Protocols   Select Another Resource Report Type

Authors: Liu Liu, Arseny Finkelstein, Susu Chen, Nuo Li, Karel Svoboda
Summary: This protocol is to prepare a mouse for head-restrained electrophysiological recordings or behavior by attaching a headbar (small titanium bar) to the skull. Standard antiseptic surgery procedures are used. Animals are anesthetized with isofluorane (2-4 %). Following deep anesthesia, a flap of skin approximately 1cm2 covering the skull is removed. Liquid marcaine is applied to the wound margins for topical anesthesia. A custom machined titanium bar (22 x 3 mm) is glued and cemented to the animal's head using cyanoacrylate and dental acrylic.

Proper citation: Liu Liu, Arseny Finkelstein, Susu Chen, Nuo Li, Karel Svoboda 2020. Headbar implantation . protocols.io https://dx.doi.org/10.17504/protocols.io.bcrsiv6e Copy   

•   Source:

Authors: Alice Lee
Group: Whiteson Lab - Phage Team
Summary: Bacteriophages (phage) are viruses that infect bacteria and can be found anywhere that bacteria is found. Performing plaque assays is a technique to purify a population of viruses and can also be used to determine the viral concentration of a given sample. This protocol will outline the steps to carry out plaque assays.

Proper citation: Alice Lee 2020. Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.be6sjhee Copy   

•   Source:

Authors: Doug Campbell, Natalie Donaher
Summary: Antibody incubation steps for quantitative immunoblotting in the Campbel Lab.

Proper citation: Doug Campbell, Natalie Donaher 2017. Antibody Incubation Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.jwrcpd6 Copy   

•   Source:

Authors: Ray Norbury
Summary: The ability to respond quickly in a flexible and changing environment is advantageous in many settings (Dalley & Robbins, 2017). However, if such impulsive behaviours are chronically expressed they become maladaptive and salient to a number of brain disorders and damaging behaviours such as smoking and binge eating.Emerging evidence suggests that chronotype, which is an individual’s preference for waking and sleeping with morning types preferring to rise and go to bed early and evening-types preferring to go to bed late and rise late, is related to impulsivity. For example, Kang and colleagues (2015) observed a significant association between subjective trait impulsivity (as measured by the Barratt Impulsivity Scale (BIS  11, Patton, Stanford, & Barratt, 1995) and chronotype in healthy young adults (Kang et al., 2015). Similarly, Hwang et al., (2016) reported that morningness-eveningness was related to both impulsivity and anger (Hwang, Kang, Gwak, Park, & Lee, 2016). Limited data, therefore, point to a link between eveningness and impulsivity (Hwang et al., 2016; Kang et al., 2015). However, although self-report questionnaires are often structured according to different subtypes of impulsivity (e.g. the BIS includes measures of attentional, motor and non-planning impulsivity) impulsivity if often condensed to a single metric (Hwang et al., 2016; Kang et al., 2015). In addition, few studies have supplemented subjective outcomes with objective laboratory-based measures and related these to chronotype. One study, Berdynaj et al., (2016) found no difference between early/intermediate chronotypes and late chronotypes using a computer-based delay discounting task (Berdynaj et al., 2016). However, the modest sample size (n = 86) and the collapsing of early and intermediate chronotypes into a single group limits the interpretation these data (Berdynaj et al., 2016).The aim of the current study, therefore, is to extend previous findings (Berdynaj et al., 2016; Hwang et al., 2016; Kang et al., 2015) to include both subjective and objective metrics of impulsivity. Decisional impulsivity can be objectively measured using: 1) Delay discounting, which is the preference for small, immediate rewards versus larger but delayed rewards. An impulsive choice in a temporal discounting task is reflected as a preference for smaller, more-immediate outcomes and follows a delay-dependent hyperbolic function. And 2) The jumping to conclusions task (as measure of reflection impulsivity) which assays the tendency to make rapid decisions without adequate accumulation and consideration of the available evidence. Motor impulsivity can be assessed using the stop-signal reaction time (SSRT) which measures the ability to inhibit a response after it has been initiated (please see below for experimental details). Based on the extant literature, it is expected that later chronotype will be associated with increased self-report impulsivity. The proposed work also provides a unique opportunity to assess (in an exploratory manner) the relationship between chronotype and objective-measures of impulsivity.

Proper citation: Ray Norbury 2018. Impulsivity. protocols.io https://dx.doi.org/10.17504/protocols.io.ptfdnjn Copy   

•   Source:

Authors: Haseena Khan

Proper citation: Haseena Khan 2017. Protoplast Isolation from Zymoseptoria tritici. protocols.io https://dx.doi.org/10.17504/protocols.io.k2mcyc6 Copy   

•   Source:

Authors: Emil Boros, Marina Kolpakova
Summary: The major ion concentration data of sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), chloride (Cl), sulphate (SO4), bicarbonate (HCO3), carbonate (CO3) and pH (if it was coupled with ion data) were input into the database. The data were drawn from a large geographic scale across Eurasia (Austria, China, Hungary, Kazakhstan, Mongolia, Russia, Serbia, Turkey) and from a large number of saline lakes and pans (N=220) with minimum a 1.0 g L–1 salinity threshold. The 1.0 g L–1 salinity threshold was selected based on a former study (Boros et al., 2014), where this threshold was experimentally found to be the characteristic boundary of soda ecosystems. Salinity was estimated by the sum of measured concentrations of eight major ions (Na, K, Ca, Mg, Cl, SO4, HCO3, CO3). As generally known, sodium is by far the most common cation in saline lakes and necessarily the dominant cation in soda type lakes. Therefore, sites were excluded from the dataset if Na was not the most abundant ion. If seasonal or annual water data were available, mean values were put into database. Most of the data came from papers (sources are indicated in the table).

Proper citation: Emil Boros, Marina Kolpakova 2018. An assessment on a large geographic scale of Eurasian inland saline surface waters. protocols.io https://dx.doi.org/10.17504/protocols.io.rikd4cw Copy   

•   Source:

Authors: Yingyu Hu, Zoe V Finkel
Group: Marine Microbial Macroecology Lab

Proper citation: Yingyu Hu, Zoe V Finkel 2020. Inorganic polyphosphate in microalgae: A DAPI-based quantification in microtiter plate . protocols.io https:// Copy   

•   Source:

Authors: Alan Cone
Group: Ju Lab

Proper citation: Alan Cone 2016. Destain Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.fw9bph6 Copy   

•   Source:

Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Case 1: Quick check of viral concentration. Use this protocol when you can count your samples in a few days.For when long term storage of slide is required, see Case 2.

Proper citation: Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 1). protocols.io https://dx.doi.org/10.17504/protocols.io.c69zh5 Copy   

•   Source:

Authors: Sam Li
Group: BioLegend
Summary: BioLegend MojoSort™ nanobeads work in commonly used separation columns, based on our internal research as well as validation by external testing by academic labs. This simple protocol consists of following the MojoSort™ protocol to label the cells with pre-diluted MojoSort™ reagents and using the columns as indicated by the manufacturer.Note: Due to the properties of our beads, it may be possible to use far fewer beads that with other commercial suppliers. We recommend a titration to find the best dilution factor. However, as a general rule, dilutions ranging from 1:3 to 1:20 for the Nanobeads can be used. Please contact BioLegend Technical Service ([email protected]) if further assistance is needed.

Proper citation: Sam Li 2019. MojoSort™ Mouse CD4 Nanobeads Column Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.696hh9e Copy   

•   Source:

Authors: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward
Group: Neurodegeneration Method Development Community
Summary: Live imaging permits visualization of molecular and organellar dynamics within the neuron. While a standard confocal microscope is sufficient for short imaging experiments, extended imaging applications (>1 hr) are best served by a 37 °C live imaging chamber outfitted onto the microscope. CM should also be changed to Hibernate A Low Fluorescence Medium (BrainBits LLC, cat. no. SKU#HAPR) for extended imaging.

Proper citation: Michael S. Fernandopulle, Ryan Prestil, Christopher Grunseich, Chao Wang, Li Gan, Michael E. Ward 2019. LIVE IMAGING OF i3NEURONS (Support Protocol 5) . protocols.io https://dx.doi.org/10.17504/protocols.io.5w7g7hn Copy   

•   Source:

Authors: Yaowu Yuan
Group: Mimulus
Summary: This collection consists of three protocols: 1. Agro Transformation a) Using Electropotator b) Using Freeze-Thaw Method2. Agro Preparation 3. Plant infiltration

Proper citation: Yaowu Yuan 2019. Mimulus in planta Transformation. protocols.io https://dx.doi.org/10.17504/protocols.io.3tkgnkw Copy   

•   Source:

Authors: Brenton Paolella
Summary: This protocol is for performing Cell Hashing only. Sample multiplexing and super-loading on single cell RNA-sequencing platforms.Cell Hashing uses a series of oligo-tagged antibodies against ubiquitously expressed surface proteins with different barcodes to uniquely label cells from distinct samples, which can be subsequently pooled in one scRNA-seq run. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its sample of origin, and robustly identify doublets originating from multiple samples.

Proper citation: Brenton Paolella 2019. Cell Hashing. protocols.io https://dx.doi.org/10.17504/protocols.io.yp6fvre Copy   

•   Source:

Authors: Ashley Jones, Neeraj Purushotham, Jamila Nasim, Benjamin Schwessinger
Group: High molecular weight DNA extraction from all kingdoms
Summary: DNA extractions often contain impurities which limit the output of long-read sequencing technologies. Here a protocol is provided which removes impurities and size selects for longer fragments. To remove residual RNA and protein, an additional RNAse A and Proteinase K treatment is performed. A clean-up with chloroform: isoamyl alcohol (24:1) removes these proteins and other hydrophobic organics such as lipids. A low volume ethanol precipitation and wash is used to concentrate the DNA, hopefully also reducing polysaccharides. Finally, a Short Read Eliminator (SRE) kit by Circulomics is utilised for size selection, which also appears to clean the DNA. This has been trialled for the sorghum rot fungus Macrophomina phaseolina, providing highly promising results with an Oxford Nanopore MinION. One strain yielded 13.71 Gbases with an N50 of 21.75 kb, another strain yielded 9.72 Gbases with an N50 of 43.50 kb. Similar results are expected across many organisms, but have not been tested.

Proper citation: Ashley Jones, Neeraj Purushotham, Jamila Nasim, Benjamin Schwessinger 2019. DNA clean-up and size selection for long-read sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.6kahcse Copy   

•   Source:

Authors: Marco Cosentino, Elisa Storelli, Alessandra Luini, Massimiliano Legnaro, Emanuela Rasini, Marco Ferrari, Franca Marino
Summary: List of published works using this protocol:- Kustrimovic N., Comi C., Magistrelli L., Rasini E., Legnaro M., Bombelli R., Aleksic I., Blandini F., Minafra B., Riboldazzi G., Struchio A., Mauri M., Bono G., Marino F., Cosentino M. 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 (2018). Journal of neuroinflammation, 15(1), 205. https://doi.org/10.1186/s12974-018-1248-8- Kustrimovic, 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/srep33738- Cosentino 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. PBMC- 02 - CD4+ T cell Isolation from PBMC with “Dynabeads CD4 Positive Isolation Kit”. protocols.io https://dx.doi.org/10.17504/protocols.io.bpxqmpmw Copy   

•   Source:

Authors: Antoine ZILLER

Proper citation: Antoine ZILLER 2016. Digestion NotI. protocols.io https://dx.doi.org/10.17504/protocols.io.ecubaww Copy   

•   Source:

Authors: New England Biolabs
Group: New England Biolabs (NEB)

Proper citation: New England Biolabs 2020. Typical Protocol for NEBExpress GamS Nuclease Inhibitor when used with the NEBExpress Cell-free E. coli Protein Synthesis System (NEB #E5360). protocols.io https:// Copy   

•   Source:

Authors: Anna Behle
Group: Axmann Lab
Summary: Protocol for radioactive labelling of RNA using T7-Polymerase and α-[32P]-UTP.

Proper citation: Anna Behle 2017. Radioactive in vitro transcription. protocols.io https://dx.doi.org/10.17504/protocols.io.gudbws6 Copy   

•   Source:

Authors: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko
Group: Human Cell Atlas Method Development Community
Summary: Protocol for extraction of nuclei from frozen tissue in preparation for single-nuclei sequencing (droplet-based/10X). This protocol is based strongly on a similar extraction protocol from the McCarroll lab.

Proper citation: Carly Martin, Abdul Abdul, Charles Vanderburg, Naeem Nadaf, Ashley Feirrera, Evan Macosko 2019. Frozen Tissue Nuclei Extraction (v2). protocols.io https://dx.doi.org/10.17504/protocols.io.7xchpiw Copy   

•   Source:

Authors: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores
Group: Coronavirus Method Development Community, PATH
Summary: This is Appendix A of "Phase 3 randomized, double-blinded, placebo-controlled trial to evaluate the safety, immunogenicity, and efficacy of Vaccine Candidate against COVID-19 in adults > 18 years of age"This generic Phase 3 protocol was developed by the PATH team with support of the Bill and Melinda Gates Foundation. The aim of the collection is to share recommended best practices in designing and implementing a Phase 3 study of a COVID-19 vaccine candidate. As Phase 3 trials of different Vaccine Candidates proceed around the world, following the same protocols will ensure consistency and comparability of the Phase 3 trial results.Please note that this is an evolving document, to be versioned and updated, based on community feedback and new data.

Proper citation: Chris Ockenhouse, Chris Gast, Renee Holt, Jorge Flores 2020. Schedule of Study Visits and Evaluations (Appendix A of Phase 3 study of Vaccine Candidate for COVID-19). protocols.io https://dx.doi.org/10.17504/protocols.io.bj6bkran Copy   

•   Source: