1Application Development, Akonni Biosystems, Inc., 2Manufacturing, Akonni Biosystems, Inc., 3Engineering, Akonni Biosystems, Inc., 4Research & Development, Akonni Biosystems, Inc.
TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. Consequently, the sample preparation format is compatible with most liquid handling instruments, and can be used for many medium to high-throughput clinical applications and sample types.
Published June 11, 2013. Keywords: Genetics, Bioengineering, Biomedical Engineering, Molecular Biology, Automation, Laboratory, Clinical Laboratory Techniques, Molecular Diagnostic Techniques, Analytic Sample Preparation Methods, Clinical Laboratory Techniques, Molecular Diagnostic Techniques, Genetic Techniques, Molecular Diagnostic Techniques, Automation, Laboratory, Chemistry, Clinical, DNA/RNA extraction, automation, nucleic acid isolation, sample preparation, nasopharyngeal aspirate, blood, plasma, high-throughput, sequencing
1Department of Immunology, National Jewish Health, 2Department of Pharmacology, School of Medicine, University of Colorado Denver
The reliability of results in metabolomics experiments depends on the effectiveness and reproducibility of the sample preparation. Described is a rigorous and in-depth method that enables extraction of metabolites from biological fluids with the option of subsequently analyzing up to thousands of compounds, or just the compound classes of interest.
Published July 11, 2014. Keywords: Bioengineering, plasma, chemistry techniques, analytical, solid phase extraction, mass spectrometry, metabolomics, fluids and secretions, profiling, small molecules, lipids, liquid chromatography, liquid-liquid extraction, cerebrospinal fluid, bronchoalveolar lavage fluid
1Bioprocess Engineering, Wageningen University and Research Center, 2AlgaePARC, Wageningen University and Research Center, 3Food and Biobased Research, Wageningen University and Research Center
A method for the determination of fatty acid content and composition in microalgae based on mechanical cell disruption, solvent based lipid extraction, transesterification, and quantification and identification of fatty acids using gas chromatography is described. A tripentadecanoin internal standard is used to compensate for the possible losses during extraction and incomplete transesterification.
Published October 1, 2013. Keywords: Environmental Sciences, chemical analysis techniques, Microalgae, fatty acid, triacylglycerol, lipid, gas chromatography, cell disruption
1Life Sciences Division, Lawrence Berkeley National Laboratory, 2Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 3National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory
The bottleneck for cellular 3D electron microscopy is feature extraction (segmentation) in highly complex 3D density maps. We have developed a set of criteria, which provides guidance regarding which segmentation approach (manual, semi-automated, or automated) is best suited for different data types, thus providing a starting point for effective segmentation.
Published August 13, 2014. Keywords: Bioengineering, 3D electron microscopy, feature extraction, segmentation, image analysis, reconstruction, manual tracing, thresholding
1Department of Chemistry, Union College, 2Department of Mechanical Engineering, Union College
This article describes a rapid supercritical extraction method for fabricating silica aerogels. By utilizing a confined mold and hydraulic hot press, monolithic aerogels can be made in eight hours or less.
Published February 28, 2014. Keywords: Chemistry, Aerogel fabrication, Silica aerogels, Aerogel monoliths, Rapid supercritical extraction, Hot press, Tetramethylorthosilicate (TMOS)
1Materials Engineering Division, Lawrence Livermore National Laboratory, 2UCSF Center for Integrative Neuroscience and the Department of Physiology, University of California, San Francisco
Insertion of flexible neural microelectrode probes is enabled by attaching probes to rigid stiffeners with polyethylene glycol (PEG). A unique assembly process ensures uniform and repeatable attachment. After insertion into tissue, the PEG dissolves and the stiffener is extracted. An in vitro test method evaluates the technique in agarose gel.
Published September 27, 2013. Keywords: Bioengineering, Nervous System Diseases, Surgical Procedures, Operative, Investigative Techniques, Nonmetallic Materials, Engineering (General), neural interfaces, polymer neural probes, surgical insertion, polyethylene glycol, microelectrode arrays, chronic implantation
JoVE Clinical and Translational Medicine
1Africa Centre for Health and Population Studies, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa, 2Unit D11, Jembi Health Systems, 3Academic Medical Center, Department of Global Health, Amsterdam Institute for Global Health and Development (AIGHD), University of Amsterdam, 4Division of Infectious Diseases and Geographic Medicine, Centre for AIDS Research, Stanford Medical School
Drug resistance testing for HIV-1 infected individuals failing antiretroviral therapy (ART) can guide future therapies and improve treatment outcomes. Optimizing individual and population health outcomes in high HIV prevalence but resource-limited settings will ultimately require affordable and accessible drug resistance genotyping and interpretation methods.
Published March 30, 2014. Keywords: Medicine, Biomedical Technology, HIV-1, HIV Infections, Viremia, Nucleic Acids, genetics, antiretroviral therapy, drug resistance, genotyping, affordable
1Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, University of Pennsylvania, 2Department of Pharmacology, University of Pennsylvania
This protocol will demonstrate the extraction and analysis of free and esterified bioactive fatty acids from cells. Fatty acids are accurately quantified using stable isotope dilution, chiral liquid chromatography, electron capture atmospheric chemical ionization multiple reaction monitoring mass spectrometry (SID-LC-ECAPCI-MRM/MS).
Published November 17, 2011. Keywords: Bioengineering, lipids, extraction, stable isotope dilution, chiral chromatography, electron capture, mass spectrometry
JoVE Clinical and Translational Medicine
1Medical School and Stanley S. Scott Cancer Center, LSU Health Sciences Center, 2Department of Biomedical, Surgery and Dental Sciences, University of Milan
We describe a protocol of real time PCR to profile microRNAs in the cerebrospinal fluid (CSF). With the exception of RNA extraction protocols, the procedure can be extended to RNA extracted from other body fluids, cultured cells, or tissue specimens.
Published January 22, 2014. Keywords: Medicine, microRNAs, biomarkers, miRNA profiling, qPCR, cerebrospinal fluid, RNA, DNA
1CUBRC, Inc., 2Department of Microbiology and Immunology, State University of New York at Buffalo, School of Medicine and Biomedical Sciences
A tool and chemistries are described to sequentially isolate nucleic acids followed by proteins from a sample without the need for electricity. The tool consists of a sorbent held within a transfer pipette while the isolation chemistries are based on solid-phase extraction principles. The isolated macromolecules can be analyzed by immuno-based and PCR-based assays.
Published May 15, 2012. Keywords: Chemistry, Solid phase extraction, nucleic acid, protein, isolation, silica, Guanidine thiocyanate, isopropanol, remote, DTRA