Protocols   Select Another Resource Report Type

Authors: Mattia Bottacini, Annalisa Scollo, Sandra A. Edwards, Barbara Contiero, Martina Veloci, Vincenzo Pace, Flaviana Gottardo
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Sara Beier
Summary: 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.

Proper citation: Sara Beier 2019. allele.variability. protocols.io https://dx.doi.org/10.17504/protocols.io.7vvhn66 Copy   

•   Source:

Authors: Torsten Thomas
Group: CMSI protocols

Proper citation: Torsten Thomas 2016. Extraction of surface-community DNA from Ulva sp.. protocols.io https://dx.doi.org/10.17504/protocols.io.f3xbqpn Copy   

•   Source:

Authors: Ryoji Amamoto, Constance L. Cepko
Summary: 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.

Proper citation: Ryoji Amamoto, Constance L. Cepko 2019. Probe-Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.6j3hcqn Copy   

•   Source:

Authors: Kenneth Schackart, Kattika Kaarj
Group: 481b Laboratory
Summary: 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: .

Proper citation: Kenneth Schackart, Kattika Kaarj 2019. E. coli K12 DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.yujfwun Copy   

•   Source:

Authors: Tim Mercer
Summary: 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.

Proper citation: Tim Mercer 2020. Using sequins in metagenome experiments.. protocols.io https://dx.doi.org/10.17504/protocols.io.bic3kayn Copy   

•   Source:

Authors: João Vitor Molino

Proper citation: João Vitor Molino 2021. Chlamydomonas reinhardtii nuclear transformation by electroporation.. protocols.io https:// Copy   

•   Source:

Authors: Tiffany Borbon, Corey Parlet, Gwendolyn Clay, Mary E. Wilson
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Odette Wegwarth*, Gert G. Wagner**, Gerd Gigerenzer*
Summary: 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

Proper citation: 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 Copy   

•   Source:

Authors: Fabio Gomes
Group: PlasmoVet

Proper citation: Fabio Gomes 2020. Preparo de Meio L15. protocols.io https:// Copy   

•   Source:

Authors: april woods
Group: Environmental Biotechnology Lab
Summary: 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

Proper citation: 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 Copy   

•   Source:

Authors: Stephanie Rosales

Proper citation: Stephanie Rosales 2020. Homogenate of A. cervicornis. protocols.io https:// Copy   

•   Source:

Authors: Hongwei Dong
Summary: 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).

Proper citation: Hongwei Dong 2019. TRIO tracing. protocols.io https://dx.doi.org/10.17504/protocols.io.4xsgxne Copy   

•   Source:

Authors: Serhat Sevli, C. Yunus Sahan
Summary: Nehir Biyoteknoloji Ltd. www.nehirbt.com

Proper citation: Serhat Sevli, C. Yunus Sahan 2017. SNP Analysis 1: DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.gycbxsw Copy   

•   Source:

Authors: Ken Christensen, Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the Addgene protocol page.

Proper citation: Ken Christensen, Addgene The Nonprofit Plasmid Repository 2020. Agarose Gel Electrophoresis-Chem 584 . protocols.io https://dx.doi.org/10.17504/protocols.io.bjvnkn5e Copy   

•   Source:

Authors: Alba Balletbó
Group: iGEM Wageningen 2019
Summary: 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.

Proper citation: 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 Copy   

•   Source:

Authors: Ada de la Cruz
Group: Hillesland Lab

Proper citation: Ada de la Cruz 2020. General Salts + Sodium Bicarbonate Solutions. protocols.io https://dx.doi.org/10.17504/protocols.io.bpfkmjkw Copy   

•   Source:

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

Proper citation: 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 Copy   

•   Source:

Authors: Adolfo Maria TAMBELLA, Evelina SERRI, Anna Rita ATTILI
Summary: 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

Proper citation: 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 Copy   

•   Source:

Authors: Chris Berndsen

Proper citation: Chris Berndsen 2021. Fitting of SAXS data using SCATTER . protocols.io https:// Copy   

•   Source: