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Authors: 301910411478

Proper citation: 301910411478 2020. Yoga compared to non-exercise or physical therapy exercise on pain, disability, and quality of life for patients with chronic low back pain: A systematic review and meta-analysis of randomized controlled trials. protocols.io https://dx.doi.org/10.17504/protocols.io.bi6gkhbw Copy   

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Authors: Alba Balletbó
Group: iGEM Wageningen 2019

Proper citation: Alba Balletbó 2019. Antibiotic Stocks. protocols.io https://dx.doi.org/10.17504/protocols.io.7krhkv6 Copy   

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Authors: Livia Tenuta, Tarcísio Leitão, Jaime A. Cury

Proper citation: Livia Tenuta, Tarcísio Leitão, Jaime A. Cury 2018. Calcium release from calcium pretreated S. mutans at low pHs. protocols.io https://dx.doi.org/10.17504/protocols.io.mapc2dn Copy   

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Authors: Mari Golub
Group: Mouse Metabolic Phenotyping Centers
Summary: The y-maze is a modification of the T- maze which evaluates memory and special learning in rodents though quantification of spontaneous alternation (a measure of spatial cognition). This measure has previously been shown to be affected in mouse models of Alzheimer’s. References: Ohno et al. Neuron 41:27-33, 2004. Oakley et al. J Neuroscience 26(40):10129-10140, 2006. Ohno et al. Neurobiol Dis 26:134-145, 2007. Holcomb et al. Nat Med 4:97-100, 1998.

Proper citation: Mari Golub 2019. UC Davis - Y-Maze. protocols.io https://dx.doi.org/10.17504/protocols.io.yw7fxhn Copy   

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Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses The VOCs (Virus Orthologous Clusters) database is at the heart of our system. The database links directly to integrated tools for comparative analyses. VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval. Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu). design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists. Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations Linking to research reviews/papers for the research community. Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases Building new features into our tools Help with genome annotation

Proper citation: Nick Tang 2016. VBRC Base By Base: Import genes from Genbank file. protocols.io https://dx.doi.org/10.17504/protocols.io.ecxbaxn Copy   

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Authors: Shuntai Zhou
Summary: This is the protocol to prepare Primer ID MiSeq sequencing library. Viral RNA was first extracted using QIAamp viral RNA extraction kit.  The block of random nucleotides (Ns) in the cDNA primers served as the Primer ID. The Superscript III kit was used for the cDNA synthesis. We used two rounds of PCR to amplify the cDNA and incorporate Illumina indexed adapters with KAPA2G Robust and KAPA HiFi PCR kits, respectively. 

Proper citation: Shuntai Zhou 2018. Primer ID MiSeq Library Prep. protocols.io https://dx.doi.org/10.17504/protocols.io.useewbe Copy   

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Authors: Kristin Evans
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary: Vertical sleeve Gastrectomy (VSG) is a common surgical treatment of obesity, type-2 diabetes, and other comorbidities of obesity. The VSG mouse surgical model provides researchers with a mechanism to evaluate mechanistic studies to explore the methods by which VSG bariatric surgery produces beneficial effects on obesity. The surgical procedure is performed under sterile conditions in accordance with AAALAC standards. Surgical animals will be able to ship 2 weeks after the post-operative monitoring period is completed. Cohorts of Vertical Sleeve gastrectomy (VSG), a pair fed SHAM, and an ad lib SHAM will be provided with each cohort ordered.

Proper citation: Kristin Evans 2019. UC Davis - Vertical Sleeve Gastrectomy. protocols.io https://dx.doi.org/10.17504/protocols.io.za3f2gn Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: This reagent can be used in ELISA, Western blotting and Dot blot to detect antigens and antibodies. It is important in the immunodiagnosis of infectious diseases and other problems. I find this useful in the detection of anti-HIV antibodies by ELISA.

Proper citation: Angel Justiz-Vaillant 2020. Preparation of staphylococcal protein-A conjugated to horseradish peroxidase by the periodate method.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjk5kky6 Copy   

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Authors: yalhiyari
Group: XPRIZE Rapid Covid Testing

Proper citation: yalhiyari 2020. C-19 protocol. protocols.io https:// Copy   

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Authors: Roey Angel
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: Standard operating procedure for using the gassing manifoldThe gassing manifold is used for replacing the headspace of vials with N2 (or N2:CO2) or for degassing solutions. It is useful for preparing anoxic incubations, media and buffers before bringing them in closed vials into the anoxic chamber. The manifold is equipped with an electronic controller that automatically switches between the gas inlet and the vacuum pump and performs multiple cycles of headspace flushing.

Proper citation: Roey Angel 2019. Operating the gassing manifold. protocols.io https://dx.doi.org/10.17504/protocols.io.vcue2ww Copy   

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Authors: A. Townsend Peterson, Alex Asase, Dora L. Canhos, Sidnei de Souza, John Wieczorek
Summary: Biodiversity data exist in large quantities, which is a boon to biodiversity science. In spite of large numbers of data records being available, however, the proportion of those records that is readily usable for science applications is quite small. The difference between the full number of data records existing versus the records that are ready for use is the result of what we call "leakage" of data, in the form of steps that have not been taken or errors that remove the utility of the data. In this contribution, we explore several large-scale biodiversity data sets in terms of why they contain data records that are or are not ready for use.

Proper citation: A. Townsend Peterson, Alex Asase, Dora L. Canhos, Sidnei de Souza, John Wieczorek 2017. Characterizing Biodiversity Data Leaks. protocols.io https://dx.doi.org/10.17504/protocols.io.kebctan Copy   

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Authors: Daniel Vaulot
Group: Ecology of Marine Plankton (ECOMAP) team - Roscoff, Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: Concentrate phytoplankton samples about 100-fold typically from 5L down to 20 mL. Takes about 1 hour per sample. Samples can be used for flow cytometry sorting or for cultures. Enrichment by TFF usually keep growing for a longer time than unconcentrate samples.ReferenceMarie, D., Shi, X.L., Rigaut-Jalabert, F. & Vaulot, D. (2010). Use of flow cytometric sorting to better assess the diversity of small photosynthetic eukaryotes in the English Channel. FEMS Microbiology Ecology. 72. p.pp. 165–178.

Proper citation: Daniel Vaulot 2016. Tangential flow filtration (TFF) concentration of phytoplankton. protocols.io https://dx.doi.org/10.17504/protocols.io.gpybvpw Copy   

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Authors: Mariam Awlia, Magdalena Julkowska
Group: Salt Lab KAUST
Summary: The following protocol on plant material preparation and salt imposition for PlantScreen analysis will cover:Agar preparation for seedsSowing germination traysSowing PlantScreen traysPlantScreen preparationSalt stress impositionPlantScreen protocol

Proper citation: Mariam Awlia, Magdalena Julkowska 2019. Plant material preparation and salt imposition for PlantScreen analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.4xzgxp6 Copy   

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Authors: ShiNan Dong
Summary: To prepare the genomic DNA of microsporidia, 400 ll suspension of purified spores (1010 spores/ml) was mixed with 40 ll KOH (2 mol/l) in a 1.5 ml Eppendorf tube and incubated at 27C for 1 h, TEK buffer (1 mmol/l Tris–HCl, 10 mmol/l EDTA, 0.17 mol/l KCl, pH 8.0) was added and continued incubating at 27C for 1 h. Adjusted pH to 8.0 with 1 mol/l HCl, added 10% SDS in order to attain 0.5% in the mixture and kept it in ice-bath for 15 min. 20 mg/ml proteinase K (TaKaRa Biotechnology Co. LTD) was added in order to attain 200 lg/ml in the mixture and incubated at 50C for 4 h. Subsequently, isovolumetric tris–phenol extraction was performed twice, and washed with chloroform: isoamyl alcohol (24:1 v/v). 10% NaOAC was added to the recovered aqueous phase after centrifuging (10,000 r/min, 5 min), and then the DNA was precipitated by 2.5 times volume of cold ethanol at -20C for 40 min before centrifuging (12,000 r/min, 10 min). In addition, the precipitated DNA was rinsed twice with 500 ll cold 70% ethanol before drying at 37C for 5–10 min. Then, the extracted DNA was stored at -20C after dissolution in 50 ll TE buffer at 65C for 10 min. 

Proper citation: ShiNan Dong 2017. Preparation of Genomic DNA of Microsporidia. protocols.io https://dx.doi.org/10.17504/protocols.io.igacbse Copy   

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Authors: yang1832 , Julia Laskin
Group: NanoDESI MSI Julia Laskin group Purdue
Summary: Scope: Annotate protein species detected by Nano-DESI IMS analysis.

Proper citation: yang1832 , Julia Laskin 2020. Proteins annotation of Nano-DESI MSI datasets. protocols.io https://dx.doi.org/10.17504/protocols.io.bm2rk8d6 Copy   

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Authors: Sarah Hu
Group: Protist Research to Optimize Tools in Genetics (PROT-G), Caron Lab - Protistan Ecology, SCOPE
Summary: This protocol describes steps and considerations for working in the field to collect samples to be used for molecular work targetting marine (or freshwater) microbial eukaryotes. See downstream protocols for DNA/RNA extraction and library prep (pending) for 18S rRNA gene tag sequencing.Many steps in this protocol can be modified to fit a users' specific needs or environment type. Here, we strive to make recommendations that consider the delicate nature of single-celled eukaryotes and collect samples in the field as cleanly as possible. We use this approach for RNA and DNA-based sequencing - both for tag sequencing and metatranscriptomics.This protocol is based off of the field work we conduct at the San Pedro Ocean Time-series (SPOT) station. We go out to the SPOT station once a month. Once we arrive at the SPOT station, we try to sample at the same time of day each month. Timelapse video for sampling SPOT: https://youtu.be/1US3h_qD00wMaterials required:(1) 20 L carboys (volume amount flexible)(2) Covers for carboys (we use pizza bags, black trash bags, or coolers)(3) Ice packs(4) Tubing for Niskin (5) Vacuum pump filtration system (see time-lapse video)    - trap flask    - pump    - extra tubing & rubber/silicon stopper (to fit filter towers)(6) Filter towers that fit in vacuum pump filtration system(7) In-line filters, 47 mm(8) Nitex mesh, cut for 47 mm - 200 um & 80 um(9) RNase-spray(10) Absorbent pads (for reducing water spillage & covering countertops)(11) Liquid nitrogen - make sure to check regulations on transporting liquid nitrogen and storing it on-site/shipboard(12) 15 mL falcon tubes - RNase/DNase-free(13) RNA later or Lysis buffer (e.g. RLT buffer from this protocol)(14) Filters for collecting material, we use 0.7um GF/F filters**Our reasoning to use this filter size is that the 0.7um nominal pore size will collect the protistan fraction of the community, but it is a woven filter style, so more water can be filtered through without clogging.

Proper citation: Sarah Hu 2017. Sample collection from the field for downstream molecular analysis - microbial eukaryote-focused. protocols.io https://dx.doi.org/10.17504/protocols.io.hisb4ee Copy   

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Authors: Monserrat López-Sanmartín, Gaetano Catanese, Amalia Grau, Jose María Valencia, Jose Rafa García-March, José Ignacio Navas
Summary: The aim of this study has been to develop species-specific quantitative PCR (qPCR) protocol carrying out a fast, specific and effective molecular diagnose of Haplosporidium pinnae. In this sense, the detection limit for qPCR was equal to 30 copies of SSU rDNA / ng of DNA using plasmid alone and when 100ng DNA of non-infected oyster were added.

Proper citation: Monserrat López-Sanmartín, Gaetano Catanese, Amalia Grau, Jose María Valencia, Jose Rafa García-March, José Ignacio Navas 2019. Species-specific quantitative PCR (qPCR) protocol developed to identify Haplosporidium pinnae. protocols.io https://dx.doi.org/10.17504/protocols.io.xe7fjhn Copy   

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Authors: Benjamin Istace, Anne Friedrich, Léo dAgata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury
Group: GigaScience Press
Summary: This protocol describes the library preparation for Nanopore sequencing according to the SQK-MAP005 protocol. It accompanies the GigaScience publication:Benjamin Istace, et al. (2017) De novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer. GigaScience...

Proper citation: Benjamin Istace, Anne Friedrich, Léo dAgata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury 2017. SQK-MAP005 protocol for library preparation for Nanopore sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.gvubw6w Copy   

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Authors: Kelsey Miller
Group: BioLegend
Summary: This protocol is essentially the same as a standard ELISA protocol, with one major exception – all animal compounds must be avoided in buffers, etc. because they contain Neu5Gc, which will interfere with antibody activity and result in misleading data. Essentially, the glycoconjugate to be evaluated is immobilized on an ELISA plate and exposed to a primary antibody. The antibody provided in this kit has been shown to identify as little as 5 pmol of Neu5Gc per microgram glycoprotein, which is at or below the current detection limit for conventional DMB HPLC analysis. An advantage of the ELISA procedure is that it confirms the presence of Neu5Gc on the glycoconjugate of interest, but use caution, as it also reacts with solution/media that contains glycoconjugate.

Proper citation: Kelsey Miller 2017. Anti-Neu5Gc Antibody Kit Protocol - ELISA. protocols.io https://dx.doi.org/10.17504/protocols.io.hvpb65n Copy   

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Authors: Fernanda Svedman, Warangkana Lohcharoenkal, Matteo Bottai, Suzanne Egyhazi Brage, Enikö Sonkoly, Johan Hansson, Andor Pivarcsi, Hanna Eriksson

Proper citation: Fernanda Svedman, Warangkana Lohcharoenkal, Matteo Bottai, Suzanne Egyhazi Brage, Enikö Sonkoly, Johan Hansson, Andor Pivarcsi, Hanna Eriksson 2018. Plasma-derived exosomal preparation and isolation of RNA. protocols.io https://dx.doi.org/10.17504/protocols.io.tuienue Copy   

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