Mentors at Your Benchside

#35 — A smooth, perfect agar plate will make your microbial experiments a lot easier. Whether you're using LB, M9 or blood agar, tune in to this episode to learn how to pour the perfect plates every time.

Visit our website to read the full article. [1]

Explore other practical secrets of the bacterial world [2] on our website or find out how to avoid lab disasters. [3]

Resources:
1.  How to Make the Perfect Agar Plate Every Time. Available at: https://bitesizebio.com/6938/how-to-make-the-perfect-agar-plate-every-time/
2.  Practical Secrets of the Bacterial World for the Uninitiated. Available at: https://bitesizebio.com/26345/practical-microbiology-for-the-uninitiated/
3.  Rookie Researcher Disasters. Available at: https://bitesizebio.com/194/rookie-researcher-disasters/

#34 — Whether you like it or not, you need to know the concentration of your protein samples accurately. Binding constants, enzyme kinetics, and activity assays all need accurately-quantified protein to deliver accurate results.

But there's a head-spinning amount of protein quantification assays out there! The BCA assay, Bradford assay, biuret reaction, the Folin–Lowry assay—but hold on.

Which assay is appropriate for your sample and why? In this episode of Mentors At Your Benchside, we break down our top 5 protein quantification assays, go into their advantages and disadvantages, and suggest what types of proteins they are appropriate for.

Be sure to visit the corresponding article for table breakdown of the assays discussed. [1] You can also follow up this podcast by reading our article on how colorimetric assays work. [2]

Resources:
1. Top 5 Protein Quantification Assays. Available at:
https://bitesizebio.com/23824/top-5-protein-quantification-assays/
2. Ask a Chemist: How Colorimetric Assays Work. Available at:
https://bitesizebio.com/7214/ask-a-chemist-how-colorimetric-assays-work/

#33 — Your lab. It probably doesn't look very nice, and often enough, it probably doesn't smell very nice either. Lumps of E. coli, fishy amines, eggy reducing agents. All uniquely rotten. What's your candidate for the worst lab smell? In this episode of Mentors At Your Benchside, we go through our top ten picks for the worst lab smell. Do you agree with us?

Be sure to visit the original article, where you can see what others have to say about our top ten picks. [1] You can also contribute your own worst-smelling chemical in the comments! Also check out the top ten stupid safety mistakes we've made. [2]

Resources:
1. The Top 10 Worst Lab Smells. Available at:
https://bitesizebio.com/6935/top-10-worst-lab-smells/
2. 10 Stupid Lab Safety Mistakes. Available at:
https://bitesizebio.com/1899/stupid-lab-safety-mistakes/

#32 — How do you know if your bacteria culture is ready for your experiment? In this episode of Mentors At Your Benchside we take a close look at the popular method of OD600 measurements as well as some other techniques you can use to find out if your bacterial culture is still growing.

You can find the full article on our website. [1]

Learn more about different bacterial strains [2] and get to grips with growth curves [3], or find out how to train yourself to measure OD600 by eye [4]. And if you're curious about sporulating bacteria, read this article about endospores [5].

Resources:
1. Is Your Bacterial Culture Still Growing? A Primer on OD­600 Measurements. Available at: https://bitesizebio.com/41100/is-your-bacterial-culture-still-growing/
2. Choosing the Right Bacterial Strains for Your Lab. Available at: https://bitesizebio.com/55858/bacterial-strains-for-lab/
3.Why Isn’t My Culture Growing? The S-Curve Explained. Available at: https://bitesizebio.com/37809/culture-growing-s-curve-explained/
4.How To Train Yourself to Measure OD600 by Eye. Available at: https://bitesizebio.com/7271/how-to-train-yourself-to-measure-od600-by-eye/
5.Meet Nature’s Oldest Doomsday Preppers: Endospores. Available at: https://bitesizebio.com/38204/meet-natures-oldest-doomsday-preppers-endospores/

#31 — CRISPR can do more than edit DNA. Cas13, a CRISPR-associated protein that can bind and cut RNA, provides the power of CRISPR for studying RNA. Listen to the episode to discover how you can use Cas13 to knock-down, modify or track RNAs in mammalian cells. Plus learn how Cas13 can help you detect specific RNAs in patient samples in a matter of minutes.

Visit the original article on CRISPR-Cas13 to see helpful diagrams and a table summarizing where to buy Cas13 plasmids. [1]

Want to know more about how CRISPR can help your research? Visit our CRISPR hub, [2] where you can find articles explaining the basics of how CRISPR works, [3] discover the wealth of CRISPR nucleases available, [4] get advice on using CRISPR in your research, [5] and more.

Resources:
1. CRISPR-Cas13: How to Revolutionize Your RNA Research. Available at: https://bitesizebio.com/64751/crispr-cas13/
2. CRISPR Hub. Available at: https://bitesizebio.com/CRISPR/
3. CRISPR Technology Explained: Towards a CRISPR Genome! Available at: https://bitesizebio.com/32581/crispr-technology-explained/
4. CRISPR Nucleases: The Ultimate Guide To Selection. Available at: https://bitesizebio.com/46146/crispr-nucleases-the-ultimate-guide/
5. CRISPR Gene Editing: Considerations and Getting Started. Available at: https://bitesizebio.com/47239/crispr-gene-editing-getting-started/

#30 — We have all heard about centrifugation, or more specifically, the horror stories associated with centrifugation going wrong.

But don't let centrifugation scare you! In this episode, you'll learn how to properly balance, when to use the brake, what the difference is between RCF and RPM, and more.

Read the full Whats and Whys of Centrifugation article for some of the most common issues that can be easily overlooked during centrifugation and why they are so important for the proper handling of a centrifuge. [1] Discover why RPM Does Not Equal RCF, and get top tips for Proper Use and Handling of Centrifugal Filters. [2,3]

Resources:
1. Keep Calm and Spin On: The Whats and Whys of Centrifugation. Available at: https://bitesizebio.com/47991/centrifuges-centrifugation/
2. RPM Does Not Equal RCF. Available at: https://bitesizebio.com/1777/rpm-does-not-equal-rcf/
3. Spinning Around: Tips and Tricks for Using Centrifugal Filters. Available at: https://bitesizebio.com/44738/spinning-around-tips-and-tricks-for-using-centrifugal-filters/

#29 — Ever wondered why you have to add protease inhibitors to your lysis buffer? In this episode of Mentors At Your Benchside we’ll tell you all about protease inhibitors, why they’re important and how to use and store them.

To learn more about protease inhibitors and to access the table with information about common protease inhibitors, read the full article on our website [1].

Read more about how protease inhibitors work [2], learn about protein expression [3] and find out what you need to consider during cell lysis [4].

Resources:
1. Protease Inhibitors 101: How They Work and How to Use Them. Available at: https://bitesizebio.com/58195/protease-inhibitors-101/
2. How Proteases and Protease Inhibitors Work. Available at: https://bitesizebio.com/8845/how-proteases-and-protease-inhibitors-work/
3. The Bitesize Bio Guide to Protein Expression – a Bitesize Bio eBook. Available at: https://bitesizebio.com/webinar/the-bitesize-bio-guide-to-protein-expression-a-bitesize-bio-ebook/
4. Four Important Considerations for Your Cell Lysis. Available at: https://bitesizebio.com/40942/4-important-considerations-for-your-cell-lysis/

#28 — SDS-PAGE gels can be run at constant current, constant voltage or constant power. But which is best? Listen to this episode of Mentors at Your Benchside to discover the differences between current, voltage and power, and how they affect how your gels run.

Visit the original article to see a summary table of running your SDS-PAGE gels at a constant voltage, current or power. [1] We've also got tips and tricks for casting the perfect SDS-PAGE gel, [2] or read a refresher on how SDS-PAGE works. [3]

Resources:
1. Constant Current or Voltage in SDS-PAGE: The Great Debate. Available at: https://bitesizebio.com/51744/constant-current-or-voltage-in-sds-page/.
2. A Simple SDS-PAGE Gel Recipe and 10-Step Casting Protocol for Perfect Gels. Available at: https://bitesizebio.com/59429/sds-page-gel-recipe/.
3. How SDS-PAGE Works. Available at: https://bitesizebio.com/580/how-sds-page-works/.

#27 — Optimal conditions for DNA ligation reactions are a delicate balance between DNA molecules interacting and the enzymatic ligation reaction.

In this episode, you'll discover our top 6 DNA ligation tips to improve the efficiency of your ligations and increase your cloning success rate!

Read the full article to get more practical advice for optimizing DNA ligation reactions for cloning. [1] Want more cloning advice? Read about Cloning with Compatible Cohesive Ends, [2] and discover how to Remove Unwanted DNA from Vectors. [3] Also, find out why T4 DNA ligase is such a popular ligase and perhaps the only ligation enzyme you’ll ever need. [4]

Resources:
1. DNA Ligation: How it Works & 6 Top Tips. Available at: https://bitesizebio.com/10279/how-dna-ligation-works/
2. Assembling the Puzzle: Cloning with Compatible Cohesive Ends. Available at: https://bitesizebio.com/21716/assembling-the-puzzle-cloning-with-compatible-cohesive-ends/
3. Tech Clinic #1: Removing Unwanted DNA from Vectors — beat Murphy’s Law. Available at: https://bitesizebio.com/10228/removing-unwanted-dna-from-vectors-how-to-beat-murphys-law/
4. T4 DNA Ligase: The Only Ligase You’ll Ever Need? Available at: https://bitesizebio.com/46482/t4-dna-ligase-the-only-ligase-youll-ever-need/

#26 — Cryo-EM is a revolutionary imaging method that lets us see complex biostructures at higher and higher resolutions.

But do you understand the mind-blowing science behind this technique? And what is cryo-electron microscopy, anyway? Why is the cryogenic aspect important, and how did it seemingly go from nothing to the big time? In the latest episode of Mentors At Your Benchside, we answer all of these questions and more!

Check out the corresponding online article to access loads of follow-up resources to deepen your understanding of this topic.[1] Also, check out our related articles covering crucial sample preparation considerations for cryo-EM and its history from obscure to Nobel Prize winner. [2,3]

Resources:
1. What Is Cryo-Electron Microscopy? Available at: https://bitesizebio.com/62871/what-is-cryo-electron-microscopy/
2. Cryo-EM Sample Prep: 5 Crucial Considerations. Available at: https://bitesizebio.com/62619/cryo-em-sample-prep/
3. A Short History of Cryo-Electron Microscopy: Available at: https://bitesizebio.com/62839/history-of-cryo-electron-microscopy/