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Authors: Debora Ferreira Barreto-Vieira, Fernanda Cunha Jácome, Marcos Alexandre Nunes da Silva, Gabriela Cardoso Caldas, Elen Mello de Souza, Audrien Alves Andrade, Ortrud Monika Barth.
Proper citation: Debora Ferreira Barreto-Vieira, Fernanda Cunha Jácome, Marcos Alexandre Nunes da Silva, Gabriela Cardoso Caldas, Elen Mello de Souza, Audrien Alves Andrade, Ortrud Monika Barth. 2017. Ultra-thin section staining. protocols.io dx.doi.org/10.17504/protocols.io.jqwcmxe Copy
Authors: Anton Du Plessis
Summary: MicroCT is a well known technique and is often used for non-destructive analysis of parts produced by additive manufacturing. This is especially useful to inspect the parts for potential defects such as excessive porosity or layered defects due to imperfect powder levelling in individual layers. While various online monitoring methods are under development, there is currently not yet any accepted method to identify such defects during the building process. Post-production microCT of the entire part allows for the identification of such errors, but its limitation is the resolution which depends on part size. Hence a large part may have small but important porosities which may be missed by microCT. This can be overcome by using a witness specimen built in the same process, and analysing this smaller sample at a high resolution. The porosity information from the smaller part can be used to evaluate the acceptability of the entire build. The workflow presented here serves to standardize this process: with a simple process, a standard geometry witness specimen and hence standardized scan and analysis procedures. A layered stop-start flaw is shown in the witness specimen to demonstrate the ability to detect this type of flaw.
Proper citation: Anton Du Plessis 2018. Standard method for microCT-based additive manufacturing quality control 5: witness specimen analysis. protocols.io dx.doi.org/10.17504/protocols.io.sbzeap6 Copy
Authors: Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm
Summary: Display of proteins on the bacterial cell surface has always been an attractive technique for the production of functional cell-anchored proteins, thereby reducing the cost, time and effort related to enzyme purification. Thus, surface display can enable fast and easy screening of protein libraries, e.g. activity variants, or screening of different enzyme substrates, while maintaining a connection between the phenotype and the genotype. Additionally, cells displaying functional enzymes can potentially be used as whole-cell catalysts.This protocol describes how to express proteins on the surface of E. coli BL21 (DE3) using a L-rhamnose inducible expression system.
Proper citation: Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm 2020. Protein expression on the surface of Escherichia coli. protocols.io dx.doi.org/10.17504/protocols.io.bfh4jj8w Copy
Authors: Ken Christensen
Group: Re-Entering Labs Post COVID-19 Shutdown
Summary: Working alone in the laboratory should be minimized; however, CHEM 584 students can work alone in the laboratory if they adhere to the following Standard Operating Procedure (SOP).Also, the doors to the laboratory must remain closed during times when the class is not in a scheduled session.
Proper citation: Ken Christensen 2020. Working Alone in the Lab--CHEM 584. protocols.io dx.doi.org/10.17504/protocols.io.bmnwk5fe Copy
Authors: Bhavesh Patel, Yanmin Wang
Summary: This protocol describes the step followed to conduct ex vivo triaxial mechanical testing (inflation, extension, torsion) of dog colon samples on our custom build testing platform.
Proper citation: Bhavesh Patel, Yanmin Wang 2021. Triaxial mechanical testing of dog colon samples. protocols.io dx.doi.org/10.17504/protocols.io.bp7qmrmw Copy
Authors: Tjusls China
Group: Chemistry Method Development Community
Proper citation: Tjusls China 2019. 10 Affinity Chromatography. protocols.io dx.doi.org/10.17504/protocols.io.5cgg2tw Copy
Authors: Hannah Zurcher
Summary: This protocol is designed for use with food-safe materials. It may be used to illustrate principles of gel electrophoresis for children, or as a party novelty for scientifically-minded adults. It is currently a work in progress and will be updated as necessary. Currently different colors of food dye will run for different times but will not form distinct bands.
Proper citation: Hannah Zurcher 2018. Edible Gel Electrophoresis. protocols.io dx.doi.org/10.17504/protocols.io.t3neqme Copy
Authors: Charles Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar
Group: SPARC
Summary: This protocol provides the steps for recording the gastrointestinal myoelectric responses and stimulation of the abdominal vagus nerve from the behaving ferret. These tests occur after an animal is surgically implanted with gastrointestinal and vagus nerve electrodes (see the protocol "SPARC - Chronic implantation of gastrointestinal and vagus nerve electrodes in the ferret" for implantation methods).Funding: This protocol was developed with funding from the NIH Common Fund’s Stimulating Peripheral Activity to Relieve Conditions (SPARC) program (Award U18TR002205). To learn more about the SPARC program, visit https://sparc.science.
Proper citation: Charles Horn, Derek M. Miller, Stephanie Fulton, Bill J. Yates, Lee E. Fisher, Ameya C. Nanivadekar 2019. SPARC - Gastrointestinal myoelectric recordings from the behaving ferret. protocols.io dx.doi.org/10.17504/protocols.io.6a8hahw Copy
Authors: P. Dreux Chappell, Bethany D. Jenkins
Summary: A protocol to separate chloroplasts from diatom cells using ammonium fluoride to permeate the silica frustrule and a percoll gradient to separate the plastid from other cellular components.
Proper citation: P. Dreux Chappell, Bethany D. Jenkins 2017. Diatom Chloroplast Isolation Steps. protocols.io dx.doi.org/10.17504/protocols.io.hjsb4ne Copy
Authors: Megan Settell, Bruce E Knudsen, Andrea L McConico, Kip A Ludwig
Proper citation: Megan Settell, Bruce E Knudsen, Andrea L McConico, Kip A Ludwig 2020. Protocol for Pig Vagus Nerve Microdissection and Histology. protocols.io dx.doi.org/10.17504/protocols.io.9ieh4be Copy
Authors: Zhujun Wei
Group: 2020 iGEM NEFU China
Proper citation: Zhujun Wei 2020. DNT Induction. protocols.io dx.doi.org/10.17504/protocols.io.bnxsmfne Copy
Authors: Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf
Summary: Gastruloid generation protocol as performed in the Lutolf Lab, EPFL.For previously published protocols, see:Baillie-Johnson, Peter, et al. "Generation of aggregates of mouse embryonic stem cells that show symmetry breaking, polarization and emergent collective behaviour in vitro."JoVE (Journal of Visualized Experiments)105 (2015): e53252. andMehmet, G., et al. "Generating Gastruloids from Mouse Embryonic Stem Cells."Protocol Exchange (2018).
Proper citation: Stefano Vianello, Mehmet Girgin, Giuliana Rossi, Matthias Lutolf 2020. Protocol to generate Gastruloids (LSCB, EPFL). protocols.io dx.doi.org/10.17504/protocols.io.9j5h4q6 Copy
Authors: Andrew Potter
Group: Human Cell Atlas Method Development Community
Summary: Protocol for human intestine cell dissociation.
Proper citation: Andrew Potter 2018. Intestine cell dissociation. protocols.io dx.doi.org/10.17504/protocols.io.nf3dbqn Copy
Authors: Teri Stevenson, Vance L. Albaugh
Group: Mouse Metabolic Phenotyping Centers
Summary: This is the protocol for the vertical sleeve gastrectomy in the mouse. This procedure eliminates the greater curvature of the stomach leaving approximately 30% of the preoperative stomach capacity. Specifically, this procedure eliminates the greater curvature of the stomach where the ghrelin-producing cells are located.
Proper citation: Teri Stevenson, Vance L. Albaugh 2019. Vandy - Vertical Sleeve Gastrectomy in Mice. protocols.io dx.doi.org/10.17504/protocols.io.zcjf2un Copy
Authors: Giana Schena, Emma Murray
Group: Coronavirus Method Development Community
Summary: During the height of the COVID-19 outbreak, personal protective equipment shortages are felt around the world, in spite of the fact that traditional face masks are not even sufficient to fully protect against the 0.125 micron SARS-CoV-2 virus. Medical personnel, more than any other sector, are being hit hardest by this shortage, given their close contact with infected persons. During this time of crisis and shortage, alternative and atypical solutions are necessary to ensure the protection of those who are on the front lines against this disease. One solution is the creation of reusable 3D-printed personal protective equipment (PPE) in conjunction with appropriate disposable filtration.3D-printed face masks are available on a variety of different open source 3D-printing online platforms. Unfortunately, the general public remains largely unaware of these potential solutions and can also be intimidated by the lack of information available regarding how to integrate scientifically appropriate filters. The intention of this white paper is to make available the information needed for simple construction of effective 3D-printed masks. We recommend a 3D printed face mask design made available by CREALITY, a leader in 3D-printing machines. By using CREALITY’s open source designs and easily obtainable air filters, cut to a desired size, we can increase our ability to protect medical workers against this disease. Additionally, CREALITY offers designs for a 3D-printed eye mask that can be used with plexiglass to protect eyes against airborne droplets. In practice, CREALITY’s 3D model object STL files can be uploaded into any available slicer software allowing for creation of specific commands for 3D printers. Within the slicer, face mask and eye mask models can be scaled to small, medium, or large to fit a variety of face sizes. We have also included strap adjustment clip models for use with facemasks and a face shield to extend the life of traditional facemasks.We also propose a plan to coordinate large-scale construction of crowd-sourced 3D printed masks with collection and delivery of said masks to at-risk businesses, in particular hospitals and care facilities.
Proper citation: Giana Schena, Emma Murray 2020. 3D Printing Of Personal Protective Equipment And Repurposing Of Common Household Air Filters. protocols.io dx.doi.org/10.17504/protocols.io.bd77i9rn Copy
Authors: Isabel Gautreau
Group: New England Biolabs (NEB)
Proper citation: Isabel Gautreau 2020. NEBNext Ultra End Prep Mixture E7442. protocols.io dx.doi.org/10.17504/protocols.io.bpiumkew Copy
Authors: Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson
Summary: This protocol describes methods for detecting cell-surface markers by indirect immunofluorescence after treatment with BiTE®. Cells are analyzed by cellular imaging.
Proper citation: Sandra L. Ross, Marika Sherman, Patricia L. McElroy, Julie A. Lofgren, Gordon Moody, Patrick A. Baeuerle, Angela Coxon, Tara Arvedson 2017. Immunofluorescence: EGFR, ICAM-1 and FAS detection. protocols.io dx.doi.org/10.17504/protocols.io.hwgb7bw Copy
Authors: Leigh Propper, Marda Jorgensen
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This method details the microtomy process for specimens that will be stained and analyzed using the Akoya CODEX® system.This process applies to paraffin embedded blocks containing tissue of no more than 1cm x 1cm in size.FFPE tissues for CODEX® analysis must be sectioned onto prepared poly-l-lysine coated coverslips.Cut and mounted tissue sections can be stored at 4°C for up to one(1 )month prior to staining.
Proper citation: Leigh Propper, Marda Jorgensen 2019. HuBMAP - Tissue Sectioning for CODEX Specimens. protocols.io dx.doi.org/10.17504/protocols.io.basdiea6 Copy
Authors: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Kara A. Clissold, Warren M. Grill
Group: SPARC
Summary: The protocol describes immunohistochemistry with anti-claudin-1, imaging, image segmentation, and image analysis methods to quantify human vagus nerve morphology.
Proper citation: Nicole A. Pelot, J. Ashley Ezzell, Gabriel B. Goldhagen, Kara A. Clissold, Warren M. Grill 2020. SPARC_Duke_PelotGrill_OT2-OD025340_PigVagusNerve_FibronectinIF_Morphology. protocols.io dx.doi.org/10.17504/protocols.io.bfwtjpen Copy
Authors: Cj Xia
Group: Boster Bio
Summary: Immunohistochemistry (IHC) is a method that combines biochemical, histological and immunological techniques into a simple but powerful assay for protein detection. IHC provides valuable information as it visualizes the distribution and localization of specific cellular components within cells and in proper tissue context.This protocol describes the steps for performing ICC/IF.
Proper citation: Cj Xia 2018. ICC/IF Protocol. protocols.io dx.doi.org/10.17504/protocols.io.mgcc3sw Copy
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