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amplification and sequencing of the mitochondrial gene cytochrome c oxidase subunit I (COI) in Sabellidae polychaetes Resource Report Resource Website |
Michela Del Pasqua, Anja Schulze, María Ana Tovar-Hernández, Erica Keppel, Marco Lezzi, Maria Cristina Gambi, Adriana Giangrande | 10.17504/protocols.io.nx6dfre | Pasqua MD, Schulze A, Tovar-Hernández MA, Keppel E, Lezzi M, Gambi MC, Giangrande A (2018) Clarifying the taxonomic status of the alien species Branchiomma bairdi and Branchiomma boholense (Annelida: Sabellidae) using molecular and morphological evidence. PLoS ONE 13(5): e0197104. doi: 10.1371/journal.pone.0197104 | Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, CoNISMa Unit, 73100 Lecce, Italy, Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX 77554, USA., Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Laboratorio de Biosistemática, San Nicolás de los Garza, Nuevo León, 66455, México, Smithsonian Environmental Research Center, 647 Contees Wharf Road, Edgewater, Maryland, 21037, USA, ARPAT, Environmental Protection Agency of Tuscany, A.V. Costa - Laboratory Sector - U.O. Biologia, Pisa 56127, Italy, Stazione Zoologica Anton Dohrn di Napoli, Department of Integrative Marine Ecology, Villa Dohrn- Benthic Ecology Center, Punta S. Pietro, 80077 Ischia (Napoli), Italy, Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, CoNISMa Unit, 73100 Lecce, Italy | https://doi.org/10.1371/journal.pone.0197104 | 1 | 2018 | Michela Del Pasqua, Anja Schulze, María Ana Tovar-Hernández, Erica Keppel, Marco Lezzi, Maria Cristina Gambi, Adriana Giangrande 2018. amplification and sequencing of the mitochondrial gene cytochrome c oxidase subunit I (COI) in Sabellidae polychaetes. protocols.io dx.doi.org/10.17504/protocols.io.nx6dfre | 2021-03-29 03:08:35 | |||
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Method for electroporation of Isochrysis galbana CCMP1323 Resource Report Resource Website |
Glen Wheeler, Rowena Stern, Cecilia Balesteri | 10.17504/protocols.io.hmab42e | Protist Research to Optimize Tools in Genetics (PROT-G) | Faktorová D, Nisbet RER, Robledo JAF, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget F, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano J, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Vanclová AMGN, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Smith GJ, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, Dassow Pv, Haar Tvd, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J, Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods 17(5). doi: 10.1038/s41592-020-0796-x | Marine Biological Association, Marine Biological Association, Marine Biological Association | https://doi.org/10.1038/s41592-020-0796-x | 1 | 2017 | Glen Wheeler, Rowena Stern, Cecilia Balesteri 2017. Method for electroporation of Isochrysis galbana CCMP1323. protocols.io dx.doi.org/10.17504/protocols.io.hmab42e | 2021-03-29 03:08:35 | ||
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S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient Resource Report Resource Website |
Luciano Martelotto | 10.17504/protocols.io.brdcm22w | This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq experiments using droplet-based methods, and is an extension of the Frankenstein (S.O.F means Son Of Frankenstein). Developed to prepare nuclei isolates from fresh and frozen material of small-to-large sizes. The good thing is that it does not uses FACS but OptiPrep® discontinuous gradient to remove debris. It is the alternative protocol when FACS is not available. | Harvard Medical School | https://research.unimelb.edu.au/centre-for-cancer-research/our-research/single-cell-innovation-lab | 1 | 2021 | Luciano Martelotto 2021. S.O.F protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® discontinuous gradient . protocols.io dx.doi.org/10.17504/protocols.io.brdcm22w | 2021-03-29 03:08:35 | |||
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Determination of flavonoid content Resource Report Resource Website |
Jorge Carlos Ruiz Ruiz | 10.17504/protocols.io.sfnebme | Flavonoid content determination using the aluminum chloride method. | Rodríguez-García CM, Ruiz-Ruiz JC, Peraza-Echeverría L, Peraza-Sánchez SR, Torres-Tapia LW, Pérez-Brito D, Tapia-Tussell R, Herrera-Chalé FG, Segura-Campos MR, Quijano-Ramayo A, Ramón-Sierra JM, Ortiz-Vázquez E (2019) Antioxidant, antihypertensive, anti-hyperglycemic, and antimicrobial activity of aqueous extracts from twelve native plants of the Yucatan coast. PLoS ONE 14(3): e0213493. doi: 10.1371/journal.pone.0213493 | Universidad Anáhuac Mayab | https://doi.org/10.1371/journal.pone.0213493 | 1 | 2018 | Jorge Carlos Ruiz Ruiz 2018. Determination of flavonoid content. protocols.io dx.doi.org/10.17504/protocols.io.sfnebme | 2021-03-29 03:08:35 | ||
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In situ sequencing for RNA analysis in tissue sections Resource Report Resource Website |
Chika Yokota, Daniel Gyllborg, Mats Nilsson | 10.17504/protocols.io.bb2giqbw | Molecular Diagnostics - Mats Nilsson Group | In situ sequencing method for parallel targeted analysis of short RNA fragments in morphologically preserved tissue. This protocol can be used to detect RNA molecules at the single cell level to aid in the identification of cell types according to their gene expression. The technique uses padlock probes to target desired genes of interest and rolling circle amplification to amplify signal for a high throughput methodolgy of spatial transcriptomics. With the use of barcode sequencing, identification of numerous genes is possible through multiplexing.Version 2 Update: Only minor mistakes were corrected for version 2 of this protocol, no major changes to protocol were done. Some references were also updated. | Gyllborg D, Langseth CM, Qian X, Choi E, Salas SM, Hilscher MM, Lein ES, Nilsson M, Hybridization-based sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue. Nucleic Acids Research 48(19). doi: 10.1093/nar/gkaa792 | Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden | https://www.nature.com/articles/nmeth.2563 | 2 | 2020 | Chika Yokota, Daniel Gyllborg, Mats Nilsson 2020. In situ sequencing for RNA analysis in tissue sections. protocols.io dx.doi.org/10.17504/protocols.io.bb2giqbw | 2021-03-29 03:08:35 | |
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Extracorporeal membrane oxygenation meta-analysis of time-to-event data in cardiopulmonary disease in adults Resource Report Resource Website |
Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim | 10.17504/protocols.io.bb3tiqnn | Purpose:Time-to-event data of hazard ratios were used to generate a forest plot of all-cause mortality on extracorporeal membrane oxygenation (ECMO) in both overall and individual indications of cardiopulmonary disease in adults.Materials and Methods:A systemic search was conducted in PubMed from 1975 to 2018. Among 4,121 articles, a total of 34 clinical reports comprising 20,610patients (1,631 of the patients who underwent ECMO and 18,979 of the patients who did not undergo ECMO) met the inclusion criteria.Results:The pooled hazard ratio of 1.2828 (95% confidence interval: 0.9649, 1.7054) suggests that the ECMO group was not significantly associated with a reduction in mortality compared with the no-ECMO group in the overall ECMO indications. The results of subgroup analyses showed a significantly improved patient survival in respiratory failure with 0.6308 (0.5037, 0.7900), and a worse patient survival after lung transplantation with 2.0600 (1.6987, 2.4981), in bridging to heart transplantation with 1.4212 (1.0309, 1.9592), and after heart transplantation with 5.6365 (1.7569, 18.0827).Conclusions:Most of the included studies are retrospective, which diminishes the significance of the findings due to a higher risk of selection bias, which was exemplified by the allocation of ECMO based on the patients’ severity condition. | Emergency Medicine and Echocardiography Laboratory, Dongjak Kyunghee Hospital, Seoul, Korea. nGene Hemodynamic Research Center, Seoul, Korea., Department of Medicine, Hanyang University College of Medicine, Seoul, Korea., Department of Thoracic and Cardiovascular Surgery, Hando General Hospital, Ansan City, Gyunggi, Korea., Department of Microbiology and Biomedical Science, Hanyang University College of Medicine and Graduate School of Biomedical Science and Engineering, Seoul, Korea. | 1 | 2020 | Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim 2020. Extracorporeal membrane oxygenation meta-analysis of time-to-event data in cardiopulmonary disease in adults. protocols.io dx.doi.org/10.17504/protocols.io.bb3tiqnn | 2021-03-29 03:08:35 | ||||
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Isolation of cell fractionation Resource Report Resource Website |
Mengchen Shi | 10.17504/protocols.io.kcfcstn | Shi M, Zhou L, Zhao L, Shang M, He T, Tang Z, Sun H, Ren P, Lin Z, Chen T, Yu J, Xu J, Yu X, Huang Y (2017) Csseverin inhibits apoptosis through mitochondria-mediated pathways triggered by Ca2 + dyshomeostasis in hepatocarcinoma PLC cells. PLoS Negl Trop Dis 11(11): e0006074. doi: 10.1371/journal.pntd.0006074 | Sun Yat-Sen University | https://doi.org/10.1371/journal.pntd.0006074 | 1 | 2017 | Mengchen Shi 2017. Isolation of cell fractionation. protocols.io dx.doi.org/10.17504/protocols.io.kcfcstn | 2021-03-29 03:08:35 | |||
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Protocol for a reproducible circRNA analysis using Docker4Circ Resource Report Resource Website |
Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli | 10.17504/protocols.io.9vmh646 | Q-Bio Turin | Despite many computational tools were developed to predict circular RNAs (circRNAs), a limited number of work-flows exists to fully analyse a circRNA set ensuring the computational reproducibility of the whole analysis.For this purpose, we designed Docker4Circ, a computational work-flow for a comprehensive circRNAs analysis of a circRNAs composed of four modules: the circRNAs prediction (module 1), the circRNAs classification and annotation (module 2), the circRNAs sequence analysis (module 3), and circRNAs expression analysis (module 4).To ensure reproducibility each function of Docker4Circ was embeded into a docker image following guideline provided by Reproducible Bioinformatics Project (RBP, http://reproducible-bioinformatics.org/). Each function is included in the Docker4Seq R package which already includes different solutions for reproducible bioinformatic analyses.This protocol describes the use of each function of Docker4Circ to analyse the circRNAs predicted from a set of RNA-Seq experiments performed in normal colon and colorectal cancer cell lines. Furthermore, the description of the functions required to compute the expression level of the analysed circRNAs in a set of RNA-Seq experiments of colorectal primary tumors is provided. | University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin, University of Turin | 4 | 2019 | Giulio Ferrero, Nicola Licheri, Lucia Coscujuela Tarrero, Carlo De Intinis, Valentina Miano, Raffaele Adolfo Calogero, Francesca Cordero, Marco Beccuti, Michele De Bortoli 2019. Protocol for a reproducible circRNA analysis using Docker4Circ. protocols.io dx.doi.org/10.17504/protocols.io.9vmh646 | 2021-03-29 03:08:35 | |||
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Step 2: Preparing amino acid, polyphosphates, and maltodextrin-based energy solutions for cell-free reactions Resource Report Resource Website |
Anibal Arce Medina, Fernan Federici | 10.17504/protocols.io.j2ncqde | Laboratorio de Tecnologias Libres | Pontificia Universidad Católica de Chile, | 2 | 2017 | Anibal Arce Medina, Fernan Federici 2017. Step 2: Preparing amino acid, polyphosphates, and maltodextrin-based energy solutions for cell-free reactions. protocols.io dx.doi.org/10.17504/protocols.io.j2ncqde | 2021-03-29 03:08:34 | ||||
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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 | 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 dx.doi.org/10.17504/protocols.io.ugketuw | 2021-03-29 03:08:34 | ||
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Dietary rotenone and paraquat on larval development Resource Report Resource Website |
Wen Aw | 10.17504/protocols.io.rs8d6hw | Cage Studies | Aw WC, Towarnicki SG, Melvin RG, Youngson NA, Garvin MR, Hu Y, Nielsen S, Thomas T, Pickford R, Bustamante S, Vila-Sanjurjo A, Smyth GK, Ballard JWO (2018) Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness. PLoS Genet 14(11): e1007735. doi: 10.1371/journal.pgen.1007735 | [email protected] | https://doi.org/10.1371/journal.pgen.1007735 | 1 | 2018 | Wen Aw 2018. Dietary rotenone and paraquat on larval development. protocols.io dx.doi.org/10.17504/protocols.io.rs8d6hw | 2021-03-29 03:08:34 | ||
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DAB Solutions Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bctkiwkw | BICCN, Allen Institute for Brain Science | 3, 3´ Diaminobenzidine (DAB) is a commonly used chromogen for histological staining. In the presence of peroxidase enzyme, DAB produces a brown precipitate that is insoluble in alcohol and xylene. Peroxidase catalyzes hydrogen peroxide oxidation of substrate DAB. This SOP provides instructions to prepare four different formulations of DAB. DAB for Immunohistochemical staining (IHC), DAB for Acetylcholinesterase (AChE) Staining, Nickel Enchanced DAB for Biocytin staining, and DAB for Biocytin staining. | Allen Institute | 1 | 2020 | Allen Institute for Brain Science 2020. DAB Solutions. protocols.io dx.doi.org/10.17504/protocols.io.bctkiwkw | 2021-03-29 03:08:34 | |||
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Monterey Wharf II Weekly Phytoplankton Monitoring Sample Collection and Processing Notes Resource Report Resource Website |
april woods | 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 dx.doi.org/10.17504/protocols.io.f2pbqdn | 2021-03-29 03:08:34 | |||
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Assembling Cooled LED Illuminator Resource Report Resource Website |
Jakub Nedbal | 10.17504/protocols.io.bcrniv5e | The cooled LED illuminator is a large heatsink with self-adhesive LED strips, four axial fans, and the LED controller attached to it.This document is part of the Illuminated Orbital Shaker for Microalgae Culture project:Procuring Parts for Algal ShakerAssembling LED Controller Electronics3D Printing Case for LED ControllerAssembling Cooled LED Illuminator (this document)Cutting and Drilling Clear Acrylic SheetAssembling Algal Shaker | Nedbal J, Gao L, Suhling K, Bottom-illuminated orbital shaker for microalgae cultivation. Hardwarex doi: 10.1016/j.ohx.2020.e00143 | King's College London | https://app.labstep.com/sharelink/8f145ee3-eecc-4f9f-8e99-fc7b4f41d12e | 1 | 2020 | Jakub Nedbal 2020. Assembling Cooled LED Illuminator. protocols.io dx.doi.org/10.17504/protocols.io.bcrniv5e | 2021-03-29 03:08:34 | ||
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ELISA for quantification of IL-29 in human serum. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bj3ykqpw | University of the West Indies, [email protected] | Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. IL-29 is a type-3 interferon and produced by virus-infected cells, dendritic cells, and regulatory T-cells. It upregulates viral protective responses. Virus-infected cells may regulate IL-29 genome. [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. ELISA for quantification of IL-29 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj3ykqpw | 2021-03-29 03:08:34 | |||
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Part 1: Preparation of lipid films for phospholipid liposomes Resource Report Resource Website |
James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy | 10.17504/protocols.io.hasb2ee | Van Mooy Lab @ WHOI | This protocol (like its companion protocol for liposome suspension and extrusion) was original created by Krista Longnecker and Jamie Collins for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in Chapter 4 of:Collins, J. R. 2017. The remineralization of marine organic matter by diverse biological and abiotic processes. Ph.D. thesis. Cambridge, Massachusetts: Massachusetts Institute of Technology, 300 pp; doi:10.1575/1912/8721A manuscript of the chapter is forthcoming. | Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution | 2 | 2017 | James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy 2017. Part 1: Preparation of lipid films for phospholipid liposomes. protocols.io dx.doi.org/10.17504/protocols.io.hasb2ee | 2021-03-29 03:08:34 | |||
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Attenuated expression of MTR in both prenatally androgenized mice and women with the hyperandrogenic phenotype of PCOS Resource Report Resource Website |
Lei Lei1, Lijun Ding, Jing Su, Mengyuan Liu, Qingqing Shi, Jianjun Zhou, Haixiang Sun, Guijun Yan | 10.17504/protocols.io.jiuckew | Lei L, Ding L, Su J, Liu M, Shi Q, Zhou J, Sun H, Yan G (2017) Attenuated expression of MTR in both prenatally androgenized mice and women with the hyperandrogenic phenotype of PCOS. PLoS ONE 12(12): e0187427. doi: 10.1371/journal.pone.0187427 | Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210029, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China, Center for Reproductive Medicine, Drum Tower Clinic Medical College of Nanjing Medical University, Nanjing 210029, Jiangsu, China, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, China | https://doi.org/10.1371/journal.pone.0187427 | 1 | 2017 | Lei Lei1, Lijun Ding, Jing Su, Mengyuan Liu, Qingqing Shi, Jianjun Zhou, Haixiang Sun, Guijun Yan 2017. Attenuated expression of MTR in both prenatally androgenized mice and women with the hyperandrogenic phenotype of PCOS. protocols.io dx.doi.org/10.17504/protocols.io.jiuckew | 2021-03-29 03:08:34 | |||
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Adipose depot innervation: whole mount staining, imaging, quantification Resource Report Resource Website |
Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz | 10.17504/protocols.io.brs2m6ge | Townsend Lab Neurobiology & Energy Balance | AbstractLittle is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses a method of mechanically compressing tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit imaging of intact whole tissues on both widefield and confocal microscopes and a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within the inguinal subcutaneous white adipose tissue in mice. | Ohio State University, Columbus, Ohio State University, Ohio State University, Columbus | 2 | 2021 | Jake Willows, Kristy Townsend, Magdalena Blaszkiewicz 2021. Adipose depot innervation: whole mount staining, imaging, quantification. protocols.io dx.doi.org/10.17504/protocols.io.brs2m6ge | 2021-03-29 03:08:34 | |||
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Nucleic Acid Extraction, Amplification and Library Construction for Viral Metagenomic Sequencing. Resource Report Resource Website |
Jing-Zhe (Ginger) Jiang, Hong-Ying Wei | 10.17504/protocols.io.m5vc866 | Suttle Laboratory of Marine Molecular Microbiology and Virology | This protocol is a continuation of the previous protocol (dx.doi.org/10.17504/protocols.io.m4yc8xw) for viral metagenomic researches with the tissues of Molluscs, such as abalone, oyster, clam, scallop and so on. This maybe also applicable for other animals, such as shrimp and fish, based on the principle of the protocol. But we havn't verified this idea yet. | Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Product Processing, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences | 1 | 2018 | Jing-Zhe (Ginger) Jiang, Hong-Ying Wei 2018. Nucleic Acid Extraction, Amplification and Library Construction for Viral Metagenomic Sequencing.. protocols.io dx.doi.org/10.17504/protocols.io.m5vc866 | 2021-03-29 03:08:34 | |||
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Semi-quantitative measure of roots colonization by arbuscular mycorrhizal fungi using standard light microscopy Resource Report Resource Website |
Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté | 10.17504/protocols.io.zbgf2jw | Plant Functional Ecology Lab | Université de Montréal, Université de Montréal, Université de Montréal, Université de Montréal | 1 | 2019 | Florence Blanchard, Alexis Carteron, Xavier Guilbeault-Mayers, Etienne Laliberté 2019. Semi-quantitative measure of roots colonization by arbuscular mycorrhizal fungi using standard light microscopy. protocols.io dx.doi.org/10.17504/protocols.io.zbgf2jw | 2021-03-29 03:08:34 |
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