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Biotechnology and Bioengineering

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https://www.readbyqxmd.com/read/30414290/rislnet-rapid-identification-of-smart-mutant-libraries-using-protein-structure-network-application-to-thermal-stability-enhancement
#1
Roopali Upadhyay, Jin Young Kim, Eun Young Hong, Sun-Gu Lee, Joo-Hyun Seo, Byung-Gee Kim
A key point of protein stability engineering is to identify specific target residues whose mutations can stabilize the protein structure without negatively affecting the function or activity of the protein. Here, we propose a method, called RiSLnet (Rapid identification of Smart mutant Library using residue network), to identify such residues by combining network analysis for protein residue interactions, identification of conserved residues, and evaluation of relative solvent accessibility. To validate its performance, the method was applied to four proteins, i...
November 10, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30414273/growth-kinetics-and-mathematical-modeling-of-synechocystis-sp-pcc-6803-under-flashing-light
#2
Levi Straka, Bruce E Rittmann
In photobioreactors and natural systems, microalgae are subjected to rapidly changing light intensities (LI) due to light attenuation and mixing. A controlled way to study the effect of rapidly changing LI is to subject cultures to flashing light. In this study, series of flashing-light experiments were conducted using Synechocystis sp. PCC6803 with constant overall average LI of ~84 μmol m-2 s-1 , and relative times in the light and dark varied. The results were also compared to simulated results using a mathematical model including an absorbed pool of light energy, photoacclimation, and photoinhibition...
November 10, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30414271/assessing-the-ability-of-human-endothelial-cells-derived-from-induced-pluripotent-stem-cells-to-form-functional-microvasculature-in-vivo
#3
Jonathan R Bezenah, Ana Y Rioja, Benjamin Juliar, Nicole Friend, Andrew J Putnam
Forming functional blood vessel networks is a major clinical challenge in the fields of tissue engineering and therapeutic angiogenesis. Cell-based strategies to promote neovascularization have been widely explored, but cell sourcing remains a significant limitation. Induced pluripotent stem cell-derived endothelial cells (iPSC-ECs) are a promising, potentially autologous, alternative cell source. However, it is unclear whether iPSC-ECs form the same robust microvasculature in vivo documented for other EC sources...
November 10, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30411322/metabolic-flux-balance-analysis-during-lactate-and-glucose-concomitant-consumption-in-hek293-cell-cultures
#4
I Martínez-Monge, J Albiol, M Lecina, L Liste-Calleja, J Miret, C Solà, J J Cairó
At early stages of the exponential growth phase in HEK293 cell cultures, tricarboxylic acid cycle is unable to process all the amount of NADH generated in the glycolysis pathway, being lactate the main by-product. However, HEK293 cells are also able to metabolize lactate depending on the environmental conditions. It has recently been observed that one of the most important modes of lactate metabolization is the co-metabolism of lactate and glucose, observed even during the exponential growth phase. Extracellular lactate concentration and pH appear to be the key factors triggering the metabolic shift from glucose consumption and lactate production to lactate and glucose concomitant consumption...
November 8, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30411315/an-ultra-scale-down-method-to-investigate-monoclonal-antibody-processing-during-tangential-flow-filtration-tff-using-ultrafiltration-membranes
#5
Lara Fernandez-Cerezo, Andrea C M E Rayat, Alex Chatel, Jennifer M Pollard, Gary J Lye, Michael Hoare
The availability of material for experimental studies is a key constraint in the development of full-scale bioprocesses. This is especially true for the later stages in a bioprocess sequence such as purification and formulation, where the product is at a relatively high concentration and traditional scale-down models can require significant volumes. Using a combination of critical flow regime analysis, bioprocess modelling and experimentation, ultra scale-down (USD) methods can yield bioprocess information using only millilitre quantities prior to embarking on highly demanding full-scale studies...
November 8, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30397916/on-fiber-display-of-a-functional-peptide-at-sites-distant-from-the-cell-surface-using-a-long-bacterionanofiber-of-a-trimeric-autotransporter-adhesin
#6
Hajime Nakatani, Junichi Kanie, Katsutoshi Hori
In the cell surface display system, the distance of a surface-displayed molecule from the cell surface should influence its functionality due to the interference by other surface structures. For the purpose of developing this distance-variable surface display system, we utilized a long fibrous adhesin, Acinetobacter trimeric autotransporter adhesin (AtaA) of the strain Tol 5. We constructed His-tagged full length and shorter AtaA fibers designed by N-terminal deletion and expressed them in the ΔataA mutant...
November 5, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30367820/3d-tumor-spheroids-as-in-vitro-models-to-mimic-in-vivo-human-solid-tumors-resistance-to-therapeutic-drugs
#7
REVIEW
Ana S Nunes, Andreia S Barros, Elisabete C Costa, André F Moreira, Ilídio J Correia
Three-dimensional cell culture models, such as spheroids, can be used in the process of the development of new anticancer agents because they are able to closely mimic the main features of human solid tumors, namely their structural organization, cellular layered assembling, hypoxia, and nutrient gradients. These properties imprint to the spheroids an anticancer therapeutics resistance profile, which is similar to that displayed by human solid tumors. In this review, an overview of the drug resistance mechanisms observed in 3D tumor spheroids is provided...
October 27, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30345505/local-fk506-dose-dependent-study-using-a-novel-three-dimensional-organotypic-assay
#8
Kasra Tajdaran, Katelyn Chan, Jennifer Zhang, Tessa Gordon, Gregory H Borschel
Local administration of FK506, an FDA approved immunosuppressant with neuroregenerative properties, is a promising technique to achieve improved peripheral nerve regeneration while preventing the side effects associated with the systemic administration of this drug. Whilst considerable research has been devoted to the development of clinically suitable systems for local delivery of FK506 to the site of nerve injury and repair, the optimal dose of FK506 for enhancement of axon regeneration in the peripheral nerve has not yet been established...
October 21, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30345503/serine-integrase-recombinational-engineering-sire-a-versatile-toolbox-for-genome-editing
#9
Nico Snoeck, Maarten L De Mol, Dries Van Herpe, Anke Goormans, Isabelle Maryns, Pieter Coussement, Gert Peters, Joeri Beauprez, Sofie L De Maeseneire, Wim Soetaert
Chromosomal integration of biosynthetic pathways for the biotechnological production of high-value chemicals is a necessity to develop industrial strains with a high long-term stability and a low production variability. However, the introduction of multiple transcription units into the microbial genome remains a difficult task. Despite recent advances, current methodologies are either laborious or efficiencies highly fluctuate depending on the length and the type of the construct. Here we present SIRE, Serine Integrase Recombinational Engineering, a novel methodology which combines the ease of recombinase mediated cassette exchange (RMCE) with the selectivity of orthogonal att sites of the PhiC31 integrase...
October 21, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30345502/whole-synthetic-pathway-engineering-of-recombinant-protein-production
#10
Adam J Brown, Suzanne J Gibson, Diane Hatton, Claire L Arnall, David C James
The output from protein biomanufacturing systems is a function of total host cell biomass synthetic capacity and recombinant protein production per unit cell biomass. In this study we describe how these two properties can be simultaneously optimized via design of a product-specific combination of synthetic DNA parts to maximize flux through the protein synthetic pathway and the use of a host cell chassis with an increased capability to synthesise both cell and product biomass. Using secreted alkaline phosphatase (SEAP) production in Chinese hamster ovary cells as our example, we demonstrate how an optimal composition of input components can be assembled from a minimal toolbox containing rationally designed promoters, untranslated regions, signal peptides, product coding sequences, cell chassis and genetic effectors...
October 21, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30320445/a-microfluidic-gradient-mixer-flow-chamber-as-a-new-tool-to-study-biofilm-development-under-defined-solute-gradients
#11
Yingdan Zhang, Cheng Li, Yichao Wu, Yilei Zhang, Zhi Zhou, Bin Cao
Understanding the dynamics of biofilm development in response to chemical cues and signals is required toward the development of controllable biofilm-mediated bioprocesses. In this study, we report a new biofilm growth system that integrates a microfluidic gradient mixer with a biofilm growth chamber. The biofilm growth system allows biofilms grow under defined solute gradients and enables non-destructively monitor the biofilm development dynamics in response to the defined gradients. The solute gradients generated in the system were simulated and then validated experimentally...
October 15, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30298908/trophoblast-endothelium-signaling-involves-angiogenesis-and-apoptosis-in-a-dynamic-bioprinted-placenta-model
#12
Che-Ying Kuo, Mariya Shevchuk, Justin Opfermann, Ting Guo, Marco Santoro, John P Fisher, Peter Cw Kim
Trophoblast invasion and remodeling of the maternal spiral arteries are required for pregnancy success. Aberrant endothelium-trophoblast crosstalk may lead to preeclampsia, a pregnancy complication that has serious effects on both the mother and the baby. However, our understanding of the mechanisms involved in this pathology remains elementary because the current in vitro models cannot describe trophoblast-endothelium interactions under dynamic culture. In this study, we developed a dynamic three-dimensional (3D) placenta model by bioprinting trophoblasts and an endothelialized lumen in a perfusion bioreactor...
October 9, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30298905/model-assisted-process-characterization-and-validation-for-a-continuous-two-column-protein-a-capture-process
#13
Daniel Baur, James Angelo, Srinivas Chollangi, Thomas Müller-Späth, Xuankuo Xu, Sanchayita Ghose, Zheng Jian Li, Massimo Morbidelli
In this study we introduce three process characterization approaches toward validation of continuous twin-column capture chromatography (CaptureSMB), referred to as "standard," "model assisted" and "hybrid." They are all based on a traditional risk-based approach, using process description, risk analysis, Design-of-Experiments (DoE), and statistical analysis as essential elements. The first approach, the "standard" approach uses a traditional experimental DoE to explore the design space of the high-ranked process parameters for the continuous process...
October 9, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30267586/enhancing-h-2-dependent-growth-of-and-co-2-fixation-by-clostridium-ljungdahlii-through-nitrate-supplementation
#14
David Frederic Emerson, Benjamin Michael Woolston, Nian Liu, Mackenzie Donnelly, Devin H Currie, Gregory Stephanopoulos
Syngas fermentation via the Wood-Ljungdahl pathway is receiving growing attention as a possible platform for the fixation of CO2 and renewable production of fuels and chemicals. However, the pathway operates near the thermodynamic limit of life, resulting in minimal ATP production and long doubling times. This calls into question the feasibility of producing high-energy compounds at industrially relevant levels. In this work, we investigated the possibility of co-utilizing nitrate as an inexpensive additional electron acceptor to enhance ATP production during H2 -dependent growth of Clostridium ljungdahlii, Moorella thermoacetica, and Acetobacterium woodii...
September 29, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30267585/incorporating-hydrodynamics-into-spatiotemporal-metabolic-models-of-bubble-column-gas-fermentation
#15
Xiangan Li, Derek Griffin, Xueliang Li, Michael A Henson
Gas fermentation has emerged as a technologically and economically attractive option for producing renewable fuels and chemicals from carbon monoxide (CO) rich waste streams. LanzaTech has developed a proprietary strain of the gas fermentating acetogen Clostridium autoethanogenum as a microbial platform for synthesizing ethanol, 2,3-butanediol, and other chemicals. Bubble column reactor technology is being developed for the large-scale production, motivating the investigation of multiphase reactor hydrodynamics...
September 29, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30267565/process-development-for-the-continuous-production-of-heterologous-proteins-by-the-industrial-yeast-komagataella-phaffii
#16
Ayca Cankorur-Cetinkaya, Nathalie Narraidoo, Ceyda Kasavi, Nigel K H Slater, David B Archer, Stephen G Oliver
The current trend in industrial biotechnology is to move from batch or fed-batch fermentations to continuous operations. The success of this transition will require the development of genetically stable production strains, the use of strong constitutive promoters, and the development of new medium formulations that allow an appropriate balance between cell growth and product formation. We identified genes that showed high expression in Komagataella phaffii during different steady-state conditions and explored the utility of promoters of these genes (Chr1-4_0586 and FragB_0052) in optimizing the expression of two different r-proteins, human lysozyme (HuLy), and the anti-idiotypic antibody fragment, Fab-3H6, in comparison with the widely used glyceraldehyde-3-phosphate dehydrogenase promoter...
September 29, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30252943/effects-of-inactivation-of-the-cyabrb2-transcription-factor-together-with-glycogen-synthesis-on-cellular-metabolism-and-free-fatty-acid-production-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#17
Yuta Kodama, Akihito Kawahara, Atsuko Miyagi, Toshiki Ishikawa, Maki Kawai-Yamada, Yasuko Kaneko, Yasushi Takimura, Yukako Hihara
Deletion of the cyAbrB2 (Sll0822) transcription factor in Synechocystis sp. PCC 6803 causes aberrant accumulation of glycogen. We previously tried to redirect the excess carbon stored as glycogen in the cyabrB2-disrupted (∆ cyabrB2) mutant by knockout of the glgC (slr1176) gene encoding glucose-1-phosphate adenylyltransferase. However, complete knockout could not be attained, suggesting that accumulation of glycogen is essential for the Δ cyabrB2 mutant. In this study, we introduced the cyabrB2 gene fused to the copper-inducible petE promoter into the ∆ cyabrB2 mutant...
September 25, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30252940/two-stage-carbon-distribution-and-cofactor-generation-for-improving-l-threonine-production-of-escherichia-coli
#18
Jiaheng Liu, Huiling Li, Hui Xiong, Xixian Xie, Ning Chen, Guangrong Zhao, Qinggele Caiyin, Hongji Zhu, Jianjun Qiao
L-Threonine, a kind of essential amino acid, has numerous applications in food, pharmaceutical, and aquaculture industries. Fermentative l-threonine production from glucose has been achieved in Escherichia coli. However, there are still several limiting factors hindering further improvement of l-threonine productivity, such as the conflict between cell growth and production, byproduct accumulation, and insufficient availability of cofactors (adenosine triphosphate, NADH, and NADPH). Here, a metabolic modification strategy of two-stage carbon distribution and cofactor generation was proposed to address the above challenges in E...
September 25, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30252938/the-pearl-necklace-model-in-protein-a-chromatography-molecular-mechanisms-at-the-resin-interface
#19
Goncalo L Silva, Jacek Plewka, Helga Lichtenegger, Ana C Dias-Cabral, Alois Jungbauer, Rupert Tscheließnig
Staphylococcal protein A chromatography is an established core technology for monoclonal antibody purification and capture in the downstream processing. MabSelect SuRe involves a tetrameric chain of a recombinant form of the B domain of staphylococcal protein A, called the Z-domain. Little is known about the stoichiometry, binding orientation, or preferred binding. We analyzed small-angle X-ray scattering data of the antibody-protein A complex immobilized in an industrial highly relevant chromatographic resin at different antibody concentrations...
September 25, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/30229866/drug-delivering-nerve-conduit-improves-regeneration-in-a-critical-sized-gap
#20
Pratima Labroo, David Hilgart, Brett Davis, Christopher Lambert, Himanshu Sant, Bruce Gale, Jill E Shea, Jayant Agarwal
Autologous nerve grafts are the current "gold standard" for repairing large nerve gaps. However, they cause morbidity at the donor nerve site and only a limited amount of nerve can be harvested. Nerve conduits are a promising alternative to autografts and can act as guidance cues for the regenerating axons, without the need to harvest donor nerve. Separately, it has been shown that localized delivery of GDNF can enhance axon growth and motor recovery. FK506, an FDA approved small molecule, has also been shown to enhance peripheral nerve regeneration...
September 19, 2018: Biotechnology and Bioengineering
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