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Authors: Yongbo Cui
Summary: Provide a modified Bradford method to determine the residual protein content in the bio-synthesis product. The product may be obtained from enzymatic reaction and extract from organic solvent, and /or insoluble in water.
Proper citation: Yongbo Cui 2017. modified Bradford procedure for residual protein testing in enzyme catalysis synthesis products. protocols.io dx.doi.org/10.17504/protocols.io.k4kcyuw Copy
Authors: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber
Group: Human Cell Atlas Method Development Community, Coronavirus Method Development Community
Summary: This protocol describes the isolation of lymphocytes and pan-mononuclear cells from human whole blood for scRNAseq analysis.
Proper citation: Peter Szabo, Steven Wells, Peter A. Sims, Donna Farber 2020. COVID Blood Processing for scRNAseq. protocols.io dx.doi.org/10.17504/protocols.io.bjm6kk9e Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: This experiment measures blood or plasma glucose concentration using Analox GM9 Glucose Analyzer or GM7 Micro-Stat Rapid Multi-assay Analyzer. The measurement is based on the rate of oxygen uptake in the reaction between sample glucose and glucose oxidase. Plasma glucose levels are elevated (i.e., hyperglycemia) in obesity, insulin resistance, and type 2 diabetes.
Proper citation: Jason Kim 2019. U Mass - Glucose. protocols.io dx.doi.org/10.17504/protocols.io.xw5fpg6 Copy
Authors: Jacob Marsh, Rj Martinez, Celeste Karch
Group: Neurodegeneration Method Development Community
Proper citation: Jacob Marsh, Rj Martinez, Celeste Karch 2020. Thawing, Expanding, and Freezing Human Fibroblasts. protocols.io dx.doi.org/10.17504/protocols.io.bgunjwve Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Proper citation: Allen Institute for Brain Science 2020. PCR Prep from cDNA for IVT Reactions. protocols.io dx.doi.org/10.17504/protocols.io.bdpni5me Copy
Authors: Cibrián Angelica, Sánchez Miguel, García Sara, Pérez Eduardo, Bernal German, Castañon Migel, Jiménez Laura, Toledano Cairo
Summary: The third report of the National Cholesterol Education Program guidelines recommend calculating the 10-year morbidity of atherosclerotic cardiovascular disease using risk calculators when treating high blood cholesterol in adults. We analyzed the changes in cardiovascular risk (CVR) among patients with human immunodeficiency virus (HIV) from México.Materials and MethodsThis observational, prospective cohort study compared the cardiovascular risk after one year of usual treatment among 460 HIV patients in México. Changes using the atherosclerotic cardiovascular disease risk estimator and changes in clinical outcomes were analyzed. The results were categorized as low or high CVR using a cut-off of 7.5%.The cardiovascular risk at baseline showed a mean of 4.45% ± 6.1% (0.2% to 50.1%), which changed to 4.48% ± 5.4% (0.2% to 33.2one year later . After cardiovascular risk stratification at baseline, we found that 84.3% of patients had a low CVR, and 18% of this group had metabolic syndrome. Moreover, 15.7% of this population was at high cardiovascular risk and 47% had metabolic syndrome. Approximately 4.3% of patients had a CVR increase and 2.6% had a cardiovascular risk decrease. Of the total patients, 22.3% had metabolic syndrome at baseline.
Proper citation: Cibrián Angelica, Sánchez Miguel, García Sara, Pérez Eduardo, Bernal German, Castañon Migel, Jiménez Laura, Toledano Cairo 2017. Changes in cardiovascular risk and clinical outcomes in a HIV/AIDS cohort study over a one-year period at a specialized clinic in Mexico. protocols.io dx.doi.org/10.17504/protocols.io.mcqc2vw Copy
Authors: Yuan Yao
Proper citation: Yuan Yao 2018. Expression and purification of protein. protocols.io dx.doi.org/10.17504/protocols.io.qaadsae Copy
Authors: Rosa Leon
Group: Leon Zayas Lab
Summary: This protocol series will guide students through the experience of analyzing metagenomic data.
Proper citation: Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io dx.doi.org/10.17504/protocols.io.nnuddew Copy
Authors: J Jobu Babin, Haritima Chauhan, Feng Liu
Summary: Workers in online labor markets routinely misrepresent the value of effort, both through shirking and misreporting performance. We execute a field experiment on Amazon MTurk to determine whether honesty oaths impact the cost of worker lies. Employing a design that follows the “die roll” paradigm, we determine that oaths elicit more truthful behavior, although they primarily impact extreme lies. Oath-taking decreased the cost of misreportingby 12%. While shirking is widespread, oaths marginally decrease it. Male workers misreport performance more often on average than females, yet both sexes are equally responsive to oath-taking.JEL Codes: D90, D91, C8, C93, J9
Proper citation: J Jobu Babin, Haritima Chauhan, Feng Liu 2020. Clever Pennies: Honesty Oaths, Misreporting Performance, and MTurk. protocols.io dx.doi.org/10.17504/protocols.io.bix7kfrn Copy
Authors: James Fraser
Group: Fraser Lab
Proper citation: James Fraser 2015. BL21 Electrocompetent Prep. protocols.io dx.doi.org/10.17504/protocols.io.dim4c5 Copy
Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: This collection contains protocols that explains how to use serial dilutions of sample protein to determine the linear ranges of detection for a target and internal loading control, and choose an appropriate amount of sample to load for QWB analysis.
Proper citation: LI-COR Biosciences 2017. Protocols for Determining the Linear Range for Quantitative Western Blot Detection. protocols.io dx.doi.org/10.17504/protocols.io.g78bzrw Copy
Authors: Patrick Tso, Dana Lee
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:
Food Intake Monitoring - Oxymax/CLAMS monitors the cumulative amount of food eaten as well as the amount eaten in each bout with the use of a Mettler Toledo balance with a resolution of 0.01g. Feeders are designed to account for spillage of food and to prevent foraging, a combination which provides the most accurate food intake monitor on the market.
Food Access Control - Access to food can be placed under automatic computerized control. A pneumatic driven shield prevents access to the food, and can be controlled by times intervals and/or by mass of food. Additionally, this option also includes paradigms for Yolked or Paired feeding.
Center Feeder Cages: The Center Feeder Cage maintains the same sealed environment but adds a feeder to the center of the cage to allow food intake measurements. The Center Feeder is the most popular and universal in application, supporting all subject body types from lean to obese. An adjustable food guard allows mechanical fine tuning of food access to minimize foraging.
Proper citation: Patrick Tso, Dana Lee 2019. U Cinn - Meal Pattern Analysis Food Intake Procedure. protocols.io dx.doi.org/10.17504/protocols.io.xjqfkmw Copy
Authors: Anna Behle
Group: Axmann Lab, CyanoWorld, Roscoff Culture Collection, iGEM Duesseldorf 2018
Summary: Stanier RY, Deruelles J, Rippka R, Herdman M, Waterbury JB: Generic Assignments, Strain Histories and Properties of Pure Cultures of Cyanobacteria. Microbiology 1979, 111:1–61.Recipes for standard and alternative BG11 for culturing freshwater cyanobacteria, such as Synechocystis sp. PCC 6803, as described.Media is usually not suitable for marine cyanobacteria.
Proper citation: Anna Behle 2018. Recipe for standard BG-11 media. protocols.io dx.doi.org/10.17504/protocols.io.mmvc466 Copy
Authors: George Carnell, Fabrizio Biuso, Emanuele Montomoli, Nigel Temperton
Summary: Lentiviral vectors pseudotyped with influenza surface glycoproteins represent an alternative to wild type virus for serological assays. The influenza neuraminidase (NA) has the ability to bud and release new virions with or without the contribution of Haemagglutinin (HA). Influenza pseudotypes expressing NA alone, or with HA, can be produced to evaluate the antibody response against NA using an enzyme-linked lectin assay (ELLA). The expression of an avian HA with human NAs has enabled the detection of specific antibody reponses against the human circulating subtypes of NA. This protocol describes the efficient production of NA pseudotypes for these ELLA assays. The pseudotypes have H11 HA on the surface as this will not react with human sera.Figure 1. Cartoon schematic of lentiviral vectors pseudotyped with NA or HA+NA for use in ELLA assays.
Proper citation: George Carnell, Fabrizio Biuso, Emanuele Montomoli, Nigel Temperton 2018. Production of lentiviral vectors pseudotyped with influenza neuraminidase (NA). protocols.io dx.doi.org/10.17504/protocols.io.rkkd4uw Copy
Authors: Ariana Hirsh
Group: Innovative Genomics Institute
Proper citation: Ariana Hirsh 2017. Cas9 Expression and Purification Protocol. protocols.io dx.doi.org/10.17504/protocols.io.hagb2bw Copy
Authors: Karen Maciel de Oliveira
Summary: Lipid peroxidation (LP) is determined by quantifying the malondialdehyde (MDA) content in the homogenate supernatant in the caudal adjacent segment to epicenter by colorimetric reaction with thiobarbituric acid (TBA) at high temperatures. Malondialdehyde is the principal and most studied product of polyunsaturated fatty acid peroxidation.
Proper citation: Karen Maciel de Oliveira 2018. Lipid peroxidation assessment. protocols.io dx.doi.org/10.17504/protocols.io.rujd6un Copy
Authors: Kenneth Schackart, Kattika Kaarj
Group: 481b Laboratory
Summary: This protocol details how to use ImageJ software to create a composite image from fluorescence images taken with a microscope.
Proper citation: Kenneth Schackart, Kattika Kaarj 2019. ImageJ Fluorescence Image Composition. protocols.io dx.doi.org/10.17504/protocols.io.yc8fszw Copy
Authors: Alba Balletbó
Group: iGEM Wageningen 2019
Summary: Gel purification allows you to isolate and purify DNA fragments based on size. The procedure starts with standard agarose gel electrophoresis, which separates DNA by their length in base pairs. Following electrophoresis, you can cut DNA bands out of the agarose gel and purify the DNA samples.
Proper citation: Alba Balletbó 2019. DNA Purification from an Agarose Gel (Protocol for NucleoSpin® PCR clean-up Gel Extraction Kit). protocols.io dx.doi.org/10.17504/protocols.io.7hrhj56 Copy
Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: Separation of Human Neutrophils (PMN) from Buffy Coat: list of published papers using this protocol- Boydum A.Isolation of mononuclear cells and granulocytes from human blood. Scand.J.Clin.Lab. Invest. 21 (Suppl.97): 77-89, 1968- Alex Mabou Tagne, Franca Marino, Massimiliano Legnaro, Alessandra Luini, Barbara Pacchetti and Marco Cosentino. A Novel Standardized Cannabis sativa L. Extract and Its Constituent Cannabidiol Inhibit Human Polymorphonuclear Leukocyte Functions. Int J Mol Sci2019 Apr; 20(8): 1833. Published online 2019 Apr 13. doi: 10.3390/ijms20081833.- Angela Scanzano, Laura Schembri, Emanuela Rasini, Alessandra Luini, Jessica Dallatorre, Massimiliano Legnaro, Raffaella Bombelli, Terenzio Congiu, Marco Cosentino, Franca Marino. Adrenergic Modulation of Migration, CD11b and CD18 Expression, ROS and interleukin-8 Production by Human Polymorphonuclear Leukocytes. Inflamm Res. 2015 Feb;64(2):127-35. doi: 10.1007/s00011-014-0791-8. Epub 2015 Jan 6.
Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. PMN- 01a - Isolation of Human PMN from Buffy Coat. protocols.io dx.doi.org/10.17504/protocols.io.bpxxmppn Copy
Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is a generic PNGase F protocol with denaturing reaction conditions. It is appropriate for both P0704 and P0708.
Proper citation: New England Biolabs 2015. PNGase F Protocol, Denaturing Conditions. protocols.io dx.doi.org/10.17504/protocols.io.cqfvtm Copy
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