Mentors at Your Benchside

#105 — You may be familiar with standard single fragment ligations: insert, vector, ligase—done! But what if you have a complex cloning project with a massive region of DNA to clone? You can’t PCR the whole thing, and you can’t cut the entire thing out from somewhere else. What do you do? In this episode, we explain the answer: multiple fragment ligation. Check out the corresponding article for some handy illustrations and links to related resources. [1] To discover more ways to go about molecular cloning, check out these five approaches. [2] And read this article to dive deeper into how ligation works. [3] Resources: 1. Multiple Fragment Ligation: The Why and How. Available at: https://bitesizebio.com/67124/multiple-fragment-ligation/ 2. Cloning Methods: 5 Different Ways to Assemble. Available at: https://bitesizebio.com/26961/cloning-methods-5-different-ways-to-assemble/ 3. DNA Ligation: How it Works & 6 Top Tips. Available at: https://bitesizebio.com/10279/how-dna-ligation-works/

#104 — What funding stream is right for you? Industry or government? Non-profits or crowdfunding? It depends on what you're researching, but also where you want to take your career. In this episode, Joel Berry, Founder, and Chief Scientist at Astound Research, breaks down the different funding streams and flow of money in bioscience research. Discover the scope and requirements of each type of funding source, and get a breakdown of the overall funding landscape so you can pick the funding stream that works best for you. Check out the corresponding online article for links to more helpful funding resources. [1] Plus, discover how you can advocate for science funding [2] and dive deeper into whether crowdfunding will work for your project. [3] Resources: 1. Funding Opportunities and the Flow of Money in Science. Available at: https://bitesizebio.com/77353/funding-opportunities-landscape/ 2. Defend Science Funding! A Brief Guide. Available at: https://bitesizebio.com/36701/defend-science-funding/ 3. Kick Start Your Research With Crowdfunding! Available at: https://bitesizebio.com/20876/kick-start-your-research-with-crowdfunding/

#103 — DNA sequencing is a fundamental technique in modern molecular biology that has revolutionized the study of genes. In the old days, Maxam–Gilbert sequencing was the method of choice, but it has mostly been replaced by Sanger sequencing and Next-Generation methods. Yet, it still has some niche uses, and in the historical context of DNA sequencing, it’s hugely important! So, in this episode, learn about what Maxam–Gilbert sequencing is, why it lost popularity, and why some researchers still use it today. Check out the corresponding article to see if you can read a Sanger sequencing gel and decipher the final amino acid code. [1] And check out our primer on the Sanger sequencing method to learn why it was so advantageous over the Maxam–Gilbert method. [2] Resources: 1. Maxam–Gilbert Sequencing: What It Is and 3 Modern Applications. Available at: https://bitesizebio.com/36696/maxam-gilbert-sequencing/ 2. Sanger Sequencing: How the Genome Was Won. Available at: https://bitesizebio.com/27985/sanger-sequencing-genome-won/

#102 — Fluorescence microscopy images not only look great but also allow us to get a better understanding of cells, structures, and tissues. And confocal laser scanning microscopy lets us construct 3D images from 2D micrographs. In this episode, learn the basic principles of confocal laser scanning microscopy, how the microscopes work, and some of its applications in bioscience and beyond. Check out the corresponding article for a handy confocal laser scanning microscope diagram. [1] Learn about the Airy unit [2] and check out our guide to choosing a fluorescent protein for your experiments. [3] Resources: 1. Confocal Laser Scanning Microscopy Explained In 3 Easy Steps. Available at: https://bitesizebio.com/19958/confocal-laser-scanning-microscopy/ 2. Rubbing Your Microscope’s Eyes: A Guide to Optical Resolution. Available at: https://bitesizebio.com/13415/rubbing-your-microscopes-eyes-a-guide-to-optical-resolution/ 3. The Ultimate Guide to Choosing a Fluorescent Protein. Available at: https://bitesizebio.com/54287/choosing-a-fluorescent-protein/

#101 — Discover what it takes to become an expert at getting funded, from simple habits such as summarizing what you read in the literature, to big steps such as organizing your very own conference to establish your name in your field. With over 30 years of experience as a biomedical engineering researcher seeking grants, Joel Berry, Founder, and Chief Scientist at Astound Research, shares his hard-won insights on strategizing your approach to seeking grants. [1] Take a listen to what he has to say. If you're struggling to keep up to date with the literature in your field, read our tips for staying on top of new publications [2] and get more grant writing advice from a grant reviewer! [3] Resources: 1. How to Become an Expert at Getting Funded. Available at: https://bitesizebio.com/77308/how-to-become-an-expert-at-getting-funded/ 2. Useful Tips to Keep on Top of New Literature. Available at: https://bitesizebio.com/10532/search-engines-for-literature-searching/ 3. What I Learned as a Grant Reviewer. Available at: https://bitesizebio.com/30909/learned-grant-reviewer/

#100 — Science attracts so many different and quirky personalities that you are bound to have some people you just don’t get along with. Conflicts happen, and there are many strategies you can take to deal with conflict in the lab. But when your lab supervisor is the problem, it can be a big issue for you. In this episode, delve into the challenges of dealing with difficult lab supervisors. [1] We identify five common problematic personality traits: passive-aggressive, manipulative, unfocused, micro-manager, and negative reinforcement. Listen and explore practical strategies for addressing each type while remaining professional and constructive. Check out our related article for further advice on dealing with conflicts in a busy research lab. [2] Resources: 1. Five Types of Difficult Lab Supervisor and How to Handle Them. Available at: https://bitesizebio.com/1540/6-types-of-bad-boss-and-how-to-handle-them/ 2. Dealing with Tension and Conflict in the Lab. Available at: https://bitesizebio.com/27373/dealing-tension-conflict-lab/

#99 — So you’ve got your flow cytometry training booked and are one step closer to that precious data. But if you want to hit the ground running and get some useful data from your samples, there are some little things you'll need to do. These include reading up on a bit of background theory, understanding the capabilities of different types of cytometers, and thinking about what you want to learn from your experiment. In this episode of Mentors At Your Benchside, we've compiled cytometry training advice from a core facility manager to help you get the most out of your training sessions and early experiments. [1] While you are here, why not learn about the components inside cytometers and what they do? [2] Plus, take a step towards fully understanding your data and explore the difference between forward scatter, side scatter, and their corresponding plots. [3] Resources: 1. Seven Top Tips to Make the Most of Your Flow Cytometry Training. Available at: https://bitesizebio.com/75182/flow-cytometry-training/ 2. Demystifying the Flow Cytometry Optics System: A Peek Under the Hood. Available at: https://bitesizebio.com/31638/flow-cytometry-optics-system/ 3. Basic Parameters Measured by a Flow Cytometer: What is Scattered Light and Absolute Fluorescence? Available at: https://bitesizebio.com/25310/basic-parameters-measured-by-a-flow-cytometer-what-is-scattered-light-and-absolute-fluorescence/

#98 — Our labs can contain thousands of chemicals, many of which will be past their given expiry date and many of which are expensive to buy and replace. Replacing them when you don't need to can be a waste of time and grant money. On the other hand, using expired chemicals can lead to failed experiments and confusing results. In this episode of Mentors At Your Benchside, learn what types of chemicals are safe to use past their expiry date, which ones you should probably throw out, and why. Read out the corresponding article for a handy summary table. [1] And while you're diving into reagents, why not check out the different types of antibiotics in molecular biology? [2] Resources: 1. What Reagents Can You Use Past Their Chemical Expiry Date? Available at: https://bitesizebio.com/74311/chemical-expiry-date/ 2. Antibiotics Used in Molecular Biology. Available at: https://bitesizebio.com/10288/antibiotics-used-in-molecular-biology/

#97 — A research interest statement is essential to successfully apply for an academic job. In this episode, we delve into how to craft an outstanding one. [1] We cover strategies to outline your past, current, and future research in a concise format. We also explain other key elements such as, creating a compelling introduction, detailing research plans, aligning with targeted labs or departments, and writing a strong conclusion. Plus, get tips on personalizing your applications while maintaining clarity and conciseness. While you're here, check out our related article packed with tips to help you shine at your next job interview. [2] Or, if you're considering working abroad, check out some of its pros and cons. [3] Resources: 1. How to Write a Killer Research Interest Statement. Available at: https://bitesizebio.com/35364/position-research-interest-statement/ 2. How To Shine in a Job Interview. Available at: https://bitesizebio.com/2599/how-to-shine-in-a-job-interview/ 3. The Pros and Cons of a PhD or Post-doc in a Foreign Country. Available at: https://bitesizebio.com/7300/the-pros-and-cons-of-a-phd-or-post-doc-in-a-foreign-country-2/

#96 — An appropriate microorganism preservation method can make all the difference in maintaining the viability of your microbial strains because it plays a crucial role in ensuring reproducible results and continuity in research. In this episode, learn the preservation methods for short- and long-term microbe storage, their pros and cons, and the kit you need to do them. Check out the corresponding article for a list of helpful references. [1] Learn the main ingredients of cell culture media [2] and the steps you can take to keep mammalian cell cultures healthy. [3] Resources: 1. How to Preserve Microorganisms: Store Your Cells Better. Available at: https://bitesizebio.com/45159/how-to-preserve-microorganisms/ 2. What’s in Your Cell Culture Medium? Available at: https://bitesizebio.com/37034/cell-culture-medium/ 3. How To Keep Your Mammalian Cells Happy And Healthy. Available at: https://bitesizebio.com/8146/how-to-keep-your-cells-happy-and-healthy/

#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/