinely achieve 〉5 g/L titers in fed-batches. This progress is partly due to the rapid adaptability of CHO cells to various genetic manipulations and changing process conditions. An inherently plastic genome allows for this adaptability; however, it also gives CHO cells the propensity for genomic rearrangements. In combination with the genomic and metabolic demand of high producer cells, CHO cell plasticity manifests itself in the bioproduction process as 〈strong〉cell line instability〈/strong〉, by way of a decline in productivity and product quality. In this review, we provide a definition for titer and quality stability and discuss the main causes of the CHO instability phenomenon and advances in clone selection and genetic manipulations. We also discuss advances in systems biology efforts that can provide new strategies for early prediction of CHO cell instability, which will help to identify multi-gram per liter titer cell lines that can maintain production stability and reproducible product quality over extended culture durations.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302039-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 7 January 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology〈/p〉 〈p〉Author(s): Saulius Klimašauskas, Linas Mažutis〈/p〉

Description: 〈p〉Publication date: June 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 21〈/p〉 〈p〉Author(s): Sudip Kumar Sen, Prasanta Patra, Chitta Ranjan Das, Smita Raut, Sangeeta Raut〈/p〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉In the present investigation, a number of experiments have been conducted for mineralization of wastewater containing methyl orange (MO) in integrated biofilm bioreactor with coconut fiber as natural bio-material. The color removal expected from the standard curve of dye versus optical density at its maximum absorption wavelength (460 nm) were 87% and COD removals were 69〈em〉%. Pseudomonas putida〈/em〉 showed a strong ability to decolorize methyl orange under aerobic conditions at pH 7.0 and ambient temperature were considered to be the optimum decolorizing conditions under static state. The spectral analysis of UV–Visible spectroscopy, Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (〈sup〉1〈/sup〉H NMR) corrugated the metabolic products formed during the degradation. The nutritional profile of wheat grains irrigated with TTW has enhanced with respect to Energy 241%, Carbohydrate 212% and Protein 402% in comparison to grains obtained on irrigation with Textile wastewater (TWW).〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371718300489-fx1.jpg" width="252" alt="fx1" title="fx1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Vladimir Kubyshkin, Nediljko Budisa〈/p〉 〈div〉〈p〉Can we make life with a different genetic amino acid repertoire? Can we expect organisms which would keep newly given genetic code associations permanently? To address these questions, we would like to analyze the existent genetic code amino acid repertoire as formed from derivatives of alanine. Derivation from alanine leads to the α-helix based biological world, the 〈em〉Alanine World〈/em〉, whereas variations in the side-chains enable tertiary folding and subsequent chemical versatility of the proteome. Proline, glycine and pyrrolysine are the rudiments in the current genetic code, indicating that the original set could be different. Furthermore, from the perspective of peptide chemistry, it shall be possible to recruit these alternative scaffolds for the construction of synthetic or alternative life. This would allow for a completely new biological world, potentially as functional and versatile as the existing one. Pursuing these options offers a strategy for a complete re-design or even 〈em〉de-novo〈/em〉 creation of living organisms based on entirely different chemical make-up, with completely new set of solutions for both near and distant future biotechnologies.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918302064-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Jasmin E Fischer, Anton Glieder〈/p〉 〈div〉〈p〉In the past two to five years innovative DNA tools and inventive methodologies accelerated the speed of engineering of 〈em〉Komagataella phaffii〈/em〉 (〈em〉Pichia pastoris〈/em〉) for the efficient expression of intracellular and secreted proteins. Going beyond the standard approaches employing single heterologous genes or simultaneous expression of several different genes under the control of identical promoter and terminator sequences, balanced and consecutive co-expression of multiple genes (a, b) combined with simple host genome editing (c) now opens new opportunities for manufacturing of recombinant proteins or chemicals made by whole cell biocatalysis or synthetic biology.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301939-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: February 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 61〈/p〉 〈p〉Author(s): Janina Metje-Sprink, Thorben Sprink, Frank Hartung〈/p〉 〈div〉〈p〉The application of site directed nucleases (SDN) for Genome Editing (GE) in plant breeding and research increases exponentially in the last few years. The main research so far was on ‘proof of concept’ studies or improvement of the precision and delivery of the SDN. Nevertheless, a reasonable amount of research is present on market-oriented applications for cash crops such as rice but also for commercially lesser interesting crops and vegetables. Reported field trials involving GE plants are scarce around the world and almost not existing in Europe. This is due to the regulatory landscape for GE plants, which is quite distinct and especially in the European Union very demanding. By far the most field trials involve GE rice varieties in the Asian area, followed up by tomato and other vegetables and crops.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300618-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: February 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 61〈/p〉 〈p〉Author(s): Angelina Schindele, Annika Dorn, Holger Puchta〈/p〉 〈div〉〈p〉CRISPR/Cas is in the process of inducing the biggest transformation of plant breeding since the green revolution. Whereas initial efforts focused mainly on changing single traits by error prone non-homologous end joining, the last two years saw a tremendous technical progress achieving more complex genetic, epigenetic and transcriptional changes. The efficiencies of inducing directed changes by homologous recombination have been improved significantly and strategies to break genetic linkages by inducing chromosomal rearrangements have been developed. Cas13 systems have been applied to degrade viral and mRNA in plants. Most importantly, a historical breakthrough was accomplished: By introducing multiple genomic changes simultaneously, domestication of wild species in a single generation has been demonstrated, speeding up breeding dramatically.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300606-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Kun Liu, Shengying Li〈/p〉 〈div〉〈p〉Enormous fuel consumption and growing environmental concerns have been spurring development of renewable biofuels. Among various biofuels, fatty acid-derived biohydrocarbons are ideal alternatives to non-renewable fossil fuels due to their closest properties to petroleum-based fuels. In the past decade, novel hydrocarbon-producing enzymes have continuously been discovered and engineered. Here, we review the recent advances in biosynthesis of fatty acid-derived hydrocarbons with emphasis on enzymology and enzyme engineering, based on which some outlooks are provided.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300485-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Doug K Allen, Jamey D Young〈/p〉 〈div〉〈p〉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 novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301132-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 23〈/p〉 〈p〉Author(s): Hussein I. Abdel-Shafy, Madiha A. Shoeib, Mohamed A. El-Khateeb, Ahmed O. Youssef, Omar M. Hafez〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Cooling tower blowdown water (CTBW) was treated with simple electrocoagulation (EC) using magnesium-rod electrode. This study examined the effects of the treatment parameters (current density, electrolysis time, electrode distance, initial pH and stirring speed) on the EC ability to remove hardness ions (Ca〈sup〉2+〈/sup〉, Mg〈sup〉2+〈/sup〉) and dissolved silica from CTBW. Under the optimized condition, magnesium-rod electrode removed 51.80% and 93.70% respectively for total hardness and silica; with an operating cost of 0.88 US$/m〈sup〉3〈/sup〉 treated CTBW. EC sludge has been characterized by SVI, SEM-EDX, XRD, and FTIR exploring the ability of sludge to settle, surface morphology, elemental composition, crystalline type, and functional groups. It can be concluded that EC using magnesium-rod electrode can be successfully applied for the treatment of CTBW to facilitate its reuse.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371719300381-fx1.jpg" width="256" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 65〈/p〉 〈p〉Author(s): Jose L Garcia-Cordero, Sebastian J Maerkl〈/p〉 〈div〉〈p〉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 some cases, integrated microfluidic technologies, coupled with biosensors, are proving to be more sensitive and precise in the detection of cancer biomarkers than conventional assays. Based on the current state-of-the-art and the rapid progress over the past decade, we also briefly discuss the next evolutionary steps that these technologies are likely to take.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301405-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 65〈/p〉 〈p〉Author(s): Erkko Ylösmäki, Vincenzo Cerullo〈/p〉 〈div〉〈p〉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 tumours into immunologically hot tumours, and to increase immune cell and cytokine infiltration, can be further enhanced by arming OVs with transgenes that increase their immunostimulatory activities and direct immune responses specifically towards cancer cells. These OVs, specifically engineered to be used as cancer immunotherapeutics, can be synergized with other immune modulators or cytotoxic agents to achieve the most potent immunotherapy for cancer.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301326-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 1 November 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry〈/p〉 〈p〉Author(s): Niels van Linden, Ran Shang, Georg Stockinger, Bas Heijman, Henri Spanjers〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉 〈p〉The application of zero liquid discharge (ZLD) results in the generation of solid residual streams, which are often not fit for reuse. In this study, we assessed the separation of natural organic matter (NOM) and sodium chloride (NaCl) by nanofiltration (NF), electrodialysis (ED) and ion exchange (IEX) in the reverse osmosis brine and by SALEX in the generated mixed solids from a full-scale ZLD wastewater treatment plant.〈/p〉 〈p〉The NaCl recovery by NF, ED and IEX ranged 69–99%. The rejection of NOM by NF, ED and IEX ranged 18–19%, 43–65% and 53–76%, respectively. Finally, the recovery of NaCl by SALEX ranged 52–99%, while the rejection of NOM ranged 59–80%. The results showed that NOM and NaCl can be separated both in reverse osmosis brine and mixed solids, opening opportunities for recovery of reusable salt from brines in ZLD.〈/p〉 〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371719300666-fx1.jpg" width="399" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Sami Ben Said, Robin Tecon, Benedict Borer, Dani Or〈/p〉 〈div〉〈p〉Traditional biotechnological applications of microorganisms employ mono-cultivation or co-cultivation in well-mixed vessels disregarding the potential of spatially organized cultures. Metabolic specialization and guided species interactions facilitated through spatial isolation would enable consortia of microbes to accomplish more complex functions than currently possible, for bioproduction as well as biodegradation processes. Here, we review concepts of spatially linked microbial consortia in which spatial arrangement is optimized to increase control and facilitate new species combinations. We highlight that genome-scale metabolic network models can inform the design and tuning of synthetic microbial consortia and suggest that a standardized assembly of such systems allows the combination of ‘incompatibles’, potentially leading to countless novel applications.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300904-fx1.jpg" width="284" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 23〈/p〉 〈p〉Author(s): Fallah Hashemi, Hassan Hashemi, Mohammad Shahbazi, Mansooreh Dehghani, Mohammad Hoseini, Azita Shafeie〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉The refining industry is one of the most water consuming industries. Hence, reclamation of effluents can be useful as a sustainable, permanent, and available source of water for refineries. Therefore, this research was conducted aimed to evaluate the efficiency of integrated processes of ultrafiltration, mixed bed ion exchange and multioxidant disinfectant (MOX) as an advanced treatment of oil refinery effluent in order to provide makeup water in cooling towers. Integrated pilot including polysulfone membrane, two types of strong acid cationic resin and strong base anionic resin were used for real effluent reclamation. Finally, the treated effluent was disinfected using on site generated solution of MOX disinfectant. In the optimum Trans Membrane Pressure of 1 bar, removal efficiency of COD (57%), TDS (80%), Turbidity (94%), SiO2 (67%), Oil (88%), HPC (99%) was achieved. Integrated processes was efficient in reclamation of oily effluents in order to provide makeup water in cooling towers.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371719300629-fx1.jpg" width="371" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 65〈/p〉 〈p〉Author(s): Armand Kurum, Min Gao, Li Tang〈/p〉 〈div〉〈p〉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 〈em〉in vivo〈/em〉 to enhance cell modulation. Recent research has focused on designing three-dimensional (3D) scaffolds with specific properties to modulate the antitumor response at various stages of the cancer immunity cycle. As the number of immunotherapies in clinical trials is soaring, it is essential to critically evaluate the role that scaffolds can play in improving the safety and efficacy of existing and future therapies.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691930120X-fx1.jpg" width="245" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 22〈/p〉 〈p〉Author(s): S. Vaca-Jiménez, P.W. Gerbens-Leenes, S. Nonhebel〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Hydropower, biomass and thermal power plants (HPPs, BPPs and TPPs) consume water. The WF tool quantifies freshwater consumption. We calculated direct and indirect WFs of 255 Ecuadorian power plants using different technologies and fuels classified into eleven subclasses. Median WFs are largest for BPPs, followed by HPPs, while WFs of TPPs were smallest, but variation in subclasses is enormous. For HPPs, dammed HPPs have relatively large blue WFs, run-of-the-river HPPs have relatively small WFs, although they are significant to their electricity output. The cooling system is paramount for TPPs subclasses. Water-efficient cooling systems (once-through and dry-cooling) have 20% smaller WFs than wet-tower systems. Moreover, the fuel used affects the direct WF of TPPs significantly. Fuel and residue oil require water-intensive preheating; some diesel-fired TPPs use water as GHG control. BPPs are water-intensive because biomass has a large WF. Technology and fuel variation indicate pathways towards more water-efficient electricity mixes.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371718301501-fx1.jpg" width="487" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Nico J Claassens, Simon Burgener, Bastian Vögeli, Tobias J Erb, Arren Bar-Even〈/p〉 〈div〉〈p〉Conversion of biological feedstocks into value-added chemicals is mostly performed via microbial fermentation. An emerging alternative approach is the use of cell-free systems, consisting of purified enzymes and cofactors. Unfortunately, the 〈em〉in vivo〈/em〉 and 〈em〉in vitro〈/em〉 research communities rarely interact, which leads to oversimplifications and exaggerations that do not permit fair comparison of the two strategies and impede synergistic interactions. Here, we provide a comprehensive account for the advantages and drawbacks associated with each strategy, and further discuss recent research efforts that aim to breach the limits of cellular and cell-free production. We also explore emerging hybrid solutions that integrate the benefits of both worlds and could expand the boundaries of biosynthesis.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301861-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Michaela Gebauer, Arne Skerra〈/p〉 〈div〉〈p〉Initially emerging as a highly innovative concept in the late 1990s, the concept of creating novel binding reagents based on stable protein scaffolds from outside the immunoglobulin (Ig) superfamily has become a well-developed area of research and discovery today. Numerous scaffolds based on extracellular, membrane-bound or intracellular proteins (or their domains) have been recruited, yielding versatile research reagents and even biological drug candidates to serve as a viable alternative to antibodies. This minireview discusses both established and novel concepts in this field and summarizes the current state of clinical development of the more advanced protein scaffolds, in particular Affibody, Adnectin, Anticalin and DARPin drug candidates.〈/p〉〈/div〉

Description: 〈p〉Publication date: December 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 60〈/p〉 〈p〉Author(s): Yi Liu, Jens Nielsen〈/p〉 〈div〉〈p〉Microbe-mediated chemical production can replace traditional fossil-dependent production and hereby ensure sustainable production of chemicals that are important for our society. Significant success in economical chemical bioproduction has been accomplished by improving the cellular properties of microbial cells through metabolic engineering. The emergence of new techniques and strategies has led to a significant reduction in the turnaround time in the classic design-build-test-learn (DBTL) cycle in metabolic engineering. Here, we summarize the recent achievements and trends in microbial production of chemicals, with a focus on biofuels and high-value natural compounds. In addition, we offer perspectives on the challenges and opportunities for the successful establishment of future microbial chemical factories.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301976-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Shanshan Li, Wenqing Shui〈/p〉 〈div〉〈p〉The recent rapid advance of systematic mapping of protein–metabolite interactions (PMIs) in both prokaryotic and eukaryotic cells has been catalyzed by development of innovative and effective proteomics or metabolomics strategies all based on large-scale mass spectrometry (MS) analysis of biomolecules. Both metabolite-centric and protein-centric approaches have been established to profile PMIs in the native cellular matrix treated by specific metabolites or proteins. Here we will review the development and application of versatile MS-based proteomics and metabolomics techniques for global PMI mapping in different species, which lead to the discovery of numerous uncharacterized PMIs that may reveal new interaction-derived functionality. We further discuss the strengths and limitations of different PMI mapping approaches as well as the key elements in MS quantification and data mining for reliable PMI identification.〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Sebastian Gude, Michiko E Taga〈/p〉 〈div〉〈p〉Nearly all microbes rely on other species in their environment to provide nutrients they are unable to produce. Nutritional interactions include not only the exchange of carbon and nitrogen compounds, but also amino acids and cofactors. Interactions involving cross-feeding of cobamides, the vitamin B〈sub〉12〈/sub〉 family of cofactors, have been developed as a model for nutritional interactions across species and environments. In addition to experimental studies, new developments in culture-independent methodologies such as genomics and modeling now enable the prediction of nutritional interactions in a broad range of organisms including those that cannot be cultured in the laboratory. New insights into the mechanisms and evolution of microbial nutritional interactions are beginning to emerge by combining experimental, genomic, and modeling approaches.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691930059X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Antonin Prévoteau, Jose M Carvajal-Arroyo, Ramon Ganigué, Korneel Rabaey〈/p〉 〈div〉〈p〉Microbial electrosynthesis (MES) is an electrochemical process used to drive microbial metabolism for bio-production, such as the reduction of CO〈sub〉2〈/sub〉 into industrially relevant organic products as an alternative to current fossil-fuel-derived commodities. After a decade of research on MES from CO〈sub〉2〈/sub〉, figures of merit have increased significantly but are plateauing yet far from those expected to allow competitiveness for synthesis of commodity chemicals. Here we discuss the substantial technological shortcomings still associated with MES and evoke possible ways to mitigate them. It appears particularly challenging to obtain both relevant production rates (driven by high current densities) and energy conversion efficiency (i.e. low cell voltage) in microbial-compatible electrolytes. More competitive processes could arise by decoupling effective abiotic electroreductions (e.g. CO〈sub〉2〈/sub〉 to CO or ethanol; H〈sub〉2〈/sub〉 evolution) with subsequent fermentation processes.〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Juhyun Kim, Alexander Darlington, Manuel Salvador, José Utrilla, José I Jiménez〈/p〉 〈div〉〈p〉Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise growth (e.g. ribosome synthesis) and the rest of cellular functions. Limitations in gene expression also play a role in generating phenotypic diversity, which is advantageous in fluctuating environments, at the expenses of decreasing growth rates. Our current understanding of these trade-offs can be exploited for biotechnological applications benefiting from the selective manipulation of the allocation of resources.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300588-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Gi Bae Kim, Won Jun Kim, Hyun Uk Kim, Sang Yup Lee〈/p〉 〈div〉〈p〉Systems metabolic engineering allows efficient development of high performing microbial strains for the sustainable production of chemicals and materials. In recent years, increasing availability of bio big data, for example, omics data, has led to active application of machine learning techniques across various stages of systems metabolic engineering, including host strain selection, metabolic pathway reconstruction, metabolic flux optimization, and fermentation. In this paper, recent contributions of machine learning approaches to each major step of systems metabolic engineering are discussed. As the use of machine learning in systems metabolic engineering will become more widespread in accordance with the ever-increasing volume of bio big data, future prospects are also provided for the successful applications of machine learning.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300643-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Anamika Chatterjee, Drew M DeLorenzo, Rhiannon Carr, Tae Seok Moon〈/p〉 〈div〉〈p〉The production of fuels and chemicals from renewable feedstocks is necessary for a fossil fuel independent economy. Lignin and other industrial wastes represent sustainable, non-food feedstocks that can be tapped for microbe-based bioproduction. 〈em〉Rhodococcus opacus〈/em〉 is a gram-positive bacterium capable of catabolizing a broad range of feedstocks, and recent technological advances have further established its potential for lignin and industrial waste valorization. In the process of developing 〈em〉R. opacus〈/em〉 as a platform for bioproduction, metabolic profiling has elucidated its native mechanisms of bioconversion, adaptive evolution has enhanced its tolerance towards inhibitory feedstocks, and genetic engineering has enabled it to produce novel products, such as wax esters, free fatty acids, and long chain hydrocarbons. Here, we present recent examples of broad feedstock utilization and value-added chemical production by 〈em〉R. opacus〈/em〉, demonstrating its potential as an industrially relevant strain.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300679-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: Available online 23 November 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry〈/p〉 〈p〉Author(s): Bushra Fatima, Sharf Ilahi Siddiqui, Rabia Ahmed, Saif Ali Chaudhry〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Cadmium tungstate, CdWO〈sub〉4〈/sub〉, is well-known semiconductor which exhibit good photocatalytic properties but its preparation is usually carried out at very high temperature. Hardly any report is available for its preparation through green route, and its application for water treatment. Therefore, the functionalized cadmium tungstate, f-CdWO〈sub〉4〈/sub〉, nanoparticles synthesis through green, environmentally benign route using 〈em〉Brassica rapa〈/em〉 leave extract and sodium tungstate and cadmium iodide was objective of the present work. The formation of f-CdWO〈sub〉4〈/sub〉 was confirmed from FT-IR, XRD, and TEM, SEM and UV/Visible spectroscopic techniques. The average size of 54 nm was calculated from XRD analysis, 37.23 nm radius was determined from UV-Visible spectrum, whereas average 27 nm breadth and 120 nm length was found from TEM imaging showing rod shaped f-CdWO〈sub〉4〈/sub〉 nanoparticles. The f-CdWO〈sub〉4〈/sub〉 was used for removal of toxic Bismarck brown R dye from aqueous solution through adsorption and photocatalytic degradation under sun light. The coloured water containing 10 mgL〈sup〉−1〈/sup〉 concentration of dye could be cleaned with 1.5 gL〈sup〉-1〈/sup〉 dose of f-CdWO〈sub〉4〈/sub〉 at optimum condition. The adsorption capacity of f-CdWO〈sub〉4〈/sub〉 for Bismarck brown R was found to be 46.5, 49.50, and 51.54 mgg〈sup〉−1〈/sup〉 at 30, 40 and 50 °C, respectively. The endothermic adsorption of Bismarck brown R followed pseudo-second order kinetics. The interaction between f-CdWO〈sub〉4〈/sub〉 and Bismarck brown R, on molecular level, was investigated from FT-IR studies clubbed with isotherm, kinetics, and thermodynamics. The f-CdWO〈sub〉4〈/sub〉 also showed good photocatalytic degradation activity and degraded 82.70% of Bismarck brown R in 50 mL solution having 20 mgL〈sup〉−1〈/sup〉 dye concentration, with 1.5 gL〈sup〉-1〈/sup〉 dosage of f-CdWO〈sub〉4〈/sub〉. Therefore, f-CdWO〈sub〉4〈/sub〉, prepared through green route, would be efficient for water treatment through both photocatalytic and adsorption activities.〈/p〉〈/div〉 〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S2212371719300915-fx1.jpg" width="335" alt="Image 1" title="Image 1"〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Rufeng Wang, Shujuan Zhao, Zhengtao Wang, Mattheos AG Koffas〈/p〉 〈div〉〈p〉The microbial production of natural products has been traditionally accomplished in a single organism engineered to accommodate target biosynthetic pathways. Often times, such approaches result in large metabolic burdens as key cofactors, precursor metabolites and energy are channeled to pathways of structurally complex chemicals. Recently, modular co-culture engineering has emerged as a new approach to efficiently conduct heterologous biosynthesis and greatly enhance the production of natural products. This review highlights recent advances that leverage 〈em〉Escherichia coli〈/em〉-based modular co-culture engineering for making natural products. Potential future perspectives for studies in this promising field are addressed as well.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300734-fx1.jpg" width="244" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2019〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 59〈/p〉 〈p〉Author(s): Xiaolin Shen, Jia Wang, Chenyi Li, Qipeng Yuan, Yajun Yan〈/p〉 〈div〉〈p〉Taking inspiration from natural dynamic regulatory mechanisms in microbes, construction of dynamic regulatory networks has recently emerged as a promising strategy for metabolic pathway engineering. Over the past years, a variety of dynamic control systems have been developed to maximize the production by balancing cell growth and product formation. Here, we review the attractive dynamic regulation tools that have been applied in biosynthetic pathway optimization. We particularly put emphasis on the recent successful implementations in pathway engineering by utilization of fermentation parameters-based, metabolites-based and quorum sensing system-based dynamic control networks, and the future challenges in extending the application of those promising dynamic regulation tools in industrial manufacturing.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166918301472-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Water Resources and Industry, Volume 23〈/p〉 〈p〉Author(s): R. Lutze, M. Engelhart〈/p〉 〈div xml:lang="en"〉 〈h5〉Abstract〈/h5〉 〈div〉〈p〉Process stability and limitations of loading capacity of anaerobic membrane bioreactors (AnMBRs) and continuously stirred tank reactors (CSTRs) for the treatment of WAS and a lipid-rich flotation sludge from the dairy industry were investigated in pilot scale. The digesters were operated with increasing shares of lipids up to 85% at low sludge retention times (SRT) down to 10 days. High shares of lipids are favorable for treating wastewater sludges from industrial WWTPs on-site instead of their disposal, but often lead to long chain fatty acid (LCFA) accumulations and digester failures. In this study, high COD removals were obtained in all digesters resulting in methane yields over 250 L/kg COD〈sub〉in〈/sub〉. Methane production and COD removal followed substrate first-order kinetics. High lipid shares of COD〈sub〉lipid〈/sub〉 〉 80% did not inhibit COD degradation. Process stability was determined based on the ratio of specific methanogenic activity and mean acetate conversion in the digesters. Process stability depended mainly on SRT and lipid shares in the substrate as both parameters affected the degradable lipid content in the anaerobic sludge. Shorter SRTs and higher shares of lipids in particular reduced process stability as observed by inhibitions of acetoclastic methanogenesis. The OLR was not a decisive factor. When treating COD shares of lipids higher than 80%, SRT should exceed 15 d. COD shares of lipids below 80% were also successfully treated at SRT of 10 d. Residual degradable lipid content of anaerobic sludge negatively influenced process stability starting from 50 mg lipid/g TS. The performance of an AnMBR in terms of COD degradation and process stability corresponds to a CSTR with equal SRT, but can be operated with higher OLRs. At equal HRT compared to a CSTR, the AnMBR offers a higher process stability by extending the SRT.〈/p〉〈/div〉 〈/div〉

Description: 〈p〉Publication date: October 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 65〈/p〉 〈p〉Author(s): Ines Carqueijeiro, Chloe Langley, Dagny Grzech, Konstantinos Koudounas, Nicolas Papon, Sarah E O’Connor, Vincent Courdavault〈/p〉 〈div〉〈p〉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 agents.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301338-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: October 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 65〈/p〉 〈p〉Author(s): Christoph Rader〈/p〉 〈div〉〈p〉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 〈em〉in situ〈/em〉. In cancer immunotherapy, T-biAbs are facing fierce competition with chimeric antigen receptor T cells (CAR-Ts), a battle for clinical and commercial viability that will be closely watched. However, innovative combinations of T-biAbs and CAR-Ts have also transpired. NK-cell engaging biAbs (NK-biAbs) are reemerging as an alternative that addresses liabilities of T-biAbs. Beyond NK-biAbs, other biAbs designed to recruit cellular and molecular components of the innate immune system will be covered in this reflection on new tools, technologies, and targets.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301363-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Pratip Rana, Carter Berry, Preetam Ghosh, Stephen S Fong〈/p〉 〈div〉〈p〉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 contrarily, constraint-based model simulation results are analyzed by machine learning and reconciled with experimental data. This can iteratively refine a constraint-based model until there is consistency between experimental data, machine learning results, and constraint-based model simulations.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691930117X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 63〈/p〉 〈p〉Author(s): Maike Spöring, Monika Finke, Jörg S Hartig〈/p〉 〈div〉〈p〉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 expression platforms. RNA-based switches have been constructed that allow for controlling gene expression in diverse contexts. Here we discuss latest developments and applications of aptamer-based gene expression switches in eukaryotes.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301181-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 63〈/p〉 〈p〉Author(s): Christian Dusny, Alexander Grünberger〈/p〉 〈div〉〈p〉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 that enable us to control cellular input parameters such as environmental conditions and to measure intracellular processes, as well as novel approaches that enable for the first time to quantify non-averaged cell-specific rates and yields. Finally, we demonstrate how integrating microfluidic single-cell analysis into established population-based experimental workflows might unlock its full potential for biotechnology research in the future.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301119-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: June 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 63〈/p〉 〈p〉Author(s): Wojciech Kajetan Kasprzak, Nour Ali Ahmed, Bruce Allen Shapiro〈/p〉 〈div〉〈p〉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-trivial aspect to the modeling and characterization of the RNA structures. This short review introduces the issues involved in RNA structure prediction and modeling, dynamics of RNA structures, the influence of ligands on the structure and the dynamics, and ways to incorporate this information in the design of RNA-based nanostructures.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919301090-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Robert L. Shahab, Simone Brethauer, Jeremy S. Luterbacher, Michael H. Studer〈/p〉 〈div〉〈p〉The design of controllable artificial microbial consortia has attracted considerable interest in recent years to capitalize on the inherent advantages in comparison to monocultures such as the distribution of the metabolic burden by division of labor, the modularity and the ability to convert complex substrates. One promising approach to control the consortia composition, function and stability is the provision of defined ecological niches fitted to the specific needs of the consortium members. In this review, we discuss recent examples for the creation of metabolic niches by biological engineering of resource partitioning and syntrophic interactions. Moreover, we introduce a complementing process engineering approach to provide defined spatial niches with differing abiotic conditions (e.g. O〈sub〉2〈/sub〉, T, light) in stirred tank reactors harboring biofilms. This enables the co-cultivation of microorganisms with non-overlapping abiotic requirements and the control of the strain ratio in consortia characterized by substrate competition.〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): In Young Hwang, Matthew Wook Chang〈/p〉 〈div〉〈p〉There has been a growing emphasis on understanding the important relationship between human-associated microbial communities and disease development. With technological advancements, we are able to gain further insights into host–microbiome interactions at a deeper level. In order to fully leverage the close associations between microbes and their host, development of therapeutics targeting the microbiome has surged in recent years. In this review, we discuss advances made in engineering gut bacteria to develop novel therapeutic modalities that aim to rewire host–microbiome interactions such as host metabolism and immune functions for prevention and treatment of various diseases. In particular, applications of these engineered bacteria against diseases such as metabolic, immune disorders and cancer are covered.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691930076X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Djordje Bajic, Alvaro Sanchez〈/p〉 〈div〉〈p〉Free-living microbes are generally capable of growing on multiple different nutrients. Some of those nutrients are used simultaneously, while others are used sequentially. The pattern of nutrient preferences and co-utilization defines the metabolic strategy of a microorganism. Metabolic strategies can substantially affect ecological interactions between species, but their evolution and distribution across the tree of life remain poorly characterized. We discuss how the confluence of better computational models of genotype-phenotype maps and high-throughput experimental tools can help us fill gaps in our knowledge and incorporate metabolic strategies into quantitative predictive models of microbial consortia.〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Xiaoqun Nie, Qiang Hua, Ping Xu, Chen Yang〈/p〉 〈div〉〈p〉Stable-isotope metabolic flux analysis is an important approach to unravel the metabolic network and its regulation in organisms. It has become a key analytical technology for biotechnological applications. During recent years non-model microorganisms have received increasing attention because they possess unique metabolic capabilities and can serve as a host for production of biofuels and biochemicals. Stable-isotope metabolic flux analysis has been widely used in these microorganisms for exploring novel pathways, elucidating the operation of central metabolic networks, and revealing the metabolic changes that result from genetic manipulations. Here, we review recent applications of stable-isotope metabolic flux analysis in characterizing non-model microbial hosts, guiding the development of rational engineering strategies for enhancement of biochemical production and extension of substrate range, and understanding of industrial production processes.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300795-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Toshihiro Obata〈/p〉 〈div〉〈p〉Intermediates of metabolic pathways are sometimes contained within cavities of enzyme molecules and passed directly from active centers of one to next enzymes without diffusing into bulk matrix. This ‘metabolite channeling’ is postulated to have various advantages in enhancing and regulating pathway reactions and considered as a central unit to control metabolic network. Therefore, it has a strong potential in applications to metabolic engineering to enhance the production of desired molecules. Quantitative evaluation of the effects of metabolite channeling is crucial for its appropriate application and further understanding of its functions. In the present review, current approaches to demonstrate functional metabolite channeling will be reviewed and their extension toward quantitative evaluation of channeling effects 〈em〉in vivo〈/em〉 will be discussed.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300886-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Nancy M Kim, Riley W Sinnott, Nicholas R Sandoval〈/p〉 〈div〉〈p〉Genetic diversity within the geobiosphere encompasses enormous sensing capabilities and many non-model bacteria are of biotechnological interest. Biosensing, or more generally inducible, systems are a vital component of metabolic engineering, as they allow tight control of gene expression as well as the basis for high-throughput screens on non-growth-related phenotypes. While these inducible systems, primarily transcription factor/promoter pairs, have been utilized extensively in 〈em〉Escherichia coli〈/em〉, progress in other bacteria is limited because of differences in transcription machinery, physiological compatibility of parts and proteins, and other nuances. Here, we provide an overview of the available genetic biosensing elements in non-model organisms and state-of-the-art efforts to engineer them, and then discuss challenges preventing these methods from common use in non-model bacteria.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S0958166919300783-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉

Description: 〈p〉Publication date: August 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 64〈/p〉 〈p〉Author(s): Chao Wu, Melissa Cano, Xiang Gao, Jonathan Lo, PinChing Maness, Wei Xiong〈/p〉 〈div〉〈p〉Quantitative understanding of clostridial metabolism is of longstanding interest due to the importance of Clostridia as model anaerobes, biotechnology workhorses, and contributors to evolutionary history and ecosystem. Current computational methods such as flux balance analysis-based construction of clostridial metabolism in genome scale provide a fundamental framework for metabolic analysis. However, this method alone is inadequate to characterize cellular metabolic activity. Experiment-driven approaches including isotope tracer-based fluxomics in association with genetic and biochemical methods are needed to gain a more comprehensive understanding. Here we focus on typical examples where these integrated approaches have contributed to the identification of new metabolic pathways and quantification of metabolic fluxes in Clostridia. We also highlight the opportunities and challenges of cutting-edge fluxomics approaches such as machine learning modeling, deuterium tracer approach, and high throughput flux phenotyping in exploring clostridial metabolism with respect to inorganic carbon utilization, redox cofactor interconversion, and other key metabolic features.〈/p〉〈/div〉

Description: 〈p〉Publication date: April 2020〈/p〉 〈p〉〈b〉Source:〈/b〉 Current Opinion in Biotechnology, Volume 62〈/p〉 〈p〉Author(s): Jan-Ulrich Kreft, Benjamin M Griffin, Rebeca González-Cabaleiro〈/p〉 〈div〉〈p〉Metabolic division of the labour of organic matter decomposition into several steps carried out by different types of microbes is typical for many anoxic — but not oxic environments. An explanation of this well-known pattern is proposed based on the combination of three key insights: (i) well-studied anoxic environments are high flux environments: they are only anoxic because their high organic matter influx leads to oxygen depletion; (ii) shorter, incomplete catabolic pathways provide the capacity for higher flux, but this capacity is only advantageous in high flux environments; (iii) longer, complete catabolic pathways have energetic happy ends but only with high redox potential electron acceptors. Thus, aerobic environments favour longer pathways. Bioreactors, in contrast, are high flux environments and therefore favour division of catabolic labour even if aeration keeps them aerobic; therefore, host strains and feeding strategies must be carefully engineered to resist this pull.〈/p〉〈/div〉 〈h5〉Graphical abstract〈/h5〉 〈div〉〈p〉〈figure〉〈img src="https://ars.els-cdn.com/content/image/1-s2.0-S095816691930062X-fx1.jpg" width="301" alt="Graphical abstract for this article" title=""〉〈/figure〉〈/p〉〈/div〉