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Journal of Biological Engineering

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https://www.readbyqxmd.com/read/28191036/influence-of-gold-nanoparticle-surface-chemistry-and-diameter-upon-alzheimer-s-disease-amyloid-%C3%AE-protein-aggregation
#1
Kelly A Moore, Kayla M Pate, Deborah D Soto-Ortega, Samuel Lohse, Nicholas van der Munnik, Mihyun Lim, Kaliah S Jackson, Venetia D Lyles, Lemeisha Jones, Nisha Glassgow, Vanessa M Napumecheno, Shanee Mobley, Mark J Uline, Rahina Mahtab, Catherine J Murphy, Melissa A Moss
BACKGROUND: Deposits of aggregated amyloid-β protein (Aβ) are a pathological hallmark of Alzheimer's disease (AD). Thus, one therapeutic strategy is to eliminate these deposits by halting Aβ aggregation. While a variety of possible aggregation inhibitors have been explored, only nanoparticles (NPs) exhibit promise at low substoichiometric ratios. With tunable size, shape, and surface properties, NPs present an ideal platform for rationally designed Aβ aggregation inhibitors. In this study, we characterized the inhibitory capabilities of gold nanospheres exhibiting different surface coatings and diameters...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28127399/future-developments-in-biosensors-for-field-ready-zika-virus-diagnostics
#2
REVIEW
Ariana M Nicolini, Katherine E McCracken, Jeong-Yeol Yoon
Since early reports of the recent Zika virus outbreak in May 2015, much has been learned and discussed regarding Zika virus infection and transmission. However, many opportunities still remain for translating these findings into field-ready sensors and diagnostics. In this brief review, we discuss current diagnostic methods, consider the prospects of translating other flavivirus biosensors directly to Zika virus sensing, and look toward the future developments needed for high-sensitivity and high-specificity biosensors to come...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28127398/pretreatment-of-vinasse-from-the-sugar-refinery-industry-under-non-sterile-conditions-by-trametes-versicolor-in-a-fluidized-bed-bioreactor-and-its-effect-when-coupled-to-an-uasb-reactor
#3
Elda España-Gamboa, Teresa Vicent, Xavier Font, Jorge Dominguez-Maldonado, Blondy Canto-Canché, Liliana Alzate-Gaviria
BACKGROUND: During hydrous ethanol production from the sugar refinery industry in Mexico, vinasse is generated. Phenolic compounds and melanoidins contribute to its color and make degradation of the vinasse a difficult task. Although anaerobic digestion (AD) is feasible for vinasse treatment, the presence of recalcitrant compounds can be toxic or inhibitory for anaerobic microorganism. Therefore, this study presents new data on the coupled of the FBR (Fluidized Bed Bioreactor) to the UASB (Upflow Anaerobic Sludge Blanket) reactor under non-sterile conditions by T...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28127397/synthetic-photosynthetic-consortia-define-interactions-leading-to-robustness-and-photoproduction
#4
Stephanie G Hays, Leo L W Yan, Pamela A Silver, Daniel C Ducat
BACKGROUND: Microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs: Bacillus subtilis, Escherichia coli, or Saccharomyces cerevisiae...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28101135/towards-the-10-year-milestone-of-journal-of-biological-engineering
#5
EDITORIAL
Jeong-Yeol Yoon
October 10(th), 2016 marked the 9(th) anniversary for the Journal of Biological Engineering (JBE), the official journal of Institute of Biological Engineering (IBE), published by BioMed Central. We are entering into the 10(th) year of its exciting and productive history. In this editorial, a brief history of JBE is summarized, along with a series of analyses on average number of citations, breakdown of topical subjects, geographical representations and so forth for all published articles in JBE. Future prospects and new directions of JBE are also described in this editorial...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28101134/single-cell-isolation-process-with-laser-induced-forward-transfer
#6
Yu Deng, Philippe Renaud, Zhongning Guo, Zhigang Huang, Ying Chen
BACKGROUND: A viable single cell is crucial for studies of single cell biology. In this paper, laser-induced forward transfer (LIFT) was used to isolate individual cell with a closed chamber designed to avoid contamination and maintain humidity. Hela cells were used to study the impact of laser pulse energy, laser spot size, sacrificed layer thickness and working distance. The size distribution, number and proliferation ratio of separated cells were statistically evaluated. Glycerol was used to increase the viscosity of the medium and alginate were introduced to soften the landing process...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28074108/cellulolytic-robolector-towards-an-automated-high-throughput-screening-platform-for-recombinant-cellulase-expression
#7
Martina Mühlmann, Martin Kunze, Joaquim Ribeiro, Bertram Geinitz, Christian Lehmann, Ulrich Schwaneberg, Ulrich Commandeur, Jochen Büchs
BACKGROUND: Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the enzymes. To overcome this draw back, a lot of effort is put into the area of protein engineering, to modify these enzymes by directed evolution or rational design. Huge clone libraries are constructed and have to be screened for improved variants. High-throughput screening is the method of choice to tackle this experimental effort, but up to now only a few process steps are adapted to automated platforms and little attention has been turned to the reproducibility of clone rankings...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28018483/can-terminators-be-used-as-insulators-into-yeast-synthetic-gene-circuits
#8
Wenjiang Song, Jing Li, Qiang Liang, Mario Andrea Marchisio
BACKGROUND: In bacteria, transcription units can be insulated by placing a terminator in front of a promoter. In this way promoter leakage due to the read-through from an upstream gene or RNA polymerase unspecific binding to the DNA is, in principle, removed. Differently from bacterial terminators, yeast S. cerevisiae terminators contain a hexamer sequence, the efficiency element, that strongly resembles the eukaryotic TATA box i.e. the promoter sequence recognized and bound by RNA polymerase II...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28018482/algae-based-biofilm-productivity-utilizing-dairy-wastewater-effects-of-temperature-and-organic-carbon-concentration
#9
Zachary T Fica, Ronald C Sims
BACKGROUND: Biofilm-based microalgal growth was determined as functions of organic chemical loading and water temperature utilizing dairy wastewater from a full-scale dairy farm. The dairy industry is a significant source of wastewater worldwide that could provide an inexpensive and nutrient rich feedstock for the cultivation of algae biomass for use in downstream processing of animal feed and aquaculture applications. Algal biomass was cultivated using a Rotating Algal Biofilm Reactor (RABR) system...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27999616/bioelectronic-nose-and-its-application-to-smell-visualization
#10
REVIEW
Hwi Jin Ko, Tai Hyun Park
There have been many trials to visualize smell using various techniques in order to objectively express the smell because information obtained from the sense of smell in human is very subjective. So far, well-trained experts such as a perfumer, complex and large-scale equipment such as GC-MS, and an electronic nose have played major roles in objectively detecting and recognizing odors. Recently, an optoelectronic nose was developed to achieve this purpose, but some limitations regarding the sensitivity and the number of smells that can be visualized still persist...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27895704/the-extracellular-microscape-governs-mesenchymal-stem-cell-fate
#11
REVIEW
William J Hadden, Yu Suk Choi
Each cell forever interacts with its extracellular matrix (ECM); a stem cell relies on this interaction to guide differentiation. The stiffness, nanotopography, protein composition, stress and strain inherent to any given ECM influences stem cell lineage commitment. This interaction is dynamic, multidimensional and reciprocally evolving through time, and from this concerted exchange the macroscopic tissues that comprise living organisms are formed. Mesenchymal stem cells can give rise to bone, cartilage, tendon and muscle; thus attempts to manipulate their differentiation must heed the physical properties of incredibly complex native microenvironments to realize regenerative goals...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27872658/exploiting-the-dynamic-properties-of-covalent-modification-cycle-for-the-design-of-synthetic-analog-biomolecular-circuitry
#12
Mathias Foo, Rucha Sawlekar, Declan G Bates
BACKGROUND: Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours - ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic. RESULTS: In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27795735/respiration-activity-monitoring-system-for-any-individual-well-of-a-48-well-microtiter-plate
#13
David Flitsch, Sebastian Krabbe, Tobias Ladner, Mario Beckers, Jana Schilling, Stefan Mahr, Uwe Conrath, Werner K Schomburg, Jochen Büchs
BACKGROUND: Small-scale micro-bioreactors have become the cultivation vessel of choice during the first steps of bioprocess development. They combine high cultivation throughput with enhanced cost efficiency per cultivation. To gain the most possible information in the early phases of process development, online monitoring of important process parameters is highly advantageous. One of these important process parameters is the oxygen transfer rate (OTR). Measurement of the OTR, however, is only available for small-scale fermentations in shake flasks via the established RAMOS technology until now...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27777616/significantly-enhancing-recombinant-alkaline-amylase-production-in-bacillus-subtilis-by-integration-of-a-novel-mutagenesis-screening-strategy-with-systems-level-fermentation-optimization
#14
Yingfang Ma, Wei Shen, Xianzhong Chen, Long Liu, Zhemin Zhou, Fei Xu, Haiquan Yang
BACKGROUND: Alkaline amylase has significant potential for applications in the textile, paper and detergent industries, however, low yield of which cannot meet the requirement of industrial application. In this work, a novel ARTP mutagenesis-screening method and fermentation optimization strategies were used to significantly improve the expression level of recombinant alkaline amylase in B. subtilis 168. RESULTS: The activity of alkaline amylase in mutant B. subtilis 168 mut-16# strain was 1...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27752283/design-and-engineering-of-a-transmissible-antiviral-defense
#15
Matthew L Paff, Scott L Nuismer, Andrew D Ellington, Ian J Molineux, Ryan H May, James J Bull
BACKGROUND: We propose, model, and implement a novel system of population-level intervention against a virus. One context is a treatment against a chronic infection such as HIV. The underlying principle is a form of virus 'wars' in which a benign, transmissible agent is engineered to protect against infection by and spread of a lethal virus. In our specific case, the protective agent consists of two entities, a benign virus and a gene therapy vector mobilized by the benign virus. RESULTS: Numerical analysis of a mathematical model identified parameter ranges in which adequate, population-wide protection is achieved...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27733867/probing-unnatural-amino-acid-integration-into-enhanced-green-fluorescent-protein-by-genetic-code-expansion-with-a-high-throughput-screening-platform
#16
Georg Wandrey, Joel Wurzel, Kyra Hoffmann, Tobias Ladner, Jochen Büchs, Lorenz Meinel, Tessa Lühmann
BACKGROUND: Genetic code expansion has developed into an elegant tool to incorporate unnatural amino acids (uAA) at predefined sites in the protein backbone in response to an amber codon. However, recombinant production and yield of uAA comprising proteins are challenged due to the additional translation machinery required for uAA incorporation. RESULTS: We developed a microtiter plate-based high-throughput monitoring system (HTMS) to study and optimize uAA integration in the model protein enhanced green fluorescence protein (eGFP)...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27688801/design-and-integration-of-a-problem-based-biofabrication-course-into-an-undergraduate-biomedical-engineering-curriculum
#17
Ritu Raman, Marlon Mitchell, Pablo Perez-Pinera, Rashid Bashir, Lizanne DeStefano
BACKGROUND: The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27582873/treatment-of-saline-municipal-wastewater-using-hybrid-growth-system
#18
N Salmanikhas, M Tizghadam, A Rashidi Mehrabadi
BACKGROUND: In this study, a hybrid treatment system (Fluidized Bed positioned in a biological reactor of an Activated Sludge process) was used to treat saline domestic wastewater. The performance of the mentioned hybrid system was compared with the conventional activated sludge. A pilot study was conducted, and Chemical Oxygen Demand (COD), Electrical Conductivity (EC), Total Dissolved Solids (TDS) and pH were measured to investigate treatment efficiency. Three saline wastewater samples with salt concentrations of 0...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27347005/optimization-of-the-fermentation-process-of-cordyceps-sobolifera-se-ceps-and-its-anti-tumor-activity-in-vivo
#19
Shengli Yang, Hui Zhang
BACKGROUND: Cordyceps sobolifera (C. sobolifera) isolated from cicadae was used as the starting fungus to produce selenium-enriched C. sobolifera extracellular polysaccharide (Se-CEPS). An orthogonal experimental design based on a single-factor experiment was used to optimize the C. sobolifera fermentation conditions, including the potato juice, peptone, and KH2PO4 concentrations. Ultraviolet (UV) and infrared (IR) analyses of CEPS and Se-CEPS were conducted, as well as an in vivo anti-tumor analysis...
2016: Journal of Biological Engineering
https://www.readbyqxmd.com/read/27200108/ce-uv-vis-and-ce-ms-for-monitoring-organic-impurities-during-the-downstream-processing-of-fermentative-produced-lactic-acid-from-second-generation-renewable-feedstocks
#20
Hendrik Laube, Frank-Michael Matysik, Andreas Schmidberger, Kerstin Mehlmann, Andreas Toursel, Jana Boden
BACKGROUND: During the downstream process of bio-based bulk chemicals, organic impurities, mostly residues from the fermentation process, must be separated to obtain a pure and ready-to-market chemical. In this study, capillary electrophoresis was investigated for the non-targeting downstream process monitoring of organic impurities and simultaneous quantitative detection of lactic acid during the purification process of fermentatively produced lactic acid. The downstream process incorporated 11 separation units, ranging from filtration, adsorption and ion exchange to electrodialysis and distillation, and 15 different second-generation renewable feedstocks were processed into lactic acid...
2016: Journal of Biological Engineering
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