NerdRx Podcast: Recent Episodes

Barkha Yadav-Samudrala

Hello everyone, NerdRx podcast brings you a new scientific technique every week. I will invite scientists from various backgrounds and discuss their favorite lab techniques. Stay tuned every Tuesday for a new episode. If you have any topic suggestions or if you would like to join me for an episode please email me at barkha@nerdrxpodcast.com

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Hello listeners,
Today is an exciting one, Microscopy. Out guest Dr. Saurabh Mehta will discuss the differences between light, confocal and super resolution microscopy. And wait till you hear the fun fact about microscopy. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Nikon MicroscopyU. The source for microscopy educationhttps://www.microscopyu.com

Dr. Eric Betzig – UC Berkeley Physicshttps://physics.berkeley.edu/people/faculty/eric-betzig

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Hello listeners,
This week on NerdRx podcast, we have a novel cell culture technique called bacteria spheroid co-cultures. Dr. Deb will discuss how these bacteria thrive within cancerous tumors and can be used as therapies in the future. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
A rapid screening platform to coculture bacteria within tumor spheroids
https://www.nature.com/articles/s41596-022-00723-5Design of combination therapy for engineered bacterial therapeutics in non-small cell lung cancer.
https://www.nature.com/articles/s41598-022-26105-1

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Hello listeners,

This week we will discuss a behavior technique different from what we usually discuss. Our guest Subhajit Sarkar, a PhD student at IIT Kharagpur in India, will talk about the nitty-gritty of how to perform memory assays in a fruit fly!Thank you for joining us, and I hope you keep listening. Reading suggestions:Plasticity of local GABAergic interneurons drives olfactory habituationhttps://www.pnas.org/doi/10.1073/pnas.1106411108

A simplified courtship conditioning protocol to test learning and memory in Drosophilahttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9843266/

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Hello listeners,
Today we will talk about BRET, which is short for Bioluminescence Resonance Energy Transfer, with a fellow content creator and podcaster, David Lakhter. Hear it from David about his journey and how he got into creating content. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Application of BRET to monitor ligand binding to GPCRs

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488387/

Get in touch with David: https://www.linkedin.com/in/davidlakhter

Follow The Shane Hummus Show: https://www.youtube.com/@theshanehummusshow/featured

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Hello listeners, 
I am so excited that this week my former mentor and the person who made me fall in love with Chemistry is with us tonight. This podcast began with high-throughput screening and Dr. Malaika Argade will take a step further and discuss what happens next. Thank you for joining us, and I hope you keep listening. 

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Hello listeners,

This week we are going to discuss how scientists use sound waves to dispense liquids at a nano scale. Joining us for this episode is Dr. Julia Hottinger. Thank you for joining us, and I hope you keep listening.

Reading suggestion:
A review on acoustic droplet ejection technology and systemhttps://pubs.rsc.org/en/content/articlelanding/2021/sm/d0sm02193h

Acoustic Droplet Ejection Applications for High-Throughput Screening of Infectious Agentshttps://journals.sagepub.com/doi/full/10.1177/2211068215620345

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Hello listeners,

I have been waiting for this one for a long time, CRISPR/Cas9. In this episode, our guest Dr. Carla Belmonte gives us the details of the beauty of CRISPR/Cas9 and how it is evolving as a therapy. Thank you for joining us, and I hope you keep listening.

Reading suggestion:
A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunityhttps://www.science.org/doi/full/10.1126/science.1225829 TEMPO enables sequential genetic labeling and manipulation of vertebrate cell lineageshttps://pubmed.ncbi.nlm.nih.gov/36417906/ Cas9 gene therapy for Angelman syndrome traps Ube3a-ATS long non-coding RNAhttps://doi.org/10.1038/s41586-020-2835-2

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Hello listeners,

This week Dr. Thomas Bonacci will talk about the method he uses to study every stage of cell cycle. Yes, going to the basics with Cell-free systems. Thank you for joining us, and I hope you keep listening. Reading suggestions:What makes the cell cycle tick? a celebration of the awesome power of biochemistry and the frog egghttps://pubmed.ncbi.nlm.nih.gov/33320710/Email me your suggestions at barkha@nerdrxpodcast.com

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Hello listeners,
We all have hear about cell cultures but do you that there are 3D-cell cultures too? This week we have Dr. Nishant Kulkarni, who will talk all about his experience with 3D cell cultures. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Three-Dimensional in Vitro Cell Culture Models in Drug Discovery and Drug Repositioninghttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5787088/

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Hello listeners, 

This week Dr. Crystal Starbird, Assistant Professor at UNC Chapel Hill will talk about X-Ray Crystallography, a rival to CryoEM. Thank you for joining us, and I hope you keep listening. 

Reading Suggestion:
RCSB Protein Data Bankhttps://www.rcsb.org 

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Hello listeners,
Well if you thought only clothes or shoes can be designers, you are wrong! This week Sophie Bendrath will tell us about a fascinating technique of Designer Receptors Exclusively Activated by Designer Drugs aka DREADDs. Thank you for joining us, and I hope you keep listening.

Reading suggestion:
DREADDs for Neuroscientistshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759656/

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Hello listeners,

Today we will talk about one of my favorite techniques, Chromatography. Join me with Dr. Abha Jain, a postdoc at UNC Chapel Hill, for this episode, where we discuss three different types of chromatography, ion exchange, size exclusion, and affinity chromatography. Thank you for joining us, and I hope you keep listening.

Reading suggestion:

Separation techniques: Chromatographyhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206469/

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Hello listeners,

This week we have a UNC Ph.D. candidate Alexis Stutzman. Alesis will dive into a genomic technique called Hi-C that is used to measure DNA-DNA contacts. Thank you for joining us, and I hope you keep listening.

Reading suggestion:

Advancements in Mapping 3D Genome Architecturehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391055/

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcriptionhttps://www.sciencedirect.com/science/article/pii/S0092867417303434

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Hello listeners, 

For our March special, we dive into something new. Dr. Sharena Rice will walk us through Neurotechnology and how it can be life-changing and can be used in treating so many issues, we are currently facing. Thank you for joining us, and I hope you keep listening. 

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Hello listeners, 

This week we have Christa Frodella who will be discussing the technical side of RNA sequencing. RNAseq is a technique used to quantify RNA in a biological sample and has the ability to look at gene fusion, post translation modifications and more. Thank you for joining us, and I hope you keep listening.

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Hello listeners,

This week we discuss immunocytochemistry (ICC) with Dr. Hallie Blevins who I know from my graduate school at VCU. ICC is a great way to identify and quantify the distribution of your target proteins and is routinely used in many labs. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Immunocytochemistry and quantification of protein colocalization in cultured neuronshttps://www.nature.com/articles/nprot.2006.220

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Hello listeners,

This week we have Dr. Emily Witt, who discusses a behavioral technique called Self-administration and how do we use this technique to understand the abuse liability of a molecule. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Behavioural assessment of drug reinforcement and addictive features in rodents: an overviewhttps://pubmed.ncbi.nlm.nih.gov/16759333/

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Hello listeners,

You do not want to miss it. We hear so many stories about cannabinoids these days but do you know how the cannabinoid receptor was discovered and the story behind it? Join me for this week’s episode where we have the scientist who actually discovered the cannabinoid receptor, Dr. Allyn Howlett. Thank you for joining us, and I hope you keep listening.

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Hello listeners,

We all would love if we lived our lives without any fear but did you know that fear is our survival mechanism? This week on NerdRx podcast we have Dr. Ian Jacobs who will discuss the ins and out of how do we study fear in a lab setting. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Context, Ambiguity, and Unlearning: Sources of Relapse after Behavioral Extinction https://www.appstate.edu/~steelekm/classes/psy5150/Documents/Bouton2002.pdf

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Hello listeners,

This week allow me to take you back to the basics of Thermodynamics. We have Dr. Shashank Chavali for our discussion on ITC and find out at the end and find out which disease utilized ITC to help develop treatment. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and cellshttps://pubmed.ncbi.nlm.nih.gov/34767799/

A small RNA that cooperatively senses two stacked metabolites in one pocket for gene controlhttps://www.nature.com/articles/s41467-021-27790-8

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Hello listeners,

This week we have a graduate student Natalie Harris joining us to discuss the details of BioID. This recently developed technique helps identify your target protein’s “neighbors”. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Meet the neighbors: Mapping local protein interactomes by proximity‐dependent labeling with BioIDhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5053326/

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Hello listeners,

The opioid epidemic is an ongoing issue we are currently facing., For our January special episode, we have Dr. Samuel Obeng, Assistant Professor, who will discuss the problems of opioid use and how we can develop therapies for opioid use disorder.

Reading suggestions:

Bias Factor and Therapeutic Window Correlate to Predict Safer Opioid Analgesicshttps://pubmed.ncbi.nlm.nih.gov/29149605/

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Hello listeners,

This week we discuss a routine and an essential technique used in numerous labs called IHC. Dr. Shveta Parekh will talk about the nitty-gritty details that go into performing IHC. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Beautiful Minds: Imaging Cells of the Nervous System [Slide Show]https://www.scientificamerican.com/slideshow/brain-beautiful-minds-pics/

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Hello listeners,

Today we discuss a cell viability assay called MTT assay. We have graduate student Marzia Pendino joining us to walk us through this technique. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assayshttps://pubmed.ncbi.nlm.nih.gov/6606682/

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Hello listeners,

In today’s episode, we discuss Immunoprecipitation. We have graduate student Erin Hughes joining us for this episode. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Protein-Protein Interactions: Co-Immunoprecipitationhttps://pubmed.ncbi.nlm.nih.gov/28667615/

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Hello listeners,

I wish you all a very happy new year! As promised, we will kick off our new year with icy, and here it is ICE assay. Dr. Jay Anand will discuss his experience with ICE assay and its importance. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Detection of Topoisomerase Covalent Complexes in Eukaryotic Cellshttps://link.springer.com/protocol/10.1007/978-1-4939-7459-7_20

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Hello listeners,

This week we discuss a routine but handy technique called FTIR. Cameron Jordan, a Graduate student will discuss how FTIR can help us determine various structural features in a molecule. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

A novel handheld FT-NIR spectroscopic approach for real-time screening of major cannabinoids content in hemphttps://www.sciencedirect.com/science/article/abs/pii/S0039914022003551

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Hello listeners,

In this episode, we discuss microscale thermophoresis (MST). We have Connor O’Hara, PhD Candidate, joining us for this episode. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Nanotemper website:
https://nanotempertech.com/monolith/

Protein-binding assays in biological liquids using microscale thermophoresishttps://www.nature.com/articles/ncomms1093

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Hello listeners, 

This week we take a step back from the bench and dive into our minds. Biomedical mind mapping has been used by geniuses such as DaVinci, Michelangelo, and many others. Dr. Jimita Toraskar talks about biomedical mind mapping and how we can use it in our day-to-day life. Thank you for joining us, and I hope you keep listening. 

Reading suggestions:

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Hello listeners,

Antimicrobial drug resistance is a significant issue we are facing, and we just saw what COVID-19 did to this world. Let’s hear from Dr. Aurijit Sarkar, Assistant Professor, about his thoughts on the issue of drug resistance and the one question he would like to get answered in his lifetime. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

Antibacterial drug discovery in the resistance era
https://www.nature.com/articles/nature17042

Antibiotic resistance is ancient
https://pubmed.ncbi.nlm.nih.gov/21881561/

Hospitalizations for Endocarditis and Associated Health Care Costs Among Persons with Diagnosed Drug Dependence - North Carolina, 2010-2015
https://pubmed.ncbi.nlm.nih.gov/28594786/

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Hello listeners,

Did you know facial expressions can be used to measure pain in mammals? Join us this week for a behavior technique where Rahul Patel, PhD candidate, talks about a relatively novel method, Grimace. Thank you for joining us, and I hope you keep listening.
Reading suggestions:

Development and validation of PainFace, a software platform that simplifies and standardizes mouse grimace analyseshttps://www.biorxiv.org/content/10.1101/2022.08.12.503790v1

Visit Hypothesis to Hardware to know more about the grimace test chambers https://www.hypothesistohardware.com

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Hello listeners,

The Nobel Prize 2022 in Chemistry was shared between three scientists, Carolyn R. Bertozzi, Morten P. Meldal, and Karl Barry Sharpless, for their work on click chemistry and bioorthogonal chemistry. And for this episode, my former mentor, Dr. Umberto Maria Battisti, will talk about his work on biorthogonal chemistry. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Catalytic Click Reactionshttps://onlinelibrary.wiley.com/doi/10.1002/9783527651733.ch32

Recent Advances in the Development of Tetrazine Ligation Tools for Pretargeted Nuclear Imaginghttps://www.mdpi.com/1424-8247/15/6/685/htm

Inverse electron demand Diels–Alder reactions in chemical biologyhttps://pubs.rsc.org/en/content/articlelanding/2017/cs/c7cs00184c

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Hello everyone,

Today we have an exciting episode because we will discuss one of my favorite techniques, IR MALDI ESI. Dr. Megan Knuth will be joining us today to walk us through the nitty-gritty of IR MALDI ESI. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
Methods for Cryosectioning and Mass Spectrometry Imaging of Whole-Body Zebrafish
https://pubs.acs.org/doi/10.1021/jasms.9b00097

IR-MALDESI Mass Spectrometry Imaging of Biological Tissue Sections using Ice as a Matrix
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950934/

Vitamin D deficiency promotes accumulation of bioactive lipids and increased endocannabinoid tone in zebrafish
https://pubmed.ncbi.nlm.nih.gov/34673019/

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Hello listeners,

In this episode, we discuss a routinely and important technique called Fluorescent competition assay. We have Dr. Deepika Jayaprakash joining us for this episode. Thank you for joining us, and I hope you keep listening.

Reading suggestions:
A comprehensive phenotypic CRISPR-Cas9 screen of the ubiquitin pathway uncovers roles of ubiquitin ligases in mitosishttps://pubmed.ncbi.nlm.nih.gov/33539788/

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Hello listeners,
This week we dive into Cryo-EM, a Nobel Prize winning technique. Joining us this week is Dr. Claudio Catalano who has worked with Cryo-EM for many years. Thank you for joining us, and I hope you keep listening.

Reading suggestions:

  • Cryo-EM—the first thirty years. https://doi.org/10.1111/j.1365-2818.2011.03569.x
  • Cryo-electron microscopy wins chemistry Nobel. https://doi.org/10.1038/nature.2017.22738
  • Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise.https://www.pnas.org/doi/10.1073/pnas.1314449110

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Hey guys, 
This episode is all about my journey and why I am creating this podcast. 
Send me you suggestions at barkha@nerdrxpodcast.com 

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Welcome to the very first episode of NerdRx Podcast. As this is the first one, who better to join me than my best friend? We have Dr. Shravan Morla joining us today, and he will walk us through the ins and outs of high-throughput screening. Thank you for joining us, and I hope you keep listening.

Reading suggestion: Impact of high-throughput screening in biomedical research. https://www.nature.com/articles/nrd3368

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Hello everyone, 
Welcome to NerdRx podcast and I am your host Barkha. Please join me every Tuesday for a new episode where I discuss a new lab technique with a scientist. 
Email me your suggestions at barkha@nerdrxpodcast.com