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Authors: Silva HR, Nucci MP, Mamani JB, Mendez-Otero R, Nucci LP, Tannus A, Gamarra LF
Group: Nanobiotecnholgy
Summary: The thermocoagulation model is a type of focal cerebral ischemia with craniectomy. It represents an opportunity to study permanent ischemic brain lesions with good reproducibility and low mortality

Proper citation: Silva HR, Nucci MP, Mamani JB, Mendez-Otero R, Nucci LP, Tannus A, Gamarra LF 2018. Thermocoagulation induced focal ischemic model. protocols.io https://dx.doi.org/10.17504/protocols.io.pasdiee Copy   

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Authors: Marcello Zala
Group: Zymoseptoria community protocols (STBnet)

Proper citation: Marcello Zala 2018. Sexual crosses of Zymoseptoria tritici. protocols.io https://dx.doi.org/10.17504/protocols.io.s22egge Copy   

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Authors: Pringle Lab
Group: Aiptasia-Symbiodiniaceae Model System
Summary: This protocol describes the basic steps neccessary to maintain and propagate Aiptasia as they are done in the Pringle lab.

Proper citation: Pringle Lab 2018. General Aiptasia husbandry - Pringle lab. protocols.io https://dx.doi.org/10.17504/protocols.io.rkud4ww Copy   

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Authors: Hye-k

Proper citation: Hye-k 2018. untitled protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.subeesn Copy   

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Authors: Fabio Gomes
Group: PlasmoVet

Proper citation: Fabio Gomes 2020. Rotina de Manutenção e Infecção de Células C6/36_v2. protocols.io https:// Copy   

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Authors: Erin Garza, Vincent Bielinski
Group: Protist Research to Optimize Tools in Genetics (PROT-G), JCVI West Protocols
Summary: This method can be used to increase the efficiency of Gibson Assemblies containing many pieces and/or difficult to assemble DNA fragments.

Proper citation: Erin Garza, Vincent Bielinski 2020. Nested Gibson Assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.bbikikcw Copy   

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Authors: Test McTester
Group: PDI Test

Proper citation: Test McTester 2021. 2009 Deep Soil Core Protocol. protocols.io https:// Copy   

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Authors: lewis.bingle
Group: SunMedMicro

Proper citation: lewis.bingle 2020. Preparation of electrocompetent Escherichia coli. protocols.io https:// Copy   

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Authors: Fergal Waldron, Katy Monteith, Pedro Vale
Summary: Infomration about the creation and maintenance of Ashworth outcrossed DGRP population

Proper citation: Fergal Waldron, Katy Monteith, Pedro Vale 2019. Creation and maintenance of Ashworth outcrossed DGRP population. protocols.io https://dx.doi.org/10.17504/protocols.io.zbuf2nw Copy   

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Authors: Angelina Spotts
Summary: Ingredients3/4 cup butter, softened1 cup sugar1 large egg, room temperature1/4 cup molasses2 cups all-purpose flour2 teaspoons baking soda1 teaspoon ground cinnamon1 teaspoon ground cloves1 teaspoon ground ginger1/4 teaspoon saltAdditional sugarDirectionsIn a bowl, cream butter and sugar. Beat in egg and molasses. Combine the flour, baking soda, cinnamon, cloves, ginger and salt; gradually add to creamed mixture. Chill.DirectionsRoll into 1-1/4-in. balls and dip into sugar. Place 2 in. apart on ungreasedbaking sheets. Bake at 375° for about 10 minutes or until set and surface cracks. Cool on wire racks.

Proper citation: Angelina Spotts 2020. Swedish Traditional Gingersnaps. protocols.io https://dx.doi.org/10.17504/protocols.io.bb5tiq6n Copy   

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Authors: Alexi Mcadams, Tavé van Zyl
Group: Human Cell Atlas Method Development Community
Summary: Fresh trabecular meshwork tissue is dissected from post-mortem human eyes and dissociated into a single cell suspension.

Proper citation: Alexi Mcadams, Tavé van Zyl 2020. Single-Cell Dissociation of Human Trabecular Meshwork . protocols.io https://dx.doi.org/10.17504/protocols.io.bfdyji7w Copy   

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Authors: Elizabeth Fozo

Proper citation: Elizabeth Fozo 2020. 1.1 Bead beating. protocols.io https:// Copy   

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Authors: Klinger Vagner Teixeira Da Costa, Pedro Menezes, Ana Frizzo
Summary: Trata-se de 0um protocolo de avaliação auditiva multiprofissional para crianças com microcefalia na síndrome congênita do vírus da zica. Este protocolo contempla a avaliação clinica por neuropediatra, otorrinolaringologista e fonoaudiólogo de forma simultânea. A seguir, a criança é avaliada por exames eletrofisiológicos para pesquisa de perdas auditivas tanto periféricas como centrais.

Proper citation: Klinger Vagner Teixeira Da Costa, Pedro Menezes, Ana Frizzo 2019. Permanent multiprofessional auditory assessment protocol for children with congenital zika virus syndrome. protocols.io https://dx.doi.org/10.17504/protocols.io.5hvg366 Copy   

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Authors: Monica Hassan

Proper citation: Monica Hassan 2020. Public protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bms2k6ge Copy   

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Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory. The assay specifically targets the 3' UTR region of DENV-2 strains and is designed as a qualitative screening test for human cases of DENV-2 infection, but not for infection due to other known DENVs.

Proper citation: Ian Mackay, Judy Northill 2018. Dengue virus type 2 (DENV-2) MGB TaqMan (DENV2-2016MGB) assay. protocols.io https://dx.doi.org/10.17504/protocols.io.n7kdhkw Copy   

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Authors: Gloria Pryhuber, Ravi Misra, Heidie Huyck, Gautam Bandyopadhyay
Group: Human Cell Atlas Method Development Community, LungMap2 Consortium, URMC Pryhuber Lab
Summary: Lung MAP HTC - BioRepository for Investigation of Neonatal Diseases of the Lung (BRINDL)Standard Operating Procedures 703.2_HTC102314rev061019Cryopreservation of Isolated CellsPurpose and Scope of the Procedure or Laboratory Assay

Proper citation: Gloria Pryhuber, Ravi Misra, Heidie Huyck, Gautam Bandyopadhyay 2020. 703.3 URMC HTC_Cryopreservation_of_Isolated_Cells_061220. protocols.io https://dx.doi.org/10.17504/protocols.io.biz6kf9e Copy   

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Authors: Seth John
Group: John Lab
Summary: Protocol for cleaning new and old teflon products.

Proper citation: Seth John 2016. Cleaning for new teflon (PFA/FEP/PTFE). protocols.io https://dx.doi.org/10.17504/protocols.io.fvabn2e Copy   

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Authors: Benjamin Bolduc, Simon Roux
Group: Sullivan Lab, iVirus
Summary: Cluster genomes is script that clusters genomes at a set nucleotide identity and coverage length. Additonally, it offers the ability to cluster sequences whose ends may not align correspondingly, i.e. the special cases of assembled, circular viral genomes that are treated as 'linear' by other sequence-clustering software (that can "miss" the ends).This is 'beta-like' software that has been vetted, though has not been as thoroughly tested as other widely-recognized clustering tools, such as CD-HIT, UCLUST, etc... As with all software, please examine the final results to see if they make sense.

Proper citation: Benjamin Bolduc, Simon Roux 2017. Clustering Viral Genomes in iVirus. protocols.io https://dx.doi.org/10.17504/protocols.io.gwebxbe Copy   

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Authors: Xinpei Yue, Xinkui Liu
Summary: The Coronavirus disease 2019 (COVID-19) was first identified in Wuhan, China during December of 2019. Previous studies have described clinical aspectsof the COVID-19 illness;however, insufficient literature currently exists regarding detecting severe conditions in patients during the early diagnosisstage. Patients admitted to a designated hospital in the Henan Province of China with outcomes of either discharge or death before February 15, 2020 were enrolled retrospectively as a cohort study population. Patients who underwent at least one of the following treatments were considered a severe group: continuous renal replacement therapy (CRRT), high-flow oxygen absorption, noninvasive and invasive mechanical ventilation, or extracorporeal membrane oxygenation (ECMO); while,the remaining patients were considereda non-severe group. Data regarding basic information, initial symptoms, and first visit examination results were collected from electronic medical records (EMR) and compared between the severe and non-severe groups. Multivariate logistic regression analysis was performed to determine predictors. Areceiver operating characteristic (ROC) curve was applied to find threshold for each predictor. Altogether,104 patients were enrolled to our study with 30 and 74 patients in the severe and non-severe groups, respectively. A majority of older patients werein the severe group. In addition,patients in the severe group had higher direct bilirubin, lactate dehydrogenase, C-reactive protein (CRP), and procalcitonin along witha lower absolute lymphocyte value. Multivariate logistic analysis indicated that patients aged ≥63-years (odds ratio 41.0, 95% CI 2.8~592.4)，with an absolute lymphocyte value≤1.02×10^9/L (odds ratio 6.1, 95% CI 1.5~25.2), CRP≥65.08mg/L (odds ratio8.9, 95% CI 1.0~74.2) had more risk being diagnosed as severe condition.

Proper citation: Xinpei Yue, Xinkui Liu 2020. Analysis of clinical features and early warning signs in patients with severe COVID-19: a retrospectivecohort study. protocols.io https://dx.doi.org/10.17504/protocols.io.bfpejmje Copy   

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Authors: Jian Guo, Alexandra Worden, Grant Hartzog, and Manuel Ares
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: We have available several plasmids designed for expression of Cas9, guide RNA, chloramphenicol acetyl-transferase, GFP, and beta-lactamase in Micromonas CCMP1545. For protein expression we used the promotor and 3' end elements from the endogenous RPS9 gene, and codon optimized the coding region.  For expression of guide RNAs we used the Micromonas U6 snRNA promoter.  DNA is available by contacting M. Ares .We have constructed and sequence verified 9 plasmids which we would like to make available to others attempting to detect transformation of DNA into Micromonas. Using the CCMP1545 genome as a source for the U6 promoter sequence, and for the promoter and 3' UTR sequences of ribosomal protein RPS9, we built the following plasmids:CRISPR/Cas9 plasmids for Micromonas1. Mp U6 promoter driving Bae cassette for guide RNA expression in pUC132. Mp RPS9-Cas9SV40-RPS9 in pUC133. Both Mp U6 promoter driving Bae cassette for guide RNA expression and Mp RPS9-Cas9SV40-RPS9 in pUC13These first three plasmids were anticipated to enable stable incorporation of transgenes at specific genomic locations. BaeI is a type IIS restriction enzyme that leaves noncompatible sticky ends. In the context of the gRNA cassette, a pair of 24 nt oligos designed to have the sticky ends compatible with BaeI cleaved plasmid are annealed and cloned into the plasmid, replacing the BaeI cassette while adding the 20 nt target complementary sequence of the desired guide RNA.Selectable/Detectable Marker genes4. Mp RPS9-codon optimized GFPsv40-RPS9 in pUC135. Mp RPS9-codon optimized chloramphenicol acetyltransferase-RPS9 in pUC13 6. Mp RPS9-codon optimized beta-lactamase-RPS9 in pUC13 These three plasmids have the indicated coding regions codon optimized for Micromonas flanked by RPS9 promoter and 3' end sequences. In the case of GFP, a nuclear localization signal from SV40 has been added to the C-terminus. Plasmids for Agrobacterium-mediated gene transfer 7. Mp RPS9-codon optimized GFPsv40-RPS9 in pOSCAR 8. Mp RPS9-codon optimized chloramphenicol acetyltransferase-RPS9 in pOSCAR 9. Mp RPS9-codon optimized beta-lactamase-RPS9 in pOSCAR

Proper citation: Jian Guo, Alexandra Worden, Grant Hartzog, and Manuel Ares 2018. Plasmid DNAs designed for expression in Micromonas CCMP1545. protocols.io https://dx.doi.org/10.17504/protocols.io.i9wch7e Copy   

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