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How to lose a tail in 25 million years

Coccydynia, also known as tailbone pain, is perhaps the rare moment when we are actually aware of the presence of our vestigial tail. But let’s delve deeper. Imagine the convenience of living with a tail.* Both hands are occupied and you need to grasp something else? Just take a cue from the opossum with its prehensile tail adept at grabbing branches – it seems so effortless. If only it were not for an event that transpired around 25 million years ago, we might have been sipping our favourite drink while wielding cutlery in both hands. Instead, evolutionary pressure compelled us to abandon the arboreal lifestyle and adapt to a new style of locomotion. So, time to go back in time to unravel the genetic basis of tail-loss with researchers from New York University.

Without a time machine, teams led by Jef Boeke and Itai Yanai had to begin their detective work somewhere. Comparing sequences of genes predicted to be involved in tail-loss between two evolutionary closest animal lineages – one with tails and the other without, sounded like a reasonable starting point. Among these relatives were hominoids, encompassing humans and apes, thought to have lost their tails around 25 million years ago. This pivotal moment coincided with their divergence from their evolutionary siblings, ancient Old World monkeys, whose tailed family members include baboons, macaques, and mandrills. As genes involved in the loss of shortening of the tail were previously selected, scientists could narrow down their search to these specific genome parts of hominoids and Old World monkeys.

Genes are composed of coding segments known as exons and non-coding parts called introns. Despite being labelled as ‘non-coding’, these sequences are integral to a process called alternative splicing, where introns are removed from mRNA (messenger molecule carrying gene sequence). This process is incredibly powerful, as it can lead to rearrangements of various exons. Consequently, these mRNAs can be translated into different forms, known as isoforms, of a protein, that will eventually serve diverse functions within a cell.

Upon closer investigation of gene sequences associated with the absence of a tail or its reduced forms, scientists made a significant discovery. They found an insertion within one of the introns of the hominoid TBXT gene. This inserted sequence to a type of Alu element, known as a transposable element or transposon. Transposons, also dubbed as ‘jumping genes’ or ‘tiny genome travellers’ are relics of an ancient virus infection. They populate up to 50% of our genome and their selfish goal is to replicate themselves. Hence, they jump around and insert in different regions of host genomes, sometimes disrupting genes in the process.** In this case, an insertion of the Alu element occurred around the same time when hominoids lost their tails. Moreover, it happened in a gene crucial for tail development. After a series of few elegant experiments later, researchers uncovered the mechanistic explanation of what transpired, leading to the birth of mice without tails.

The inserted Alu element interacts with the different Alu element that has been present before in the next intron. Together, they form a loop, causing an exon located between these two elements to be excised during alternative splicing. This results in the production of a shorter isoform of TBXT mRNA. However, merely generating a slightly shorter TBXT isoform is not sufficient to cause tail loss. Tail-less mice are only born in cases where there is either a lack of full-length TBXT or a significantly higher proportion of the shorter isoform.

Proposed mechanism of tail loss

As science is an endless journey of discovery, every result leads to new questions. This time was no different. Some of the mice without tails also exhibited defects in neural tube closure, a condition similar to the spina bifida in humans. While it may not be surprising given the importance of the TBXT gene during embryo development, it raises the question: Why would evolution deprive us of tails but leave us with the (rare) risk of developing serious health conditions?

* It is worth noting that animals also experience tail pain. Whether with or without a tail, life is not devoid of suffering.

** Rest easy knowing your cells have evolved mechanisms to curb the activity transposons.

References:

Xia, B., Zhang, W., Zhao, G., Zhang, X., Bai, J., Brosh, R., Wudzinska, A., Huang, E., Ashe, H., Ellis, G., et al. (2024). On the genetic basis of tail-loss evolution in humans and apes. Nature 626, 1042-1048. 10.1038/s41586-024-07095-8.

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Lake Malawi: A haven of biodiversity

Nestled between the countries of Malawi, Mozambique, and Tanzania, lies a long, thin, and deep Lake Malawi, also known as Lake Nyasa or Lago Niassa. Despite its status as a natural wonder, the shimmering waters of Lake Malawi serve a vital earthly function – sustaining the livelihoods of countless local fishermen and their families. For generations, these fishermen have practiced their craft on traditional wooden boats, using techniques passed down from their fathers and grandfathers. Little could they have imagined that their daily routines would play a crucial role in a scientific article.

What truly sets Lake Malawi apart is its astonishing biodiversity, harbouring around 15% of all freshwater fish species on Earth. Interestingly, the lake is a home to more than 800 species found only in this specific space (scientifically called “endemic”), all descending from a common ancestor that lived there 800 years ago. One might immediately assume their genomes are vastly different, but that’s a near shot. There is basically no difference. So where is the rub? That’s what caught the interest of a group of scientists from the UK. From awakened curiosity to experiments, just one step…

As we read in the “Methods” section of the original article “All cichlid specimens were bought dead from local fisherman…”. Armed with curiosity (and fish samples straight from Africa), scientists decided to unravel the mysteries of Lake Malawi’s inhabitants.

On the researchers’ table lay a diverse array of specimens, each representing a distinct ecological niche and dietary preferences. Among them were the livers and muscles of six different species: the pelagic piscivore, Rhamphochromis longiceps, the deep-water pelagic carnivore, Diplotaxodon limnothrissa, two rock-dwelling algae eaters, Maylandia zebra and Petrotilapia genalutea, the benthic invertebrate-eating sand and rock-dweller, Aulonocara stuartgranti, and the inhabitant of rivers and lake margins, Astatotilapia calliptera. Upon closer look at DNA, scientists pinpointed a potential culprit – DNA methylation. More just than a decorative motif, this reversible modification of DNA, when present at sites of transcription initiation, modulates expression of genes. Such methylation effectively turns off genes, making them no longer active inside a cell. The most prominent differences between investigated fish from Malawi Lake were observed in the methylations of liver-specific genes that encode proteins involved in metabolism of specific dietary components. Further investigation led scientists to discovery of another significant disparity, common across multiple tissues within one species. Researchers hypothesised that the lack of methylation in genes important for eye development, leading to larger eye size of Diplotaxodon limnothrissa,represents an evolutionary adaptation to life in the deepest, darkest depths of the lake. Altogether, this study highlights  DNA methylation as an evolutionary trick to adapt to various environments.

Having had the pleasure of listening to the leader of the above-mentioned group of scientists at a recent conference, I can attest to the fact that the pursuit of scientific discoveries frequently leads researchers to breathtaking locations to personally collect specimens. As readers, all we can do is eagerly await the fruits of their labour. So, stay tuned, there is surely much more to come from the depths of Lake Malawi.

References:

Vernaz, G., Malinsky, M., Svardal, H., Du, M., Tyers, A.M., Santos, M.E., Durbin, R., Genner, M.J., Turner, G.F., and Miska, E.A. (2021). Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes. Nat Commun 12, 5870. 10.1038/s41467-021-26166-2.

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CRISPR. How to edit DNA and develop new therapies: lessons from bacteria?

In the last months, the scientific community welcomed the news that the first CRISPR gene therapy (Casgevy) was approved by the regulatory agencies1 around the world. This therapy is being used to treat blood disorders and sets the stage for the approval of other CRISPR-based treatments. While we wait for these, we decided to dive into the basics of this technology that have been widely used by scientists to edit DNA2 and answer several questions in biology.

The CRISPR (short name for clustered regularly interspaced short palindromic repeats) system was discovered in bacteria as a defense mechanism against viruses (yes, bacteria can be also attacked by viruses; we call them bacteriophages or simply phages).  Briefly, this system works by detecting DNA from phages, cutting it into small pieces and then integrating those into the bacteria’s own DNA. If the bacteria get attacked again by the same type of the phage, they have a “memory” that allows them to find and destroy the invader (see illustration below).

To accomplish this, the CRISPR system works together with several Cas proteins that are responsible for “cutting” the phage DNA in the right way (e.g. with the specific length) but also participate in the later stages of recognizing DNA from the same type of phage during new attacks.

So, the next question was: how do the Cas proteins recognize and destroy the phage DNA? This is where another important piece of the system comes to action- the RNA (a molecule that is similar to DNA and is produced when the DNA is “read”, thus codes the same “information”).  When the phage DNA is cut and pasted in the bacteria’s own DNA, it will be “read” and RNA that guides the Cas proteins will be produced. Just like a puzzle, where the different edges of one piece match another piece, the RNA will pair with the phage DNA , and will trigger the destruction of the phage DNA by the Cas proteins3

Figure 1- CRISPR molecular mechanism in bacterias.

Now, how did we learn from bacteria and start applying this mechanism to humans, allowing the creation of new therapies?  

Although CRISPR can be used in different ways to treat human diseases, the current approaches use both Cas proteins (mostly a very well-studied one, Cas9) and a guide RNA. The guide RNA informs the Cas9 protein which piece of the human DNA should be cut. The way we use this system can vary from disease to disease.

In most diseases, to precisely correct DNA errors, another element is needed: the template DNA.  In CRISPR therapies currently being tested, the Cas9 will first cut the part of the DNA that has errors. Then, a template DNA that does not contain those errors will be offered to the cells that will uptake this new DNA copy and repair the cut.  

Figure 2- Strategy used for most CRISPR therapies being tested and Casgevy.

Although this is a very elegant and smart way to correct genetic diseases, scientists are still trying to show that this cut and replacement of DNA is safe for human therapies. So why is Casgevy different and why did it become the first-approved CRISPR treatment?

Well, Casgevy was created to treat patients with sickle cell disease. These patients have an error in the part of DNA that gives the cells the information how to produce haemoglobin (a protein present in our red blood cells and is needed to transport the oxygen from the lungs to the rest of our body). The trick is, in our DNA we have the information to produce 2 types of haemoglobin: the adult haemoglobin, that we have after birth and that contains errors in sickle cell disease patients and the fetal haemoglobin, the one we had when we were just a baby inside our moms’ womb.  Thus, in this therapy, CRISPR is used to remove the part of the DNA that stops our cells from producing the fetal haemoglobin after birth. With this strategy, no extra DNA is added to the cells, making it a safer approach.

CRISPR is then a promising technology that has been explored to precisely correct genetic errors that give origin to diseases. While scientists have already used it broadly in the laboratory for several years, its application for human therapies is still in the beginning but holds the promise of new treatment possibilities for many people in the world.  

 

1. Regulatory agencies- Before a new medicine enters the market it should be approved by regulatory agencies (e.g. FDA in the US, EMA in the European Union/EU) that ensure a medicine is safe to be used by people. 

2. DNA- Check our previous post- “What If a Cell Was a City? – The Industry of Protein Production”

3. For more information on CRISPR biology we recommend you this page: https://innovativegenomics.org/crisprpedia/crispr-in-nature/

2024-03-11

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But That’s Not The Shape of My Heart

(no, not the Sting’s song)

Ah… Valentine’s Day. Love is in the air? Quoting the character Sheldon Cooper from the sitcom The Big Bang Theory: “Wrong. Nitrogen, oxygen, argon and carbon dioxide are in the air”.

And if this wasn’t nerdy enough, we are going to ruin another Valentine’s Day symbol: the heart.

The truth is that the typical symbol for love – this shape that you see everywhere from emojis to chocolate boxes – has nothing to do with the actual shape of the human heart. And why is that?

The silphium plant

If we scan through history, the heart symbol is very clearly visible in the shape of a seed from an ancient plant, the silphium, native to Cyrene, an old region in North Africa. The exact identity of this plant remains unknown to this day, as it is thought to have gone extinct. However, it was a highly valuable plant with various uses, including as a contraceptive.

According to this theory, through the association of the silphium plant with lovemaking, and considering the heart was believed to be the origin of the soul and feelings, these concepts got associated and, therefore, the shape of the silphium seed became a symbol for love.

As weird as this might sound, we also know that, historically, animal intestines were utilized as condoms, serving as another form of contraceptive. If their association had not been with the silphium seed but rather with a cow’s intestine, today we would be offering each other gut-shaped chocolates. How lovely.

Aristotle’s misconception of the human heart

The Greek philosopher Aristotle was known to be a great polymath (no, this doesn’t mean that he was married to different forms of math. It means he studied and had knowledge of various fields). He’s the one who first defended that the heart was the place for all mental functions (including love).
Besides, Aristotle also believed that the human heart was divided into three chambers instead of the four, as we today know. This could have led illustrators to draw the heart based on this misconception, leading to that symbolic shape instead of an anatomically correct one.

Scientifically accurate or not, the truth is that we have all learned to associate the “heart” symbol with love in many different ways. Either through emojis sent to lovers and friends or with bent thumbs and pointy fingers forming a very rectilineal heart in the middle of a concert.

From the Science As We Know It team to all our loving readers, we wish you a happy Valentine’s Day.

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Anatomy

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When Science Goes Wrong

Ah, the wonders of pursuing knowledge… The ambition of achieving more and more…

We might be led to think that scientific progress is a straight line. But science, as we know it, (see what I did here?) is a path made of ups and downs. Things do not always work out well. And as important as it is to highlight the successes and achievements from the past, it is also valuable to talk about the wrongs, the errors, the mistakes. Because, as every cheap self-help book will tell you, we are meant to learn from our mistakes. And what is science if not a learning process?

“What seems like a plot from a science fiction novel”

Paolo Macchiarini, at that time a researcher at Karolinska Institute, claimed he had developed a groundbreaking technology in bioengineering: the ability to replace a patient’s trachea with a synthetic one. This brought a huge amount of hope for patients who, for different reasons including some forms of cancer affecting the trachea, were in life-threatening need of a transplant.

The thing about transplants is that they usually rely on external donors. Someone else who can donate the tissue or organ in question. In this case, a trachea. Which, unlike kidneys (which we have two of), can only be taken by a cadaver. And this, as you might imagine, raises many problems. The first challenge is donor availability, as one cannot just get a catalog of recently deceased people to choose from (is this metaphor a little too much?). But even after this, there are always concerns about immune rejection. Our immune systems are very good at flagging and fighting things that are external to them. This works for viruses or bacteria, but also for perfectly fine human tissues or organs that come from someone else. Therefore, prior tests must be made to assess the “compatibility”, checking how much the donor and receiver are “similar” enough not to cause a huge dangerous immune reaction on the receiver’s organism. These tests are not only expensive, but might actually not even be 100% accurate, and end up in a rejection reaction on the receiver’s despite some apparent compatibility.

With Macchiarini’s new technology, these issues were no longer a concern. The trachea structure for transplantation was fully artificially made of a nanofiber scaffold, which mimicked the natural tissues. Then, these artificial trachea were coated with cartilage cells from the patient. For this, stem cells were taken from the patient’s own bone marrow. These stem cells have the potential to give rise to any other cell of the body and, in this case, were differentiated into cartilage cells which then would seed the synthetic structure. And since they come from the patients themselves, there are no concerns for any kind of rejection reaction.

This new approach seemed “nothing short of miraculous”, and would, hopefully, soon be expanded to the generation of other organs for transplantation: kidneys, livers, hearts…

The only problem was that… it was all a lie.

Many patients were subjected to this transplant. However, after surgery, their conditions kept worsening. Some of them started accumulating “mucus and blood which had to be pumped out several times a day” (we apologize if you are having a meal while reading this). And, at some point, they started dying. Despite this, Macchiarini kept performing these surgeries around the world, claiming patients’ good responses and diverging from any possible raised issues.

Why was it not working? The reasons could be many. Although in theory the idea of making an artificial organ that is fully coated with real cells from a patient seems completely plausible (even you, probably, reading this thought it was great! That it solved all the issues), there are many things that we cannot predict. This is why procedures like these must be very well studied and validated before moving on to actual patients.

News pieces started appearing about possible issues, and by 2016, Swedish TV channel SVT made a documentary piece, which set the ground for the situation to be fully exposed, culminating in Macchiarini’s final incarceration.

Macchiarini’s fraudulent behavior went way beyond its formal academic side. His personal involvement with an American news producer elevated this to a worldwide story of love, money, and scam. This mediatic side of the story has been covered in many works, including a recent documentary on Netflix.

This initially though “groundbreaking” scientific discovery created hope, a hope which Macchiarini exploited and used as a ramp for his popularity amongst the general public which, unfortunately, also affected his scientific peers.
Part of a scientist’s duty is to bring it to the general public. And this, just like the science done in the lab, has to be done with the same amount of ethics, transparency, and integrity. 

Scientists are, at the end of the day, not superheroes. They are humans. Humans which, inherent to their occupation, work with knowledge. And we know knowledge is power. So please allow me an exception and let me quote a super-hero proverb: with great power comes great responsibility.

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mRNA – a molecule with life-saving potential

The life-saving success of mRNA COVID-19 vaccines draws collective attention to a molecule called RNA and its therapeutic potential. Today we celebrate the birthday of Katalin Karikó, , who, alongside Drew Weissman, was awarded last year with the Nobel Prize in Physiology or Medicine for their groundbreaking findings concerning nucleoside base modification and mRNA interactions with the immune system.

Coming from Kisújszállás, Hungary, Katalin Karikó has been enamoured with the beauty and complexity of nature since early life. Her scientific journey has been far from a smooth ride. However, fuelled by curiosity, persistence, and resilience, Katalin Karikó turned her dreams into reality, saving millions of human lives and paving the way for the future of medicine. Let’s reflect on the scientific odyssey that has propelled mRNA to the forefront of modern medicine.

In 1961, scientists discovered messenger RNA (mRNA), a middle man between stable genome (DNA) and creation of proteins. As they learned to produce mRNA in a tube and deliver this mRNA to cells, a challenge arose – the mRNA was short-lived, prompted cells to recognize it as an invader and triggered a defence response – inflammation. This raised a puzzling question: our cells have mRNA, and they are not inflamed, so what was the difference?

The breakthrough happened at a photocopying machine at University of Pennsylvania, US, where Katalin Karikó and Drew Weissman joined forces. Determinant to find out why would mRNA tigger an immune response, they fed immune cells with various types of mRNA: mitochondrial, bacterial, their lab-made mRNA, mammalian mRNA, bacterial tRNA (transfer RNA – a special kind of RNA that helps making proteins), and mammalian tRNA.

Their eureka moment came when they noticed that the last three types did not cause much trouble – in fact, they barely provoked the immune response. What made them special? It turned out to be all about modifications in their building blocks.

Here is the twist: the lab-made mRNA lacked these modifications. One troublemaker stood out – uridine, one of the four building blocks of mRNA. When left unmodified, it caused all the fuss. By tweaking it to pseudouridine, this not only stopped the inflammation, but also made mRNA more stable and better in protein production.

How pseudouridine affects mRNA properties?

In essence, Katalin Karikó and Drew Weissman modified the mRNA to make its job effectively and even gave it a little upgrade along the way. This discovery marked a turning point, unleashing the incredible potential of mRNA in medicine.

The implications extend beyond COVID-19 and other infectious diseases, offering a novel approach for cancer. This Nobel Prize celebrates not just a discovery but a transformative leap in medical science, opening exciting possibilities for the future of mRNA therapeutics.

Katalin Kariko is undeniably a remarkably scientist whose research has saved millions people worldwide. Yet, she transcends the realm of scientific achievement, serving as an inspiration to countless young individuals, particularly researchers, navigating a challenging journey to realize their dreams – a path often hindered by obstacles beyond their intelligence and hard work.

If you would like to know more about unlikely journey of Katalin Karikó, read her autobiography “Breaking through. My life in science”.

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Charting human development: Nature’s Method of the Year 2023

As we approach the eagerly awaited New Year of 2024, let’s rewind the clock and reflect on years-long research that has been revolutionizing our understanding of human development. Scientists keep creating embryos in a dish solely from stem cells, bypassing the use of human embryos. This approach offers hope for addressing questions once deemed impossible. Why and how so many pregnancies end in loss? How can we prevent this? How tissues and organs are formed? And how can this knowledge aid in repairing and constructing organs in the lab for patients in need? While knowing the answers edges into the future, let’s delve into the past and present to understand how it can be achieved.

In nature, the union of a male gamete (sperm) and a female one (egg) results in the formation of a zygote, marking the beginning of a new life. As the zygote divides, it transforms into a blastocyst—a ball of cells that eventually implants into the inner lining of the uterus (endometrium). At this point, cells within the embryo specialise into extraembryonic tissues, serving to safeguard and provide essential resources during development. Simultaneously, they organize into germ layers that will eventually give rise to diverse tissues and organs of the organism. The challenge with understanding the earliest stages of human development is that it occurs hidden from our view, inside the mother.

A recent solution to this challenge is the development of various systems for culturing human embryos outside the uterus until 14 days after fertilization. This aligns with the internationally agreed limit for human embryo culture.

In one approach, researchers led by Magdalena Zernicka-Goetz genetically-modified human embryonic stem cells to guide their development towards formation of extraembryonic tissues. These modified cells were then combined with unaltered human embryonic stem cells, resulting in the self-organization of embryo-like structures. Alternatively, a team spearheaded by Berna Sozen took a distinct route, opting to grow cells in medium containing specific factors to program the fate of extraembryonic tissues. But these models are not flawless, they lack trophoblast-derived cells, crucial stem cells that eventually contribute to the formation of placenta.

As we forge ahead in crafting more advanced in vitro models of human embryos, there is a growing need for tools that let us study them in setting closely resembling the natural environment of the uterus. This marks an exciting moment as scientists from diverse fields – embryologists, bioengineers and computational biologists – join their forces to unravel the intricacies how embryo is developed inside mother’s womb and figure out ways to mimic this process outside the body. But that’s just a glimpse into the future of science…

Despite the ethical and technical considerations arising from advances in modelling human development, these breakthroughs open up tremendous possibilities in addressing pregnancy-related disorders and gaining insights into the formation of tissues and organs.

Methods for modelling development were named Method of the Year 2023 by renowned scientific journal, Nature.

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Nobel Prizes – Bon Appétit!

In the middle of all the holiday festivities, last week was particularly important in science. Between snowflakes falling all over the world, Mariah Carey echoing through the ear canals of millions and millions of people, the Nobel Prize Award Ceremony took place last Sunday, the 10th of December. During this big event, eleven laureates were awarded for their accomplishments that have benefited humanity so much. And still, we haven’t figured out a way of communicating the sense of smell through computers or smartphones… Maybe next year.
The ceremony took place at the Stockholm Concert All, after what we assume might have been a nice dinner with unpronounceable dishes. As a way to celebrate this day, here in the Science As We Know It, we propose you come with us through a brief overview of some of the recent Nobel Prizes in Physiology or Medicine. On the menu today we have: evolution, the organism’s internal clock and cells eating themselves. You are welcome to have a small taste of each of them.

2016 – Yoshinori Ohsumi “for his discoveries of mechanisms for autophagy”

“Autophagy” means “to self-eat”. And although this might sound cannibalistic, it is actually a very smart mechanism through which cells can adapt to extreme conditions, like starvation or infection.
Yoshinori Ohsumi’s groundbreaking studies identified genes that are essential for autophagy. By using yeast (because of their simplicity), Ohsumi and his team characterized different events that take place during the autophagy process: how stress signals give the cell the cue to initiate the formation of the vesicles that will engulf some of the cellular components. These will then be recycled to provide the cell with what it needs.

By degrading some of its own inner components, although causing some self-harm by losing them, the cell is able to rapidly get some more building blocks for renewing other components that might be more important at that time. It’s like we chose to destroy a cookie factory to get some materials to build a huge protective wall in case of an alien invasion. Cookies are nice, I know. But if an alien species is trying to conquer your planet, maybe our priorities need to be changed (Apocalyptic scenarios are always fun, aren’t they?).

 

2017 – Jeffrey C. Hall, Michael Rosbash, and Michael W. Young “for their discoveries of molecular mechanisms controlling the circadian rhythm”

You are probably aware that your body seems to have its internal way of telling time. Maybe you are able to wake up at a specific time, even though you set no alarm (or on weekends, when you really really reeeally don’t need to).

The 2017 Nobel laureates looked under the hood and unveiled the mechanism through which a key protein named “Period”, in an intricate system involving other proteins named “Timeless” and “Doubletime”, accumulates inside the cell during nighttime and is then degraded during the day.

This oscillation throughout 24 hours is, therefore, the reason why cells are “aware” of time.

Besides the creativity in naming these proteins – we have to admit – these were also pioneering discoveries leading to a better understanding of our intracellular clockwork. Our biological clocks regulate so many different things like metabolism, hormone levels, or sleep. Now you know why you felt jet-lagged after traveling to distant time zones.

Figure 1- Illustration for the Nobel Prizes in Physiology and Medicine, 2016, 2017 and 2022. In 2016, Yoshinori Ohsum was awarded the Prize for his discoveries in autophagy, a process where cells “eat” old cellular components to renew them. Jeffrey C. Hall, Michael Rosbash and Michael W. Young won in 2017, for describing the proteins and cellular processes that control the circadian cycle. In 2022, Svante Pääbo was awarded the Prize for his studies in Human evolution and the discovery of a Denisovan. 

2022 – Svante Pääbo “for his discoveries concerning the genomes of extinct hominins and human evolution”

Where do we come from? What is our story? These are 2 essential questions every now and then we might ask ourselves. Svante Pääbo went a little bit further and tried to figure out not only his past but the history of all humans. 
We, modern humans, or as scientists like to call Homo sapiens, have been here for 300,000 years (despite the word modern don’t get confused, this means humans with our physical features, not humans carrying phones everywhere). However, before us, there were other relatives very close to what we might call a human now, like Homo erectus. More interesting, other relatives were co-existing with us, the Neanderthals. This raises several questions: Why have our relatives gone extinct? If we co-exist with Neanderthals, were we interacting with each other?  Well, as you can imagine my dear reader, this is not easy to understand as our relatives went extinct. All we have to tell us about our past is ancient bones and teeth. This is where Svante Pääbo entered in scene, taking advantage of multiple lab technologies, Pääbo and his team made it possible to analyze DNA from those old bones*. Why is this so important? Multiple years after body death there is only very few amounts of DNA that we can take and analyze. Now we know that some percentage of Neanderthal DNA is present in today’s humans, meaning that at some point Neanderthals and Homo sapiens mate. We understand better how our immune system (the system we have to fight bacteria and viruses) adapted and survived to new environments while we were spreading through the entire world and finally, we discovered another relative that existed at the same time as us- Denisovan (Ah! The classic big family dinner, where you find out that you have another cousin). 


*In this post, we refer to nuclear DNA, as we will later explain to you other DNAs exist, which were explored in the first evolution studies by Allan Wilson.

2023-12-18

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Let’s jump around – how DNA moves between organisms

I bet your first thought when you hear “gene transfer” is creation of a little cute human being by combining genetic material of parents. And you are certainly right. That is so-called vertical gene transfer. Apart from it, there is also horizontal gene transfer (HGT). While well studied in bacteria, this non-sexual exchange of DNA helps bacteria adapt to a changing environment (check what is “DNA” in our last post). The concept of HGT in more complicated organisms might seem unlikely at first glance due to various reasons from a DNA perspective, logistically speaking. How could genetic material leave a donor cell? How could it get inside a germ cell – the one which gives rise to gametes – sperm and egg cells, and therefore can pass genetic information to offspring. Finally, how foreign DNA could be inserted into the genome of germ cells (genome is all the genetic information of the organism that consists of DNA or, in case of viruses, RNA)?

Figure 1. Remaining questions about nonsexual movement of genetic material.

Examples such as the transfer of antifreeze genes between Atlantic herring and Japanese smelt enabling survival in icy sea waters, and the hijacking of plant detoxification gene by whiteflies to neutralise plant toxins underscore that HGT occurs even in complex organisms. Yet, the question of precisely how that happens remains.Here comes viruses, those invisible culprits responsible for our latest pandemic and the common cold. But what exactly do they do? They excel at grabbing pieces of DNA and inserting them into the genome of infected cells.

Adding a touch of complexity, or beauty, depending on your perspective, are the descendants of ancient viruses, known as transposons, “jumping genes”, “tiny genome travellers” (read more about them here). These elements populate large proportions of eukaryotic DNA and are termed “selfish” because their primary goal is to replicate, even if it means disrupting genes of their host.

Now, let me introduce you to the stars of the show – Maverick elements – creatures that share features of transposons and viruses. Known already for many years but just recently discovered by a group led by Alejandro Burga in Vienna, Austria, as mediators of HGT  in  nematodes – tiny worms, only 1 mm long, that inhabit diverse locations worldwide. Due to their minimal dietary and living requirements, they are perfect organisms for laboratory studies.

Much like viruses, Mavericks have the ability to invade other organisms. Combining characteristics of both transposons and viruses, Maverick elements have been transferred between different worm species on a global scale, some of these events dating back to the era when dinosaurs ruled the world. In essence, the transferred cargo consists of genes that provide fitness advantage to offspring – a story awaiting exploration in the next post.

Figure 2. Maverick elements mediate HGT in nematodes.

If you are now curious about whether the above findings hold true for humans, we still do not know. But hopefully, we will find out soon.

References:

Graham, L.A., Lougheed, S.C., Ewart, K.V., and Davies, P.L. (2008). Lateral transfer of a lectin-like antifreeze protein gene in fishes. PLoS One 3, e2616. 10.1371/journal.pone.0002616.

Xia, J., Guo, Z., Yang, Z., Han, H., Wang, S., Xu, H., Yang, X., Yang, F., Wu, Q., Xie, W., et al. (2021). Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184, 1693-1705 e1617. 10.1016/j.cell.2021.02.014.

Widen, S.A., Bes, I.C., Koreshova, A., Pliota, P., Krogull, D., and Burga, A. (2023). Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 380, eade0705. 10.1126/science.ade0705.

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What If a Cell Was a City? – The Industry of Protein Production

Dear reader, I will ask you right now to imagine the voice of your favorite teacher saying:

A cell is the smallest unit of life.

Also, since you already tuned their voice in your head, keep going:

Drugs are bad.
Stay in school.
Donate a lot of money to the Science as We Know It team so that they can go on vacation to Hawaii.

Indeed, your teacher was right. Every living thing is composed of cells. And inside those cells, there are other structures that do their own things – the organelles.

Perhaps the most famous organelle, the mitochondria, is usually known for being “the powerhouse of the cell”.
But… what other interesting comparisons can we make with these organelles? If we imagine a cell as a city, what are the infrastructures that allow this urban paradise of life to thrive like a metropolis?

Today, let’s focus on the “industrial process” occurring inside the cells. A very well-organized assembly line that starts in the “books” of DNA and ends on the packaging and transportation of the vital molecules for the cell – the proteins.

Nucleus – The Library

Ah, the most noble place in the cell… The nucleus is where the DNA – that long molecule (both in name and in size) – is stored.
DNA is like a textbook, composed of long lines of smaller molecules. These molecules are the alphabet to “write” the instructions to produce all proteins in the cell. And the smart thing about life is that every cell* contains, in its nucleus, all the DNA containing the instructions to assemble all proteins. The information is always there, in this repository of information.
And yes, if you are wondering, you must always be quiet in the nucleus. Come on, people are trying to read some DNA there. Be respectful!

*Apart from reproductive cells. But let’s ignore those for now. It’s too early to talk about how babies are made.

Ribosomes – The Factories

If the nucleus is the quiet place where the information is stored, the ribosomes are the workplace where hardworking laborers get their hands dirty to make proteins. The information comes from the nucleus, but not in the form of DNA. Nah nah nah, the librarians do not let you bring the DNA books directly. Do you want some information, honey? Then copy it into a new piece of paper.
And that’s exactly what the messenger RNA is – a draft copy from DNA which is brought to the ribosomes where it is translated into proteins.
24 hours a day, 7 days a week, nightshifts… Ribosome production can’t stop, or else… Well, you die. So, let’s really hope ribosomes never think about going on strike.

Endoplasmic Reticulum – The Refinery

You probably can tell that protein production is a big thing for the cell, right? It’s what keeps it together and functioning properly. Therefore, it is also a rather complex process. And, sometimes, the proteins coming straight from the ribosomes are still not in their final form. So, in the endoplasmic reticulum, which is right beside the ribosomes, some freshly produced proteins are then further… Let’s say… Refined, processed. They are folded in a more sophisticated way and made so their function is best once they go out of the process.

Golgi Apparatus – The Transportation Terminal

This is where the whole chain of protein production comes to an end. After being manufactured in the ribosomes and refined in the endoplasmic reticulum, proteins are brought to the Golgi Apparatus where they can be ultimately packaged for transport and delivery throughout (or even out of) the cell.
We can call it the transportation company of the cell.

CellEx.
DHCell.
UPS(ell).
All right, I stopped now.

Illustration by Inês Caiado

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‘Science as We Know It’ Is (Back) Online!

And what can be a better way to (re)start this blog than by saying:

Let there be light

A quote from the Book of Genesis, upon the creation of the universe. Translated from the Latin sentence “Fiat lux”. Which, if we think about it, could be a great name for a car model from a famous Italian car brand.

A depiction of the Big Bang. The beginning of the universe. Used here to imply that it has the same amount of importance as the beginning of this blog. (We know it doesn’t).

Is this relevant to what we are doing here? No.

Does this illustrate how things can be somehow interestingly interconnected and somewhat related to each other even without us noticing at first glance? Yes.

After a long creative break, the Science as We Know It blog is back online. With a new team motivated to write about science in the most accessible and captivating way. To de-construct, de-complexify, and de-other things that the person who was writing this wasn’t able to think more thoroughly.

We share the idea that, sometimes, scientific facts and new discoveries become so over-complicated in the jungle of countless plots that their true wow factor is lost for most people (even scientists!). Here, we want to grab these amazing facts by a leg and pull them out. Exposing them to everyone (this metaphor sounds more violent than it actually should be).

Check out the new About Us page to get to know who we are. Also, connect to us on social media! We are so excited we now have Twitter, Instagram, Facebook, and LinkedIn pages. Connecting with us on social media is the easiest way to stay up to date on any new posts and other updates.

If you like the old-school way, you can also subscribe to the blog by email, and you will then receive a weekly email about the last posts that you might have missed.
If you are more old-school than this, send us your home address and we will send you printed versions of our blog posts.
If you are even more old-school than this, we are currently working on a rock art version of our blog. Here, is a quick preview:

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Everything is connected: Neuroimmunology

By Niklas Krausse

Neuroimmunology combines neuroscience with immunology to better understand the interactions of the two systems.

How does our immune system control our behavior?

The immune system is the body’s defense system, whereas the central nervous system is the control unit. It is easy to think about them as separate and isolated – but they are much more closely interwoven than one would think.

Pathogens have always been a driving force in human evolution. Harmful viruses, bacteria and parasites have forced us to adapt and develop better defense strategies. One theory suggests the co-evolution of the immune and the central nervous system. At least partly, our cognitive development could be the result of pathogen evading strategies. The never-ending arms race between pathogens and our immune system may also have influenced our highly adaptive central nervous system. New behavior strategies could have evolved to prevent the spread of infections. In turn, the immune system might have evolved ways to communicate with the nervous system in order to respond to a threat. Undoubtable, however, are the similarities between the molecular and cellular features of the two systems1,2.

In a study from 2016, researchers found that mice without an adaptive immune system (which mostly consists of B and T cells) showed despaired social behavior3. They observed that these immune-deficient mice lacked a social preference for another mouse over an object, unlike wild-type mice which always chose to socialize with other mice. Interestingly, this disturbed social behavior could be reversed by simply injecting immune cells in the immune-deficient mice.

The same group of researchers were able to show that loss of meningeal T cells causes the disturbance in social behavior. The “meninges” are the three membranes that enclose and protect the brain and the spinal cord4. These membranes, and the spaces between them, harbor a variety of immune cells that are in close contact with the central nervous system without actually infiltrating it – communication between the two systems takes place via soluble molecules known as cytokines. Consequently, the research team identified the T cell-derived cytokine “interferon-gamma” (IFN-γ) as the mediator between immunity and the neuronal connections that control social behavior.

In an earlier study from 2010, researchers had found a similar connection between meningeal T cells and the regulation of learning and memory behavior in mice5. They showed that the number of T cells increased in the meninges of mice trained in a learning and memory test. Depletion of these cells caused mice to perform worse in the same test. The learning and memory performance was regulated by another cytokine secreted by meningeal T cells, “interleukin-4” (IL-4). Besides other effects, IL-4 was increasing the production of a molecule in neural cells that is key for learning and memory processes.

It is easy to think of an organism as the sum of different, strictly separated systems – all required for a specialized task, but living organisms cannot be described in the same way as artificial objects. There is much more exchange and interaction between the different parts. Neuroimmunology is a great example how the combination of different research fields may help to better understand complex biological processes such as learning and memory, social behavior, and the development of neurodegenerative and autoimmune diseases.

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