Cystic Hallelujah


Cystic Fibrosis is an inherited genetic condition, where specialised cells called epithelial cells, found in the lining of vessels (like the lungs, the intestines, the reproductive ducts…) do not function correctly. Normally, they would produce mucus, a slimy substance that reduces friction and allows substances to pass through the tracts more easily, but when suffering from Cystic Fibrosis, the mucus becomes less runny, so it is not as efficient at lubricating.

The most common treatment is physiotherapy, where an expert massages the chest area to help move the mucus along. This is an important area to do so, since if the mucus in the lungs gets stuck, it could house bacterial infections and cause trouble breathing. But as much as this may help, it still doesn’t cure CF, so infected people may still die quite young (around 40 years old).

A possible solution which has been considered for over a quarter of a century, since the single gene responsible for causing CF had been identified, has been gene therapy. This technique consists of introducing a healthy version of the gene into the cells of an infected person, and using it to replace the mutated version. However, there are several complications involved, and it has never been fully possible to carry this out and obtain good results. But not anymore.

liposome

A liposome is a phospholipid bilayer, which can fuse with cell membranes and release the gene it contains

In a new study carried out on 116 infected people, half received a gene therapy treatment, and half received a placebo. The treatment was a solution of liposomes that carried the desired gene inside them, and which the participants had to inhale so it could easily reach the lung cells. Although both were administered for 9 months, their effects were measured until after 12 months, and to do so researchers in charge measured the volume of air participants would breathe in and out in a set period of time. The results didn’t disappoint. People treated with gene therapy not only saw a stabilisation in their lung performance, instead of the disease’s characteristic downfall, but also had 3.7% better breathing capability than those people who had been given a placebo.

Although it may not sound like an impressive feat, it certainly is. Consider this is only the first time this has ever actually worked, and that it was a scaled down version of the treatment. The dose could definitely be increased so the effects are much greater. And even if the change seems small, it could postpone the need for lung transplants for decades.

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Equalitarian Blood


Blood flows around the body all the time, yet we barely see it unless we suffer from an accident. If this were the case, and we lost too much of it, we’d need a blood transfusion. But it is not as easy as just putting blood from one individual into another: you need to test it and make sure the blood is compatible.

RBC

Can you guess what antigens these red blood cells have?

This occurs because human blood can be divided into many categories. The most common one is the ABO group classification, which divides blood into four types: A, B, AB and O. In each, red blood cells (those cells specialised in carrying oxygen around the body) have a specific antigen depending on the blood type. For example, if you have group A blood, you will have A antigens; if you have AB blood, you will have A and B antigens; and most importantly, if you have O blood, you will have no antigens.

Each antigen stimulates a response from our immune system to produces antibodies against the other antigens. So if you have blood group A, you will produce antibodies that will destroy cells with antigen B, and vice versa. This is potentially very dangerous, because if you give someone of type A blood from a person of type B, the antibodies can attack each other’s red blood cells and wreck havoc in our bodies.

When it comes to transfusing blood, the best one is group O- since it has no antigens, so there is no way your body can attack it. That is why we call it universal, since it works for anyone, no matter their blood type. This makes it very sought after for blood transfusions, but there isn’t always plenty of it available.

But what if we could convert all blood into O type blood? We can’t change the genotype of adults so that their body produced it, but we can change the blood itself after the blood has been donated. The most successful way to do this would be to insert bacterial enzymes into the blood which can recognise antigens in the red blood cells and cut them off so they are just like red blood cells from O group blood.

In the experiment which created this mechanism, the original enzyme worked mostly with cells from group B only, so to make it effective on cells from group A too they used a very interesting method called directed evolution. It’s just as it sounds: they grew the bacteria that produce this type of enzyme, and slowly mutated their genome (by adding bases to their DNA) so that every generation produced a better enzyme. At the end of the experiment, after 5 generations of bacteria, the final enzyme was produced, which not only could severe A antigens, but was also an impressive 170 times more efficient than the original one.

Yet this method is still not perfect: the enzyme can’t modify all the thousands of red blood cells in a sample of blood and therefore can’t make it completely safe, as there will still be some red blood cells with antigens present. But with enough time, the scientists hope to perfect it and make the technique available so blood transfusions are easier to carry out.

Evil Twin’s Downfall


So what if we have an evil twin, like in the movies? If he/she commits a murder, and DNA evidence is found in the crime scene, both you and your evil twin will be suspects, since you share the same genetic material. Although this is a rare and unlikely scenario, it is definitely a possibility, and has actually happened several times throughout the years.

Usually, this will end in no one being prosecuted, since it would be impossible to determine which twin did it, and sending both to jail would be terribly unfair to the innocent sibling. A new option for the police in these cases is to analyse the DNA of both twins in incredible detail, searching for any slight variations that may have randomly occurred due to mutations and changed the genetic code, but this option takes a lot of time (over a month) and also happens to be very costly.

twins

Now we can find out which twin actually did it

However, scientists have now come up with a sort of an upgrade to this method. Instead of looking for mutations, which occur randomly, they would look for differences in the DNA strands that have been caused by their way of life. These modifications are called epigenetic changes, and instead of causing a gene to change its sequence of bases, it just modifies how it is expressed into a protein. It can do this by adding a methyl group (-CH3) or by altering the histones in our DNA: the proteins that help condense our genetic information into a more compact shape so it can all fit into the nucleus of a cell.

These changes can be inherited, which would be unhelpful since both twins can have them, or caused by environmental factors, which would also be unhelpful if the twins have lived close together in the same conditions. Fortunately, very small differences can cause these changes, specifically in the early stages of the embryo’s development, so although still rare, these changes do exist in twins.

In the specific case of epigenetic changes by methylation, this would mean that the DNA strand is now larger, and has more molecules in it. This would increase the forces of attraction and increase its melting point. Since both twins will have different changes, and therefore different amounts of methyl groups, their DNA would not melt at the same temperature. So comparing their DNA’s melting temperature with that of the DNA found in the crime scene can tell the police which of the two twins did it, and solve the mystery in a much faster and cheaper process, as you only have to heat the suspects’ sample.

Mom, Dad and the Mitochondrial Donor


They say three is a party. But in this case, three parents may be just enough parents to save future babies from suffering a crippling disease for the rest of their lives.

We are talking about the mitochondrial replacement procedure. Found in the cytoplasm of a cell, mitochondria are powerhouses which supply it with energy to function and survive. However, they are not perfect organelles, and may sometimes have mutations which cause disease. Unfortunately, this can be passed on to children, since when fertilisation occurs, it uses the mother’s egg cell as the starter cell, and so all of her mitochondria, meaning that any subsequent cells that form from that zygote will carry the mother’s defective mitochondria.

zygote

A human zygote, which would contain a nucleus with genes from the mother and the father, and mitochondria from a donor

To prevent this, scientists have designed a new process, called mitochondrial replacement, to be carried out on women with mitochondrial diseases, allowing them to have children and prevent these from also suffering from the disease. It is done by a form of In Vitro Fertilisation. An egg cell from the mother and a sperm cell from the father are taken, like in normal IVF. The change comes when we add another egg cell, this time from a different woman (a donor). The nucleus of the mother’s egg cell is taken and it replaces the nucleus from the donor egg cell. The sperm is then allowed to fertilise the new egg cell and a zygote is formed which can then be implanted onto the mother and allowed to grow into a healthy baby. This way, the zygote will develop from a cell which contains the mother’s genes, but none of her mitochondria, so the baby is safe.

Messing around with zygotes is never child’s play, and always carries some controversy. In this case, it is due to the questionable effects of adding a third group of genes to a person. Since mitochondria are essential for life, having them come from a different source than the rest of the genome could have unpredictable consequences.

Despite some uncertainty, the UK government has approved this measure, saying there is no real proof it is unsafe. Rest assured, there will be plenty of human trials before it becomes a standard procedure, but at least it’s a brave step towards helping people suffering from these diseases improve their lives.

Micro Slavery


bacteria culture

This is the only way these modified organisms can live: in a dish in the lab

Bacteria can be both useful and lethal. In either case, scientists want total control over them to maximise their efficiency or prevent any diseases. However, it does sounds impossible: how can humans control a bacterium, which is a free living organism so small we can’t see it with our naked eye and is incapable of understanding our commands? But of course they have accomplished this, or otherwise I wouldn’t be writing an article on it.

Subjugating bacteria is done by a simple method. All living organisms require proteins made out of amino acids to live, and bacteria are no different. They use them to carry out many varied functions: they act as enzymes, hormones, connective tissue… so if you control how bacteria make proteins, you can basically dictate how they live their lives. Since proteins are coded by the DNA, scientists tweaked the genetic information so that bacteria didn’t code for proteins they way they would usually do. But changing the whole genome is a long, tiresome process; so instead, they targeted a specific set of genes which code for a specific set of proteins: those that are crucial for a bacterium to make other proteins. It is quite effective. If bacteria can’t make the proteins that guide DNA transcription and translation (the processes that produce proteins), then the bacteria are hindered and can’t work any further.

The modifications involved changing the bases in the DNA sequence so they didn’t code for the usual, natural amino acids. Instead, some new bases introduced coded for an artificial amino acid, created and only found in the lab, so proteins could only be made if this one artificial amino acid was present. This idea, although creative, was developed by two independent teams, one of which used a large, artificial amino acid and the other used three different artificial amino acids. Either way, if these bacteria wanted to survive, they would have to stay in the lab, the only place where they can obtain the amino acid necessary for creating proteins.

The main implications of this development are related to genetically modified organisms (GMOs). People fear that creating beings with features enhanced in the laboratory is dangerous, and if they somehow make it into the wild and grow there, they can harm other, more natural species, or reproduce with them, which would destroy the natural balance of natural selection. This technique solves both of those problems, since the new GMOs developed with dependency on this amino acid would only be able to live in the lab, and could be easily controlled and kept in small numbers.

Antibiotic Hero


Antibiotics are the real wonder drug. They were a revolution in the 20th century, capable of fighting the most powerful bacterial infections. Scientists understood their potential and worked tirelessly to create a wide variety of them to harness their power, but eventually they stopped. Since the 1980s, no new antibiotic has been discovered. Since we have a great amount of them, it wouldn’t be too big of an issue, if it weren’t for a growing problem: resistance.

Due to the threat antibiotics represent to bacteria, these organisms feel a high selection pressure to evolve and develop new ways to defend themselves from these drugs. And they have succeeded. Many strains of bacteria, especially for diseases like MRSA and TB, have become immune to many antibiotics and are proving really hard to fight. Due to the increase in antibiotic resistance, there has been a hunt for new antibiotics in the recent years, and it has finally paid off.

The most common way to obtain an antibiotic is from bacteria themselves. We are not the only ones who want to get rid of them; competing bacteria do too. So when these bacteria develop chemicals to destroy other bacteria, we need to extract them and use them to our advantage. But to extract the chemicals, bacteria need to be cultured in the lab, which can be difficult at time, since the most used bacteria for this process are found in the soil, which has conditions difficult to recreate in the lab. A new method created by researchers in Boston could solve this: it consists of creating a culture with three layers: two layers of soil on either side of a semi permeable membrane. These are perfect conditions for bacteria and have made it possible for thousands of them to grow and for a possible new antibiotic to be isolated.

teixobactin

Teixobactin could fight TB and other diseases which, over the years, have become immune to our medications

 It’s called teixobactin, and it targets proteins on the membrane of bacteria, eventually killing them. Because of its complicated mechanism, it is very hard for bacteria to develop resistance to its action. However, it is not impossible. Scientists predict that if used correctly (that is, without overprescribing), teixobactin could be effective for over 30 years, quite a long lifespan for an antibiotic. As it is completely new and bacteria have never been exposed to it, many say it could be the key to fight multidrug resistant bacteria, fighting superbugs and giving us and edge over the most fierce and dangerous infections. These hopeful results have yet to be confirmed in human trials, but the effectiveness of the new antibiotic seems to be as good as it sounds in animal tests.

 With this new method and this new antibiotic, the future of medicine could prosper, and bacterial infection could remain an enemy we can defeat.

2014 Science Highlights: Part 2


Continuing last week’s list of the most interesting scientific events of 2014, here I present 5 more discoveries that marked this year.

6. Curious Curiosity

moon earth curiosity

The picture Curiosity took in which the Moon and Earth can be seen together

2014 was Curiosity’s year. It was always present in the news, whether it was because of its 2 Earth years anniversary, its 1 Martian year anniversary, the popular selfie it took of itself or the breathtaking picture of the Moon and the Earth. But Curiosity is not only a great photographer; it’s a great researcher too. Since its arrival on Mars, it has provided us with a lot of information about the Red planet. It has made some curious discoveries on the methane gas concentrations in Mars’ atmosphere, and the deuterium to hydrogen ratio, to shed some light on the controversial history of water in Mars.

 7. ALS Fever

als icebucketchallenge

ALS got lots of attention from the insanely popular Ice Bucket Challenge

The Ice Bucket Challenge swept the world; almost everyone, from celebrities to normal citizens did it, and most donated some amount of money to the ALS Association. Overall, $115 million dollars were raised, and the money will now go into helping people with this condition and into research for a treatment and a cure. Although ALS is not a very common disease, it is a crippling one and can leave those affected with a very disabled life. Therefore, it is absolutely amazing to see the amount of support this charity received, and very hopeful how much effort was put into spreading awareness.

 8. The $1000 Genome

genome 1000

By making reading genomes cheaper, we are getting closer to personalized medicine

A machine that could effectively read a person’s whole genome for less than 1000 dollars was invented this year. This has been a very sought after discovery, and a milestone in the genetic field. Scientists have expected this for years, and it is such an important creation that even prizes were created for those who could accomplish this feat to motivate scientists into researching it. Now that we finally have it, it’s better than we imagined. The machine can actually sequence 5 sets of genomes per day. This could set off a revolution in genomics, and fasten the pace of discovery tremendously.

 9. Giant Dinosaur

giant dinosaur

A drawing of the largest creature ever; its size is roughly that of a seven-story biulding

Dinosaurs have always been known for their size, ferocity and majesty. A new species of dinosaur discovered in Patagonia has been calculated to measure 40m long and 20m high, with an estimated weight of 77 tonnes; that’s 77000 kg! Not only is this the largest dinosaur ever found, but it is also the largest animal to ever walk the Earth. What’s also great bout this discovery is that there were dozens of bones from this creature and allconserved in a great condition, so investigating these bones won’t be too difficult. Unfortunately, it still doesn’t have a name; it is such an important aspect that archeologists want time to think of a name that can represent the importance of this animal.

 10. Fake Life Flourishes

X and Y

Base X (left) and base Y (right), completely new bases which act like the natural ones

Synthetic biology grew greatly this year. On one hand, scientists were able to create a synthetic version of yeast’s chromosome, by substituting the original, natural genes by artificial ones created in the lab. But also, two new bases were proven effective this year. All animals use the usual 4 bases (A, G, C, T) in their genes to code for proteins. But new research has created a bacterium that uses two extra bases, named X and Y, which can code for new amino acids and extend the range of chemicals organisms can produce.

 

2014 was a great year for science; let’s hope 2015 has even more interesting and fascinating discoveries in store for us!

Smoking Out Y


When people smoke, not only do they inhale burnt pieces of paper which damage their lungs, or have tar accumulate inside of them, which is likely to cause lung cancer, or inject nicotine into their bloodstream, which increases heart rate and blood pressure; it also causes the Y chromosome to eventually disappear. Of course, this only affects males, since the presence of a Y chromosome determines you’re male in gender, but for women smoking is still unhealthy and should be stopped.

Chemicals in tobacco affect this chromosome during cell division or mitosis when the chromosomes are being separated to either sides of the cell. Damage to the chromosome can build up until it eventually disappears. The study, carried out in Sweden, showed that people (men, specifically) who smoked had 33% more chances of loosing their Y chromosome compared to men who didn’t smoke.

However, it has been widely thought for many years that the Y chromosome is so small (in fact, it’s the smallest out of our 46 chromosomes), that its loss wouldn’t have too dire consequences. Past experiments on cells show that they can survive just as well without said chromosome. But new studies show that the lack of this chromosome, although not directly fatal, can shorten life duration and causes an increase in the likelihood of developing cancer. Lung cancer or any other cancer having to do with the respiratory system aside, male smokers are twice as likely to develop cancer as female smokers.

A possible explanation for this is that the Y chromosome contains tumour suppressing genes, so if it disappears, tumours are not going to be controlled and inhibited and therefore will be able to reproduce uncontrollably, causing cancer.

The newest research shows that this effect changes intensity depending on the dose of tobacco smoked. Obviously, the more tobacco you smoke, the more likely you are to suffer from its negative effects. But there’s a silver lining: this process is reversible. If you were to stop smoking, your cells would stop taking damage and after some time they’d be repaired, so you would have the same percentage of healthy cells with a Y chromosome as a non-smoker.

y chromosome

The Y chromosome is more important than you think in the fight against cancer

 

XNA Alternative


DNA and RNA have always been considered miracle molecules thanks to their ability to self-replicate and create life. Everyone thought that they were the only molecules that could carry information on how to code for an organism and pass this down for generations. But what if I told you there were other molecules capable of doing the same thing?

This group of molecules is called XNAs (Xeno Nucleic Acids) and they all are a polynucleotide strands but each with a different repeating monomer. They still have a base and a phosphate group attached; what changes is the sugar in them. Whilst DNA uses deoxyribose and RNA uses ribose, XNA can use a wide variety of sugars, like theorose, or other unrelated chemicals, like peptides.

DNA XNA

This is a normal DNA strand – XNA is the same but with a different sugar in the nucleotide

Not only do they copy the structure of a nucleotide and therefore form a nucleic acid, but they can also store information in the form of bases. However, to make XNA carry bases in a desired order, scientists have to use an enzyme that copies the coding from a DNA strand and passes it onto an XNA strand. Once there, another enzyme can read the bases in the XNA and copy them onto DNA, and if needed, back to XNA. This means that an old XNA can technically pass information to a new XNA molecule, even if it uses an intermediate molecule; this process is basically evolution.

But this discovery is from back 2012. The current news involves XNA being able to act as enzymes, apart from encoding possible genetic information. They still can’t form copies of themselves in the traditional sense, but they can manipulate RNA and even add XNA fragments to an XNA strand. The fact these molecules are enzymes and can modify themselves to some extent makes it more feasible that at some point they will be able to self-replicate, and behave just like DNA did, to evolve into a new type of life.

It is also further proof showing that XNA is a viable alternative to both DNA and RNA, and that the reality that all living organisms we know use these nucleic acids could be arbitrary. In fact, it could be perfectly possible than in other galaxies, organisms use XNAs instead of DNA. Of course, this is only a theory, and we have to take into account the conditions of an environment without any life. RNA and DNA could have developed because they were more likely to appear in the first place, for a reason unbeknownst to us yet.

Genesexual


gene

Although genes could now have a very important effect on men’s sexuality, the environmental impact is still significant

In the largest study on the matter up to date, scientists from Illinois have investigated the DNA of hundreds homosexual men and have found revolutionising results that show that being gay could have a strong genetic influence.

Although the genome is a vast structure, home to thousands of genes, there were two very specific areas contained in it that were analysed in detail. Both these areas have been known by the scientific community for quite some years. For example, one of them, located in the X chromosome, and called Xq28, was first suspected to be related to homosexuality in a smaller study in 1993; whereas the other one, 8q12 in chromosome 8, was discovered in 2005. The aim of this experiment was to confirm these areas had some effect on sexuality in men and investigate how they caused this effect.

Overall, 818 men, all gay, volunteered for this project. This is almost 20 times more people than in the study in 1993. But to make it reliable as well as statistically accurate, many of the test subjects were brothers; in some cases, even non-identical twins! Having two closely related individuals with similar genetic makeup can make differences in their genome stand out and their distinct effect on the phenotype much easier to find. Using DNA collected over many years from blood samples, the scientific team looked closely at these men’s gene sequence. They were looking for small differences in the coding between brothers, specifically for single nucleotide polymorphisms, which are changes of only one base or nucleotide in a gene. After all the DNA samples were analysed, 5 single changes in the nucleotides were observed, and most occurred in these two regions of the genome.

What makes this study’s results worth considering is the fact that the only feature all these men shared was their sexuality: they were all gay. They varied in every other physical feature; so any change in those areas of their genome that was common to all men had to be related to their sexual orientation.

But both Xq28 and 8q12 are filled with genes, so although we know almost certainly that there are genes in there related to homosexuality, there is still not a distinct list of genes that could cause someone to be gay. Finding them hidden in these large areas full of coding is the team’s next task.

This discovery has, as could be expected, grave implications. It could help resolve all discrimination against gay people, and show that their sexual orientation is not a choice, but actually who they are. But unfortunately, it could lead some people to consider homosexuality as a biological mistake or a negative mutation, and even resort to genetic engineering to identify and remove ‘gay genes’ from embryos. This is wrong on many levels, but the most related to this article is that a person’s sexuality is not only defined by their genes, but is also affected by the environment they live in, so changing their genes is unnecessary and would not prevent homosexual people from being born.