Foundational Skills in Life Sciences Dr. Synaptologica

We will experience the fascinating world of scientific troubleshooting. In this episode, we will revisit a life-science experiment where researchers aimed to see if a specific chemical compound could enhance a particular function in cultured cells. Their plan seemed straightforward - a pilot experiment with a positive control (active compound) and a negative control (inactive compound). They wanted to confirm everything worked as expected. But the results were strange! Both the positive and negative controls showed unexpectedly high cell function, leaving the researchers scratching their heads. Join us as we explore the initial troubleshooting steps. Help us by showing your idea: where in the protocol the problem could be hiding. Stay tuned for the next episode where we continue this exciting discussion.    

This is Part 13 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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There are many reasons why life-science experiments do not work well. Today, I will tell you a real story about an experiment. It is an experiment that did not go well. We will explore the problem that researchers encountered. In the following episodes), we will discuss how they identified the problem, and how they solved the problem. The story will help us understand the importance of negative controls, especially how to design them for the experiments, and how to use them for trouble-shooting problematic experiments.   

This is Part 12 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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Today's focus: negative controls. In life-science experiments, negative controls play critical roles. In my view, they are more important than the positive controls! They form such a rich topic that we will spend at least a few episodes on discussing them. Today, we introduce basic aspects: 1) what the negative controls do in life-science experiments, 2) our practical definition by modifying the typical and ideal one, 3) how the negative control was used in our milestone graph (Fig. 3D of milestone article 1 by the Laureates of the Nobel Prize in Physiology or Medicine 2023), and 4) two critical assumptions for negative controls to work properly.   

This is Part 11 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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I will list four sets of links mentioned in this episode. All are related to the Laureates, Dr. Katalin Karikó & Dr. Drew Weissman of the Nobel Prize in Physiology or Medicine 2023.

Milestone Article 1: Immunity, 2005
- DOI: https://doi.org/10.1016/j.immuni.2005.06.008   
- PDF: https://www.cell.com/immunity/pdf/S1074-7613(05)00211-6.pdf   
- PubMed: https://pubmed.ncbi.nlm.nih.gov/16111635/   

Milestone Article 2: Molecular Therapy, 2008
- DOI: https://doi.org/10.1038/mt.2008.200   
- PDF: https://www.cell.com/action/showPdf?pii=S1525-0016%2816%2932681-8   
- PubMed: https://pubmed.ncbi.nlm.nih.gov/18797453/   

Milestone Article 3: Nucleic Acids Research, 2010
- DOI: https://doi.org/10.1093/nar/gkq347   
- PDF: https://academic.oup.com/nar/article-pdf/38/17/5884/16767310/gkq347.pdf   
- PubMed: https://pubmed.ncbi.nlm.nih.gov/20457754/   

YouTube video of Nobel announcement
- Embedded in Nobel website: https://www.nobelprize.org/prizes/medicine/2023/prize-announcement/   
- Standalone with time stamp: https://www.youtube.com/watch?v=0JP-yDsLc3k&t=2m20s    

Enjoy and let's learn from them!

This is Part 10 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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Today's focus: the power of text elements in figures. We explore how category axis labels in bar graphs, when meticulously organized, reveal key experimental conditions at a glance. For a prime example, take Fig. 2B from our milestone article 1 by the Laureates of the Nobel Prize in Physiology or Medicine 2023. Here, the labels use two key strategies: 1) precise keywords accurately represent each condition, and 2) a three-layered structure visually communicates relationships between conditions. The next time you encounter a graph, take a moment to appreciate the labels and how they efficiently convey information.   

This is Part 9 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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Dive deep into Step 11 of reading the milestone article written by Nobel Laureates. We will examine the most important bar graph. We will read the labels and the legend, and combine our knowledge with the Nobel Committee video. We will use the information flexibly to understand the story the graph tells.   

This is Part 8 of the reading mini-series "Let’s read a paper written by Nobel Prize Laureates, 2023."    

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