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Authors: Matthew Fox
Summary: This protocol will guide you through the process of extracting embryos from adult mice and the manipulation of embryos in order to obtain palatal tissue.
Proper citation: Matthew Fox 2019. Collection of Mammalian Embryonic Palate Tissue. protocols.io dx.doi.org/10.17504/protocols.io.5tag6ie Copy
Authors: Marijn Ceelen
Group: iGEM Wageningen 2019
Summary: This is a protocol for the quantification of phage lamba and T7 titers by counting plaques.
Proper citation: Marijn Ceelen 2019. Plaque assay. protocols.io dx.doi.org/10.17504/protocols.io.7i8hkhw Copy
Authors: Victor Rodriguez
Summary: The aim of this protocol is to extract and analyze the starch content of a plant in order to gain data into its metabolism and photosynthetic properties.
Proper citation: Victor Rodriguez 2019. Starch Concentration Protocol. protocols.io dx.doi.org/10.17504/protocols.io.8gbhtsn Copy
Authors: Zhong Hui LIU, Dominic Chi Chung Foo, Wai Lun LAW, Fion Siu Yin CHAN, Joe King Man FAN, Jun Sheng PENG
Summary: Backgrounds and aims: The association of melanosis coli with the development ofcolorectal polyps remains uncertain.Methods: From a total of 18263 patients who had received colonoscopy in our hospital,219 with melanosis coli cases and 438 controls matched by age and sex (at 1:2 ratio)were included in this study. The association of incidence, number, location, andpathology of colorectal neoplasm with grades and distribution of melanosis coli wereanalyzed.Results: Melanosis coli was associated with significantly more colorectal polyps thancontrol, a higher incidence of numerous colorectal polyps (number ≥ 20) (7.3% vs0.5%; p 0.01). Patients with melanosis coli had higher incidences of low-grade adenomas(31.1% vs 23.3%, p the controls. On multivariate analysis, melanosis coli was independently associatedwith increased detecting rates of low grade adenoma (OR = 1.54; 95%: 1.06-2.23; p .05), non-adenoma polyp (OR = 1.72; 95%: 1.11-2.70; p (OR = 16.2, 95%: 3.66-71.6; p incidence of high-grade adenomas or adenocarcinomas in the two population groups,but the numbers of these lesions were insufficient to permit firm conclusions. Nosignificant differences in incidence, number, and pathology of colorectal polypsbetween individuals with melanosis coli of three different grades of severity were found.Melanosis located predominantly in the right colon had an interestingly lower incidenceof colonic polyps in right colon than did melanosis located predominantly in the leftcolon or total colon (8.9% vs. 26.3%, 24.0%, p had significantly more nonspecific distal ileal ulcers than did controls (8.0% vs 0%, p 0.001).Conclusion: Melanosis coli is associated with a higher incidence and number of colonicnon-adenoma polyps and low-grade adenomas, and higher incidence of distal ilealulcers. Melanosis coli may not be a harmless pigmentation, but a sign of chronic injuryof colonic and intestinal mucosa.
Proper citation: Zhong Hui LIU, Dominic Chi Chung Foo, Wai Lun LAW, Fion Siu Yin CHAN, Joe King Man FAN, Jun Sheng PENG 2017. Melanosis coli: harmless pigmentation? A case-control retrospective study of 657 cases. protocols.io dx.doi.org/10.17504/protocols.io.j6rcrd6 Copy
Authors: Frank Brosius
Group: Diabetic Complications Consortium
Summary: This protocol describes a validated protocol used by some DiaComp members to determine podocyte numbers in rodent glomeruli.Edited by: Brosius LaboratoryDiabetic Complication:Reference: Sanden SK, Wiggins JE, Goyal M, Riggs LK, and Wiggins RC. Evaluation of a thick and thin section method for estimation of podocyte number, glomerular volume, and glomerular volume per podocyte in rat kidney with Wilms' tumor-1 protein used as a podocyte nuclear marker. J Am Soc Nephrol 14: 2484-2493, 2003.
Proper citation: Frank Brosius 2019. Determination of Podocyte Number and Density in Rodent Glomeruli. protocols.io dx.doi.org/10.17504/protocols.io.8eyhtfw Copy
Authors: Aizea Morales Kastresana, Bryce Killingsworth, Joshua Welsh, Tim Traynor, Jennifer Jones
Group: Translational Nanobiology Section
Summary: This protocol describes a method to prepare bovine EV-depleted 10% FBS cell culture media by ultracentrifugation of 20% FBS media and subsequent dilution.
Proper citation: Aizea Morales Kastresana, Bryce Killingsworth, Joshua Welsh, Tim Traynor, Jennifer Jones 2020. Preparing EV-depleted media. protocols.io dx.doi.org/10.17504/protocols.io.biihkcb6 Copy
Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol goes through AAV titration by qPCR using SYBR Green Technology. To see the full abstract and additional resources, visit the Addgene protocol page.Sample DataReferencesAurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, Nitschko H, Busch U, Sing A, Ehrhardt A, Baiker A. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Hum Gene Ther Methods. 2012 Feb;23(1):18-28.PMID: 22428977
Proper citation: Addgene The Nonprofit Plasmid Repository 2019. AAV Titration by qPCR Using SYBR Green Technology. protocols.io dx.doi.org/10.17504/protocols.io.bawrifd6 Copy
Authors: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
Group: RENE FLORES
Proper citation: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones 2021. Actinobacteria collection, enrichment and isolation. protocols.io dx.doi.org/10.17504/protocols.io.brztm76n Copy
Authors: Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin
Summary: The ARF-AID (Auxin Response Factor-Auxin Inducible Degron) system is a re-engineered auxin-inducible protein degradation system. Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological system under study remains intact and functional until perturbation. This feature necessitates that the endogenous levels of the protein are maintained. However, endogenous tagging of genes with AID can result in chronic, auxin-independent proteasome-mediated degradation. The additional expression of the ARF-PB1 domain in the re-engineered ARF-AID system prevents chronic degradation of AID-tagged proteins while preserving rapid degradation of tagged proteins. Here we describe the protocol for engineering human cell lines to implement the ARF-AID system for specific and inducible protein degradation. These methods are adaptable and can be extended from cell lines to organisms.
Proper citation: Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin 2020. The ARF-AID system: Methods that preserve endogenous protein levels and facilitate rapidly inducible protein degradation. protocols.io dx.doi.org/10.17504/protocols.io.bc7ciziw Copy
Authors: Sam Li
Group: BioLegend
Summary: Product description and procedure summary:The cells targeted by the Nanobeads are either selected or depleted by incubating your sample with the directly conjugated magnetic particles. The magnetically labeled fraction is retained by the use of a magnetic separator. After collection of the targeted cells, downstream applications include functional assays, gene expression, phenotypic characterization, etc.Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Scale up volumes if using 14 mL tubes and Magnet, and place the tube in the magnet for 10 minutes.
Proper citation: Sam Li 2019. MojoSort™ Human CD14 Nanobeads Protocol. protocols.io dx.doi.org/10.17504/protocols.io.7x4hpqw Copy
Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.Modified from Rioux, C., Jordan, D., & Rattray, J. B. (1983). Colorimetric determination of catechol siderophores in microbial cultures. Analytical Biochemistry,133(1), 163-169. doi:10.1016/0003-2697(83)90238-5
Proper citation: Dr. Steven Wilhelm 2017. Rioux Test for Catecholates. protocols.io dx.doi.org/10.17504/protocols.io.icrcav6 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io dx.doi.org/10.17504/protocols.io.dpa5id Copy
Authors: David Milner
Group: Richards Lab
Summary: Complementation of a S. cerevisiae Δpho84 strain with putative phosphate transporter(s)
Proper citation: David Milner 2018. S. cerevisiae Δpho84 complementation: growth curves. protocols.io dx.doi.org/10.17504/protocols.io.kw5cxg6 Copy
Authors: Seth Currlin, Marda Jorgensen, Jerelyn Nick
Group: Optical Clearing of Tissue, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is a guide for immunostaining CLARITY-processed samples. dx.doi.org/10.17504/protocols.io.8jihukeThese steps are meant to be a guide for immunostaining large samples and should be optimized to suit your particular tissues and reagents. Large tissue volumes and dense tissue types will require longer incubation and wash times. The parameters suggested below are for a piece of human tissue (thymus, spleen, or lymph node) approximately 5 mm3 in size.A useful link: http://wiki.claritytechniques.org/index.php/Immunostaining
Proper citation: Seth Currlin, Marda Jorgensen, Jerelyn Nick 2020. Large Volume Immunostaining for Cleared Samples. protocols.io dx.doi.org/10.17504/protocols.io.bprtmm6n Copy
Authors: Ben Pascoe
Summary: Protocol for DNA extraction from Campylobacter isolates using the QIAGEN QIAamp DNA Mini Kit (QIAGEN, Crawley, UK).
Proper citation: Ben Pascoe 2019. DNA extraction: Campylobacter. protocols.io dx.doi.org/10.17504/protocols.io.wzbff2n Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the steps for processing post-mortem human brain, starting from whole brain or a single hemisphere.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U01MH114812. 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. Human Post Mortem Brain Processing. protocols.io dx.doi.org/10.17504/protocols.io.bezcjf2w 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. Phagocytes mainly make IL-36. It acts on T lymphocytes and NK cells regulating the IFN-γ synthesis. It stimulates the hematopoiesis and expression of both MHC class I and II molecules as well as intracellular adhesion molecules (ICAM)-1. [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-36 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj38kqrw Copy
Authors: Qiaoshan Lin
Proper citation: Qiaoshan Lin 2017. Reads trimming & Quality control & Reads alignment. protocols.io dx.doi.org/10.17504/protocols.io.k7qczmw Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Keyhole limpet hemocyanin (KLH) is a cooper-containing protein comprising of subunits with MW of 400 kDa. This protein is found in the hemolymph of the sea mollusk Megathura crenulata. It has the ability to enhance the host’s immune response by interacting with monocytes, T cells and macrophages. KLH has been used primarily as a carrier for vaccines and antigens [1]. It was found that chicken immunized with KLH bound peptide raised an anti-KLH immunoresponse [2]. This can be tested by a single method such as the Ouchterlony technique.Reference1. Aarntzen EH, de Vries IJ, Göertz JH, et al. Humoral anti-KLH responses in cancer patients treated with dendritic cell-based immunotherapy are dictated by different vaccination parameters.Cancer Immunol Immunother. 2012;61(11):2003-2011. doi:10.1007/s00262-012-1263-z2. Justiz Vaillant AA, Anderson MF, Smikle M, Wisdom B, Mohammed W, et al. (2013) Development of Anti HIV Gp120 and HIV Gp41 Peptide Vaccines. J Vaccines Vaccin 4: 206. doi: 10.4172/2157-7560.1000206
Proper citation: Angel Justiz-Vaillant 2020. Detection of anti- SpA antibodies in egg white tested by double immunodiffusion (Ouchterlony) technique.. protocols.io dx.doi.org/10.17504/protocols.io.bjsqkndw Copy
Authors: Shunsuke Taito, Kota Yamauchi, Yuki Kataoka
Summary: BackgroundTelerehabilitation is delivery of therapeutic rehabilitation at a distance or offsite using telecommunication technologies. However, telerehabilitation for respiratory diseases and respiratory infections is not known. During the COVID-19 pandemic, telerehabilitation may represent the first option for people at home. The COVID-19 is one of respiratory tract disease, and rapid and widespread transmission was demonstrated. Therefore, it is necessary consider telerehabilitation in patients with respiratory tract disease in the acute phase in hospital as well as chronic phase from the perspective of infection prevention.AimThe purpose of this scoping review is to assess the intervention program, safety and feasibility of telerehabilitation for patients with respiratory tract diseases in the COVID-19 era.Methods and analysisWe describe this protocol that follows the PRISMA extension for scoping reviews (PRISMA-ScR) statement. We also use the scoping review framework by The Joanna Briggs Institute following five stage approach: (1) identify the research question; (2) identify relevant studies; (3) select studies; (4) chart the data and (5) collating, summarize and report the results.Ethics and disseminationIn this scoping review, only data from previously conducted studies will be analyzed. We will publish this scoping review in peer-reviewed journals.
Proper citation: Shunsuke Taito, Kota Yamauchi, Yuki Kataoka 2020. Telerehabilitation in patients with respiratory tract diseases: protocol for a scoping review. protocols.io dx.doi.org/10.17504/protocols.io.bf6wjrfe Copy
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