Can gold cure us?

No it can’t. But in a recent report (1) scientists show how using tiny gold particles they were able to deliver a therapeutic agent called siRNA to cells and tissues.

siRNA are two short stretches of ribonucleic acid (RNA), chemically very similar to DNA. siRNA molecules whose sequence is properly designed can be very powerful in reducing the level of a target gene’s activity, most commonly by stopping the production of the protein the gene encodes for. In their paper, the authors focused on a protein called endothelial growth factor receptor, or EGFR, which is known to be hyperactive in certain types of cancer. As you probably figured out by now, reducing the levels of EGFR protein by siRNA might therefore be a very powerful way of helping some cancer patients. This study did not involve any human patients, but it did show that gold nanoparticles coated with siRNA molecules designed to reduce EGFR levels were successful in doing so in cultured cells and even in the skin of mice.

The facts that EGFR is hyperactive in some malignancies as well as that siRNA can reduce levels of proteins have been known for decades. So why has it taken so long for the scientists to come up with an effective way of combining the two pieces of knowledge into something effective. The problem is, putting siRNA into cells, especially when they are a part of a living organism, is not a straightforward task. It’s a bit simpler when the cells grow in culture – we can mix siRNA with some chemicals or stick it into modified viruses, which have the natural ability to inject DNA or RNA into cells. But when it comes to patients, using these chemicals or viruses is not something you can get patients to agree to easily. The mentioned chemicals can be simply toxic and viruses are, well, viruses. These two methods can not only be harmful to cells or organisms, but they can also modify the so-called gene expression, i.e. set of genes that are active in given cells. For example, cells in our bodies usually know that they have been infected by a virus and they activate all sorts of genes to alert the body’s immune system, often resulting in phenomena such as inflammation. Scientists do have means of checking how the profile of active genes inside cells changes after they’ve been subject to a certain type of treatment, and one of the fascinating things about the gold nanoparticles was that they changed the activity of only seven genes in cultured cells. Is that a lot? Well, a chemical reagent used to deliver the same siRNA to the same cells affected 427 genes. On top of that, the siRNA delivered on gold nanoparticles was still about 50% active after 4 days, at which time the siRNA delivered by the compared chemical completely lost its activity. But most importantly, when tested in animals, the gold-delivered siRNA managed to get into the majority of cells, stayed active in there for a long time, exerted a prominent effect, and no obvious signs of toxicity were apparent in the skin (site of application) or any other tested organ.

This approach, obviously, has its limitations. In the mentioned study, the researchers applied the gold nanoparticles only to the skin. They did not mention or speculate about how the golden spheres could be delivered to another organ. After all, it’s not only skin that might require some siRNA. Direct injections might be effective, but this certainly requires testing. Additionally, it would be hard to imagine this technique being used systematically, say, to treat metastatic cancer. After all the authors point out just how localised the action of this method is. Nonetheless, this is a very promising discovery that seems to have a whole multitude of pros and limited number of cons. Hopefully, in the near future some of our conditions will get treated by rubbing some gold into our skin…

1. Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation.

Evolution of music

OK, this isn’t really totally in line with the life science theme of this blog, but I personally found it really cool! And this is because on one hand I am interested in biology and its concepts in general, and that includes evolution, and on the other hand – I love music. Additionally, I have always wondered, what makes popular music… popular? How come “Poker face” by Lady Gaga was such a hit while “Dance in the dark” not so much? And this study that I stumbled upon combines these two phenomena – evolution under selective pressure and music.

So, evolution under pressure. Without going into too much detail, when some organisms, which can be as simple as bacteria or as complex as humans, start living in a new environment that is in some way different than the previous one, they evolve. For instance, a long time ago people from Africa – where it’s hot – migrated north, where it’s colder. Breathing in cold air through black people’s wide nostrils was probably not very healthy as it cooled downs their respiratory tracts easily and facilitated viral infections. But some people randomly developed more narrow noses. The air takes slightly longer to go through such a narrow passage and so gets warmed up before it reaches deeper parts of our air pipes. Warm air is something viruses don’t like, so they were less likely to cause respiratory infections in narrow-nosed people. Less infections equals less death equals longer life equals more time and opportunity to produce offspring who would also have the narrow nostrils. And so, in the European climate the narrow-nose trait took over the wide-nose one.

The study I’m going to talk about next (1), conducted at Imperial College London, subjected music to a similar process of evolution under pressure. It infused short pieces of music with genetic features and as the selective pressure – it used human taste. How did they make the evolution of music happen? Well, first they designed some programs that created pieces of music made of notes occurring at pretty much random pitches and timings, or in other words, made of random melody and rhythm. Then they had several thousands of people listen to those musical samples and rate them based on how pleasant they were to listen to. The half of the samples that was least pleasant was eliminated (died), while the other half was allowed to randomly pair. Within pairs, bits of musical samples were exchanged between one another to create a new “daughter” piece of music, the same way that we get the genes from each of our two parents randomly. At this stage, the authors allowed for rare random changes in the “daughter” music samples, i.e. bits of music or rhythm not present in either of the “parent” tunes. This was mirroring mutations, like the occurrence of the narrow nostrils in white people. Obviously these random changes in the daughter pieces could be either pleasant for the listener or unpleasant and contributed to either higher or lower score they received. And then, again, the highest-scoring 50% of samples was allowed to “survive” and “have sex” and produce the next generation of musical offspring. If you go to http://soundcloud.com/uncoolbob/sets/darwintunes/, you will be able to listen to the whole concept presented by Dr. MacCallum, the lead author of the whole project (the first track on the list), as well as music samples selected at certain “generations”. It is fascinating to hear how music in these samples gradually changes from random noise-like sequences of sounds to quite organised, structured and pleasant pieces of music.

Obviously, the study doesn’t exactly mirror how pop music is created. Firstly, music as we know it did not start as a random collection of sounds that sounded plain annoying. Secondly, new pieces of music do not arise as hybrids of existing songs (well, for the most). I mean, even if someone did put together “Bad romance” with “Like a prayer”, I can imagine this mix gaining some popularity but I struggle to see it staying at the top of pop lists as long as either of these two songs did.

Nonetheless, the whole concept is very interesting and the samples are just fun to listen to!

1. Evolution of music by public choice.

An old protein with a new anti-HIV role

There are many viruses that you can have yourself vaccinated against, and sometime, like in the case of small pox, the vaccination can completely eradicate the virus from the face of the planet. HIV, however, is not one of them. It changes frequently and has evolved into many different strains presenting with varying behaviour. These strains can be so different that some antiviral drugs can be efficient only against one of them but not another.

One of the ways these strains differ is how they enter cells. You can think of a cell as a large room with many doors leading to it. And of HIV virus as a small malicious robot that enters these rooms and consumes them from the inside to manufacture its own copies. To open the doors, the robots have specialised arms. However some strains of the virus have arms that can only pull handles, while others can only turn knobs. This is mirrored in anti-HIV medications. For example, following this analogy, some drugs act as attachments that you put on the knobs to give them rectangular shape. The knob-turning virus won’t be able to grab it and get inside the cell anymore. However, the same drug won’t affect the handles and therefore have no effect on the handle-pulling virus. There are also strains of HIV that can both pull handles and turn knobs, but that’s a different story.

A recent publication (1) has revealed that our platelets (the tiny cell-like structures in our blood responsible for clotting) can secrete quite large amounts a long known protein called platelet factor 4 (PF4) that actually gets in the way of HIV infection. It does so by a mechanism similar to the one of the drug turning a round knob into a rectangle, but this protein does not bind to the doors on the cells, but instead to the virus arms. The data suggests that PF4 does not attach to the “fingers” of the viral arm, but rather in some way grabs it by the wrist and gets in the way of it getting a hold of the handle. Or the knob for that matter, as the researchers have shown that PF4 can affect both handle-pulling and knob-turning HIV strains. However, HIV virus isolated from a small number of people seemed to be unaffected by PF4. And this is another example of HIV diversity – most of the analysed strains are inhibited by PF4, but some – are not.

The research is interesting for a few reasons. Firstly, it identifies an important part of the HIV “arm” – the wrist. Much research has been focused on the fingers or the handles/knobs as it is them that interact with each other directly. It was interesting to see how grabbing the wrist can also significantly affect the ability of the virus to open the doors. Secondly, as the authors point out, PF4 not only binds the viral arm, but also activates the immune system cells, which might in turn further facilitate fending off the virus. Thirdly, identifying a new way by which body’s own proteins interfere with viral infection can open some doors to development of new drugs. And finally, as mentioned before, it further highlights the diversity of HIV, as there was a small number of patients whose virus did not seem to have been affected by PF4. This in turn further underlines the fact that, unlike for many other viruses, HIV therapy should be personalised to the behaviour of the particular strain infecting the particular patient.

1. Identification of the platelet-derived chemokine CXCL4/PF-4 as a broad-spectrum HIV-1 inhibitor.

HIV therapies: new challenges, new hopes

HIV is a very sneaky virus that has developed many strategies of evading the immune system. One of the strategies is direct transmission of viral particles from cell to cell. What other viruses normally do, is they infect a cell, use it to multiply themselves in the thousands and make the cell release the new viral particles ready to infect further cells. But cells infected by HIV also do something else. They create tiny channels by which they connect their content with the content of another cell. And HIV uses these channels like a motorway to quickly travel to a new cell and establish a new replication centre.
In a recently published study (1), scientists hypothesised that this highway route of transmission might not only be faster and more efficient in infecting new cells, but also increase the chances of the virus escaping the action of anti-retroviral drugs. Here’s what their theoretical idea was.
If an infected cell releases viruses to the environment, the new virus, before infecting the next cell, drifts around in the solution randomly, as HIV has no mechanism to home onto target cells. It’s a little bit like standing with your mouth open when it’s snowing: even though there are thousands and thousands of snowflakes around, only a small number will make it on your tongue. Let’s call this way a drifting virus infection. However, imagine there was a tube that you put in your mouth that has a large funnel on the other side. Hundreds of snowflakes would find it much easier to travel directly through the tune into your mouth. Let’s call this funnelled infection. Now, let’s change the analogy and think of the virus as wasps invading your house and travelling straight onto the doughnuts on your kitchen table, and your anti-wasp spray will be the anti-retroviral drug. When you get the odd wasp every now and then (drifting infection), you can easily fend them off with your spray. But when you get hundreds of them barging through your window in an instant (funnelled infection), chances are, you will miss a few and they will reach the doughnuts. In the viral terms, it means escaping the anti-retroviral drugs and establishing an replication centre in a new cell. So this was the scientists’ theory, but how did they test it? Quite simply. They took some cells and mixed them with a solution of the virus, and either mixed in some drugs or not. As expected, many cells got successfully infected in the absence of the drug, while in its presence, very little did. For the second part of the experiment, they mixed some cells which were already infected by the virus and were red with some uninfected cell, which were green. And again, they did it in the presence or absence of the drug. After some time they removed all the red cells, and counted how many of the green ones were infected. And consistently with their theory – even though the drug decreased the number of green cells getting infected, this reduction was nowhere near as successful as that observed in the first part of the experiment. The wasps flew in in their hundreds and often managed to escape the spray.
AIDS is one of the worst pandemics to have ever affected the world. There is no cure, and the development of a successful vaccine is still in infant stages. Currently, the only thing that can be done is to use anti-retroviral therapy to control the virus and minimise the damage it does to patient’s body. The research I mentioned here can be seen as both bad news and good news. Bad news, because it shows the weakness of the current anti-retroviral therapy. Good news, because it showed how important this alternative way of virus transmission is. Now that we realise it, we can try to develop new drugs, which will close the connections between the cells. Or, using our metaphor, close the window and not let any wasps in. There’s a new challenge, a new hope.

1. Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy

Protein crowding can harm and help

Some time ago, I wrote about how mislocalised proteins get binned immediately. Otherwise they might form dangerous clusters, such as those that cause the human form of mad cow disease. It turns out that this process – protein aggregation – might actually play an important role in our bodies and help protect us against viruses.
Faulty prion proteins are deadly not because their localisation and shape is incorrect, but because they cause deformation of other proteins which were normal to that point. Then, the newly distorted protein deforms another one and so on. This chain reaction on one hand partially depletes the cell of normally shaped and functional proteins and on the other, causes aggregation of the misfolded ones, which you might think of as a big pile of sticky rubbish. When a neuron cell is overwhelmed by such a pile, it can no longer function normally and decides to die. Such a decision, a cell suicide, by scientists called ‘apoptosis’, is nothing unusual and happens to many cells in every healthy person’s body. Normally, a suicide cell partially digests itself from the inside and the “corpse” is removed by other cells. But the problem with a prion aggregates from a dead cell is that they are very resistant to digestion. They persist and can come in contact with normal proteins on surrounding cells, causing them to misfold. This process is similar to a viral infection: a virus, after killing one cell, in which it copied itself thousands of times – infects further cells. And similarly, a misfolded prion protein – after forcing other proteins to misfold and killing the cell it originated in – moves on to other cells and causes more damage.
All of the above makes it seem like the progressive aggregation of proteins is something dangerous and deadly. But scientists in Texas found that there is another protein that behaves in a very prion-like way, but actually does it to protect us (1). The protein is called MAVS and it was known for quite a while that it responds to viral infections: when a virus enters a cell, the MAVS protein is able to pick it up and instruct the cell to activate an anti-viral programme. Fajian Hou and colleagues showed that what viral infection actually does, is aggregation of the MAVS protein, and only in this clustered form can it start the virus defence. They also found that even MAVS aggregates made synthetically (and not by viral infection) are able to activate the anti-viral programme. And these aggregates, just like prions, after enzymatic digestion don’t get destroyed and are still functional. Another similarity to prions came from the observation that pre-made MAVS clusters can enforce aggregation of natural MAVS proteins. And all this happens to help our cells fight the viral invaders.
From all of the above it appears that MAVS can very much behave like a prion protein – it aggregates, it doesn’t get digested easily and it can make other MAVS proteins aggregate too. But instead of making us worse – this actually helps to make us better. It is not clear however, what happens next. Since the aggregates are so resistant to digestion – how are they cleared? Is there another yet-unknown enzyme that actually can digest or untangle them? Do they de-aggregate spontaneously? Hopefully, one day these questions will find answers and the answers will help fight diseases caused by the evil prions.


1. MAVS Forms Functional Prion-like Aggregates to Activate and Propagate Antiviral Innate Immune Response

New hope for after-stroke treatment

But the message is not crystal-clear

Researchers from Stanford, California, have found that a protein well-known to be a part of our eyes might provide protection after stroke. The protein is called crystallin and is called so because it was discovered as a protein that supports our eye lens structure and is responsible for its optical properties. It was later found to be produced by other tissues of the body including many kinds of brain cells. Ahmet Arac and colleagues set out to investigate if the protein might have any function in the aftermath of a brain stroke.
When mice suffered stroke, the researchers discovered that animals that were not able to produce crystallin, showed larger area of brain injury and the stroke itself affected their motor functions to a much greater extent. When they looked closer at the lesions, they found there was much more inflammation going on in the animals without crystallin. Even though inflammation is there to fight damage, when excessive, can cause even more of it. To make sure that it is crystallin that makes the difference, the scientists went on to inject it into the mice that couldn’t produce it themselves. And as expected, this procedure made the brain lesions size comparable to that seen in mice which can readily produce their own crystallin. But then they thought – that’s not actually a real-life situation, because all humans produce crystallin, so we could never use it to help people who don’t. So they decided to check if they will see any difference after injecting crystallin to mice that can produce their own. And indeed – when the protein was given to these animals after the stroke their lesion area was much smaller than when they received no treatment. And importantly, this effect was apparent even when they waited with the injections until 12 hours after the injury. Now that seems to be more applicable in real-life situations, especially when something stands in the way of immediate treatment of a stroke victim. And apart from experiments in mice, the researchers also asked whether crystallin might be important in human strokes. They tested the blood of several patients who have suffered stroke and discovered that indeed the protein levels are higher than in healthy people, which might suggest that human body after stroke also uses that protein to minimise the damage caused.
So is this discovery a new hope for stroke patients? Might very well be. The research quite convincingly shows that crystallin plays an important part in minimising the damage done to the brain following a stroke, by alleviating the severity of the inflammation. It even shows that injecting crystallin as a post-stroke intervention can do the trick. But what I found missing from these studies, is looking at how the animals did in terms of motor functions after they were given the protein, as the authors did not show that. Obviously having less inflammation in your brain is an encouraging result, but is it still any good if there is no difference in the damage caused? Hopefully they will address this issue soon and a new treatment for stroke patients might soon be under way.


Systemic augmentation of αB-crystallin provides therapeutic benefit twelve hours post-stroke onset via immune modulation

Undelivered items go to BAG6

A story of how bin men work at the post office in our cells

Our cells produce all sorts of proteins with all sorts of functions. But to fulfil these functions the proteins must be in the right place. There’s no use for a protein that should be in the nucleus to stick around the outer membrane and like wise. When a protein needs to go to a specific compartment of the cell, this information is encoded in the protein itself. It’s like the address on an envelope. And interestingly, the machinery responsible for protein delivery starts working even before the synthesis of the protein is finished. It’s like we addressed an envelope, then started writing a letter, and before we finished it, our personal postman was already putting the address from the envelope into his sat nav.
Because there is so many various proteins being synthesised in the cell at any given moment, these postmen sometimes can’t keep up and happen miss a “protein letter”. The protein would then just stick around and clutter the wrong compartment of the cell. Now obviously, apart from post men, our cells are also equipped with bin men, who take care of such undelivered protein mail. A recent discovery (1) found that these bin men are actually very vigilant and work in a fashion very similar to the postmen. They hang around the protein factories, and as soon as they see a protein addressed to the membrane that wasn’t spotted by any of the postmen, they grab it and put it in their trash bag. Interestingly, one of the proteins responsible for this process is called BAG6.
You might wonder, is this discovery really that important? Isn’t it science just for the sake of it? Would a cell really mind having some litter laying around its protein synthesis offices? Well, actually, it would. Apart from just not being able to fulfil its function at the right compartment of the cell, a protein that isn’t where it’s supposed to be, can behave in an unpredicted and sometimes harmful way. This is one of the causes for Creutzfeldt-Jakob disease, otherwise known as the human form of mad cow disease. A so-called prion protein, the cause of this disease, is normally supposed to find itself in the cell membrane. But when it doesn’t and stays in the cell cytoplasm (where protein synthesis occurs) it tends to form aggregates which are very resistant to being cleaned up. These aggregates start affecting the functioning of the whole cell, and because the protein is mainly produced in the brain cells, the brain’s function gets severely impaired. If this research goes further, maybe the scientists will be able to better understand the onset of the disease, and maybe even come up with novel therapies to either treat patients affected by it, or prevent its development in people who have a family history.
So that’s the story. In our cells, bin men work as fast as they can to remove junk proteins which are undelivered. And wouldn’t it be great if all the junk mail we receive was binned just as it’s being put in its envelope?

1. Protein targeting and degradation are coupled for elimination of mislocalized proteins.