Mentors at Your Benchside

#95 — Have you ever accidentally forgotten to add the Kozak consensus sequence to the start of a coding gene? Or forgotten to include the stop codon? Did you clone something, then realize you wanted to tag it with something? Or do you want to add restriction enzymes to your PCR product to make it easier to clone into a plasmid? Overhang PCR may be your answer!

In this episode, we discuss what overhang PCR is, its benefits, and how to perform it in the lab. [1] While you are here, check out our article on TA cloning? [2]

Resources:
1. Overhang PCR: Add Missing DNA Sequences Using Primers. Available at: https://bitesizebio.com/20786/overhang-pcr/
2. Ta-Da! The Magic of Taq and TA Cloning. Available at: https://bitesizebio.com/19709/ta-da-the-magic-of-taq-and-ta-cloning/

#94 — While there are lots of methods to choose from for cleaning up your RNA or DNA samples, for many researchers, phenol-chloroform is the go-to technique.

In this episode, go beyond the basics of how the method works and get expert practical guidance on performing and optimizing it.

Plus, learn the differences between the common solvents, how to check and adjust the pH of the phenol phase, and get tips to reduce the amount of interphase. 

Check out the corresponding online article for a diagram illustrating how you can reduce the interphase. [1] Learn the theory behind the technique in our easy explainer [2] and explore four other ways you can clean up DNA samples. [3]

Resources:
1. Practical Application of Phenol-Chloroform Extraction. Available at: https://bitesizebio.com/3651/practical-application-of-phenol-chloroform-extraction/
2. The Basics: How Phenol Extraction of DNA Works. Available at: https://bitesizebio.com/384/the-basics-how-phenol-extraction-works/
3. Five Ways to Clean Up A DNA Sample. Available at: https://bitesizebio.com/142/5-ways-to-clean-up-a-dna-sample/

#93 — Bioinformatics is an interdisciplinary field that combines mathematics, computer science, physics, and biology to help answer key questions in modern biological sciences research.

In this episode, we’ve got the lowdown on the training you’ll need to pursue this career path, and a handy list of resources to get you started on your learning. [1] Plus, check out our related article on some of the ways that scientists from diverse fields use bioinformatics. [2]

Resources:
1. How to Become a Bioinformatician. Available at: https://bitesizebio.com/38236/how-to-become-a-bioinformatician/
2. Bioinformatics: It’s Not All About Genomics. Available at: https://bitesizebio.com/46495/bioinformatics-its-not-all-about-genomics/

#92 — We all need to lyse cells to extract the goodness—our samples—from them.

However, there are many cell lysis methods. Some are harsh, while some are gentle. Some are laborious, while some are easy. Some require dedicated equipment, while some do not. So which one do you choose?

In this episode, we cover eight cell lysis methods for your experiments. [1] For extra information to help you pick a lysis method, check out our article on the different types of cell walls. [2]

Resources:
1. 8 Cell Lysis Methods to Break Cell Walls. Available at: https://bitesizebio.com/13536/cell-lysis-methods/
2. Cell lysis 101: 5 types of cell walls you need to understand. Available at: https://bitesizebio.com/13535/tutorial-cell-lysis-5-types-of-cell-walls/

#91 — Genomes are complex and encode a vast quantity of information. One of their key features is genetic variants—aberrations in the genetic sequence, usually in the form of insertions, deletions, repeats, and translocations of genetic material.

This episode explains the different types of genetic variants, introduces their key features, and gives you some top tips for studying them.

Read the corresponding online article for links to helpful resources and a handy figure. [1] While you're here, check out how to identify protein binding sequences on DNA using chip ChIP-seq [2] and learn about some of the fascinating applications of genome sequencing. [3]

Resources:
1. Genetic Variants Explained. Available at: https://bitesizebio.com/23996/whats-so-important-about-variants/
2. An Introduction To ChIP-seq. Available at: https://bitesizebio.com/13541/an-introduction-to-chip-seq/
3. Decoding the Genome: Applications of DNA Sequencing. Available at: https://bitesizebio.com/27892/decoding-the-genome-applications-of-dna-sequencing/

#90 — Are you confused about the banding pattern of DNA on agarose gels? DNA can take many structural forms depending on its source and how you have isolated and purified it. And those forms, including linear, nicked, closed circled, and supercoiled, all migrate at different rates on agarose gels.

But how do you identify which band corresponds to which structural form? And why do some of these occur during plasmid preps but not others? Listen to this episode to find out. [1]

Since you're here, check out our article explaining how to get more supercoiled DNA from your plasmid preps [2] and learn how alkaline lysis works. [3]

Resources:
1. How to Identify Supercoils, Nicks and Circles in DNA Plasmid Preps using Gel Electrophoresis. Available at: https://bitesizebio.com/13524/how-to-identify-supercoils-nicks-and-circles-in-plasmid-preps/
2. 6 Ways to Show Your Plasmid Preps Some Tlc and Get More Supercoiled Plasmid in Return. Available at: https://bitesizebio.com/13525/6-ways-to-show-your-plasmid-preps-some-tlc-and-get-more-supercoiled-plasmid-in-return/
3. Lab Basics: How The Alkaline Lysis Method Works. Available at: https://bitesizebio.com/180/the-basics-how-alkaline-lysis-works/

#89 — "Achieve more by doing less" sounds like a piece of cheap advice, but there is a lot of wisdom in it.

Research is complicated. You must choose the best questions to ask, techniques, controls, organisms, and equipment, to name just a few things that make up good experiments. With so much to focus on, it becomes harder to do each of these things well.

This episode explains three actionable steps you can take to simplify your research and become more effective at it.

Check out the corresponding online article for links to related resources. [1] and listen to our The Happy Scientist podcast for advice to stay happy, focused, and satisfied in the lab. [2]

Resources:
1. Simplicity in Science: How to Increase your Research Effectiveness by Doing Less. Available at: https://bitesizebio.com/63207/become-an-effective-researcher/
2. The Happy Scientist: Available at: https://thehappyscientist.bitesizebio.com/

#88 — Getting the best out of your in situ hybridizations requires choosing the correct protocol, deciding if sections or whole mount is better, using the right equipment, making fresh buffers, careful planning for all steps, optimizing your probe concentration, and taking the time to get the development step right. In other words, there are a lot of ways in situ hybridizations can go wrong!

This episode walks you through your first in situ hybridization and how to totally nail it! [1] When you've finished listening, why not check out our article on fluorescence in situ hybridization (FISH)? [2]

Resources:
1. How to Totally Nail Your First in situ Hybridization. Available at: https://bitesizebio.com/44651/how-to-totally-nail-your-first-in-situ-hybridization/
2. Do You Know Where Your mRNAs Are? Available at: https://bitesizebio.com/13391/its-10-am-do-you-know-where-your-mrnas-are/

#87 — Selecting the right blood collection tubes for your experiment is crucial. But do you know what tubes to use for which type of blood sample?

In this episode, we cover the nuances of choosing the appropriate blood collection tubes, a choice that hinges largely on whether you're aiming to collect serum or plasma samples. Understand the vital role that different tubes play in either fostering or preventing blood clotting and how these subtle differences can significantly impact the outcomes of your experiments. [1]

Whether you are venturing into the world of hematology microscopy, exploring genetic material, or identifying circulating biomarkers, choosing the correct tube can be a game-changer. Download our handy poster to illuminate the intricacies of plasma and serum tubes and how the type of tube you choose aligns with your scientific objectives. [2]

Resources:
1. Blood Collection Tubes: How to Pick the Correct One. Available at: https://bitesizebio.com/23701/choosing-the-right-blood-collection-tubes/
2. Poster. Available at: https://bitesizebio.com/blood-collection-tube-chart/

#86 — qPCR primer design is a bit of science, a bit of magic, and a little bit of luck. In this episode, we cover the science of qPCR primer design, a cornerstone in conducting successful qPCR or RT-qPCR assays for gene expression analysis. [1] Get top tips and learn why dedicating time to crafting high-quality primers can save your experiment from poor data and resource wastage. [2]

We guide you through utilizing popular tools like NCBI's Primer-BLAST for your qPCR primer designs, alongside introducing alternative online resources to aid in your experimentation journey. [3] Whether you're beginning your research journey or looking to hone your skills further, this episode promises to equip you with the knowledge to navigate the complex yet captivating world of qPCR primer design proficiently.

Resources:
1. A Step-by-Step Guide to Designing qPCR Primers. Available at: https://bitesizebio.com/10041/designing-qpcr-primers/
2. 10 Tips for Consistent qPCR. Available at: https://bitesizebio.com/1118/10-tips-for-consistent-real-time-pcr-rtpcr/
3. NCBI tool Primer-BLAST. Available at: https://www.ncbi.nlm.nih.gov/tools/primer-blast/