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Journal of Biological Engineering

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https://www.readbyqxmd.com/read/29213305/a-multiplexed-magnetic-tweezer-with-precision-particle-tracking-and-bi-directional-force-control
#1
Keith C Johnson, Emilie Clemmens, Hani Mahmoud, Robin Kirkpatrick, Juan C Vizcarra, Wendy E Thomas
Background: In the past two decades, methods have been developed to measure the mechanical properties of single biomolecules. One of these methods, Magnetic tweezers, is amenable to aquisition of data on many single molecules simultaneously, but to take full advantage of this "multiplexing" ability, it is necessary to simultaneously incorprorate many capabilities that ahve been only demonstrated separately. Methods: Our custom built magnetic tweezer combines high multiplexing, precision bead tracking, and bi-directional force control into a flexible and stable platform for examining single molecule behavior...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29213304/engineering-the-human-blood-brain-barrier-in-vitro
#2
REVIEW
John J Jamieson, Peter C Searson, Sharon Gerecht
The blood-brain barrier (BBB) is the interface between the vasculature and the brain, regulating molecular and cellular transport into the brain. Endothelial cells (ECs) that form the capillary walls constitute the physical barrier but are dependent on interactions with other cell types. In vitro models are widely used in BBB research for mechanistic studies and drug screening. Current models have both biological and technical limitations. Here we review recent advances in stem cell engineering that have been utilized to create innovative platforms to replicate key features of the BBB...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29213303/climbing-the-mountain-experimental-design-for-the-efficient-optimization-of-stem-cell-bioprocessing
#3
REVIEW
Derek Toms, Rob Deardon, Mark Ungrin
"To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of." - R.A. Fisher While this idea is relevant across research scales, its importance becomes critical when dealing with the inherently large, complex and expensive process of preparing material for cell-based therapies (CBTs). Effective and economically viable CBTs will depend on the establishment of optimized protocols for the production of the necessary cell types...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29204185/bioengineering-considerations-in-liver-regenerative-medicine
#4
REVIEW
Ogechi Ogoke, Janet Oluwole, Natesh Parashurama
Background: Liver disease contributes significantly to global disease burden and is associated with rising incidence and escalating costs. It is likely that innovative approaches, arising from the emerging field of liver regenerative medicine, will counter these trends. Main body: Liver regenerative medicine is a rapidly expanding field based on a rich history of basic investigations into the nature of liver structure, physiology, development, regeneration, and function...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29204184/viral-cre-loxp-tools-aid-genome-engineering-in-mammalian-cells
#5
Ranjita Sengupta, Amy Mendenhall, Nandita Sarkar, Chandreyee Mukherjee, Amirali Afshari, Joseph Huang, Biao Lu
Background: Targeted nucleases have transformed genome editing technology, providing more efficient methods to make targeted changes in mammalian genome. In parallel, there is an increasing demand of Cre-LoxP technology for complex genome manipulation such as large deletion, addition, gene fusion and conditional removal of gene sequences at the target site. However, an efficient and easy-to-use Cre-recombinase delivery system remains lacking. Results: We designed and constructed two sets of expression vectors for Cre-recombinase using two highly efficient viral systems, the integrative lentivirus and non-integrative adeno associated virus...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29201140/expression-of-the-entire-polyhydroxybutyrate-operon-of-ralstonia-eutropha-in-plants
#6
Rita Mozes-Koch, Edna Tanne, Alexandra Brodezki, Ran Yehuda, Ofer Gover, Haim D Rabinowitch, Ilan Sela
Background: Previously we demonstrated that an entire bacterial operon (the PRN operon) is expressible in plants when driven by the Tomato -yellow-leaf-curl-virus (TYLCV) -derived universal vector IL-60.Petroleum-derived plastics are not degradable, and are therefore harmful to the environment. Fermentation of bacteria carrying operons for polyhydroxyalkanoates (PHAs) produces degradable bioplastics which are environmentally friendly. However, bacterial production of bioplastics is not cost-effective, and attention is turning to their production in plants...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29201139/structural-properties-of-starch-chitosan-gelatin-foams-and-the-impact-of-gelatin-on-mc3t3-mouse-osteoblast-cell-viability
#7
Gregory E Risser, Brittany L Banik, Justin L Brown, Jeffrey M Catchmark
Background: This study examines the effects of adding gelatin to a starch-chitosan composite foam, focusing on the altered structural and biological properties. The compressive modulus of foams containing different gelatin concentrations was tested in dry, wet, and lyophilized states. MC3T3 mouse osteoblast cells were used to test the composite's ability to support cell growth. The stability of the foams in α-MEM culture media with and without cells was also examined. Results: It was found that for dry foams, the compressive modulus increased with increasing gelatin content...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29201138/implementation-and-use-of-cloud-based-electronic-lab-notebook-in-a-bioprocess-engineering-teaching-laboratory
#8
Erin M Riley, Holly Z Hattaway, P Arthur Felse
Background: Electronic lab notebooks (ELNs) are better equipped than paper lab notebooks (PLNs) to handle present-day life science and engineering experiments that generate large data sets and require high levels of data integrity. But limited training and a lack of workforce with ELN knowledge have restricted the use of ELN in academic and industry research laboratories which still rely on cumbersome PLNs for recordkeeping. We used LabArchives, a cloud-based ELN in our bioprocess engineering lab course to train students in electronic record keeping, good documentation practices (GDPs), and data integrity...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29177007/a-simplified-microwave-based-motion-detector-for-home-cage-activity-monitoring-in-mice
#9
Andreas Genewsky, Daniel E Heinz, Paul M Kaplick, Kasyoka Kilonzo, Carsten T Wotjak
Background: Locomotor activity of rodents is an important readout to assess well-being and physical health, and is pivotal for behavioral phenotyping. Measuring homecage-activity with standard and cost-effective optical methods in mice has become difficult, as modern housing conditions (e.g. individually ventilated cages, cage enrichment) do not allow constant, unobstructed, visual access. Resolving this issue either makes greater investments necessary, especially if several experiments will be run in parallel, or is at the animals' expense...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29177006/tissue-specific-microenvironments-a-key-tool-for-tissue-engineering-and-regenerative-medicine
#10
REVIEW
Patrick C Sachs, Peter A Mollica, Robert D Bruno
The accumulated evidence points to the microenvironment as the primary mediator of cellular fate determination. Comprised of parenchymal cells, stromal cells, structural extracellular matrix proteins, and signaling molecules, the microenvironment is a complex and synergistic edifice that varies tissue to tissue. Furthermore, it has become increasingly clear that the microenvironment plays crucial roles in the establishment and progression of diseases such as cardiovascular disease, neurodegeneration, cancer, and ageing...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29158775/evaluation-of-microbial-globin-promoters-for-oxygen-limited-processes-using-escherichia-coli
#11
Alvaro R Lara, Karim E Jaén, Juan-Carlos Sigala, Lars Regestein, Jochen Büchs
Oxygen-responsive promoters can be useful for synthetic biology applications, however, information on their characteristics is still limited. Here, we characterized a group of heterologous microaerobic globin promoters in Escherichia coli. Globin promoters from Bacillus subtilis, Campylobacter jejuni, Deinococcus radiodurans, Streptomyces coelicolor, Salmonella typhi and Vitreoscilla stercoraria were used to express the FMN-binding fluorescent protein (FbFP), which is a non-oxygen dependent marker. FbFP fluorescence was monitored online in cultures at maximum oxygen transfer capacities (OTRmax) of 7 and 11 mmol L(-1) h(-1)...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29151885/treatment-of-old-landfill-leachate-with-high-ammonium-content-using-aerobic-granular-sludge
#12
Yanan Ren, Fernanda Ferraz, Abbass Jafari Kang, Qiuyan Yuan
Background: Aerobic granular sludge has become an attractive alternative to the conventional activated sludge due to its high settling velocity, compact structure, and higher tolerance to toxic substances and adverse conditions. Aerobic granular sludge process has been studied intensively in the treatment of municipal and industrial wastewater. However, information on leachate treatment using aerobic granular sludge is very limited. Methods: This study investigated the treatment performance of old landfill leachate with different levels of ammonium using two aerobic sequencing batch reactors (SBR): an activated sludge SBR (ASBR) and a granular sludge SBR (GSBR)...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29142590/birdcage-volume-coils-and-magnetic-resonance-imaging-a-simple-experiment-for-students
#13
Dwight E Vincent, Tianhao Wang, Thalia A K Magyar, Peni I Jacob, Richard Buist, Melanie Martin
Background: This article explains some simple experiments that can be used in undergraduate or graduate physics or biomedical engineering laboratory classes to learn how birdcage volume radiofrequency (RF) coils and magnetic resonance imaging (MRI) work. For a clear picture, and to do any quantitative MRI analysis, acquiring images with a high signal-to-noise ratio (SNR) is required. With a given MRI system at a given field strength, the only means to change the SNR using hardware is to change the RF coil used to collect the image...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29118850/study-of-in-vitro-transcriptional-binding-effects-and-noise-using-constitutive-promoters-combined-with-up-element-sequences-in-escherichia-coli
#14
Qiang Yan, Stephen S Fong
Background: UP elements (upstream element) are DNA sequences upstream of a promoter that interact with the α-subunit of RNA polymerase (RNAP) and can affect transcription by altering the binding RNAP to DNA. However, details of UP element and binding affinity effects on transcriptional strength are unclear. Results: Here, we investigated the effects of UP element sequences on gene transcription, binding affinity, and gene expression noise. Addition of UP elements resulted in increased gene expression (maximum 95...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29075321/modeling-the-behavior-of-human-induced-pluripotent-stem-cells-seeded-on-melt-electrospun-scaffolds
#15
Meghan E Hall, Nima Khadem Mohtaram, Stephanie M Willerth, Roderick Edwards
BACKGROUND: Human induced pluripotent stem cells (hiPSCs) can form any tissue found in the body, making them attractive for regenerative medicine applications. Seeding hiPSC aggregates into biomaterial scaffolds can control their differentiation into specific tissue types. Here we develop and analyze a mathematical model of hiPSC aggregate behavior when seeded on melt electrospun scaffolds with defined topography. RESULTS: We used ordinary differential equations to model the different cellular populations (stem, progenitor, differentiated) present in our scaffolds based on experimental results and published literature...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29046717/designing-of-pla-scaffolds-for-bone-tissue-replacement-fabricated-by-ordinary-commercial-3d-printer
#16
Aleš Gregor, Eva Filová, Martin Novák, Jakub Kronek, Hynek Chlup, Matěj Buzgo, Veronika Blahnová, Věra Lukášová, Martin Bartoš, Alois Nečas, Jan Hošek
BACKGROUND: The primary objective of Tissue engineering is a regeneration or replacement of tissues or organs damaged by disease, injury, or congenital anomalies. At present, Tissue engineering repairs damaged tissues and organs with artificial supporting structures called scaffolds. These are used for attachment and subsequent growth of appropriate cells. During the cell growth gradual biodegradation of the scaffold occurs and the final product is a new tissue with the desired shape and properties...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/29026441/modeling-the-architecture-of-the-regulatory-system-controlling-methylenomycin-production-in-streptomyces-coelicolor
#17
Jack E Bowyer, Emmanuel Lc de Los Santos, Kathryn M Styles, Alex Fullwood, Christophe Corre, Declan G Bates
BACKGROUND: The antibiotic methylenomycin A is produced naturally by Streptomyces coelicolor A3(2), a model organism for streptomycetes. This compound is of particular interest to synthetic biologists because all of the associated biosynthetic, regulatory and resistance genes are located on a single cluster on the SCP1 plasmid, making the entire module easily transferable between different bacterial strains. Understanding further the regulation and biosynthesis of the methylenomycin producing gene cluster could assist in the identification of motifs that can be exploited in synthetic regulatory systems for the rational engineering of novel natural products and antibiotics...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28919925/in-vitro-evaluation-of-polylactic-acid-pla-manufactured-by-fused-deposition-modeling
#18
Matthias C Wurm, Tobias Möst, Bastian Bergauer, Dominik Rietzel, Friedrich Wilhelm Neukam, Sandra C Cifuentes, Cornelius von Wilmowsky
BACKGROUND: With additive manufacturing (AM) individual and biocompatible implants can be generated by using suitable materials. The aim of this study was to investigate the biological effects of polylactic acid (PLA) manufactured by Fused Deposition Modeling (FDM) on osteoblasts in vitro according to European Norm / International Organization for Standardization 10,993-5. METHOD: Human osteoblasts (hFOB 1.19) were seeded onto PLA samples produced by FDM and investigated for cell viability by fluorescence staining after 24 h...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28883890/facing-the-challenge-of-sustainable-bioenergy-production-could-halophytes-be-part-of-the-solution
#19
REVIEW
Ahmed Debez, Ikram Belghith, Jan Friesen, Carsten Montzka, Skander Elleuche
Due to steadily growing population and economic transitions in the more populous countries, renewable sources of energy are needed more than ever. Plant biomass as a raw source of bioenergy and biofuel products may meet the demand for sustainable energy; however, such plants typically compete with food crops, which should not be wasted for producing energy and chemicals. Second-generation or advanced biofuels that are based on renewable and non-edible biomass resources are processed to produce cellulosic ethanol, which could be further used for producing energy, but also bio-based chemicals including higher alcohols, organic acids, and bulk chemicals...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28878819/construction-of-an-easy-to-use-crispr-cas9-system-by-patching-a-newly-designed-exit-circuit
#20
Qiang Tang, Chunbo Lou, Shuang-Jiang Liu
BACKGROUND: Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing plasmid elimination methods impedes follow-up genetic manipulation or application. Conventional strategies including exposure to physical and chemical treatments, or exploiting temperature-sensitive replication origins have several drawbacks (e.g., they are limited for efficiency and are time-consuming)...
2017: Journal of Biological Engineering
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