The ASAP-sponsored interview series, Protocol Particulars, highlights ASAP-generated protocols. Featured guests include the protocol authors, who provide an overview of their protocol, describe how the protocol relates to their ASAP project, and present detailed troubleshooting tips.
Protocol Particulars is designed to further the spread of knowledge and enhance equity across the scientific community through promoting transparent research practices and enabling others to replicate the work. We are excited to share these interviews with the research community, in hopes that they will help to accelerate discoveries for Parkinson’s disease.
Watch Protocol Particulars
Watch the videos or listen in audio-only mode. To receive notifications when there are new interviews, subscribe to ASAP’s YouTube channel.
Open-Source Platform for Kinematic Analysis of Mouse Forelimb Movement with Daniil Berezhnoi, PhD
In this episode of Protocol Particulars, Daniil Berezhnoi, a staff scientist on Team Wichmann, discusses his paper in STAR Protocols, a start-to-finish protocol for simultaneous recording of reaching behavior and calcium imaging and subsequent kinematic analysis.
Read the full paper and check out the related GitHub and website. Learn more about Team Wichmann.
Open-Source Platform for Kinematic Analysis of Mouse Forelimb Movement with Daniil Berezhnoi, PhD
In this episode of Protocol Particulars, Daniil Berezhnoi, a staff scientist on Team Wichmann, discusses his paper in STAR Protocols, a start-to-finish protocol for simultaneous recording of reaching behavior and calcium imaging and subsequent kinematic analysis.
Read the full paper and check out the related GitHub and website. Learn more about Team Wichmann.
Culturing and Passaging of iPSC-derived Intestinal Organoids with Rachel Bates, PhD
Culturing and Passaging of iPSC-derived Intestinal Organoids with Rachel Bates, PhD
Introducing the Tagless LysoIP Method with Daniel Saarela, BSc
Team ASAP sits down with Daniel Saarela, BSc, from Team Alessi to discuss critical steps in his protocol for tagless LysoIP. Daniel and other members of Team Alessi developed a video to show the exact steps of the protocol. Here, Daniel shares his motivations for making this video available to the scientific community.
Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Introducing the Tagless LysoIP Method with Daniel Saarela, BSc
Team ASAP sits down with Daniel Saarela, BSc, from Team Alessi to discuss critical steps in his protocol for tagless LysoIP. Daniel and other members of Team Alessi developed a video to show the exact steps of the protocol. Here, Daniel shares his motivations for making this video available to the scientific community.
Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Pulling back the CURTAIN on Mass Spec Dataset Exploration with Enrico Bagnoli, PhD
Enrico Bagnoli, a postdoc on Team Alessi, chats with ASAP about Team Alessi’s mass spectrometry analysis tools, CURTAIN and CURTAIN-PTM, and provides an inside look at the utility of these web-based tools in their work. In addition, Enrico describes a series of how-to videos that Team Alessi created which provide a step-by-step demonstration of analyzing MS data through the CURTAIN tool.
Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Pulling back the CURTAIN on Mass Spec Dataset Exploration with Enrico Bagnoli, PhD
Enrico Bagnoli, a postdoc on Team Alessi, chats with ASAP about Team Alessi’s mass spectrometry analysis tools, CURTAIN and CURTAIN-PTM, and provides an inside look at the utility of these web-based tools in their work. In addition, Enrico describes a series of how-to videos that Team Alessi created which provide a step-by-step demonstration of analyzing MS data through the CURTAIN tool.
Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Isolation of PBMCs with Gerardo Ongari, PhD
Team ASAP chats with Garardo Ongari, PhD, a postdoctoral fellow on Team Schapira, about the steps required to isolate plasma and PBMCs from whole blood samples.
Read the full protocol. Learn more about Team Schapira.
Production and Purification of AAVs with Damien Wolfe, MS
For this episode of Protocol Particulars, Damien Wolfe, MS, a lead research technician and program manager at Clover Center CalTech, provides insight into the generation of AAVs.
Read the full protocol. Learn more about Team Gradinaru. Watch the full video or listen to the audio transcript to learn more.
Production and Purification of AAVs with Damien Wolfe, MS
For this episode of Protocol Particulars, Damien Wolfe, MS, a lead research technician and program manager at Clover Center CalTech, provides insight into the generation of AAVs.
Read the full protocol. Learn more about Team Gradinaru. Watch the full video or listen to the audio transcript to learn more.
Verifying the Integrity of Data Sets Uploaded to Amazon S3 with Sonia García-Ruiz, PhD
Sonia García-Ruiz, a postdoctoral fellow on Team Hardy, chatted with ASAP about the challenges associated with generating and storing large biomedical data sets and a new tool that enables users to determine if any unwanted changes occurred when uploading a dataset to Amazon S3.
Read the full protocol. Learn more about Team Hardy. Watch the full video or listen to the audio transcript to learn more.
Verifying the Integrity of Data Sets Uploaded to Amazon S3 with Sonia García-Ruiz, PhD
Sonia García-Ruiz, a postdoctoral fellow on Team Hardy, chatted with ASAP about the challenges associated with generating and storing large biomedical data sets and a new tool that enables users to determine if any unwanted changes occurred when uploading a dataset to Amazon S3.
Read the full protocol. Learn more about Team Hardy.
Uncovering Mitochondrial Antigen Presentation with Ahmed Fahmy, PhD
In this episode of Protocol Particulars, ASAP speaks with Ahmed Fahmy, PhD from Team Desjardins to learn more about best practices when conducting mitochondrial antigen presentation assays.
Read the full protocol. Learn more about Team Desjardins. Watch the full video or listen to the audio transcript to learn more.
Uncovering Mitochondrial Antigen Presentation with Ahmed Fahmy, PhD
In this episode of Protocol Particulars, ASAP speaks with Ahmed Fahmy, PhD from Team Desjardins to learn more about best practices when conducting mitochondrial antigen presentation assays.
Read the full protocol. Learn more about Team Desjardins.
Assessing Cellular Uptake of Fluorescently-Labeled Polyamines with Mujahid Azfar, MSc
In this episode, Protocol Particulars host, Devin Snyder, chats with Mujahid Azfar, MSc, a graduate student at KU Leuven and member of Team Vangheluwe about the protocol, “Fluorescently-labeled Polyamine Uptake (via Flow Cytometry),” which is authored by Team Vangheluwe alum Marine Houdou.
Read the full protocol. Learn more about Team Vangheluwe. Watch the full video or listen to the audio transcript to learn more.
Free-floating immunohistochemistry with Jonathan Breiter, MSc
Jonathan Breiter, MSc, joins ASAP’s Protocols Particulars in a discussion on the protocol, “Free-floating Mouse Brain Immunohistochemistry.” Here, Jonathan provides insight into the pros and cons of free-floating vs. slide-mounted tissue staining and gives a few tricks for ensuring that the tissue remains intact.
Read the full protocol. Learn more about Team Wood. Watch the full video or listen to the audio transcript to learn more.
Free-floating Mouse Brain Immunohistochemistry with Jonathan Breiter, MSc
Jonathan Breiter, MSc, joins ASAP’s Protocols Particulars in a discussion on the protocol, “Free-floating Mouse Brain Immunohistochemistry.” Here, Jonathan provides insight into the pros and cons of free-floating vs. slide-mounted tissue staining and gives a few tricks for ensuring that the tissue remains intact.
Read the full protocol. Learn more about Team Wood. Watch the full video or listen to the audio transcript to learn more.
Free-floating immunohistochemistry with Jonathan Breiter, MSc
Jonathan Breiter, MSc, joins ASAP’s Protocols Particulars in a discussion on the protocol, “Free-floating Mouse Brain Immunohistochemistry.” Here, Jonathan provides insight into the pros and cons of free-floating vs. slide-mounted tissue staining and gives a few tricks for ensuring that the tissue remains intact.
Read the full protocol. Learn more about Team Wood. Watch the full video or listen to the audio transcript to learn more.
Rapid Purification of Intact Golgi with Rotimi Fasimoye, PhD
On this episode of Protocol Particulars, ASAP staff are joined by Team Alessi member, Rotimi Fasimoye, PhD. Here, Rotimi describes the ins and outs of his protocol, “Introducing GolgiTag to Cells and Immunoprecipitation of Golgi.”
Read the full protocol. Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Rapid Purification of Intact Golgi with Rotimi Fasimoye, PhD
On this episode of Protocol Particulars, ASAP staff are joined by Team Alessi member, Rotimi Fasimoye, PhD. Here, Rotimi describes the ins and outs of his protocol, “Introducing GolgiTag to Cells and Immunoprecipitation of Golgi.”
Read the full protocol. Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
iNeuron Differentiation on EM Grids with Cristina Capitanio, MSc
Cristina Capitanio, MSc, a graduate student at the Max Planck Institute of Biochemistry and member of Team Harper, joins ASAP’s Protocol Particulars to share her protocol on neural differentiation on EM grids – iNeurons Sample Preparation for Cryo-ET and CLEM.
Read the full protocol. Learn more about Team Harper. Watch the full video or listen to the audio transcript to learn more.
iNeuron differentiation on EM grids with Cristina Capitanio, MSc
Cristina Capitanio, MSc, a graduate student at the Max Planck Institute of Biochemistry and member of Team Harper, joins ASAP’s Protocol Particulars to share her protocol on neural differentiation on EM grids – iNeurons sample preparation for cryo-ET and CLEM.
Read the full protocol. Learn more about Team Harper. Watch the full video or listen to the audio transcript to learn more.
Immunoblotting Methods for LRRK2 Signaling with Francesca Tonelli, PhD
On this episode of Protocol Particulars, Francesa Tonelli, PhD, a senior research scientist at the University of Dundee and project manager for Team Alessi, joins ASAP to discuss her protocol for the quantitative immunoblotting analysis of the LRRK2 signaling pathway.
Read the full protocol. Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Immunoblotting Methods for LRRK2 Signaling with Francesca Tonelli, PhD
On this episode of Protocol Particulars, Francesa Tonelli, PhD, a senior research scientist at the University of Dundee and project manager for Team Alessi, joins ASAP to discuss her protocol for the quantitative immunoblotting analysis of the LRRK2 signaling pathway.
Read the full protocol. Learn more about Team Alessi. Watch the full video or listen to the audio transcript to learn more.
Examining the Ultrastructural Components of Dopamine Neurons with Natalie Doig, PhD
Natalie Doig, PhD, a postdoc at the University of Oxford and member of Team Cragg, joins ASAP’s Protocol Particulars to discuss her collection of protocols on the quantitative analysis of ultrastructural features of dopaminergic axon terminals.
Read the full protocol. Learn more about Team Cragg. Watch the full video or listen to the audio transcript to learn more.
Examining the Ultrastructural Components of Dopamine Neurons with Natalie Doig, PhD
Natalie Doig, PhD, a postdoc at the University of Oxford and member of Team Cragg, joins ASAP’s Protocol Particulars to discuss her collection of protocols on the quantitative analysis of ultrastructural features of dopaminergic axon terminals.
Read the full protocol. Learn more about Team Cragg. Watch the full video or listen to the audio transcript to learn more.
