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Authors: Terri Bryson, Steven Henikoff
Summary: Here we describe the method used to purify and load pATn5 for CUT&Tag, https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6/abstract. This protocol was modeled after that in Picelli et al (Picelli et al., 2014) using the pTXB1-rbs_3XFlag-pATn5-FL plasmid available from Addgene: https://www.addgene.org/124601/. It yields, as written, used at 1:200 dilution in CUT&Tag reactions, and for future use, both of which should be stored at -20C and can easily be scaled down.
Proper citation: Terri Bryson, Steven Henikoff 2019. 3XFlag-pATn5 Protein Purification and MEDS-loading (5x scale, 2L volume). protocols.io dx.doi.org/10.17504/protocols.io.8yrhxv6 Copy
Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The steps describe how to prepare each virus concentrate. There are multiple options for many of the steps; in the case where there is more than one option they are noted in annotations.
Proper citation: André M. Comeau and Rachel T. Noble 2016. Concentration of viruses and preparation of FLVs for tracer assays. protocols.io dx.doi.org/10.17504/protocols.io.dzv765 Copy
Authors: Sungwoo Bae
Proper citation: Sungwoo Bae 2019. Experiment protocol: a syringe-filter based DNA extraction. protocols.io dx.doi.org/10.17504/protocols.io.ysqfwdw Copy
Authors: RACHELE CESARONI, Rachele Cesaroni
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: RACHELE CESARONI, Rachele Cesaroni 2019. Dot blot to verify microinjection efficacy in Euplotes crassus. protocols.io dx.doi.org/10.17504/protocols.io.2aqgadw Copy
Authors: Vidur Sabharwal
Proper citation: Vidur Sabharwal 2019. Protein Estimation by BCA. protocols.io dx.doi.org/10.17504/protocols.io.zn4f5gw Copy
Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: 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. Different cells in both innate and acquired immunities produce IL-22, but the primary sources are T cells. Th22 cell is a new line of CD4+ T cells, which differentiated from naive T cells in the presence of various pro-inflammatory cytokines including IL-6. IL-22 inhibits IL-4 production. It also has essential functions in mucosal surface protection and tissue repairy. [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.
Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-22 in human serum.. protocols.io dx.doi.org/10.17504/protocols.io.bj3rkqm6 Copy
Authors: Jack Cerchiara, Kerry Kim, Eli Meir, Mary Pat Wenderoth, Jennifer H. Doherty
Summary: The basis for understanding neurophysiology is understanding ion movement across cell membranes. Students in introductory courses recognize ion concentration gradients as a driving force for ion movement but struggle to simultaneously account for electrical charge gradients. We developed and validated a 17-multiple-choice item assessment of students’ understanding of electrochemical gradients and resistance in neurophysiology, the Electrochemical Gradients Assessment Device (EGAD). We investigated the internal validity of the assessment by analyzing item characteristic curves of score probability and student ability for each question, as well as a Wright Map of student scores and ability. We used linear mixed-effect regression to test student performance and ability as well as learning gains. Our assessment discriminated students with average ability (WLE -2 to 1.5 Θ), however, was not as effective at discriminating students at the highest ability (WLE > 2 Θ). We determined the assessment could capture changes in both assessment scores (model r2 = 0.51, p2= 0.47, p2 = 0.51, p=0.014, n=444) and had higher ability scores (p=0.003) on the EGAD assessment. Caucasian students of both genders were positively correlated with score (r2 = 0.51, p2= 0.47, p<0.001, n=444). Based on the evidence gathered through our analyses, the scores obtained from the EGAD can validly and reliably distinguish between levels of content knowledge on introductory neurophysiology principles for students in introductory plant and physiology courses.
Proper citation: Jack Cerchiara, Kerry Kim, Eli Meir, Mary Pat Wenderoth, Jennifer H. Doherty 2019. Electrochemical Gradients Assessment Device (EGAD). protocols.io dx.doi.org/10.17504/protocols.io.z4ff8tn Copy
Authors: Lara Shepherd
Summary: A non-destructive DNA extraction method suitable for robust herbarium specimens and potentially useful for specimens with high levels of secondary compounds.
Proper citation: Lara Shepherd 2017. A non-destructive DNA sampling technique for herbarium specimens. protocols.io dx.doi.org/10.17504/protocols.io.i3jcgkn Copy
Authors: Bioo Scientific
Summary: This protocol is for the NEXTflex™ Small RNA Sequencing Kit v2, designed to prepare small RNA libraries for sequencing using Illumina® sequencers. This kit utilizes adapters with randomized ends to greatly reduce sequence bias in small RNA sequencing library construction.Please see the full manual for additional details.(The protocol below describes preparation of small RNA sequencing libraries from Total RNA starting material; for small RNA samples, please see this protocol.)
Proper citation: Bioo Scientific 2015. NEXTflex™ Small RNA Sequencing for Total RNA Starting Material. protocols.io dx.doi.org/10.17504/protocols.io.dnc5av Copy
Authors: Mohd Khubaib
Summary: this protocol describes the maintainance and treatment of RAW 264.7 macrophage cell lines with Mycobacterial PE/PPE proteins. It also describes estimation of secreted cytokines through ELISA. Estimation of level of IgG subclass from the serum is also described here.
Proper citation: Mohd Khubaib 2018. Cell Culture and estimation of cytokines by ELISA. protocols.io dx.doi.org/10.17504/protocols.io.p2hdqb6 Copy
Authors: Stefanie Andrew, Carol Clark, Sheppard Z.A., Evans M., Hutt J., Crook T. B.
Summary: BackgroundThe use of virtual reality to aid rehabilitation of upper-limb conditions has been an emerging field over the past decade. The majority of research seems to focus on post-stroke therapies with major advances in improving hand function through various robotic and digital techniques (1), however it is still not standard practice. With the recent crisis of COVID 19, home therapy has been thrust into the forefront of rehabilitation.At present a wide variety of technology has been developed to target rehabilitation in the upper limb.This includes hand tracking technology (e.g. Leap Motion) where various prototypes have been tested using haptics (2), robotic-assisted movement devices which predominantly target stroke or neurorehabilitation by means of exoskeleton prototypes (3,4), and exercise programmes through telerehabilitation and virtual reality (5). The majority of hand devices that have been developed are bulky and can impact on the accuracy of functional measurements (6).In terms of virtual reality, studies suggest that patients find it enjoyable and are as, if not more, motivated in these rehabilitation sessions when compared to traditional exercises, even in the older population (7). Hoffman et al in 2020 (8) found that patients undergoing hand rehabilitation with virtual reality felt that their pain was reduced, they had increased levels of motivation and therefore felt more able to perform exercises. This has been matched by studies looking at pain and anxiety levels whilst using virtual reality during wide awake anaesthesia with a significant reduction in both (9). Hand rehabilitation outside of stroke and neurological disorders, for example post-surgery or trauma, involves intensive hand rehabilitation by the hand therapy team but there is a global shortage of this service. Current practice is one-to-one patient-to-therapist and involves intensive rehabilitation, assessment and documentation. Virtual reality could prove a vital technology to develop to enable patients to undertake immersive therapy within their own homes whilst allowing remote assessment of their progress and function from the hand therapy and clinical teams.AimsThe overarching aim of this review is to identify the range and variety of virtual reality tools that are available and effective for upper limb conditions.Review objectives1) What is the “extent (size), range (variety) and nature (characteristics) of the evidence” of virtual tools to enhance hand rehabilitation?2) Do these tools have the potential to be used in the field of hand surgery and hand rehabilitation?3) What are the barriers and facilitators to hand rehabilitation using virtual tools? Design The scoping review will be conducted in accordance with PRISMA-ScR guidelines (10) and the frameworks developed by Arksey and O’Malley (11) and Levac et al. (12). Preliminary searches will be conducted and two librarians will be consulted to create a comprehensive search strategy. Screening of titles and abstracts will be undertaken by three independent reviewers, with conflicts resolved by discussions and consensus. Full-text screening will be undertaken following this same approach. A charting form will be developed based on the objectives of the review and refined by the research team. Data will be collated and summarised, with quantitative sources described descriptively and qualitative data analysed thematically (13). Results will be presented using summary tables and/or using pictorial/flow charts, if appropriate.References1) Saposnik G, Levin M, Outcome Research Canada (SORCan) Working Group. Virtual reality in stroke rehabilitation: a meta-analysis and implications for clinicians. Stroke. 2011 May;42(5):1380-1386. DOI: 10.1161/strokeaha.110.605451.2) Placidi G, Avola D, Iacoviello D, Cinque L. Overall design and implementation of the virtual glove. Comput Biol Med. 2013 Nov;43(11):1927-40. doi: 10.1016/j.compbiomed.2013.08.026. Epub 2013 Sep 25. PMID: 24209938.3) Ghassemi M, Ochoa JM, Yuan N, Tsoupikova D, Kamper D. Development of an Integrated Actuated Hand Orthosis and Virtual Reality System for Home-Based Rehabilitation. Annu Int Conf IEEE Eng Med Biol Soc. 2018 Jul;2018:1689-1692. doi: 10.1109/EMBC.2018.8512704. PMID: 30440720.4) Osuagwu BAC, Timms S, Peachment R, Dowie S, Thrussell H, Cross S, Shirley R, Segura-Fragoso A, Taylor J. Home-based rehabilitation using a soft robotic hand glove device leads to improvement in hand function in people with chronic spinal cord injury:a pilot study. J Neuroeng Rehabil. 2020 Mar 5;17(1):40. doi: 10.1186/s12984-020-00660-y. PMID: 32138780; PMCID: PMC7057671.5) Levanon Y. The advantages and disadvantages of using high technology in hand rehabilitation. J Hand Ther. 2013 Apr-Jun;26(2):179-83. doi: 10.1016/j.jht.2013.02.002. PMID: 23598084.6) Rose CG, Pezent E, Kann CK, Deshpande AD, O'Malley MK. Assessing Wrist Movement With Robotic Devices. IEEE Trans Neural Syst Rehabil Eng. 2018 Aug;26(8):1585-1595. doi: 10.1109/TNSRE.2018.2853143. Epub 2018 Jul 5. PMID: 29994401.7) Van Schaik P, Blake J, Pernet F, Spears I, Fencott C. Virtual augmented exercise gaming for older adults. Cyberpsychol Behav. 2008 Feb;11(1):103-6. doi: 10.1089/cpb.2007.9925. PMID: 18275322.8) Hoffman HG, Boe DA, Rombokas E, Khadra C, LeMay S, Meyer WJ, Patterson S, Ballesteros A, Pitt SW. Virtual reality hand therapy: A new tool for nonopioid analgesia for acute procedural pain, hand rehabilitation, and VR embodiment therapy for phantom limb pain. J Hand Ther. 2020 Apr-Jun;33(2):254-262. doi: 10.1016/j.jht.2020.04.001. Epub 2020 May 30. PMID: 32482376; PMCID: PMC7719341.9) Hoxhallari E, Behr IJ, Bradshaw JS, Morkos MS, Haan PS, Schaefer MC, Clarkson JHW. Virtual Reality Improves the Patient Experience during Wide-Awake Local Anesthesia No Tourniquet Hand Surgery: A Single-Blind, Randomized, Prospective Study. Plast Reconstr Surg. 2019 Aug;144(2):408-414. doi: 10.1097/PRS.0000000000005831. PMID: 31348351.10) Tricco, AC, Lillie, E, Zarin, W, O'Brien, KK, Colquhoun, H, Levac, D, Moher, D, Peters, MD, Horsley, T, Weeks, L, Hempel, S et al. (2018b) PRISMA extension for scoping reviews (PRISMA-ScR): checklist and explanation. Ann Intern Med. 2018,169 (7):467-473. doi:10.7326/M18-0850.11) Arksey H and O’Malley L (2005) Scoping studies: towards a methodological framework International Journal of Social Research Methodology 8(1): 19-3212) Levac D, Colquhoun H and O’Brien K (2010) Scoping studies: advancing the methodology Implementation Science 5: 6913) Braun, V. and Clarke, V. (2006). Using thematic analysis in psychology. Qualitative Research in Psychology, 3, 77–101. doi:10.1191/1478088706qp063oa14) World Health Organisation (2018) Classification of digital health interventions v1.0: A shared language to describe the uses of digital technology for health. WHO/RHR/19.06. Pages 1-20. https://www.who.int/reproductivehealth/publications/mhealth/classification-digital-health-interventions/en/
Proper citation: Stefanie Andrew, Carol Clark, Sheppard Z.A., Evans M., Hutt J., Crook T. B. 2021. Exploration of rehabilitation through the use of virtual reality interventions for patients with upper limb conditions: protocol for scoping review.. protocols.io dx.doi.org/10.17504/protocols.io.bq6smzee Copy
Authors: ZengU19 BRAIN Grant
Group: BICCN, Allen Institute for Brain Science
Summary: Protocol to generate Nextera libraries using 0.2x reagents in a 96-well PCR plate using the Formulatrix Mantis instrument.
Proper citation: ZengU19 BRAIN Grant 2019. Nextera XT at 0.2X On the Mantis. protocols.io dx.doi.org/10.17504/protocols.io.63rhgm6 Copy
Authors: Addgene The Nonprofit Plasmid Repository
Summary: This protocol describes how to design a primer. To see the full abstract and additional resources, visit https://www.addgene.org/protocols/primer-design/.
Proper citation: Addgene The Nonprofit Plasmid Repository 2020. How to Design a Primer. protocols.io dx.doi.org/10.17504/protocols.io.4r5gv86 Copy
Authors: Emily Lingeman
Group: Innovative Genomics Institute
Proper citation: Emily Lingeman 2017. T7 Endonuclease Assay. protocols.io dx.doi.org/10.17504/protocols.io.g93bz8n Copy
Authors: Rachele Cesaroni
Group: Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: Rachele Cesaroni 2019. Small-scale silencing experiment in vegetative Euplotes crassus (provisional). protocols.io dx.doi.org/10.17504/protocols.io.2asgaee Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the preparation of 1x3 glass slides for mounting embedded mouse brain samples for subsequent imaging and sectioning on TissueCyte 1000. 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 2020. Slide Preparation for Mounting Samples for TissueCyte 1000 Sectioning and Imaging. protocols.io dx.doi.org/10.17504/protocols.io.ber8jd9w Copy
Authors: Sarah Giuliani
Group: Coleman Lab
Summary: This sampling protocol is designed to collect two fractions: cell pellets and cell-free filtered supernatants. The cell pellets are used for gene expression analyses by RNA-Seq and proteomics. The cell-free fraction is used for analysis of dissolved analytes (e.g. N, P, DOC). Volumes are based on our experience with cyanobacterial cultures at cell densities ~ 5E7/ml. For more/less concentrated cultures, adjust volumes accordingly.
Proper citation: Sarah Giuliani 2016. Sampling for RNA / Protein/ dissolved nutrients from phage infection experiments. protocols.io dx.doi.org/10.17504/protocols.io.f27bqhn Copy
Authors: Dr. Steven Wilhelm
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 2017. Propagating T5-phages for Fluorescent Staining. protocols.io dx.doi.org/10.17504/protocols.io.igzcbx6 Copy
Authors: Henri Brunengraber
Group: Mouse Metabolic Phenotyping Centers
Summary: Mouse Insulin ELISA kit is used for the non radioactive quantification of insulin in mouse plasma.
Proper citation: Henri Brunengraber 2019. Case - Plasma Insulin Measurement by ELISA. protocols.io dx.doi.org/10.17504/protocols.io.yesftee Copy
Authors: Franchesca Farris
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is an appendix for spleen SOP.
Proper citation: Franchesca Farris 2020. Appendix for Spleen SOP. protocols.io dx.doi.org/10.17504/protocols.io.bbcwiixe Copy
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