BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: #mutations

Can CRISPR Gene Editing Cause Problems in the Embryos it is Meant to Customize?

Researchers from around the Tri-State area came together in 2020 to examine the effectiveness of the Crispr-Cas9 double stranded DNA break (DSB) induction on human embryos to repair a chromosomal mutation. The study, which was published in Cell, began with sperm from a mutated male patient at the EYS locus, which causes retinitis pigmentosa blindness. The researchers then attempted to use CRISPR-Cas9 technology to repair the blindness gene in a number of fertilized embryonic stem cells that carried the EYS mutation.  The results showed that about half of the breaks in the experiment went unrepaired, which resulted in an undetectable paternal allele. After mitosis, the loss of one or both the chromosomal arms was also common. This study shows that using CRISPR-Cas9 technology is still in its early days, and needs to be further vetted before it is used to treat patients.

CRISPR Cas9 technology

Instead of correctly and consistently editing the genome of the embryos, the Crispr-Cas9 wreaked havoc, leaving behind chromosomal trauma. The data shows that the embryos started to tear apart and get rid of big pieces of the chromosome that had the EYS mutation, some losing the entire chromosome. The promise of Crispr technology is about changing one gene, but how can that be done when a larger, untargeted part of the genome is also being altered? Dr. Egli, the paper’s main author, brought up a more likely use for the Crispr editing: deploying it as a form of “moleculure bomb”, sent in to shred unwanted chromosomes. An important part of using gene editing is the ability to consistently predict the outcome, However, the resulting “mosaicism prevents inferring the genotype of the fetus from a biopsy and is thus incompatible for clinical use”, according to the Cell authors.

There were many rarities that appeared in the alleles of the embryos used. With a small sample size, due to the difficulty to acquire human embryos, there was no ability to rule out rare events. Although there were combinations of maternal and paternal alleles that showed interhomolog events, they occurred after the two-cell-stage injections, all mosaic. A single Cas9-induced break can result in outcomes in the human embryo that suggest species-specific differences in repair. In on-target sequencing of the cells, the detection of only a wild-type maternal allele might have been because of the unrepaired breaks and the loss of the chromosomal arm or the loss of the entire chromosome. This study shines light on the dangers of Crispr gene editing. The quotes from researchers, doctors, and genealogists all echo the same risk, we must walk before we can run. Testing and ensuring the safety of using Crispr on an embryo before the first round of DNA replication happens is crucial to the ultimate promise of gene repair. If it can’t be done safely with no off target effects, then Crispr “would be deeply unethical”, according to Dr Faraheny from Duke University.

How Does Activation of p53 Effect the Use of CRISPR?

In a study conducted at Karolinska Institutet in Sweden, researchers looked into CRISPR gene editing and how that can play a critical role in mutated cancer cells as well as the medical field. CRISPR is “programmed to target specific stretches of genetic coding and to edit DNA at the precise location;” specifically, the CRISPR system binds to the DNA and cuts it, therefore, shutting the targeted gene off. Researchers can also permanently alter genes in living cells and organisms, and in the future, using this method they may even be used to treat genetic causes of diseases. Although CRISPR sounds amazing, will it really be as great as it seems?

CRISPR CAS9 technology

CRISPR

There are a few obstacles that need to be overcome before CRISPR can even become regularly administered in hospitals. The first is to understand how cells will behave once they are subjected to DNA damage which is caused by CRISPR in a controlled manner. When cells are damaged they activate a protein called p53 which has negative and positive effects on the procedure. The technique is less effective when p53 is activated, however, when p53 is not activated cells can grow uncontrollably and become cancerous. Cells, where p53 is not activated, have a higher survival rate when subjected to CRISPR and because of this can accumulate in mixed cell populations. Researchers have also found a network of linked genes that have a similar effect to p53 mutations, so inhibiting p53 also prevents these cells from mutating. 

Long Jiang, a doctoral student at the Department of Medicine at Karolinska Institutet, says that “it can be contrary to inhibit p53 in a CRISPR context. However, some literature supports the idea that p53 inhibition can make CRISPR more effective.” By doing this it can also counteract the replication of cells with mutations in p53 as well as genes that are associated with the mutations. This research established a network of possible genes that should be carefully controlled for mutations during CRISPR. This will hopefully allow for mutations to be regulated and contained more efficiently.

DNA, or deoxyribonucleic acid, is a long molecule that contains a genetic code; “like a recipe book it holds all the instructions for making the proteins in our bodies.” Most DNA is found in the nucleus of the cell, but a small amount can also be found in the mitochondria. DNA is a key part of reproduction because genetic heredity comes from the passing down of DNA from parents to offspring. Altering this DNA can have an impact on a number of someone’s physical characteristics. CRISPR does just that. It can be used to edit genes by finding a specific piece of DNA inside a cell and then modifying it. Since CRISPR is so new, it has its positives and negatives, but overall it is a groundbreaking discovery. 

DNA double helix horizontal

DNA

In conclusion, even though cells seem to gain p53 mutations from CRISPR, it has been discovered that most of the cell mutations were there from the start. Even though this is still an issue, we don’t know to what extent it can cause greater harm, so it will be exciting to see the new discoveries in the future!

What is the Real Reason Dog Breeds Vary in Size?

Dog (Canis lupus familiaris) (6)

Do you like big dogs or small dogs? This question is frequently asked, but how did we even come about having this option? Ancient domesticated dogs in the past 30,000 years differed in size but nothing as extreme as the modern size differences. Dogs now can range from 40 times in size, and these drastic differences emerged just in the past 200 years as humans started establishing more and more breeds. In a study conducted by Ewen Callaway, he looked at why dogs differ so much in size and how a mutation could be the cause of this. The mutation behind all of this has been traced all the way back to ancient wolves. It lies near a gene called IGF1(insulin growth factor) which researchers found to have a major role in the size variations of domestic dogs. IGF1 is a hormone that manages the effects of growth hormones and is primarily produced by the liver so liver diseases can cause its levels to change.

One variant stood out when comparing the region around IGF1 and dog sizes. This variant “lies in the stretch of DNA that encodes a molecule called a long non-coding RNA which lives in controlling levels of the IGF1 protein.” A gene variant is a permanent change in the DNA sequence that makes up a gene. Variants can be inherited from a parent or can just occur during a person’s lifetime. If a variant is inherited from a parent they are present in pretty much every cell of the body while a variant that occurs during someone’s lifetime is present only in certain cells. Most variants that lead to disease are not common in the general population; however, some variants occur often enough in the general population to be considered common genetic variations. Examples of this would be eye color, hair color, and blood type. Even though DNA variants can be seen as a negative, as it is explained not all variants produce fatalistic effects.

There are two identified versions (alleles) of the variant, which Callaway identified. An allele is a form of a gene and each organism inherits two alleles, one from each parent. Dogs who have two copies of one allele typically weigh more than 55 pounds and have higher IGF1 protein levels in their blood. Whereas, dogs with two copies of the other allele tend to weigh less than 33 pounds. In addition, there are dogs with one copy of each version and they tend to be intermediate in size. Researchers determined that the same relationship was present in other canids as well, such as foxes, coyotes, and wolves.

Protein IGF1R PDB 1igr

IGF1 structure

The allele linked to small-bodied animals is seen to be much more evolutionary than alleles linked to large-bodied animals. Coyotes, jackals, foxes, and a lot of other candids have two copies of the small version, suggesting that this variation could have been present in their ancestors. However, it is not as clear as to when the large-bodied allele formed. It has been traced back 53,000 years ago to an ancient wolf living in Siberia, and since then has been found in other ancient wolves. Robert Wayne, an evolutionary biologist at UCLA, states that the view used to be that animals that have a small body size can be linked to genetic changes that could be unique to domestic dogs. This study could be a sign that dogs were domesticated from smaller wolves rather than present-day gray wolves.

Overall researchers have discovered a big part as to why dogs vary so much in size, however, the story of dog size is far from complete as IGF1 proteins only make up 15% of the difference in dog size. Even though this is such a small percentage, we are 85% closer to finding the whole meaning.

How are new COVID variants identified?

COVID variants are of high concern for scientists studying the disease. Some variants can be more infectious or cause more severe illness. Additionally, some variants can evade vaccines by having different surface proteins than the variant the vaccine was created for. This causes the antibodies produced from the vaccine to be less effective against other variants. In AP Biology class we discussed how the Delta Variant, first identified in December 2020, has a different spike protein structure than the original virus from which the vaccine was created from. This allows the variant to be more infectious, and make the vaccine less effective against it. But, what are COVID variants? And how are they discovered? Hand with surgical latex gloves holding Coronavirus and A Variant of Concern text

COVID variants are “versions” of the virus with a different genetic code than the original one discovered. However, not every mutation leads to a new variant. This is because the genetic code of the virus codes for proteins. Some mutations will not change the structure of the protein and thus not change the virus. So, COVID variants can be defined as versions of the virus with a significantly different genetic code than the original virus.

To detect new COVID variants, scientists sequence the genetic code of virus which appears in positive COVID tests. Scientists look at the similarity of the genetic sequences they find. Then, if many of the sequences they get look very similar to each other, but different to any other known virus, a variant has been discovered.

To sequence the RNA of the virus, scientists use what is called Next Generation Sequencing (NGS). To understand how NGS works, it is best to start with what is called Sanger Sequencing. Sanger Sequencing utilizes a modified PCR reaction called chain-termination PCR to generate DNA or RNA fragments of varying length. The ending nucleotide of each sequence is called a ddNTP, which contains a florescent die corresponding to the type of nucleotide. The addition of a ddNTP also terminates the copying of the particular sequence. The goal of this PCR reaction is to generate a fragment of every length from the start to the end of the sequence. The sequences can then be sorted by length using a specialized form of gel electrophoresis. The sequence is then read by using a laser to check the color of the fluorescent die at the end of each sequence. Based on the color and size, the nucleotide at that position of the genomic sequence can be found.

Sanger Sequencing Example

The difference with NGS is that many sequences can be done in parallel, allowing for very high throughput. In other words, with NGS many COVID tests can be sequenced in once.

Mu Vs. Delta: Which is the Scarier SARS-CoV-2 Variant?

The Mu variant has been a term of interest in a lot of peoples conversations. This is due to the fact that it has been getting a lot of news coverage as one of the latest variants of the world wide virus SARS-CoV-2. It has been portrayed to be the next big virus ready to take over the world, but, does it have the legs to do so and how much more dangerous is it than other mutations such as the Delta variant?

Laboratoire de Physique de la Matière Condensée laboratoire PMC - 46940329992

The Mu variant first popped up on January 2021 in Columbia and has spread to about 39 countries since then. Mu is very similar to the original version of the SARS-CoV-2 virus. However, where it differs is at the two mutations E484K and K417N. These are what cause Mu to be seen as a variant of the original virus. The traditional anti-bodies that would normally be able to stop SARS-CoV-2 are seemingly ineffective against Mu leading the World Health Organization to classify it as a “Variant of Interest”. This classification means that it will continue to be monitored closely to derive the best possible plan on how to contain it. The mutations of Mu give it different properties such as mutation E484K, this mutation caused a drastic change in the structure of the original Covid-19 protein and thus made it so that it is able to by pass the human immune system easier. This is seen as a big problem because studies of how the anti-bodies effect SARS-CoV-2 conducted in US and UK compared to those conducted African countries have shown that African cases seem to be severely less effective against SARS-CoV-2. Researchers believe this is due to Africa being exposed to significantly more cases with the E484K mutation. As discussed in class this sequence of numbers and letters means that in the original amino acid sequence at spot 484 there was a Glutamic Acid amino acid (which is a negatively charged), and then once the mutation occurred it then became Lysine which is positively charged. This change in properties is what causes the protein to fold differently thus causing a severe changes as to how it behaves in humans. The Mu variant seems to have been able to disregard the anti-bodies and still effect the human body. However this seems to be the reach of its dangerous mutations because as of now scientist have no reason to believe that Mu is any more transmissible than the original virus which is a good sign.

The Delta variant has been an extremely worrisome mutation for some time now with the first case being noted back in October of 2020 believing to have originated in India. The Delta variant has been one that has taken over the world recently and it seems as though the former version of Covid-19 is a thing of the past and that Delta is the new pandemic. This is due to Delta’s interesting mutation P681R. The original amino acid at place 681 was Proline which has no charge, however after the mutation occurred it became Arginine which is negatively charges causing the amino acids to behalves differently with each other and the environment. This mutation is the cause of Delta’s incredibly rapid spread throughout the world. This ability to be globally spread in months is just one of the reasons why it has also taken the lives of so many as more people are getting Delta over the initial virus now.

Ultimately, it is clear which variant has been seen as the more dangerous by the media: Delta. However, while the Delta variant is scary in it’s own right, it just seems to be a faster spreading SARS-CoV-2. Meanwhile Mu has a way to almost be a completely different virus as it spreads just as fast as the original virus (it only took 4-5 months to completely shut down the world). It is also able to completely bypass the anti-bodies if you already had Covid-19 or have the vaccine. If this virus reaches levels of spread to the likes of Delta then scientist are going to have to create a new vaccine for Mu as it is simply to dangerous to ignore. Feel free to share how you feel about all of this and let me hear your take on the more menacing variant!

A New Way to “Tangle” with Diseases? British Scientists Think They’ve Stumbled Upon the Future

A team of scientist from the Universities of Bath and Birmingham have made a discovery that is making noise in the world of Biology. Ironically, they had the realization while studying silent mutations in DNA. What they found is a new method of evolution. Well not a new method per say as the scientists predict this method is being used in all forms of life; however, new in the sense that it was only recently realized. What they have discovered is a trend of tangles in DNA strands. This tangling occurs in DNA strands that are not in a double helix as DNA typically is. However The DNA strands are separated during copying. This task is done by DNA polymerase enzymes. During the copying process, the enzymes are often disrupted by the tangles in the strand. The resulting skipping of genes causes specific mutations to the DNA.

DNA replication split horizontal

The scientists then tested their hypothesis by way of experiment. They did so by studying the evolution of soil bacteria called Pseudomonas fluorescens (SBW25 and Pf0-1). They began by removing the gene that give the bacteria the ability to swim. They then observed the re-evolution of the strains to regain the ability swim. Both strains evolved quickly; however, there was a clear differences in predictability. One strain (SBW25) mutated the same part of a particular gene in every trial. The other strain (Pf0-1) varied in which gene and where the mutation occurred in each trial. Upon further observation, this contrast coincided with a hair-pin shaped tangle in the SBW25 strain. As the DNA polymerase enzymes would pass this tangle they would be effected in a predictable manner that would disrupt copying of DNA and result in a mutation that allows for the bacteria to swim. The scientists tested the theory by removing the tangle. They did so using 6 silent mutations so that the DNA sequence would not have a relevant change. The trials after the change showed that both strains showed inconsistent areas being mutated.

 

DNA are the dictators of protein synthesis in the body. The DNA sequences code for the types of proteins that are created. Proteins perform many of the bodies function. This means that even the slightest change in the sequencing of DNA can have major effects on the functioning of a human body or any organism. The process of evolution was thought to be caused by random errors in DNA sequencing that coincidentally gave an organism a survival advantage. These mutations would then be tested in the concept of survival of the fittest. While this is still thought to be the most prevalent form of evolution, especially with eukaryotic organisms, the tangling of DNA strands proposes a form of evolution that would be easier to study and predict.

 

The predictability of such a phenomenon is where the intrigue in viruses arises. “If we knew where the potential mutational hotspots in bacteria or viruses were, it might help us to predict how these microbes could mutate under selective pressure.” says Dr. Tiffany Taylor, from the Milner Centre for Evolution. Mutational hotspots have already been found in cancer, and the new information on their significance is getting scientists excited about the opportunities present. The new ways to understand and predict evolution of bacteria and viruses may allow scientists to be a step ahead on vaccines and be able to anticipate and understand new variants. It’s hard not to think this information would’ve been nice before the rise of SARS-CoV-2.

Progress Towards Solving a 50-year-old Problem in Biology

Protein structures revealed at record pace

One of the hardest problems in biology is predicting the structure of a protein. Proteins are complicated. There are many interactions  between both the side chains and backbones of the proteins, making it very difficult to predict how a protein will fold into its 3D structure solely based on the amino acid sequence (primary structure). In our AP Biology class, we talked extensively about how this 3D (tertiary) structure of the protein is extremely important as it determines the function of the protein. For example, the success of the delta variant of SARS-CoV-2 is largely due to the change in the tertiary structure of it’s spike proteins. Thus, if the 3D structure of a protein is known, it is much easier to predict the function of that protein, and how well it performs the function. However, the methods of determining the tertiary structure of proteins is extremely costly. To determine the structure of a single protein, it can take up to $120,000 and one year.

AlphaFold 2.0 is a breakthrough in this long thought impossible problem. AlphaFold, created by Deepmind, uses deep learning to predict protein’s tertiary structures. In particular, it uses an architecture of transformers, a relatively new and increasingly popular deep learning technique. Using this method AlphaFold is able to achieve remarkably accurate and detailed results, even on an atomic level.

Because of its ability to predict the structure of unknown proteins, AlphaFold can be used to determine how a single nucleotide mutation can affect the structure of a protein. Interestingly, many diseases result from an improperly folded protein, these include: Cystic Fibrosis, Alzheimer’s, and Parkinson’s. While the protein structures themselves do not often lead to the creation of new treatments, they do offer a better understanding of how the protein works. This deeper understanding can then be used to develop new therapies. Thus, AlphaFold has the potential to accelerate new treatments for many untreatable diseases at a much lower cost.

In addition to diseases resulting from misfolded proteins, AlphaFold can be used to predict the effect mutations will have on the folding of the SARS-CoV-2 spike proteins. This can help to quickly determine how a mutation will change the shape (and thus function) of the spike proteins. This makes it much easier to predict how these mutations will affect the spread and severity of the new variants and, using this info, classify the new variants.

However, AlphaFold is not perfect. While most predictions are quite good, a small percentage of the protein structures generated are clearly  inaccurate, putting hydrophobic amino acids on the outside of the protein. Knowing this, it is still necessary to analyze any prediction made by the computational model before using it for biological analysis.  Nonetheless, AlphaFold is a powerful tool for prediction of protein structure and will revolutionize the field of computational protein structure prediction.

If you want to experiment yourself with AlphaFold, a working notebook can be found here. Any PDB sequence can be queried, and the AlphaFold model will predict the structure to the best of its ability.

 

 

CRAZY NEW COVID-19 Mutation Makes Virus Weaker Against Antibodies

As revealed in a fascinating article that details a study conducted by the University of North Carolina at Chapel Hill, a mutated form of the virus has been discovered to be much more susceptible to antibodies produced by antibody drugs. This means that it is more easily disabled by antibodies produced by drugs such as the new vaccine. However, this may not all be good news as this new strain, called D614G, is also much more transmissible. D614G originated in Europe and has quickly become the most prevalent form of the virus. According to professor of epidemiology at UNC Ralph Baric, “The virus outcompetes and outgrows the ancestral strain by about 10-fold and replicates extremely efficiently in primary nasal epithelial cells, which are a potentially important site for person-to-person transmission.” These nasal epithelial cells act as a physical barrier against any pathogens attempting to enter the body and play a significant part in the control of the innate and acquired immune response. As we learned in biology, one method of innate immune response that our bodies have is mucous that traps pathogens. The nasal epithelial cells contain cilia that act to push the mucous and the pathogen contained inside out of the body. This means that if this new virus reproduces exceptionally well within the nasal epithelial cells, then it is extremely transmissible through any expulsion of mucous by either sneezing or coughing. It is also far more capable of bypassing the barrier of the mucous and entering the body. These epithelial cells also help the innate immune system by producing various cytokines. If a virus manages to make it past the barrier defenses, the epithelial cells will secrete cytokines. These cytokines will attract a type of cell called a neutrophil that digests pathogens. This means that these nasal epithelial cells are vital to the innate immune response and having a virus strain reproduce so effectively inside of them is extremely worrying.

The researchers believe that D614G is so effective at reproducing because it increases the virus’ ability to enter cells. The D614G mutation opens a flap on the tip of one of the spikes on the side of the virus which allows it to infect cells more effectively. However, this mutation also creates a weakness in the virus. When the flap is open, it becomes much easier for antibodies to bind to the spike proteins, preventing the virus from attacking additional cells.

Two researchers from the University of Wisconsin contributed to this study by experimenting with hamsters. To test the airborne aspect of this mutation, the hamsters were placed into different cages and groups so they could not touch and inoculated with either the original strain or D614G. By day two, in the group exposed to the mutation, six out of the eight hamsters were infected with D614G. In the group of hamsters exposed to the original virus, no additional hamsters were infected by day 2. This shows that this D614G is extremely effective at being transmitted airborne. However, the mutation had the same symptoms and effects as the original virus meaning it is not more severe. The researchers have also noted that these results may not be the same in human studies. I think that this study is equal parts of good and bad news. I am glad that the most prevalent form of the virus is much easier to deal with, but it is quite terrifying that it could mutate to be so much more contagious. How do you feel about this new development? Let me know in the comments. 

Some People Can’t Smell Stinky Fish?!

A New York Times article has just reported a new “mutant superpower.” In Iceland, a brand new genetic trait was discovered, in which 2% of the population can’t smell the stinky odor of fish. 

A study of 11,326 Icelanders was conducted, in which each participant was given six “Sniffin’ Sticks (pens imbued with synthetic odors)” of cinnamon, peppermint, banana, licorice, lemon, and fish. The participants were then asked to identify the odors based on how strong each smell was and how good each Sniffin’ Stick smelled. Across the majority, the fish was rated the lowest in pleasantness. However, a small group of people actually enjoyed the scent, noting that it smelled like caramel or even a rose. 

This small group of participants was discovered to have a genetic mutation that enables the TAAR5 gene to form. TAAR5 (Trace Amine Associated Receptor 5) aids in making proteins that recognize trimethylamine (TMA), a chemical found in rotten and fermented fish, and some bodily fluids, including sweat and urine.  TAAR5 is also a G Protein, meaning that it binds guanine nucleotides. And, like other coding proteins, TAAR5 is a quaternary structured protein that has three subunits. Because this protein is incapable of binding guanine nucleotides, it means that there will be at least one “broken” copy of the gene that codes for the inability to smell fish. 

To simplify: TAAR5 recognizes the chemical of smell in fish (TMA), however, with the mutation that prevents the TAAR5 from forming, the smell of fish (TMA) is unrecognizable.

Interestingly, research has shown that this mutation may be a reaction to the customs of Iceland and a possible next step in the evolution of the region. In Iceland, fish takes a prominent place on most menus including dishes like “rotten shark.” These cultural and possibly smelly dishes may explain why this mutation is much more prominent in Iceland compared to Sweden, Southern Europe, and Africa (where the study was repeated). Bettina Malnic, an olfaction expert at the University of Sao Paulo in Brazil, commented on the luck of the region study took place, saying, “if they hadn’t looked at this population, they might not have found the variant [of TAAR5].”

I am VERY sensitive to smell and, at the same time, a lover of sushi, so it definitely fascinates me that there are people out there who don’t have to deal with the odor of smelly fish. This mutation is definitely one I wish I obtained. What do you think about this? Do you think you could have this mutation?!

 

Meeting Your Great Great Great… Grandchildren

The MDI Biological Lab along with the Buck Institute of Research on Aging have discovered cell pathways that could increase the human lifespan by 400-500%. “The increase in lifespan would be the equivalent of a human living for 400 or 500 years.” The implications this would have are immense along with some potential drawbacks, but let’s get into the science first.

The research was conducted on C. elegans, a nematode, because “it shares many of its genes with humans and because its short lifespan of only three to four weeks.” The short lifespan allows scientists to quickly see the effects of their efforts to extend the healthy lifespan. The keyword here is “healthy” because prolonging life means nothing unless you can extend the quality as well. The scientists used a double mutant in the insulin signaling and TOR pathways. The alteration in the insulin pathway yields a 100% increase in lifespan and the TOR pathway yields a 30% increase. The incredible discovery though was that when combined the new lifespan was amplified by 500%!! The expected yield was 130%.

Image result for double mutant "

Here depicted is a diagram showing the meaning of a double mutant.

Researchers still say “the discovery in C. elegans of cellular pathways that govern aging, it hasn’t been clear how these pathways interact.” This discovery does lead to the mindset that the important methods of anti-aging are in the interactions between cellular pathways rather than singular pathways. This newly found interaction could also explain why scientists have had trouble discovering “the gene” the governs aging. The combinations of these treatments are described as being similar to the “way that combination therapies are used to treat cancer and HIV.”

It’s odd to picture a world where this treatment could be considered “cosmetic” in a way. Eventually, the human lifespan could expand to hundreds of years with some even living to 1000. The implications that this could have are a current problem we have of overpopulation. It is farfetched, but this would help immensely with the mission to expand into space. The ability to survive with hundreds of years on a potential “colony ship” allows humans to expand to other planets where we would be able to expand greatly. I’ll end with a question: If this treatment was 100% safe and affordable, would you get it? Why or why not?

How did butterflies evolve to eat poison?!

A recent article confirms that scientists have researched that caterpillars are now eating milkweed (which is supposed to kill them). How is this happening? “Scientists have unraveled the sequence of gene mutations that enabled the monarch butterfly to thrive on toxic milkweed.” We learn at a young age that caterpillars turn into beautiful butterflies, so something must be happening before metamorphosis. There are three gene changing mutation amino acid sites including, 111, 119, and 122. Mutation 122 had the biggest boost in resistance. Another article states that ‘monarch flies’ continue to have small amounts of cardiac glycosides through metamorphosis, which is a trait that has been developed in monarch butterflies to restrain predators.

Monarch butterfly eating milkweed

Monarch butterflies can eat milkweed due to a peculiarity in a crucial protein in their bodies, which is a sodium pump, that the cardenolide(steroid) toxins intervene with. How the pumps work? They move positively charged sodium atoms out of the cell resulting in the inside of the cell is negatively charged. In order for a heart to beat, the sodium pump has to build up enough electric charge and then nerves use the pumps to send signals to the brain.

Potassium pump diagram where the pump moves the sodium and potassium ions through the membrane

What does milkweed have to do with this? In the study, they first addressed how milkweed is toxic to almost all insects, but caterpillars depend on milkweed. Females use milkweed to lay eggs and caterpillars eat as much as they can before chrysalis. In the article, they are referred to as “flying poison” because the milkweed toxin gets send from their gut to their wings and anything that tries to eat it immediately vomits it up.  After these mutations, they now NEED milkweed to live and it altered the sodium pumps, so cardiac glycosides in the monarchs cells don’t affect them.

This mutation allowed butterflies to have their own food supply since milkweed is poisonous to other insects. Noah Whiteman, a biologist at the University of California, Berkely used CRISPR to try the mutations on fruit flies. The fruit fly experiment resulted in the findings that mutation 122 has bad side effects and is only useful if followed by another mutation. Other researchers say the order that mutations are done can make a big difference as well.

 

The Collateral Damage of CRISPR-Cas9

 

CRISPR’s ‘precise’ gene-editing has actually been damaging other parts of the DNA sequence, according to a recent study. Photo from this source.

Of the various gene-editing techniques, CRISPR-Cas9 is the fastest, simplest, and most accurate gene-altering method known to date. Comprised of simply two parts, CRISPR-Cas9 snips through targeted segments of DNA and causes a change in the genetic code. Scientists are hopeful that we can soon use this method to cut out mutations that code for HIV, cancer, and sickle cell disease. However, a study published in Nature Biotechnology has revealed an unwanted side-effect of CRISPR.

When using CRISPR-Cas9, there are two major molecules that create a mutation, or change, in a DNA segment. The first is an enzyme called Cas9. This enzyme works like a pair of scissors and that cuts the two helices at a specific location so DNA can be altered. The second tool used in this process is the guide RNA (gRNA) that binds to the DNA and ensures that the Cas9 molecule cuts the DNA in the correct place. Finally, after the incision, the DNA will seal itself back together, without a trace of the deleted segment.

Such a precise process seems flawless. In theory, one should be able to cut out the unwanted genetic material and our DNA should perfectly repair itself. Unfortunately, senior group leader and director of the study at Wellcome Sanger Institute in England, Allan Bradley, stated that “CRISPR is not as safe as we thought.” Through a systematic and tedious approach, Bradley and his colleagues edited a series of mouse and human cells with CRISPR and then examined DNA base pairs father and farther away from the cut site. By examining millions of base pairs, the team landed upon unsettling news.

Bradley and his team found that huge chunks of DNA were inadvertently deleted, mutated, and rearranged millions of base pairs away from the cut site. The DNA was mutated so immensely that cells lost function in 15% of cases. Because these CRISPR-induced mutations were shown so far away from the cut site, this information could have easily been overlooked in other studies.  

This research poses questions on the accuracy of such gene-editing methods. What are the long-term effects of genetic engineering with CRISPR? How can we ensure that base pairs so far away from the cut site aren’t altered? Although this is somewhat discouraging news for the CRISPR community, this newfound information is motivating more researchers to improve CRISPR technology before making it widely accessible.

Read the full article here.

Crispr-Cas9 is the gateway to a new frontier in genetic engineering. Here’s The good and the bad.

For a number of years now, molecular biologists have been diving increasingly further into the field of genome editing. The latest development into the field is the emergence of CRISPR-Cas9. CRISPR-Cas9 has risen to prominence over other potential methods of genome editing due to its relatively simple construction and low cost. CRISPR-Cas9’s original primary and intended purpose was to help fix mutations within DNA, and with this it could theoretically help eradicate entire diseases. This application of CRISPR is wholly positive, however with the increasing prevalence of the technique other potential uses have been discovered, and some of these potential uses raise profound ethical questions.

One of the main concerns of people skeptical about CRISPR is their assertion that once the door to the wholesale genetic editing of offspring is open, there is no going back. This, on its own, is a reasonable concern. The ability to choose a child’s sex, eye color, hair color and skin complexion is very likely to be made available to by CRISPR in the coming years. CRISPR does not yet have the capability to influence more abstract elements of the genome, such as intelligence and athletic ability, but this may not be far off. There are legitimate concerns that this is a slippery slope towards a dystopian society similar to the one seen in the movie Gattaca, where society is stratified into two distinct classes: those who are genetically engineered and those who are not.

Another concern raised by some scientists is the overall safety of genetic editing. A potentially very hazardous negative result of CRISPR is the possibility of an “off target mutation.” An off target mutation is the result of CRISPR mutating something other than the intended part of the genome and it could have disastrous consequences. Now, many scientists believe that with further advancements in the field the likelihood of something like an off target mutation occurring could be reduced to almost zero. However, it is important to examine the risks of any new process, and the prospect of something like an off target mutation occurring is certainly noteworthy.

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How DNA damaged from radiation causes cancer

In a recent study, professors from the Wellcome Trust Sanger Institute sought to see the similarity between spontaneous cancerous tumors and cancer caused by ionized radiation. By looking at the molecular fingerprint of different types of cancers, they were able to differentiate between cancers that formed by radiation and cancers that were not formed by radiation.

In the study, they studied the mutational signatures of the DNA. Mutational signatures are just ways in which the DNA is affected by cancerous mutations. They studied the DNA mutational signatures from DNA exposed to radiation, but not necessarily cancerous, and the mutational signatures of the DNA of cancerous cells of which some were caused by radiation exposure and some were not. Both included the same signatures.

The two mutational signatures that were observed were deletion of segments of DNA bases and balanced inversion, where the DNA is cut in two places, the middle piece flips around, and the pieces are joined back in the opposite orientation from before the flip. High energy radiation is the cause for balanced inversion, since it does not happen naturally in the body. After the mutation, the DNA cannot repair itself.

This gives us a better understanding of cancer and how ionized radiation affects DNA and produces these mutational signatures. Knowing this information, this helps us recognize which tumors are caused by radiation. Once we have a better understanding of this, it will prove important for determining how each cancer should be treated. But for now, this is a strong step forward in the battle against cancer and every step of the way is crucial if we are to be victorious.

 

Potential New Treatment Strategy for Brain Cancer!

Cancer is a disease characterized by the up-regulation of cell growth and it usually develops when normal cells are not able to repair damaged genetic material. New studies are revealing insights into the function of genetic mutations commonly found in a form of brain cancer, specifically the IDH mutation. Isocitrate Dehydrogenase(IDH) is a metabolic enzyme found in more than 70% of low grade gliomas and secondary glioblastomas, types of malignant brain tumors. In a normal cell, IDH enzymes help to break down nutrients and generate energy cells. When mutated, IDH creates a molecule that alters cells genetic programming and instead of maturing, the cell remain primitive. Studies have shown that cells holding this mutation also have an impaired ability to repair DNA. Strangely enough, low grade gliomas that have the IDH mutation are typically more sensitive to chemotherapy than those that lack the mutation. Why does this occur? We still don’t really know the answer.  Yet, researchers have discovered a potential new treatment option for the glial cells harvesting the IDH mutation– PARP Inhibitors.   A super cool future is waiting ahead.

When treating the IDH mutated cells with PARP Inhibitors, a substance in the form of a drug that blocks an enzyme called PARP, the cells were effectively killed. When the drug blocks PARP, it keeps the cancer cells from repairing their damaged DNA, and eventually they die off. The cells are extremely sensitive after the effects of the inhibitors, especially after taking the most common PARP drug called oliparib. PARP inhibitors are a form of targeted therapy–meaning the inhibitors work within a similar approach as radiation and chemotherapy– they simply damage or prevent the repair the DNA. Researchers have also found the up regulation of the unusual molecule called  2-HG(2-Hydroxyl-glutarate) within the IDH mutated enzymes. In a study with Dr. Brinda’s team at Yale, they found that 2-HG may be responsible for the defect, DNA repair inabilities, in these cells. When the production of 2-HG was blocked in these cells, the DNA repair defect was reversed and cells became unresponsive to the PARP inhibitor treatment. This finding further solidifies that PARP inhibitors may be the best new effective brain cancer treatment method. What do you think? I think this is pretty cool news!

Jto410 is the username of the radiologistwho took the picture

Low grade glioma MRI scan. Creative Commons Attribution-Share Alike 3.0 Unported license.

There are also many clinical trials occurring currently to observe 2-HG as a definite IDH biomarker for cells that are sensitive to treatment with PARP inhibitors. In addition, labs are also designing a clinical trial of olaparib and temozolomide, two PARB inhibitor drugs, in patients with low-grade gliomas. The results of these trials, are for sure going to make headlines within the Biology and Medical field! Even though, there are still many questions to answers and studies to conduct regarding brain cancer and the IDH mutation, we are definitely on the right track to cure the monster a.k.a “cancer.”

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