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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the blunting protocol for NEB PCR Cloning Kit (E1202)

Proper citation: New England Biolabs 2015. Blunting Protocol for NEB PCR Cloning Kit (E1202). protocols.io https://dx.doi.org/10.17504/protocols.io.crpv5m Copy   

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Authors: Boaz Mohar
Summary: The purpose of this protocol is to compare the intake and clerance kinatics of JF dye systemic delivery using retro orbital injections.We image a mouse with a crenial window before and after systemic dye injection.We want to fit the clearance of the dye with a double exponanatial decay function:y = \textbf a*e^{-\frac{1}{\textbf b*x}}+\textbf c*e^{-\frac{1}{\textbf d*x}} + \textbf e

Proper citation: Boaz Mohar 2020. Mesuring JF dye kinetics in the brain of C57/Bl mice. protocols.io https://dx.doi.org/10.17504/protocols.io.5vmg646 Copy   

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Authors: Fabio Gomes

Proper citation: Fabio Gomes 2015. Genomic DNA extraction from mosquitoes. protocols.io https://dx.doi.org/10.17504/protocols.io.d7h9j5 Copy   

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Authors: Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton
Group: Temperton Lab
Summary: Working protocol

Proper citation: Holger Buchholz, Michelle Michelsen, Michael Allen, Ben Temperton 2020. Viral isolation for SAR11 and OM43 hosts. protocols.io https://dx.doi.org/10.17504/protocols.io.bb73irqn Copy   

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Authors: Steven Burgess
Group: OpenPlant Project, Plantae
Summary: Sueoka's High Salt Medium is used for photoautotrophic growth of the green alga Chlamydomonas reinhardtii. The medium is also known as HS or HSM.Source:Sueoka, N. (1960) Proc. Natl. Acad. Sci. USA 46, 83-91.http://www.chlamycollection.org/Sueoka.html

Proper citation: Steven Burgess 2016. Sueoka's High Salt Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.fdebi3e Copy   

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Authors: G-Biosciences
Group: G-Biosciences
Summary: This protocol is part of the FOCUS™ Mitochondria Kit collection. Please refer to the appropriate protocol depending on your application.

Proper citation: G-Biosciences 2016. Fractionation of Light and Heavy Mitochondria by Gradient Cushion using the FOCUS™ Mitochondria Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.e88bhzw Copy   

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Authors: Giulio Cordaro
Group: SOFC Procedures

Proper citation: Giulio Cordaro 2021. Preparation of ink for electrode deposition via paint brushing using oxide powders . protocols.io https:// Copy   

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Authors: Rachel Howard-Till, Claudia Osorio, Marcos Olivos, Bradley Till
Summary: This protocol describes how to build your own agarose gel documentation system to create digital images for quantification of DNA stained with dyes that fluoresce under blue LED light. Free software and inexpensive materials are used that can save tens of thousands of dollars when compared to similar commercial products.

Proper citation: Rachel Howard-Till, Claudia Osorio, Marcos Olivos, Bradley Till 2020. A do-it-yourself low-cost agarose gel documentation and DNA quantification system . protocols.io https://dx.doi.org/10.17504/protocols.io.bdtpi6mn Copy   

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Authors: Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness
Summary: Enteroendocrine cells are important regulators of gastrointestinal, digestive and metabolic function. Here we describe protocols for investigating nerve fiber populations that may innervate these cells, using immunohistochemistry and high resolution microscopy techniques in the human gastric mucosa and muscle.

Proper citation: Madeleine Di Natale, Josiane Fakhry, Martin Stebbing, Billie Hunne, John B. Furness 2019. Identification of different EEC types and nerve fiber types in human gastric mucosa. protocols.io https://dx.doi.org/10.17504/protocols.io.8u7hwzn Copy   

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Authors: Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru
Group: Optical Clearing of Tissue, Neurodegeneration Method Development Community
Summary: To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1–2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.

Proper citation: Jennifer B Treweek, Ken Y Chan, Nicholas C Flytzanis, Bin Yang, Benjamin E Deverman, Alon Greenbaum, Antti Lignell, Cheng Xiao, Long Cai, Mark S Ladinsky, Pamela J Bjorkman, Charless C Fowlkes, Viviana Gradinaru 2019. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. protocols.io https://dx.doi.org/10.17504/protocols.io.8xehxje Copy   

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Authors: Matus Valach
Summary: A brief protocol for the preparation of glyoxal used in glyoxal/borate and RNase T1-based detection of inosine residues in RNAs.

Proper citation: Matus Valach 2016. Preparation of deionized glyoxal. protocols.io https://dx.doi.org/10.17504/protocols.io.ejsbcne Copy   

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Authors: Tim Mercer

Proper citation: Tim Mercer 2020. Using sequins with RNA sequencing.. protocols.io https:// Copy   

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Authors: Katie Pitz, Nathan Truelove, Charles Nye, Reiko P Michisaki, Francisco Chavez
Group: MBON eDNA
Summary: The 12S protocol is aimed at amplifying the hypervariable region of the mitochondrial DNA 12S rRNA gene in eukaryotes. The primers (MiFish-U-F & MiFish-U-R) used in this protocol were developed by Miya et al., 2015 for metabarcoding environmental DNA (eDNA) from fishes. Touchdown thermocycling protocols were adapted from the CALeDNA group.This work was supported by NASA grant NNX14AP62A ‘National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)’ funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), and the U.S. Integrated Ocean Observing System (IOOS) Program Office.Citations1) Miya M et al. 2015 MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R.Soc.opensci. 2: 150088. http://dx.doi.org/10.1098/rsos.1500882) CALeDNA. 2019. University of California Conservation Genomics Consortium.

Proper citation: Katie Pitz, Nathan Truelove, Charles Nye, Reiko P Michisaki, Francisco Chavez 2020. Environmental DNA (eDNA) 12S Metabarcoding Illumina MiSeq NGS PCR Protocol (Touchdown). protocols.io https://dx.doi.org/10.17504/protocols.io.bcppivmn 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. Regulatory T-cells synthesize IL-28, which acts on keratinocytes and melanocytes. It stimulates cell presentation of viral antigens to CD8+T lymphocytes. IL-28 also upregulates TLR-2 and TLR-3 expression. IL-28 enhances the keratinocyte capacity to recognize pathogens in the healthy skin. [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-28 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj3xkqpn Copy   

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Authors: Chuck Vanderburg, Carly Martin, Velina Kozareva, Naeem Nadaf, Nehal Patel, Evan Macosko

Proper citation: Chuck Vanderburg, Carly Martin, Velina Kozareva, Naeem Nadaf, Nehal Patel, Evan Macosko 2020. Fresh Frozen Mouse Brain Preparation (for Single Nuclei Sequencing). protocols.io https://dx.doi.org/10.17504/protocols.io.bcbrism6 Copy   

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Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community
Summary: This is part 6 of: "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.Note: Study procedures are vaccine-specific and will depend upon vaccine administration days (Day 1 and Day 15 versus Day 1 and Day 29) and serology collection days. The below section assumes that vaccine administrations take place on Days 1 and 15 with procedures as indicated.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Study Procedures (Part 6 of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj5ckq2w Copy   

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Authors: Rattanawat Chaiyarat, Namphung Youngpoy, Praeploy Kongsurakan, Seree Nakbun
Group: WILDREC
Summary: Banteng (Bos javanicus) underwent general medical checkups and received minimal human contact in 302 ha enclosure.They were train in transportation boxes(1 m × 2.5 m × 1.8 m, width × long × high)over6 months.They werekept in groups in soft release cage for 4 months. Natural food plants,fresh water and artificial salt licks were provided.Immobilizations were controlledwith anesthetic drugsby veterinarians and fitted with radio collars.The radio signals were monitored every week through ground tracking, using homing in and triangulation techniquesvia VHF signals.Cameras traps were installed,memory cards and batteries were changed every month in each location.

Proper citation: Rattanawat Chaiyarat, Namphung Youngpoy, Praeploy Kongsurakan, Seree Nakbun 2020. Methods and protocols from Chaiyarat et al. (2019) for systematic reintroduction of bateng (Bos javanicus). protocols.io https://dx.doi.org/10.17504/protocols.io.ba8zihx6 Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant 2020. Determination of C3 concentration by the Mancini test.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj94kr8w Copy   

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Authors: Gloria Patricia Barrera, Deisy Liseth Toloza, Laura Fernanda Villamizar, Carlos Espinel.
Summary: Diatraea spp. (Lepidoptera: Crambidae) are a group of insects considered as an agriculture pest in many economically relevant crops such as sugarcane, sorghum, corn and rice. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. We described a protocol based on a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene and Single-Strand Conformation Polymorphism (SSCP) methodology to properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.

Proper citation: Gloria Patricia Barrera, Deisy Liseth Toloza, Laura Fernanda Villamizar, Carlos Espinel. 2017. Identification of Diatraea spp (Lepidoptera: Crambidae) based on Cytochrome oxidase II and SSCP. protocols.io https://dx.doi.org/10.17504/protocols.io.ipqcdmw Copy   

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Authors: Plínio Luna de Albuquerque
Summary: It is a crossover, double-blind, sham-controlled, pseudorandomized, and counterbalanced study at the Laboratory of Applied Neuroscience (LANA) of the Federal University of Pernambuco (UFPE). We performed a double-blind, randomized, sham-controlled crossover study with 12 healthy volunteers who underwent single sessions of rTMS (1Hz, 20Hz and Sham) and tsDCS (anodal, cathodal and Sham) associated with 20 minutes of treadmill walking. Cortical excitability was assessed by motor evoked potential (MEP) and spinal cord excitability by the Hoffmann reflex (Hr), nociceptive flexion reflex (NFR) and homosynaptic depression (HD). All measures were assessed before, immediately, 30 and 60 minutes after the experimental procedures.

Proper citation: Plínio Luna de Albuquerque 2018. Effect of different types of non-invasive central nervous system stimulation on pain perception, cortical and spinal cord excitability in healthy individuals.. protocols.io https://dx.doi.org/10.17504/protocols.io.nkidcue Copy   

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