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Authors: Diego Bonatto
Group: Grupo de Estudos de Leveduras Cervejeiras
Summary: 12Ampicillin100 mg/mL100 µg/mL3Bleocin5 mg/mL5 µg/mL4Carbenicillin*100 mg/mL100 µg/mL5Chloramphenicol25 mg/mL(dissolve in EtOH)25 µg/mL6Coumermycin25 mg/mL(dissolve in DMSO)25 µg/mL7Gentamycin10 mg/mL10 µg/mL8Kanamycin50 mg/mL50 µg/mL9Spectinomycin50 mg/mL50 µg/mL10Tetracycline10 mg/mL10 µg/mLNote: Unless otherwise indicated, the antibiotic powder can be dissolved in dH2O.*Note: Carbenicillin can be used in place of ampicillin. Carbenicillin is more stable, so it is potentially more effective at selecting only bacteria containing the plasmids of interest (for example, fewer satellite colonies will grow). However, it is also more expensive.
Proper citation: Diego Bonatto 2018. Antibiotics solutions. protocols.io dx.doi.org/10.17504/protocols.io.puednte Copy
Authors: Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li
Group: GigaScience Press
Summary: As one of the most recognizable characteristics in birds, plumage colour has a high impact on understanding the evolution and mechanisms of colouration. Feather and skin are ideal tissues to explore the genomics and complexity of colour patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst’s pheasant (Chrysolophus amherstiae), exhibit brilliant colours in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage colouration mechanisms in birds. Here we provide details of the protocols used for plumage pigments identification by High-performance liquid chromatography. The fat-soluble pigments (carotenoids) and oxidation products of melanins (TTCA and PTCA) can be qualitatively and quantificationally analyzed by HPLC with the corresponding standards, respectively.
Proper citation: Guangqi Gao, Meng Xu, Yongchun Zuo, Yulan Yang, Chunling Bai, Junyang Xu, Zhuying Wei, Jiumeng Min, Guanghua Su, Xianqiang Zhou, Jun Guo, Yu Hao, Guiping Zhang, Xukui Yang, Xiaomin Xu, Randall B Widelitz, Cheng-Ming Chuong, Chi Zhang, Jun Yin, Guangpeng Li 2018. Plumage pigments identification by High-performance liquid chromatography. protocols.io dx.doi.org/10.17504/protocols.io.sjtecnn Copy
Authors: Michelle Lent
Summary: Bariatric surgery patients may experience significant psychosocial changes after surgery, but littlepsychological support is available beyond support groups postoperatively. We evaluated the feasibility of apostoperative support program targeting quality of life, psychosocial functioning and adherence to behavior change in bariatric surgery patients. This prospective, randomized pilot trial evaluated a comprehensive postoperative behavioral support intervention using a 4-month bi-weekly program in 24 bariatric surgery patients compared to 26 usual care patients that completed bariatric surgery within one year. Outcomes included feasibiilty and the difference in quality of life (as measured by the Short Form-36) between groups, as well as differences in psychosocial functioning (mood, eating behaviors) and adherence (diet, physical activity, appointments). Outcomes were assessed at baseline and treatment completion (4 months). The intervention focused on addressing psychosocial changes after surgery, strategies for postoperative diet and adherence, and preventing weight regain. Patients collaboratively set goals for diet, physical activity, adherence and other behavioral changes tailored to the needs of each participant. Intervention patients were asked to attend 8, one-hour bi-weekly treatment sessions in a 4-month time period.
Proper citation: Michelle Lent 2019. A Randomized Trial of a Pilot Behavioral Support Intervention After Bariatric Surgery. protocols.io dx.doi.org/10.17504/protocols.io.2bagaie Copy
Authors: Kailong Ma
Group: GigaScience Press, BGI
Summary: This protocol is used to clarity the process of total DNA extraction for our Betta splendens genome.
Proper citation: Kailong Ma 2018. DNA extraction for the Betta splendens genome. protocols.io dx.doi.org/10.17504/protocols.io.qvedw3e Copy
Authors: Alice Jones, XB Wu, YW Bai, Jia Han, Elizabeth Dean
Summary: This protocol describes the methods for a study aimed to investigate perceptions of Chinese physical therapy students on the use of the Health Improvement Care (HIC) as a clinical tool to assess lifestyle behaviors/attributes and provide lifestyle education advice to others. Title of the study: Use of Health Improvement Card by Chinese physical therapy students: A pilot study. Xubo Wu, Alice YM Jones, Yiwen Bai, Jia Han, Elizabeth Dean.
Proper citation: Alice Jones, XB Wu, YW Bai, Jia Han, Elizabeth Dean 2019. Use of Health Improvement Card by Chinese physical therapy students: A pilot study. protocols.io dx.doi.org/10.17504/protocols.io.54kg8uw Copy
Authors: Miten Jain
Summary: Reverse Transcription-free (RT-free) poly(A) RNA protocol for Nanopore Direct RNA SequencingThis protocol was developed as a collaboration between NASA Houston, Oxford Nanopore Technologies, and UC Santa Cruz to support direct RNA Nanopore sequencing on the International Space Station (ISS). Contributors: NASA JSC Houston: Sarah Stahl, Aaron S. Burton, Kristen K. John, Sarah L. Castro-WallaceOxford Nanopore Technologies: Daniel Jachimowicz, Daniel R. GaraldeUniversity of California Santa Cruz: Mark Akeson, Benedict Paten, Miten JainOxford Nanopore Technologies: Daniel Jachimowicz, Daniel R. GaraldeUniversity of California Santa Cruz: Mark Akeson, Benedict Paten, Miten Jain
Proper citation: Miten Jain 2020. RT-free Nanopore direct RNA sequencing v1. protocols.io dx.doi.org/10.17504/protocols.io.bpiimkce Copy
Authors: Mihai IONITA
Proper citation: Mihai IONITA 2019. SSH Amazon EC2. protocols.io dx.doi.org/10.17504/protocols.io.xjcfkiw Copy
Authors: Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert
Group: GigaScience Press
Summary: This protocol allows for adequate DNA extraction from fresh blood samples.
Proper citation: Faezah Mohd Salleh, Jazmin Ramos-Madrigal, Fernando Penaloza, Shanlin Liu, Mikkel-Holger S Sinding, Riddhi P Patel, Renata Martins, Dorina Lenz, Jorns Fickel, Christian Roos, Mohd Shahir Shamsir, Mohammad Shahfiz Azman, Burton K Lim, Stephen J Rossiter, Andreas Wilting, M Thomas P Gilbert 2017. Extraction method B (FMS and CR). protocols.io dx.doi.org/10.17504/protocols.io.im9cc96 Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hens was a reproducible and feseable test used to meassure IgY development after vaccination.
Proper citation: Angel Justiz-Vaillant 2020. Enzyme-linked immunosorbent assay (ELISA) for studying the presence of anti-Salmonella antibody in layer hen's egg yolks.. protocols.io dx.doi.org/10.17504/protocols.io.bjj3kkqn Copy
Authors: karen maciel de oliveira
Summary: This assay is used to measure cell viability. Dead cells have damage membranes. The ethidium homodimer-1 enters damaged cells and is fluorescent when bound to nucleic acids, producing a bright red fluorescence in damaged or dead cells.
Proper citation: karen maciel de oliveira 2018. Assessment of cell death. protocols.io dx.doi.org/10.17504/protocols.io.ruhd6t6 Copy
Authors: Alba Balletbó
Group: iGEM Wageningen 2019
Proper citation: Alba Balletbó 2019. Transformation using Electroporation. protocols.io dx.doi.org/10.17504/protocols.io.7jzhkp6 Copy
Authors: Emily Bellis, Elizabeth Kelly
Summary: This protocol describes a standard germination assay for Striga hermonthica carried out in the Penn State quarantine facility.
Proper citation: Emily Bellis, Elizabeth Kelly 2019. Striga hermonthica germination assay. protocols.io dx.doi.org/10.17504/protocols.io.2wdgfa6 Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using Hexamine Cobalt Chloride. protocols.io dx.doi.org/10.17504/protocols.io.eq7bdzn Copy
Authors: Lawrence A. Klobutcher
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: The electroporation procedure and conditions described allow for the entry of DAPI into the cell, resulting in nuclear staining. We have not yet been successful in using these conditions for transformation of Euplotes crassus, but only a couple of constructs have been tried to date.
Proper citation: Lawrence A. Klobutcher 2017. Electroporation of Euplotes crassus: conditions that allow for the uptake of DAPI.. protocols.io dx.doi.org/10.17504/protocols.io.gwmbxc6 Copy
Authors: Anbarasu Karthikaichamy, Jackie Collier
Group: Collier Lab
Summary: Transformation protocol for electroporation of CRISPR/Cas9 ribonucleoprotein (RNP) complex in urantiochytrium limacinum (ATCC MYA-1381; Stramenopile/ Heterokont, Thraustochytrid).
Proper citation: Anbarasu Karthikaichamy, Jackie Collier 2019. CRISPR/Cas9 based knockout generation in Aurantiochytrium limacinum (ATCC MYA-1381). protocols.io dx.doi.org/10.17504/protocols.io.baeyibfw Copy
Authors: Shuo Liu
Proper citation: Shuo Liu 2017. Oral versus intravenous methylprednisolone for treatment of relapses in multiple sclerosis?a meta-analysis of randomized controlled trials.. protocols.io dx.doi.org/10.17504/protocols.io.j5hcq36 Copy
Authors: Kenji Tsuchiya
Proper citation: Kenji Tsuchiya 2018. Experimental procedure of Household Activities and Physical Activity. protocols.io dx.doi.org/10.17504/protocols.io.jatcien Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukin-10 is a pleiotropic cytokine playing a critical role as a regulator of myeloid and lymphoid cell function. Due to the ability of IL-10 to blocking cytokine synthesis and many accessory cell functions of antigen-presenting cells such as macrophages this cytokine is a potent suppressor of the effector functions of macrophages, T-cells and NK cells. IL-10 also participates in regulating proliferation and differentiation of B-lymphocytes, mast cells and thymocytes [1]. Reference1. Ouyang W, O'Garra A. IL-10 Family Cytokines IL-10 and IL-22: from Basic Science to Clinical Translation.Immunity. 2019;50(4):871-891. doi:10.1016/j.immuni.2019.03.020
Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-6 in human serum or plasma.. protocols.io dx.doi.org/10.17504/protocols.io.bjy7kpzn Copy
Authors: Bioline
Group: Bioline
Summary: The steps for preparing the lysate are different depending on the starting material. Please ensure you follow the correct procedure for your starting material (see the section Disrupting and Homogenizing Starting Materials and the different lysate preparation protocols here). The subsequent steps detailed in Genomic DNA removal and total RNA purification are the same in all cases.This protocol describes the isolation of viral RNA from small amounts of tissue (up to 20 mg for most types of tissue).
Proper citation: Bioline 2016. Lysate Preparation from Viruses in Mammalian Tissue. protocols.io dx.doi.org/10.17504/protocols.io.f5gbq3w Copy
Authors: Rebecca Nance, Payal Agarwal, Maninder Sandey, Dmytro Starenki, Jey Koehler, Abdul Mohin Sajib, Bruce F Smith
Summary: Extracting sufficient quantity and quality RNA from bone is essential for downstream application, such as transcriptomic sequencing, to evaluate gene expression. Isolation of RNA from bone presents a unique challenge owing to the hypocellular, brittle and mineralized matrix, which makes homogenizing the tissue difficult and provides little RNA to work with. Removal of contaminating tissue, such as bone marrow and connective tissue, is essential for isolating RNA that is unique to osteoblasts, osteoclasts and osteocytes. This protocol establishes a method to effectively isolate RNA from normal canine bone cells using the second phalanx, without contamination from other tissue types, for downstream transcriptomic analysis.This method combines physical manipulation to remove exterior tissue, washing and centrifugation to remove cells and fat within the diaphysis, homogenization using a mortar and pestle on dry ice prior to bead dissociation, followed by acid guanidinium thiocyanate-phenol-chloroform extraction and column purification to yield sufficiant quantity and quality RNA from canine phalanges. The second phalanx was chosen due to its size small enough to fit into a 1.7 mL microfuge tube, but large enough to provide enough RNA. Mean RNA obtained using this protocol was 14.7 ug of RNA per gram of frozen bone.
Proper citation: Rebecca Nance, Payal Agarwal, Maninder Sandey, Dmytro Starenki, Jey Koehler, Abdul Mohin Sajib, Bruce F Smith 2020. A method for isolating RNA from canine bone . protocols.io dx.doi.org/10.17504/protocols.io.be86jhze Copy
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