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Authors: BioLegend, Inc.
Group: BioLegend
Proper citation: BioLegend, Inc. 2016. True-Nuclear™ Transcription Factor Staining Protocol for 96-Well, U-Bottom Plate. protocols.io dx.doi.org/10.17504/protocols.io.gq5bvy6 Copy
Authors: Ken Youens-Clark
Group: Metafunc Course 2017
Proper citation: Ken Youens-Clark 2017. Hello (bash). protocols.io dx.doi.org/10.17504/protocols.io.jvgcn3w Copy
Authors: Kiran B
Proper citation: Kiran B 2017. Purification of pooled PCR amplicon libraries using SPRI beads. protocols.io dx.doi.org/10.17504/protocols.io.fnvbme6 Copy
Authors: Ravi More
Summary: Integrated Whole Exome Sequencing (WES) analysis pipline using various tools and databases, developed as part of the Accelerator program for Discovery in Brain disorders using Stem cells (ADBS) program at National Centre for Biological Sciences (NCBS), Bangalore.
Proper citation: Ravi More 2018. ADBS Whole Exome Sequencing (WES) Analysis Pipeline. protocols.io dx.doi.org/10.17504/protocols.io.vrhe536 Copy
Authors: BioLegend, Inc.
Group: BioLegend
Proper citation: BioLegend, Inc. 2016. Immunofluorescence Microscopy Protocol. protocols.io dx.doi.org/10.17504/protocols.io.eyubfww Copy
Authors: John Stack, Gary Cline
Group: Mouse Metabolic Phenotyping Centers
Summary: Procedure used to measure glucose concentrations. Glucose is measured by the enzymatically coupled reactions of hexokinase and glucose-6-P dehydrogenase. The rate of NADH formation is monitored by the change in absorbance at 340 nm.
Proper citation: John Stack, Gary Cline 2019. Yale - Blood Glucose. protocols.io dx.doi.org/10.17504/protocols.io.y2kfycw Copy
Authors: Ken Stedman
Group: VERVE Net
Summary: For use in "PCTE Protocol for VLP enumeration"
Proper citation: Ken Stedman 2016. PCTE filter staining. protocols.io dx.doi.org/10.17504/protocols.io.eavbae6 Copy
Authors: Jitka Marencakova, Frantisek Zahalka
Summary: The protocol describes guidelines and steps for taking repeated measurements of sportive population: postural stability, body weight distribution during quiet stance, and the foot type diagnostic. The parameters calculated from repeated measurements can be used for separate analyses: analysis of center of pressure displacement, represented by total travelled way parameter; analysis of body weight distribution and loading of the lower limbs; and foot typology. The guidelines are mostly based on recommendations of the literature, partly on our own research experiences. It is important to remain consistent during all of the measurements and follow the guidelines as they control important aspects of the measurements. Any changes of any aspects can signifficantly alter the final results.
Proper citation: Jitka Marencakova, Frantisek Zahalka 2018. Postural stability, body weight distribution, and foot typology of sportsmen . protocols.io dx.doi.org/10.17504/protocols.io.qp8dvrw Copy
Authors: Roey Angel, Eva Petrova
Group: SoWa RI Anaerobic and Molecular Microbiology (public)
Summary: The following protocol is intended for the quantification of double-stranded DNA using Quant-iT™PicoGreen® dsDNA Assay Kit (ThermoFisher). This protocol is a simplified and condensed version of the full protocol from the manufacturer. The procedure described here is for 96 reactions. If samples are run in duplicates, then this should allow quantifying 40 samples.
Proper citation: Roey Angel, Eva Petrova 2020. Qant-iT™ PicoGreen® dsDNA Quantification. protocols.io dx.doi.org/10.17504/protocols.io.bftfjnjn Copy
Authors: Prajakta Bendre, Vanessa Melino
Summary: Nitrogen (N) in the form of nitrate (NO3-) can move radially from roots to the vascular tissue from where it is transported to the above-ground organs. Roots are the first to sense the scarcity of nitrogen in the soil. The following protocol describes the step-wise procedure for performing unidirectional root NO3- influx with the use of 15N labelled NO3- at a concentration that stimulates the inducible high-affinity nitrate transporters. Stable isotopes such as 15N can be used to trace the movement of NO3- through the plant. This protocol uses a split-root design where only embryonic roots are treated with the 15N label. The remaining, non-embryonic roots are not labelled but similarly treated. this split-root design can be modified to select and label specific root types based on your interest.
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Proper citation: Prajakta Bendre, Vanessa Melino 2020. Root nitrate influx . protocols.io dx.doi.org/10.17504/protocols.io.biibkcan Copy
Authors: Amy Oreskovic, Barry Lutz
Summary: Overview: This protocol describes a method for highly sensitive sequence-specific purification of short tuberculosis (TB) urine cell-free DNA (cfDNA) from large-volume (10 mL) urine samples. Biotinylated oligonucleotide capture probes complementary to the target of interest are immobilized on streptavidin-coated magnetic beads and used to capture, concentrate, and purify target DNA via hybridization. This protocol improves upon the analytical performance of both existing silica-based extraction methods for urine cfDNA and previous hybridization capture protocols, and meets several previously unmet design criteria for urine cfDNA: (1) high recovery of short fragments, (2) large sample input volume, and (3) . There are two key innovations that contribute to the robustness and unprecedented sensitivity of this method: dual biotinylated capture probes, which increase recovery compared to single biotinylated probes by moderating probe density on the bead surface (a key variable affecting efficiency of surface-based hybridization), improving thermostability of the bead-probe linkage, and eliminating interference by endogenous biotin in urine, and a two-probe system for each target region, which enables recovery of both strands of double-stranded DNA. We designed this hybridization method for capture of short, dilute TB cfDNA fragments from urine, but anticipate that it will be versatile and may be useful for other applications and sample types requiring sensitive and efficient purification of DNA from large sample volumes. Design of primer and probe sequences for new targets is straightforward (see "Materials" tab).Expected performance:Near 100% recovery (95% CI: 82.6 - 117.6%) of synthetic ssDNA or dsDNA spiked into 10 mL urine samples, verified across concentrations of at least 1 – 10,000 copies/mL and fragment lengths of at least 25 – 150 bpLimit of detection of ≤5 copies of dsDNA in 10 mL urine (0.5 copies/mL)Enables amplification of DNA from 10 mL urine in a single PCR well (500X concentration factor)Tolerant to variations in sample composition, including pH (5 – 8), salt (0 – 500 mM), and non-target DNA (0 – 10 µg)Graphic abstract: (A) Schematic of capture probe design. (B) Overview of workflow.
Proper citation: Amy Oreskovic, Barry Lutz 2021. Ultrasensitive hybridization capture of short tuberculosis cell-free DNA from urine. protocols.io dx.doi.org/10.17504/protocols.io.bep4jdqw Copy
Authors: Sergio Cervera-Torres, Susana Ruiz Fernández, Martin Lachmair, Peter Gerjets
Summary: Embodied cognition research suggests that bodily experiences might ground mental representations of emotional valence in the vertical dimension of space (i.e., positive is up and negative is down). Accordingly, recent studies show that upward and downward arm movements may also influence the evaluation of valence-laden stimuli, suggesting that upward (downwards) movements lead to more positive (negative) evaluations. Interestingly, these studies typically did not investigate paradigms that require a direct hand interaction with the stimuli. With the advent of touchscreen devices and their use for experimental environments, however, a direct and more natural hand interaction with the stimuli has come to the fore. In this regard, the goal of the present study is to examine how direct hand interaction with valence-laden stimuli on a touchscreen monitor affects their perceived valence. To do so, participants evaluated emotional pictures after touching and moving them either upwards or downwards across a vertically mounted touchscreen. In contrast to previous findings, the results suggest that positive pictures were evaluated as more positive after downward movements while negative pictures were evaluated as less negative following upward movements. This finding may indicate that a matching between the pictures’ valence and the valence associated with their vertical touch location leads to more positive evaluations. Thus, the present study extends earlier results by an important point: Touching the emotional pictures during movement may influence their valence processing.
Proper citation: Sergio Cervera-Torres, Susana Ruiz Fernández, Martin Lachmair, Peter Gerjets 2018. Valence-space associations in vertical touchscreen interactions. protocols.io dx.doi.org/10.17504/protocols.io.qagdsbw Copy
Authors: Thomas Plümper, Vera Troeger, Eric Neumayer
Summary: Traditionally, social scientists perceived causality as regularity. As a consequence, qualitative comparative case study research was regarded as unsuitable for drawing causal inferences. Apparently, few cases cannot establish regularity. The dominant perception of causality has changed, however. Nowadays, social scientists define and identify causality through the counterfactual effect of a treatment. This brings causal inference in qualitative comparative research back on the agenda since obviously comparative case studies can identify treatment effects. We argue that the validity of causal inferences from the comparative study of cases depends on the employed case-selection algorithm. We employ Monte Carlo techniques to demonstrate that different case-selection rules strongly differ in their ex ante reliability for making valid causal inferences and identify the most and the least reliable case selection rules.
Proper citation: Thomas Plümper, Vera Troeger, Eric Neumayer 2017. Case selection and causal inferences in qualitative comparative research. protocols.io dx.doi.org/10.17504/protocols.io.kjccuiw Copy
Authors: Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan
Group: Human Cell Atlas Method Development Community
Summary: CODEX is a technology that uses oligo labeled antibodies, specialized fluorescent probes, and a companion instrument along-side a standard fluorescence microscope to create single-cell resolution fluorescence data across a multitude of parameters within spatial context in a single tissue. CODEX was developed by Yury Goltsev and Nikolay Samusik in the laboratory of Garry Nolan at Stanford. The technology is being commercialized by Akoya Biosciences.
Proper citation: Yury Goltsev, Nikolay Samusik, Julia Kennedy-Darling, Salil Bhate, Matthew Hale, Gustavo Vazquez, Sarah Black, Garry Nolan 2019. CODEX Oligo-labeled Antibody Conjugation. protocols.io dx.doi.org/10.17504/protocols.io.3fugjnw Copy
Authors: New England Biolabs
Group: Grupo de Estudos de Leveduras Cervejeiras
Proper citation: New England Biolabs 2018. SOC Media. protocols.io dx.doi.org/10.17504/protocols.io.pngdmbw Copy
Authors: Harley King
Summary: Quantifying the change in fluorescent status of cells over time can be an important data point in experimental analysis. Optimally, quantification can be accomplished with flow cytometers. However, these instruments are not available to every lab. Routine analysis and multi-sample preparation can be both time and cost prohibitive.Fluorescent cell quantifcation in cell culture requires a fluorescent microscope and freely available imaging software like Image J.
Proper citation: Harley King 2019. Quantifying Fluorescent Cells in Mammalian Cell Tissue Culture. protocols.io dx.doi.org/10.17504/protocols.io.y2nfyde Copy
Authors: Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres
Summary: The sterile insect technique (SIT) is an environmentally friendly control tactic based on the sequential, inundative releases of sterile insects in a targeted area. Recently, this technique has been suggested as a potential complementary control method as part of an area-wide insect pest management program (AW-IPM) against D. suzukii. One of the key issues for the SIT application is to determine the radiation dose since the doses used to induce reproductive sterility can vary between sexes and among species. Treating insects with a lower oxygen atmosphere before and during exposure to radiation can mitigate some of the negative physiological effects due to the irradiation. The irradiation of pupae under the oxygen-reduced environments such as hypoxia is routinely used in the SIT operational programs of some tephritid species as it provides radiological protection. This treatment allows to have the sterile pupae already in sealed containers to facilitate their shipment. Therefore, it is crucial to study the effects of irradiation on the reproductive sterility in D. suzukii males and females under low-oxygen atmosphere (hypoxia) compare to normal oxygen level conditions (normoxia).
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This protocol describes step-by-step the irradiation of D. suzukii pupae under hypoxia and normoxia atmosphere conditions. This protocol may be utilized for a further assessment concerning the quality of the sterile versus non-sterile D. suzukii adults such as laboratory and/or field behavioral studies. Additionally, the description of the hypoxia treatment in this protocol may allow for the evaluation of the handling and release processes of the sterile males. The adoption of this protocol by different laboratories should increase further studies for the applicability of SIT on D. suzukii or for continuing assessments to improve SIT technology and decrease the variability in data between different studies.
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Proper citation: Fabiana Sassu, Katerina Nikolouli, Rui Pereira, Marc Vreysen, Christian Stauffer, Carlos Cáceres 2019. Gamma radiation of Drosophila suzukii under hypoxia and normoxia atmosphere conditions.. protocols.io dx.doi.org/10.17504/protocols.io.76whrfe Copy
Authors: David Booth
Group: King Lab, Protist Research to Optimize Tools in Genetics (PROT-G)
Proper citation: David Booth 2018. Protocol G: Preparation of reporter DNA. protocols.io dx.doi.org/10.17504/protocols.io.h8yb9xw Copy
Authors: Crystal M. Gigante, Rene Edgar Condori, Lillian Orciari, Todd G. Smith, Yu Li
Summary: Patterns of rabies virus spread within the central nervous system suggest that a thorough examination of the brain stem is critical for rabies diagnosis. Viral RNA is widespread in the brain of most animals positive for rabies. However, because virus spread may be unilateral, especially in larger animals, a negative finding for rabies can be made only if a complete cross section of the brain stem is examined. Examination may be made at the level of the pons, medulla, or midbrain of the brain stem.While a negative finding for rabies can be made only if a full cross section of brain stem tissue is examined, incomplete or suboptimal specimens should be tested, if possible. Identification of rabies virus RNA in any tissue is diagnostic of rabies infection [1, 2]. Examples of samples that may be tested for rabies virus RNA to rule-in (but not rule-out) rabies infection are hippocampus, cerebellum, cortex, saliva, and nuchal skin biopsy.
Proper citation: Crystal M. Gigante, Rene Edgar Condori, Lillian Orciari, Todd G. Smith, Yu Li 2018. Collection of brain stem for post-mortem diagnosis of rabies in animals by the LN34 pan-lyssavirus real-time RT-PCR assay. protocols.io dx.doi.org/10.17504/protocols.io.n4sdgwe Copy
Authors: Wei Tang, Xuepeng Sun, Junyang Yue, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shenxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei, Yongsheng Liu
Summary: This protocol includes a computational pipeline used in assembly and annotation of Kiwifruit Actinidia eriantha genome.
Proper citation: Wei Tang, Xuepeng Sun, Junyang Yue, Xiaofeng Tang, Chen Jiao, Ying Yang, Xiangli Niu, Min Miao, Danfeng Zhang, Shenxiong Huang, Wei Shi, Mingzhang Li, Congbing Fang, Zhangjun Fei, Yongsheng Liu 2018. Chromosome-scale genome assembly of kiwifruit Actinidia eriantha with single-molecule sequencing and chromatin interaction mapping. protocols.io dx.doi.org/10.17504/protocols.io.vgse3we Copy
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