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Journal of Biological Engineering

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https://www.readbyqxmd.com/read/28592992/streamlining-recombination-mediated-genetic-engineering-by-validating-three-neutral-integration-sites-in-synechococcus-sp-pcc-7002
#1
Anne Ilse Maria Vogel, Rahmi Lale, Martin Frank Hohmann-Marriott
BACKGROUND: Synechococcus sp. PCC 7002 (henceforth Synechococcus) is developing into a powerful synthetic biology chassis. In order to streamline the integration of genes into the Synechococcus chromosome, validation of neutral integration sites with optimization of the DNA transformation protocol parameters is necessary. Availability of BioBrick-compatible integration modules is desirable to further simplifying chromosomal integrations. RESULTS: We designed three BioBrick-compatible genetic modules, each targeting a separate neutral integration site, A2842, A0935, and A0159, with varying length of homologous region, spanning from 100 to 800 nt...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28592991/aav-based-dual-reporter-circuit-for-monitoring-cell-signaling-in-living-human-cells
#2
Zhiwen Zhang, Zachary Stickney, Natalie Duong, Kevin Curley, Biao Lu
BACKGROUND: High-throughput methods based on molecular reporters have greatly advanced our knowledge of cell signaling in mammalian cells. However, their ability to monitor various types of cells is markedly limited by the inefficiency of reporter gene delivery. Recombinant adeno-associated virus (AAV) vectors are efficient tools widely used for delivering and expressing transgenes in diverse animal cells in vitro and in vivo. Here we present the design, construction and validation of a novel AAV-based dual-reporter circuit that can be used to monitor and quantify cell signaling in living human cells...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28484513/significantly-enhanced-biomass-production-of-a-novel-bio-therapeutic-strain-lactobacillus-plantarum-as-14-by-developing-low-cost-media-cultivation-strategy
#3
Asma Manzoor, Javed Iqbal Qazi, Ikram Ul Haq, Hamid Mukhtar, Akhtar Rasool
BACKGROUND: Probiotic bacteria are becoming an important tool for improving human health, controlling diseases and enhancing immune responses. The availability of a cost effective cultivation conditions has profound effect on the efficiency and role of probiotic bacteria. Therefore the current study was conducted with an objective to develop a low cost growth medium for enhancing the biomass production of a bio-therapeutic bacterial strain Lactobacillus plantarum AS-14. In this work the isolation of Lactobacillus plantarum AS-14 bacterial strain was carried out from brinjal using cheese whey as a main carbon source...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28469703/application-of-denitrifying-wood-chip-bioreactors-for-management-of-residential-non-point-sources-of-nitrogen
#4
REVIEW
E V Lopez-Ponnada, T J Lynn, M Peterson, S J Ergas, J R Mihelcic
Two important and large non-point sources of nitrogen in residential areas that adversely affect water quality are stormwater runoff and effluent from on-site treatment systems. These sources are challenging to control due to their variable flow rates and nitrogen concentrations. Denitrifying bioreactors that employ a lignocellulosic wood chip medium contained within a saturated (anoxic) zone are relatively new technology that can be implemented at the local level to manage residential non-point nitrogen sources...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28396694/synthesis-of-umbelliferone-derivatives-in-escherichia-coli-and-their-biological-activities
#5
Luan Luong Chu, Ramesh Prasad Pandey, Haet Nim Lim, Hye Jin Jung, Nguyen Huy Thuan, Tae-Su Kim, Jae Kyung Sohng
BACKGROUND: Umbelliferone, also known as 7-hydroxycoumarin, is a phenolic metabolite found in many familiar plants. Its derivatives have been shown to have various pharmacological and chemo-preventive effects on human health. A uridine diphosphate glycosyltransferase YjiC from Bacillus licheniformis DSM 13, a cytochrome P450BM3 (CYP450 BM3) variant namely mutant 13 (M13) from Bacillus megaterium, and an O-methyltransferase from Streptomyces avermitilis (SaOMT2) were used for modifications of umbelliferone...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28392831/directing-three-dimensional-multicellular-morphogenesis-by-self-organization-of-vascular-mesenchymal-cells-in-hyaluronic-acid-hydrogels
#6
Xiaolu Zhu, Shiva Gojgini, Ting-Hsuan Chen, Peng Fei, Siyan Dong, Chih-Ming Ho, Tatiana Segura
BACKGROUND: Physical scaffolds are useful for supporting cells to form three-dimensional (3D) tissue. However, it is non-trivial to develop a scheme that can robustly guide cells to self-organize into a tissue with the desired 3D spatial structures. To achieve this goal, the rational regulation of cellular self-organization in 3D extracellular matrix (ECM) such as hydrogel is needed. RESULTS: In this study, we integrated the Turing reaction-diffusion mechanism with the self-organization process of cells and produced multicellular 3D structures with the desired configurations in a rational manner...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28360935/portable-nuclear-magnetic-resonance-biosensor-and-assay-for-a-highly-sensitive-and-rapid-detection-of-foodborne-bacteria-in-complex-matrices
#7
Yilun Luo, Evangelyn C Alocilja
BACKGROUND: Nuclear magnetic resonance (NMR) technique is a powerful analytical tool in determining the presence of bacterial contaminants in complex biological samples. In this paper, a portable NMR-based (pNMR) biosensor and assay to detect the foodborne bacteria Escherichia coli O157:H7 is reported. It uses antibody-functionalized polymer-coated magnetic nanoparticles as proximity biomarker of the bacteria which accelerates NMR resonance signal decay. RESULTS: The pNMR biosensor operates at 0...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28344644/strategies-for-using-nanoprobes-to-perceive-and-treat-cancer-activity-a-review
#8
REVIEW
Byunghoon Kang, Aastha Kukreja, Daesub Song, Yong-Min Huh, Seungjoo Haam
Nanomedicine has seen a significant increase in research on stimuli-responsive activatable nanoprobes for tumor-specific delivery and diagnosis. The tumor microenvironment has particular characteristics that can be exploited to implement therapeutic strategies based on disparities between normal tissues and tumor tissues, including differences in pH, oxygenation, enzymatic expression, gene activation/inactivation, and vasculature. The nanocarriers of activatable nanoparticles maintain their structure while circulating in the body and, upon reaching the tumor site, are altered by unique tumoral stimuli, leading to the release of a drug or other agent...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28293287/aptamer-based-sandwich-type-biosensors
#9
REVIEW
Ho Bin Seo, Man Bock Gu
Sandwich-type biosensor platforms have drawn lots of attentions due to its superior features, compared to other platforms, in terms of its stable and reproducible responses and easy enhancement in the detection sensitivity. The sandwich-type assays can be developed by utilizing a pair of receptors, which bind to the different sites of the same target. In this mini-review paper, the sandwich-type biosensors using either pairs of aptamers or aptamer-antibody pairs are reviewed in terms of its targets and platforms, the schematic designs, and their analytical performance...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28289439/detection-of-extremely-low-concentration-waterborne-pathogen-using-a-multiplexing-self-referencing-sers-microfluidic-biosensor
#10
Chao Wang, Foram Madiyar, Chenxu Yu, Jun Li
BACKGROUND: It is challenging to achieve ultrasensitive and selective detection of waterborne pathogens at extremely low levels (i.e., single cell/mL) using conventional methods. Even with molecular methods such as ELISA or PCR, multi-enrichment steps are needed which are labor and cost intensive. In this study, we incorporated nano-dielectrophoretic microfluidic device with Surface enhanced Raman scattering (SERS) technique to build a novel portable biosensor for easy detection and characterization of Escherichia coli O157:H7 at high sensitivity level (single cell/mL)...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28261325/technical-advances-in-global-dna-methylation-analysis-in-human-cancers
#11
REVIEW
Basudev Chowdhury, Il-Hoon Cho, Joseph Irudayaraj
Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28239411/reliable-measurement-of-e-coli-single-cell-fluorescence-distribution-using-a-standard-microscope-set-up
#12
Marilisa Cortesi, Lucia Bandiera, Alice Pasini, Alessandro Bevilacqua, Alessandro Gherardi, Simone Furini, Emanuele Giordano
BACKGROUND: Quantifying gene expression at single cell level is fundamental for the complete characterization of synthetic gene circuits, due to the significant impact of noise and inter-cellular variability on the system's functionality. Commercial set-ups that allow the acquisition of fluorescent signal at single cell level (flow cytometers or quantitative microscopes) are expensive apparatuses that are hardly affordable by small laboratories. METHODS: A protocol that makes a standard optical microscope able to acquire quantitative, single cell, fluorescent data from a bacterial population transformed with synthetic gene circuitry is presented...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28191036/influence-of-gold-nanoparticle-surface-chemistry-and-diameter-upon-alzheimer-s-disease-amyloid-%C3%AE-protein-aggregation
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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