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Authors: Natalie Solonenko
Group: Sullivan Lab

Proper citation: Natalie Solonenko 2020. Ampure bead clean up for high molecular weight DNA . protocols.io https://dx.doi.org/10.17504/protocols.io.6kphcvn Copy   

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Authors: Brett Rasile, Kendra Maas
Group: Coronavirus Method Development Community, 2019-nCoV Wastewater Epidemiology, UConn Mars
Summary: Process

Proper citation: Brett Rasile, Kendra Maas 2021. SARS-CoV-2 Wastewater RNA Concentration and Extraction (Nanotrap® and NucleoMag® RNA Water). protocols.io https://dx.doi.org/10.17504/protocols.io.bn58mg9w Copy   

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Authors: Bonnie Poulos, Melissa Duhaime, Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Here, we adapt the linker amplified shotgun library (LASL) approach to next generation sequencing by offering an alternate polymerase for challenging samples, developing a more efficient sizing step, integrating a “reconditioning PCR” step to increase yield and minimize late-cycle PCR artifacts. Our optimized linker amplification method requires as little as 1 pg of DNA and is the most precise and accurate available, with amplification biases less than 1.5-fold, even for complex samples as diverse as a wild virus community. While optimized here for 454 sequencing, this linker amplification method can be used to prepare metagenomics libraries for sequencing with next-generation platforms, including Illumina and Ion Torrent.Adapted from the Broad’s LASL Sanger Seq’g Protocol, and optimized for low template work.

Proper citation: Bonnie Poulos, Melissa Duhaime, Li Deng 2016. DNA Preparation and Linker Amplification for Pyrosequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.c9zz75 Copy   

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Authors: John Stack, Gary Cline
Group: Mouse Metabolic Phenotyping Centers
Summary: Procedure used to determine the concentration of triglycerides in blood, serum, and plasma. Triglycerides are determined by coupling lipase, glucokinase, glycerol phosphate oxidase, and peroxidase to form a quinonemine dye which is measured at 500 nm.

Proper citation: John Stack, Gary Cline 2019. Yale - Triglycerides. protocols.io https://dx.doi.org/10.17504/protocols.io.y4bfysn Copy   

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Authors: Pierre Teodosio

Proper citation: Pierre Teodosio 2020. AMOVA AND PHILOGENY IN HIV-1 PROTOCOLS. protocols.io https://dx.doi.org/10.17504/protocols.io.bixqkfmw Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. Roseobacter Screening Of Surface Waters For Viruses. protocols.io https://dx.doi.org/10.17504/protocols.io.dbt2nm Copy   

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Authors: Andrea Argouarch
Group: Neurodegeneration Method Development Community
Summary: Protocol includes splitting growing cell line from a T75 flask into two T150 flasks for expansion.

Proper citation: Andrea Argouarch 2020. Splitting p1 (1xT75) to p2 (2xT150). protocols.io https://dx.doi.org/10.17504/protocols.io.8gnhtve Copy   

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Authors:
Group: UCSC BME 22L

Proper citation: 2020. Lab 6 Notebook. protocols.io https:// Copy   

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Authors: Francisco Herrera
Summary: The use of extracts obtained from various plants is an activity developed for years with the purpose of taking advantage of resources from the regions to prevent or cure a specific disease. On the other hand, the application of in vitro techniques, as angiotensin-converting enzyme inhibitory assay have allowed finding the relationship of organic compounds with biological activities and thus be able to determine which type of plants or their extracts are suitable to be used as a treatment for hypertension. In this protocol is described a method based on the colorimetric reaction of the hippuric acid with trichloro-triazine (TT).

Proper citation: Francisco Herrera 2018. Angiotensin-converting enzyme inhibitory assay. protocols.io https://dx.doi.org/10.17504/protocols.io.tb4eiqw Copy   

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Authors: Emma C Wall, Mavuto Mukaka, Brigitte Denis, Veronica S Mlozowa, Malango Msukwa, Khumbo Kasambala, Mulinda Nyrienda, Theresa J Allain, Brian Faragher, Robert S Heyderman, David G Lalloo

Proper citation: Emma C Wall, Mavuto Mukaka, Brigitte Denis, Veronica S Mlozowa, Malango Msukwa, Khumbo Kasambala, Mulinda Nyrienda, Theresa J Allain, Brian Faragher, Robert S Heyderman, David G Lalloo 2017. Early goal directed therapy for adult bacterial meningitis in Malawi . protocols.io https://dx.doi.org/10.17504/protocols.io.j5kcq4w Copy   

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Authors: Zymo Research
Group: Zymo Research - The Epigenetics Company
Summary: Highlights Quick (15 minute) high-yield recovery of ultra-pure DNA from agarose gels. Column design permits DNA elution at high concentrations into minimal volumes (≥ 6 μl). Eluted DNA is well suited for use in DNA ligation, sequencing, labeling, PCR, etc.

Proper citation: Zymo Research 2016. Zymoclean™ Gel DNA Recovery Kit. protocols.io https://dx.doi.org/10.17504/protocols.io.gitbuen Copy   

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Authors: Brian Kenn Baltzar.
Summary: A protocol to cast a polyacrylamide gel. Used in for iGEM SDU 2016

Proper citation: Brian Kenn Baltzar. 2017. Casting of a polyacrylamide gel. protocols.io https://dx.doi.org/10.17504/protocols.io.hchb2t6 Copy   

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Authors: Sarah Hessen-Schmidt

Proper citation: Sarah Hessen-Schmidt 2016. Dishwashing. protocols.io https://dx.doi.org/10.17504/protocols.io.e7xbhpn Copy   

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Authors: Josh Quick

Proper citation: Josh Quick 2019. Amplicon clean-up using SPRI beads. protocols.io https://dx.doi.org/10.17504/protocols.io.7nxhmfn Copy   

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Authors: Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton
Group: Coronavirus Method Development Community
Summary: Viral RNA isolation kits used in PCR based tests for the novel coronavirus (SARS-Cov2) are in short supply. Our group sought to identify a method to isolate viral RNA without the use of a kit or other supplies in high demand by clinical labs. Using a TRIzol based RNA extraction, followed by a glycogen precipitation, we are able to isolate a sufficient quality and quantity of RNA for quantitative PCR, and/or droplet digital PCR. This method has been confirmed to work as well as a viral RNA isolation kit, shown to work with SARS-Cov2 RNA-spiked into human samples, and in detecting SARS-Cov2 in known positive cases of COVID-19.

Proper citation: Joseph Patterson, Allyson Cole-Strauss, John Beck, Caryl Sortwell, Jack Lipton 2020. Isolation of SARS-Cov2 RNA from Humans Without High Demand Reagents. protocols.io https://dx.doi.org/10.17504/protocols.io.be8ujhww Copy   

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Authors: Gianpaolo Coro
Group: Coronavirus Method Development Community
Summary: This image reports a Maximum Entropy model that estimates suitable locations for COVID-19 spread, i.e. places that could favour the spread of the virus just in terms of environmental parameters.The model was trained just on locations in Italy that have reported a rate of new infections higher than the geometric mean of all Italian infection rates. The following environmental parameters were used, which are correlated to those used by other studies:Average Annual Surface Air Temperature in 2018 (NASA)Average Annual Precipitation in 2018 (NASA)CO2 emission (natural+artificial) averaged between January 1979 and December 2013 (Copernicus Atmosphere Monitoring Service)Elevation (NOAA ETOPO2)Population per 0.5° cell (NASA Gridded Population of the World)The model file (in ASC format) and all parameters used are attached.A higher resolution map and also the model file (in ASC format) and all parameters are available at the external link (Zenodo).The model indicates highest correlation with infection rate for CO2 around 0.03 gCm^−2day^−1, for Temperature around 11.8 °C, and for Precipitation around 0.3 kg m^-2  s^-1, whereas Elevation and Population density are poorly correlated with infection rate.One interesting result is that the model indicates, among others, the Hubei region in China as a high-probability location, and Iran (around Teheran) as a suited location for virus' spread, but the model was not trained on these regions, i.e. it did not know about the actual spread in these regions.Evaluation:A risk score was calculated for each country/region reported by the JHO monitoring system (https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html). This score is calculated as the summed normalised probability in the populated locations divided by their total surface. This score represents how much the zone would potentially foster the virus' spread.We assessed the reliability of this score, by selecting the country/regions that reported thehighest rates of infection. These zones were selected as those with a rate higher than the upper confidence of a log-normal distribution of the rates.The agreement between the two maps (covid_high_rate_vs_high_risk.png, where violet dots indicatehigh infection ratesand countries' colours indicate estimatedhigh risk score) is the following:Accuracy(overall percentage of correctly predicted high-rate zones): 77.25%Kappa(agreement between the two maps):0.46(Good, according to Fleiss' intepretation of the score) This assessment demonstrates that our map can be used to estimate the risk of a certain country to have a high rate of infection, and indicates that the influence of environmental parameters on virus's spread should be further investigated.FilesName (Size) (5.7 MB) md5:dea4e66a1c66d0dfc3b0872adfaa020f (47.3 MB) md5:069727a6c5656d276c475606c9b96d47 (1.9 MB) md5:ca91c4d56654b77bf572eef1a42af7a5 (5.1 MB) md5:0ed217e20ab32aad4ab96e5403670ee4 (2.8 MB) md5:79639fd3540c68450d86fde288edb264 (4.6 MB)md5:57aa6c172b3fc036c08d0560f01436ba (5.5 MB) md5:3ab587ea0e0fbe3fcbd9ea6b7844271a (4.7 MB) md5:7ea930f59e5ff627a18383f02737f78dReferences

Proper citation: Gianpaolo Coro 2020. Suitability Map of COVID-19 Virus Spread. protocols.io https://dx.doi.org/10.17504/protocols.io.bd88i9zw Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Chicken immunization with peptides is inefective if only just the peptides are being inoculated. However, to make the immune response effective the fragment 254-274 of HIV-1 was conjugated with a carrier protein (KLH) that produced a critical immune response, assessed by ELISA, Immunoblot analysis and dot blot [1-4]. The Polson method (1990) can be used effectively to separate the IgY antibody from the egg yolk of immunized chickens [5].References1. Schade R, Pfister C, Italatsch R, Henklien P (1991) Polyclonal antibodies from chicken egg yolk-an alternative to the production of mammalian IgG type antibodies in rabbits. ATLA 19: 403-419. 2. Justiz Vaillant AA, Akpaka PE, Smikle M, McFarlane-Anderson N (2012) In vitro Inhibition of Staphylococcus aureus Isolates by Anti-Anti-Idiotypic Antibodies to Staphylococcal Protein (SpA). J Vaccines Vaccin 3: 127-131.3. Collins AM, Roberton DM, Hosking CS, Flannery GR (1991) Oral immunization with xenogeneic antibodies stimulates the production of systemic and mucosal anti-idiotypic antibodies. Immunology 73: 388-393. 4. Ho DD, Kaplan JC, Rackauskas IE, Gurney ME (1988) Second conserved domain of gp120 is important for HIV infectivity and antibody neutralization. Science 239: 1021-1023. 5. Polson A (1990) Isolation of IgY from the yolks of eggs by a chloroform polyethylene glycol procedure. Immunol Invest 19: 253-258.

Proper citation: Angel Justiz-Vaillant 2020. Chicken immunization with Keyhole limpet hemocynin (KLH)-gp120 fragment (254-274) conjugate raises anti-KLH antibodies in egg yolks.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjvtkn6n Copy   

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Authors: Yuki Kataoka, Yasushi Tsujimoto, Masahiro Banno, Shunsuke Taito, Ryuhei So, Jun Watanabe, Akihiro Shiroshita

Proper citation: Yuki Kataoka, Yasushi Tsujimoto, Masahiro Banno, Shunsuke Taito, Ryuhei So, Jun Watanabe, Akihiro Shiroshita 2020. protocol_template_for_intervention_review. protocols.io https://dx.doi.org/10.17504/protocols.io.biqrkdv6 Copy   

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Authors: Ken Christensen
Summary: General Information: VWR Life Science AMRESCO’s NEXT GEL® products for denaturing gel electrophoresis are proprietary, ready-to-pour solutions comprised of acrylamide, bis-acrylamide, gel buffer, and SDS. The unique chemistry of NEXT GEL® eliminates the need for a stacking gel, thus reducing gel preparation time and extending the separation matrix available for electrophoresis, enabling the resolution of small peptides and high molecular weight proteins in the same gel.NEXT GEL® solutions polymerize upon addition of ammonium persulfate and TEMED and are fully compatible with all standard electrophoresis equipment, SDS-PAGE staining procedures, and downstream applications including 2D electrophoresis, western blot, transfer, protein sequencing, and MALDI analysis. Each NEXT GEL® acrylamide solution is supplied with NEXT GEL® Running Buffer, 20X, which is essential for optimal gel performance.

Proper citation: Ken Christensen 2020. NEXT Gel - CHEM 584 . protocols.io https://dx.doi.org/10.17504/protocols.io.bj5dkq26 Copy   

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Authors: Daniel Manrique-Castano

Proper citation: Daniel Manrique-Castano 2021. Human Brain Vascular Pericytes (HBVP) Fixation and Staining . protocols.io https:// Copy   

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