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Authors: Ekaterina Pokrant, Francisca Medina, Aldo Maddaleno, Betty San Martin, Javiera Cornejo
Summary: Analytical methodology for the detection of sulfachloropyridazine (SCP) in samples of feathers via LC-MS/MS was implemented based on techniques previously published by other authors:
1- Hindle R. A validated atmospheric pressure chemical ionization method for analysing sulphonamides in pork muscle. 2013. Available at http://www.youngin.com/application/0411-0045EN-E.pdf. Accessed October 12, 2017.
2- Renew JE, Huang CH. Simultaneous determination of fluoroquinolone, sulfonamide, and trimethoprim antibiotics in wastewater using tandem solid phase extraction and liquid chromatography–electrospray mass spectrometry. J Chromatogr A 2004; 1042: 113-21.
3- Shao B, Dong D, Wu y, Hu J, Meng J, Tu X, Xu S. Simultaneous determination of 17 Sulfonamide residues in porcine meat, kidney and liver by solid phase extraction and liquid chromatography-tandem mass spectrometry. Anal Chim Acta 2005; 546:174-81.
4- Pang G, Cao YZ, Zhang JJ, Jia GQ, Fan CL, Li XM, Liu YM, Li ZY, Shi YQ. Determination of sulfonamides in honey by liquid chromatography- tandem mass spectrometry. J AOAC Int 2005; 88:1304-11.
5- Stubbings G, Bigwood T. The development and validation of a multi-class liquid chromatography tandem mass spectrometry (LC– MS/MS) procedure for the determination of veterinary drug residues in animal tissue using a QuEChERS (QUick, Easy, CHeap, Effective, Rugged and Safe) approach. Anal Chim Acta 2009; 637:68-78.
6- Bedendo GC, Jardim IC, Carasek E. A simple hollow fiber renewal liquid membrane extraction method for analysis of sulphonamides in honey samples with determination by liquid chromatography-tandem mass spectrometry. J Chromatogr A 2010; 1217:6449-54.
7- Yu H, Tao Y, Chen D, Wang Y, Huang L, Peng D, et al. Development of a high-performance liquid chromatography method and a liquid chromatography-tandem mass spectrometry method with the pressurized liquid extraction for the quantification and confirmation of sulphonamides in the foods of animal origin. J Chromatogr B 2011; 879:2653-62.
The method is based mainly on a solid-liquid extraction with organic solvents. The analyte was concentrated using a water bath at 40-50°C under a mild nitrogen flow. For the instrumental analysis, a Symmetry C8 analytical column of 3.5μm and 2.1 x 100mm (Waters®) was fitted in an Agilent 1290 infinity series liquid-chromatograph equipment, coupled to an API 3200 (AB Sciex, Darmstadt, Germany) triple-quadrupole mass-spectrometer. The analytical data was then integrated using the Analyst® version 1.5 software package (SCIEX, Framingham, Massachusetts).
Proper citation: Ekaterina Pokrant, Francisca Medina, Aldo Maddaleno, Betty San Martin, Javiera Cornejo 2018. Chemical extraction of sulfachloropyridazine from muscle samples. protocols.io dx.doi.org/10.17504/protocols.io.pvcdn2w Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. Th2 lymphocytes synthesize IL-19 and acts on resident vascular cells in addition to immune cells. It is an anti-inflammatory molecule. It promotes immune responses mediated by regulatory lymphocytes and has substantial activity on microvascular.[1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.
Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-19 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj3jkqkn Copy
Authors: Serena Ding
Group: Behavioural Genomics
Summary: For imaging swarming behaviour of 40 young adult C. elegans on agar using the Phoenix multi-worm tracker system. Worms are synchronised by bleaching and refeeding for 72 hours, and then 40 young adult hermaphrodites are transferred by glass pipette onto a 35 mm regular NGM plate for imaging for 7 hours at 25 fps.
Proper citation: Serena Ding 2019. bright field standard swarming imaging. protocols.io dx.doi.org/10.17504/protocols.io.vybe7sn Copy
Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:This experiment provides the quantification of multiple hormones using multiplexed-Luminex technology based on beads containing specific antibodies. Sample matrices include plasma, serum, tissue culture supernatants, and tissue or cell lysates. Serum C-peptide levels reflect insulin secretion and pancreatic -cell function. Serum C-peptide levels are altered in obesity, insulin resistance, and type 1 and type 2 diabetes.
Proper citation: Jason Kim 2019. U Mass - C-Peptide. protocols.io dx.doi.org/10.17504/protocols.io.xttfnnn Copy
Authors: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
Group: Neurodegeneration Method Development Community
Summary: Live imaging permits visualization of molecular and organellar dynamics within the neuron. While a standard confocal microscope is sufficient for short imaging experiments, extended imaging applications (>1 hr) are best served by a 37 °C live imaging chamber outfitted onto the microscope. CM should also be changed to Hibernate A Low Fluorescence Medium (BrainBits LLC, cat. no. SKU#HAPR) for extended imaging.
Proper citation: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward 2019. LIVE IMAGING OF i3NEURONS (Support Protocol 5) . protocols.io dx.doi.org/10.17504/protocols.io.5w7g7hn Copy
Authors: Timothy Nichols, David Clemmons
Group: Diabetic Complications Consortium
Summary: This assay is used by the DiaComp to measure glucose tolerance and insulin sensitivity in pigs.Diabetic Complications:Reference:1. Bergman RN, Finegood DT, Ader M: Assessment of insulin sensitivity in vivo. Endocr Rev 1985, 6:45-86.
Proper citation: Timothy Nichols, David Clemmons 2019. Frequently sampled Insulin glucose tolerance test. protocols.io dx.doi.org/10.17504/protocols.io.8e8hthw Copy
Authors: John Hickey
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: See our detailed protocol published with the following title: CODEX multiplexed tissue imaging with DNA-conjugated antibodies.
Proper citation: John Hickey 2021. Imaging - Stanford TMC. protocols.io dx.doi.org/10.17504/protocols.io.be8qjhvw Copy
Authors: Elizabeth Allen
Summary: This protocol is used to stain late larval Drosophila lipid droplets in fat bodies and intestines with Nile Red, which emits fluorescence in the 552/636 nm range.
Proper citation: Elizabeth Allen 2019. Nile Red Staining of Drosophila Larval Tissues. protocols.io dx.doi.org/10.17504/protocols.io.5x7g7rn Copy
Authors: Franchesca Farris, Maigan Brusko
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This protocol is for the generation of 3' (chemistry version 3) cDNA libraries from individual cells via droplet generation utilizing the 10x Genomics Chromium Controller and associated reagents. Paired end libraries are then sequenced on Illumina instruments.
Proper citation: Franchesca Farris, Maigan Brusko 2020. HuBMAP UF TMC - Single Cell RNA Seq (10x Genomics) Library Preparation and Sequencing . protocols.io dx.doi.org/10.17504/protocols.io.bffvjjn6 Copy
Authors: Jon Eilers
Summary: This is a protocol for sea cucumber gonad removal without killing the sea cucumber or causing evisceration.
Proper citation: Jon Eilers 2019. Surgical Removal of Sea Cucumber Gonads. protocols.io dx.doi.org/10.17504/protocols.io.5pag5ie Copy
Authors: Marijn Ceelen
Group: iGEM Wageningen 2019
Summary: This protocol explains how to use the Abor BiosciencesSigma 70 TXTL mix to produce bacteriophages. This protocol works for bacteriophage T7. It has been tested on phage lambda. However, it seems that the current protocol does not work for phage lambda.
Proper citation: Marijn Ceelen 2019. TXTL phage production. protocols.io dx.doi.org/10.17504/protocols.io.77thrnn Copy
Authors: Andrea Argouarch
Group: Neurodegeneration Method Development Community
Summary: Protocols included in this collection describe cell isolation from human dura mater, culturing, and banking.
Proper citation: Andrea Argouarch 2020. Dural Cell Isolation and Culturing - Collection. protocols.io dx.doi.org/10.17504/protocols.io.8m2hu8e Copy
Authors: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder
Group: VERVE Net
Summary: The viral concentrate used for PFGE analysis must be molded into plugs, followed by lysis of the virus particles to release their DNA. It is possible to run solution-based preparation of viral DNA for PFGE (Steward 2001); however, large DNA molecules (>100 kb) are extremely sensitive to mechanical shearing in aqueous solution (Bouchez and Camilleri 1997). The consensus is that lysis inside viral plugs prevents mechanical shearing of the DNA, resulting in more discrete PFGE bands. Intact viral genomes are then separated by size by PFGE. After separation, the banding pattern is visualized by staining with a fluorescent DNA stain. This banding pattern provides a visual record of the genome size distribution that can be used for qualitative and quantitative comparisons between samples.
Proper citation: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Fingerprinting aquatic virus communities using pulsed field gel electrophoresis (PFGE). protocols.io dx.doi.org/10.17504/protocols.io.dy27yd Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare Phosphate Buffered Saline (PBS). PBS (-) and PBS (+) which includes Tween are used as biologically neutral wash solutions in many processes including In Situ Hybridization (ISH), Immunohistochemistry (IHC) and Fixation.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. Phosphate Buffered Saline (PBS). protocols.io dx.doi.org/10.17504/protocols.io.bezgjf3w Copy
Authors: Roey Angel, Eva Petrova, Ana Lara
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: Universal 16S rRNA probe-based-qPCR assay for bacteria.The primers and probe are taken from Yu et al. (2005).
Proper citation: Roey Angel, Eva Petrova, Ana Lara 2020. qPCR: Bacterial SSU rRNA 338F-516P-805R. protocols.io dx.doi.org/10.17504/protocols.io.bqx5mxq6 Copy
Authors: Diep Ganguly, Asmini Athman
Group: Pogson Genomics Group
Summary: Method for visualizing cell-localized gene expression patterns.Adapted from: Athman, A., Tanz, S.K., Conn, V.M., Jordans, C., Mayo, G.M., Ng, W.W., Burton, R.A., Conn, S.J., and Gilliham, M. (2014). Protocol: a fast and simple in situ PCR method for localising gene expression in plant tissue. Plant Methods 10: 29.Also, for more information on epidermal peels: Chen, Z.-H., Eisenach, C., Xu, X.-Q., Hills, A., and Blatt, M.R. (2012). Protocol: optimised electrophyiological analysis of intact guard cells from Arabidopsis. Plant Methods 8: 15.
Proper citation: Diep Ganguly, Asmini Athman 2019. In situ PCR using leaf epidermal peels. protocols.io dx.doi.org/10.17504/protocols.io.p85dry6 Copy
Authors: Alice Lee
Group: Whiteson Lab - Phage Team
Summary: Bacteriophages (phage) are viruses that infect bacteria and can be found anywhere that bacteria is found. Performing plaque assays is a technique to purify a population of viruses and can also be used to determine the viral concentration of a given sample. This protocol will outline the steps to carry out plaque assays.
Proper citation: Alice Lee 2020. Plaque Assay. protocols.io dx.doi.org/10.17504/protocols.io.be6sjhee Copy
Authors: Souza TKF, Nucci MP, Mamani JB, Silva HR, Fantacini DMC, Souza LEB, Picanço-Castro V, Covas DT, Vidoto EL, Tannús A, Gamarra LF
Group: Nanobiotecnholgy
Proper citation: Souza TKF, Nucci MP, Mamani JB, Silva HR, Fantacini DMC, Souza LEB, Picanço-Castro V, Covas DT, Vidoto EL, Tannús A, Gamarra LF 2018. Image and behavior analysis in C6 glioma model. protocols.io dx.doi.org/10.17504/protocols.io.p4hdqt6 Copy
Authors: Paul Whaley
Group: Systematic Reviews
Summary: A protocol template to help researchers follow the COSTER recommendations for conduct of systematic reviews. This instance covers the planning steps of a systematic review and will help with writing up the systematic review protocol.The intent is to convert COSTER from a checklist of things which need to be done into a sequence of actions which can be followed by a research team.When completing the protocol and either registering it or submitting it to a journal, please cite this instance of the protocol template and the parent manuscript, DOI 10.1016/j.envint.2020.105926.
Proper citation: Paul Whaley 2020. Generic Protocol for Environmental Health Systematic Reviews Based on COSTER Recommendations. protocols.io dx.doi.org/10.17504/protocols.io.biktkcwn Copy
Authors: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko
Group: Human Cell Atlas Method Development Community
Summary: Protocol for extraction of nuclei from frozen tissue in preparation for single-nuclei sequencing (droplet-based/10X). This protocol is based strongly on a similar extraction protocol from the McCarroll lab.
Proper citation: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko 2019. Frozen Tissue Nuclei Extraction (v2). protocols.io dx.doi.org/10.17504/protocols.io.7xchpiw Copy
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