Full disclosure, this is outside my area of expertise (whatever that means…).
I want to talk about the thymus and its importance in aging. I recently came across a fascinating paper that builds on a model of human lymphopoiesis across development and aging, and I wanted to share it with you all: (https://pubmed.ncbi.nlm.nih.gov/38908962).
The thymus plays a key role in the immune system, especially in the production and maturation of T-cells, which are crucial for immune responses. One of the things that really piqued my interest is how the paper discusses developmental transitions in the thymus and how these changes potentially affect the immune system throughout life. It’s especially interesting how thymic involution with age may impact immune health, and how this could tie into the overall aging process.
To me, it's wild that the thymus pretty much "dies" before we’re even out of our teens... Seriously, look at Figure 5. This idea has kept me up at night for about a decade now. Anyway, I’m in a transition phase of my career and am fortunate enough to have the latitude to start thinking deeply about the thymus. So let’s chat—we can struggle through my learning phase together!
While I’m still learning the specifics, this got me thinking about the potential implications for therapies aimed at rejuvenating or maintaining thymic function in older individuals. Could these interventions help us preserve immune function as we age? You ever hear of this guy Greg Fahy? Interesting person. He has a fascinating publication history in the area of cryopreservation (another field I want to dive into, and we should totally discuss), but he’s also attempting to rejuvenate the thymus. Here’s one of his papers: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6826138.
Honestly, I’m not sure where I stand on this yet. I find the hypothesis really interesting, but I’m in no way an immunologist. I’d love to hear your thoughts! If you’ve worked in this space or know of any relevant research, feel free to share. And if you haven’t but have a hot take, I’d love to hear that too! No barrier to entry—feel free to open this up.
What areas in aging or immunology are you curious about? What do you think will get us to 130+ years on this planet!?
My suspicion is that a big part of this discussion revolves around integrating vs. non-integrating gene therapies, so let’s start there.
At a high level, viral gene therapies use a viral vector (the capsid or container) to deliver a genetic payload into a cell. That payload can then integrate into the host’s genome if the lysogenic machinery is part of the payload—but that doesn’t necessarily have to be the case.
Plasmid therapies, on the other hand, involve non-chromosomal DNA that stays outside the host’s genome but can still express the proteins it encodes independently. In most cases, plasmids don’t come with the machinery that promotes integration with the host genome, but it’s not an absolute safeguard against integration either. Additionally, a plasmid cargo still needs a vector to gain access into the cell.
In the follistatin gene therapy paper, the authors use a plasmid (the genetic cargo) to encode instructions for follistatin. They deliver this via polyethyleneimine (PEI), a cationic polymer that helps get the plasmid into cells—so PEI acts as the vector here, instead of a virus.
Now, the superiority of either approach really depends on the use case:
Integrating Gene Therapies (more commonly viral-based, since many naturally have integrating machinery that can be included as part of the cargo) are ideal when you want a one-time, permanent fix—for example, in conditions like sickle cell anemia, where a single gene mutation needs to be corrected. In this case, you’d want the therapeutic gene to integrate into the genome for long-term expression and potentially a cure with just one treatment.
Non-integrating Therapies (more commonly plasmid + non-viral vector based) are ‘better’ when you want temporary gene expression. For example, if you're priming the body to fight a new pathogen or delivering a protein with a temporary therapeutic effect, plasmid-based therapies are argued to be more practical. These are also great for delivering proteins that need short-term action but shouldn’t stick around indefinitely, especially if there’s a risk of side effects from prolonged exposure.
That said, I don’t see why viral/non-plasmid strategies couldn’t do these things as well. In fact, many such strategies are in development.
Other Considerations for Viral vs. Plasmid-Based Therapies: Viral Vectors: These also come with higher risks like immune responses, insertional mutagenesis (which can potentially lead to cancers), and limited payload sizes. There are some neat solutions to these in the research sector that we should chat about in the future.
Plasmid Vectors: Generally less immunogenic, but they offer shorter-lived expression, meaning you might need repeated doses to maintain effects. The big benefit in my opinion is they deliver a much larger payload when compared to viruses. Not relevant if you are aiming for a single gene therapeutic but I feel it's the big draw.
Now, About the Follistatin Paper... I’ll hold back some of my critiques of the paper that are beyond the scope of your question, but let me address the safety aspects they mention:
Inherently Transient Expression: This is generally true for plasmids since they don’t integrate into the genome. However, I’m cautious about saying this is 100% guaranteed. There’s always a small risk of integration, even with non-integrating strategies, although the probability is low.
Drug-Inducible Reversibility: The paper mentions this, but it’s not clear how exactly they plan to achieve it. They didn’t include details about the plasmid construct or any antibiotic kill switch, which would be crucial to back up their claim. If such a switch were tied to any potential integrations, in theory, it could allow them to kill off any cells where integration occurred—but more details are needed here. This strategy also isn’t 100% effective, by the way.
Excision of Transfected Tissue: This one made me laugh a bit—“Oops, we made a tumor—CUT IT OUT!” Brilliant and novel, guys. Thanks for mentioning it. While theoretically possible, it doesn’t seem like a reasonable safety net for a clinical approach. Given that cancer development is one of the big concerns with these therapies, and cancer is notoriously slippery, this doesn’t offer much reassurance.
In my opinion, the advantages of plasmids mentioned in the paper could also apply to viral vectors.
So, Where Do I Stand? Both viral and plasmid approaches have their place, and the choice really depends on the situation and how the technology evolves. I suspect that in the long term, viral vectors will be the better choice, despite their risks. There’s a lot of work going into custom capsid design, which will allow for specific targeting and immune evasion. I think the idea that plasmid-based therapies are "safer" may be leading to a false sense of security.
That said, I’m definitely flirting with both. Can you ask me again in 5 years? Maybe 10?
What are your thoughts?
Great question! I don’t want to downplay the utility of multiplex PCR—we have in-house panels that we frequently rely on. However, there are two key drawbacks: cost and breadth. The reagents for these assays are quite expensive, and they can only detect what is on the panel, which is dictated by the species-specific primers. We use the BioFire system here, which you can look up if you’re curious about the panels. Another sequence-based option would be using assays like Karius (also Google-able), which is an unbiased approach that detects microbial cell-free DNA and attempts to match it to a library. When it first came out, Karius was supposed to revolutionize infectious disease diagnostics but failed to gain strong footing due to its cost, turnaround time, and the ambiguity of the data you get back.
MALDI-TOF proteomics is the gold standard because it’s fast, cost-effective, and requires minimal sample preparation compared to sequencing.
MALDI-TOF is not highly targeted in the sense of picking specific proteins of interest. Instead, it generates a broad mass spectrum “fingerprint” of all the proteins (primarily ribosomal proteins) present in the organism (we can do fungi too). The key is that the spectrum is matched against a reference database of known profiles. So, it’s a comparative method, rather than specifically aiming for certain proteins. The spectra tend to be consistent and reproducible for each species, which is why it works so well for identification. The reference library is massive and constantly growing with more samples, so generally speaking, you are not restricted to a panel of select organisms (there are caveats to this, but you know, generally speaking).
Typically, there are about 10-20 prominent proteins, with most of these being small, abundant proteins like ribosomal proteins. These are what the machine "sees" best and uses to generate the profile. It’s not that we have ‘proteins of interest’ per se—it’s more that each organism presents a predictable set of proteins to the MALDI. If we know that, we can identify the organism. For many organisms, they present ribosomal proteins, which is convenient because ribosomes are a classic marker for identifying organisms through speciation. However, some organisms present other proteins as well.
Let me know if you have any other questions!
Yes, that is exactly why! The safety concerns around using spectrometry for anthrax primarily stem from how the samples are handled and prepared. Nuance incoming!
The dogma in our lab is that mass spectrometry, especially MALDI-TOF, involves creating an aerosol or vapor from the sample, which could potentially release live spores or other dangerous particles into the environment. In the case of anthrax, because it’s a highly infectious pathogen, this aerosolization could pose serious biohazard risks if the spores aren’t completely neutralized.
In reality, it's much more likely that the true concern lies in the upstream processing. In fact, many labs have the capacity to, and ultimately do, run anthrax samples on the MALDI. This is because the samples are chemically deactivated with reagents like trifluoroacetic acid and α-cyano-4-hydroxycinnamic acid, which also aid in the production of adduct ions that are ultimately detected by the machine.
A key difference between most hospital microbiology labs is the biosafety classification. At my location, for example, the only part of the lab that is rated Biosafety Level (BSL) 2 is the mycology suite. To handle anthrax safely, you would want manipulations performed in a BSL-3 lab within a class 2 safety cabinet, which is what the reference labs would do. Then, once the sample is inactivated, they proceed to MALDI. In hospital labs, we usually limit our manipulations of possible anthrax and therefore use quick assays to rule it out. If we can’t, we send it to other labs... through the mail... there may be a dark joke somewhere in there.
Fun fact: most of Robert Koch’s (a, if not the, father of germ theory) early work was actually with the anthrax bacillus, long before our BSL equipment existed!
Hello Mainlined Science! We’re always looking for new topics and ideas to dive into, so we’d like to start getting some engagement! Got a question, a research area you’re curious about, or just something science-related that you’ve been pondering? Let’s talk about it! Even if it's outside our fields, no wrong answers!
Whether it’s a specific field you want to explore or a “random thought of the day,” feel free to start up the chat, we will reply. We’re here to start discussions, share knowledge, and learn together. Drop your ideas below—there are also no wrong questions!
I’m also thinking about occasionally hosting some hypothesis-generating sessions, starting small research projects, and maybe even setting up a little DIY lab. If there’s interest of course.. Maybe we could get into some 3D printing or simple bio experiments too! Let's see where this can go. Let's get the hive mind goin!
Ok, so I had a patient. The actual history isn't terribly important because this sort of thing happens relatively frequently, but to give you a quick one-liner: he was an older male with rheumatoid arthritis admitted for Staph bacteremia. In cases of blood infections, we order tests called "clearance cultures" to track and confirm that the organism we're fighting disappears with treatment. In this case, 1 out of 4 of these samples tested positive for a potential Bacillus species—the genus to which anthrax belongs. That being said, completely inert species of Bacillus are common contaminants in this setting, and the fact that only 1 out of 4 samples tested positive definitely makes you think this is such a case of contamination.
However, we treat it as if it were anthrax until we're completely certain it isn't. It's Schrödinger's anthrax! After all, you don’t want to be the lab that missed anthrax.
Bacillus anthracis Identification Colonies of B. anthracis appear non-hemolytic, consist of gram-variable rods with spore forms, and are non-motile. In other words, when grown on sheep's blood agar, they do not break down hemoglobin (a feature many microorganisms possess), appear elongated and purple or pink under a microscope after staining (gram-variable), produce spores (a survival mechanism), and lack motility (i.e., they don’t move via structures like flagella). We use these properties to rule out B. anthracis. While mass spectrometry is the gold standard for organism identification in modern microbiology, when it comes to potential anthrax, we revert to basic microbiological methods for safety reasons (which we can discuss more in the comments if you're interested).
Bacillus anthracis: What Sets It Apart? Bacillus anthracis, the causative agent of anthrax, is a zoonotic disease, meaning it can be transmitted to humans through the handling or consumption of contaminated animal products. Due to its potential use as a bioweapon, B. anthracis is classified as a Tier I Category A agent by the CDC. Even though infection is rare in the United States, the micro lab remains vigilant in identifying this organism due to its serious implications.
Plasmids and Virulence Factors What makes B. anthracis particularly dangerous are its virulence plasmids, pXO1 and pXO2, which carry the genes responsible for toxin production and capsule formation, respectively. These plasmids play a crucial role in the organism’s ability to cause disease, enabling it to evade the immune system and produce lethal toxins.
But what exactly is a plasmid?
What is a Plasmid? A plasmid is a small, circular piece of DNA that exists independently of the bacterial chromosome. Unlike the bacterial genome, which contains essential genes for the organism’s survival, plasmids often carry genes that provide advantages under certain conditions—such as antibiotic resistance or, in the case of B. anthracis, virulence factors.
Plasmids are particularly interesting biologically and evolutionarily because they can be transferred between bacteria via a process called horizontal gene transfer. This means bacteria can acquire new traits, such as antibiotic resistance or enhanced pathogenicity, from other bacteria without evolving them slowly over generations. In essence, plasmids allow bacteria to adapt quickly to new challenges, making them highly versatile and resilient organisms. From an evolutionary standpoint, plasmids accelerate genetic diversity and adaptability, giving certain bacteria a survival edge in hostile environments.
Think of it this way: plasmids let bacteria "plug and play" abilities. Imagine if I could transfer my height, immune system, or ability to play the ocarina just by touching you... now you're getting it. Because of these abilities plasmids are, in many ways, the cornerstone of modern biomedical tech. We will definitely be talking about them again.
What is Bacillus cereus biovar anthracis and why use it to intro plasmids? Now, why bring up plasmids in this way? Because I can. Stories are nice. Anyway, plasmids are key to understanding another entity: Bacillus cereus biovar anthracis. This variant of B. cereus (the contaminant in our story) has acquired plasmids nearly identical to those found in B. anthracis, meaning it can cause anthrax-like diseases, particularly in animals. While B. cereus is more commonly known for causing food poisoning or being a random contaminant, its biovar anthracis variant is a real concern due to its ability to acquire these plasmids, making it capable of causing serious infections similar to anthrax. Mother nature is getting scarier!
In 2016, this variant was added to the CDC’s select agent list, emphasizing the significance of monitoring its presence, especially in cases involving animals. Though not as common in humans, its existence underscores the evolutionary importance of plasmids in spreading virulence factors across bacterial species.
Conclusion To wrap it up: Plasmids are fascinating, highly relevant to the changing landscape of infectious diseases, and, as will be discussed later, they might even change what it means to be human.
OK, Time for Something Random: Lyme disease and its strange connection to lizards.
Lyme disease is a big deal. Especially, or at least historically, here on the east coast US. Did you know that some animals can actually cure infected tick carriers!? I didn't either.
In parts of California, western fence lizards play a surprising role in controlling Lyme disease. When ticks feed on these lizards, a protein in their blood kills the bacteria (Borrelia burgdorferi) that causes Lyme disease. Some factor in the lizards blood is ingested and kills the bacteria present in the gut of the tick.
To conclude, nature is wild. Much of our innovation in biology/medicine, including CRISPR (see earlier related posts) and the majority of our antibiotics, aren't so much inventions but are more accurately 'discoveries.'
Relevant papers I happened upon: https://pubmed.ncbi.nlm.nih.gov/9488334/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5413869/
Let’s continue our dive into gene therapy with one of my favorite papers. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6876218/
In this study, researchers delivered three longevity-associated genes (FGF21, αKlotho, and sTGFβR2) to mice using a gene therapy cocktail. These genes target metabolism, heart function, and kidney health—three areas that typically decline with age. Here’s why this is a big deal:
Obesity & Diabetes? Reversed. Mice fed a high-fat diet lost weight and saw their diabetes symptoms disappear, just by tweaking how their cells handled energy.
Heart Failure? Improved. The therapy improved heart function by 58%, meaning it could help tackle the leading cause of death worldwide.
Kidney Disease? Protected. Mice treated with this gene therapy avoided the typical kidney damage seen with age-related conditions.
What’s most exciting is that a single gene therapy cocktail—combining just two of the three genes—was able to treat all of these diseases simultaneously. Imagine being able to tackle multiple age-related health issues with just one treatment!
This approach could be a game-changer in how we think about aging and disease. Instead of targeting one condition at a time, we might be able to treat aging itself by addressing the root causes of multiple diseases.
What do you think—are we on the verge of a breakthrough in how we fight age-related diseases?
See this similar paper here targeting TERT and follistatin: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9171804/
Do these papers pass our threshold of believability? Are we concerned that one of these papers had a few post publication amendments? I may circle back to poke holes in them (if I can find any) at a later time. Feel free to beat me to it!
Let’s talk CRISPR-Cas9 and why it’s one of the most significant breakthroughs in modern biology.
At its core, CRISPR-Cas9 is a tool for precise genome editing. Before CRISPR, genetic modification was a slow, expensive, and often imprecise process. CRISPR changed the game by allowing scientists to cut DNA at specific sites, guided by an RNA molecule that can be customized to target nearly any gene. Once the DNA is cut, it can be repaired in a way that adds, deletes, or alters the genetic sequence. This kind of precision has opened up endless possibilities.
Why is this such a big deal?
Speed and Efficiency: CRISPR allows scientists to make changes to the DNA of organisms in weeks, not years. You want to knock out a gene? You can do that. Want to introduce a new one? Done. The speed and flexibility are revolutionary compared to older methods.
Precision: CRISPR can zero in on specific genes with high accuracy, reducing the risk of off-target effects (though this is still an area of research). Precision matters when you’re editing the building blocks of life.
Wide Applications: It’s not just a tool for basic research—CRISPR is shaping medicine, agriculture, and even biotechnology. Scientists are working on curing genetic disorders, creating disease-resistant crops, and engineering cells to fight cancer. The potential here is massive.
How is CRISPR shaping biology today?
Gene Therapy: One of the most exciting applications is in treating genetic diseases like sickle cell anemia, muscular dystrophy, and certain forms of blindness. By directly editing the faulty genes responsible for these conditions, CRISPR could offer permanent cures rather than just treating symptoms.
Cancer Research: CRISPR is being used to edit immune cells, making them better at recognizing and attacking cancer. We’re moving closer to personalized medicine where your immune system can be genetically fine-tuned to fight off specific diseases.
Agriculture: In crops and livestock, CRISPR is being used to enhance yields, create resistance to pests and disease, and improve nutritional content. This could help address food security as populations grow and climates change.
Basic Research: Perhaps one of its most profound impacts is that CRISPR makes it easier to explore how genes work. We’re learning more about gene functions at a faster pace than ever before, and this knowledge feeds into all other areas of biology.
Of course, with great power comes great responsibility. There are ethical considerations around using CRISPR, especially when it comes to editing human embryos or making changes that can be passed down to future generations. The technology is advancing quickly, but society will need to decide how to handle the moral implications.
In summary, CRISPR-Cas9 is a huge deal because it makes genome editing faster, cheaper, and more accurate than ever before. It’s shaping everything from how we fight diseases to how we grow food, and it’s rapidly transforming the future of biology. We’re just starting to scratch the surface of its potential.
Suggested reading:
The paper that started all https://pubmed.ncbi.nlm.nih.gov/22745249/
A look at a future where everyone has access to the power of CRISPR https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297044/