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Nuclei Isolation from Human Brain Using Sucrose Gradient Resource Report Resource Website |
Fatma Ayhan, Genevieve Konopka | 10.17504/protocols.io.scneave | Human Cell Atlas Method Development Community, Neurodegeneration Method Development Community | This protocol outlines our preparation of single-nuclei suspension from surgically acquired fresh human adult brain tissue. | Neurocrine Biosciences, UT Southwestern Medical Center | 1 | 2018 | Fatma Ayhan, Genevieve Konopka 2018. Nuclei Isolation from Human Brain Using Sucrose Gradient. protocols.io dx.doi.org/10.17504/protocols.io.scneave | 2021-03-29 03:10:00 | |||
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cpf1 cloning Resource Report Resource Website |
Jaclyn Winter | 10.17504/protocols.io.8f4htqw | University of Utah | 1 | 2019 | Jaclyn Winter 2019. cpf1 cloning. protocols.io dx.doi.org/10.17504/protocols.io.8f4htqw | 2021-03-29 03:10:00 | |||||
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Miracle Prep for Plasmid Isolation Resource Report Resource Website |
Blake Flood | 10.17504/protocols.io.8p2hvqe | Based on:https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0160509 | University of Chicago | 1 | 2019 | Blake Flood 2019. Miracle Prep for Plasmid Isolation. protocols.io dx.doi.org/10.17504/protocols.io.8p2hvqe | 2021-03-29 03:10:01 | ||||
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Labyrinthula growth medium Resource Report Resource Website |
Janina Brakel | 10.17504/protocols.io.ehkbb4w | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Stony Brook University | 1 | 2016 | Janina Brakel 2016. Labyrinthula growth medium. protocols.io dx.doi.org/10.17504/protocols.io.ehkbb4w | 2021-03-29 03:10:01 | ||||
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Western blot, ELISA and enzymatic assays of reference proteins for subcellular fractionation Resource Report Resource Website |
Saumel Perez Rodriguez, María De Jesús Ramírez-Lira, Tune Wulff, Bjørn Gunnar Voldbor, Octavio T Ramírez, Mauricio A Trujillo-Roldán, Norma A Valdez-Cruz | 10.17504/protocols.io.bgc4jsyw | Subcellular fractionation of mammalian cells has been applied for the study of morphology, composition, structure and interactions between organelles, cellular and molecular biology and, more recently, the cell composition through omics approaches . Advantages of fractionation comprise but are not limited to obtaining fractions enriched in certain compartments for the study of cellular processes in vitro , locate and track proteins and analyze post-translational modifications (PTM) of proteins processed along the secretory pathway and protein composition of organelles. Despite the existence of a wide variety of cell fractionation protocols and techniques, most of them are based on the identification or assignment of a certain isolated fraction to one or more subcellular compartments from the enrichment of this fraction in certain markers, the which are mostly protein. The quantification of these protein markers can be done through western blot, ELISA, enzymatic assays or proteomic studies. The present protocol is focused in the identification of proteins markers from several organelles, by WB, ELISA and enzymatic assays. The enrichment of isolated fractions in endoplasmic reticulum (ER), cytosol, nucleus, mitochondria, plasma membrane (PM), cis-Golgi and trans-Golgi can be assessed by detection of 78 kDa glucose-regulated protein (Grp78), glyceraldehyde 3-phosphate dehydrogenase (Gapdh), histone H3, heat shock protein 60 (Hsp60), flotilin 1, golgin A5 and golgin-97, respectively, by WB, and also by ELISA in case of golgin-97. Enrichment of peroxisomes in fractions collected from sucrose gradients can be assessed by a catalase assay adapted from . This protocol can be applied to any mammalian cell line during subcellular fractionation in order to quantify the enrichment of several organelles in the isolated fractions. | Pérez-Rodriguez S, Ramírez-Lira MdJ, Wulff T, Voldbor BG, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA (2020) Enrichment of microsomes from Chinese hamster ovary cells by subcellular fractionation for its use in proteomic analysis. PLoS ONE 15(8): e0237930. doi: 10.1371/journal.pone.0237930 | Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México | https://doi.org/10.1371/journal.pone.0237930 | 1 | 2020 | Saumel Perez Rodriguez, María De Jesús Ramírez-Lira, Tune Wulff, Bjørn Gunnar Voldbor, Octavio T Ramírez, Mauricio A Trujillo-Roldán, Norma A Valdez-Cruz 2020. Western blot, ELISA and enzymatic assays of reference proteins for subcellular fractionation . protocols.io dx.doi.org/10.17504/protocols.io.bgc4jsyw | 2021-03-29 03:10:01 | ||
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LCMS-SOP Determination of Microcystins in Water Samples by High Performance Liquid Chromatography (HPLC) with Single Quadrupole Mass Spectrometry (MS) Resource Report Resource Website |
Gregory L Boyer | 10.17504/protocols.io.bck2iuye | Metabolomics Protocols & Workflows | This standard operating procedure is used to determine and quantify microcystins and nodularin (intracellular and/or extracellular) in whole water samples or filter samples using HPLC-coupled with single quadrupole mass spectrometry (LC-MS). The method described here is a modification of the methods described in Boyer (2007) for particulate microcystins in water samples and does not use solid phase extraction. It was designed to use a 50% acidified methanolic extraction solvent, but is compatible with protocols for direct water analysis (US-EPA, 2016) and higher concentration methanolic extracts (Cerasino et al., 2017). It is not suitable for use with tissues samples or other samples with complex matrix interferences, such as soil or sediments. The method is designed for high throughput (1000-1500 injections per month) using a low-resolution (unit mass) mass spectrometer. It gives results of similar accuracy to the commonly used Abraxis ADDA ELISA with additional information on the microcystin congener profiles. | Department of Chemistry, State University of New York (SUNY), College of Environmental Science and Forestry, Syracuse, NY | 1 | 2020 | Gregory L Boyer 2020. LCMS-SOP Determination of Microcystins in Water Samples by High Performance Liquid Chromatography (HPLC) with Single Quadrupole Mass Spectrometry (MS). protocols.io dx.doi.org/10.17504/protocols.io.bck2iuye | 2021-03-29 03:10:00 | |||
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PRUEBA DE HEMOLISIS DE ERITROCITOS HUMANOS Resource Report Resource Website |
Germán Alberto Téllez Ramírez, Lily Johanna Toro, Diana Carolina Henao, Juan David Rivera, Jhon Carlos Castaño Osorio | 10.17504/protocols.io.jh9cj96 | Grupo de inmunología molecular | Esta prueba evalúa la actividad hemolítica de péptidos o moleculas sobre eritrocitos humanos como criterio de selectividad ante las células eucariotas. La realizacion de este protocolo fue posible gracias al apoyo del departamento administrativo de ciencia tecnología e innovacion, Colciencias a traves del proyecto 111356933173 convocatoria569-2012. | Centro de investigaciones biomédicas. Universidad del Quindío, Centro de Investigaciones Biomédicas - Universidad del Quindío, Centro de investigaciones biomédicas. Universidad del Quindío, Centro de investigaciones biomédicas. Universidad del Quindío, Centro de investigaciones biomédicas. Universidad del Quindío | 1 | 2017 | Germán Alberto Téllez Ramírez, Lily Johanna Toro, Diana Carolina Henao, Juan David Rivera, Jhon Carlos Castaño Osorio 2017. PRUEBA DE HEMOLISIS DE ERITROCITOS HUMANOS. protocols.io dx.doi.org/10.17504/protocols.io.jh9cj96 | 2021-03-29 03:10:01 | |||
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Evaluation of stability of balance recovery from unpredictable perturbations through the compensatory arm and leg movements (CALM) scale Resource Report Resource Website |
Marina Torres Betelli, Patrícia Sayuri Takazono, Caroline Ribeiro de Souza, Julia Ávila de Oliveira, Daniel Boari Coelho, Luis Augusto Teixeira | 10.17504/protocols.io.2p2gdqe | The scale for evaluation of compensatory arm and leg movements (CALM) was developed to evaluate balance stability recovery after unpredictable displacements of the support base in the mediolateral direction. The mediolateral perturbations are applied in three modes: rotation, translation or combined rotation-translation, to either side, in three platform peak velocities: 20º-20 cm/s (low), 30º-30cm/s (intermediate) or 0º-40 cm/s (high), keeping peak acceleration of 500o/s2(cm/s2) and displacement amplitude of 7o (cm) constant across perturbations. The factors perturbation mode (3), direction (2) and velocity (3) of platform displacement are combined to generate 18 distinct stance perturbations. To create the context of unpredictability, perturbations are pseudorandomly sequenced. To become aware of the stance perturbations, participants watch a video demonstrating a person responding to the different platform perturbations included in the protocol. After video watching, subjects are warmed up for 5 min. with global movements. Initial feet positions are marked on the support base with adhesive tapes (5-cm width). Other adhesive tape marks are fixed 15 cm away from the outer border of the feet to either side, in parallel to the feet orientation. The initial participant’s posture on the platform is keeping the Romberg’s stance, with the feet oriented forward, touching each other, maintaining both arms relaxed hanging beside the trunk, and palms of the hands lightly touching the upper legs. Participants wear a safety harness supported by two ropes tied at the shoulders height with the other end attached overhead. The participant’s aim across perturbations is to recover balance after support base displacements trying to maintain the initial body posture. Participants’ responses are filmed from behind using a commercial digital camera (Sony), for off-line analysis based on the CALM scale. | Souza CRd, Betelli MT, Takazono PS, Oliveira J | 1 Human Motor Systems Laboratory, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil , Human Motor Systems Laboratory, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil, Human Motor Systems Laboratory, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil , Human Motor Systems Laboratory, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil , Centre for Engineering, Modeling and Applied Social Sciences (CECS), Federal University of ABC, São Paulo, Brazil, Human Motor Systems Laboratory, School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil | https://doi.org/10.1371/journal.pone.0221398 | 1 | 2019 | Marina Torres Betelli, Patrícia Sayuri Takazono, Caroline Ribeiro de Souza, Julia Ávila de Oliveira, Daniel Boari Coelho, Luis Augusto Teixeira 2019. Evaluation of stability of balance recovery from unpredictable perturbations through the compensatory arm and leg movements (CALM) scale. protocols.io dx.doi.org/10.17504/protocols.io.2p2gdqe | 2021-03-29 03:09:57 | ||
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Associations between three XRCC1 polymorphisms and the hepatocellular carcinoma risk: a meta-analysis of case-control studies Resource Report Resource Website |
Yao Xiong, Qian Zhang, Jiaxiang Ye, Shan Pan, Lianying Ge | 10.17504/protocols.io.sqwedxe | Conflicting results have been obtained regarding the association between X-ray repair cross complementation group 1 (XRCC1) and susceptibility to hepatocellular carcinoma (HCC). In this study, associations between HCC and three polymorphisms (Arg194Trp, Arg280His, and Arg399Gln) were evaluated using a meta-ananlysis approach. PubMed, Web of science, Cochrane Library, the Chinese National Knowledge Infrastructure, and the Wanfang standard database were systematically searched to identify all relevant case-control studies published through March 2018. A total of 32 case-control studies, including 13 that evaluated Arg194Trp, 14 that evaluated Arg280His, and 26 that evaluated Arg399Gln, were analyzed. In the entire study population, XRCC1 Arg399Gln was significantly associated not only with the overall risk of HCC (homozygous model, OR = 1.53, 95% CI: 1.34–1.76, P = 0.00; recessive model, OR = 1.31, 95% CI:1.15–1.49, P = 0.00), but also with the risk of HCC in Chinese patients (homozygous model, OR = 1.78, 95% CI: 1.53–2.08, P = 0.00; recessive model, OR = 1.47, 95% CI: 1.27–1.70, P = 0.00). Limiting the analysis to studies demonstrating Hardy–Weinberg equilibrium (HWE), the results were consistent and robust. Similarly, a significant association between XRCC1 Arg399Gln and HCC risk was found in healthy controls in the general population but not in hospital controls. Trial sequential analysis (TSA), the false-positive report probabilities (FPRP) and the combined genotype analysis revealed that XRCC1 Arg399Gln is mainly associated with susceptibility to liver cancer. However, there was no association between Arg194Trp or Arg280His and the risk of HCC. These results, indicating that the Arg399Gln polymorphism of XRCC1 is associated with the risk of HCC in the Chinese population, provide a basis for the development of improved detection and treatment approaches. | Department of Medical Oncology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China, Department of Gynecologic Oncology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China, Department of Medical Oncology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China, Department of Medical Oncology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China, Department of Medical Oncology, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China | 1 | 2018 | Yao Xiong, Qian Zhang, Jiaxiang Ye, Shan Pan, Lianying Ge 2018. Associations between three XRCC1 polymorphisms and the hepatocellular carcinoma risk: a meta-analysis of case-control studies. protocols.io dx.doi.org/10.17504/protocols.io.sqwedxe | 2021-03-29 03:09:59 | ||||
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Unsucessful atemps on transfromation of the Icthyosporean Sphaeroforma artica Resource Report Resource Website |
Elena Casacuberta, Cristina Aresté, Omaya Dudin , Elena Casacuberta | 10.17504/protocols.io.z6ef9be | Protist Research to Optimize Tools in Genetics (PROT-G), Multicellgenomelab, Emerging Organisms for Biology | Testing electroporation on Spaheroforma artica with two different electroporatorsNeon (invitrogen)Lonza (nucleofector) | Institute of Evolutionary Biology, IIBB, Institute of Evolutionary Biology, Institute of Evolutionary Biology | 1 | 2019 | Elena Casacuberta, Cristina Aresté, Omaya Dudin , Elena Casacuberta 2019. Unsucessful atemps on transfromation of the Icthyosporean Sphaeroforma artica. protocols.io dx.doi.org/10.17504/protocols.io.z6ef9be | 2021-03-29 03:09:59 | |||
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CZV8CS - liquid medium for fungal culture Resource Report Resource Website |
Oliver Mead | 10.17504/protocols.io.f7cbriw | Solomon Lab - Australian National University | prepare 100 mL per 250 mL flask for each overnight culturefor CZV8CS - liquid media for flask cultureprepare 100 mL per 250 mL flask for each overnight culture for 100 mL: 300 mLCzapek-Dox liquid medium 4.54 g 13.62 g centrifuged V8 juice 20 mL 60 mLadd H20 to 95 mL 285 mL adjust to pH 6.0 transfer totransfer to flask(s) and autoclaveadd 5 mL sterile complete supplement to media after autoclavingComplete Supplement (CS)Bacto-casamino acids 20 g/lBacto-peptone 20 g/lBacto-yeast extract 20g/lAdenine 3 g/l 9Biotin 0.02 g/lNicotinic acid 0.02 g/lP-aminobenzoic acid 0.02 g/l 10Pyridoxine 0.02 g/lThiamine 0.02 g/l | Australian National University | 1 | 2016 | Oliver Mead 2016. CZV8CS - liquid medium for fungal culture. protocols.io dx.doi.org/10.17504/protocols.io.f7cbriw | 2021-03-29 03:09:57 | |||
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Acid nucleic extraction from rice dried leaves Resource Report Resource Website |
Martine Bangratz, Charlotte Tollenaere | 10.17504/protocols.io.bcntiven | Acid nucleic extraction of rice dried leaves by a CTAB method adapted from Li et al 2008. Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. Journal of Virological Methods. 2008;154(1):48-55. doi: 10.1016/j.jviromet.2008.09.008. | Bangratz M, Wonni I, Kini K, Sondo M, Brugidou C, Béna G, Gnacko F, Barro M, Koebnik R, Silué D, Tollenaere C (2020) Design of a new multiplex PCR assay for rice pathogenic bacteria detection and its application to infer disease incidence and detect co-infection in rice fields in Burkina Faso. PLoS ONE 15(4): e0232115. doi: 10.1371/journal.pone.0232115 | IRD, Montpellier, France, IRD, Montpellier, France | https://doi.org/10.1371/journal.pone.0232115 | 1 | 2020 | Martine Bangratz, Charlotte Tollenaere 2020. Acid nucleic extraction from rice dried leaves . protocols.io dx.doi.org/10.17504/protocols.io.bcntiven | 2021-03-29 03:09:58 | ||
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DNA size selection (>3-4kb) and purification of DNA using an improved homemade SPRI beads solution. Resource Report Resource Website |
Ramawatar, Benjamin Schwessinger | 10.17504/protocols.io.n7hdhj6 | High molecular weight DNA extraction from all kingdoms | Most noncommercial tradition DNA extraction protocols result in a crude DNA preparation. If the DNA is intended to be used for a high-end application like Nanopore sequencing, it requires a thorough clean-up and size selection before it could be used for sequencing. Solid Phase Reversible Immobilisation (SPRI) magnetic beads is a quick and convenient way of purifying and size selecting intact double-stranded DNA from crude DNA. Most commercially available SPRI beads based DNA purification mix is quite expensive so our lab endeavored to develop an inexpensive beads mix which is as good as the commercially available ones. In this effort, our lab has optimized a beads mix for purifying and size selecting crude DNA extracted from eucalyptus and posted on protocol.io, https://www.protocols.io/edit/high-purity-high-molecular-weight-dna-extraction-f-n5ydg7w?step=16.However, this solution was not very effective in purifying crude DNA extracted from fungal material. DNA extracted from fungal material is highly viscous which is indicative of high levels of impurities in the DNA preparation. I tried to improve the beads mix for purifying rust DNA by adding 0.25 % (v/v) Tween-20 into the beads mix.I tested beads mix with Tween-20 to see if adding tween into the solution makes any difference in the recovery, purity and size selection. Turns out that bead solutions with Tween-20 make big difference in the size selection and recovery of the DNA compared to the bead solutions without. I calibrated/tested the bead solution with and without Tween-20 on the 1 kb DNA ladder to establish which DNA solution to beads volume ratio gives optimal recovery and size selection. We found that beads mix with 0.25 % Tween-20 works much better in size selection and recovery than beads mix without Tween-20. The best DNA to beads volume ratios were 1.0: 0.9 and 1.0: 1.0. | Schalamun M, Nagar R, Kainer D, Beavan E, Eccles D, Rathjen JP, Lanfear R, Schwessinger B, Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from . Molecular Ecology Resources 19(1). doi: 10.1111/1755-0998.12938 | Australian National University, Australian National University | https://doi.org/10.1111/1755-0998.12938 | 1 | 2018 | Ramawatar, Benjamin Schwessinger 2018. DNA size selection (>3-4kb) and purification of DNA using an improved homemade SPRI beads solution.. protocols.io dx.doi.org/10.17504/protocols.io.n7hdhj6 | 2021-03-29 03:09:58 | |
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MG_HW9: Getting started with Anvi'o Resource Report Resource Website |
Murat Eren and Bonnie Hurwitz | 10.17504/protocols.io.gc3bsyn | Hurwitz Lab, MetaFunc Course | Adapted from http://merenlab.org/2016/06/22/anvio-tutorial-v2/ | University of Chicago and University of Arizona | http://merenlab.org/2016/06/22/anvio-tutorial-v2/ | 1 | 2016 | Murat Eren and Bonnie Hurwitz 2016. MG_HW9: Getting started with Anvi'o. protocols.io dx.doi.org/10.17504/protocols.io.gc3bsyn | 2021-03-29 03:09:56 | ||
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Extracting DNA from bananas Resource Report Resource Website |
Melissa Wilson Sayres | 10.17504/protocols.io.esvbee6 | For more information and for the Spanish version of this protocol, please see here.The protocol is based on: http://www.scientificamerican.com/article/find-the-dna-in-a-banana-bring-science-home/. | protocols.io | 1 | 2016 | Melissa Wilson Sayres 2016. Extracting DNA from bananas. protocols.io dx.doi.org/10.17504/protocols.io.esvbee6 | 2021-03-29 03:09:58 | ||||
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Mapping and Counting High-Intensity Perineuronal Nets in the Somatosensory Cortex Resource Report Resource Website |
Dana Layo, Billy Y.B. Lau, Keerthi Krishnan | 10.17504/protocols.io.bcf8itrw | The purpose of this protocol is to outline the process by which we count high-intensity perineuronal nets (PNNs) in whole brain analysis. Specifically, high-intensity PNNs within the primary somatosensory cortex of adult mouse brain sections cut in a sagittal orientation. This protocol accompanies the paper “Lateralized expression of cortical perineuronal nets during maternal experience is dependent on MECP2” (https://doi.org/10.1101/787267).First, we align a digital map from the Franklin & Paxinos Mouse Brain Atlasonto individual brain sections. We then explain the process by which the S1 and its subregions areoutlined based on this atlas overlay. Finally, we outline the process of counting high-intensity PNNs within these regions.High-intensity PNNs are thought to be more mature structures due to a larger accumulation of the proteoglycans that make-up the structures1–3. We look at PNNs as a marker for changes in experience-dependent plasticity within the brain, where it can inhibit plasticity or solidify the changes that occurred in response to an experience.Video tutorial accompanying this protocol: Different regions of the mouse brain have differing densities of PNNs. Adult somatosensory cortex has the highest density based on what we have observed. This protocol can also be used to count all PNNs, just skip the contrast step (7.2) in PNN analysis.Citations1.Slaker, M. L., Harkness, J. H. & Sorg, B. A. A standardized and automated method of perineuronal net analysis using Wisteria floribunda agglutinin staining intensity.IBRO reports 1, 54–60 (2016).2.Carulli, D.et al.Composition of perineuronal nets in the adult rat cerebellum and the cellular origin of their components.The Journal of Comparative Neurology 494, 559–577 (2006).3.Foscarin, S.et al.Experience-Dependent Plasticity and Modulation of Growth Regulatory Molecules at Central Synapses.PLoS ONE 6, e16666 (2011). | Lau BYB, Layo DE, Emery B, Everett M, Kumar A, Stevenson P, Reynolds KG, Cherosky A, Bowyer SH, Roth S, Fisher DG, McCord RP, Krishnan K, Lateralized Expression of Cortical Perineuronal Nets during Maternal Experience is Dependent on MECP2. eNeuro 7(3). doi: 10.1523/ENEURO.0500-19.2020 | University of Tennessee, Knoxville, University of Tennessee, Knoxville, University of Tennessee, Knoxville | https://doi.org/10.1101/787267 | 2 | 2020 | Dana Layo, Billy Y.B. Lau, Keerthi Krishnan 2020. Mapping and Counting High-Intensity Perineuronal Nets in the Somatosensory Cortex. protocols.io dx.doi.org/10.17504/protocols.io.bcf8itrw | 2021-03-29 03:09:58 | ||
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Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing Resource Report Resource Website |
Franziska Aron, Gunnar Neumann, Guido Brandt | 10.17504/protocols.io.bakricv6 | WarinnerGroup, MPI-SHH Archaeogenetics | Protocol for the preparation of double-stranded genomic libraries for Illumina sequencing, optimised for ancient DNA (aDNA). This protocol generates adapter ligated DNA fragments that can be used in conjunction with downstream Indexing protocols.This protocol does not include UDG (USER) treatment, in order to retain molecular 'damage' in the form of deaminated cytosines characteristic of aDNA. This protocol is modified after Meyer & Kircher (2010) Cold Spring Harb. Protoc. (doi: 10.1101/pdb.prot5448). | Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Department of Archaeogenetics, Max Planck Institute for the Science of Human History | 1 | 2020 | Franziska Aron, Gunnar Neumann, Guido Brandt 2020. Non-UDG treated double-stranded ancient DNA library preparation for Illumina sequencing . protocols.io dx.doi.org/10.17504/protocols.io.bakricv6 | 2021-03-29 03:09:58 | |||
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Hepatotoxicity during 6-thioguanine treatment: protocol for a systematic review Resource Report Resource Website |
Linea Natalie Toksvang, Rikke Hebo Larsen, Thomas Leth Frandsen, Kjeld Schmiegelow, Cecilie Utke Rank | 10.17504/protocols.io.zjnf4me | Hepatotoxicity was recognised as a complication of 6-thioguanine (6TG) in 1976. Since then, 6-TG associated hepatotoxicity in the form of acute sinusoidal obstruction syndrome (SOS), also known as veno-occlusive disease (VOD), has notably been reported in childhood acute lymphoblastic leukaemia (ALL), whereas chronic nodular regenerative hyperplasia (NRH) has been reported in adults with inflammatory bowel disease (IBD) as well as in childhood ALL. However, SOS and NRH should be considered part of a spectrum of microvascular disorders caused by endothelial injury. Nevertheless, the cellular mechanisms responsible for the sinusoidal damage, being pivotal to their development, remain to be established. 6TG-related SOS and NRH have been hypothesised to be dose-related, since they do not seem to occur with low cumulative doses. .justify:after { content: ""; display:inline-block; width: 100%; } The recent finding that higher levels of thioguanine nucleotides incorporated into leucocyte DNA (DNA-TGN) correlate to a lower relapse risk, calls for reappraisal of the feasibility of prolonged 6TG treatment for childhood ALL, while avoiding the risk of SOS and NRH. .justify:after { content: ""; display:inline-block; width: 100%; } .justify:after { content: ""; display:inline-block; width: 100%; } Objectives .justify:after { content: ""; display:inline-block; width: 100%; } - Primary objective: To assess the incidence of hepatotoxicity in patients treated with 6TG compared to 6MP or standard care. .justify:after { content: ""; display:inline-block; width: 100%; } - Secondary objective: To explore if a safe dose of 6TG can be established. .justify:after { content: ""; display:inline-block; width: 100%; } | Toksvang LN, Schmidt MS, Arup S, Larsen RH, Frandsen TL, Schmiegelow K, Rank CU (2019) Hepatotoxicity during 6-thioguanine treatment in inflammatory bowel disease and childhood acute lymphoblastic leukaemia: A systematic review. PLoS ONE 14(5): e0212157. doi: 10.1371/journal.pone.0212157 | Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark, Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark, Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark, Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Institute of Clinical Medicine, The Faculty of Medicine, University of Copenhagen, Denmark. , Department of Hematology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Pediatric Oncology Research Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark. | https://doi.org/10.1371/journal.pone.0212157 | 1 | 2019 | Linea Natalie Toksvang, Rikke Hebo Larsen, Thomas Leth Frandsen, Kjeld Schmiegelow, Cecilie Utke Rank 2019. Hepatotoxicity during 6-thioguanine treatment: protocol for a systematic review. protocols.io dx.doi.org/10.17504/protocols.io.zjnf4me | 2021-03-29 03:09:56 | ||
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Protocol : Cement augmentation of internal fixation for trochanteric fracture: protocol for a systematic review and meta-analysis Resource Report Resource Website |
Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki | 10.17504/protocols.io.bkg2ktye | Department of Orthopedic Surgery, Kagawa Prefectural Central Hospital, Kagawa, Japan, Department of Orthopedic Surgery, Tokyo Medical and Dental University, Tokyo, Japan, Systematic Review Workshop Peer Support Group (SRWS-PSG), Japan, Systematic Review Workshop Peer Support Group (SRWS-PSG), Japan, Department of Musculoskeletal Traumatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan, Department of orthopedics ,Foot and Ankle Research and Innovation Laboratory, Massachusetts General Hospital, Boston, USA, Department of Orthopaedic Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Science, Okayama, Japan | 6 | 2020 | Norio Yamamoto, Takahisa Ogawa, Masahiro Banno, Jun Watanabe, Tomoyuki Noda, Haggai Schermann, Toshifumi Ozaki 2020. Protocol : Cement augmentation of internal fixation for trochanteric fracture: protocol for a systematic review and meta-analysis. protocols.io dx.doi.org/10.17504/protocols.io.bkg2ktye | 2021-03-29 03:09:56 | |||||
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How to make a 50 mg/ml Kanamycin Stock Solution Resource Report Resource Website |
Sean Seaver | 10.17504/protocols.io.ci2ugd | How to make a 50 mg/ml Kanamycin Stock Solution | P212121 | http://store.p212121.com/kanamycin-monosulfate/ | 1 | 2014 | Sean Seaver 2014. How to make a 50 mg/ml Kanamycin Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.ci2ugd | 2021-03-29 03:09:56 |
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