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Authors: Nichola Calvani

Proper citation: Nichola Calvani 2017. Fasciola spp. faecal sedimentation protocol for concentration of eggs and DNA isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.jw9cph6 Copy   

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Authors: New England Biolabs
Summary: This protocol defines methods for the Q5® Site-Directed Mutagenesis Kit without competent cells.

Proper citation: New England Biolabs 2020. Q5® Site-Directed Mutagenesis (E0552). protocols.io https://dx.doi.org/10.17504/protocols.io.beurjev6 Copy   

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Authors: Shiqi Xie, Anne Cooley, Gary Hon

Proper citation: Shiqi Xie, Anne Cooley, Gary Hon 2018. Preparation of the sgRNA-Barcode Amplicon Library. protocols.io https://dx.doi.org/10.17504/protocols.io.pufdntn Copy   

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Authors: Zeljka Smit-Mcbride
Summary: Sample collection, isolation of miRNAs, and quality control Aqueous and vitreous humor, as well as plasma samples, have been collected from Diabetes mellitus (DM) and control patients during the standard-of-the-care eye surgery. Samples of 100-200ul were collected, aliquoted in 100ul aliquots, frozen on dry ice immediately and stored at -80oC. RNA was isolated using Exiqons’ modification of Qiagen’s microRNeasy kit. Quantification and quality check of isolated miRNAs was performed on BioAnalyzer (Agilent) with Small RNA microfluidics Chips. Affymetrix microarray probe labelingProbe labeling was done from 10 ng of aqueous, 20ng of vitreous and 20ng of plasma miRNA samples from a total of 24 aqueous, 24 vitreous and 25 plasma samples using FlashTag (Affymetrix) procedure. Labeled probes were hybridized to Affymetrix miRNA Array 3.0 in UC Davis Genome Center Microarray Core Facility using the standard procedure (Affymetrix, Santa Clara, CA). The total data set included 73 Affymetrix miRNA 3.0 microarrays. Upon scanning of the hybridized and washed Chips, data was obtained in a set of Affymetrix data files (.cel, .arr, .jpg).

Proper citation: Zeljka Smit-Mcbride 2020. MicroRNA Affymetrix microarray probe labeling from ocular fluids. protocols.io https://dx.doi.org/10.17504/protocols.io.bc7pizmn Copy   

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Authors: Fang Liu, Yuanjun Yang, Jianwei Gao, Changle Ma, Yuping Bi
Summary: This is a protocol for extraction and purification of anthocyanin from potato.

Proper citation: Fang Liu, Yuanjun Yang, Jianwei Gao, Changle Ma, Yuping Bi 2018. Extraction and Purification of Anthocyanin from Potato. protocols.io https://dx.doi.org/10.17504/protocols.io.ma4c2gw Copy   

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Authors: Lluvia Vargas-Gastélum, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme
Group: Marine Fungi, Riquelme CICESE
Summary: The study of fungi in marine sediments has received a growing attention in the recent years. Recent advances in metagenomics have allowed the discovery of a wide diversity of fungi in deep-sea environments, although standardized methods are needed to process the samples and to analyze the data. This protocol is a guidance to obtain good quality samples and subsequent ITS1 (Internal Transcribed Spacer 1) amplicons to be prepared for sequencing by Illumina platform. The collection of marine sediments is described, as well as the processing of the samples in laboratory; also, pertinent controls that should be included during all the processing steps to identify potential sources of contamination that could affect the sequencing and bias the interpretation of results are suggested.

Proper citation: Lluvia Vargas-Gastélum, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme 2019. Illumina metabarcoding protocol for the study of fungi in marine sediments. protocols.io https://dx.doi.org/10.17504/protocols.io.yupfwvn Copy   

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Authors: G-Biosciences
Group: G-Biosciences
Summary: This is a collection of protocols for high quality genomic DNA extraction using the OmniPrep™ kit. Please refer to the appropriate protocol below depending on your application.

Proper citation: G-Biosciences 2016. OmniPrep™ Protocol Collection for High Quality Genomic DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.e7rbhm6 Copy   

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Authors: Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million
Group: SPARC
Summary: This protocol describes a process for the measurement of acute electrical stimulation-induced effects on colonic motility in anesthetized young adult Yucatan minipigs. Signals recorded from manometry probes inserted into the proximal, transverse and distal colonic regions were used to measure the effect of stimulation by serosally placed electrodes opposed to the colonic tissue at multiple sites in an acute anesthetized preparation. The effect of stimulation was quantified as motility index assessments before, during and after stimulation, and the data was used to create a functional map of colonic motor response to localized colon stimulation.

Proper citation: Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million 2020. Tache_Mulugeta_OT2OD024899_Colon tissue electrical stimulation and colonic motility measurements. protocols.io https://dx.doi.org/10.17504/protocols.io.3rmgm46 Copy   

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Authors: Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro
Group: Ribeiro Lab
Summary: This is a protocol to generate axenic fly cultures by sterilizing embryos. It is part of the manuscript: Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr 18.The protocol was adapted from:Wayland MT, Defaye A, Rocha J, Jayaram SA, Royet J, Miguel-Aliaga I, et al. Spotting the differences: Probing host/microbiota interactions with a dedicated software tool for the analysis of faecal outputs in Drosophila. J Insect Physiol. 2014;69: 126–135. doi:10.1016/j.jinsphys.2014.05.023with the help of the Leulier laboratory.

Proper citation: Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro 2017. Generating and Rearing Axenic Drosophila. protocols.io https://dx.doi.org/10.17504/protocols.io.hebb3an Copy   

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Authors: Yawei Xing

Proper citation: Yawei Xing 2019. Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states Short title: Dynamic distribution of gallbladder microbiota in rabbits. protocols.io https://dx.doi.org/10.17504/protocols.io.xarfid6 Copy   

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Authors: Philip D. Weyman
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: A sequence-independent method to turn genomic DNA into libraries of hairpins. An efficient way to get a different adapter on each end of a DNA fragment is to clone it and digest the fragment back out. Design the vector to have unique restriction sites outside the unique regions you want to put on each end. After digestion, your DNA fragments will have two different "adapters" on each end.Adapted from: Wang L., Zheng J., Luo Y., Xu T., Zhang Q., Zhang L., Xu M., Wan J., Wang MB., Zhang C., Fan Y. 2013. Construction of a genomewide RNAi mutant library in rice. Plant Biotechnology Journal 11:997–1005. DOI: 10.1111/pbi.12093.

Proper citation: Philip D. Weyman 2017. Rolling circle amplification-mediated hairpin (hp)-RNA libraries. protocols.io https://dx.doi.org/10.17504/protocols.io.hnrb5d6 Copy   

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Authors: Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N.
Group: GigaScience Press
Summary: These methods accompany the following publication:Hebert, F, O; Grambauer, S; Barber, I; Landry, C, R; Aubin-Horth, N (2016): Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite. GigaScience Database. http://dx.doi.org/10.5524/100197

Proper citation: Hebert F.O., Grambauer S., Barber I., Landry C.R., Aubin-Horth N. 2016. Reference transcriptome sequence resource for the study of the Cestode Schistocephalus solidus, a threespine stickleback parasite.. protocols.io https://dx.doi.org/10.17504/protocols.io.ew9bfh6 Copy   

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Authors: Elizabeth Fozo

Proper citation: Elizabeth Fozo 2021. Frozen stocks. protocols.io https:// Copy   

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Authors: Tanja Bosak
Group: Bosak Lab

Proper citation: Tanja Bosak 2020. BG11 hypersaline medium. protocols.io https://dx.doi.org/10.17504/protocols.io.bg5rjy56 Copy   

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Authors: David Booth, Nicole King
Group: King Lab
Summary: The attached file is the full sequence for a plasmid that uses gene regulatory elements from S. rosetta to drive the expression of nanoluc luciferase upon transfection in S. rosetta. The plasmid is backbone is pUC19 and can be propagated in E. coli with Ampicillin selection.

Proper citation: David Booth, Nicole King 2019. Plasmid: NK588 (pAct-nanoluc). protocols.io https://dx.doi.org/10.17504/protocols.io.8uuhwww Copy   

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Authors: Greg Blonder

Proper citation: Greg Blonder 2020. WASP-D Field Protocol. protocols.io https:// Copy   

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Authors: Angel Justiz-Vaillant
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. [1]The immunoregulatory cytokine IL-41 (also known as meteorin-like protein) is expressed at high levels in the synovium of patients with psoriatic arthritis (PsA).[2]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.2.Onuora S. Novel cytokine, IL-41, linked with PsA.Nat Rev Rheumatol. 2019;15(11):636. doi:10.1038/s41584-019-0314-7

Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of macrophage-colony stimulating factor (M-CSF) in human serum or plasma.. protocols.io https://dx.doi.org/10.17504/protocols.io.bksskwee Copy   

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Authors: Robert Dobos
Summary: This spreadsheet contains map unit agggregated output of the cocci soil habitat model. Table headers are State, Area Symbol, Area Name, Map Unit Name, Map Unit Acres, Max HSI, and Mukey. Mukey is the link to the SSURGO spatial data, which can be obtained from the Geospatial Data Gateway:https://gdg.sc.egov.usda.gov/.This spreadsheet can be joined to the spatial data using Arc-GIS. The Mukey field must explicitly be formatted as text.The data was extracted from the NASIS transactional database 20 June 2020, and reflect the data present at that time. The states reported are Arizona, California, Colorado, Idaho, Kansas, Montana, Nebraska, Nevada, New Mexico, North Dakota, Oklahoma, Oregon, South Dakota, Texas, Utah, Washington and Wyoming. These are the states thought to have at least some area hot, dry, and salty enough for cocci to exist. This data may be available for some of these states on Web Soil Survey:https://websoilsurvey.sc.egov.usda.gov/App/HomePage.htm.

Proper citation: Robert Dobos 2020. 2020_cocci_mapping_export_western_USA. protocols.io https://dx.doi.org/10.17504/protocols.io.bia7kahn Copy   

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Authors: Angel Justiz-Vaillant, Belkis Ferrer-Cosme
Group: University of the West Indies, [email protected]
Summary: IgD is a monomer with a molecular weight of 184 Kd. IgD is present in a meager amount in the serum (0.03 mg/mL) and has an unknown function against pathogens. It is regarded as a BCR. IgD may play an essential role in antigen-triggered lymphocyte differentiation. [1]

Proper citation: Angel Justiz-Vaillant, Belkis Ferrer-Cosme 2020. ELISA for quantification of human immunoglobulin D (IgD) in serum or plasma.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj7wkrpe Copy   

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Authors: Eva Feldman
Group: Diabetic Complications Consortium
Summary: Summary:Phenotyping of Rodents for the Presence of Diabetic Neuropathy In man, the development of diabetic neuropathy is dependent on both the degree of glycemic control and the duration of diabetes. Diabetic neuropathy is a progressive disorder, with signs and symptoms that parallel the loss of nerve fibers over time. Consequently, assessments of neuropathy in mice are not performed at one time point, but are characterized at multiple time points during a 6 month period of diabetes. The degree of diabetes is evaluated in 2 ways: tail blood glucose measured following a 6 hour fast and glycated hemoglobin levels. The initial degree of neuropathy is screened using the methods discussed below. Detailed measures of neuropathy are employed when the initial screening instruments indicate a profound or unique phenotypic difference. This document contains protocols used by the DiaComp staff to examine and measure diabetic neuropathy at the whole animal, tissue and cellular levels.Diabetic Complication:

Proper citation: Eva Feldman 2019. Neuropathy Phentoyping Protocols - Dosages of Analgesics for Rats and Mice. protocols.io https://dx.doi.org/10.17504/protocols.io.3jrgkm6 Copy   

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