Mentors at Your Benchside

#115 — Hepatocytes are liver cells that are essential for its function. They are also essential for certain branches of drug testing and diagnostics.

However, they have irregular shapes, multiple nuclei, and can clump, which makes them difficult to process and count accurately.

In this episode, we explain how to prepare the best hepatocyte samples possible.

We also explain the latest automated machine learning-based tools that make hepatocyte counting easy and do essential sample-based calculations for you, removing tedious math. See the full article here. [1]

For more details on the machine learning technology discussed in this episode, read this technical note. [2] And to hear more from DeNovix experts on hepatocyte counting, watch their webinar Automated Hepatocyte Counting: New Technology for Simple, Reliable Counts. [3]

Resources:
1. Hepatocyte Counting Methods: From Manual Counts to Fast, Accurate Automation. Available at: https://bitesizebio.com/83141/hepatocyte-counting-methods/
2. TN 228 Automated Counting of Hepatocytes. Available at: https://www.denovix.com/tn-228-automated-counting-of-hepatocytes/?utm_source=bitesizebio&utm_medium=technicalcontent&utm_campaign=hepatocytes
3. Automated Hepatocyte Counting: New Technology for Simple, Reliable Counts. Available at: https://events.bitesizebio.com/automated-hepatocyte-counting-new/room

#114 — High-quality nuclei extraction is pivotal for many genetic and epigenetic studies, including single cell RNA-seq to describe transcriptomic profiles and gene expression dynamics and ATAC-seq to determine chromatin accessibility.

But nuclei samples are extremely delicate and can be challenging to prepare and count.

In this episode, we provide some practical tips to prepare high-quality nuclei extracts and tailor your extraction protocol to your sample.

We also compare methods to count nuclei, assess their quality, and demonstrate how automated nuclei counting can improve your workflow.

Check out the original article for a graphic that shows you the level of purity and quality you should aim for with nuclei extraction. [1] If you want to learn more about automated nuclei counting, download this free eBook. [2] Read this article to learn how to count cells quickly using fluorescence microscopy. [3] And to hear directly from DeNovix experts on nuclei counting, watch their webinar Optimizing Nuclei Extraction & Counting for Single Cell Sequencing. [4]

Resources:
1. Single Cell Sequencing: Tips to Optimize Nuclei Extraction and Counting. Available at: https://bitesizebio.com/78877/optimizing-nuclei-extraction/
2. Automated Counting of Isolated Nuclei. Available at: https://www.denovix.com/ebook/automated-counting-of-isolated-nuclei?utm_source=bitesizebio&utm_medium=technicalcontent
3. Quick and Easy Automatic Cell Counting in 4 Steps. Available at: https://bitesizebio.com/30184/quick-easy-automatic-cell-counting/
4. Optimizing Nuclei Extraction & Counting for Single Cell Sequencing. Available at: https://events.bitesizebio.com/optimizing-nuclei-extraction/room

#113 — Learning how to respond to criticism is an unavoidable aspect of grant applications. Follow all instructions from funding agencies to avoid immediate rejection.

This episode of Mentors At Your Benchside gives you some simple strategies to ensure you respond to criticism in a constructive and proportionate way.

For example, identifying reviewers can help you tailor your responses, but don't mention them by name! Plus, using a two-column document to systematize the criticisms and responses is a great way to organize feedback and distance yourself emotionally from it.

Hit play for more tips, check out the original article for links to helpful resources [1], and check out our complete guide to funding series for advice on getting your research funded—directly from a former NIH grant reviewer [2].

Resources:
1. Personal Advice on How to Respond to Criticism of Your Grant Proposal Reviews. Available at: https://bitesizebio.com/80095/respond-to-criticism/
2. The Complete Guide to Funding I: How to Become an Expert at Getting Funded. Available at: https://events.bitesizebio.com/the-complete-guide-to-funding-i-how/join

#112 — Isoelectric focusing (IEF) is a powerful technique distinct from the more familiar SDS-PAGE, [1,2] tailored for separating proteins or peptides based on their isoelectric points (pI). [3]

This method capitalizes on the migration of charged molecules through a stable pH gradient until they reach a zone where their net charge is zero, halting their movement.

Essential to setting up an IEF experiment are the IPG strips, equipped with a pH-responsive gel, and the sample, often mixed with carrier ampholytes for efficient migration.

IEF's utility spans various applications, from enhancing 2D-PAGE protein separations to analyzing post-translational modifications and preparing samples for mass spectrometry. [4]

Discover more about how this technique can advance your research and streamline your experimental workflows.

Resources:
1. How SDS-PAGE Works. Available at: https://bitesizebio.com/580/how-sds-page-works/
2. Isoelectric Focusing: A Simple Way to Enhance Your Protein Separation. Available at: https://bitesizebio.com/26811/isoelectric-focusing-separation-proteins-peptides/
3. The Definitive Guide to pH, pKa, and pI. Available at: https://bitesizebio.com/9425/what-is-ph-pka-pi/
4. Detecting Post-Translational Modifications. Available at: https://bitesizebio.com/49322/detecting-post-translational-modifications/

#111 — In this episode, we dive deep into the fascinating world of microbes and their revolutionary applications in biotechnology. From environmental solutions to breakthroughs in health and medicine, microbes hold the key to some of the most advanced scientific developments.

Discover how these microscopic organisms are transforming industries and pushing the boundaries of what's possible in science and technology. We’ll explore the latest research and applications that are shaping the future.

For an in-depth look at this topic, make sure to read the corresponding article on our website. [1] Dive into an application you almost certainly know about, yeast two-hybrid assays, [2] and check this article out to learn how to increase protein expression in plants. [3]

Resources:
1. Top 10 Uses of Microbes in Biotechnology. Available at: https://bitesizebio.com/48446/microbes-biotechnology/
2. Split Ubiquitin Yeast Two-Hybrid. Available at: https://bitesizebio.com/25286/split-ubiquitin-yeast-two-hybrid/
3. P19 to the Rescue: How to Increase Protein Expression in Agroinfiltration. Available at: https://bitesizebio.com/29964/p19-increase-expression-agroinfiltration/

#110 — Comparing two sets of data is a fundamental process in statistical analysis, crucial for drawing meaningful conclusions across various fields. Whether it's for determining the success of an intervention, understanding market trends, or validating scientific research, the need for comparison arises.

This episode delves into the essence of data comparison, focusing on two prevalent statistical tests: the Student’s t-test and the Mann–Whitney U test. [1] Each test comes with its assumptions and applicability, making the choice between them critical depending on the nature of your data.

Read our related article to learn more about comparing multiple datasets. [2]

Resources:
1. Let’s Talk About Stats: Methods for Comparing Two Sets of Data. Available at: https://bitesizebio.com/19298/comparing-two-sets-of-data/
2. Let’s Talk About Stats: Getting the Most out of your Multiple Datasets with Post-hoc Testing. Available at: https://bitesizebio.com/19318/lets-talk-about-stats-getting-the-most-out-of-your-multiple-datasets-with-post-hoc-testing/

#109 — How do you build a scientific network that gives you the best chance of getting your research funded? How can you identify who to include in your network, and how should you contact them?

This episode explains how to build a scientific network that works for you. We discuss the answers to these questions and provide some examples of collaborations that ended well—and some that didn't.

Check out our online article for additional resources to help get your research funded. [1] If you struggle to convey the impact of your research, you should definitely check out our webinar on this topic. [2] Plus, you can find more direct funding advice from Joel Berry here. [3]

Resources:
1. Personal Advice on Building Your Professional Network. It Takes a Village. Available at: https://bitesizebio.com/77734/professional-network/
2. How to Effectively Communicate Your Research. Available at: https://events.bitesizebio.com/how-to-effectively-communicate-your-1/join
3. How to Become an Expert at Getting Funded. Available at: https://bitesizebio.com/77308/how-to-become-an-expert-at-getting-funded/

#108 — What should you use to fix your cells? Alcohols or aldehydes? Gluteraldehyde or formaldehyde? And how long will your cells stay fixed?

This episode explains the four main fixatives for histology and cytometry and when to use them. It also provides some practical tips to ensure your fixation works and explains the benefits of combining fixatives.

Check out the corresponding article for links to related resources. [1] To learn more about autofluorescence and the controls you need to check for it, read this article. [2]

Resources
1. 4 Fixatives for Histology and Cytometry. Perfect Your Preservation. Available at: https://bitesizebio.com/22141/fixation-and-flow-cytometry/
2. 5 Controls for Immunofluorescence: A Beginner’s Guide. Available at: https://bitesizebio.com/44370/controls-for-immunofluorescence-a-beginners-guide/

#107 — Need to give your microscope a quick clean to get rid of some grime but unsure what cleaning agent to use? Have you had a nasty sample on there recently and need to disinfect it for the next user?

This episode gives you a quick guide to disinfecting your microscopes, including what solvents are safe to use and the parts you should tackle first.

Check out the corresponding article for helpful references. [1] To get a better understanding of the safety of your samples and other people's, read our introduction to safety datasheets. [2]

Resources:
1. Microscope Disinfection: A Quick Guide. Available at: https://bitesizebio.com/47987/microscope-disinfection/
2. Deciphering your Materials Safety Data Sheet. Available at: https://bitesizebio.com/21848/deciphering-your-materials-safety-data-sheet/

#106 — Transforming a tissue sample into a slide ready for microscopic exploration involves a series of critical steps. Among these, tissue processing is a fundamental phase bridging tissue fixation and the embedding/sectioning of paraffin blocks.

In this episode, discover what exactly happens in this vital in-between stage, and learn about the six steps that ensure your samples are ready for microscopic examination. [1]

And while you're here, check out our related articles on tissue fixation and embedding/sectioning [2,3], and the five important stages in histology slide preparation. [4]

Resources:
1. Tissue Processing For Histology: What Exactly Happens? Available at: https://bitesizebio.com/13469/tissue-processing-for-histology-what-exactly-happens/
2. An Introduction To Fixation For Histology: Think Before You Fix! Available at: https://bitesizebio.com/13401/think-before-you-fix/
3. Tissue Embedding and Sectioning: Something to Think About Whilst in the Bath. Available at: https://bitesizebio.com/13414/tissue-embedding-and-sectioning-something-to-think-about-whilst-in-the-bath/
4. How Histology Slides Are Prepared. Available at: https://bitesizebio.com/13398/how-histology-slides-are-prepared/