A collection of blog posts connected to my teaching on biomedical sciences and biochemistry degrees. All views and opinions expressed are my own, and not connected to my past, present or future employers.
In this video, I use bagels to explain how some common misconceptions about the function and shape of organelles came about. I also explore, using images of horses, how we have not fully appreciated the dynamic structure of the cell and vesicle trafficking.
In this video, I continue to look at the cytoskeleton by examining the structure and function of the Intermediate Filaments.
Intermediate filaments are made of various proteins (lamins, vimentin, desmin, keratin, and neurofilaments), and their composition can change depending on the cell's state. The filaments provide mechanical strength, line the nuclear membrane, and can form higher-order structures with or without accessory proteins.
The book is a refresher for life, biomedical sciences and chemistry students who may be a little unsure of some of the key maths and chemistry skills they need and covers: Elements, atoms, ions, molecules, and compounds; Atomic weight, isotopes and molecular weight; Amounts, volumes, and concentrations; The SI units and the SI unit prefixes (m, µ, n, p etc.); Scientific Notation; Dealing with unit prefixes (m, µ, n, p etc.) in calculations; Order of operations (BODMAS and PEMDAS) in maths; How to get the best out of your calculator; Maths 'tricks' — Logs; and, graphs
Coming soon....
The big bumper book of Biomedical Sciences Terms and Definitions.
The book will contain the definitions of over 2,000 terms used in the biomedical and life sciences, along with commonly used abbreviations, molecular structures and links through to over 40 relevant videos that place the terms in context.
In the video, I take a quick look at microtubules, one of the essential filaments that form the cytoskeleton of cells. I explore their structure, function, and dynamic nature.
In this video, I look at actin filaments, an essential component of the cell's cytoskeleton.
I examine their structure, the process of filament formation, and their diverse functions in various cellular processes. I also discuss different types of actin filament structures, including contractile bundles (loose packing with myosin-II), gel-like networks (e.g., filamin), dendritic networks of branched actin molecules, and tight parallel bundles (e.g., fimbrin).
In this video, I introduce the cytoskeleton, a complex network of protein fibres and accessory proteins that provides essential support and strength to the cell. The cytoskeleton absorbs mechanical stress, controls cell shape and movement, enables muscle contraction, and aids in chromosome separation during mitosis and meiosis. Additionally, it helps the cell divide and provides trackways for moving molecules and vesicles.
In the video, I look at how cells receive information across their membranes and the three primary methods they use to sense external molecules and ions, from diffusion through the membrane to communication via gap junctions and interactions with specialised proteins called receptors.
The video covers various receptor types, including ion-channel linked receptors, G-protein-coupled receptors (GPCRs), and enzyme-linked receptors, explaining how each type facilitates the transmission of signals inside the cell.
This is one of four videos on membranes, the other two being:
In this video, I examine cellular transport and how proteins facilitate the crucial exchange of molecules, ions, and information across cell membranes. The video explains both passive and active transport mechanisms and highlights the specialised roles of carrier and channel proteins in these processes.
This is one of four videos on membranes, the other two being:
I introduce the eight ways proteins can interact with membranes: single and multiple membrane-spanning proteins, beta barrels, and proteins anchored by lipid chains or other proteins. ion transport, enzymatic reactions, and signal transduction. The video also covers the function of some protein domains (SH2 and SH3 domains, PH domains, and PTB domains) and some of the functions carried out by proteins in the membrane, such as the transport of ions, molecules and information.
This is one of four videos on membranes, the other two being:
Maths and Chemistry Refresher for Life and Biomedical Scientists
The book is a refresher for life, biomedical sciences and chemistry students who may be a little unsure of some of the key maths and chemistry skill they need and covers:
Elements, atoms, ions, molecules, and compounds
Atomic weight, isotopes and molecular weight
Amounts, volumes, and concentrations
The SI units and the SI unit prefixes (m, µ, n, p etc.)
Scientific Notation
Dealing with unit prefixes (m, µ, n, p etc.) in calculations
In the video, I discuss why meiosis is important, meiosis I and II, the key steps in Prophase I (Leptotene, Zygotene, Pachytene, Diplotene and Diakinesis), and the consequence when it goes wrong.
In this video, I examine cell growth (hypertrophy) and proliferation (hyperplasia), with the content mainly focused on hyperplasia and the cell cycle.
The cell cycle is a sophisticated series of events that cells undergo to duplicate themselves. It's divided into four main phases:
G1 Phase: The cell grows and synthesises proteins (cells may sit in G0 phase before entering G1).
S Phase: Chromosomes are duplicated.
G2 Phase: The cell prepares for mitosis.
M Phase: Mitosis occurs, and chromosomes are separated into daughter cells.
Most of a cell's life is spent in the interphase, which includes the G1 (G0), S, and G2 phases. This period is crucial for the cell as it performs its regular functions, replicates proteins, synthesises RNAs, and maintains organelles.
The cycle is regulated by the Mitosis-Promoting Factor (MPF), consisting of cyclin and cyclin-dependent kinase (Cdk). These proteins are essential for the progression of the cell cycle, particularly in phosphorylating specific amino acids on proteins that need to be activated or deactivated for the cycle to proceed.
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.
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:
Mesoderm: Forms muscles, bones, and cartilage.
Ectoderm: Develops into nerve tissue and the epidermis.
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.
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.
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?
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.
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.
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.
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.
