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Skin lesions monitoring on slaughtered pigs Resource Report Resource Website |
Mattia Bottacini, Annalisa Scollo, Sandra A. Edwards, Barbara Contiero, Martina Veloci, Vincenzo Pace, Flaviana Gottardo | DOI:10.17504/protocols.io.ugketuw | On a high speed slaughter line for pigs, skin scratches were separately scored in the posterior region (defined as the area including the hind legs and the tail) and the anterior one (as the remaining area), while the whole carcass was examined for external hematomas. Chronic ear and tail lesions referable to the rearing phase, and bursitis were recorded as retrospective welfare indicators. | Bottacini M, Scollo A, Edwards SA, Contiero B, Veloci M, Pace V, Gottardo F (2018) Skin lesion monitoring at slaughter on heavy pigs (170 kg): Welfare indicators and ham defects. PLoS ONE 13(11): e0207115. doi: 10.1371/journal.pone.0207115 | University of Padua, Swivet Research snc, University of Newcastle-upon-Tyne, University of Padua, Suivet snc, OPAS pig farmer association, University of Padua | https://doi.org/10.1371/journal.pone.0207115 | 1 | 2018 | Mattia Bottacini, Annalisa Scollo, Sandra A. Edwards, Barbara Contiero, Martina Veloci, Vincenzo Pace, Flaviana Gottardo 2018. Skin lesions monitoring on slaughtered pigs. protocols.io https://dx.doi.org/10.17504/protocols.io.ugketuw | 2021-04-15 09:15:47 | ||
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allele.variability Resource Report Resource Website |
Sara Beier | DOI:10.17504/protocols.io.7vvhn66 | A prerequisite to improve the predictability of microbial community dynamics is to understand their assembly mechanisms. To study factors that contribute to microbial community assembly, we examined temporal dynamics of genes in five aquatic metagenome time series, originating from marine off-shore or coastal sites and one lake, while focusing on a trait-based data evaluation.We expected to find gene-specific patterns for the temporal allele variability depending on the metacommunity size of carrier-taxa and variability of the milieu and the substrates that the resulting enzymes are exposed to. In more detail we hypothesized that a larger metacommunity would cause increased temporal variability of functional units, as shown previously for taxonomic units. Furthermore, we hypothesized that multi-copy genes feature higher temporal variability then single-copy genes, because gene multiplication is often the consequence of increased variability in (subtil) changes of substrate quality and quantity. Finally, we hypothesized that direct exposure of proteins to the extracellular environment would result in increased temporal variability of the respective gene compared to intracellular proteins as they would be exposed to highly variable conditions. The first two hypotheses were confirmed in all, while an effect of the subcellular location of gene-products was only seen in three out of the five time series. The gene with highest allele variability throughout all datasets was an iron transporter, which also represents a target for phage infections. This finding points to the general importance of iron transporter mediated phage infections on the assembly and maintenance of diversity of aquatic prokaryotes. | Leibniz Institute for Baltic Sea Research | 1 | 2019 | Sara Beier 2019. allele.variability. protocols.io https://dx.doi.org/10.17504/protocols.io.7vvhn66 | 2021-04-15 09:15:56 | ||||
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Extraction of surface-community DNA from Ulva sp. Resource Report Resource Website |
Torsten Thomas | DOI:10.17504/protocols.io.f3xbqpn | CMSI protocols | 1 | 2016 | Torsten Thomas 2016. Extraction of surface-community DNA from Ulva sp.. protocols.io https://dx.doi.org/10.17504/protocols.io.f3xbqpn | 2021-04-15 09:15:47 | |||||
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Probe-Seq Resource Report Resource Website |
Ryoji Amamoto, Constance L. Cepko | DOI:10.17504/protocols.io.6j3hcqn | Recent transcriptional profiling technologies are uncovering previously-undefined cell populations and molecular markers at an unprecedented pace. While single cell RNA (scRNA) sequencing is an attractive approach for unbiased transcriptional profiling of all cell types, a complementary method to isolate and sequence specific cell populations from heterogeneous tissue remains challenging. Here, we developed Probe-Seq, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature. Dissociated cells are labelled using fluorescent in situhybridization (FISH) for RNA, and then isolated by fluorescent activated cell sorting (FACS). We used Probe-Seq to purify and profile specific cell types from mouse, human, and chick retinas, as well as the Drosophila midgut. Probe-Seq is compatible with frozen nuclei, making cell types within archival tissue immediately accessible. As it can be multiplexed, combinations of markers can be used to create specificity. Multiplexing also allows for the isolation of multiple cell types from one cell preparation. Probe-Seq should enable RNA profiling of specific cell types from any organism. | Harvard Medical School, Harvard Medical School | https://www.biorxiv.org/content/10.1101/735738v1 | 2 | 2019 | Ryoji Amamoto, Constance L. Cepko 2019. Probe-Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.6j3hcqn | 2021-04-15 09:15:47 | |||
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E. coli K12 DNA Extraction Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.yujfwun | 481b Laboratory | How to extract DNA from E. coli K12 using Wizard® Genomic DNA Purification Kit by Promega®.I do not claim any credit for the development of this protocol. It has been adapted from the protocol detailed in: . | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. E. coli K12 DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.yujfwun | 2021-04-15 09:15:49 | |||
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Using sequins in metagenome experiments. Resource Report Resource Website |
Tim Mercer | DOI:10.17504/protocols.io.bic3kayn | Metagenome sequins are a set of synthetic DNA controls that reflect the sequence complexity, GC content, phylogenetic diversity and abundance of a natural microbial community. The sequins are ‘spiked-in’ to your DNA sample, which together undergo to library preparation, sequencing and analysis. The sequins can then be distinguished from you sample DNA in the output library by their synthetic sequence, and analyzed as internal controls. Sequins are compatible with all standards library preparation and sequencing methods. This protocol describes the laboratory steps required to re-suspend and spike the sequins into your DNA sample, as well as the bioinformatic steps required to analyze sequins in your output library. For further details on the design, validation and use of sequins, we refer users to ‘Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis’ by Hardwick et. al., (2018) Nature Communications. | Garvan Institute of Medical Research | http://www.sequinstandards.com | 1 | 2020 | Tim Mercer 2020. Using sequins in metagenome experiments.. protocols.io https://dx.doi.org/10.17504/protocols.io.bic3kayn | 2021-04-15 09:15:49 | |||
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Chlamydomonas reinhardtii nuclear transformation by electroporation. Resource Report Resource Website |
João Vitor Molino | University of Zurich | https://doi.org/10.1371/journal.pone.0192433 | 2 | 2021 | João Vitor Molino 2021. Chlamydomonas reinhardtii nuclear transformation by electroporation.. protocols.io https:// | 2021-04-15 09:15:47 | |||||
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Intradermal coinfection of mice ears with L. major IA-2 and Staphylococcus aureus Newman strain Resource Report Resource Website |
Tiffany Borbon, Corey Parlet, Gwendolyn Clay, Mary E. Wilson | DOI:10.17504/protocols.io.vdse26e | Cutaneous coinfection of bacteria with Leishmania species in mice provides a model for studying the immune effects of non-sterile inoculation of Leishmania protozoa. In this protocol, we describe a method for intradermal coinfection of mice ear pinnas with Leishmania major IA-2 and a low dose of Staphylococcus aureus Newman strain. This protocol describes the methods for S. aureus and L. major preparation, mixing, mouse anesthesia and intradermal injection as well as infection monitoring and euthanasia. This protocol can be modified for the co-inoculation of other bacterial or leishmanial species in mice. | Borbón TY, Scorza BM, Clay GM, Queiroz FLNd, Sariol AJ, Bowen JL, Chen Y, Zhanbolat B, Parlet CP, Valadares DG, Cassel SL, Nauseef WM, Horswill AR, Sutterwala FS, Wilson ME (2019) Coinfection with Leishmania major and Staphylococcus aureus enhances the pathologic responses to both microbes through a pathway involving IL-17A. PLoS Negl Trop Dis 13(5): e0007247. doi: 10.1371/journal.pntd.0007247 | University of Iowa, University of Iowa, University of California San Diego, University of Iowa | https://doi.org/10.1371/journal.pntd.0007247 | 1 | 2018 | Tiffany Borbon, Corey Parlet, Gwendolyn Clay, Mary E. Wilson 2018. Intradermal coinfection of mice ears with L. major IA-2 and Staphylococcus aureus Newman strain. protocols.io https://dx.doi.org/10.17504/protocols.io.vdse26e | 2021-04-15 09:15:47 | ||
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Evidence-Based Information Halves the Influence of Physicians’ Non-Evidence-Based Cancer Screening Recommendations Resource Report Resource Website |
Odette Wegwarth*, Gert G. Wagner**, Gerd Gigerenzer* | DOI:10.17504/protocols.io.imscc6e | Randomized survey study to test whether evidence-based patient information about cancer screening provided upfront to people make them less likely to simply follow a non-evidence-based recommendation of their physician | Wegwarth O, Wagner GG, Gigerenzer G, Can facts trump unconditional trust? Evidence-based information halves the influence of physicians’ non-evidence-based cancer screening recommendations. PLoS ONE 12(8). doi: 10.1371/journal.pone.0183024 | *Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany), **German Institute for Economic Research and Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany), *Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany), **German Institute for Economic Research and Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany), *Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany), **German Institute for Economic Research and Max Planck Institute for Human Development, Lentzeallee 94, 14195 Berlin (Germany) | https://doi.org/10.1371/journal.pone.0183024 | 1 | 2018 | Odette Wegwarth*, Gert G. Wagner**, Gerd Gigerenzer* 2018. Evidence-Based Information Halves the Influence of Physicians’ Non-Evidence-Based Cancer Screening Recommendations. protocols.io https://dx.doi.org/10.17504/protocols.io.imscc6e | 2021-04-15 09:15:56 | ||
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Preparo de Meio L15 Resource Report Resource Website |
Fabio Gomes | PlasmoVet | UFRJ | 1 | 2020 | Fabio Gomes 2020. Preparo de Meio L15. protocols.io https:// | 2021-04-15 09:15:50 | |||||
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Monterey Wharf II Weekly Phytoplankton Monitoring Sample Collection and Processing Notes Resource Report Resource Website |
april woods | DOI:10.17504/protocols.io.f2pbqdn | Environmental Biotechnology Lab | A description of how samples are collected and processed as part of MLML Smith Lab's weekly HAB monitoring efforts in Monterey, CA.Sampling Location: Monterey Commercial Wharf, Monterey, CA. 36° 36.3' N 121° 53.3' WOceanographic and meteorological observations for the time of sampling are referenced from the Monterey, CA NOAA station ID: 9413450 | Moss Landing Marine Labs | 1 | 2016 | april woods 2016. Monterey Wharf II Weekly Phytoplankton Monitoring Sample Collection and Processing Notes. protocols.io https://dx.doi.org/10.17504/protocols.io.f2pbqdn | 2021-04-15 09:15:47 | |||
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Homogenate of A. cervicornis Resource Report Resource Website |
Stephanie Rosales | (University of Miami) | 1 | 2020 | Stephanie Rosales 2020. Homogenate of A. cervicornis. protocols.io https:// | 2021-04-15 09:15:55 | ||||||
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TRIO tracing Resource Report Resource Website |
Hongwei Dong | DOI:10.17504/protocols.io.4xsgxne | TRIO (Tracing the Relationship of Inputs and Outputs) experiments systematically inject complementary viruses into different target brain regions to monosynaptically label inputs to a specific projection neuron population. TRIO experiments use 3 different viruses (AAVretro-Ef1a-Cre, AAV8-hSyn-FLEX- TVA-P2A-GFP-2A-oG helper virus, and EnvA pseudotyped G-deleted Rabies mCherry (EnvA RVdG-4mCherry). | USC Mark and Mary Stevens Neuroimaging and Informatics Institute | https://cic.ini.usc.edu/protocols/trio-tracing | 1 | 2019 | Hongwei Dong 2019. TRIO tracing. protocols.io https://dx.doi.org/10.17504/protocols.io.4xsgxne | 2021-04-15 09:15:55 | |||
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SNP Analysis 1: DNA Extraction Resource Report Resource Website |
Serhat Sevli, C. Yunus Sahan | DOI:10.17504/protocols.io.gycbxsw | Nehir Biyoteknoloji Ltd. www.nehirbt.com | Nehir Biyoteknoloji Ltd. www.nehirbt.com, Nehir Biyoteknoloji Ltd. www.nehirbt.com | 1 | 2017 | Serhat Sevli, C. Yunus Sahan 2017. SNP Analysis 1: DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.gycbxsw | 2021-04-15 09:15:55 | ||||
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Agarose Gel Electrophoresis-Chem 584 Resource Report Resource Website |
Ken Christensen, Addgene The Nonprofit Plasmid Repository | DOI:10.17504/protocols.io.bjvnkn5e | This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the Addgene protocol page. | Brigham Young University, Addgene | https://www.addgene.org/protocols/gel-electrophoresis/ | 1 | 2020 | Ken Christensen, Addgene The Nonprofit Plasmid Repository 2020. Agarose Gel Electrophoresis-Chem 584 . protocols.io https://dx.doi.org/10.17504/protocols.io.bjvnkn5e | 2021-04-15 09:15:55 | |||
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Colony PCR (Protocol for Thermo Scientific™ Phire™ Hot Start II DNA Polymerase) Resource Report Resource Website |
Alba Balletbó | DOI:10.17504/protocols.io.7kkhkuw | iGEM Wageningen 2019 | Thermo Scientific™ Phire™ Hot Start II DNA Polymerase is a novel DNA polymerase designed for use in all routine and high throughput PCR applications. A special DNA binding domain linked to the Phire Hot Start II DNA Polymerase enhances the processivity of the polymerase, enabling short extension times and improved yields. The polymerase is also capable of amplifying long DNA fragments, such as the 7.5 kb genomic DNA used in Thermo Scientific quality control assays. Phire Hot Start II DNA Polymerase provides 2-fold fidelity compared to Taq DNA polymerase. The hot start modification of the polymerase is based on the Affibody™ inactivation method1,2 . It inhibits DNA polymerase activity at ambient temperatures, thus preventing amplification of non-specific products. At polymerization temperatures the Affibody molecule is released, rendering the polymerase fully active. Phire Hot Start II DNA Polymerase generates blunt ends in the amplification products. It does not possess the 5’→3’ exonuclease activity needed for hydrolysis experiments. | Wageningen University | 1 | 2019 | Alba Balletbó 2019. Colony PCR (Protocol for Thermo Scientific™ Phire™ Hot Start II DNA Polymerase). protocols.io https://dx.doi.org/10.17504/protocols.io.7kkhkuw | 2021-04-15 09:15:51 | |||
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General Salts + Sodium Bicarbonate Solutions Resource Report Resource Website |
Ada de la Cruz | DOI:10.17504/protocols.io.bpfkmjkw | Hillesland Lab | University of Washington | 1 | 2020 | Ada de la Cruz 2020. General Salts + Sodium Bicarbonate Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bpfkmjkw | 2021-04-15 09:15:55 | ||||
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Universal sandwich ELISA for investigating the binding of avian immunoglobulins to Staphylococcal protein-A (SpA) using anti-IgY-peroxidase conjugate. Resource Report Resource Website |
Angel Justiz-Vaillant, Monica F. Smikle | DOI:10.17504/protocols.io.bjqxkmxn | University of the West Indies, [email protected] | University of the West Indies St. Augustine, University of the West Indies. Mona Campus | 1 | 2020 | Angel Justiz-Vaillant, Monica F. Smikle 2020. Universal sandwich ELISA for investigating the binding of avian immunoglobulins to Staphylococcal protein-A (SpA) using anti-IgY-peroxidase conjugate.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjqxkmxn | 2021-04-15 09:15:55 | ||||
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Autologous platelet-rich plasma for topical application as regenerative therapy in dogs Resource Report Resource Website |
Adolfo Maria TAMBELLA, Evelina SERRI, Anna Rita ATTILI | DOI:10.17504/protocols.io.nb6dare | This protocol describes a step-by-step procedure for the production of autologous platelet-rich plasma for topical application in dogs.This protocol was used in the following publication:Tambella AM, Attili AR, Dini F, Palumbo Piccionello A, Vullo C, Serri E, Scrollavezza P, Dupré G. Autologous platelet gel to treat chronic decubital ulcers: a randomized, blind controlled clinical trial in dogs. Veterinary Surgery, 43(6), 2014: 726-733. (ISSN: 0161-3499) (DOI: 10.1111/j.1532-950X.2014.12148.x).http://onlinelibrary.wiley.com/doi/10.1111/j.1532-950X.2014.12148.x/full | School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy, School of Biosciences and Veterinary Medicine, University of Camerino, Matelica, MC, Italy | http://onlinelibrary.wiley.com/doi/10.1111/j.1532-950X.2014.12148.x/full | 1 | 2018 | Adolfo Maria TAMBELLA, Evelina SERRI, Anna Rita ATTILI 2018. Autologous platelet-rich plasma for topical application as regenerative therapy in dogs. protocols.io https://dx.doi.org/10.17504/protocols.io.nb6dare | 2021-04-15 09:15:55 | |||
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Fitting of SAXS data using SCATTER Resource Report Resource Website |
Chris Berndsen | James Madison University | 1 | 2021 | Chris Berndsen 2021. Fitting of SAXS data using SCATTER . protocols.io https:// | 2021-04-15 09:15:55 |
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