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Authors: Lynn Doran
Group: Ag SynBio Lab UIUC

Proper citation: Lynn Doran 2021. Transplanting Tobacco Seedlings in the Greenhouse. protocols.io https:// Copy   

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Authors: John Palmer
Summary: A protocol for sampling people for purposes of understanding patterns of mobility and activity-space segregation at the scale of city-days.

Proper citation: John Palmer 2018. Human Trajectory Sampling at the City-Day Scale. protocols.io https://dx.doi.org/10.17504/protocols.io.njgdcjw Copy   

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Authors: Klinger Vagner Teixeira Da Costa, Luis Pedro Coelho
Summary: Trata-se de uma ficha de anamneses direcionada para avaliação audiológica em crianças com a síndrome congênita do vírus da Zica.

Proper citation: Klinger Vagner Teixeira Da Costa, Luis Pedro Coelho 2019. Protocolo de avaliação clínica audiológica para crianças com microcefalia. protocols.io https://dx.doi.org/10.17504/protocols.io.5czg2x6 Copy   

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Authors: Judy Northill, Ian Mackay
Group: Public Health Virology, Forensic and Scientific Services, Coronavirus Method Development Community
Summary: A real-time RT-PCR to specifically detect SARS-CoV-2 betacoronavirus also called nCoV-2019 or Wuhan seafood market pneumonia virus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region is within the ORF1ab sequence.NotesAssay is fully optimised (as of 24Jan2020).This test has identified a clinical positive cases of coronavirus disease (COVID-19)

Proper citation: Judy Northill, Ian Mackay 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) real-time RT-PCR ORF1ab 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bgtmjwk6 Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: This is the protocol for dephosphorylation of 5'-ends of DNA using AnP (Antarctic Phosphatase - M0289).

Proper citation: New England Biolabs 2014. Dephosphorylation using AnP (M0289). protocols.io https://dx.doi.org/10.17504/protocols.io.cdns5d Copy   

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Authors: Dave Lunt
Group: EvoHull
Summary: Nauplii, ie newly hatched Artmemia (3-5 days), are processed to concentrate and separate from the eggs, before a DNA extraction

Proper citation: Dave Lunt 2017. Isolation of Artemia nauplii for DNA extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.ifbcbin Copy   

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Authors: Kevin Crouse
Summary: Teachers’ Sense of Efficacy is the beliefs in their capability to make a difference in student learning, to be able to get through even to students who are difficult or unmotivatedd. The Teacher Sense of Efficacy Scale asks teachers to assess their capability concerning instructional strategies, student engagement, and classroom management.This protocol taken from Megan Tschannen-Moran's classic work on Teacher Self-Efficacy.

Proper citation: Kevin Crouse 2020. Teacher Sense of Efficacy Scale Short Form. protocols.io https://dx.doi.org/10.17504/protocols.io.2j2gcqe Copy   

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Authors: Sarah Hessen-Schmidt

Proper citation: Sarah Hessen-Schmidt 2016. Zobell Broth. protocols.io https://dx.doi.org/10.17504/protocols.io.e7wbhpe Copy   

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Authors: Elena Dorando, Thilo Sachse, Tim Mathes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper
Summary: Please find detailed information on our protocol in the attached PDF file.

Proper citation: Elena Dorando, Thilo Sachse, Tim Mathes, Simone Heß, Petra Thürmann, Sven Schmiedl, Salmaan Kanji, Carole Lunny, Pierre Thabet, Dawid Pieper 2020. Overviews on adverse events in pharmacological interventions. protocols.io https://dx.doi.org/10.17504/protocols.io.bfgqjjvw Copy   

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Authors: Brett Hanzlicek, Dennis Bourbeau, Margot Damaser
Group: SPARC
Summary: In this study, we will be using Yorkshire Pigs, 50-70kg. The purpose of this study is to develop a tool to measure bowel fullness and activity. This system will eventually be able to provide continuous, wireless, battery−powered data and ultimately be translated for use in research and clinicalapplications of bowel function. We will measure porcine bowel compliance, pressures, and dimensions in acute live animal studies.

Proper citation: Brett Hanzlicek, Dennis Bourbeau, Margot Damaser 2021. SPARC Pig2 acute wired ColoMOCA implantation. protocols.io https://dx.doi.org/10.17504/protocols.io.bfxgjpjw Copy   

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Authors: Don Cooper

Proper citation: Don Cooper 2020. Mobile Device Quantification of Lateral Flow Tests: Modular illumination and sensor chamber (US patent US20160131592A1). protocols.io https://dx.doi.org/10.17504/protocols.io.bmmwk47e Copy   

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Authors: Stefania Marcotti, Koichiro Maki, Gwendolen C Reilly, Damien Lacroix, Taiji Adachi
Summary: Four different samples were employed for experiments, designed as follows:HABP/HA: cantilever functionalised with hyaluronic acid binding protein, untreated cell sample;BSA/HA: cantilever functionalised with bovine serum albumin, untreated cell sample;untreated/HA: non-functionalised cantilever, untreated cell sample;HABP/HAase: cantilever functionalised with hyaluronic acid binding protein, cell sample treated with HAaseThe steps of activation are listed in this protocol and were the same for Sample 1 (HABP/HA, functionalisation molecule: hyaluronic acid binding protein), Sample 2 (BSA/HA, functionalisation molecule: bovine serum albumin) and Sample 4 (HABP/HAase, functionalisation molecule: hyaluronic acid binding protein). The cantilevers used to test cells in Sample 3 (untreated/HA) were not treated.Similar protocols were described in:* Maki K et al. Mechano-adaptive sensory mechanism of α-catenin under tension. Sci Rep 2016;6: 24878. doi:10.1038/srep24878* Maki K et al. Real-time TIRF observation of vinculin recruitment to stretched α-catenin by AFM. Sci Rep 2018;8: 1–8. doi:10.1038/s41598-018-20115-8

Proper citation: Stefania Marcotti, Koichiro Maki, Gwendolen C Reilly, Damien Lacroix, Taiji Adachi 2018. Cantilever functionalisation for AFM single molecule force spectroscopy. protocols.io https://dx.doi.org/10.17504/protocols.io.ra4d2gw Copy   

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Authors: Claudia Pogoreutz, Christian Voolstra
Group: reefgenomics, Aiptasia-Symbiodiniaceae Model System
Summary: Endozoicomonas are gram-negative bacteria widely and often abundantly associated with marine invertebrates and fish (Yang et al., 2010; Bayer et al., 2013; Nishijima et al., 2013; Hyun et al., 2014; Katharios et al., 2015; Ding et al., 2016; Neave et al., 2017a; Schreiber et al., 2016; Pogoreutz et al., 2018). Despite their ubiquitous distribution, only few cultured strains are available, as Endozoicomonasare supposedly difficult to isolate and to maintain in pure cultures (Neave et al., 2017b). Here we detail a protocol that allowed us to reproducibly isolate Endozoicomonasfrom stony corals (Acropora humilis) from the Red Sea. This protocol should be useful in isolating abundant Endozoicomonasfrom other corals or marine invertebrates.ReferencesBayer, T., Neave, M.J., Alsheikh-Hussain, A., Aranda, M., Yum, L.K., Mincer, T., et al. (2013) The microbiome of the Red Sea coral Stylophora pistillatais dominated by tissue-associated Endozoicomonasbacteria. Appl. Environ. Microbiol.79: 4759–4762.Ding, J.Y., Shiu, J.H., Chen, W.M., Chiang, Y.R., and Tang, S.L. (2016) Genomic insight into the host-endosymbiont relationship of Endozoicomonas montiporaeCL-33T with its coral host. Front. Microbiol.7: 251.Hyun, D.W., Shin, N.R., Kim, M.S., Oh, S.J., Kim, P.S., Whon, T.W., and Bae, J.W. (2014) Endozoicomonas atrinaesp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. Int. J. Syst. Evol. Microbiol.64: 2312–2318.Katharios, P., Seth-Smith, H.M.B., Fehr, A., Mateos, J.M., Qi, W., Richter, D., et al. (2015) Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: Striking genomic and morphological features of novel Endozoicomonassp. Sci. Rep.5: 1–13.Neave, M.J., Michell, C.T., Apprill, A., and Voolstra, C.R. (2017a) Endozoicomonasgenomes reveal functional adaptation and plasticity in bacterial strains symbiotically associated with diverse marine hosts. Sci. Rep.7: 40579.Neave, M. J., Apprill, A., Ferrier-Pagès, C., & Voolstra, C. R. (2016) Diversity and function of prevalent symbiotic marine bacteria in the genus Endozoicomonas. App. Microbiol. Biotech., 100:8315-8324.Neave, M.J., Rachmawati, R., Xun, L., Michell, C.T., Bourne, D.G., Apprill, A., and Voolstra, C.R. (2017b) Differential specificity between closely related corals and abundant Endozoicomonasendosymbionts across global scales. ISMEJ 11: 186-200.Nishijima, M., Adachi, K., Katsuta, A., Shizuri, Y., and Yamasato, K. (2013) Endozoicomonas numazuensissp. nov., a gammaproteobacterium isolated from marine sponges, and emended description of the genus EndozoicomonasKurahashi and Yokota 2007. Int. J. Syst. Evol. Microbiol.63: 709–714.Pogoreutz, C., Rädecker, N., Cárdenas, A., Gärdes, A., Wild, C., and Voolstra, C.R. (2018) Dominance of Endozoicomonasbacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosamicrobiome.Ecol. Evol.8: 2240–2252.Schreiber, L., Kjeldsen, K.U., Funch, P., Jensen, J., Obst, M., Lopez-Legentil, S., and Schramm, A. (2016) Endozoicomonasare specific, facultative symbionts of sea squirts. Front. Microbiol. 7: 1–15.Yang, C.-S., Chen, M.-H., Arun, A.B., Chen, C.A., Wang, J.-T., and Chen, W.-M. (2010) Endozoicomonas montiporaesp. nov., isolated from the encrusting pore coral Montipora aequituberculata. Int. J. Syst. Evol. Microbiol.60: 1158–1162.

Proper citation: Claudia Pogoreutz, Christian Voolstra 2018. Isolation, culturing, and cryopreservation of Endozoicomonas (Gammaproteobacteria: Oceanospirillales: Endozoicomonadaceae) from reef-building corals. protocols.io https://dx.doi.org/10.17504/protocols.io.t2aeqae Copy   

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Authors: Gergely Nagymáté, Rita M Kiss
Summary: The protocol provides guidelines, preparation and execution instructions to perform and process a gait analysis trial by a novel motion capture method using virtually calibrated anatomical points tracked by augmented reality (AR) markers.

Proper citation: Gergely Nagymáté, Rita M Kiss 2018. Gait analysis using augmented reality markers. protocols.io https://dx.doi.org/10.17504/protocols.io.qkzdux6 Copy   

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Authors: Jernej Turnsek, Chris Dupont
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Here we present an efficient way to grow Tp colonies inside a 0.25% superclean agar matrix. This protocol could possibly be applicable to other marine microeukaryotes that are problematic to grow on fully solid support.

Proper citation: Jernej Turnsek, Chris Dupont 2017. Pour plating of Thalassiosira pseudonana (Tp). protocols.io https://dx.doi.org/10.17504/protocols.io.jfncjme Copy   

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Authors: David Frommholz, Alexandra Ehl, Nadine Stefanczyk
Summary: Purification Guide for the Isolation of Antibodies with ChroSpin Columns by DALEX Biotech.Easy and quick small scale antibody purification from various sources and species.Each ChroSpin column has a binding capacity of > 2 mg (tested with human polyclonal Ig, binding varies between species and clones).The proprietary resin does not shrink or swell in aqueous buffers.High pressure stability.pH stability short term 2 - 8, long term 3 - 8.Excellent thermal stability up to 15 minutes at 80 °C in aqueous buffers at neutral pH.Can be dried for long term storage (80 °C for > 2 h).

Proper citation: David Frommholz, Alexandra Ehl, Nadine Stefanczyk 2018. ChroSpin - ProteinA/G. protocols.io https://dx.doi.org/10.17504/protocols.io.vvte66n Copy   

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Authors: Michael Henson, Ben Temperton, Cameron Thrash
Group: Thrash Lab
Summary: Modified 1D Native Barcoding genomic DNA protocol (v. NBE_9006_v103_revO_21Dec2016 for SQK-LSK108) from the Temperton Lab (University of Exeter)

Proper citation: Michael Henson, Ben Temperton, Cameron Thrash 2020. Modified 1D Native Barcoding genomic DNA protocol from the Temperton Lab (University of Exeter). protocols.io https://dx.doi.org/10.17504/protocols.io.bixskfne Copy   

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Authors: Fabien Vincent

Proper citation: Fabien Vincent 2017. cGAS Enzymatic Assay – cGAMP Fluorescence Polarization Format. protocols.io https://dx.doi.org/10.17504/protocols.io.jaycifw Copy   

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Authors: Magdalena Julkowska
Group: Salt Lab KAUST
Summary: The standard protocol to propagate TOP10 Competent cells for Heatshock transformation method

Proper citation: Magdalena Julkowska 2020. Home-made TOP10 competent heat-shock cells. protocols.io https://dx.doi.org/10.17504/protocols.io.pbtdinn Copy   

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Authors: Matus Valach
Summary: Simple protocol for mapping 5′-P RNA termini by RT-PCR after the addition of a 5′ adaptor using T4 RNA ligase 1.

Proper citation: Matus Valach 2019. Addition of the adaptor to RNA substrates for 5′ RACE. protocols.io https://dx.doi.org/10.17504/protocols.io.xsrfnd6 Copy   

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