BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Genome (Page 1 of 2)

Are You Predisposed to Being Overweight? New Genetic Variations Say Yes.

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On January 8, 2023

In Student Post

Recent studies composed by researchers from the Spanish National Cancer Research Centre and the IMDEA Food Institute show that people with a specific variation or version of a gene crucial to cell nutrition tend to accumulate less fat. This means that those with a particular change or alteration in this gene may be inclined to store less fat in their bodies. Prior research has shown that genetics only play a role in 20% of our body weight for the general population. This means that other external factors such as diet, exercise, and overall lifestyle have much more of an impact on body weight.

Past research has identified nearly 100 genetic variants which slightly increase one’s likelihood of having a high BMI. This new research identifies one additional variant. Typically genetic variations are only slightly different versions of a gene and often do not result in visible changes. But, this new variation challenges this idea. It affects the amount of fat the body stores, something which can strongly alter one’s physical appearance. What’s more, the researchers of this gene have found that it is more prevalent in Europe with just under 60% of the population having it.

Ácido desoxirribonucleico (DNA)

 

According to Alejo Efeyan, the head of CNIO’s Metabolism and Cell Signalling Group, the new research can help us to further understand the role which genes play in obesity, body weight, and fat accumulation. Efeyan says, “the finding is a step forward in the understanding of the genetic components of obesity.” Additionally, Ana Ramirez de Molina, the director of the IMDEA Food Institute, claims that a key understanding of cell pathways regarding cell nutrition may affect and spur the creation of not only obesity prevention but also personalized treatments. Essentially, understanding the new gene can help us to target obesity and body weight on an individual level rather than the population as a whole. She believes, “a deep knowledge of the involvement of the cellular nutrient-sensing pathway in obesity may have implications for the development and application of personalized strategies in the prevention and treatment of obesity.”

To find and research the genetic variant which influences fat storage and obesity a team from the IMDEA Food institute collected a variety of data from 790 healthy volunteers. This included body weight, muscle mass, genetic material, and more. The researchers found a “significant correlation between one of these variants in the FNIP2 gene and many of these obesity-related parameters.” Essentially their research proved that there is a connection between the specific gene and factors of obesity. The study has also been published in the scientific journal of Genome Biology. Although this gene may play a role in keeping body fat storage lower than others, it is important to note that it is not entirely a preventative measure against obesity or fat gain. Efeyan clarifies, “It is not at all the case that people with this genetic variant can overeat without getting fat.”

The genetic variation is present in a gene that specifically partakes in a signaling pathway that tells the cell what nutrients are available and needed. The gene signals to the cell what nutrition is necessary at a given moment. In our AP Bio class, we learned the intricacies of cell communication; how and why it can occur, the stages of it, and even the differences in the distances of communication. Connecting back to our AP Bio class, I wonder whether the gene interacts in an adjacent, paracrine, or long-distance manner. Also, how the distance can affect the communication of the gene to the cell regarding cell nutrition. We also learned about how genes in the nucleus of our cells can code for specific factors in our bodies and how they are a sort of ‘instructions’ for us to carry out. This connects to the research as we can see that a change in a gene can alter our body’s fat storage and connection to obesity. The genetic variation changed the ‘instructions’ for weight, fat storage, and obesity disposition. Additionally, the research stated that 60% percent of Europeans have genetic variation, I wonder what may have caused this. Was it a result of their diets, lineage, geography, or just a scientific anomaly? I invite any and all comments with a perspective and an idea as to what may have caused this, along with any comments regarding this research as a whole.

Obesity-waist circumference

 

 

CRISPR Gene Editing: The Future of Food?

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On March 16, 2022

In Student Post

Biology class has taught me a lot about genes and DNA – I know genes code for certain traits, DNA is the code that makes up genes, and that genes are found on chromosomes. I could even tell two parents, with enough information, the probabilities of different eye colors in their children! However, even with all this information, when I first heard “gene editing technology,” I thought, “parents editing what their children will look like,” and while this may be encapsulated in the CRISPR gene editing technology, it is far from its purpose! So, if you’re like me when I first started my CRISPR research, you have a lot to learn! Let’s dive right in!

CRISPR

Firstly, what is CRISPR Gene Editing? It is a genetic engineering technique that “edits genes by precisely cutting DNA and then letting natural DNA repair processes to take over” (http://www.crisprtx.com/gene-editing/crispr-cas9).  Depending on the cut of DNA, three different genetic edits can occur: if a single cut in the DNA is made, a gene can be inactivated; if two separate DNA sites are cut, the middle part of DNA will be deleted, and the separate cuts will join together; and if the same two separate pieces of DNA are cut, but a DNA template is added, the middle part of DNA that would have been deleted can either be corrected or completely replaced. This technology allows for endless possibilities of advancements, from reducing toxic protein to fighting cancer, due to the countless ways it can be applied. Check out this link for some other incredible ways to apply CRISPR technology!

In this blog post however, we will focus on my favorite topic, food! Just a few months ago, the first CRISPR gene-edited food went on the market! In Japan, Sicilian Rouge tomatoes are now being sold after the Tokyo-based company, Sanatech Seed, edited them to contain an increased amount of y-aminobutyric acid (GABA). “GABA is an amino acid and neurotransmitter that blocks impulses between nerve cells in the brain” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). It supposedly (there is scarce scientific evidence of its role as a health supplement) lowers blood pressure and promotes relaxation. In the past, bioengineers have used CRISPR technology to “develop non-browning mushrooms, drought-tolerant soybeans and a host of other creative traits in plants,” but this is the first time the creation is being sold to consumers on the market (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/)!

Tomatoes

So, how did Sanatech Seed do it? They took the gene editing approach of disabling a gene with the first method described above, making a single cut in the DNA. By doing so, Sanatech’s researchers inactivated the gene that “encodes calmodulin-binding domain (CaMBD)” in order to increase the “activity of the enzyme glutamic acid decarboxylase, which catalyzes the decarboxylation of glutamate to GABA, thus raising levels of the molecule” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). These may seem like big words, but we know from biology that enzymes speed up reactions and decarboxylation is the removal of carbon dioxide from organic acids so you are already familiar with most of the vocabulary! Essentially, bioengineers made a single cut in DNA inside of the GABA shunt (a metabolic pathway) using CRISPR technology. They were therefore able to disable the gene that encodes the protein CaMBD, and by disabling this gene a certain enzyme (glutamic acid decarboxylase) that helps create GABA from glutamate, was stimulated. Thus, more activity of the enzyme that catalyzes the reaction of glutamate to GABA means more GABA! If you are still a little confused, check out this article to read more about how glutamate becomes GABA which will help you better understand this whole process – I know it can be hard to grasp!

After reading all of this research, I am sure you are wondering if you will soon see more CRISPR-edited food come onto the market! The answer is, it depends on where you are asking from! Bioengineered crops are already hard to sell – many countries have regulations against such food and restrictions about what traits can actually be altered in food. Currently, there are some nutritionally enhanced food on the market like soybeans and canola, and many genetically modified organisms (GMOs), but no other genome-edited ones! The US, Brazil, Argentina, and Australia have “repeatedly ruled that genome-edited crops fall outside of its purview” and “Europe has essentially banned genome-edited foods” (https://www.scientificamerican.com/article/crispr-edited-tomatoes-are-supposed-to-help-you-chill-out/). However, if you are in Japan, where the tomatoes are currently being sold, expect to see many more genome edited foods! I know I am now hoping to take a trip to Japan soon!

Thank you so much for reading! If you have any questions, please ask them below!

Migraines Are Just in my DNA

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On February 16, 2022

In Student Post

           While over a billion people suffer from migraines, there is not much knowledge about what causes them or how they can be treated. This uncertainty led to a study in which researchers from Europe, Australia, and America all worked together to find how genetics might play a role in migraines. In this study data from over 800,000 individuals, around 100,000 of which had migraines, was collected, which led to the discovery of tons of new genetic risk factors. While it is understood that the recurrence of migraines in certain individuals is very likely due to genetics, it is unclear if the different types of migraines have the same genetic background such as migraines with aura vs. without aura. To test this, the International Headache Genetics Consortium acquired data on genetics in order to hold a “Genome-wide association study” to find specific genetic mutations commonly in migraines with aura and/or migraines without aura. The results found suggested that there are both genetic risk factors shared by the two main types of migraines, as well as some specific to each. The results also backed the belief that migraines are a neurovascular disorder by showing that neuronal and vascular genetic factors contribute to them. 

DNA orbit animated         

           As we are learning in AP Biology class, the genome is a person’s complete set of DNA. A person’s genetic risk factors are passed down from their parents through their genes, and while all humans have genes, everyone has slightly different variations of them inherited from their parents.  Humans typically receive 23 of their 46 chromosomes from each parent, as the two haploid sets of chromosomes join to make a diploid set.  This diploid set is the human’s genome, and holds the coding for genetic risk factors, such as the ones that contribute to migraines in some individuals.

               So many people are living susceptible to migraines with little ways to treat them, however with the new discoveries about what genetic causes may lead to migraines there is more hope for treatments in the future. One specific medication that has recently been developed is a CGRP inhibitor which prevents “calcitonin gene-related peptide”, which is a molecule playing a large role in the occurrence of migraines. Dr. Matti Pirinen from the Institute for Molecular Medicine Finland, University of Helsinki, commented on his optimism for finding “other potential drug targets among the new genomic regions” as well as the ability to learn even more about the issue through larger studies. Despite little known information about migraines causes and treatments in the past, recent studies offer a brighter future to finding out why some people are so susceptible to them, as well as new ways to provide relief for those who suffer from migraines.  

Is Junk DNA Really Junk?

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On October 27, 2021

In Student Post

DNA is the base code of all living creatures. It is in every plant, animal, and single-cell organism, yet  50% of human DNA is seen to be irrelevant to bodily function. While some DNA is responsible for synthesizing materials within cells, much of it is in essence, spare genes, or ancient viruses that have become part of the human genome over time. Moreover, it has been debated whether the 50% of DNA that is not seen to be relevant is truly essential for survival. That is, can humans live without unused genetic code, or is it vital to the survival of the species?

Ácido desoxirribonucleico (DNA)

One specific element of junk DNA is transposons. Transposons are sequences of DNA that have the ability to mutate a cell or change its function as a whole. A study was conducted at the University of California, Berkley, and Washington University on transposons, as written in the So-called Junk DNA – Genetic “Dark Matter” – Is Actually Critical to Survival in Mammals, by the University of California, Berkley. The studies looked at a specific transposon in mice called MT2B2, one that controlled the growth rate of cells in a fertilized embryo, and when the embryo would implant in the uterus of the mother by initiating the short gene Cdk2ap1. When the researchers disabled the MT2B2 transposon using CRISPR-EZ, the mice created a longer version of the gene Cdk2ap2. This new version of the gene decreased cell growth and increased the period of implantation. The teams found that half of the baby mice died before birth without this transposon in their DNA. When the transposon was disabled, the mice sort randomly instead of uniformly in the uterus, and some may cause the death of a developed fetus and or the mother.

The team at Washington University researched the transposons turned on before embryos are impacted into the uterus in humans, rhesus monkeys, marmosets, mice, goats, cows, pigs, and opossums. The team used scRNA-seq, which records messenger RNA levels to indicate which genes are being used. With this technique,  the team saw that in every animal, a group of species-specific transposons was turned on. While the transposons were different for each species, the result of their use was nearly the same for all eight cases. Moreover, the gene Cdk2ap1 was expressed by all eight animals, but the amount of short and long versions of the gene expressed was unique for each one. While an animal that needs fast implantation uses more of the short version of the gene, like the mouse, animals with little to none of the shorter version of Cdk2ap1 took two weeks to longer for implantation to occur, like the cow.

Baby Mouse Rehabber

For these transposons to be promoting the expression of the Cdk2ap1 gene, at a certain point in history, a virus entered the organism and eventually part in a mutually beneficial symbiotic relationship with the organism until it evolved into the current iteration of the transposon. When viruses blend into the DNA of a species, they can be used to regulate and perform tasks that the cell could not previously perform. This can create a wide range of evolutionary options in species. Additionally, the main difference between the different genomes of species is the regulation of genes. By studying transposons, scientists can better understand differences in the genome of one species to another. With the understanding of this transposon, scientists could now begin searching further into junk DNA, as the removal of the transposon studies by the two universities proved lethal 50% of the time. Moreover, undiagnosed patients could have junk DNA mutations that lead to health problems, but those cases are currently a mystery to the medical world. Transposons are just the beginning of scientists dive into junk DNA, and who knows what wonders they will find next?

Mutation in the Nation

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On January 12, 2021

In Student Post

We constantly think of SARS-CoV-2, the virus that causes COVID-19, as a single virus, one enemy that we all need to work together to fight against. However, the reality of the situation is the SARS-CoV-2, like many other viruses, is constantly mutating. Throughout the last year, over 100,000 SARS-CoV-2 genomes have been studied by scientists around the globe. And while when we hear the word mutation, we imagine a major change to how an organism functions, a mutation is just a change in the genome. The changes normally change little to nothing about how the actual virus functions. While the changes are happening all the time since the virus is always replicating, two viruses from anywhere in the world normally only differ by 10 letters in the genome. This means that the virus we called SARS-CoV-2 is not actually one species, but is a quasi-species of several different genetic variants of the original Wuhan-1 genome.

The most notable mutation that has occurred in SARS-CoV-2 swapped a single amino acid in the SARS-CoV-2 spike protein. This caused SARS-CoV-2 to become significantly more infective, but not more severe. It has caused the R0 of the virus, the number of people an infected person will spread to, to go up. This value is a key number in determining how many people will be infected during an outbreak, and what measures must be taken to mitigate the spread. This mutation is now found in 80% of SARS-CoV-2 genomes, making it the most common mutation in every infection.

Glycoproteins are proteins that have an oligosaccharide chain connect to them. They serve a number of purposes in a wide variety of organisms, one of the main ones being the ability to identify cells of the same organism.  The spike protein is a glycoprotein that is found on the phospholipid bilayer of SARS-CoV-2 and it is the main tool utilized in infecting the body. The spike protein is used to bind to host cells, so the bilayers of the virus fuse with the cell, injecting the virus’s genetic material into the cell. This is why a mutation that makes the spike protein more efficient in binding to host cells can be so detrimental to stopping the virus.

In my opinion, I find mutations to be fascinating and terrifying. The idea that the change of one letter in the sequence of 30,000 letters in the SARS-CoV-2 genome can have a drastic effect on how the virus works is awfully daunting. However, SARS-CoV-2 is mutating fairly slowly in comparison to other viruses, and with vaccines rolling out, these mutations start to seem much less scary by the day.

 

File:New COVID19 mutant.jpg - Wikimedia Commons

Diagram of the SARS-Cov-2 mutation

Embryo Gene Editing can Ensure Offspring Do Not Inherit a Deafness Gene!

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On January 23, 2020

In Student Post

Denis Rebrikov, A scientist in Russia has done research regarding ways in which he can edit the genome sequence of an embryo in order to prevent the fetus from developing certain gene mutations, specifically in this case a hearing problem or possible complete deafness. His plans are very controversial to some, who believe the possible risks of very harmful mutations to DNA that would be passed onto direct and future offspring, outweigh the possible benefits. However, some people find this scientific possibility to be worth the risk, if it means not passing a potentially very harmful gene down to offspring. If these methods are done correctly, it should alter the genome sequence in the embryo so that future offspring off that embryo will not inherit the negative mutation.

One couple shared their story in detail, in which both parties have a hearing deficiency, the man with partial deafness, and the woman completely deaf. Their biggest hope is to have children who will not inherit hearing issues, because of the apparent challenges they have had to face themselves because of them. They would be the first couple to perform this gene editing on an IVF embryo, so they obviously have some reservations. One of those being publicity, but more importantly the potential risks of using the CRISPR genome editor. They already have a daughter with hearing loss, but they never chose to test her genes for mutations, nor did they get her a cochlear implant to aid her hearing, because of the potential risks of that. When they finally tested her genes, they learned that she had the same common hearing loss mutation called 35delG in both her copies of a gene called GJB2. The parents then tested themselves, realizing they were both 35delG homozygous, meaning their daughter’s mutations were not unique to her, they had been inherited.

If either the mother or father had a normal copy of the GJB2 gene, a fertility clinic could have more easily created embryos by IVF and tested a few cells in each one to select a heterozygote–with normal hearing–to implant. At this stage, Denis Rebrikov informed them that CRISPR genome editing would be their only option. However, the process presents possibly deal breaking risks, such as mosaicism, in which a gene edit might fail to fix the deafness mutation, which could create other possible dangerous mutations like genetic disorders or cancer. The couple has not decided to go through with the editing just yet, but it is something they are open to in the future as more possible new research or test subjects become available.

Explaining the CRISPR Method: “The CRISPR-Cas9 system works similarly in the lab. Researchers create a small piece of RNA with a short “guide” sequence that attaches (binds) to a specific target sequence of DNA in a genome. The RNA also binds to the Cas9 enzyme. The modified RNA is used to recognize the DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location… Once the DNA is cut, researchers use the cell’s own DNA repair machinery to add or delete pieces of genetic material, or to make changes to the DNA by replacing an existing segment with a customized DNA sequence.” -US National Library of Medicine Genetics Home Reference

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Woman with a hearing aid 

If you had the opportunity to alter something in the gene’s of your baby’s embryo, would you? Under what circumstances would you consider this, and what risks might stop you from deciding to do it? Comment down below.

 

 

How Old “Chewing Gum” Allows Us To See Into The Past

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On January 21, 2020

In Student Post

In a recent study conducted by the University of Copenhagen, scientists have discovered a complete human genome extracted from a sample of old birch pitch “chewing gum”.

 

While excavating in Lolland, and island in Denmark, archeologists found a sample of 5,700 thousand year old birch pitch sealed in mud. Since the sample was sealed in mud, it was preserved very well. The birch pitch was found in a place called Syltholm, a site where many past archaeological finds have been made.

 

Why is this Discovery Important?

This is the first time a complete ancient genome has been extracted from something other than a bone sample. Samples of oral DNA as well as other human pathogens were found which are very important finds due to the fact that there are no other human remains left from that time period. From the initial birch pitch sample, scientists could figure out that the person who chewed the birch pitch was a female who most likely had dark hair, dark skin, blue eyes, and was genetically related to hunter-gatherers.

Scientists also made bacterial discoveries. Bacteria that come from oral microbiomes were found which allows us to also study the diet and microbiomes of  the people living 5,700 years ago. Scientist Hannes Schroeder says that studying these DNA samples will help us understand ancient microbiomes as well as the evolution of human pathogens.

I think it is interesting that so much information could be uncovered from a sample of ancient tree bark tar. What do you think?

Meet Your New Favorite Fruit, The Groundcherry

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On March 12, 2019

In Student Post

Groundcherries are small orange fruits that are in the same plant family as tomatoes. However, they taste nothing like tomatoes. Instead, some taste like pineapples while others have a hint of vanilla. These yummy, mysterious fruits are uncommon because farmers have not grown them in sizable numbers. This is because the berries tend to drop off the branch and onto the ground before they are ripe which makes the plant unreliable for farmers to harvest.

https://upload.wikimedia.org/wikipedia/commons/3/36/Ground_Cherry_Festival_at_the_Sensō-ji.jpg

These types of crops were known as “orphans” because they have some appealing traits but also come with challenges which is why farmers don’t plant them in large numbers.

 

However, researchers Lippman and Van Eck wanted to develop a groundcherry that eliminated those challenges by domesticating the crop using a tool called CRISPR. CRISPR allowed scientists to make changes to the plant’s genome, developing new varieties more efficiently than ever before. The researchers wanted to make the groundcherry a more manageable plant and they were able to do that by making small modifications to its genome.

By doing this, they made the groundcherry plant more compact and therefore more manageable for growers. Now, culinary experts even recommend using groundcherries in cakes, pies, spicy salsas and savory appetizers. So Lippman and Van Eck really did help the groundcherry to become the next specialty crop!

 

 

A Fintastic Discovery

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On October 10, 2018

In Student Post

Sharks have interesting biological features: a cartilage skeleton, highly developed senses, dermal denticles, and an oil-storing liver. However, these traits are difficult to identify within the huge genomes of sharks.

 

Previously, the genomes for sharks were larger than many other organisms, making it difficult for scientists to decode and understand the genetic background behind the lifestyle of sharks. However, the Japanese team at RIKEN Center for Biosystems Dynamics Research managed to decode whole genomes of two species of shark: the brown banded bamboo shark and the cloudy catshark. They also improved the genome sequences of the whale shark.

Image result for whale shark of sharks

Whale shark Photo Credit: Zac Wolf

Whale Shark

According to the RIKEN team, the large genomes in many shark species was a result of huge, repetitive insertions within the genome. Additionally, it was discovered that these shark genomes have been evolving at a slow rate, suggesting that sharks have kept some characteristics that were similar to distant ancestors.

 

Already, particular parts of the shark genome revealed certain characteristics of sharks. Using the DNA from the shark genomes, researchers discovered that the rhodopsin pigments in a whale shark can sense short wavelengths, allowing them to see at 2000 meters below the water level when they aren’t hunting on the surface. Furthermore, the team determined that there were too few olfactory genes in the shark genomes, meaning that the highly developed navigation system is not done through smell.

 

These results help fill the gaps in the genetic background in sharks while understanding the way sharks live. Keiichi Sato, deputy director of Okinawa Churaumi Aquarium, says, “Such understanding should contribute to the marine environments as well as to sustainable husbandry and exhibitions at aquariums that allow everyone to experience biodiversity up close.”

What does the future hold for CRISPR-Cas9?

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On March 13, 2018

In Student Post

Genome editing, or the technologies in which scientists can change the DNA of an organism, is on the rise, especially with its latest development, CRISPR-Cas9, the most efficient method of all of the methods to edit DNA.

Like many other discoveries in science, CRISPR-Cas9 was discovered through nature. Scientists learned that certain bacteria capture snippets of DNA from invading viruses, making DNA segments called CRISPR arrays, helping them remember the virus to prepare for future invasions of that virus. When they are confronted with that virus again, RNA segments from the CRISPR arrays are created which target the DNA of the virus, causing the enzyme Cas9 to cut the virus’ DNA apart, which would destroy the virus.

 

We use the same method in genome editing with CRISPR-Cas9 by creating RNA that binds to a specific sequence in a DNA strand and the Cas9, causing the Cas9 to cut the DNA at that specific sequence. Once this is done, the scientists create a sequence to replace the one that was cut to get the desired genome.

This technology is most prominently used to attempt to treat diseases, where the somatic cells’ genomes are altered which affect tissues, as well as prevent genetic diseases where the sperm or egg’s genome is changed. However, the latter causes some serious ethical concerns of whether we should use this technology to enhance human traits. But this begs the question that if we start using it more and more to prevent genetic diseases, will this open the door for it to be used in new ways?

Inside Out

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On March 12, 2018

In Student Post

CRISPR is a revolutionary tool used for editing the human genome. It allows for the altering of  any given DNA sequence and ability to modify any one specific genes’ function. Its applicability consists of correcting genetic defects, treating and preventing the spread of diseases, and improving crops. However, it also raises some ethical concerns, that of which mainly is the idea that practicing CRISPR technology could be considered as playing the role of “God”.

CRISPR was adapted from the natural defense mechanisms of bacteria, which use CRISPR-derived RNA and Cas proteins, to prevent attacks by viruses and other intruding organisms. They do so by chopping up and destroying the DNA of the virus. When these components are derived and applied to more complex, organisms, it allows for the manipulation of genes.

Disregarding its ethical concerns, CRISPR can provide substantial support to a previously uncharted area of medicine; the diagnosing and treating of genetic disorders, which was previously thought to be that if one had a genetic disorder it would be incurable.  Clinical trials are set to take place both in Europe and in North America, where patients with rare genetic disorders will give cellular samples in an attempt to alter their genome, implant them back into the individual, and hopefully cure the genetic abnormality.

With CRSPR taking such progressive strides in the past year, it is not outrageous to predict what its usage could end up providing society with.  With the ability to edit the human genome there are endless possibilities in which science could evolve this area of study to benefit the human race.  CRISPR can even be used to boost the expected intelligence of an embryo.  Who knows, thirty years from now we could be watching the news and hear of the first ever “superhuman”, a genetically modified human that has been hand-coded for optimality in all human functions.

Sperm Epigenetics and the Next Generation

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On April 5, 2017

In Student Post

Jerome Jullien from the Welcome Trust CRUK Gurdon Institute in Cambridge experimented with frogs to see if more than just DNA is passed on to the second generation offspring.  Sperm contain something called epigenetic tags which are “chemical switches attached to the genomes of sperm.”  (It is important to understand that epigenetics does not alter an organism’s DNA.)  In order to test if these sperm epigenetics influence offspring Jullien used two types of sperm; regular frog sperm and spermatids which had different epigenetic tags.  They then injected the sperm and spermatid into genetically engineered eggs which took away some of the epigenetic tags (with specific enzymes) on the sperm.  This lead to abnormal gene expression causing problems for the offspring.

This basically shows that a male does not simply pass down his DNA to his offspring but other factors like epigenetic tags can also effect the life of their kids.  As Jullien says, “The obvious implication is that whatever experiences the father has in life that end up epigentically modifying sperm cells might also be transmitted to the offspring and affect their genetic development and characteristics.”  There is still disagreement over whether epigenetic tags on sperm influence offspring.  For example some feel the experiment tested was not realistic because the frogs were not exposed to different environments as a human would be in his lifetime.  What do you think; would epigenetic tags on male sperm have an effect on a mans offspring?

CRISPR/Cas9 Provides Promising Treatment for Duchenne Muscular Dystrophy

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On May 1, 2016

In Student Post

There are nine kinds of muscular dystrophy and of these, Duchenne MD is the most common severe form of childhood MD. It affects about 1 in 5000 newborn males, only in very rare cases has it affected females. DMD is a genetic disorder that causes progressive muscle degeneration and weakness. Patients usually die by age 30 to 40.

DMD is caused by the absence of a protein, dystrophin, that helps keep muscle cells intact. In 1986 it was discovered that there was a gene on the X chromosome that, when mutated, lead to DMD. Later, researchers discovered that the protein associated with this gene was dystrophin. From this information, we can tell that this disorder is sex-linked, which explains why women are mainly carriers.

No one has found an absolute cure for this genetic disorder until now. Even in recent years, people have discovered treatments that will make patients’ lives more bearable, but never reverse the disorder. As a result of these advances, mostly in cardiac and respiratory care, patients are able to live past teen year and as long as in to their fifties, though this is rare. Although there are still drugs being tested like Vamorolone (a “dissociative steroid,” is an anti-inflammatory compound), more treatments on the molecular level are now being considered. However, thanks to recent discoveries and research with the new genetic technology, CRISPR/ Cas9, scientists may have found a treatment for DMD.

This new approach to gene correction by genome editing has shown promise in studies recently. This particular correction can be achieved in a couple ways: one is by skipping exon 51 of the DMD gene using eterplirsen (a morpholino-based oligonucleotide). Studies over four years show prolonged movement abilities, and a change in the rate of decline compared to controls. The newest approach to gene correction using CRISPR/Cas9, which the article I’m writing about focuses on, was performed in this study as next described: the CRISPR/Cas9 system targets the point mutation in exon 23 of the mdx mouse that creates a premature stop codon and serves as a representative model of DMD. Multiple studies in three separate laboratories have provided a path and laid the groundwork for clinical translation addressing many of the critical questions that have been raised regarding this system. The labs also discovered by further demonstrations, that this is a feasible treatment for humans. Functional recovery was demonstrated in the mice, including grip strength, and improved force generation- all of which are very important and hopeful discoveries. It is estimated from these studies that this new method will pass clinical trials and go on to benefit as many as 80% of DMD sufferers. Even greater success rates are expected if this is performed in young and newborn DMD patients.

Gaining a CRISPR Understanding

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On April 13, 2016

In Student Post

There have been some very exciting, recent biological findings involving gene editing. The CRISPR-Cas9 findings allow for the exact and purposeful changes to the genome of a cell. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats, and it is used in bacteria and archaea as a way to protect the bacteria from intruding genetic material. Essentially, CRISPR is used to remove a faulty gene and put another in its place. This is exciting because in humans, this technology could be used to remove extremely harmful DNA from our bodies, only to be replaced by healthy DNA. This method could then be used to cure cancer. In fact, another genome editing technology, called TALEN, was actually used to cure  an 11 month old girl named Layla who had what doctors thought was an untreatable form of leukemia. Described as “biological scissors”, doctors editing genes in cells in the immune system. The new genes then hunted down the dangerous red blood cells that were putting Layla’s life at risk. What is so exciting about CRISPR, however, is that unlike TALENS, which used proteins to edit genes in a very time consuming process, CRISPR uses nucleic acids such as RNA, which are significantly easier to use. Ultimately, these findings should bring a lot of good to the world and are a promising step towards curing cancer and other dangerous diseases.CRISPR-Cas9_mode_of_actionImage creator unknown. https://commons.wikimedia.org/wiki/File:CRISPR-Cas9_mode_of_action.png

HIV > CRISPR-Cas 9

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On April 13, 2016

In Student Post

https://commons.wikimedia.org/wiki/Category:HIV#/media/File:HIV-infected_H9_T_Cell_(6813314147).jpg

HIV Infecting a Cell

CRISPR-Cas 9 is an extremely advanced gene editing tool. This tool has efficiently created ways to make precise and targeted changes to the genome of living cells. However, in a study in the journal Cell Reports, scientists from the McGill University AIDS Center in Canada discovered drawbacks in using CRISPR to treat HIV. Instead of simply removing the virus from affected cells, the process of using CRISPR can also strengthen the infection by causing it to replicate at a much faster rate.

HIV has always been a popular disease to conduct research on. Scientists are constantly attempting to come up with ways to kill HIV. Several cures to HIV have been developed such as various as antiretroviral drugs, however, these medicines stop being effective after the patient has ceased to take them. As scientists have started to utilize gene editing tools to remove HIV they have been noticing the huge drawback. They realize that while the gene alteration allows the virus to be killed off in some cases, the resulting scar tissue can lead to the infection becoming stronger! Kamel Khalili, a scientist at Temple University, pointed out that the key to eliminating HIV could lie in attacking the virus at different sites using CRISPR.

Link to Original Study

Link to Original Article 

Link to Original Photo

CRISPR: Is Science Going Too Far?

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On April 13, 2016

In Student Post

CRISPR is a some-what new genetic tool in the field of science to edit human embryos. Using CRISPR, scientists can edit the genes of organisms more precisely than ever before. It uses RNA and an enzyme that slices up invading virusesF. One use of this new technology is to fix mutations that cause genetic diseases.

Crispr

https://en.wikipedia.org/wiki/CRISPR

Ethical concerns arose in April of 2015 when Chinese research used CRISPR to edit nonviable human embryos. In addition, some fear that the use of CRISPR to give the embryo traits not found in their genetic code can lead to a obsessive gene culture like the one found in Gattaca. This ethical debates caused scientists to meet at an international summit hosted by the United States National Academies of Sciences and Medicines, where the scientists discussed the ethical concerns of CRISPR but agreed to continue researching it cautiously.

In addition, some argue that using CRISPR for gene editing defeats the sacredness of the human genome and is unnatural. To this point, Sarah Chan from the EuroStemCell argues, “There is nothing sacred or sacrosanct about the genome as such. The human genome – the genome of humanity as a whole, and the unique individual genome we each possess – is merely the product of our evolutionary history to date”. From this point of view, the genome is merely a record of one’s history, but to some religious groups it is a symbol of life which should not be tainted with.

So readers, what do you think? Should we use this tool to help cure treatable diseases, or does this new technology cross the line between scientific mechanisms and morality? What type of genes should this new tool be allowed to edit?

 

Other sources

https://www.sciencenews.org/article/year-review-breakthrough-gene-editor-sparks-ethics-debate

http://www.sciencemag.org/news/2016/04/crispr-debate-fueled-publication-second-human-embryo-editing-paper

http://www.wired.com/2015/12/stop-dancing-around-real-ethical-problem-crispr/

http://www.eurostemcell.org/commentanalysis/ethics-changing-genes-embryo

Epigenetics – Exercise Runs In The Family

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On March 18, 2015

In Student Post

It is common fact that people who exercise frequently are more likely to live a longer healthier life, but now new studies show that if a person exercises it can also result in a better life for his or her children and even grandchildren. Before the study of epigenetics people always thought the genome they are born with it the genome they are stuck with. However new science has shown exercise not only changes the outward appearance of our muscles and overall physical health, but also changes our DNA.

Exercise, astonishingly, can effect gene shape, function, and turn them on and off. Scientists now know that genes can actually be quieted or amplified through exercise because biochemical signals are sent out every time a person exercises. This is where epigenetics comes in. Epigenetics doesn’t simply change the gene all together, but instead works its magic on the outside of each gene through a process called methylation. A cluster of atoms surround the genes either denying or amplifying biochemical signals. Scientists believe that even one day of exercise can change methylation patterns.

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One study done by scientists at the Karolinska Institute in Stockholm put the theory of exercise and epigenetic’s to the test. They studied 23 young and healthy men and women. They asked all the participants to work out half of their lower body for three months. This way each member of the study was his or her own control and experimental group. Obviously, after the three months each members leg that was worked out was stronger than the other, but what was much more intriguing was the results at the molecular level. The scientists found significant methylation changes in the cells of the leg that were worked out, averaging 5,000 sights on the genome where there was a new methylation pattern. Many of these methylation patterns were changed on enhancers, which are important for amplifying gene expression. The genes that were most affected were those that play a role in energy metabolism, insulin response, and inflammation within muscles. Exercise, along with many other healthy lifestyle tasks, has shown to cause changes in a persons epigenome. Changes that make a person healthier, but perhaps even more significantly, can make his or her children and grandchildren healthier.

 

http://well.blogs.nytimes.com/2014/12/17/how-exercise-changes-our-dna/?_r=0

 

The Harm Stress Causes

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On March 10, 2015

In Student Post

http://upload.wikimedia.org/wikipedia/commons/c/c6/DNA_double_helix_45.PNG

https://www.sciencenews.org/article/chronic-stress-can-wreak-havoc-body

Recently scientists have begun to discover why stress can have a negative effect on the human body. Although stress is needed when dealing with situations which require hormones to trigger a fight or flight, consistent stress can lead to a multitude of health problems. Chronic stress can lead to mental instability, and an increased risk in heart attacks, strokes, infection, etc. The decrease in health is due to inflammation and warped genetic material caused by epigenetics (chemical interactions that activate and deactivate regions of a genome to carry out specific functions). Recently scientists have discovered that  changes in epigenetics can affect activity levels in genes which directly change responsibilities of certain cells including immune cells. The stress causes a genetic response that deactivates certain areas of a genome which stops an immune cell from working properly, which of course leads to an increase in diseases that cannot be properly taken care of. Hopefully, as we continue to understand epigenetics, we will be able to take appropriate steps that will both further our understanding of the human genome, as well as help increase the longevity and immune system of individuals.

Epigenetic breakthrough: A first of its kind tool to study the histone code

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On March 10, 2015

In Student Post

 

DNA_methylation

Scientists at the University of North Carolina have recently made a breakthrough in the study of epigenetics, particularly enzyme modification of histones. Histones, the structures to which our DNA binds in the nucleus, play a pivotal role in gene expression. In other words, histone and enzyme interaction control which genes are expressed in which cells during certain times. Epigenetics is the study of how this process works. Tightening or loosening histones can turn a certain gene off or on. The study of this process has been difficult given the size of the genome and number of different histone-enzyme interactions dispersed through the sizable sequence of DNA. The Enzymes place specific chemical markers on the histones that cause the gene regulation to occur, but scientists have been unable to determine which enzymes affect what genes and how. However, the scientists at UNC have recently conducted a study with the fruit fly genome that has given them a large amount of data. The fruit fly genome contains all of its epigenetic markers in the same place. The scientists were able to insert synthesized gene regulating enzymes in place of the originals and determine the function of each individual enzyme by simply observing what was affected by the new enzymes. This research is crucial for the understanding of how the human genome is regulated, possibly leading to the cure for many illnesses.

Article Link: http://www.sciencedaily.com/releases/2015/02/150210142008.htm

Identical Twins, Identical Lives, Different Disease

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On March 9, 2015

In Student Post

Jack and Jeff Gernsheimer are identical twins. Jack has Parkinson’s disease, and his twin Jeff does not. Up until recently, because they have identical genomes, it would have been a mystery as to why Jack could develop Parkinson’s but not Jeff. However, with the discovery of epigenetics, scientists know that genes alone cannot explain why some people get Parkinson’s and other do not. While there are some genetic mutations linked to Parkinson’s, 90 percent of cases are “sporadic”, meaning that the disease did not run in the family. Even twins often do not develop Parkinson’s in tandem. Naturally, if genes don’t explain the development of Parkinson’s, scientists look to environment. There are several environmental factors that are known to link to the disease. People who were POW’s in WWII, for example, have a higher rate of developing Parkinson’s. But, and here’s the interesting part, Jack and Jeff have lived almost identical lives. For almost all of their lives, they have lived less than half a mile apart. Throughout their lives, they have been exposed to the same air, water, pesticides, etc. When they grew up, they built homes five minutes apart (by walk) on their father’s farm in Pennsylvania. Then, when they entered the professional life, they co-founded a design firm, working with their desks pushed up against each other.

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This anomaly, where a pair of humans exist with the same genetics and the same environment yet only one of them got sick is a research “bonanza” for scientists. All expected variables are being held constant, thus whatever is left must be deeply linked to the origins of Parkinson’s. However, there was a small difference in their lives that could provide insight into this anomaly. in 1968, Jack was drafted into the army and Jeff was not. This led to a series of unfortunate events in Jack’s life: first he served two years stateside in the military, got married, had two children, became involved in a long divorce, and suddenly his teenage son died. After this traumatic event, Jack went on to develop Parkinson’s, glaucoma, and prostate cancer, none of which Jeff has.

Jeff and Jack have been more than willing to undergo several studies in hope of finding something that could alleviate Jack’s Parkinson’s. The first study involved collecting embryonic stem cells from the twins. The benefit of stem cell cultures is that they act similarly to how they would in the body even though they are in a petri dish. The mid-brain dopaminergic neurons grown from Jack’s cells created abnormally low amounts of dopamine. Jeff’s produced normal amounts. Surprisingly, even though Jeff showed no signs of Parkinson’s, both twins had a mutation on a gene called GBA. This gene is known to be associated with Parkinson’s. As a result, both of their brain culture cells produced half the normal amount of beta-glucocerebrosidase, an enzyme linked to that gene. Instead of answering questions, this study only raised more to the fascinating case of Jeff and Jack.

I want to add a bit about how Jack’s son died, because it is unimaginably tragic and can show you just how much Jack had to face. Especially if we are considering Jack’s trauma as a contributor to his development of Parkinson’s, it is important to know the story. When Gabe, Jack’s son, was 14 in 1987, he became fascinated with the Vietnam War. Like any good father, Jack rented his son some movies on the war. One of those being The Deer Hunter, in which there is a scene where two prisoners of the Viet Cong are forced to play Russian Roulette. Gabe told his friend that if it were him, he wouldn’t just sit there. He would rather just get it over with. With that conversation, Gabe got his dad’s pistol, that he knew was hidden in the closet drawer, put one bullet in the chamber, put the gun to his head, and shot.

Jack rarely shows emotion. This “pressure cooker” way of dealing with things could explain his illness. Jeff thinks that the parkinson’s is a physical manifestation of how Jack deals with stress, rather how he doesn’t deal with stress. The connection between stress and disease is a very active research topic. And while their lives were very similar, if compared, Jack’s is by far the life with a more stressful environment. Some research might suggest that this stress differential can have a relation to Parkinson’s disease. In 2002, neuroscientists at UPitt subjected rats to stress, and they found that the stressed rats were more likely to experience damage to their dopamine-producing neurons than the non-stressed rats. This led to the term “neuroendangerment”, which means “rather than stress producing damage directly and immediately, it might increase the vulnerability of dopamine-producing cells to a subsequent insult.”

Another hypothesis as to what caused Jack’s Parkinson’s is that it could be linked to chronic inflammation.  Chronic inflammation is the mechanism by which stress can create neurodegeneration. Evidence that suggests this could be the case in Jack and Jeff is presented in their skin. Jack has psoriasis, a condition linked to chronic inflammation, and Jeff does not.

To this day, the search for what caused Jack’s Parkinson’s continues. Last year, NYSCF scientists conducted a study on the twins’ stem cells. They found a few functional differences between their cells. After finding the GBA mutation, they searched harder for other clues as to what might differentiate their brains. They screened 39,000 SNV’s, single nucleotide variants, which are instances where a single nucleotide in the human genome has been altered (either switched, deleted, or duplicated). They found 11 SNV’s, nine of which are linked to Parkinson’s disease. However, all 9 were found in both twins, meaning that this did not explain why Jack was sick and Jeff wasn’t.

Finally, they were able to uncover a relevant difference. Jack had high levels of MAO-B, which is involved in the breakdown of dopamine, whereas Jeff’s levels were close to normal.This hypothesis supposed that there exists a possible molecular mechanism by which stress could lead to neurodegeneration. What’s nice about this finding is that it could present a possible treatment for Parkinson’s. MAO-B inhibitors exist and are actually drugs currently on the market. They were given to Jack, and while it’s too soon to see the effects and to recommend them as treatment for Parkinson’s disease, it’s definitely a start.

Source: http://nautil.us/issue/21/information/did-grief-give-him-parkinsons

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