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Biotechnology and Bioengineering

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https://www.readbyqxmd.com/read/28322442/systems-analysis-of-dynamic-transcription-factor-activity-identifies-targets-for-treatment-in-olaparib-resistant-cancer-cells
#1
Joseph T Decker, Eric C Hobson, Yining Zhang, Seungjin Shin, Alexandra L Thomas, Jacqueline S Jeruss, Kelly B Arnold, Lonnie D Shea
The development of resistance to targeted therapeutics is a challenging issue for the treatment of cancer. Cancers that have mutations in BRCA, a DNA repair protein, have been treated with poly (ADP-ribose) polymerase (PARP) inhibitors, which target a second DNA repair mechanism with the aim of inducing synthetic lethality. While these inhibitors have shown promise clinically, the development of resistance can limit their effectiveness as a therapy. This study investigated mechanisms of resistance in BRCA-mutated cancer cells (HCC1937) to Olaparib (AZD2281) using TRACER, a technique for measuring dynamics of transcription factor (TF) activity in living cells...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28322439/modeling-multidimensional-and-multispecies-biofilms-in-porous-media
#2
Youneng Tang, Haihu Liu
Modeling multidimensional and multispecies biofilm in porous media at the pore scale is challenging due to the need to simultaneously track the microbial community in the biofilms and the interfaces between the biofilms and the fluid. Therefore, researchers usually assume that the model has only one dimension in space or has only one microbial species. This work uses bioremediation of U(VI)-contaminated groundwater as the context to develop a two-dimensional and multispecies biofilm model. The model simulates the transverse mixing zone in which U(VI) is mixed with propionate, a nutrient externally supplied to stimulate the growth of microorganisms...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28322436/modelling-hydraulic-transport-and-anaerobic-uptake-by-paos-and-gaos-during-wastewater-feeding-in-ebpr-granular-sludge-reactors
#3
David G Weissbrodt, Christof Holliger, Eberhard Morgenroth
New-generation bioprocesses using granular sludge aim for a high-rate removal of nutrients from wastewater with low footprint. Achieving enhanced biological phosphorus removal (EBPR) relies on the design of sludge beds and wastewater feeding conditions to optimally load the biomass and to select for polyphosphate- (PAOs) over glycogen-accumulating organisms (GAOs) and other heterotrophs. A hydraulic-metabolic mathematical model was developed to elucidate the impact of hydraulic transport patterns and environmental conditions on the PAO/GAO competition during up-flow feeding through an EBPR granular sludge bed...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28322433/a-9-pool-metabolic-structured-kinetic-model-describing-days-to-seconds-dynamics-of-growth-and-product-formation-by-penicillium-chrysogenum
#4
Wenjun Tang, Amit T Deshmukh, Cees Haringa, Guan Wang, Walter van Gulik, Wouter van Winden, Matthias Reuss, Joseph J Heijnen, Jianye Xia, Ju Chu, Henk J Noorman
A powerful approach for the optimization of industrial bioprocesses is to perform detailed simulations integrating large scale computational fluid dynamics (CFD) and cellular reaction dynamics (CRD). However, complex metabolic kinetic models containing a large number of equations pose formidable challenges in CFD-CRD coupling and computation time afterward. This necessitates to formulate a relatively simple but yet representative model structure. Such a kinetic model should be able to reproduce metabolic responses for short-term (mixing time scale of tens of seconds) and long-term (fed-batch cultivation of hours/days) dynamics in industrial bioprocesses...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28295202/in-situ-esterification-and-extractive-fermentation-for-butyl-butyrate-production-with-clostridium-tyrobutyricum
#5
Zhong-Tian Zhang, Steven Taylor, Yi Wang
Butyl butyrate (BB) is a valuable chemical that can be used as flavor, fragrance, extractant, etc. in various industries. Meanwhile, BB can also be used as a fuel source with excellent compatibility as gasoline, aviation kerosene and diesel components. The conventional industrial production of BB is highly energy-consuming and generates various environmental pollutants. Recently, there have been tremendous interests in producing BB from renewable resources through biological routes. In this study, based on the fermentation using the hyper-butyrate producing strain Clostridium tyrobutyricum ATCC 25755, efficient BB production through in situ esterification was achieved by supplementation of lipase and butanol into the fermentation...
March 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28295162/evaluation-of-two-public-genome-references-for-chinese-hamster-ovary-cells-in-the-context-of-rna-seq-based-gene-expression-analysis
#6
Chun Chen, Huong Le, Chetan T Goudar
RNA-Seq is a powerful transcriptomics tool for mammalian cell culture process development. Successful RNA-Seq data analysis requires a high quality reference for read mapping and gene expression quantification. Currently, there are two public genome references for Chinese hamster ovary (CHO) cells, the predominant mammalian cell line in the biopharmaceutical industry. In this study, we compared these two references by analyzing 60 RNA-Seq samples from a variety of CHO cell culture conditions. Among the 20,891 common genes in both references, we observed that 31...
March 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28295160/a-novel-sugar-analog-enhances-sialic-acid-production-and-biotherapeutic-sialylation-in-cho-cells
#7
LETTER
Bojiao Yin, Qiong Wang, Cheng-Yu Chung, Rahul Bhattacharya, Xiaozhi Ren, Juechun Tang, Kevin J Yarema, Michael J Betenbaugh
A desirable feature of many therapeutic glycoprotein production processes is to maximize the final sialic acid content. In this study, the effect of applying a novel chemical analog of the sialic acid precursor N-acetylmannosamine (ManNAc) on the sialic acid content of cellular proteins and a model recombinant glycoprotein, erythropoietin (EPO), was investigated in CHO-K1 cells. By introducing the 1,3,4-O-Bu3 ManNAc analog at 200-300 µM into cell culture media, the intracellular sialic acid content of EPO-expressing cells increased ∼8 fold over untreated controls while the level of cellular sialylated glycoconjugates increased significantly as well...
March 15, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28295166/engineering-oxidative-stress-defense-pathways-to-build-a-robust-lipid-production-platform-in-yarrowia-lipolytica
#8
Peng Xu, Kangjian Qiao, Gregory Stephanopoulos
Microbially-derived lipids have recently attracted renewed interests due to their broad applications in production of green diesels, cosmetic additives and oleochemicals. Metabolic engineering efforts have targeted a large portfolio of biosynthetic pathways to efficiently convert sugar to lipids in oleaginous yeast. In the engineered overproducing strains, endogenous cell metabolism typically generates harmful electrophilic molecules that compromise cell fitness and productivity. Lipids, particularly unsaturated fatty acids, are highly susceptible to oxygen radical attack and the resulting oxidative species are detrimental to cell metabolism and limit lipid productivity...
March 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28295163/cyanobacterial-carbon-metabolism-fluxome-plasticity-and-oxygen-dependence
#9
Ni Wan, Drew M DeLorenzo, Lian He, Le You, Cheryl M Immethun, George Wang, Edward E K Baidoo, Whitney Hollinshead, Jay D Keasling, Tae Seok Moon, Yinjie J Tang
Synechocystis sp. strain PCC 6803 has been widely used as a photo-biorefinery chassis. Based on its genome annotation, this species contains a complete TCA cycle, an Embden-Meyerhof-Parnas pathway (EMPP), an oxidative pentose phosphate pathway (OPPP), and an Entner-Doudoroff pathway (EDP). To evaluate how Synechocystis 6803 catabolizes glucose under heterotrophic conditions, we performed (13) C metabolic flux analysis, metabolite pool size analysis, gene knockouts, and heterologous expressions. The results revealed a cyclic mode of flux through the OPPP...
March 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28294302/polyclonal-and-monoclonal-igg-binding-on-protein-a-resins-evidence-of-competitive-binding-effects
#10
Justin Weinberg, Shaojie Zhang, Gillian Crews, Edward Healy, Giorgio Carta, Todd Przybycien
Protein A (ProA) chromatography is used extensively in the biopharmaceutical industry for the selective capture of both polyclonal and monoclonal antibodies (mAbs). This work provides a comparison of the adsorptive behavior of a highly heterogeneous polyclonal hIgG versus that of a mAb as well as the behavior of their mixtures on representative ProA resins. Both pH gradient elution and frontal loading experiments using human polyclonal IgG (hIgG) reveal a distribution of IgG-ProA binding strengths likely associated with multiple IgG subclasses and the heterogeneity of the variable region...
March 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28294288/engineering-saccharomyces-cerevisiae-fatty-acid-composition-for-increased-tolerance-to-octanoic-acid
#11
Pamela B Besada-Lombana, Ruben Fernandez-Moya, Jacob Fenster, Nancy A Da Silva
Biorenewable chemicals such as short and medium chain fatty acids enable functional or direct substitution of petroleum-derived building blocks, allowing reduction of anthropogenic greenhouse gases while meeting market needs of high-demand products like aliphatic alcohols and alpha olefins. However, producing these fatty acids in microorganisms can be challenging due to toxicity issues. Octanoic acid (C8) can disrupt the integrity of the cell membrane in yeast, and exogenous supplementation of oleic acid has been shown to help alleviate this...
March 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28266026/optimizing-cell-free-protein-expression-in-cho-assessing-small-molecule-mass-transfer-effects-in-various-reactor-configurations
#12
Chariz Peñalber-Johnstone, Xudong Ge, Kevin Tran, Nicholas Selock, Neha Sardesai, Chandrasekhar Gurramkonda, Manohar Pilli, Michael Tolosa, Leah Tolosa, Yordan Kostov, Douglas D Frey, Govind Rao
Cell-free protein synthesis (CFPS) is an ideal platform for rapid and convenient protein production. However, bioreactor design remains a critical consideration in optimizing protein expression. Using turbo green fluorescent protein (tGFP) as a model, we tracked small molecule components in a Chinese Hamster Ovary (CHO) CFPS system to optimize protein production. Here, three bioreactors in continuous-exchange cell-free (CECF) format were characterized. A GFP optical sensor was built to monitor the product in real-time...
March 7, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28266022/an-artificial-tca-cycle-selects-for-efficient-%C3%AE-ketoglutarate-dependent-hydroxylase-catalysis-in-engineered-escherichia-coli
#13
Eleni Theodosiou, Marina Breisch, Mattijs K Julsing, Francesco Falcioni, Bruno Bühler, Andreas Schmid
Amino acid hydroxylases depend directly on the cellular TCA cycle via their cosubstrate a-ketoglutarate (α-KG) and are highly useful for the selective biocatalytic oxyfunctionalization of amino acids. This study evaluates TCA cycle engineering strategies to force and increase α-KG flux through proline-4-hydroxylase (P4H). The genes sucA (α-KG dehydrogenase E1 subunit) and sucC (succinyl-CoA synthetase β subunit) were alternately deleted together with aceA (isocitrate lyase) in proline degradation-deficient Escherichia coli strains (ΔputA) expressing the p4h gene...
March 7, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28266015/understanding-of-decreased-sialylation-of-fc-fusion-protein-in-hyperosmotic-recombinant-chinese-hamster-ovary-cell-culture-n-glycosylation-gene-expression-and-n-linked-glycan-antennary-profile
#14
Jong Hyun Lee, Yeong Ran Jeong, Yeon-Gu Kim, Gyun Min Lee
To understand the effects of hyperosmolality on protein glycosylation, recombinant Chinese hamster ovary (rCHO) cells producing the Fc-fusion protein were cultivated in hyperosmolar medium resulting from adding NaCl (415 mOsm/kg). The hyperosmotic culture showed increased specific Fc-fusion protein productivity (qFc ) but a decreased proportion of acidic isoforms and sialic acid content of the Fc-fusion protein. The intracellular and extracellular sialidase activities in the hyperosmotic cultures were similar to those in the control culture (314 mOsm/kg), indicating that reduced sialylation of Fc-fusion protein at hyperosmolality was not due to elevated sialidase activity...
March 7, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28266013/optical-coherence-tomography-in-biofilm-research-a-comprehensive-review
#15
REVIEW
Michael Wagner, Harald Horn
Imaging of biofilm systems is a prerequisite for a better understanding of both structure and its function. The review aims to critically discuss the use of optical coherence tomography (OCT) for the visualization of the biofilm structure as well as its dynamic behavior. A short overview on common and well-known, established imaging techniques for biofilms such as scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), Raman microscopy (RM), and magnetic resonance imaging (MRI) paves the way to imaging biofilms at the mesoscale, which is perfectly covered by means of OCT...
March 7, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28262952/mirna-engineering-of-cho-cells-facilitates-production-of-difficult-to-express-proteins-and-increases-success-in-cell-line-development
#16
Simon Fischer, Kim F Marquart, Lisa A Pieper, Juergen Fieder, Martin Gamer, Ingo Gorr, Patrick Schulz, Harald Bradl
In recent years, coherent with growing biologics portfolios also the number of complex and thus difficult-to-express (DTE) therapeutic proteins has increased considerably. DTE proteins challenge bioprocess development and can include various therapeutic protein formats such as monoclonal antibodies (mAbs), multi-specific affinity scaffolds (e.g. bispecific antibodies), cytokines or fusion proteins. Hence, the availability of robust and versatile Chinese hamster ovary (CHO) host cell factories is fundamental for high-yielding bioprocesses...
March 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28262949/enabling-complex-genetic-circuits-to-respond-to-extrinsic-environmental-signals
#17
LETTER
Allison Hoynes-O'Connor, Tatenda Shopera, Kristina Hinman, John Philip Creamer, Tae Seok Moon
Genetic circuits have the potential to improve a broad range of metabolic engineering processes and address a variety of medical and environmental challenges. However, in order to engineer genetic circuits that can meet the needs of these real-world applications, genetic sensors that respond to relevant extrinsic and intrinsic signals must be implemented in complex genetic circuits. In this work, we construct the first AND and NAND gates that respond to temperature and pH, two signals that have relevance in a variety of real-world applications...
March 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28262915/glutathione-and-thioredoxin-systems-contribute-to-recombinant-monoclonal-antibody-interchain-disulfide-bond-reduction-during-bioprocessing
#18
Michael W Handlogten, Min Zhu, Sanjeev Ahuja
Antibody interchain disulfide bond reduction during biopharmaceutical manufacturing has received increased attention since it was first reported in 2010. Antibody reduction leads to loss of product and reduced product stability. It is therefore critical to understand the underlying mechanisms of reduction. To date, the thioredoxin system has been reported as the sole contributor to antibody reduction during bioprocessing. In this work, we show that the glutathione system, in addition to the thioredoxin system, is involved in reducing antibody molecules and the contributions of the two systems can vary depending upon the cell culture process...
March 6, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28244592/exo-exo-synergy-between-cel6a-and-cel7a-from-hypocrea-jecorina-role-of-carbohydrate-binding-module-and-the-endo-lytic-character-of-the-enzymes
#19
Silke Flindt Badino, Stefan Jarl Christensen, Jeppe Kari, Michael Skovbo Windahl, Søren Hvidt, Kim Borch, Peter Westh
Synergy between cellulolytic enzymes is essential in both natural and industrial breakdown of biomass. In addition to synergy between endo-lytic and exo-lytic enzymes, a lesser known but equally conspicuous synergy occurs among exo-acting, processive cellobiohydrolases (CBHs) such as Cel7A and Cel6A from Hypocrea jecorina. We studied this system using microcrystalline cellulose as substrate and found a degree of synergy between 1.3 and 2.2 depending on the experimental conditions. Synergy between enzyme variants without the carbohydrate binding module (CBM) and its linker was strongly reduced compared to the wild types...
February 28, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28244589/mechanistic-kinetic-models-of-enzymatic-cellulose-hydrolysis-a-review
#20
REVIEW
Tina Jeoh, Maria J Cardona, Nardrapee Karuna, Akshata R Mudinoor, Jennifer Nill
Bioconversion of lignocellulose forms the basis for renewable, advanced biofuels and bioproducts. Mechanisms of hydrolysis of cellulose by cellulases have been actively studied for nearly 70 years with significant gains in understanding of the cellulolytic enzymes. Yet, a full mechanistic understanding of the hydrolysis reaction has been elusive. We present a review to highlight new insights gained since the most recent comprehensive review of cellulose hydrolysis kinetic models by Bansal et al. (2009). Recent models have taken a two-pronged approach to tackle the challenge of modeling the complex heterogeneous reaction - an enzyme-centric modeling approach centered on the molecularity of the cellulase-cellulose interactions to examine rate limiting elementary steps and a substrate-centric modeling approach aimed at capturing the limiting property of the insoluble cellulose substrate...
February 28, 2017: Biotechnology and Bioengineering
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