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Authors: Sean Seaver
Summary: How to make a IPTG – 1 M (100 x) Stock Solution

Proper citation: Sean Seaver 2014. IPTG – 1 M (100 x) Stock Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.ci3ugm Copy   

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Authors: Bonnie Hurwitz
Group: Hurwitz Lab, MetaFunc Course

Proper citation: Bonnie Hurwitz 2016. MG_HW8: Optimized assembly, read recruitment, and gene finding. protocols.io https://dx.doi.org/10.17504/protocols.io.gbhbsj6 Copy   

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Authors: Adam Hunter
Group: Human Cell Atlas Method Development Community

Proper citation: Adam Hunter 2018. CGAP Human Lung Dissociation. protocols.io https://dx.doi.org/10.17504/protocols.io.qz9dx96 Copy   

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Authors: Wolfgang Teufl, Markus Miezal, Bertram Taetz, Michael Fröhlich, Gabriele Bleser
Summary: Find enclosed the Bland-Altman plots of hip-, knee-, ankle joint and the global pelvis felxion, obliquity and rotation belonging to the publication “Validity of inertial sensor based 3D joint kinematics of static and dynamic functional movement tasks”.

Proper citation: Wolfgang Teufl, Markus Miezal, Bertram Taetz, Michael Fröhlich, Gabriele Bleser 2019. Bland-Altman plots Squat, Single Leg Squat, Countermovement Jump. protocols.io https://dx.doi.org/10.17504/protocols.io.sj4ecqw Copy   

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Authors: Nus Igem

Proper citation: Nus Igem 2019. Transformation of Chemically Competent Cells. protocols.io https://dx.doi.org/10.17504/protocols.io.8achsaw Copy   

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Authors: Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste Karch
Group: Neurodegeneration Method Development Community
Summary: This protocol outlines the derivation of Hematopoietic Progenitor Cells and differentiation of iMGLs using iPSC cultures. This protocol is modified the following papers.

Proper citation: Fabia Filipello, Jacob Marsh, Rj Martinez, Celeste Karch 2020. Differentiation of iPSC into Microglia-Like Cells (iMGL). protocols.io https://dx.doi.org/10.17504/protocols.io.bkrvkv66 Copy   

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Authors: Federica Dal Pesco, Franziska Trede, Dietmar Zinner, Fischer Julia
Summary: This protocol provides a standardized methodology for the analyses of genetic relatedness and paternity assignment in wild Guinea baboons (Papio papio) based on 24 microsatellite markers. It describes all methodological steps from sample collection and storage, DNA extraction, microsatellite amplification, and genotyping to a detailed explanation of the analyses regarding loci descriptive statistic, dyadic relatedness, and parentage analysis. This protocol was developed as a standardized method utilized by the Cognitive Ethology Laboratory (German Primate Center) to analyse fecal samples from the wild Guinea baboon population at the CRP Simenti field site, PNNK, Senegal. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Federica Dal Pesco, Franziska Trede, Dietmar Zinner, Fischer Julia 2020. Analysis of genetic relatedness and paternity assignment in wild Guinea baboons (Papio papio) based on microsatellites. protocols.io https://dx.doi.org/10.17504/protocols.io.bfdmji46 Copy   

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Authors: Nicola O'Reilly, Svend Kjaer
Group: Coronavirus Method Development Community, Crick COVID-19 Consortium
Summary: Purpose of examination / Clinical relevanceAt the end of 2019, several pneumonia cases were reported in Wuhan, China and the pathogen was confirmed as a new viral strain. World Health organization has named the newly identified coronavirus as 2019-nCoV, also known as COVID19. The disease developed into a dangerous pandemic, posing major challenges to the NHS. Although more research is necessary to better understand the virus, in response to the emergency, simple and rapid testing is essential to identify the virus in infected individuals. This will aid the implementation of efficient interventions to contain the spread, and distinguish healthcare workers who have been infected, and are required to self-isolate, from those showing similar symptoms but which are not 2019-nCoV associated. The latter category may continue to work, alleviating stress on hard-pressed healthcare resources. 2019-nCoV is an RNA virus, and the diagnostic tests detect viral RNA in swabs from patient airways using a reverse transcriptase PCR assay. Samples are submitted to HSL, an accredited reporting laboratory, and transferred to the Crick for testing.Principles of ExaminationThis procedure involves the preparation of L6 5M Guanidine thiocyanate virus inactivation buffer for the viral inactivation protocol.

Proper citation: Nicola O'Reilly, Svend Kjaer 2020. Preparation of 5M Guanidine thiocyanate L6 Inactivation Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.bfevjje6 Copy   

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Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for general transfection. To see the full abstract and additional resources, visit the Addgene protocol page.Sample Data

Proper citation: Addgene The Nonprofit Plasmid Repository 2019. General Transfection. protocols.io https://dx.doi.org/10.17504/protocols.io.4xqgxmw Copy   

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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. Dendritic cells produced predominantly IL-25. It acts on various types of cells, including Th2 cells. It stimulates the synthesis of Th2 cytokine profile including IL-4 and IL-13. [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-25 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj3tkqnn Copy   

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Authors: Eva Feldman, Frank Brosius
Group: Diabetic Complications Consortium
Summary: Describes the protocol used by the DiaComp to detect and quantify catalase activity in a tissue. Diabetic Complications:

Proper citation: Eva Feldman, Frank Brosius 2019. Catalase. protocols.io https://dx.doi.org/10.17504/protocols.io.3e6gjhe Copy   

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Authors: Trevor Ho, Baojun Wang
Summary: Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on four proteins, converting them into AND or NAND logic gates. In this protocol we provide details in executing the IBM method.

Proper citation: Trevor Ho, Baojun Wang 2020. Intein-assisted Bisection Mapping (IBM). protocols.io https://dx.doi.org/10.17504/protocols.io.bpqdmms6 Copy   

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Authors: Elaina Graham, Benjamin Tully
Summary: Making a Phylogenetic TreeIn this procedure we are going to build a phylogenetic tree! Throughout I'll refer to scripts available on my github here. We will be using the 16 ribosomal proteins used in Hug et al. 2016. The HMM models for these are available on my github in a file called `hug_ribosomalmarkers.hmm`. We will be running this tutorial using the genomes and files found in the folder `Example`.As an overview I will be explaining1. How to generate gene predictions using prodigal for genomes of interest2. How to identify ribosomal proteins using an hmm model3. How to align, trim, and concatenate proteins for a phylogenetic tree4. building a phylogenetic treeTo cite this workflow reference this paper:Graham, E. D., J. F. Heidelberg, and B. J. Tully. 'Potential for primary productivity in a globally-distributed bacterial phototroph.' The ISME journal (2018)doi: https://doi.org/10.1038/s41396-018-0091-3

Proper citation: Elaina Graham, Benjamin Tully 2018. Building Phylogenetic Tree. protocols.io https://dx.doi.org/10.17504/protocols.io.q2pdydn Copy   

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Authors: Tamara Matute, Isaac Núñez
Group: Laboratorio de Tecnologias Libres

Proper citation: Tamara Matute, Isaac Núñez 2017. Segregation of plasmids in bacterial colonies. protocols.io https://dx.doi.org/10.17504/protocols.io.jbncime Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukin 23 activates the production of IL-17A, which is a pro-inflammatory cytokine, produced by a group of T helper cell known as T- helper17 lymphocytes in response to the said IL-23 [1,2].Reference1. Cho ML, Kang JW, Moon YM, Nam HJ, Jhun JY, Heo SB, Jin HT, Min SY, Ju JH, Park KS, Cho YG, Yoon CH, Park SH, Sung YC, Kim HY (May 2006). Journal of Immunology. 176 (9): 5652–61. 2. Nobee A, Justiz-Vaillant A, Akpaka PE, Poon-King P (2016) Levels of Interleukin 17 and 23 in Patients with Systemic Lupus Erythematosus (SLE) in Trinidad and Tobago. Immunochem Immunopathol 2: 115. doi: 10.4172/2469- 9756.1000115

Proper citation: Angel Justiz-Vaillant 2020. Enzyme linked immunosorbent assay (ELISA) for determining the serum concentration of IL-23 in humans.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjy2kpye Copy   

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Authors: Hector Silva
Summary: Solução para fixar tecidos

Proper citation: Hector Silva 2020. Protocolo para PFA 4%. protocols.io https://dx.doi.org/10.17504/protocols.io.bcjaiuie Copy   

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Authors: Chi-Kuang Yao, Yu-Tzu Liu, I-Chi Lee, You-Tung Wang, Ping-Yen Wu
Summary: This protocol is from 'Flower Ca2+ channel in CME and ADBE' of Yao CK et al. Please see the manuscript for the full method details.

Proper citation: Chi-Kuang Yao, Yu-Tzu Liu, I-Chi Lee, You-Tung Wang, Ping-Yen Wu 2017. FM1-43 dye uptake (loading/unloading assays) from Yao CK et al. (2017). protocols.io https://dx.doi.org/10.17504/protocols.io.hjvb4n6 Copy   

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Authors: Elizabeth Fozo

Proper citation: Elizabeth Fozo 2021. Site Directed Mutagenesis 2016. protocols.io https:// Copy   

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Authors: Maria Kupper
Group: Mealybug Team
Summary: This protocol describes how to perform DNA FISH on dissected tissue of Planococcus citri. While the aim of this experiment was to distinguish localisation of the P. citri endosymbionts in ovarian and bacteriome tissue, the protocol can be easily adjusted for other tissues or the use of different probes.The probes used here were designed according to the works of von Dohlen et al. (Nature, 2001) and Lopez-Madrigal et al. (PLOS ONE, 2013).In brief, tissues were isolated in 1xPBS and transferred to various fixatives. After fixation samples were dehydrated and pre-incubated in hybridisation buffer before adding probes. After hybridisation, samples were washed and counter stained with Hoechst. FInally, stained tissues were transferred to microscopy slides, briefly air-dried and mounted in FLuorSave Reagent (Millipore).

Proper citation: Maria Kupper 2018. Whole mount DNA fluorescence in situ hybridisation (DNA-FISH) on Planococcus citri tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.p9vdr66 Copy   

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Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: Published work using this protocol:- Kustrimovic N., Comi C., Magistrelli L., Rasini E., Legnaro M., Bombelli R., Aleksic I., Blandini F., Minafra B., Riboldazzi G., Struchio A., Mauri M., Bono G., Marino F., Cosentino M. Parkinson’s disease patients have a complex phenotypic and functional Th1 bias: cross-sectional studies of CD4+ Th1/Th2/T17 and Treg in drug-naïve and drug-treated patients (2018). Journal of neuroinflammation, 15(1), 205. https://doi.org/10.1186/s12974-018-1248-8- Kustrimovic, N., Rasini, E., Legnaro, M., Bombelli, R., Aleksic, I., Blandini, F., Comi, C., Mauri, M., Minafra, B., Riboldazzi, G., Sanchez-Guajardo, V., Marino, F., & Cosentino, M. (2016). Dopaminergic Receptors on CD4+ T Naive and Memory Lymphocytes Correlate with Motor Impairment in Patients with Parkinson's Disease. Scientific reports, 6, 33738. https://doi.org/10.1038/srep33738- Cosentino M., Ferrari M., Kustrimovic N., Rasini E., Marino F. (2015). Influence of dopamine receptor gene polymorphisms on circulating T lymphocytes: A pilot study in healthy subjects. Human immunology, 76, 10, 747-752. https://doi.org/10.1016/j.humimm.2015.09.032- 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. CELL COUNT- 01 - Manual cell count with Trypan Blue. protocols.io https://dx.doi.org/10.17504/protocols.io.bpxrmpm6 Copy   

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