Monday 6 May 2024

Mastering the Art of Graphing: A Step-by-Step Guide

Drawing graphs is essential in educational and professional settings, as it helps communicate information clearly and efficiently. Whether you're a student, a scientist, or just looking to present data compellingly, knowing how to create an effective graph is invaluable. Here’s a guide to help you draw graphs that are not only informative but also visually appealing.

1. Utilise Your Graph Paper Fully

The first step in drawing a graph is to make the best use of the available space on your graph paper. Avoid cramming all data into one corner; instead, spread out your data across the graph. This approach helps in better visualisation and interpretation later on.

2. Tools of the Trade

Always use a sharp pencil to mark points and draw lines. This ensures precision in your work, making your graph more readable and professional.

3. Plotting Your Points

Begin by placing your data points on the graph. Be precise and ensure each point is placed correctly according to the values it represents. This accuracy is crucial for the reliability of your graph.

4. Deciding on the Line of Best Fit

Once your points are plotted, decide whether to connect the dots directly or to use a line of best fit. If you opt for a line of best fit, ensure it appropriately represents the trend in your data, with the points evenly distributed around the line.

5. Drawing Lines

Whether connecting points directly or drawing a line of best fit, use a ruler to keep your lines straight and neat. For curves, maintain a smooth, consistent shape.

6. Labelling is Key

Clearly label your axes and include units of measurement. This step is crucial as it provides context to your data, making the graph informative and easy to understand. Remember to label both the x-axis and y-axis accurately. Don't forget the units.

7. Title Your Graph

Always give your graph a descriptive title that captures the essence of the data it represents. A well-chosen title can effectively communicate the purpose of the graph at a glance.

8. Setting Up Axes

Select sensible ranges for your axes to avoid data clustering that can occur if the ranges are too narrow. Proper scaling enhances the graph's clarity and makes it easier to interpret the data.

9. Interpreting Data

For instance, plotting a standard curve for protein concentration against absorbance, start with known concentrations on the x-axis and absorbance on the y-axis. Adjust the axis range to ensure all points are visible and not squished at the bottom.

10. Calculating and Using the Gradient

Once your graph is complete if you need to calculate the gradient of a straight line, draw the largest possible triangle under the line and use the formula (rise/run). This gradient could represent a specific value of interest, such as an extinction coefficient in spectrophotometry.

11. Dealing with Multiple Data Sets

If your graph contains multiple data sets, differentiate each set using various styles of points and lines. This distinction makes it easier to compare and contrast the data sets visually.

12. Avoid Extrapolation

Never extrapolate your data beyond the measured range. Doing so can lead to inaccurate conclusions. For data points that exceed the range of your graph, note that these values are beyond measured limits.

Final Thoughts

Graphing doesn't have to be daunting. With the right tools and a careful approach, anyone can create clear, informative, and visually appealing graphs. Remember, a good graph tells a story that speaks with clarity and impact.

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.

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.

Friday 3 May 2024

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:

I then moved on to the all-important three Rs of DNA - replication (copy), repair and recombination:
Next, I asked the important question of how cells regulate the processes of transcription and translation:
I finished off the series by looking at some lab techniques we use to work with DNA:

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 say thanks for the fact sheet, then please feel free to Buy me a coffee

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. 

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.

DNA gel showing a DNA ladder and a band

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.

Agarose gel showing the DNA ladder and the band of unknown size, plus a table of data constructed from the gel for the grapg

From the table, you plot the calibration curve.

Calibration curve for determining the size of a band on a DNA gel

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. 

For a step-by-step guide to the process, please download the free guide.

Wednesday 1 May 2024

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 thank me for the video, please feel free to Buy me a coffee.

 

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 say thanks for the video, then please feel free to Buy me a coffee.

Tuesday 30 April 2024

New video posted: Gene Regulation - how do cells control the expression of genes?

I have just posted a video that looks at the complex processes of gene regulation and protein production within cells. In the video, I explore six key stages where cells regulate protein synthesis, ensuring precise protein production according to cellular needs. These stages include:

  1. Transcriptional Control: The initiation of RNA production and the involvement of transcription factors.
  2. RNA Processing: The conversion of pre-messenger RNA to mature mRNA, including splicing and editing.
  3. Transport and Localisation: The transportation of mRNA to the correct cellular locations for protein synthesis.
  4. Translational Control: Regulation of mRNA translation within the cellular environment.
  5. RNA Degradation: Mechanisms that determine the lifespan of mRNA molecules.
  6. Protein Regulation: Various methods cells use to control protein activity, such as chemical modifications and localisation.
If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Monday 29 April 2024

New video posted: Translation - making proteins from DNA - decoding mRNA to make the protein

This is the second of two videos on how cells make proteins using DNA. In the first video, I looked at the first step, which is making the messenger RNA (mRNA) a process called transcription - Transcription - making proteins from DNA - the mRNA.

In this video, I will guide you through the process of producing the protein from the mRNA, also known as translation. I will look at the coding problem (how many mRNA bases do you need to code from an amino acid), the number of reading frames in a DNA molecule, and how the cell produces protein from the mRNA.

If you would like to say thanks for the video, then please feel free to Buy me a coffee?

 

Friday 26 April 2024

New video posted: Transcription - making proteins from DNA - the mRNA

This is the first of two videos on how cells make proteins using DNA. The second video looks at how we go from messenger RNA (mRNA) to protein - Translation - making proteins from DNA - decoding mRNA to make the protein

In this video, I will guide you through the first steps in the process of producing RNA from DNA, also known as transcription. In the next video, we will take the next step and examine how we produce the protein from mRNA.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

The video looks at the five steps of mRNA production:

  • initiation — activators bind upstream, often thousands of bases upstream, of the gene. The activators assemble the required proteins (the mediator, chromatin remodelling complex, the RNA polymerase and transcription factors) at the TATA box, which is a DNA sequence close to the gene
  • production — DNA is transcribed into the pre-messenger RNA
  • five prime capping — the five prime end of the pre-messenger RNA is capped with some modified nucleotides
  • splicing — introns are spliced out of the pre-messenger RNA to leave just the exons (exons provide the sequence for the protein)
  • three prime polyadenylation — addition of a polyadenylated tail to the three prime end of the pre-messenger RNA to give the final mature messenger RNA molecule

The video not only looks at mRNA production but also introduces the idea of non-coding RNA (ncRNA), which are RNA molecules that do not encode proteins. ncRNAs are essential in regulating gene expression and various cellular processes. For example:

  • transfer RNA (tRNA) — involved in protein synthesis
  • ribosomal RNA (rRNA) — involved in protein synthesis
  • microRNA (miRNA) — control gene expression
  • small interfering RNA (siRNA) — control gene expression 
  • long non-coding RNA (lncRNA) — diverse functions
  • circular RNA (circRNA) — gene regulation
  • Piwi-interacting RNA (piRNA) — genome protection
  • enhancer RNAs (eRNAs) — modulate gene activity
Finally, I cover how to write out DNA sequences, the means of the terms sense and antisense strands, and what we mean by upstream and downstream when talking about DNA and RNA molecules.

Thursday 25 April 2024

New video posted: DNA Recombination and Holiday Junction: The Key to Genetic Variation

In this video, I explore DNA recombination, a process where DNA strands swap segments, usually between similar sequences on sister chromatids. This swapping creates brand-new genetic combinations. DNA recombination isn't just a biological curiosity; it's crucial for increasing genetic diversity and ensuring the stability of our genome.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Wednesday 24 April 2024

New video posted: DNA Repair - BER, direct, proofreading, HR, MMR, NHEJ and NER

DNA can be damaged in a number of ways (see How can DNA become damaged in the cell? for more information— and the damage must be corrected for the cell to function correctly. 

There are seven ways cells can repair damage to their DNA: 

  • Base Excision Repair (BER)
  • Direct repair
  • DNA proofreading
  • Homologous recombination repair (HR)
  • Mismatch Repair (MMR)
  • Non-homologous end joining (NHEJ)
  • Nucleotide Excision Repair (NER)
And in this video, I look at the seven methods.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Thursday 18 April 2024

New video posted: How can DNA become damaged in the cell?

In this video, I look at how DNA can become damaged in cells and introduce four ways damage can occur:

  • deletions
  • insertions
  • substitutions
  • transitions
  • and transversions.
I also look at exogenous and endogenous damage sources of the damage.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Wednesday 17 April 2024

New video posted: DNA replication: How does a cell make a copy of its DNA?

Have you ever been curious about the precision with which DNA is replicated in our cells, or why human pregnancies don't extend to an unimaginable sixteen years?

In my latest video, I examine the process of DNA replication. First, I explore how the DNA double helix is unwound by DNA helicase and how the unwound DNA is stabilised by Single Stranded Binding Proteins. I look at the replication fork and how DNA polymerases copy the DNA strands.

I also cover the formation of Okazaki fragments—short sequences of DNA synthesised on the lagging strand—and how DNA ligase is responsible for stitching these fragments together. Additionally, the video highlights the importance of topoisomerase in preventing the DNA from becoming overly twisted and tangled during replication.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Monday 15 April 2024

New video posted: DNA Packaging - how do we package DNA into the nucleus?

In the video, I examine how the long DNA molecule is packaged into the relatively small nucleus of a cell. I examine how DNA is broken up into chromosomes, how the DNA wraps around the histones to form nucleosomes and chromatosomes, and finally, chromatin.

Please use the form below to download a fact sheet for the video. The fact sheet contains twenty-four key facts from the video, a summary of the packing of DNA into the nucleus and the definitions of twenty-five key terms used in the video.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Thursday 11 April 2024

New video posted: How long is the DNA in a human cell?

In this video, I calculate the length of the DNA in one human cell and my answer may surprise you.

How long do you think? 0.2 mm, less? 2 mm, 2 cm, 2 m, 2 km? Watch the video to find out.

The video walks you through the math I used to calculate the length of DNA, and then I will reveal the length it would be if the cell were the size of a football.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Wednesday 10 April 2024

New video posted: Genetics and Mendel — DNA, genes, dominant and recessive traits

In this video, I examine Genetics and Mendel and discuss DNA, genes, and dominant and recessive traits.

The video introduces Gregor Mendel, an Austrian scientist and Augustinian friar known as the "father of modern genetics". I discuss his classic rounded and wrinkly pea experiments and describe how he came up with the idea of dominant and recessive traits.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

Monday 8 April 2024

New video posted: DNA and Genes

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?

In the video, we will look at the genetic material — DNA (deoxyribonucleic acid) — in cells and explore how many genes humans have and whether we, as complex organisms, have more genes than a tree, a potato or a tomato. What do you think?

If you would like to say thanks for the video, then please feel free to Buy me a coffee.

New video posted: What is a cell?

This is an interesting question... what is a cell? What makes a cell a cell? Why do we have cells?

In a recent video post on YouTube, I addressed this question and explored some of the different cell types that can be found in the human body.

If you would like to say thanks for the video, then please feel free to Buy me a coffee.


To find out more, watch the video and discover the remarkable range of sizes of cells in our bodies. 

Back to blogging

After a break of nearly 8 years on this blog, I am back to blogging.


Watch this space for new posts