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Authors: Yawei Xing
Proper citation: Yawei Xing 2019. Dynamic distribution of gallbladder microbiota in rabbit at different ages and health states Short title: Dynamic distribution of gallbladder microbiota in rabbits. protocols.io dx.doi.org/10.17504/protocols.io.xarfid6 Copy
Authors: Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million
Group: SPARC
Summary: This protocol describes a process for the measurement of acute electrical stimulation-induced effects on colonic motility in anesthetized young adult Yucatan minipigs. Signals recorded from manometry probes inserted into the proximal, transverse and distal colonic regions were used to measure the effect of stimulation by serosally placed electrodes opposed to the colonic tissue at multiple sites in an acute anesthetized preparation. The effect of stimulation was quantified as motility index assessments before, during and after stimulation, and the data was used to create a functional map of colonic motor response to localized colon stimulation.
Proper citation: Muriel Larauche, Yushan Wang, Po-Min Wang, James Dunn, Wentai Liu, Mulugeta Million 2020. Tache_Mulugeta_OT2OD024899_Colon tissue electrical stimulation and colonic motility measurements. protocols.io dx.doi.org/10.17504/protocols.io.3rmgm46 Copy
Authors: Sebastião Santos
Summary: Background: Knee rehabilitation using therapeutic exercises in the aquatic environment has been used in order to initiate lower limb rehabilitation earlier and improve joint movements, as it reduces pain and allows for earlier weight bearing. Objective: To develop and describe the effects of an aquatic therapeutic exercise program in a case study of tibial osteotomy and varus femur. Methods: A 15-year-old girl undergoing a tibial and femoral varus osteotomy completed an aquatic therapeutic exercise program consisting of a total of 30 sessions (3 sessions per week of 60 minutes). The subject was evaluated at two different times (at the beginning and end of the intervention). Results: There was an improvement in the various parameters evaluated (knee flexion: 66º vs 125º; knee extension: -7º vs -1º; pain on movement: 6/10 vs 0/10). Conclusion: The aquatic therapeutic exercise program used in this study has beneficial effects in a clinical case of tibial osteotomy and varus femur.
Proper citation: Sebastião Santos 2021. Rehabilitation protocol after varization osteotomy - Case Study. protocols.io dx.doi.org/10.17504/protocols.io.bi5kkg4w Copy
Authors: Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández
Summary: Inhibitory substances can be obtained and purified by different methodologies. Free cell supernatants obtained by centrifugation and filtration are commonly used for evaluating antimicrobial metabolites produced by bacteria. In this work, a new methodology for obtaining antimicrobial metabolites is proposed, especially implemented for bacteria which are not able to produce these compounds in liquid media; based on the use of nitrocellulose filter membranes and solid culture media.
Proper citation: Catherine Cesa-Luna, Alberto Aguayo-Acosta, Antonino Baez, Jesús Muñoz-Rojas, Verónica Quintero-Hernández 2020. Cold-leaching extraction. A new methodology for obtaining inhibitory substances produced by bacteria in solid media.. protocols.io dx.doi.org/10.17504/protocols.io.bhs3j6gn Copy
Authors: Steven Burgess
Group: OpenPlant Project, Plantae
Proper citation: Steven Burgess 2016. TRIS Acetate Phosphate Salts (x40). protocols.io dx.doi.org/10.17504/protocols.io.fcsbiwe Copy
Authors: Magdalena Cygan, Mariusz Szemien, Stanisław Krompiec
Group: Chemistry Method Development Community
Proper citation: Magdalena Cygan, Mariusz Szemien, Stanisław Krompiec 2017. Syntesis and kinetic study of phenol-formaldehyde resins synthesized in the presence of polyamines . protocols.io dx.doi.org/10.17504/protocols.io.ibecaje Copy
Authors: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto J O Ramos
Group: Metabolomics Protocols & Workflows
Summary: Phytohormones play a key role in regulating development and growth, as well as acting on plant responses to biotic and abiotic stresses. The following protocol describes a target specific methodology to obtaining quantitative profiles of phytohormones from plant tissues by ultra-high-performance liquid chromatograph (UHPLC) coupled to mass spectrometry.
Proper citation: Camilo E. Vital, Jenny D. Gómez, Pedro M. Vidigal, Edvaldo Barros, Claudia S.L. Pontes, Nívea M. Vieira, Humberto J O Ramos 2019. PHYTOHORMONE PROFILING BY LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS). protocols.io dx.doi.org/10.17504/protocols.io.zgff3tn Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Proper citation: Allen Institute for Brain Science 2021. 10xV3 Genomics Sample Processing Protocol. protocols.io dx.doi.org/10.17504/protocols.io.bq7cmziw Copy
Authors: Josephine Bwogi1, 2, Khuzwayo C. Jere3, 4 , Charles Karamagi2, Denis K. Byarugaba5, Prossy Namuwulya1, Frederick N. Baliraine6 , Ulrich Desselberger7 , Miren Iturriza-Gomara3.
Proper citation: Josephine Bwogi1, 2, Khuzwayo C. Jere3, 4 , Charles Karamagi2, Denis K. Byarugaba5, Prossy Namuwulya1, Frederick N. Baliraine6 , Ulrich Desselberger7 , Miren Iturriza-Gomara3. 2017. Laboratory protocols for the study “Whole genome analysis of selected human and animal rotaviruses identified in Uganda from 2012 to 2014 reveals complex genome re-assortment events between human, bovine, caprine and porcine strains”.. protocols.io dx.doi.org/10.17504/protocols.io.h4vb8w6 Copy
Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: Separation and purification of PBMC from FRESH BLOOD: list of published work using this protocolKustrimovic, N., Comi, C., Magistrelli, L., Rasini, E., Legnaro, M., Bombelli, R., Aleksic, I., Blandini, F., Minafra, B., Riboldazzi, G., Sturchio, A., Mauri, M., Bono, G., Marino, F., & Cosentino, M. (2018). Parkinson's disease patients have a complex phenotypic and functional Th1 bias: cross-sectional studies of CD4+ Th1/Th2/T17 and Treg in drug-naïve and drug-treated patients. Journal of neuroinflammation, 15(1), 205. https://doi.org/10.1186/s12974-018-1248-8Kustrimovic, N., Rasini, E., Legnaro, M., Bombelli, R., Aleksic, I., Blandini, F., Comi, C., Mauri, M., Minafra, B., Riboldazzi, G., Sanchez-Guajardo, V., Marino, F., & Cosentino, M. (2016). Dopaminergic Receptors on CD4+ T Naive and Memory Lymphocytes Correlate with Motor Impairment in Patients with Parkinson's Disease. Scientific reports, 6, 33738. https://doi.org/10.1038/srep33738Cosentino M., Ferrari M., Kustrimovic N., Rasini E., Marino F. (2015). Influence of dopamine receptor gene polymorphisms on circulating T lymphocytes: A pilot study in healthy subjects. Human immunology, 76, 10, 747-752. https://doi.org/10.1016/j.humimm.2015.09.032
Proper citation: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino 2020. Separation and purification of human PBMC from FRESH BLOOD. protocols.io dx.doi.org/10.17504/protocols.io.bfxmjpk6 Copy
Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This protocol is used to visualise sensory and autonomic neurons innervating the bladder body (dome), bladder trigone or proximal urethra in an experimental adult male or female rat. The protocol is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation, including methods of anesthesia, surgical environment, and post-operative monitoring and care.
Proper citation: Janet Keast, Peregrine Osborne 2019. Use of tracer dyes to label neural projections to lower urinary tract organs [keast-001-stage01]. protocols.io dx.doi.org/10.17504/protocols.io.w3dfgi6 Copy
Authors: Kelsey Knight
Group: BioLegend
Summary: Catalog Number: 658502
Storage Temperature: 2°C-8°C
Product Description Anti-c-Myc Tag (9E10) Affinity Gel consists of anti-c-myc monoclonal antibody (clone 9E10), covalently immobilized onto 6% high density glyoxal agarose beads. The affinity resin can be used in affinity purifying and immunoprecipitation of c-Myc-tagged fusion protein.
Binding Specificity Mouse monoclonal antibody 9E10 recognizes the c-myc epitope N-EQKLSEEDL-C and is purified through Protein G chromatography. The antibody conjugated affinity resin can bind to epitope at N-terminal, C-terminal, and internal locations of a fusion protein. The binding capacity is greater than 0.5mg per ml of c-myc agarose resin.
Reagent Anti-c-Myc Agarose Affinity Gel is supplied as a 50% suspension in phosphate-buffered saline, pH 7.2, containing 0.09% sodium azide.
Precautions and Disclaimer This product is for research use only. Please consult the Material Safety Data Sheet for information regarding hazards and safe handling practices.
Storage/Stability Anti-c-Myc Agarose Affinity Gel should be stored between 2°C and 8°C for maximum stability. The unopened product is stable for one year when stored as indicated. After use, the resin should be regenerated and stored in TBS or PBS buffer (pH 7.2) containing 0.09% sodium azide.
Proper citation: Kelsey Knight 2018. Anti-c-Myc Tag (9E10) Affinity Gel Protocol. protocols.io dx.doi.org/10.17504/protocols.io.tideka6 Copy
Authors: Daniel Horn, Hubert János Kiss
Summary: We attempt to link laboratory-based measures of preferences with measures of school performance. We measured in an incentivized way risk, time, social and competitive preferences and also cognitive abilities of university students and look for associations between these measures and two important academic outcome measures: exam results and GPA.We find consistently that cognitive abilities (proxied by the Cognitive Reflection Test (Frederick 2005)) are very well correlated with school performance. Regarding non-cognitive skills, we find suggestive evidence for many of our measured preferences. We used two alternative measures of time preference: patience and present bias. Present bias explains exam grades relatively better, while patience is better explaining GPA. Both measures of time preferences have a non-linear relation to school performance. Competitiveness matters, as students, who opt for a more competitive payment scheme in our experiments have a higher average GPA and better exam grades. We observe also that risk-averse students perform a little better than risk-loving students. That makes sense in case of multiple choice exams, because risk-loving students may want to try to pass the exam less prepared, as the possibility of passing as exam just by chance is not zero. Finally, we have also detected that cooperative preferences – the amount of money offered in a public good game – associates strongly with GPA, but in a non-linear way. Students who offered around half of their possible amounts had significantly higher GPAs than those, who offered none or all their money.Keywords: competititive preferences, experiment, non-cognitive skills, risk preferences, school performance, social preferences, time preferences.JEL codes: C91; D91; I20
Proper citation: Daniel Horn, Hubert János Kiss 2017. Which preferences associate with school performance? – Lessons from a university exploratory study. protocols.io dx.doi.org/10.17504/protocols.io.kepctdn Copy
Authors: Gordon Wellman
Group: Salt Lab KAUST
Summary: This protocol outlines the preparation of a basic sucrose loading dye 10 X stock solution for gel electrophoresis (DNA/RNA). Orange G runs at approximately 50 bp making this loading dye ideal for small molecular weight polynucleotides. Used mainly as an indicator for approx. 100 bp polynucleotides, where we would like to avoid contamination of small fragments with other loading dyes. It is also useful as an indicator if you have excessive primer-dimer amplification in your PCRs as these usually also run at approx. 50 bp.The origins of this protocol have been lost in the mists of time and this method been handed down from PhD student to PhD student.
Proper citation: Gordon Wellman 2018. 10 X Sucrose Orange G Loading Dye. protocols.io dx.doi.org/10.17504/protocols.io.kp7cvrn Copy
Authors: Hajime Fujishima, Shoichi Fumoto, Tomotaka Shibata, Kohei Nishiki, Yoshiyuki Tsukamoto, Tsuyoshi Etoh, Masatsugu Moriyama, Norio Shiraishi, Masafumi Inomata
Summary: BackgroundRecently, neoadjuvant chemotherapy with docetaxel/cisplatin/5-fluorouracil (NAC-DCF) was identified as a novel strong regimen with a high rate of pathological complete response (pCR) in advanced esophageal cancer in Japan. Predicting pCR will contribute to the therapeutic strategy and the prevention of surgical invasion. However, a predictor of pCR after NAC-DCF has not yet been developed. The aim of this study was to identify a novel predictor of pCR in locally advanced esophageal cancer treated with NAC-DCF.Patients and MethodsA total of 32 patients who received NAC-DCF followed by esophagectomy between June 2013 and March 2016 were enrolled in this study. We divided the patients into the following 2 groups: pCR group (9 cases) and non-pCR group (23 cases), and compared gene expressions between these groups using DNA microarray data and KeyMolnet. Subsequently, a validation study of candidate molecular expression was performed in 7 additional cases.ResultsSeventeen molecules, including transcription factor E2F, T-cell-specific transcription factor, Src (known as “proto-oncogene tyrosine-protein kinase of sarcoma”), interferon regulatory factor 1, thymidylate synthase, cyclin B, cyclin-dependent kinase (CDK) 4, CDK, caspase-1, vitamin D receptor, histone deacetylase, MAPK/ERK kinase, bcl-2-associated X protein, runt-related transcription factor 1, PR domain zinc finger protein 1, platelet-derived growth factor receptor, and interleukin 1, were identified as candidate molecules. The molecules were mainly associated with pathways, such as transcriptional regulation by SMAD, RB/E2F, and STAT. The validation study indicated that 12 of the 17 molecules (71%) matched the trends of molecular expression.ConclusionsA 17-molecule set that predicts pCR after NAC-DCF for locally advanced esophageal cancer was identified.
Proper citation: Hajime Fujishima, Shoichi Fumoto, Tomotaka Shibata, Kohei Nishiki, Yoshiyuki Tsukamoto, Tsuyoshi Etoh, Masatsugu Moriyama, Norio Shiraishi, Masafumi Inomata 2017. microarray analysis. protocols.io dx.doi.org/10.17504/protocols.io.kahcsb6 Copy
Authors: Josh Quick
Group: High molecular weight DNA extraction from all kingdoms, Long Read Club
Proper citation: Josh Quick 2019. The 'Three Peaks' faecal DNA extraction method for long-read sequencing. protocols.io dx.doi.org/10.17504/protocols.io.584g9yw Copy
Authors: Aparecido Almeida Conceição, Clemente Batista Soares Neto, José Antônio de Aquino Ribeiro, Felix Gonçalves de Siqueira, Robert Neil Gerard Miller, Simone Mendonça
Summary: This simple and rapid chromatographic detection method was developed and validated in order to accurately quantify trace levels of free gossypol in different cotton materials, including cottonseed, cottonseed cake and cottonseed cake treated with macrofungi.
Proper citation: Aparecido Almeida Conceição, Clemente Batista Soares Neto, José Antônio de Aquino Ribeiro, Felix Gonçalves de Siqueira, Robert Neil Gerard Miller, Simone Mendonça 2018. Extraction and detection of free-gossypol in cottonseed samples. protocols.io dx.doi.org/10.17504/protocols.io.krncv5e Copy
Authors: Franziska Müller, Memduha Muratoglu, Jana Jung
Summary: Following this protocol, V. Natriegens cells can be transformed with linear fragments and plasmids based on natural transformation as described in Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens Dalia et. al, 2017. ACS Synthetic Biology.
Proper citation: Franziska Müller, Memduha Muratoglu, Jana Jung 2018. Natural Transformation. protocols.io dx.doi.org/10.17504/protocols.io.uyzexx6 Copy
Authors: Dr. Steven Wilhelm, Alyssa Alsante
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Alyssa Alsante 2017. Running the PTC-0200 DNA Engine. protocols.io dx.doi.org/10.17504/protocols.io.in7cdhn Copy
Authors: Adil R. Sarhan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler
Summary: We describe a fast and efficient peripheral blood mononuclear cell (PBMC) isolation for LRRK2 kinase pathway analysis
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Gain of kinase function mutations in the Leucine rich repeat kinase 2 (LRRK2) are associated with causing Parkinson’s disease. LRRK2 phosphorylates a subgroup of Rab GTPases and their phosphorylation levels mirror LRRK2 kinase activation status. Here, we describe a facile and robust method for isolating PBMCs by facilitated density gradient centrifugation, subsequent treatment with and without the specific LRRK2 kinase inhibitor MLi-2 to ensure that any effect seen is LRRK2 kinase dependent and cell lysis. PBMC lysates can then be used to quantify LRRK2 kinase pathway activity by measuring LRRK2-mediated phosphorylation of its endogenous RabGTPase substrates in human peripheral blood neutrophils either by quantitative immunoblotting or targeted mass-spectrometry. The benefits of using PBMCs are that they are routinely used as a biomatrix for Parkinson’s research and their isolation procedure is significantly faster and easier than that for example of neutrophils or monocytes from peripheral blood. However, their heterogeneity in terms of cellular composition and highly variable expression levels of LRRK2 and its substrates including Rab10 make PBMC a suboptimal biomatrix for reliably measuring LRRK2 kinase pathway activity. A potential use could be target engagement studies in clinical trials targeting LRRK2.
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Proper citation: Adil R. Sarhan, Andrew J.M. Howden, Dario R. Alessi, Esther M. Sammler 2021. Dundee peripheral blood mononuclear cell (PBMC) isolation protocol (from whole blood). protocols.io dx.doi.org/10.17504/protocols.io.bnhxmb7n Copy
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