Mentors at Your Benchside

#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 for 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/

#25 — Phenol extraction of DNA is a commonly used method for removing proteins from nucleic acids; for example, to remove proteins from cell lysate during genomic DNA preparation.

It's commonly used, but not well understood.

Listen to this episode to get a quick explanation of how phenol extraction of DNA works.

Visit the original article to see handy diagrams on how phenol extraction works. [1] To get more help and advice on DNA extraction, read our related articles and discover how chloroform can clean up your phenol extractions, [2] learn how ethanol precipitation works, [3] and decide if ethanol or isopropanol is best for precipitating your samples. [4]

Resources:

1. The Basics: How Phenol Extraction of DNA Works. Available at: https://bitesizebio.com/384/the-basics-how-phenol-extraction-works/

2. Practical Application of Phenol-Chloroform Extraction. Available at: https://bitesizebio.com/3651/practical-application-of-phenol-chloroform-extraction/

3. Ethanol Precipitation of DNA and RNA: How it Works. Available at: https://bitesizebio.com/253/the-basics-how-ethanol-precipitation-of-dna-and-rna-works/

4. DNA Precipitation: Ethanol vs. Isopropanol. Available at: https://bitesizebio.com/2839/dna-precipitation-ethanol-vs-isopropanol/

#24 — How can you best prepare for a postdoc interview? Here we cover 10 questions that are often encountered during the job-hunting process.

Preparing answers to these questions, alongside doing some background research about the research group and PI, can give you the edge in securing that postdoc.

You can recap these top 10 questions anytime by visiting the full article on popular postdoc interview questions. [1]

If you are looking for further interview advice, make sure you check out our top 10 interview tips, consider how you might concisely describe your research so far, and get advice on what to wear for the interview.

Resources:

1. Postdoc Interview Preparation: Sample Questions and Answers. Available at: https://bitesizebio.com/10393/postdoc-interview-preparation-sample-questions-and-answers/

2. 10 Great Tips To Make A Good Impression At Your Interview. Available at: https://bitesizebio.com/6696/10-great-tips-to-make-a-good-impression-at-your-interview/

3. Can You Describe Your Research in 30 Seconds? 60? Available at: https://bitesizebio.com/13639/can-you-describe-your-research-in-30-seconds-60/

4. GOT AN INTERVIEW! What to wear? What to wear? Available at: https://bitesizebio.com/6261/got-an-interview-what-to-wear-what-to-wear/

#23 — Creativity in Science: How a Good Imagination Can Help Your Research

If you're stuck in a research rut in the lab, developing your creativity can help you find new solutions to current problems that may be impeding your scientific progress.

In this episode, we explore 3 important questions you should consider to help spark your creativity in the lab and provide 8 simple tips to help achieve this.

Read the full article on boosting your creativity in science. [1]

If you are looking for further advice, make sure you listen to our Happy Scientist Podcast episode on Imagination, which covers even more ways to boost your imagination and creativity. [2] Consider the importance of allowing yourself time to think and reflect. [3] Finally, listen to this episode of the Microscopists featuring Eric Betzig, where the Nobel Laureate reveals how his biggest ideas came during his two periods of unemployment. [3]

Resources:

1. Creativity in Science: How a Good Imagination Can Help Your Research. Available at: https://bitesizebio.com/63742/creativity-in-science/

2. Episode 33 — How to Foster Imagination. Available at : https://bitesizebio.com/podcast/episode-33-how-to-foster-imagination/

3. Time to Think. Available at: https://bitesizebio.com/146/time-to-think/

4. Eric Betzig (University of California). Available at: https://bitesizebio.com/podcast/eric-betzig/

#22 — Research often requires you to use dangerous chemicals. From caustic acids and bases to pH solutions and toxic reducing agents, chemical hazards abound in the lab.

In this episode, we'll take a look at ten dangerous chemicals in the lab and the harm they can cause you.

Want to develop your understanding of chemical safety? Why not read the full article, [1] where you'll find lots of helpful resources and further reading? If you fancy a deeper dive into all aspects of lab safety, then check out the Bitesize Bio lab safety eBook. [2]

If you're a bit rusty on your good laboratory practice, definitely read 10 Stupid Lab Safety Mistakes [3] and see how many sins you commit. And finally, we all rely on our PPE for protection and safety. Be sure to take a look at our 10 Common PPE Sins for a quick brush-up. [4]

Resources:

1. Ten Bad Chemicals in the Lab and What They do to You! Available at: https://bitesizebio.com/10470/ten-bad-chemicals-in-the-lab-and-what-they-do-to-you/

2. The Bitesize Bio Guide to Lab Safety eBook. Available at: https://bitesizebio.com/wp-content/uploads/2021/08/The-Bitesize-Bio-Guide-to-Lab-Safety.pdf

3. 10 Stupid Lab Safety Mistakes. Available at: https://bitesizebio.com/1899/stupid-lab-safety-mistakes/

4. 10 Common PPE Sins. Available at: https://bitesizebio.com/9850/10-common-ppe-sins/

#21 — Do you know the difference between cell confluency and cell number? Can you measure cell confluency accurately? Cell confluency measurements are essential in cell-based experiments. Listen to this episode to learn what cell confluency is and the different quantification methods to measure it.

Read the original article to get visual guides to help you understand and measure your cell confluency accurately. [1]

Do you want more information to help you perfect your cell culture? Check out related articles to learn how to get the right passage number for your cells and how to culture adherent cells like HEK293s. [2,3]

Resources:

1. How Confluent Are Your Cells? A Beginner’s Guide to Measuring Cell Culture Confluency. Available at: https://bitesizebio.com/63887/cell-confluency/

2. What’s in a Number: Getting the Right Passage in Cell Culture. Available at: https://bitesizebio.com/13685/cell-culture-passage-number-explained/

3. What the HEK? A Beginner’s Guide to HEK293 Cells. Available at: https://bitesizebio.com/45489/guide-to-hek293-cells/

#20 — Have you ever wondered how Laemmli buffer actually works? In this episode of Mentors At Your Benchside, we talk through the different components of Laemmli buffer, what they do and why they are essential for your SDS-PAGE experiments.

Read the full article to learn more about this buffer and get a handy Laemmli buffer recipe. [1]

Looking for more information on SDS-PAGE? Discover the theory behind SDS-PAGE and get advice on how you can cast the perfect SDS-PAGE gel. [2,3] You can also download our useful SDS-PAGE protocol PDF that contains simple buffer recipes, gel recipes, and a neat casting protocol. [4]

Resources:

1. Laemmli Buffer: What Is It for Anyway? Available at: https://bitesizebio.com/44540/laemmli-buffer-what-is-it-for-anyway/

2. How SDS-PAGE Works. Available at: https://bitesizebio.com/580/how-sds-page-works/

3. A Simple SDS-PAGE Gel Recipe and 10-Step Casting Protocol for Perfect Gels. Available at: https://bitesizebio.com/59429/sds-page-gel-recipe/

4. Bitesize Bio's SDS-PAGE Protocol PDF Cheat Sheet. Available at: https://bitesizebio.com/sds-page-protocol-pdf/