New Video: Genetically Engineering Pigs to Reduce Environmental Pollution

In this very short video - Genetically Engineering Pigs to Reduce Environmental Pollution - I look at how genetically engineering a pig has produced an animal that is less harmful to the environment.

The problem of phosphate pollution in the runoff from farms, particularly in pig farming, is a significant environmental concern. Animals' diets are often rich in grains, which contain phytic acid, a compound that pigs cannot digest due to the absence of a specific enzyme. The undigested phosphate-rich phytic acid is then excreted as waste, contributing to environmental issues like algal blooms and water contamination.

Phytic acid, found abundantly in grains, is a form of phosphorus that pigs—and many other animals—cannot utilise because they lack the phytase enzyme to break it down. Without this enzyme, the phosphorus passes through the pigs' digestive system and is excreted, leading to the concentration of phosphate in the environment.

To combat this issue, pigs have been engineered to contain the E. coli appA gene, which enables them to produce phytase, the enzyme needed to digest phytic acid. This modification allows the pigs to break down the phytic acid in their diet, effectively reducing the amount of phosphate in their waste.

What makes this solution particularly innovative is the way the gene is expressed. The E. coli appA gene is under a promoter from a mouse, which regulates the expression of proteins in the mouse salivary gland. This means that the pig only produces the phytase enzyme in its saliva. This targeted expression ensures that the enzyme is active exactly where it needs to be—in the pig's mouth. As the pig chews and swallows, the phytase is mixed with the grain, breaking down the phytic acid before it can pass through the digestive system.

This genetic modification significantly lowers the levels of phosphate pollution associated with pig farming by reducing the amount of undigested phytic acid excreted by pigs. 

New Video: How Plants Are Fighting Climate Change and Pollution?

 In this video - How Plants Are Fighting Climate Change and Pollution? - I look at how plants are being used to help fight climate change and polution.

Genetically engineered plants are being explored to combat climate change and environmental pollution. 

Slowing Climate Change with Carbon-Capturing Plants

One area of research focuses on using plants to slow climate change by enhancing their ability to capture and store carbon. Plants have been engineered to produce suberin, a cork-like substance that resists degradation and effectively traps carbon. These plants are also being developed to grow deeper root systems, ensuring that the suberin (and the carbon it contains) is buried deep within the soil, where it can remain sequestered for long periods.

This carbon sequestration will help reduce the amount of carbon dioxide in the atmosphere and slow global warming. 

Building Resilient Crops for a Changing Climate

As climate change continues to impact agricultural productivity, crops must be developed that can withstand extreme conditions such as heat, drought, disease, and high salinity. Researchers are working to make plants more resilient, ensuring that food supplies remain stable even as the environment becomes increasingly unpredictable.

By enhancing plants' natural defences, it is hoped that crops can be produced that can thrive in adverse conditions, reducing the risk of crop failures and food shortages.

Plants as Pollution Fighters

Plants are also being engineered to tackle pollution. 

A particularly interesting approach involves cloning the rabbit gene P4502E1 into Devil's Ivy, a popular houseplant. This gene encodes an enzyme that breaks down harmful chemicals, including potential carcinogens, into less toxic compounds. By introducing this gene into plants, researchers are creating a natural air purification system that can absorb and detoxify pollutants in urban environments and indoor spaces.

New Video: The genetically engineered mouse and COVID-19

 In this video - How Genetically Engineered Mice Help Us Study COVID-19 - I look at how a mouse that was genetically engineered for studying one virus, helped us understand COVID-19.

To develop effective treatments and vaccines for COVID-19, we needed to understand how the virus interacted with living organisms. For this, scientists typically use model organisms like mice. However, using mice for COVID-19 research presented a significant problem.

COVID-19, caused by a coronavirus, gains entry into human cells by binding to a specific receptor on the cell surface known as ACE2 (angiotensin-converting enzyme 2). However, the ACE2 receptor in mice differs from the human version, making it impossible for the virus to bind to mouse cells. This meant that mice could not be used to study the virus in a living organism to better understand how it works and to test potential treatments.

Fortunately, genetic engineering provided a solution. 

Back in 2007, during the outbreak of another coronavirus, SARS, scientists developed a line of genetically engineered mice that express the human version of the ACE2 receptor. These “humanised” mice could be infected with SARS-CoV-2, the virus responsible for COVID-19, making them an invaluable tool in the fight against the pandemic.

Using these genetically modified mice, researchers could study how COVID-19 interacted with cells, how it causes disease, and how different treatments might work in a living organism.

New Video: Gene Drives: A Powerful and Controversial Genetic Technology

In this video - Gene Drives: A Powerful and Controversial Genetic Technology - I look at gene drives. A genetic engineering technique that I find equally fascinating and scary.

Gene drives are a revolutionary and controversial advancement in genetic engineering. The process allows scientists to introduce self-propagating changes into an organism's genome, bypassing traditional Mendelian inheritance. By ensuring that specific mutations become homozygous in offspring, gene drives have the potential to rapidly spread these changes throughout populations.

The applications of gene drives are both promising and far-reaching. They could play a crucial role in eradicating mosquito-borne diseases such as malaria and Zika, which continue to claim millions of lives globally. Additionally, gene drives could help tackle drug-resistant fungal pathogens that pose a significant threat to human health and be employed to control or eliminate invasive species that disrupt ecosystems.

But how does this technology work? 

Gene drives use CRISPR, a gene-editing tool. In a gene drive, the CRISPR machinery is introduced along with the desired mutation. This machinery then actively copies itself onto the corresponding chromosome, ensuring the organism becomes homozygous for the mutation. This process allows the mutation to "drive" through the population, even if it does not provide a traditional selective advantage.

However, the power of gene drives comes with significant ethical concerns. The ability to alter ecosystems and species at such a fundamental level raises the question: Just because we can, should we? That is, once you introduce a change in a system using gene drive, how could you change or reverse it, or stop it spreading to other organisms?

CRISPR Case Studies: HIV resistant babies, cancer and blindness

In the video - CRISPR Case Studies: Ethical Dilemmas and Revolutionary Applications - I look at the illegal use of CRISPR on babies and its legal use to treat some conditions.

CRISPR has emerged as a powerful genetic engineering tool. However, it does come with the ethical implications.

CRISPR

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a gene-editing tool that allows scientists to alter DNA sequences within organisms. Using this technology, researchers can add, remove, or modify genetic material, leading to potential cures for genetic diseases, improved agricultural practices, and innovative solutions to environmental issues.

However, using CRISPR, especially in humans, raises significant ethical issues.

The CRISPR Babies

One of the most shocking uses of CRISPR on humans occurred when the genomes of human embryos were edited, leading to the birth of two genetically modified babies. The primary goal was to disable the CCR5 gene to produce babies that were HIV-resistant. That is, remove the receptor that HIV uses to enter human cells.

The CCR5 gene was selected because a naturally occurring mutation in this gene provides resistance to HIV and the Black Death in about 1% of Northern Europeans.

Researchers attempted to mimic this natural 32-base pair deletion using CRISPR, disrupting the CCR5 receptor's function and preventing HIV infection.

Outcomes and Concerns

The resulting edits did not replicate the exact natural mutation. One baby had a 15-base pair deletion in one copy of the gene, while the other had different insertions and deletions across both gene copies.

These unintended mutations raise serious health concerns as studies suggest that individuals with CCR5 mutations may have a 20% lower likelihood of reaching age 76 and could be more susceptible to other infections and diseases.

There is also the risk of off-target edits, where CRISPR inadvertently alters other parts of the genome, potentially leading to unforeseen health issues.

The scientific community widely condemned this work for its ethical breaches, lack of transparency, and disregard for established guidelines. The researchers involved faced legal consequences, including fines and imprisonment.

This case highlights the ethical dilemmas associated with germline editing:

• Consent: The edited changes are heritable, affecting future generations who cannot consent.
• Risk vs. Benefit: The potential health risks may outweigh the intended benefits, especially given existing alternatives to prevent HIV transmission.
• Regulatory Oversight: The need for strict guidelines and oversight in genetic editing research is evident to prevent misuse and ensure ethical compliance.

Promising and Legal Applications of CRISPR

CRISPR has the potential for legitimate and beneficial medical applications. Here are two examples:

1. Cancer Treatment

Treatment of testicular cancer resistant to conventional therapies.

Patient-derived T cells are collected and genetically modified using CRISPR to disrupt three specific genes that regulate T cell targeting. 

A lentivirus is then used to introduce a new targeting mechanism, directing the T cells to recognise and attack proteins unique to the patient's cancer cells.

The modified T cells are then reintroduced into the patient, aiming to boost the immune system's ability to fight cancer effectively.

This represents a personalised and targeted approach to cancer therapy and demonstrates CRISPR's potential to improve immunotherapy treatments.

2. Treating Childhood Blindness

CRISPR is also being used to address Leber Congenital Amaurosis 10 (LCA10), a cause of blindness in children.

The procedure targets the CEP290 gene, where specific mutations disrupt normal retinal development.

The CRISPR components are packaged into adeno-associated viruses (AAVs), and the system precisely removes the mutation in the CEP290 gene, aiming to restore proper protein function and improve vision.

Exploring Genetic Engineering: How It's Protecting Crops and Enhancing Food

In this video - Exploring Genetic Engineering: Protecting Crops and Enhancing Food - I look at three examples of how genetic engineering has been used to protect crops from insects and enhance the nutritional value of food.

1. BT Cotton: A Solution with Unintended Consequences

BT cotton is a prime example of how genetic engineering can provide a targeted solution to agricultural problems. This cotton variety has been engineered to produce a toxin derived from a specific type of bacteria. The toxin crystallises within the plant, and when an insect eats the leaves, the toxin dissolves the insect’s gut, eliminating the pest without the need for widespread insecticide use. This approach has the added benefit of protecting beneficial insects, as the crop itself becomes a selective defence mechanism.

However, this crop has had some unintended consequences. For example, in India, the high cost of BT cotton seeds has created a debt cycle for many farmers. Additionally, the market has seen a rise in counterfeit seeds, complicating the situation further. 

2. Venomous Cabbage: A Controversial Defense

I do like this one.... what made the researchers think of it?

The venomous cabbage - these cabbages have been modified to express scorpion venom in their leaves. The Diamondback moth larvae, notorious for damaging cabbage crops, eat the leaves of cabbages producing the venom and dying. Luckily, this venom is not toxic to humans, making the cabbage safe to eat.

Would you be comfortable eating such a cabbage?

3. Golden Rice: Tackling Vitamin A Deficiency

I was involved in a similar project - more about that in a later video.

Golden Rice represents a more human-centric approach to genetic engineering. This rice has been enriched with beta-carotene, a compound the human body can convert into vitamin A - making it a potent tool in the fight against vitamin A deficiency, which is prevalent in many parts of the world.

The rice owes its yellow colour to the addition of genes from daffodils and bacteria.

While Golden Rice has the potential to significantly improve public health, it also raises important questions. How do we feel about consuming a staple food that contains genes from other species? This case exemplifies the broader debate surrounding genetically modified organisms (GMOs) and their role in our food supply.

What are your thoughts on these genetically engineered crops? Would you eat them? Let me know in the comments or comment on the video.

The Cavendish Banana Crisis: How CRISPR Could Save Our FavoUrite Fruit

I like bananas — there, I have said it. They are one of my go-to fruits. But did you know they are in danger of being wiped out and no longer available?

In this video - How CRISPR Could Save Bananas from Extinction | The Cavendish Crisis Explained -  I look at why bananas are in trouble and how genetic engineering may come to the rescue.

About 99% of bananas we eat come from a single strain known as the Cavendish. Unfortunately, this strain faces a threat that could wipe it out.

The Cavendish Banana: A Monoculture at Risk

As popular as it is, the Cavendish banana has a significant vulnerability. It's sterile, meaning it can’t reproduce through seeds like many other plants. Instead, it’s propagated through cuttings. While this has allowed us to produce vast quantities of genetically identical bananas, it also means that if a disease affects one plant, it can quickly spread to all Cavendish bananas worldwide.

Fusarium wilt tropical race 4, or TR4, is a fungus threatening to wipe out the Cavendish banana. TR4 attacks the plant's roots, eventually killing it. Because the Cavendish is sterile, traditional breeding methods can’t be used to introduce resistance to this fungus, making the banana especially vulnerable.

Worryingly, this isn’t the first time a banana strain has faced extinction due to a fungal disease. Before the Cavendish, the Gros Michel banana was the world's favourite. However, attacked by a different strain of Fusarium wilt, leading to its near-total disappearance from the market. The Cavendish was introduced as a replacement, but now it’s facing a similar fate.

How Can We Save the Cavendish Banana?

Traditional breeding can't be used as the Cavendish is sterile. Hence, scientists are using genetic engineering to save the banana. One of the most promising approaches involves tweaking the banana’s genome to make it resistant to TR4. 

One explored method is inserting a resistance gene from wild bananas into the Cavendish. The wild bananas have naturally evolved to resist the fungus, and by transferring their genes, we could give the Cavendish the same level of resistance.

However, an even more interesting approach would be to use CRISPR to make precise changes to the banana’s DNA. In the case of the Cavendish banana, CRISPR could be used to activate a gene that has been silenced but could provide resistance to TR4. Additionally, CRISPR could deactivate genes that make the Cavendish susceptible to the fungus.

Why CRISPR is a Game-Changer

The advantage of using CRISPR is that it doesn’t involve inserting foreign DNA into the banana. This means the resulting banana wouldn’t be considered transgenic, which could ease regulatory hurdles and public concerns about genetically modified organisms (GMOs). 

New Video Posted: Introduction to Genetic Engineering: Ethics, Science, and Innovation

I have posted a video - Introduction to Genetic Engineering: Ethics, Science, and Innovation.

Genetic engineering often evokes strong emotions and heated debates. When people hear the term, they might immediately think of genetically modified organisms (GMOs), "Frankenstein foods," or the ethical dilemmas surrounding altering life at its most fundamental level. But what exactly is genetic engineering, and what are the implications of this technology?

In its simplest form, genetic engineering directly manipulates an organism's DNA to achieve desired traits. Humans have used genetic engineering through selective breeding to cultivate crops and livestock that yield better produce and more reliable outcomes for centuries. But today’s technology allows scientists to bypass traditional breeding processes and make precise changes to DNA in a laboratory setting. This raises a profound question: just because we can modify life in this way, should we?

In the video, I look at the ethical and scientific complexities of genetic engineering and wonder where society should draw the line. Is it acceptable to engineer a potato or a chicken for better production? What about a cow? How about a human? These questions are not just theoretical but have real-world implications as technology continues to advance.

I also discuss how genetic engineering can be further divided into two broad categories of genetic engineering: research and applications. Research involves using genetic engineering to understand biological systems and diseases, while applications focus on improving crops, livestock, and human health. The ethical dilemmas become particularly acute when considering human health. Should genetic modifications be limited to somatic cells (which don’t get passed on to offspring), or is it ethical to alter germ cells, thereby affecting future generations?

Finally, I wrap up the video by explaining the difference between transgenic and non-transgenic organisms. Transgenic organisms have DNA from a different species introduced into their genome, while non-transgenic organisms involve changes made to the organism’s own DNA. But this distinction leads to another intriguing question: Is DNA truly species-specific?

New Video Posted: Site-Directed Mutagenesis Explained | Understanding the Basics

In this video - Site-Directed Mutagenesis Explained | Understanding the Basics - I look at how you can mutate DNA in the lab.

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Site-directed mutagenesis is a powerful technique in molecular biology that can introduce specific mutations into a DNA sequence. The method has been instrumental in understanding how proteins function and how genes are regulated. 

The Process of Site-Directed Mutagenesis

Site-directed mutagenesis involves several key steps:

1. Preparation of DNA: The DNA sequence of interest is either cloned into a plasmid or selected from a plasmid library.
2. Designing the Primer: A primer is designed to bind specifically to the region of DNA where the mutation is desired. This primer is about 20 bases long, with one crucial difference—it contains the new base that will introduce the mutation. More information on Primer Design.
3. Creating a Single-Stranded DNA Template: The double-stranded plasmid DNA is converted into a single-stranded form. This single strand serves as the template for the primer to bind.
4. DNA Synthesis and Ligation: Once the primer is bound, DNA polymerase synthesises the complementary strand, incorporating the new base. DNA ligase is then added to seal the DNA strand, completing the synthesis.
5. Introduction into Bacteria: The newly mutated plasmid is introduced into bacteria, where the bacteria's natural DNA repair mechanisms take over. These mechanisms either repair the mismatched DNA back to its original form or incorporate the new mutation.

Applications of Site-Directed Mutagenesis

The ability to change a single base in a DNA sequence provides scientists with a powerful tool to explore how specific mutations affect protein function and gene expression. This technique has enabled numerous studies, allowing researchers to pinpoint individual amino acids' roles in proteins and dissect complex genetic regulatory networks.

From Site-Directed Mutagenesis to CRISPR

While site-directed mutagenesis has been a common lab technique for decades, the advent of CRISPR technology has revolutionised the field of genetic engineering. CRISPR offers a more efficient and precise method for making targeted genetic changes, but the foundational principles of mutagenesis laid the groundwork for these modern advances.

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New Video Posted: DNA Sequencing: Sanger Method and Beyond Explained

In the video DNA Sequencing: Sanger Method and Beyond Explained, I explain the Sanger method and look at some of the new approaches and methods that can speed up the DNA sequencing process.

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DNA sequencing allows scientists to decode the genetic information that dictates everything from the colour of our eyes to how our cells function. One of the most widely used laboratory methods for DNA sequencing is the Sanger method, also known as the chain-terminating dideoxynucleotide method.

The Basics of Sanger Sequencing

The Sanger sequencing process begins like a PCR (Polymerase Chain Reaction), with a template DNA that you want to sequence, a single primer (and not two primers as in PCR), DNA polymerase, and nucleotides (dNTPs). However, the method also includes special nucleotides called dideoxynucleotides (ddNTPs), which play a key role in the sequencing process.

In the sequencing method, the reaction goes through 25-30 cycles of denaturing, annealing and extension, just as you would in PCR. The DNA polymerase builds new DNA strands during the reaction and adds nucleotides to the growing chain. The twist comes with the ddNTPs; when one of these is incorporated, the chain is terminated, and no further nucleotides can be added. Each ddNTP is tagged with a different fluorescent marker corresponding to one of the four DNA bases (A, T, C, or G). This allows the sequence to be read by analysing the fluorescent tags after the reaction.

Once the reaction is completed, the next step is separation. The DNA fragments are separated using gel electrophoresis. As the fragments move through the gel, a laser scans the gel for the fluorescent tags, and the sequence of the DNA is determined by the fluorescence colour at each position.

While the Sanger method has been incredibly valuable, it has limitations. It can only read between 500 to 1000 bases per reaction, making it labour-intensive and unsuitable for large-scale projects.

Moving Beyond Sanger: Advanced Sequencing Methods

As the need for faster and more efficient sequencing has grown, new methods have been developed. One such method is shotgun sequencing, where the genome is broken into random segments. Each segment is sequenced individually using the Sanger method, and then the fragments are pieced together like a puzzle to reconstruct the full genome.

Another significant advancement was Next-Generation Sequencing (NGS), also known as massively parallel sequencing. NGS technologies have revolutionised genomics by allowing the simultaneous sequencing of many DNA molecules. This high-throughput approach can detect the sequence using either fluorescent nucleotides or pH changes.

Finally, we have Third-Generation Sequencing methods, which include techniques like nanopore sequencing. In nanopore sequencing, DNA is passed through a nanopore, and the sequence can be determined by detecting changes in electrical current.

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New Video Posted: DNA Libraries: Genomic vs. cDNA - Key Differences and Applications

 I have posted a video on the key differences between genomic DNA (gDNA) and complementary DNA (cDNA) libraries - DNA Libraries: Genomic vs. cDNA - Key Differences and Applications.

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

DNA libraries are essential tools for researchers to study and manipulate genetic material. If you're working in a lab, you'll likely encounter two main types of DNA libraries: genomic DNA (gDNA) libraries and complementary DNA (cDNA) libraries. Though both serve important roles in research, they are fundamentally different in their composition, creation, and applications. 

What Are DNA Libraries?

A DNA library is a collection of DNA sequences cloned into vectors, small pieces of DNA that can carry foreign DNA into a host cell, such as bacteria. These libraries allow scientists to store, access, and manipulate specific DNA sequences for various research purposes.

Genomic DNA (gDNA) Libraries

A genomic DNA library is created from the complete genomic DNA of an organism. This means it contains all the genetic material necessary to build that organism. In eukaryotes, this includes both the coding regions (exons) and the non-coding regions (introns) of genes. 

How is a gDNA Library Made?

1. DNA Extraction: Genomic DNA is extracted from cells.
2. DNA Fragmentation: The extracted DNA is cut into smaller fragments using restriction enzymes.
3. Cloning: These fragments are then cloned into plasmids, which are circular DNA molecules.
4. Transformation: The plasmids are inserted into bacteria, which replicate the DNA fragments, creating a library.

When to Use a gDNA Library?

gDNA libraries are ideal when studying the full structure of genes, including regulatory elements, or when exploring gene functions across the genome.

However, there are some limitations. Because a gDNA library contains both introns and exons, it can complicate the task of isolating and studying the sequences that actually code for proteins. Additionally, genes in a gDNA library may be fragmented across multiple clones, making it challenging to reconstruct the complete gene sequence through sequence alignment.

Complementary DNA (cDNA) Libraries

cDNA libraries are derived from messenger RNA (mRNA) in a cell. This means that a cDNA library only contains the sequences actively expressed as proteins when the library is made. Therefore, the content of a cDNA library depends on the type of cell, the time of day, and the cell's conditions.

How is a cDNA Library Made?

1. mRNA Isolation: Cells are lysed, and the mRNA is purified from the lysate using affinity chromatography, which often involves oligo-dT beads that bind to the poly-A tails of mRNA molecules.
2. Reverse Transcription: Using reverse transcriptase, the mRNA is used as a template to synthesise complementary DNA (cDNA). This gives a mRNA/DNA molecule.
3. RNA Removal: The original mRNA is removed from the mRNA/DNA molecule using an enzyme (RNase H). The now single-stranded cDNA is converted into a double-stranded DNA molecule using DNA polymerase.
4. Cloning: The cDNA is cloned into plasmids and inserted into bacteria.

Isolating mRNA can be tricky because it is easily degraded by enzymes released during cell lysis or by RNases in the environment. Moreover, because cDNA libraries only reflect the genes being expressed at a specific time, they may not provide a complete picture of an organism's genome.

When to Use a cDNA Library?

cDNA libraries are particularly useful for studying gene expression, identifying specific mRNA sequences, and producing recombinant proteins.

Choosing the Right Library

It is essential to understand the distinctions between gDNA and cDNA libraries. A gDNA library is the right choice if the goal is to study the entire genome or understand gene regulation. However, a cDNA library must be used if you're interested in the proteins a cell produces or need to work with specific mRNA sequences.

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New Video Posted: PCR Primer Design: Tips for Accurate DNA Amplification

I have posted a video on PCR primer design - PCR Primer Design: Tips for Accurate DNA Amplification.

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

Polymerase Chain Reaction (PCR) is an important lab technique that allows scientists to amplify specific DNA sequences. However, the success of a PCR largely depends on correctly designing the PCR primers. 

Why Primer Design Matters

The importance of primer design in PCR cannot be overstated. If your primers are poorly designed, the DNA amplified during the reaction might not be the correct region of DNA, or you will get a low product yield. To avoid such issues, you must carefully consider three primary factors when designing primers: 

1. Melting temperature (Tm)
2. Disruptive secondary structures
3. Specificity of the primers

1. Melting and Annealing Temperatures

Two crucial temperatures play a role in PCR primer design:

1. the melting temperature (Tm)
2. the annealing temperature

The Tm is the temperature at which 50% of the primer would dissociate from a double-stranded to a single-stranded form. The primers bind to the denatured DNA template during each PCR cycle at the annealing temperature. Typically, the ideal Tm is 55-65 °C, and the annealing temperature is set 3-5 °C below the Tm to ensure optimal primer binding.

In the lab, you would use a computer program to determine the Tm of a primer. The program usually uses the nearest neighbour method to calculate the Tm accurately. This method considers the specific sequence of bases and the concentrations of components in the reaction.

2. Disruptive secondary structures

It is essential to ensure your primers won’t form problematic secondary structures like hairpin loops or primer-dimer pairs. Hairpin loops occur when a primer folds back on itself, creating a loop that can be difficult to melt during the PCR process, leading to inefficient amplification. Primer-dimer pairs form when two primers bind to each other instead of the target DNA. This can result in an inefficient reaction and the production of the wrong DNA.

In the lab, you would use a computer program to test for hairpin loop formation and primer-dimer pairs.

3. Specificity of the primers

A standard PCR primer is usually 20 to 30 bases long and has an ideal Tm of around 55-65 °C. The Tm and the length of the primer help ensure specificity. 

Finally, it is advisable to perform a BLAST search with your primer sequences, which can help confirm that they do not have unintended matches with other sequences in the species. If the DNA species is not human, a BLAST search against a human database should be performed to check for the possibility of a result if the reaction is contaminated with human DNA.

Advanced Techniques: Overcoming Challenges in PCR

In some cases, even with well-designed primers, you might need help getting the correct DNA to amplify, especially when dealing with low amounts of template DNA or needing to add restriction sites to your product. To address this, you can use a nested primer approach. This involves using two sets of primers, one set falling inside the other, to improve specificity and yield through a two-round PCR process.

For adding restriction sites, primers are designed with the desired restriction site sequences at the 5’ end. However, this introduces a mismatch between the primer and the template DNA. To compensate, the initial PCR cycles are performed at a lower annealing temperature to help the primers bind more effectively. Once the restriction site is incorporated into the amplified DNA, the annealing temperature is raised to the standard level for subsequent cycles. A GC clamp at the 3’ end of the primer, where the last two bases are guanine (G) or cytosine (C), can also help improve binding due to the stronger hydrogen bonds these bases form.

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New Video Posted: Bacterial Transformation: Natural vs. Artificial Methods Explained

In this video - Bacterial Transformation: Natural vs. Artificial Methods Explained - I look at how bacteria can take up DNA from the environment and how we can get bacteria to take up DNA in the lab.

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

Bacterial transformation is where bacteria take up external DNA, which can lead to genetic changes within the cell. This process can occur naturally or be induced artificially in a laboratory setting. 

Natural Transformation

In natural transformation, bacteria acquire DNA from their surroundings, typically from nearby bacteria that have lysed (broken apart). The free-floating DNA can then be integrated into the bacterial chromosome or replace an existing gene, leading to potential new traits or functions. This ability to naturally take up DNA is a trait of "competent" cells, which possess specific genes that encode the machinery necessary for DNA uptake.

Artificial Transformation 

In a lab, we can induce transformation using artificial methods. Unlike natural transformation, this process requires deliberate manipulation of the bacteria to make them more likely to accept new DNA. First, the bacteria must be made competent so they can take up the DNA. Techniques such as heat shock, electroporation, or polycations are then used to encourage bacteria to take up the DNA. Each method works differently but ultimately serves the same purpose: introducing new genetic material into bacterial cells, enabling researchers to study gene function, produce recombinant proteins, or create genetically modified organisms.

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New Video Posted: How Bacteriophages Transfer DNA Between Bacteria

In this video - Understanding Transduction: How Bacteriophages Transfer DNA Between Bacteria - I look at the process of DNA exchange, transdcution, between bacteria by bacteriophages.

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Transduction is driven by bacteriophages, which are viruses that specifically target and infect bacterial cells. In the video, I explain the mechanics of transduction and look at how bacteriophages can inadvertently transfer DNA from one bacterium to another.

Bacteriophages operate through two distinct life cycles: the lytic and lysogenic cycles. During the lytic cycle, the bacteriophage attaches to a bacterial cell, injects its DNA, and takes over the bacterium to produce new viruses. This ultimately leads to the bursting (lysis) of the bacterial cell, releasing the newly formed phages to continue the infection cycle. In the lysogenic cycle, the bacteriophage DNA is integrated into the bacterial chromosome, where it can lie dormant until conditions favour a return to the lytic cycle.

Some bacteriophages, such as the P22 phage, can mistakenly package bacterial DNA instead of their own during the assembly of new viruses. When these phages go on to infect other bacteria, they transfer the captured bacterial DNA, effectively driving genetic exchange between bacteria. This mechanism contributes to bacterial evolution in the wild and serves as a valuable tool in the lab for gene mapping and studying bacterial genetics.

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New Video Posted: Gene Mapping in Bacteria Using Conjugation and Interrupted Mating

Gene mapping in bacteria is a process that has helped scientists understand the order and location of genes on a bacterial chromosome. 

In this post, I will look at a method of gene mapping using bacterial conjugation, specifically focusing on a technique known as interrupted mating. Although this technique is historical and has been largely replaced by genome sequencing, it remains an important method that sheds light on genetic exchange in bacteria.

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

 

The Role of Hfr Cells in Gene Mapping

The process of using conjugation to map genes in bacteria was developed using a specific type of bacteria discovered in the 1950s, known as Hfr (High Frequency of Recombination) cells. These cells are particularly efficient at transferring genes during conjugation, a process where DNA is exchanged between two bacterial cells.

In Hfr cells, the F (fertility) factor, which is normally an independent plasmid, gets incorporated into the bacterial chromosome. This integration means that during conjugation, the F factor and parts of the bacterial chromosome can be transferred to a recipient cell.

Two outcomes can occur during this process:

1. F' Factors: If the F factor is excised from the chromosome, it may carry with it some bacterial genes, forming what is known as F' factors.
2. Chromosome Transfer: Alternatively, the entire bacterial chromosome, including the F factor, can be transferred to the recipient cell.

The Concept of Interrupted Mating

Interrupted mating is a technique that was used for gene mapping. To understand how it works, let’s consider an example involving two bacterial strains:

• Donor Bacteria (Hfr positive): This strain has the genes to produce amino acids leucine and threonine but is sensitive to the antibiotic ampicillin.
• Recipient Bacteria (Hfr negative): This strain lacks the genes for leucine and threonine production but is resistant to ampicillin.

In this experiment, the donor and recipient bacteria are mixed and allowed to conjugate. The goal is to map the location of the genes that produce leucine and threonine on the donor’s chromosome. Here’s how the process unfolds:

1. Conjugation Begins: The bacteria are mixed, and DNA transfer begins from the Hfr donor to the recipient.
2. Interrupted Mating: At specific time intervals, the mating process is interrupted, effectively stopping the transfer of DNA.
3. Plating on Selective Media: After interrupting the mating, the bacteria are plated on media that either lacks leucine or threonine and contains ampicillin. The donor bacteria, which are sensitive to ampicillin, will die. The recipient bacteria will only grow if they have received and integrated the necessary genes from the donor to produce the missing amino acids.
4. Mapping Gene Order: By examining which plates show bacterial growth at different time points, scientists can determine the order in which the genes were transferred. For instance, if bacteria start growing on the leucine-lacking plate before the threonine-lacking plate, it indicates that the leucine gene is closer to the origin of transfer than the threonine gene.

Applications and Limitations of the Technique

This method of mapping was useful because it allows scientists to estimate the relative positions of genes on a bacterial chromosome. For example, using this technique, researchers were able to map the E. coli K12 genetic map into a timeline of 100 minutes, representing the time required for the full chromosome to transfer at 37 °C.

However, the technique has limitations:

• It is mostly applicable to E. coli and closely related bacteria.
• Mapping the entire chromosome is rare and works best for genes that are close to each other.
• The F plasmids involved are large, of low copy number, and may not be ideal for genetic manipulation.

Despite these limitations, the interrupted mating technique provides valuable insights into genetic exchange mechanisms in bacteria. While modern approaches like genome sequencing have largely replaced it, understanding this historical method helps us appreciate the exchange of DNA between bacteria.

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New Video Posted: Genetic Exchange in Bacteria: Conjugation, Transduction, and Transformation

In this video, I look at the three methods bacteria use to share genetic information: Conjugation, Transduction, and Transformation.

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

Bacteria typically increase their numbers through a process akin to cloning; that is, they make exact copies of themselves. While this method is efficient, it presents a significant evolutionary limitation: genetic diversity can only arise through random mutations. In the absence of a mechanism for exchanging genes, bacteria would be stuck in a genetic standstill, unable to benefit from the rapid spread of advantageous traits. Bacteria solve this problem by horizontal gene transfer (HGT), which is also called lateral gene transfer (LGT).

To help the spread of advantageous genes in a bacteria population, the bacteria use three methods to exchange DNA:

1. Conjugation: This process involves direct physical contact between two bacteria through a structure called a sex pilus. A donor bacterium with an F plasmid (F+) forms a bridge to a recipient bacterium (F-), transferring a copy of its DNA. This method not only promotes genetic diversity but also allows for the rapid spread of advantageous traits such as antibiotic resistance.
2. Transduction: In this method, bacteriophages (viruses that infect bacteria) play a crucial role. When a virus infects a bacterium, it sometimes incorporates fragments of the host's DNA into its own genetic material. As the virus infects new bacterial cells, it transfers these DNA fragments, facilitating genetic exchange.
3. Transformation: This process occurs when bacteria take up free-floating DNA from their environment, often released by dead bacterial cells. The acquired DNA is then incorporated into the recipient's genome, providing new genetic traits that can be beneficial for survival and adaptation.

In the video, I examine the three methods.

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New Video Posted: Understanding Mendelian Genetics: Dominance, Codominance, and Incomplete Dominance

In this video, I explain some of the key terms in Mendelian genetics:

• dominant
• recessive
• codominance
• incomplete (partial) dominance

 

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

 

Introduction to Mendelian Genetics

Mendelian genetics is named after Gregor Mendel, who studied inheritance patterns in pea plants and published his findings in 1866. His experiments with pea plants, including traits like seed shape and flower colour, laid the foundation for understanding how traits are inherited. By cross-breeding plants with different traits, Mendel observed how traits reappear in subsequent generations, leading to the formulation of key genetic principles.

Dominant and Recessive Traits

Mendel discovered that certain traits, like round seeds, are dominant, while others, like wrinkled seeds, are recessive. Through cross-breeding experiments, he noted that in the first generation (F1) of true-bred plants that produced round or wrinkled seeds, the offspring all exhibited the dominant trait. However, when these F1 plants were self-pollinated, the second generation (F2) showed a 3:1 ratio of dominant to recessive traits (see Figure 1).

Using modern terminology, this can be explained with uppercase and lowercase letters representing dominant and recessive alleles, respectively. For instance, the round seed trait is represented by "R" and the wrinkled seed by "r." The F1 generation consists of heterozygous plants (Rr), which exhibit the dominant trait. The F2 generation reveals a combination of homozygous dominant (RR), heterozygous (Rr), and homozygous recessive (rr) plants, demonstrating Mendel's observed ratios (see Figure 1).

Figure 1: Crossing round and wrinkled pea plants

Codominance and Incomplete Dominance

Moving beyond simple dominance, we come to codominance and incomplete (partial) dominance.

In codominance, neither allele masks the other; both traits are fully expressed (see Figure 2). For example, in a hypothetical scenario with cows, crossing a blue cow (BB) and a yellow cow (bb) would result in offspring with both blue and yellow spots (Bb).

Figure 2: Codominance

In incomplete dominance (sometimes called partial dominance), the traits blend rather than mask one another (see Figure 3). Using the same example of cows, crossing a blue cow and a yellow cow would produce green offspring (Bb), illustrating a blend of the two parent traits.

Figure 3: Incomplete Dominance - also called partial dominance

Key Takeaways

1. Dominant and Recessive Traits: Dominant alleles mask recessive ones in heterozygous pairings.
2. Codominance: Both alleles are fully expressed in the phenotype.
3. Incomplete (Partial) Dominance: The traits blend, creating an intermediate phenotype.

Additional Resources

For further assistance, a Bioscience Glossary with over 2000 terms, chemical structures, and supporting videos is available. This glossary can help clarify additional terms and concepts in biosciences.

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New Video Posted: How to Calculate the Gradient (m) and Intercept (c) in y = mx + c | Gel Analysis Tutorial

This video is in response to a question I have received on YouTube:

“Thanks it is very helpful but can you present how to calculate slope and intercept in this curve”

The question often gets asked about two of my other videos:

• How to calculate the size of a DNA band on a gel?
• How to Determine Protein Size on an SDS-PAGE Gel | Step-by-Step Tutorial

In the How to Calculate the Gradient (m) and Intercept (c) in y = mx + c | Gel Analysis Tutorial, I explain how to calculate the gradient (m) and intercept (c) in the linear equation y = mx + c. I explain three methods that can be used:

1. Graph-based calculation
2. Solving simultaneous equations
3. Using Excel or Apple Numbers.

In the video, I use DNA gel data to illustrate these calculations.

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New Video Posted: Understanding Mitochondrial DNA: Structure, Function, and Disease

In this video - Understanding Mitochondrial DNA: Structure, Function, and Disease - I look at the mitochondria's circular DNA that contains 37 genes. I discuss how mitochondrial DNA (mtDNA) differs from nuclear DNA and can exhibit either homoplasmy or heteroplasmy. I then discuss how mitochondrial DNA is maternally inherited and not synchronised with cell division, leading to unique genetic traits and potential mitochondrial diseases that predominantly affect high-energy tissues. I wrap up by introducing the idea of how mitochondrial diseases can be treated using "three-parent babies" by replacing the nucleus of a donor egg with one from a mother with mitochondrial disease, effectively substituting the mutated mitochondria.

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New Video Posted: Understanding the Function of Mitochondria | Dr. Peter Mitchell's Nobel Prize-Winning Work

 In this video - Understanding the Function of Mitochondria | Dr. Peter Mitchell's Nobel Prize-Winning Work - I discuss the function of mitochondria, highlighting Dr. Peter Mitchell's Nobel Prize-winning chemiosmotic theory, which explains how mitochondria generate ATP using an electrochemical gradient across their inner membrane.  

I finish up by highlighting that while the mitochondria can give the cell the energy it needs for life, they also play a role in cell death by releasing factors that trigger apoptosis.

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New Video Posted: How to Determine Protein Size on an SDS-PAGE Gel | Step-by-Step Tutorial

retention factorThis video - How to Determine Protein Size on an SDS-PAGE Gel | Step-by-Step Tutorial - is in response to questions I have had about a video in which I show how to calculate the size in base pairs of bands on a DNA gel.

In the video, I explain how to determine the molecular weight (kilodaltons; kDa) of a protein on an SDS-PAGE gel. The method involves constructing a table with the known molecular weights of protein markers, calculating their logarithmic values, measuring the distance each band travels and determining their retention factor (Rf) values.

I then show how to plot the graph and determine the size in kilodaltons (kDa) for the protein under investigation.

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New Video Posted: The History, Structure and Functions of Mitochondria

This video - The History, Structure and Functions of Mitochondria is the first of three on the mitochondria. The other two videos are:

• The History, Structure and Functions of Mitochondria
• Understanding the Function of Mitochondria | Dr. Peter Mitchell's Nobel Prize-Winning Work
• Understanding Mitochondrial DNA: Structure, Function, and Disease

In the video, I examine the history and functions of mitochondria. I start with Rudolf Albert von Kölliker's initial description in 1852 and subsequent naming by Carl Benda in 1898. I explain how these organelles are more than just static power plants of the cell. I highlight the dynamic nature of mitochondria, their ability to form networks, and their crucial roles in energy production and cellular metabolism.

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New Video Posted: Exploring Nuclear Organisation: Chromatin, Chromosomes, and the Nucleolus

This video - Exploring Nuclear Organisation: Chromatin, Chromosomes, and the Nucleolus - is the final video in a series of four videos on the nucleus.

The other three are:

• Understanding the Nucleus: Structure and Function | Cell Biology Explained 
• Understanding the Nuclear Envelope: Protecting and Regulating the Nucleus
• Understanding the Nuclear Pore: Gatekeeper of the Nucleus

In this video, I explore the organisation within the nucleus, emphasising that it is structured rather than chaotic. I explain how Spectral Karyotyping reveals that chromosomes occupy specific territories and highlights the structured nature of chromatin, which can be either open or closed and influences transcription and replication. I also examine the nucleolus, describing its crucial role in producing ribosomes and signal recognition particles (SRP) and outlining the complex processes of ribosomal RNA (rRNA) synthesis and assembly.

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New Video Posted: Understanding the Nuclear Pore: Gatekeeper of the Nucleus

This video - Understanding the Nuclear Pore: Gatekeeper of the Nucleus - is the third in four videos on the nucleus.

The other three are:

• Understanding the Nucleus: Structure and Function | Cell Biology Explained 
• Understanding the Nuclear Envelope: Protecting and Regulating the Nucleus
• Exploring Nuclear Organisation: Chromatin, Chromosomes, and the Nucleolus

In the video, I explore the structure and function of the nuclear envelope and its critical role in maintaining the environment of the nucleus. I explain how the nuclear pore facilitates gated transport, allowing materials to move between the nucleus and the cytosol. Highlighting its complexity, I described how the nuclear pore is composed of numerous nucleoporins, forming a cylindrical channel that selectively regulates the passage of molecules based on their size, with larger molecules requiring active transport mechanisms.

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New Video Posted: Understanding the Nuclear Envelope: Protecting and Regulating the Nucleus

This video - Understanding the Nuclear Envelope: Protecting and Regulating the Nucleus - is the second of four videos on the nucleus.

The other three are:

• Understanding the Nucleus: Structure and Function | Cell Biology Explained 
• Understanding the Nuclear Pore: Gatekeeper of the Nucleus
• Exploring Nuclear Organisation: Chromatin, Chromosomes, and the Nucleolus

The video explains that the nuclear envelope, consisting of inner and outer membranes, protects DNA from mechanical stress and regulates the nucleus's internal environment, essential for proper mRNA processing. I highlight the role of the nuclear lamina in safeguarding DNA. I describe the challenges posed by the nuclear envelope, such as the need to disassemble during cell division and manage material exchange via nuclear pores. Overall, the nuclear envelope is crucial for maintaining nuclear integrity and function despite its associated complexities.

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New Video Posted: Understanding the Nucleus: Structure and Function | Cell Biology Explained

This video - Understanding the Nucleus: Structure and Function | Cell Biology Explained - is the first of four videos on the nucleus. The other three are:

• Understanding the Nuclear Envelope: Protecting and Regulating the Nucleus
• Understanding the Nuclear Pore: Gatekeeper of the Nucleus
• Exploring Nuclear Organisation: Chromatin, Chromosomes, and the Nucleolus

The video explains the cell nucleus, highlighting its roughly spherical shape and double membrane structure, which includes an inner and outer membrane with a perinuclear space. It describes the nucleus's contents, such as chromatin for gene transcription and mRNA splicing, and features like nuclear pores for transport and the nuclear lamina for structural support and various cellular functions. Additionally, I note that the outer nuclear membrane and perinuclear space are continuous with the endoplasmic reticulum.

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New Video Posted: Understanding Endosomes: The Cell's Sorting House | Quick Science Explanation

In my video on endosomes - Understanding Endosomes: The Cell's Sorting House | Quick Science Explanation - I look at the role of the endosomal system in cells.

Endosomes are cellular compartments that sort and traffic proteins from the Golgi apparatus and the plasma membrane. They are formed by vesicle fusion and are divided into three types

• Early endosomes - receive proteins and decide their next destination
• Recycling endosomes - return proteins to the plasma membrane either immediately (constitutive pathway) or based on signals (regulated pathway).
• Late endosomes - forward proteins to lysosomes or back to the Golgi.

The endosomal system relies on specific signals on proteins to direct their correct routing, ensuring efficient cellular function.

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New Video Posted: How to Calculate Protein Size on an SDS-PAGE Gel: A Step-by-Step Guide

I have just posted a video on how to determine the size of a protein on an SDS PAGE gel - How to Determine Protein Size on an SDS-PAGE Gel | Step-by-Step Tutorial.

Blog Bonus: Free step-by-step guide explaining the calculation - download.

The video is a response to two questions I was asked:

1. How do I calculate the size of a protein on an SDS-PAGE gel?
2. Can the DNA method be used for proteins?

In the video and the free step-by-step guide explaining the calculation, I go over the necessary steps for working out the size of a protein band on a gel, explain the Retention Factor (Rf value) and how to use it, and outline the method's limitations.

Feel free to leave any questions or comments below. If you need further clarification on any step or have suggestions for future topics, let me know!

If you would like to say thanks for the video, then please feel free to buy me a coffee at https://www.buymeacoffee.com/drnickm

Blog Bonus: Free step-by-step guide explaining the calculation - download.

New Video Posted: The Golgi Apparatus and Protein Processing

In the video - The Golgi Apparatus and Protein Processing - I look at the role of the Golgi in processing proteins.

The Golgi apparatus (possibly my favourite organelle) was discovered by Camillo Golgi in 1898 and confirmed in the 1950s.

Structurally, the Golgi resembles a stack of plates, and it has three distinct regions: the cis face (closest to the ER), the medial Golgi, and the trans face (furthest from the ER). The primary function of the Golgi is to process and sort proteins received from the ER, directing them to lysosomes, endosomes, or the plasma membrane.

There are two main theories for how the Golgi operates:

• Vesicle Transport Model - proteins move to the machinery.
• Cisternal Maturation Model - machinery moves to the proteins.

Evidence, such as vesicular tubular clusters and vesicles' size constraints, supports the Cisternal Maturation Model. In this model, the Golgi's cisternae mature over time, recycling enzymes via COPI vesicles.

Upon leaving the Golgi, proteins can enter one of two pathways:

• Constitutive secretory pathway - direct to the cell surface)
• Regulated secretory pathway - via secretory vesicles and requires a signal for the vesicles to traffic further.

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New Video Posted: Understanding the Endoplasmic Reticulum: Rough vs Smooth ER and Protein Import

In the video Understanding the Endoplasmic Reticulum: Rough vs Smooth ER and Protein Import, I look at the smooth and rough Endoplasmic Reticulum (ER), and discuss how proteins are targeted to and imported into the ER.

The ER is a vital cellular structure with two types: rough ER (RER) and smooth ER (SER). The RER is covered in ribosomes and is essential for protein production. Proteins are synthesised and threaded into the ER lumen via a process involving signal recognition particles (SRP) and the Sec61 complex. 

Membrane-spanning proteins are produced at the RER by using various signal sequences that direct their insertion into or through the membrane. The ER also plays a role in N-linked glycosylation, adding N-linked oligosaccharides to proteins and in quality control, ensuring proteins are correctly folded and functional. 

In contrast, the SER lacks ribosomes, synthesises lipids, and forms vesicles for transporting proteins and lipids to the Golgi apparatus.

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New Video Posted: Exploring the Endoplasmic Reticulum: Functions, Vesicle Trafficking, and Quality Control

In the video Exploring the Endoplasmic Reticulum: Functions, Vesicle Trafficking, and Quality Control, I look at the important role played in the cell by the Endoplasmic Reticulum (ER).

The endoplasmic reticulum (ER) is involved in a number of key processes in the cell connected with protein production, including:

• Disulphide Bond Formation: Occurs as proteins are imported into the ER, crucial for protein stability and function.
• Protein Glycosylation: Starts in the ER and finishes in the Golgi, important for protein folding and interactions.
• Quality Control: Marks incorrectly folded proteins for destruction, though it may sometimes incorrectly target properly folded proteins.

The newly made proteins are trafficked from the ER to the Golgi in COPII Vesicles. 

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The Biosciences Glossary

When I was a student, one of my go-to books was a glossary of terms for bioscientists. I used the glossary when I was learning new material to look up things I didn’t understand and remind myself of what I had previously learned. I found it an invaluable learning and revision tool.

Sadly, the book is no longer in print, so I decided to write my own and I have just published The Biosciences Glossary on the Google Play Book Store.

The Biosciences Glossary

The book defines over 2,000 words, phrases, terms, and abbreviations used in the biosciences. It also includes 80+ chemical structures with links to additional information and to my videos on YouTube.

If you go to The Biosciences Glossary on the Google Play Book Store, you can review 20% of the book for free and decide if it would help you in your studies.

The book is available as a PDF and an ePub.

New Video Posted: How Proteins Get Into Peroxisomes | Biology Explained

In the video - How Proteins Get Into Peroxisomes | Biology Explained - I look at how the cell targets proteins to the peroxisomes.

Peroxisomes are involved in fatty acid oxidation and detoxification. The import of proteins into the peroxisomes relies on a short SKL motif at the C-terminal of the protein, which acts as an address. 

The SKL motif binds to the PTS1R receptor in the cytosol, which then interacts with the Pex14P receptor on the peroxisome membrane. The protein can either be imported with or without the receptor entering the peroxisome.

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New video posted: Organelles: Targeting Proteins to the Mitochondria

In this video, Organelles: Targeting Proteins to the Mitochondria, I look at how the cell targets proteins to the mitochondria.

Proteins destined for the mitochondria begin their journey in the cell's cytosol, guided by a signal peptide that acts like a "postcode." This signal, located at the N-terminal of the precursor protein, directs the protein to the mitochondria.

The video looks at the role of the Translocase of the Outer Membrane (TOM) and the Translocase of the Inner Membrane (TIM), along with the OXA complex, during the import process and discusses how proteins are targeted to the outer and inner membranes, the intermembrane space and the matrix of the mitochondria.

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New Video Posted: Understanding Vesicle Trafficking and the SNARE Hypothesis

In this video, Understanding Vesicle Trafficking and the SNARE Hypothesis, I look at the SNARE hypothesis and how it helps the targetting of vesicles to the correct membrane.

 

Vesicle trafficking is a crucial cellular process where vesicles transport materials to specific organelles or membranes. This process involves the SNARE hypothesis, where vesicles have vesicle SNAREs (vSNAREs) and target membranes have target SNAREs (tSNAREs). The vSNAREs and tSNAREs recognise each other, ensuring that vesicles dock at the correct membranes.

However, the SNARE proteins are promiscuous and can bind with multiple partners, posing challenges for precise docking. To address this, cells use Tether proteins, which operate over greater distances and add an additional layer of specificity. Tether proteins help vesicles recognise their target membranes, while SNAREs facilitate the fusion process.

This combined mechanism ensures accurate vesicle targeting and fusion, which is regulated by a GTP timer that coordinates the events. 

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New Video Posted: Understanding Protein Sorting: Cellular Transport Mechanisms Explained

Protein sorting involves directing proteins, which originate on ribosomes in the cytosol, to their appropriate cellular locations using specific amino acid sequences known as sorting signals. These sorting signals function like postcodes, guiding proteins to various organelles or membranes within the cell, such as the nucleus, peroxisomes, or the endoplasmic reticulum. The cell employs different types of transport mechanisms—gated, transmembrane, and vesicular—to move proteins to their correct destinations, ensuring proper cellular function.

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New Video Posted: Vesicle Trafficking: How vesicles are formed for trafficking between membranes

Vesicles are crucial for transporting molecules, and they are formed in one of three ways:

1. Clathrin-coated vesicles - Traffic from the Golgi to the endosomes and from the plasma membrane to the endosomes.
2. COPI-coated vesicles - Move from the Golgi to the endoplasmic reticulum, within the Golgi stack, and from the Golgi to the plasma membrane.
3. COPII-coated vesicles - Travel from the endoplasmic reticulum to the Golgi.

In this video, I look at how vesicles are formed and targeted within a cell. 

In the video, I explore some common themes and look at the formation of the coat (clathrin, COPI, or COPII) and the pinching off of the vesicle from the membrane. 

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New Video Posted: Organelles and Membranes - how much membrane is in a cell?

This is an interesting question: "How much membrane is in a cell?".

In this video, I use a football and some sheets of material to explore how much membrane we have in a cell and which organelles have the most membrane.

This was a fun video to make, and I got some very odd looks from passing dog walkers.

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