323 results match your criteria Journal of Biological Engineering [Journal]


A simple approach for rapid and cost-effective quantification of extracellular vesicles using a fluorescence polarization technique.

J Biol Eng 2019 16;13:31. Epub 2019 Apr 16.

Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029 Republic of Korea.

Extracellular vesicles (EVs) are membrane-bound phospholipid vesicles actively secreted by all cells. As they carry specific markers expressed by their parental cells, EVs are utilized to identify specific cells via liquid biopsy. To facilitate EV-based clinical diagnosis, a fast and reliable method to count EVs is critical. Read More

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http://dx.doi.org/10.1186/s13036-019-0160-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469078PMC

Systematic analysis of the effects of different nitrogen source and ICDH knockout on glycolate synthesis in .

J Biol Eng 2019 4;13:30. Epub 2019 Apr 4.

1National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China.

Background: Glycolate is an important α-hydroxy carboxylic acid widely used in industrial and consumer applications. The production of glycolate from glucose in is generally carried out by glycolysis and glyoxylate shunt pathways, followed by reduction to glycolate. Glycolate accumulation was significantly affected by nitrogen sources and isocitrate dehydrogenase (ICDH), which influenced carbon flux distribution between the tricarboxylic acid (TCA) cycle and the glyoxylate shunt, however, the mechanism was unclear. Read More

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http://dx.doi.org/10.1186/s13036-019-0159-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449901PMC

Three-dimensional microengineered models of human cardiac diseases.

J Biol Eng 2019 3;13:29. Epub 2019 Apr 3.

1School of Biological and Health Systems Engineering (SBHSE), Arizona State University, 501 E Tyler Mall Building ECG, Suite 334, Tempe, AZ 85287-9709 USA.

In vitro three-dimensional (3D) microengineered tissue models have been the recent focus of pathophysiological studies, particularly in the field of cardiovascular research. These models, as classified by 3D biomimetic tissues within micrometer-scale platforms, enable precise environmental control on the molecular- and cellular-levels to elucidate biological mechanisms of disease progression and enhance efficacy of therapeutic research. Microengineered models also incorporate directed stem cell differentiation and genome modification techniques that warrant derivation of patient-specific and genetically-edited human cardiac cells for precise recapitulation of diseased tissues. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-019-0155-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448321PMC
April 2019
1 Read

Microvascular bioengineering: a focus on pericytes.

J Biol Eng 2019 29;13:26. Epub 2019 Mar 29.

Center for Heart and Reparative Medicine, Fralin Biomedical Research Institute, 2 Riverside Circle, Roanoke, VA 24016 USA.

Capillaries within the microcirculation are essential for oxygen delivery and nutrient/waste exchange, among other critical functions. Microvascular bioengineering approaches have sought to recapitulate many key features of these capillary networks, with an increasing appreciation for the necessity of incorporating vascular pericytes. Here, we briefly review established and more recent insights into important aspects of pericyte identification and function within the microvasculature. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-019-0158-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6444752PMC
March 2019
1 Read

Systems metabolic engineering of for the bioproduction of biliverdin via protoporphyrin independent pathway.

J Biol Eng 2019 29;13:28. Epub 2019 Mar 29.

1Department of Biotechnology, Korea University, Seoul, 02841 Republic of Korea.

Background: Biliverdin, a prospective recyclable antioxidant and one of the most important precursors for optogenetics, has received growing attention. Biliverdin is currently produced by oxidation of bilirubin from mammalian bile using chemicals. However, unsustainable procedures of extraction, chemical oxidation, and isomer separation have prompted bio-based production using a microbial cell factory. Read More

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http://dx.doi.org/10.1186/s13036-019-0156-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441180PMC

Analysis of the stability and affinity of BlaR-CTD protein to β-lactam antibiotics based on docking and mutagenesis studies.

J Biol Eng 2019 29;13:27. Epub 2019 Mar 29.

1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China.

Owing to the thermal instability and low affinity of BlaR-CTD to some β-lactams, the receptor assay based on BlaR-CTD is limited in the detection of abundant variety of drugs and the result is often unstable. In this study, the three-dimensional structure of BlaR-CTD from ATCC14580 was constructed by homologous modeling based on the crystal structure of BlaR-CTD from 749/I, and the binding sites of this protein to 40 β-lactams were also obtained by molecular docking. To improve the stability and affinity of the protein, 23 mutant proteins were designed based on docking and homologous alignment results as well as by inserting disulfide bond and building the salt bridge. Read More

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http://dx.doi.org/10.1186/s13036-019-0157-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6441189PMC

Improved expansion of equine cord blood derived mesenchymal stromal cells by using microcarriers in stirred suspension bioreactors.

J Biol Eng 2019 21;13:25. Epub 2019 Mar 21.

1Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4 Canada.

Equine mesenchymal stromal cells (MSCs) are increasingly investigated for their clinical therapeutic utility. Such cell-based treatments can require cell numbers in the millions or billions, with conventional expansion methods using static T-flasks typically inefficient in achieving these cell numbers. Equine cord blood-derived MSCs (eCB-MSCs), are promising cell candidates owing to their capacity for chondrogenic differentiation and immunomodulation. Read More

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http://dx.doi.org/10.1186/s13036-019-0153-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429778PMC

Identification of new glutamate decarboxylases from for efficient production of γ-aminobutyric acid in engineered .

J Biol Eng 2019 21;13:24. Epub 2019 Mar 21.

1Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT 84322-4105 USA.

Background: Gamma (γ)-Aminobutyric acid (GABA) as a bioactive compound is used extensively in functional foods, pharmaceuticals and agro-industry. It can be biosynthesized via decarboxylation of monosodium glutamate (MSG) or L-glutamic acid (L-Glu) by glutamate decarboxylase (GAD; EC4.1. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-019-0154-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6429771PMC
March 2019
3 Reads

Rational protein design of sp. MN chitosanase for altered substrate binding and production of specific chitosan oligomers.

J Biol Eng 2019 12;13:23. Epub 2019 Mar 12.

University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany.

Background: Partially acetylated chito-oligosaccharides (paCOS) have a variety of potential applications in different fields, but to harness their benefits, pure paCOS or well-defined paCOS mixtures are essential. For example, if one could produce fully acetylated (A) and fully deacetylated (D) tetramers in abundance, all possible variants of tetrameric paCOS could be generated reliably from them. A promising approach for generating defined paCOS is by enzymatic depolymerization of chitosan polymers using chitosanases, since these enzymes' subsite specificities directly influence the composition of the paCOS produced; however, enzymatic production of e. Read More

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http://dx.doi.org/10.1186/s13036-019-0152-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419424PMC

Protein-based vehicles for biomimetic RNAi delivery.

J Biol Eng 2019 26;13:19. Epub 2019 Feb 26.

1Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742 USA.

Broad translational success of RNA interference (RNAi) technology depends on the development of effective delivery approaches. To that end, researchers have developed a variety of strategies, including chemical modification of RNA, viral and non-viral transfection approaches, and incorporation with delivery vehicles such as polymer- and lipid-based nanoparticles, engineered and native proteins, extracellular vesicles (EVs), and others. Among these, EVs and protein-based vehicles stand out as biomimetically-inspired approaches, as both proteins (e. Read More

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http://dx.doi.org/10.1186/s13036-018-0130-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6390323PMC
February 2019

Human three-dimensional in vitro model of hepatic zonation to predict zonal hepatotoxicity.

J Biol Eng 2019 6;13:22. Epub 2019 Mar 6.

2Department of Predictive Toxicology, Korea Institute of Toxicology (KIT), Daejeon, 34114 Republic of Korea.

Background: Various hepatic models mimicking liver lobules have been investigated to evaluate the potential hepatotoxic effects of chemicals and drugs, but in vitro hepatic models of zonal hepatotoxicity have not yet been established. Herein, we developed a three-dimensional (3D) hepatic zonal channel to evaluate zone-specific hepatotoxicity. Based on the perivenous zone-3-like cytochrome P450 (CYP) expression patterns in metabolically active HepaRG cells treated with CHIR99021 (CHIR), which is an inducer of Wnt/β-catenin signaling, this culture model represents a novel tool for exploring hepatic zonation. Read More

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http://dx.doi.org/10.1186/s13036-019-0148-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404355PMC
March 2019
1 Read

PAMAM/polyhedral nanogold-modified probes with DNAase catalysis for the amperometric electrochemical detection of metastasis-associated lung adenocarcinoma transcript 1.

J Biol Eng 2019 6;13:21. Epub 2019 Mar 6.

Department of Clinical Laboratory, the Second Affiliated Hospital of the Army Medical University, Chongqing, 400037 China.

Abstract: Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a long non coding RNA (lncRNA) present in serum, is an important biomarker for detecting hepatocellular carcinoma (HCC). However, there are some shortcomings in current detection methods. So developing other novel MALAT1 detection methods is necessary. Read More

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http://dx.doi.org/10.1186/s13036-019-0149-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6404345PMC
March 2019
3 Reads

A frame-shifted gene, which rescued its function by non-natural start codons and its application in constructing synthetic gene circuits.

J Biol Eng 2019 1;13:20. Epub 2019 Mar 1.

Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Block A/F, Sector-I, Bidhannagar, Kolkata, 700064 India.

Background: Frame-shifted genes results in non-functional peptides. Because of this complete loss of function, frame-shifted genes have never been used in constructing synthetic gene circuits.

Results: Here we report that the function of gene circuits is rescued by a frame-shifted gene, which functions by translating from a non-natural start codon. Read More

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http://dx.doi.org/10.1186/s13036-019-0151-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397469PMC

Polymer-based controlled-release fed-batch microtiter plate - diminishing the gap between early process development and production conditions.

J Biol Eng 2019 22;13:18. Epub 2019 Feb 22.

1AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany.

Background: Fed-batch conditions are advantageous for industrial cultivations as they avoid unfavorable phenomena appearing in batch cultivations. Those are for example the formation of overflow metabolites, catabolite repression, oxygen limitation or inhibition due to elevated osmotic concentrations. For both, the early bioprocess development and the optimization of existing bioprocesses, small-scale reaction vessels are applied to ensure high throughput, low costs and prompt results. Read More

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http://dx.doi.org/10.1186/s13036-019-0147-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387502PMC
February 2019

Thematic series on emerging leaders in biological engineering: convergence and new directions.

Authors:
Raj R Rao

J Biol Eng 2019 21;13:17. Epub 2019 Feb 21.

Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR 72701 USA.

Over the past two decades, the biological engineering research community has increased its efforts to promote 'Convergence'. Many research endeavors have thus involved the synergy of multiple perspectives and approaches from originally distinct fields towards driving creative innovative solutions to address many grand challenges that face our society. Here, we introduce the JBE thematic series on emerging leaders in biological engineering. Read More

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http://dx.doi.org/10.1186/s13036-019-0146-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383241PMC
February 2019

Current trends in biomarker discovery and analysis tools for traumatic brain injury.

J Biol Eng 2019 19;13:16. Epub 2019 Feb 19.

2School of Biological and Health Systems Engineering, Ira A. Fulton School of Engineering, Arizona State University, PO Box 879709, Tempe, AZ 85287-9709 USA.

Traumatic brain injury (TBI) affects 1.7 million people in the United States each year, causing lifelong functional deficits in cognition and behavior. The complex pathophysiology of neural injury is a primary barrier to developing sensitive and specific diagnostic tools, which consequentially has a detrimental effect on treatment regimens. Read More

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http://dx.doi.org/10.1186/s13036-019-0145-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381710PMC
February 2019
2 Reads

Inhibition of bacterial toxin recognition of membrane components as an anti-virulence strategy.

J Biol Eng 2019 19;13. Epub 2019 Feb 19.

Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015 USA.

Over recent years, the development of new antibiotics has not kept pace with the rate at which bacteria develop resistance to these drugs. For this reason, many research groups have begun to design and study alternative therapeutics, including molecules to specifically inhibit the virulence of pathogenic bacteria. Because many of these pathogenic bacteria release protein toxins, which cause or exacerbate disease, inhibition of the activity of bacterial toxins is a promising anti-virulence strategy. Read More

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http://dx.doi.org/10.1186/s13036-018-0138-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6380060PMC
February 2019

Modelling cardiac fibrosis using three-dimensional cardiac microtissues derived from human embryonic stem cells.

J Biol Eng 2019 13;13:15. Epub 2019 Feb 13.

1Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 341411 Republic of Korea.

Background: Cardiac fibrosis is the most common pathway of many cardiac diseases. To date, there has been no suitable in vitro cardiac fibrosis model that could sufficiently mimic the complex environment of the human heart. Here, a three-dimensional (3D) cardiac sphere platform of contractile cardiac microtissue, composed of human embryonic stem cell (hESC)-derived cardiomyocytes (CMs) and mesenchymal stem cells (MSCs), is presented to better recapitulate the human heart. Read More

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http://dx.doi.org/10.1186/s13036-019-0139-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375184PMC
February 2019
1 Read

Direct cell reprogramming for tissue engineering and regenerative medicine.

J Biol Eng 2019 13;13:14. Epub 2019 Feb 13.

Department of Bioengineering, Northeastern University, Lake Hall 214A, 360 Huntington Avenue, Boston, MA 02115 USA.

Direct cell reprogramming, also called transdifferentiation, allows for the reprogramming of one somatic cell type directly into another, without the need to transition through an induced pluripotent state. Thus, it is an attractive approach to develop novel tissue engineering applications to treat diseases and injuries where there is a shortage of proliferating cells for tissue repair. In certain tissue damage, terminally differentiated somatic cells lose their ability to proliferate, as a result, damaged tissues cannot heal by themselves. Read More

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http://dx.doi.org/10.1186/s13036-019-0144-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373087PMC
February 2019
5 Reads

A prototype RFID tag for detecting bumblebee visitations within fragmented landscapes.

J Biol Eng 2019 7;13:13. Epub 2019 Feb 7.

1Royal Botanic Gardens, Kew, Surrey, TW9 3AB UK.

Detecting the arbitrary movements of fast-moving insects under field conditions is notoriously difficult because existing technologies are limited by issues of size, weight, range and cost. Here, we establish proof-of-concept for a prototype long-range, passive radio frequency identification (RFID) tagging system for detecting bumblebees and similar sized insects. The prototype tags, weighing 81 mg (49% of mean bee body weight), were flown by bumblebees in a glasshouse and detected at a distance of 1. Read More

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http://dx.doi.org/10.1186/s13036-019-0143-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6367791PMC
February 2019
1 Read

Quest for cardiovascular interventions: precise modeling and 3D printing of heart valves.

J Biol Eng 2019 6;13:12. Epub 2019 Feb 6.

5Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India.

Digitalization of health care practices is substantially manifesting itself as an effective tool to diagnose and rectify complex cardiovascular abnormalities. For cardiovascular abnormalities, precise non-invasive imaging interventions are being used to develop patient specific diagnosis and surgical planning. Concurrently, pre surgical 3D simulation and computational modeling are aiding in the effective surgery and understanding of valve biomechanics, respectively. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-018-0132-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366048PMC
February 2019
8 Reads

Transcriptome-guided target identification of the TetR-like regulator SACE_5754 and engineered overproduction of erythromycin in .

J Biol Eng 2019 24;13:11. Epub 2019 Jan 24.

1School of Life Sciences, Institute of Physical Science and Information Technology, Anhui University, Hefei, 230601 China.

Background: Erythromycin A (Er-A) produced by the actinomycete is an important antibiotic extensively used in human medicine. Dissecting of transcriptional regulators and their target genes associated with erythromycin biosynthesis is crucial to obtain erythromycin overproducer strains through engineering of relevant regulatory elements in .

Results: Here, we identified a TetR family transcriptional regulator (TFR), SACE_5754, negatively controlling erythromycin production. Read More

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http://dx.doi.org/10.1186/s13036-018-0135-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346578PMC
January 2019

Hydrophobins: multifunctional biosurfactants for interface engineering.

J Biol Eng 2019 23;13:10. Epub 2019 Jan 23.

1Department of Biomedical Engineering, University of Virginia, Thornton Hall, P.O. Box 400259, Charlottesville, VA 22904 USA.

Hydrophobins are highly surface-active proteins that have versatile potential as agents for interface engineering. Due to the large and growing number of unique hydrophobin sequences identified, there is growing potential to engineer variants for particular applications using protein engineering and other approaches. Recent applications and advancements in hydrophobin technologies and production strategies are reviewed. Read More

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http://dx.doi.org/10.1186/s13036-018-0136-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343262PMC
January 2019

AFM Imaging Reveals Multiple Conformational States of ADAMTS13.

J Biol Eng 2019 22;13. Epub 2019 Jan 22.

Institute of Biomechanics, School of Biosciences and Bioengineering, South China University of Technology, Guangzhou, 510006 China.

Background: ADAMTS13 (A disintegrin and metalloprotease with a thrombospondin type 1 motif 13) cleaves Von Willebrand factor (VWF) to regulate its size, thereby preventing aberrant platelet aggregation and thrombus. Deficiency of ADAMTS13 caused by either genetic mutations or by inhibitory autoantibodies against ADAMTS13 leads to thrombotic thrombocytopenic purpura (TTP). Recently, ADAMTS13 was reported to adopt a "closed" conformation with lower activity and an "open" one resulting from the engagements of VWF D4-CK domains or antibodies to the distal domains of ADAMTS13, or mutations in its spacer domain. Read More

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http://dx.doi.org/10.1186/s13036-018-0102-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343300PMC
January 2019
2 Reads

Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway.

J Biol Eng 2019 18;13. Epub 2019 Jan 18.

1Department of Bioengineering, Imperial College London, London, UK.

Background: The automation of modular cloning methodologies permits the assembly of many genetic designs. Utilising characterised biological parts aids in the design and redesign of genetic pathways. The characterisation information held on datasheets can be used to determine whether a biological part meets the design requirements. Read More

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http://dx.doi.org/10.1186/s13036-019-0141-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339355PMC
January 2019
1 Read

Nucleic acid delivery to mesenchymal stem cells: a review of nonviral methods and applications.

J Biol Eng 2019 18;13. Epub 2019 Jan 18.

Department of Biological Systems Engineering, University of Nebraska-Lincoln, 231 L.W. Chase Hall, Lincoln, NE 68583-0726 USA.

Background: Mesenchymal stem cells (MSCs) are multipotent stem cells that can be isolated and expanded from many tissues, and are being investigated for use in cell therapies. Though MSC therapies have demonstrated some success, none have been FDA approved for clinical use. MSCs lose stemness decreasing therapeutic potential, and face additional barriers decreasing therapeutic efficacy. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-019-0140-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6339289PMC
January 2019
12 Reads

An injectable sulfonated reversible thermal gel for therapeutic angiogenesis to protect cardiac function after a myocardial infarction.

J Biol Eng 2019 17;13. Epub 2019 Jan 17.

1Department of Bioengineering, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA.

Background: Cardiovascular disease and myocardial infarction are associated with high mortality and morbidity and a more effective treatment remains a major clinical need. The intramyocardial injection of biomaterials has been investigated as a potential treatment for heart failure by providing mechanical support to the myocardium and reducing stress on cardiomyocytes. Another treatment approach that has been explored is therapeutic angiogenesis that requires careful spatiotemporal control of angiogenic drug delivery. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-019-0142-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337754PMC
January 2019
7 Reads

Coatings on mammalian cells: interfacing cells with their environment.

J Biol Eng 2019 17;13. Epub 2019 Jan 17.

Chemical and Materials Engineering, University of Kentucky, 177 FPAT, Lexington, KY 40506-0046 USA.

The research community is intent on harnessing increasingly complex biological building blocks. At present, cells represent a highly functional component for integration into higher order systems. In this review, we discuss the current application space for cellular coating technologies and emphasize the relationship between the target application and coating design. Read More

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http://dx.doi.org/10.1186/s13036-018-0131-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6337841PMC
January 2019
1 Read

Bioengineered models to study tumor dormancy.

J Biol Eng 2019 10;13. Epub 2019 Jan 10.

Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487-0203 USA.

The onset of cancer metastasis is the defining event in cancer progression when the disease is considered lethal. The ability of metastatic cancer cells to stay dormant for extended time periods and reawaken at later stages leading to disease recurrence makes treatment of metastatic disease extremely challenging. The tumor microenvironment plays a critical role in deciding the ultimate fate of tumor cells, yet the mechanisms by which this occurs, including dormancy, is not well understood. Read More

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http://dx.doi.org/10.1186/s13036-018-0137-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327399PMC
January 2019
1 Read

Follicle development as an orchestrated signaling network in a 3D organoid.

J Biol Eng 2019 9;13. Epub 2019 Jan 9.

Department of Biomedical Engineering, University of Michigan, 2126 Lurie Biomedical Engineering, 1101 Beal Avenue, Ann Arbor, MI 48109 USA.

The ovarian follicle is the structural and functional unit of the ovary, composed of the female gamete (the oocyte) and supportive somatic cells. Follicles are not only the source of a female's germ cell supply, but also secrete important hormones necessary for proper endocrine function. Folliculogenesis, the growth and maturation of the follicular unit, is a complex process governed by both intrafollicular crosstalk and pituitary-secreted hormones. Read More

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http://dx.doi.org/10.1186/s13036-018-0134-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6327556PMC
January 2019
5 Reads

The effects of low-dose radiation on articular cartilage: a review.

J Biol Eng 2019 7;13. Epub 2019 Jan 7.

Department of Bioengineering, Clemson University, 301 Rhodes Research Center, Clemson, SC 29634 USA.

Articular cartilage is a specialized connective tissue, predominately composed of water, collagen, and proteoglycans, that provides a smooth, lubricated surface for articulation in joints. It has long been considered radioinsensitive and therefore unaffected by exposure to radiation in medical settings. Due to the increased amount of yearly radiation exposure through radiotherapy and ionizing radiation diagnostic procedures, there has been a renewed interest in how radioinsensitive articular cartilage actually is. Read More

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http://dx.doi.org/10.1186/s13036-018-0125-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322226PMC
January 2019
1 Read

Engineered Models of Tumor Dormancy and Reactivation.

J Biol Eng 2018 27;12:37. Epub 2018 Dec 27.

1Department of Biomedical Engineering, University of Delaware, 150 Academy Street, 161 Colburn Lab, Newark, DE 19716 USA.

Metastatic recurrence is a major hurdle to overcome for successful control of cancer-associated death. Residual tumor cells in the primary site, or disseminated tumor cells in secondary sites, can lie in a dormant state for long time periods, years to decades, before being reactivated into a proliferative growth state. The microenvironmental signals and biological mechanisms that mediate the fate of disseminated cancer cells with respect to cell death, single cell dormancy, tumor mass dormancy and metastatic growth, as well as the factors that induce reactivation, are discussed in this review. Read More

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http://dx.doi.org/10.1186/s13036-018-0120-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307145PMC
December 2018
1 Read

Tissue engineering strategies for the induction of angiogenesis using biomaterials.

J Biol Eng 2018 27;12:36. Epub 2018 Dec 27.

2Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.

Angiogenesis is touted as a fundamental procedure in the regeneration and restoration of different tissues. The induction of de novo blood vessels seems to be vital to yield a successful cell transplantation rate loaded on various scaffolds. Scaffolds are natural or artificial substances that are considered as one of the means for delivering, aligning, maintaining cell connection in a favor of angiogenesis. Read More

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http://dx.doi.org/10.1186/s13036-018-0133-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6307144PMC
December 2018
2 Reads

CD24 identifies nucleus pulposus progenitors/notochordal cells for disc regeneration.

J Biol Eng 2018 22;12:35. Epub 2018 Dec 22.

1Department of Orthopedics, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025 China.

Background: Cell-based therapy by transplantation of nucleus pulposus (NP) progenitor/notochordal cells has been proposed as a promising way to halt and reverse the progression of disc degeneration. Although some studies have provided a broad panel of potential markers associated with the phenotype of notochordal cells, suitability of these markers for isolation of notochordal cells for the treatment of disc degeneration is unclear.

Results: Here, we found that the number of CD24-positive NP cells significantly decreased with increasing severity of disc degeneration. Read More

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http://dx.doi.org/10.1186/s13036-018-0129-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303933PMC
December 2018
4 Reads

Online evaluation of the metabolic activity of on (poly)galacturonic acid.

J Biol Eng 2018 18;12:34. Epub 2018 Dec 18.

1AVT - Biochemical Engineering, RWTH Aachen University, Jochen Büchs, Forckenbeckstr. 51, 52074 Aachen, Germany.

Background: Pectin is a rather complex and highly branched polysaccharide strengthening the plant cell wall. Thus, many different pectinases are required for an efficient microbial conversion of biomass waste streams with a high pectin content like citrus peel, apple pomace or sugar beet pulp. The screening and optimization of strains growing on pectic substrates requires both, quantification of the residual substrate and an accurate determination of the enzymatic activity. Read More

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http://dx.doi.org/10.1186/s13036-018-0128-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299674PMC
December 2018
1 Read

Delivery systems of CRISPR/Cas9-based cancer gene therapy.

J Biol Eng 2018 18;12:33. Epub 2018 Dec 18.

Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale G.B. Morgagni 50 -, 50134 Florence, Italy.

CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) is today one of the most reliable method for gene-editing, supporting previous gene therapies technologies such as TALEN, Meganucleases and ZFNs. There is a growing up number of manuscripts reporting several successful gene-edited cancer cell lines, but the real challenge is to translate this technique to the clinical practice. While treatments for diseases based on a single gene mutation is closer, being possible to target and repair the mutant allele in a selective way generating specific guide RNAs (gRNAs), many steps need to be done to apply CRISPR to face cancer. Read More

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http://dx.doi.org/10.1186/s13036-018-0127-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299643PMC
December 2018
2 Reads

Lymphatic Tissue Engineering and Regeneration.

J Biol Eng 2018 17;12:32. Epub 2018 Dec 17.

1Department of Aerospace and Mechanical Engineering, Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN 46556 USA.

The lymphatic system is a major circulatory system within the body, responsible for the transport of interstitial fluid, waste products, immune cells, and proteins. Compared to other physiological systems, the molecular mechanisms and underlying disease pathology largely remain to be understood which has hindered advancements in therapeutic options for lymphatic disorders. Dysfunction of the lymphatic system is associated with a wide range of disease phenotypes and has also been speculated as a route to rescue healthy phenotypes in areas including cardiovascular disease, metabolic syndrome, and neurological conditions. Read More

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-018-0122-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6296077PMC
December 2018
18 Reads

An electrically-controlled programmable microfluidic concentration waveform generator.

J Biol Eng 2018 14;12:31. Epub 2018 Dec 14.

1Department of Electrical & Computer Engineering, University of California - Davis, Davis, CA 95616 USA.

Background: Biological systems have complicated environmental conditions that vary both spatially and temporally. It becomes necessary to impose time-varying soluble factor concentrations to study such systems, including cellular responses to pharmaceuticals, inflammation with waxing and waning cytokine concentrations, as well as circadian rhythms and their metabolic manifestations. There is therefore a need for platforms that can achieve time-varying concentrations with arbitrary waveforms. Read More

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http://dx.doi.org/10.1186/s13036-018-0126-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295081PMC
December 2018
1 Read

Cell surface engineering and application in cell delivery to heart diseases.

J Biol Eng 2018 4;12:28. Epub 2018 Dec 4.

Division of Cardio-Thoracic Surgery, Department of Surgery, University of Arizona College of Medicine, Room 4302D, 1501 N Campbell Ave, Tucson, Arizona 85724 USA.

Cell-based therapy has expanded its influence in cancer immunotherapy, regenerative medicine, and tissue engineering. Due to their secretory functions, differentiation capabilities, specific homing effects through chemotaxis, distinctive therapeutic potentials, and expandability, cells have become an attractive reagent for advanced therapeutic strategies. Therefore, the ability to modify cells and manipulate their functions according to intended therapeutic designs has been the central scientific interest in the field of biomedical research. Read More

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http://dx.doi.org/10.1186/s13036-018-0123-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6278044PMC
December 2018
2 Reads

Construction and characterization of a synthetic Baculovirus-inducible 39K promoter.

J Biol Eng 2018 4;12:30. Epub 2018 Dec 4.

1State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716 China.

Background: Silkworm genetic engineering is widely used in gene function, silk engineering and disease-resistant engineering in most of Asia. Some of the earliest promoter elements are used to control the development of silkworm transgenic expression and gene therapy. However, the low expression and specificity of natural promoters limit the applications of genetic engineering. Read More

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http://dx.doi.org/10.1186/s13036-018-0121-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280533PMC
December 2018
4 Reads

Imaging retinal melanin: a review of current technologies.

J Biol Eng 2018 4;12:29. Epub 2018 Dec 4.

1Morgridge Institute for Research, Madison, WI USA.

The retinal pigment epithelium (RPE) is essential to the health of the retina and the proper functioning of the photoreceptors. The RPE is rich in melanosomes, which contain the pigment melanin. Changes in RPE pigmentation are seen with normal aging and in diseases such as albinism and age-related macular degeneration. Read More

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http://dx.doi.org/10.1186/s13036-018-0124-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280494PMC
December 2018
1 Read

Laser MICROSAMPLING of soil microbial community.

J Biol Eng 2018 28;12:27. Epub 2018 Nov 28.

Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, 142190, Troitsk, Moscow, Russia.

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https://jbioleng.biomedcentral.com/articles/10.1186/s13036-0
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http://dx.doi.org/10.1186/s13036-018-0117-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6263061PMC
November 2018
13 Reads

In vitro culture expansion impairs chondrogenic differentiation and the therapeutic effect of mesenchymal stem cells by regulating the unfolded protein response.

J Biol Eng 2018 20;12:26. Epub 2018 Nov 20.

4National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064 China.

In vitro expansion of mesenchymal stem cells (MSCs) has been implicated in loss of multipotency, leading to impaired chondrogenic potential and an eventual therapeutic effect, as reported in our previous study. However, the precise regulatory mechanism is still unclear. Here, we demonstrate that endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) were involved in transformation of MSCs induced by in vitro culture based on the comparative profiling of in vitro cultured bone marrow MSCs at passage 3 (P3 BMSCs) vs. Read More

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http://dx.doi.org/10.1186/s13036-018-0119-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6245887PMC
November 2018
2 Reads

Bioconversion of cheese whey permeate into fungal oil by .

J Biol Eng 2018 14;12:25. Epub 2018 Nov 14.

1Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA 95616 USA.

Background: Oleaginous fungi are efficient tools to convert agricultural waste streams into valuable components. The filamentous fungus was cultivated in whey permeate, a byproduct from cheese production, to produce an oil-rich fungal biomass. Response surface methodology was used to optimize the fermentation conditions such as pH and temperature for increased biomass yield and lipid accumulation. Read More

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http://dx.doi.org/10.1186/s13036-018-0116-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237013PMC
November 2018
1 Read

Prevascularization of collagen-glycosaminoglycan scaffolds: stromal vascular fraction versus adipose tissue-derived microvascular fragments.

J Biol Eng 2018 13;12:24. Epub 2018 Nov 13.

1Institute for Clinical & Experimental Surgery, Saarland University, 66421 Homburg/Saar, Germany.

Background: The seeding of scaffolds with the stromal vascular fraction (SVF) of adipose tissue is a common prevascularization strategy in tissue engineering. Alternatively, adipose tissue-derived microvascular fragments (ad-MVF) may serve as vascularization units. In contrast to SVF single cells, they represent a mixture of intact arteriolar, capillary and venular vessel segments. Read More

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http://dx.doi.org/10.1186/s13036-018-0118-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234670PMC
November 2018
3 Reads

The genetic insulator RiboJ increases expression of insulated genes.

J Biol Eng 2018 29;12:23. Epub 2018 Oct 29.

1Department of Biology, Integrated Science Center, The College of William and Mary, 540 Landrum Drive, Williamsburg, VA 23185 USA.

A primary objective of synthetic biology is the construction of genetic circuits with behaviors that can be predicted based on the properties of the constituent genetic parts from which they are built. However a significant issue in the construction of synthetic genetic circuits is a phenomenon known as context dependence in which the behavior of a given part changes depending on the choice of adjacent or nearby parts. Interactions between parts compromise the modularity of the circuit, impeding the implementation of predictable genetic constructs. Read More

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http://dx.doi.org/10.1186/s13036-018-0115-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206723PMC
October 2018
2 Reads

Optimization of fermentation conditions for an strain engineered using the response surface method to produce a novel therapeutic DNA vaccine for rheumatoid arthritis.

J Biol Eng 2018 10;12:22. Epub 2018 Oct 10.

Department of Immunology and National Center for Biomedicine Analysis, Beijing 307 Hospital, No.8, Dongda Ave, Fengtai District, Beijing, 100071 People's Republic of China.

Background: Fermentation condition optimization and nutrients screening are of equal importance for efficient production of plasmid DNA vaccines. This directly affects the downstream purification and final quality and yield of plasmid DNA vaccines. The present study aimed to optimize the fermentation conditions for high-throughput production of therapeutic DNA vaccine pcDNA-CCOL2A1 by engineered DH5α, using the response surface method (RSM). Read More

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http://dx.doi.org/10.1186/s13036-018-0110-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180442PMC
October 2018
13 Reads

Collagen and fibronectin surface modification of nanoporous anodic alumina and macroporous silicon for endothelial cell cultures.

J Biol Eng 2018 1;12:21. Epub 2018 Oct 1.

1Departament d'Enginyeria Electrònica, Elèctrica i Automàtica, Universitat Rovira i Virgili, Països Catalans 26, 43007 Tarragona, Spain.

Background: The ability to direct the cellular response by means of biomaterial surface topography is important for biomedical applications. Substrate surface topography has been shown to be an effective cue for the regulation of cellular response. Here, the response of human aortic endothelial cells to nanoporous anodic alumina and macroporous silicon with collagen and fibronectin functionalization has been studied. Read More

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http://dx.doi.org/10.1186/s13036-018-0111-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6166296PMC
October 2018
1 Read

Native-mimicking in vitro microenvironment: an elusive and seductive future for tumor modeling and tissue engineering.

J Biol Eng 2018 12;12:20. Epub 2018 Sep 12.

Department of Biomedical Sciences, Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99210 USA.

Human connective tissues are complex physiological microenvironments favorable for optimal survival, function, growth, proliferation, differentiation, migration, and death of tissue cells. Mimicking native tissue microenvironment using various three-dimensional (3D) tissue culture systems in vitro has been explored for decades, with great advances being achieved recently at material, design and application levels. These achievements are based on improved understandings about the functionalities of various tissue cells, the biocompatibility and biodegradability of scaffolding materials, the biologically functional factors within native tissues, and the pathophysiological conditions of native tissue microenvironments. Read More

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http://dx.doi.org/10.1186/s13036-018-0114-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6136168PMC
September 2018
1 Read
1 Citation

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes.

J Biol Eng 2018 12;12:19. Epub 2018 Sep 12.

Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, 1304 W. Pennsylvania, Urbana, 61801 USA.

Background: Flow cytometry, with its high throughput nature, combined with the ability to measure an increasing number of cell parameters at once can surpass the throughput of prevalent genomic and metagenomic approaches in the study of microbiomes. Novel computational approaches to analyze flow cytometry data will result in greater insights and actionability as compared to traditional tools used in the analysis of microbiomes. This paper is a demonstration of the fruitfulness of machine learning in analyzing microbial flow cytometry data generated in anaerobic microbiome perturbation experiments. Read More

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http://dx.doi.org/10.1186/s13036-018-0112-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134764PMC
September 2018
11 Reads