New video posted: Embryonic Development: How the Frog Xenopus Sets the Stage for Life

In this video, I discuss embryonic development, a fascinating journey that can be studied in detail using the African clawed frog (Xenopus laevis) as a model organism. 

The frog oocyte (egg) is asymmetrical, with a pigmented upper half (animal pole) and a white lower half (vegetal pole), which contains most of the yolk. Development occurs outside the body of the frog and this makes it ideal for studying development.

The video covers fertilisation and the 30-degree rotation of the oocyte's cortex to form the "grey crescent" that determines the future dorsal side (back) of the embryo. This rotation begins the transformation into a three-dimensional body plan with three lines of asymmetry: left-right, anterior-posterior (top-bottom), and dorsal-ventral (back-front). 

The video also looks at the formation of the blastula, a hollow ball of about 4,000 cells. The subsequent gastrulation process establishes three germ layers:

1. Mesoderm: Forms muscles, bones, and cartilage.
2. Ectoderm: Develops into nerve tissue and the epidermis.
3. Endoderm: Creates the gut lining and related structures.

The localisation of key messenger RNAs like VegT and Wnt11 and the mapping studies which determined the fate of cells in the mature frog.

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Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

New video posted: An Introduction to Cell Differentiation and Embryonic Development

In this video, I look at how, after the haploid sperm fuses with the haploid oocyte to form a zygote, we go from one diploid cell to over 200 different cell types and 3 times 10 to the power of 13 (3 with 13 zeros after it) cells. That is a lot of cells and the process is called cellular differentiation.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

DNA - that's a wrap - 14 DNA revision videos

OK, so that is a wrap on DNA, a topic of immense significance in the world of biology and genetics.

Over the past few weeks, I have released fourteen revision videos on DNA, with accompanying posts on here and with information sheets accompanying each video (you can find a link to the information sheets in the links below).

In the videos, I have covered:

• DNA and Genes - I looked at how many genes does a human have? Do we have more genes than a plant? Do larger organisms, such as trees, have more genes than humans?
• Genetics and Mendel — DNA, genes, dominant and recessive traits - I introduced recessive and dominant genetic traits and Gregor Mendel, an Austrian scientist and Augustinian friar known as the "father of modern genetics"
• How long is the DNA in a human cell? - in this video, I had some fun with the structure of DNA and maths and showed how long the DNA is in one cell.
• DNA Packaging - how do we package DNA into the nucleus? - and in this video, I looked at how we can pack the surprisingly long DNA molecules we find in all cells, into the relatively small space of the nucleus.

I then moved on to the all-important three Rs of DNA - replication (copy), repair and recombination:

• DNA replication: How does a cell make a copy of its DNA?
• DNA repair: How can DNA become damaged in the cell?
• DNA repair: DNA Repair - BER, direct, proofreading, HR, MMR, NHEJ and NER
• DNA Recombination and Holiday Junction: The Key to Genetic Variation

After the three Rs, I looked at transcription and translation, the process of making protein from a DNA sequence:

• Transcription - making proteins from DNA - the mRNA
• Translation - making proteins from DNA - decoding mRNA to make the protein

Next, I asked the important question of how cells regulate the processes of transcription and translation:

• Gene Regulation - how do cells control the expression of genes?

I finished off the series by looking at some lab techniques we use to work with DNA:

• DNA Cloning - how do we clone DNA in the lab?
• DNA Cloning - how to overcome some common problems
• Understanding Nucleic Acid Hybridisation: Methods & Applications Explained

If you found these posts and videos useful, please consider following my YouTube Channel.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

New video posted: Understanding Nucleic Acid Hybridisation: Methods & Applications Explained

In this video, I look at Nucleic Acid Hybridisation and how it is the underlying principle for several lab techniques, such as PCR (Polymerase Chain Reaction), dot blots, colony blot hybridisation, chromosome in situ hybridisation (FISH), microarrays, Southern and Northern blotting, and CRISPR/Cas9 gene editing.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

A Comprehensive Guide on How to Calculate the Size of a DNA Band on a Gel

How do scientists determine the size of DNA bands on an agarose gel? In this guide, I will walk you through the step-by-step process of calculating the size in base pairs of a DNA band on an agarose gel. 

Blog Bonus: Free information sheet summarising the video and the steps - download.

 

Introduction

When working in a lab and running an agarose gel, you may need to determine the size of the DNA fragment, and this information may be crucial for various biological research applications. 

This approach is also described in the following video:

Setting Up the Experiment

Imagine you have loaded a DNA ladder with known sizes in one lane and your DNA sample with an unknown size in another lane of the gel and you get a result that looks like this when the gel has been run.

Before you can calculate the size of your DNA band, you must first label the gel and collect data to create a calibration curve.

Data Collection and Analysis

By measuring the distances the DNA bands in the ladder (see below) have moved and plotting the log values of their sizes against the distances travelled in millimetres (or you can do it in pixels), you can create a calibration curve. This curve will help you accurately determine the size of the DNA band in your unknown sample.

The image below shows the gel and the data table for the plot.

From the table, you plot the calibration curve.

Calculating the Size of the DNA Band

After plotting the calibration curve (above) and identifying the distance your unknown band has travelled, you can use the curve to determine the size of the DNA band in base pairs. By following a simple formula involving logarithms, you can convert the log value to the actual size in base pairs.

Conclusion

Calculating the size of a DNA band on an agarose gel requires careful data collection, analysis, and interpretation. By following the steps outlined in this guide, you can confidently determine the size of DNA fragments in your samples. 

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and the steps - download.

New video posted: DNA Cloning - how to overcome some common problems

In this video, I examine the step-by-step process of cloning DNA into plasmids and address common challenges faced in the lab. I start by preparing the DNA and then move on to using restriction enzymes like EcoRI and HindIII. I explain the importance of choosing the correct enzyme pairs to prevent self-ligation and ensure the correct orientation of the insert. I also cover the blue-white selection method to verify successful cloning and discuss using different vectors for larger DNA segments. 

     

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.

New video posted: DNA Cloning - how do we clone DNA in the lab?

In this video, I give a brief introduction to the subject of DNA cloning.

DNA cloning is an important lab skill that all life and biomedical science students should possess. In the video, I provide a summary of in vivo and in vitro cloning, along with the key steps, tools and methods you would use.

If you would like to support my blogging efforts, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free information sheet summarising the video and defining the key terms - download.