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Authors: Jon Eilers
Summary: This is a protocol for sea cucumber gonad removal without killing the sea cucumber or causing evisceration.

Proper citation: Jon Eilers 2019. Surgical Removal of Sea Cucumber Gonads. protocols.io https://dx.doi.org/10.17504/protocols.io.5pag5ie Copy   

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Authors: Laura Poza-Viejo, Ivan del Olmo, Pedro Crevillén
Summary: Chromatin Immunoprecipitation (ChIP) is a crucial technique to study chromatin regulation, epigenetic phenomena and transcription factor DNA-binding in vivo. This technique is widely used in model plant systems like Arabidopsis but reliability in other plant systems is challenging. We adapted our well-established Arabidopsis ChIP protocol to be used with leaves and inflorescences of Brassica crops species (Brassica rapa and Brassica napus). This protocol was originally based on Gendrel et al. Nature Methods volume 2, pages 213–218 (2005), but has several modifications inlcluding chromatin sonication using a BioRuptor (Diagenode), immunoprecipitation using magnetic Dynabeads (Thermofisher) and DNA elution recovery performed using Chelex 100 (Bio Rad). The protocol is quick and very reproducible and has been validated against a number of histone modifications and protein tag antibodies. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Laura Poza-Viejo, Ivan del Olmo, Pedro Crevillén 2019. Plant Chromatin Immunoprecipitation. protocols.io https://dx.doi.org/10.17504/protocols.io.zmff43n Copy   

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Authors: Brandon Willis
Group: Mouse Metabolic Phenotyping Centers
Summary: Standard PCR conditions for genotyping of mutant mouse DNA extracted from somatic (e.g., tail) tissue.

Proper citation: Brandon Willis 2019. UC Davis - Genotyping. protocols.io https://dx.doi.org/10.17504/protocols.io.yjifuke Copy   

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Authors: David O'Connor, Natan Vega Potler, Meagan Kovacs, Ting Xu, Lei Ai, John Pellman, Tamara Vanderwal, Lucas Parra, Samantha Cohen, Satrajit Ghosh, Jasmine Escalera, Natalie Grant-Villegas, Yael Osman, Anastasia Bui, R Cameron Craddock, Michael P Milham
Group: GigaScience Press
Summary: This protocol describes MRI, voice recoding, and some basic physiological measurements and questionnaires for Sessions 2-7 and 9-14 of the following work:David O'Connor, et. al. (2017) The Healthy Brain Network Serial Scanning Initiative. GigaScience...

Proper citation: David O'Connor, Natan Vega Potler, Meagan Kovacs, Ting Xu, Lei Ai, John Pellman, Tamara Vanderwal, Lucas Parra, Samantha Cohen, Satrajit Ghosh, Jasmine Escalera, Natalie Grant-Villegas, Yael Osman, Anastasia Bui, R Cameron Craddock, Michael P Milham 2017. The Healthy Brain Network Serial Scanning Initiative, Sessions 2-7 and 9-14. protocols.io https://dx.doi.org/10.17504/protocols.io.gxubxnw Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: Protocol for blunting ends by 3' overhang removal and fill-in of 3' recessed (5' overhang) ends using T4 DNA Polymerase.

Proper citation: New England Biolabs 2015. Blunting Protocol (M0203). protocols.io https://dx.doi.org/10.17504/protocols.io.cgwtxd Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol is used to prepare Phosphate Buffered Saline (PBS). PBS (-) and PBS (+) which includes Tween are used as biologically neutral wash solutions in many processes including In Situ Hybridization (ISH), Immunohistochemistry (IHC) and Fixation.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. Phosphate Buffered Saline (PBS). protocols.io https://dx.doi.org/10.17504/protocols.io.bezgjf3w Copy   

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Authors: Lucia Leierer, Caterina Rodríguez, Carolina Mallol
Group: Paleochar ERC
Summary: Protocol for the manufacture of micromorphological thin sections performed at AMBI Lab, Universidad de La Laguna, Tenerife, Spain.

Proper citation: Lucia Leierer, Caterina Rodríguez, Carolina Mallol 2019. Micromorphological thin section manufacture AMBI Lab, Universidad de La Laguna, Tenerife, Spain. protocols.io https://dx.doi.org/10.17504/protocols.io.yh8ft9w Copy   

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Authors: Chong Peng Lean, Ajay Kumar Singh , Kok Swee Leong
Summary: Electrical energy can be harvested from the living plants as a new potential renewable energy source. Characterization of the electrical signal is needed to enable an optimum energy harvesting setup conditions. In the presentpaper, an investigation is conducted to analyze the characteristic of Aloe Barbadensis Miller (Aloe Vera) leaves in terms of electrical energy generation under specific experimental setups. The experimental results show that 908.39uWelectrical power can be harvested from the Aloe Vera with 24 pairs of electrodes and this energy is capable to be stored in a capacitor. This energy has a high potential to be used to power up a low power consumption device.

Proper citation: Chong Peng Lean, Ajay Kumar Singh , Kok Swee Leong 2019. Characterization of Aloe Barbadensis Miller Leaves as a Potential Electrical Energy Source with Optimum Experimental Setup Conditions.. protocols.io https://dx.doi.org/10.17504/protocols.io.2yngfve Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes PCR1 and PCR2 reactions beginning with cDNA to generate transcript templates ready for IVT reaction. This protocol is written for 192 (2x96) reactions but can also be used for fewer or more reactions by adjusting the amount of materials and equipment appropriately.

Proper citation: Allen Institute for Brain Science 2020. PCR Prep from cDNA for IVT Reactions. protocols.io https://dx.doi.org/10.17504/protocols.io.bcsfiwbn Copy   

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Authors: James Fraser
Group: Fraser Lab

Proper citation: James Fraser 2015. QuikChange Mutagenesis. protocols.io https://dx.doi.org/10.17504/protocols.io.dij4cm Copy   

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Authors: Marie-Ka Tilak, Rémi Allio, Frédéric Delsuc
Group: High molecular weight DNA extraction from all kingdoms
Summary: This protocol was developed to optimize DNA sequencing from mammalian roadkill tissue samples using Oxford Nanopore Technology (ONT). Roadkill tissues contain necrotized cells and impurities that result in DNA degradation. First, we observed that DNA preservation was generally better in RNAlater than in 95% EtOH preserved tissues. Second, we found that physically removing necrotized and epidermal cells before DNA extraction resulted in better DNA quality and purity. Finally, adjusting the ratio of AMPure beads to 0.4x at the DNA purification step permitted optimizing size selection for subsequent ONT library construction. These optimization steps allowed to significantly increase both read length and yield per flow cell for roadkill samples sequencing on the ONT MinION device.

Proper citation: Marie-Ka Tilak, Rémi Allio, Frédéric Delsuc 2019. An optimized protocol for sequencing mammalian roadkill tissues with Oxford Nanopore Technology (ONT). protocols.io https://dx.doi.org/10.17504/protocols.io.6bthann Copy   

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Authors: Khairil Asnan, Mohd. Sadzan Asram bin Aliming, Aprialdy Idrus, Diana Eka Pratiwi
Summary: Cattle's blood component is compressed using centrifuge (5000 rpm for 10 minutes), then supernatant (erythrocytes) collected. Erythrocytes with a ratio of 3:1 (serum:supernatant), treated with initial mixing with NaOH (0.5 M) with an initial ratio 1:1 (v/v) and let it sit for 30 seconds then mixed it by centrifugation about 10 rpm for 30 seconds. Sample then treated by mixing oleic acid (2:1 v/v). The sample then dehydrated by heat about 121oC for a week. Calculated total iron mass was 240000 μg/100 ml whole blood sample (about 14.40% content of the whole sample). Sample purified by furnace using high temperature about 800oC for 2 hours and increased the iron concentration up to 46.30% (m/m%). .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Khairil Asnan, Mohd. Sadzan Asram bin Aliming, Aprialdy Idrus, Diana Eka Pratiwi 2019. New Iron Extracting Method from Cattle's Blood for Iron Concentration Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.6f2hbqe Copy   

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Authors: Zhujun Wei
Group: 2020 iGEM NEFU China
Summary: The concentration of the agarose gel is 1%.

Proper citation: Zhujun Wei 2020. Agarose Gel Electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.bnwsmfee Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant 2020. Immunoblot analyses for investigating SpLG-binding to purified mammalian and avian immunoglobulins.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjrukm6w Copy   

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Authors: Gábor Tóth, Gabor Kemenesi
Group: Szentagothai Research Centre Virology

Proper citation: Gábor Tóth, Gabor Kemenesi 2020. Lloviu cuevavirus sequencing protocol. protocols.io https:// Copy   

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Authors: Pringle Lab, Grossman Lab
Group: Aiptasia-Symbiodiniaceae Model System
Summary: This protocol describes how to perform PCR on extracted Symbiodinium DNA to amplify a fragment of the chloroplast 23S rRNA gene. It is based on the method describes in Pochon et al., 2006. The protocol then explains how to perform an RFLP (restriction fragment length polymorphism) analysis on the PCR products as well as eitherusing them directly for sequence analysis by Sanger sequencing or cloning them into a plasmid back bone to separate genes from mixed Symbiodinium populations and perform the sequence analysis on several clones per original sample.The attached file contains reference sequences of the following Symbiodinium strains: Clade A strains SSA01, SSA02, SSA03; SSB01 (clade B), SSB01del6, SSB01del136, SSE01 (clade E) and A001 (Clade D).

Proper citation: Pringle Lab, Grossman Lab 2018. Symbiodinium cp23S RFLP and sequence analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.qyjdxun Copy   

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Authors: Pietro Mannarino, Liliam Fernandes Oliveira, Thiago Torres da Matta
Summary: Habitual loading and resistance training (RT) can lead to changes in muscle and tendon morphology as well as in its mechanical properties which can be measured by Shear Wave Elastography (SWE) technique. The objective of this study was to analyze the Vastus Lateralis (VL) and patellar tendon (PT) mechanical properties adaptations to an 8-week RT protocol using SWE. We submitted 15 untrained health young men to an 8-week RT directed for knee extensor mechanism. VL and PT shear modulus (µ) were assessed pre and post intervention with SWE. PT thickness (PTT), VL muscle thickness (VL MT) and knee extension torque (KT) were also measure pre and post intervention to ensure the RT efficiency. Significant increases were observed in VL MT and KT (pre= 2.40 ±0.40 cm and post= 2.63 ±0.35 cm, p = 0.0111, and pre= 294.66 ±73.98 Nm and post= 338.93 ±76.39 Nm, p = 0.005, respectively). The 8-week RT was also effective in promoting VL µ adaptations (pre= 4.87 ±1.38 kPa and post= 9.08.12 ±1.86 kPa, p = 0.0105), but not in significantly affecting PT µ (pre= 78.85 ±7.37 kPa and post= 66.41 ±7.25 kPa, p = 0.1287) nor PTT (baseline= 0.364 ±0.053 cm and post = 0.368 ±0.046 cm, p = 0.71). The present study showed that an 8-week resistance training protocol was effective in adapting VL µbut not PT µ.Further investigation should be conducted with special attention to longer interventions, to possible PT differential individual responsiveness and to the muscle-tendon resting state tension environment.

Proper citation: Pietro Mannarino, Liliam Fernandes Oliveira, Thiago Torres da Matta 2019. An 8-week resistance training protocol is effective in adapting quadriceps but not patellar tendon shear modulus . protocols.io https://dx.doi.org/10.17504/protocols.io.ykwfuxe Copy   

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Authors: Brian Smith, [email protected] Micro.tucson
Summary: Here you will find common media recipes used in the Baltrus Lab at the University of Arizona for growing mostly Pseudomonas spp. and E. coli.

Proper citation: Brian Smith, [email protected] Micro.tucson 2019. Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.xf3fjqn Copy   

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Authors: Sonia Hall
Summary: Combine:150mls Ethanol150mls distilled water3mls Glacial Acetic AcidSplit into 4 beakers (approx 75mls each) and add a stir bar.Beaker 1 - Add: 0.5g Acid Fuchsin and 1.0g Ponceau 2RBeaker 2 - Add: 0.45g Light green, SF, yellowishBeaker 3 - Add: 0.75g Orange G and 1.5g Phosphotungstic acidBeaker 4 - Add: 1.5g Phosphomolybdic acidWhen each reagent is maximally dissolved, combine the 4 dyes and filter. Cover storage bottle in tin foil to reduce light exposure. Remake each month.

Proper citation: Sonia Hall 2015. Pollak Trichrome Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dh238d Copy   

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Authors: Dr. Steven Wilhelm, Samantha Coy
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Adapted from: Ortmann and Suttle (2009) Determination of Virus Abundance by Epifluorescence microscopy. Ch. 10 Methods of Molecular Biology. Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.

Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Epifluorescent Microscopy of Virus Particles Using SYBR Green. protocols.io https://dx.doi.org/10.17504/protocols.io.iptcdnn Copy   

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