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Biotechnology and Bioengineering

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https://www.readbyqxmd.com/read/29777597/microdevice-based-solid-phase-polymerase-chain-reaction-for-rapid-detection-of-pathogenic-microorganisms
#1
Quang Nghia Pham, Kieu The Loan Trinh, Seung Won Jung, Nae Yoon Lee
We demonstrate the integration of DNA amplification and detection functionalities developed on a lab-on-a-chip microdevice utilizing solid-phase polymerase chain reaction (SP-PCR) for point-of-need (PON) DNA analyses. First, the polycarbonate microdevice was fabricated by thermal bonding to contain microchambers as reservoirs for performing SP-PCR. Next, the microchambers were subsequently modified with polyethyleneimine and glutaraldehyde for immobilizing amine-modified forward primers. During SP-PCR, the immobilized forward primers and freely diffusing fluorescence-labeled reverse primers cooperated to generate target amplicons, which remained covalently attached to the microchambers for the fluorescence detection...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777596/morphological-analysis-of-pore-size-and-connectivity-in-a-thick-mixed-culture-biofilm
#2
Alex F Rosenthal, James S Griffin, Michael Wagner, Aaron I Packman, Oluwaseyi Balogun, George F Wells
Morphological parameters are commonly used to predict transport and metabolic kinetics in biofilms. Yet, quantification of biofilm morphology remains challenging due to imaging technology limitations and lack of robust analytical approaches. We present a novel set of imaging and image analysis techniques to estimate internal porosity, pore size distributions, and pore network connectivity to a depth of 1 mm at a resolution of 10 µm in a biofilm exhibiting both heterotrophic and nitrifying activity. Optical coherence tomography (OCT) scans revealed an extensive pore network with diameters as large as 110 µm directly connected to the biofilm surface and surrounding fluid...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777593/degradation-of-recombinant-proteins-by-cho-host-cell-proteases-is-prevented-by-matriptase-1-knock-out
#3
Holger Laux, Sandrine Romand, Sandro Nuciforo, Christopher J Farady, Joel Tapparel, Stine Buechmann-Moeller, Benjamin Sommer, Edward J Oakeley, Ursula Bodendorf
An increasing number of non-antibody format proteins are entering the clinical development. However, one of the major hurdles for the production of non-antibody glycoproteins is host cell-related proteolytic degradation, which can drastically impact developability and timelines of pipeline projects. Chinese hamster ovary (CHO) cells are the preferred production host for recombinant therapeutic proteins. Using protease inhibitors, transcriptomics and genetic knockdowns we have identified, out of the more than 700 known proteases in rodents, Matriptase-1 as the major protease involved in degradation of recombinant proteins expressed in CHO-K1 cells...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777592/early-identification-of-unusually-clustered-mutations-and-a-root-cause-in-therapeutic-antibody-development
#4
Yueming Qian, Zhiqiang Chen, Xin Huang, Xuning Wang, Xuankuo Xu, Stefan Kirov, Richard Ludwig, Nan-Xin Qian, Kandasamy Ravi, Li Tao, Michael C Borys, Zheng Jian Li
This study reports findings of an unusual cluster of mutations spanning 22 base pairs in a monoclonal antibody (mAb) expression vector. It was identified by two orthogonal methods: mass spectrometry on expressed protein and next-generation sequencing (NGS) on the plasmid DNA. While the initial NGS analysis confirmed the designed sequence modification, intact mass analysis detected an additional mass of the antibody molecule expressed in CHO cells. The extra mass was eventually found to be associated with unmatched nucleotides in a distal region by checking full-length sequence alignment plots...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777591/bioengineering-triacetic-acid-lactone-production-in-yarrowia-lipolytica-for-pogostone-synthesis
#5
James Yu, Jenny Landberg, Farbod Shavarebi, Virginia Bilanchone, Adam Okerlund, Umayangani Wanninayake, Le Zhao, George Kraus, Suzanne Sandmeyer
Yarrowia lipolytica is an oleaginous yeast that is recognized for its ability to accumulate high levels of lipids, which can serve as precursors to biobased fuels and chemicals. Polyketides such as triacetic acid lactone (TAL) can also serve as a precursor for diverse commodity chemicals. This study used Y. lipolytica as a host organism for the production of TAL via expression of the 2-pyrone synthase gene from Gerbera hybrida. Induction of lipid biosynthesis by nitrogen-limited growth conditions increased TAL titers...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777590/boosting-mediated-electron-transfer-in-bioelectrochemical-systems-with-tailored-defined-microbial-co-cultures
#6
Simone Schmitz, Miriam A Rosenbaum
Bioelectrochemical systems (BES) hold great promise for sustainable energy generation via a microbial catalyst from organic matter, e.g., from wastewater. In order to improve current generation in BES, understanding the underlying microbiology of the electrode community is essential. Electron mediator producing microorganism like Pseudomonas aeruginosa play an essential role in efficient electricity generation in BES. These microbes enable even non-electroactive microorganism like Enterobacter aerogenes to contribute to current production...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29777589/low-adhesive-ethylene-vinyl-alcohol-based-packaging-to-xenogeneic-islets-encapsulation-for-type-1-diabetes-treatment
#7
Kai-Chiang Yang, Goichi Yanai, Sin-Yu Yang, Priyadarshini Canning, Yoshio Satou, Masako Kawagoe, Shoichiro Sumi
Transplantation of encapsulated porcine islets is proposed to treat type 1 diabetes. However, envelopment of fibrous tissue and infiltration of immune cells impair islets function and eventually cause implant failure. It is known that hemodialysis using an ethylene vinyl alcohol (EVOH) membrane results in minor tissue responses. Therefore, we hypothesized that using a low adhesive EVOH membrane for encapsulation may prevent host cell accumulation and fibrous capsule formation. In this study, rat islets suspended in chitosan gel were encapsulated in bags made from highly porous EVOH membranes, and their in vitro insulin secretion function as well as in vivo performance were evaluated...
May 19, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29750332/building-a-genome-engineering-toolbox-in-non-model-prokaryotic-microbes
#8
REVIEW
Emily Freed, Jacob Fenster, Sharon L Smolinski, Julie Walker, Calvin A Henard, Ryan Gill, Carrie A Eckert
The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g. sunlight, CO2 , non-food biomass) to biofuels and bioproducts at sufficient titers and costs. For model microbes such as E. coli, advances in DNA reading and writing technologies are driving adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks such as photosynthesis, autotrophic growth, and cellulose degradation have very few, if any, genetic tools for metabolic engineering...
May 11, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29733444/building-a-minimal-and-generalizable-model-of-transcription-factor-based-biosensors-showcasing-flavonoids
#9
Heykel Trabelsi, Mathilde Koch, Jean-Loup Faulon
Progress in synthetic biology tools has transformed the way we engineer living cells. Applications of circuit design have reached a new level, offering solutions for metabolic engineering challenges that include developing screening approaches for libraries of pathway variants. The use of transcription-factor based biosensors for screening has shown promising results, but the quantitative relationship between the sensors and the sensed molecules still needs more rational understanding. Herein, we have successfully developed a novel biosensor to detect pinocembrin based on a transcriptional regulator...
May 7, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29733430/combinatorial-synthetic-pathway-fine-tuning-and-comparative-transcriptomics-for-metabolic-engineering-of-raoultella-ornithinolytica-bf60-to-efficiently-synthesize-2-5-furandicarboxylic-acid
#10
Haibo Yuan, Yanfeng Liu, Jianghua Li, Hyun-Dong Shin, Guocheng Du, Zhongping Shi, Jian Chen, Long Liu
The compound, 5-hydroxymethylfurfural (HMF), has attracted much attention due to its versatility as an important bio-based platform chemical. Here, we engineered Raoultella ornithinolytica BF60 as a whole-cell biocatalyst for highly efficient synthesis of 2,5-furandicarboxylic acid (FDCA) from HMF. Specifically, various expression cassettes of key genes, such as hmfH (gene encoding HMF/furfural oxidoreductase [HmfH]) and hmfo (gene encoding HMF oxidase [HMFO]) were designed and constructed for fine-tuning FDCA synthesis from HMF...
May 7, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29727468/michael-l-shuler-tribute
#11
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
May 4, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704461/non-newtonian-rheology-in-suspension-cell-cultures-significantly-impacts-bioreactor-shear-stress-quantification
#12
Alex Wyma, Leonardo Martin-Alarcon, Tylor Walsh, Tannin A Schmidt, Ian D Gates, Michael S Kallos
The fields of regenerative medicine and tissue engineering require large-scale manufacturing of stem cells for both therapy and recombinant protein production, which is often achieved by culturing cells in stirred suspension bioreactors. The rheology of cell suspensions cultured in stirred suspension bioreactors is critical to cell growth and protein production, as elevated exposure to shear stress has been linked to changes in growth kinetics and genetic expression for many common cell types. Currently, little is understood on the rheology of cell suspensions cultured in stirred suspension bioreactors...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704459/a-reference-genome-of-the-chinese-hamster-based-on-a-hybrid-assembly-strategy
#13
Oliver Rupp, Madolyn L MacDonald, Shangzhong Li, Heena Dhiman, Shawn Polson, Sven Griep, Kelley Heffner, Inmaculada Hernandez, Karina Brinkrolf, Vaibhav Jadhav, Mojtaba Samoudi, Haiping Hao, Brewster Kingham, Alexander Goesmann, Michael J Betenbaugh, Nathan E Lewis, Nicole Borth, Kelvin H Lee
Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704441/improving-culture-performance-and-antibody-production-in-cho-cell-culture-processes-by-reducing-the-warburg-effect
#14
Maria Buchsteiner, Lake-Ee Quek, Peter Gray, Lars K Nielsen
Lactate is one of the key waste metabolites of mammalian cell culture. High lactate levels are caused by high aerobic glycolysis, also known as the Warburg effect, and are usually associated with adverse culture performance. Therefore, reducing lactate accumulation has been an ongoing challenge in cell culture development in order to improve growth, productivity and process robustness. The pyruvate dehydrogenase complex (PDC) plays a crucial role for the fate of pyruvate, as it converts pyruvate to acetyl-CoA...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704438/crispr-interference-mediated-metabolic-engineering-of-corynebacterium-glutamicum-for-homo-butyrate-production
#15
Jinkyung Yoon, Han Min Woo
Combinatorial metabolic engineering enabled the development of efficient microbial cell factories for modulating gene expression to produce desired products. Here, we report the combinatorial metabolic engineering of Corynebacterium glutamicum to produce butyrate by introducing a synthetic butyrate pathway including phosphotransferase and butyrate kinase reactions and repressing the essential acn gene encoding aconitase, which has been targeted for down-regulation in a genome-scale model. An All-in-One CRISPR interference system for C...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704433/retrievable-hydrogels-for-ovarian-follicle-transplantation-and-oocyte-collection
#16
Peter D Rios, Ekaterina Kniazeva, Hoi Chang Lee, Shuo Xiao, Robert S Oakes, Eiji Saito, Jacqueline S Jeruss, Ariella Shikanov, Teresa K Woodruff, Lonnie D Shea
Cancer survivorship rates have drastically increased due to improved efficacy of oncologic treatments. Consequently, clinical concerns have shifted from solely focusing on survival to quality of life, with fertility preservation as an important consideration. Among fertility preservation strategies for female patients, ovarian tissue cryopreservation and subsequent re-implantation has been the only clinical option available to cancer survivors with cryopreserved tissue. However, follicle atresia post-transplantation and risk of re-introducing malignant cells have prevented this procedure from becoming widely adopted in clinics...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29704240/accurate-o-2-delivery-enabled-benzene-biodegradation-through-aerobic-activation-followed-by-denitrification-coupled-mineralization
#17
Zhuolin Liu, Chen Zhou, Aura Ontiveros-Valencia, Yi-Hao Luo, Min Long, Hua Xu, Bruce E Rittmann
Although benzene can be biodegraded when dissolved oxygen is sufficient, delivering oxygen is energy intensive and can lead to air stripping the benzene. Anaerobes can biodegrade benzene by using electron acceptors other than O2 , and this may reduce costs and exposure risks; the drawback is a remarkably slower growth rate. We evaluated a two-step strategy that involved O2 -dependent benzene activation and cleavage followed by intermediate oxidation coupled to NO3 - respiration. We employed a membrane biofilm reactor (MBfR) featuring nonporous hollow fibers as the means to deliver O2 directly to a biofilm at an accurately controlled rate...
April 28, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29689639/establishment-and-characterization-of-a-primary-murine-adipose-tissue-chip
#18
Nida Tanataweethum, Adelyn Zelaya, Feipeng Yang, Ronald N Cohen, Eric M Brey, Abhinav Bhushan
Better experimental models are needed to enhance our understanding of metabolic regulation which is seen in obesity and metabolic disorders, such as type 2 diabetes. In vitro models based on microfluidics enable physiological representations of tissues with several advantages over conventional culture systems, such as perfused flow to better mimic the physiological environment. Although cell lines such as 3T3-L1 have been incorporated in microfluidic devices, murine primary preadipocytes have not been differentiated and maintained for long-term monitoring in these culture systems...
April 24, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29679482/an-impurity-characterization-based-approach-for-the-rapid-development-of-integrated-downstream-purification-processes
#19
Steven M Timmick, Nicholas Vecchiarello, Chaz Goodwine, Laura E Crowell, Kerry R Love, J Christopher Love, Steven M Cramer
In this work, we describe a new approach for the characterization of process-related impurities along with an in silico tool to generate orthogonal, integrated downstream purification processes for biological products. A one-time characterization of process-related impurities from product expression in Pichia pastoris was first carried out using linear salt and pH gradients on a library of multimodal, salt-tolerant, and hydrophobic charge induction chromatographic resins. Reversed phase UPLC analysis of the fractions from these gradients was then used to generate large data sets of impurity profiles...
April 21, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29679475/chemically-controlled-aggregation-of-pluripotent-stem-cells
#20
Yonatan Y Lipsitz, Peter Tonge, Peter W Zandstra
Heterogeneity in pluripotent stem cell (PSC) aggregation leads to variability in mass transfer and signaling gradients between aggregates, which results in heterogeneous differentiation and therefore variability in product quality and yield. We have characterized a chemical based method to control aggregate size within a specific, tunable range with low heterogeneity, thereby reducing process variability in PSC expansion. This method enables controlled, scalable, stirred suspension based manufacturing of PSC cultures which are critical for the translation of regenerative medicine strategies to clinical products...
April 21, 2018: Biotechnology and Bioengineering
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