BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Crispr (Page 1 of 3)

Using CRISPR to Protect the World’s Chocolate

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On March 20, 2019

In Student Post

Cacao tree and bean

Around the world, in places 20º North and South of the equator, cacao is grown.  Growing in tropical environments, cacao trees grow pods that contain beans that are the primary ingredient of chocolate.  Unfortunately, fungal infestations have recently had a devastating impact on cacao farms, causing a wide range of diseases in the trees.  The worldwide chocolate business which employs 50 million people, is at serious risk.

Scientists have begun to develop CRISPR technology that can alter the DNA of cacao plants to make them more resistant to both fungal and viral diseases.  CRISPR is a gene-editing technology that works like a molecular pair of scissors, removing sections of DNA and replacing them with new ones.

Candy company Mars Inc. has supported the Innovative Genomics Institute in using CRISPR to engineer better cacao trees.  It will take five to seven years for the genetically engineered cacao trees to grow their pods, so until then, we can’t be certain that the project has been successful.

The lessons learned by the scientists on this project are important as they translate into work that can be done on other, important food plants such as cassava, rice, and wheat.

For the original article on this project, click here.

 

Stem Cells and CRISPR

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On March 17, 2019

In Student Post

Many cells can reproduce but there are a few types of cells that are not able to reproduce. One of these types are nerve cells, the cells that cary messages from your brain to your body.  There are many ways nerve cells can be destroyed or damaged, by trauma or drug use.  Millions of people are effected by losing nerve cells and for so long no one could think of a way to recreate them; until the discovery of stem cells.

After fertilization, and when the newly formed zygote is growing, it is made up of a sack of cells.  Some of these cells are stem cells which develop according to their environment. Because of the behavior of stem cells, scientists theorized that if they placed stem cells in the brain or spinal chord, two areas that have an abundance of neurons, the stem cells would turn into a neuron because of the environment it was in.  But, when they tried introducing stem cells into the body, the immune system treated them as an foreign body, as it should. Our immune system has to treat anything that does not come from our body as an enemy or we could get extremely sick.  However, the downside is organ transplants, blood transfusions, etc. are dangerous because they could cause a serious immune rejection.

Someone experiencing a spleen transplant rejection

Cells have a surface protein that displays molecular signals to identify if it is self or foreign.  Removing the protein causes NK (natural killer) cells to target the cell as foreign. Scientist haven’t been able to figure out how to make a foreign cell not seem foreign until Lewis Lanier, chair of UCSF’s Department of Microbiology and Immunology, and his team found a surface protein that, when added to the cell, did not cause any immune response.  The idea would be to use CRISPR/cas9 to edit the DNA of the stem cells, and in doing so would remove the code for the current surface protein and add the code for the new surface protein.

After the scientists had edited the stem cells, to have the correct signal protein, they released them into a mouse and observed that there was no immune rejection. Truly amazing. Maybe brain damage could be helped by this science one day. Tell me your thoughts on Stem Cells in the comments!

For more information, please go check out the primary source of this article.

 

 

New anti-CRISPR Proteins Serving as Impediments to this Miraculous System.

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On March 17, 2019

In Student Post

CRISPR-Cas9 systems are bacterial immune systems that specifically target genomic sequences that in turn can enable the bacterium to fight off infecting phages. CRISPR stands for “clusters of regularly interspaced short palindromic repeats” and was  first demonstrated experimentally by Rodolphe Barrangou and a team of researchers at Danisco. Cas9 is a protein enzyme that is capable of cutting strands of DNA, associated with the specialized stretches of CRISPR DNA.

Diagram of the CRISPR prokaryotic antiviral defense mechanism.

Recently, a blockage to the systems was found by researchers which are essentially anti-CRISPR proteins. Before, research on these proteins had only showed that they can be used to reduce errors in certain genome editing. But now, according to Ruben Vazquez Uribe, Postdoc at the Novo Nordisk Foundation Center for Biosustainability (DTU), “We used a different approach that focused on anti-CRISPR functional activity rather than DNA sequence similarity. This approach enabled us to find anti-CRISPRs in bacteria that can’t necessarily be cultured or infected with phages. And the results are really exciting.” These genes were able to be discovered by DNA from four human faecal samples, two soil samples, one cow faecal sample and one pig faecal sample into a bacterial sample. In doing so, cells with anti-CRISPR genes would become resistant to an antibiotic while those without it would simply die. Further studies found 11 DNA fragments that stood against Cas9 and through this, researchers were ultimately able to identify 4 new anti-CRIPRS that “are present in bacteria found in multiple environments, for instance in bacteria living in insects’ gut, seawater and food,”  with each having different traits and properties.  “Today, most researchers using CRISPR-Cas9 have difficulties controlling the system and off-target activity. Therefore, anti-CRISPR systems are very important, because you want to be able to turn your system on and off to test the activity. Therefore, these new proteins could become very useful,” says Morten Sommer, Scientific Director and Professor at the Novo Nordisk Foundation Center for Biosustainability (DTU). Only time will tell what new, cool, and exciting discoveries will be made concerning this groundbreaking system! What else have you guys heard? Comment below!

CRISPR and Improving Crops

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On March 17, 2019

In Student Post

CRISPR and improving crops

The Article: How scientists are using CRISPR to create non-GMO crops   by Yi Li touches upon how CRISPR can replace the usage of conventional GMO crops today. By using CRISPR to make these new crops we can solve the problems that GMO crops provide because for annual crop plants like corn, tomatoes, and rice can have the CRISPR genes bred out of their gene pool. This would make the effects of these CRISPR crops not undoable and therefore would not pose the same threats that GMO crops do. CRISPR crops could also be created faster and be more precise than GMO crops, making crops with powerful resistances to droughts, pests, and poor soil. Creating new plant technology to increase yields is essential to keeping up with the growing human population so some type of man made crop is needed to serve us. This method seems to be a very viable option to solve this problem. This CRISPR technology also will likely lower the price of crops and help boost the economy and could be used to help third world countries with their famines. Yi Li States that the CRISPR will work to change the plant by being inserted inside the plant cells. From there the CRISPR will locate and rewrite the relevant section of the DNA. Do you want your food to be cheaper? Do you want to boost the economy? Do you wanna help those who are hungry? Want to learn More about how the concept of CRISPR crops will work. This article (What are genome editing and CRISPR-Cas9?) explains what CRISPR is and how it works to change the genome. And the article Bypassing GMO regulations with CRISPR gene editing will show you how CRISPR is better than GMO and is able to be outside of those regulations.

Cocaine Addiction is Curable

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On March 12, 2019

In Student Post

University of Chicago researchers have made groundbreaking discoveries in the CRISPR field. Following malaria resistant mosquitoes and heat resistant cows, we are well on our way to creating cocaine-resistant mice. Scientists Xiaoyang Wu and Ming Xu teamed up to create a piece of technology that utilized the human body’s natural ability to break down cocaine, using an enzyme called butyrylcholinesterase, or “BCHE”.

After learning of BCHE, one may wonder, “why do people get addicted to cocaine if the human body makes an enzyme specifically to break it down?” In reality, “its short half-life makes it ineffective in a clinical scenario, since it disappears before it has any long-term impact on the body’s response to cocaine.” Researchers Wu and Xu had to find a way to prolong its life span to allow it time enough to work, as well as increase its potency to combat the severe nature of addiction. The scientists used epidermal stem cells in the mice, and using CRISPR technology, converted them into “BChE-producing factories.” The BCHE is easily distributed into the blood through the skin cells, and resulted in the inhibition of the mice’s withdrawal symptoms, and even preventing death in the case of lethal doses.

Not only did the stem cells work, but the mice responded well- producing high levels of BCHE for over two months without a negative immune system reaction.

“Apparently, the enzyme broke down the drug before much, if any, of it could reach their brains.”

A graph of showing the rapid increase of cocaine-caused deaths in the USA from 2002-2017.

The idea of cocaine-resistant mice may seem oddly specific, but cocaine addiction is a serious problem that we as Americans face. According to Ray Donovan, the special agent in charge of the Drug Enforcement Administration (DEA) New York Division, “cocaine is making a comeback in New York,”. It is a problem that we as Americans, and especially New Yorkers, will likely come into contact with some way or another. It doesn’t have to stop with one drug. While BCHE is unique to cocaine decomposition, there may be other enzymes that can similarly be implemented. The danger is this; if cocaine (or other drug) addiction is easily curable, who is to stop anyone from using it? Hopefully, the general public will have seen the aftereffects of cocaine addiction, and not use this new technology to excuse bad choices because they deem it less dangerous than before.

Editing Sickle Cell Disease…

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On March 12, 2019

In Student Post

CRISPR gene-editing has recently been involved in the studies of sickle-cell anemia, a gene mutation that causes a decline in children’s health. Sickle cell anemia makes it difficult for oxygen to transport sufficiently throughout the body due to unhealthy blood cells. Some symptoms of the condition are shortness of breath, pale skin, colder body temperatures, headaches, etc…

Photo by SciTechTrend

Looking at sickle-cell anemia from a molecular standpoint, the mutation alters the red-blood cell by producing the wrong form of molecule which is referred to as a subunit. Out of the four subunits in hemoglobin, an “adult-expressed” subunit also known as “beta” is produced. In contrast, fetal subunits create “gamma” subunits which are the appropriate molecules in red blood cell development for children. The unfortunate results of a mutated gene are crescent-like and inflexible red blood cells, which can form blockages against the flow of blood and oxygen through blood vessels.

In the past, scientists have been able to increase the gamma production in hemoglobins by “reversing” beta subunits to gamma subunits through a form of therapy, yet in a recent study scientist dove deeper to prevent the mutation as a whole. With gene editing technology, CRISPR has been reported to be useful in putting an end to the hereditary mutation. In that, scientists can identify the mutation and cut the DNA target out by using CRISPR. A specific piece of the DNA, also known as the “control section”, is introduced to gamma subunits during a  process of molecular conversion therapy and the ends of the control section are placed together after the mutated code for the gene is removed. Ultimately, this is said to reduce the adult-expressed subunits and stimulate higher levels of gamma subunits in fetal hemoglobins so that young children affected by sickle cell can avoid invasive treatments in their future.

 

Scientist from China creates a baby resistant to HIV

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On March 12, 2019

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The development of CRISPR technology has drastically progressed in the recent years, and He Jiankui, a scientist from China, took a step that most people judge to be crazy: he used CRISPR technology to create a human who is resistant to the HIV virus.

What is CRISPR? Good question.

CRISPR-Cas9 is a gene editing tool made from an ancient bacterial immune system. In bacteria, this system identifies DNA of invading viruses and send in different enzymes, such as Cas-9 to target and cut out a piece of DNA. Researchers quickly realized that almost any sequence of DNA can be cut out and modified the system to any sequence desired, even one that can prevent HIV. This is what Jianku’s work comprised of.

Jiankui and his team targeted the gene CCR5, a gene that provides the blueprint for the cell surface protein involved in the immune system, in the DNA of human embryos. The cell surface protein is usually involved in relaying information between cells, and HIV can use it to dock onto cells, infecting them with their own genetic material. Jianku eliminated the CCR5 gene to prevent HIV from docking onto any of the baby’s cells. However CRISPR-Cas9 induces mutations that scientist cannot fully control, and Jianku could not replicate the gene to the exact level. So, he instead created a “mixture of disrupted gene products”, which could potentially have a negative effect on human health.

At first glance, Jiankui’s experiment might be seen as beneficial, but Jiankui’s decision to create this human has been considered by other scientist as premature, drastic, and unethical, and has caused a lot of controversy. Although this was not the first time a scientist tampered with a human embryo, many scientists are outraged and believe that his experiment was a violation of human ethics. According to an article written by Allison Eck, the most notable ethical breach was conducting this experiment without the consent of other scientists, ethicists, regulators, or institutional review boards.

Debates over Jianku’s work have been circulating since the announcement of his experiment. Personally, I think that in the future, if we can prevent HIV and other harmful diseases that cause death, CRISPR can be an effective tool. However, as of now, we do not fully understand are aware of all of its effects. Therefore it is dangerous to test it on other humans. In the wrong hands, this powerful technology might be used in the wrong way and can cause huge repercussions. What do you think?

 

Microbial Tape Recorders: A new Application to CRISPR

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On March 12, 2019

In Student Post

Research in the new gene-editing technology CRISPR has raised many red flags and ethical dilemmas as its full capabilities prove to be more than what was thought previously possible. It is used by bacteria to combat viral infections, but now scientists have repurposed it to keep records of a given bacteria’s environmental conditions, which could have significant applications to accurate chronicling of biological changes. Scientific American’s article, “Bacterial ‘Tape-Recorder’ Could Keep Tabs on Bodily Function” outlines how CRISPR “is a DNA sequence that makes and keeps a genetic record of viruses the bacterium encounters, commanding it to kill any that try to reinfect the bacterium or its descendants”. This natural function of bacteria, though, can be manipulated so that instead of exclusively accounting viral encounters, any environmental abnormality can be captured by CRISPR. More specifically, the bacterial mechanism would sense a special signal from a change in its surroundings and create trigger DNA, which, according to the U.S. National Library of Medicine, is a noticeable sequence of DNA from the invaders, which could be used to identify what exactly caused the change.

Applications of this technology today are far-reaching. This technology can be theoretically used to measure contaminants in fresh water or saltwater, or the nutrient levels in topsoil, but the predicted first application will be in monitoring bodily function in humans, and other animals. Digestion problems seem likely to be the first human system monitored with this new tool. Fructose Malabsorption is a digestive disorder which results in high levels of fructose sugar remaining in the digestive system. This disorder results from damaged intestines, normally from serious infection. Sugar levels in the digestive tract can now be monitored precisely by using this application of CRISPR in Escherichia coli cells (bacteria which are naturally found in the human digestive system). The record of sugar can identify specific problems diseased patients, after the E. coli cells are recovered from a patient’s feces, and cause them no harm in the process.

This tool is not without its drawbacks. It is reported that millions of modified bacteria need to be placed in a given system to have an accurate reading of environmental surroundings, and these bacteria have to be in the region of interest for at least six hours. The magnitude and duration of this prospective tool leave much to be desired as initial costs would be enormous, and other limitations, which can only be found through proper testing, remain unknown. In all, this advanced tool still seems applicable for now on only a small scale, but it is an example of CRISPR as a tool for good, and shows much hope for the future.

https://commons.wikimedia.org/wiki/File:E._coli_Bacteria_(16578744517).jpg

Escherichia coli bacteria which can be modified with CRISPR to become a “tape-recorder” of the human digestive system

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!

 

 

Cas9: Dormant Killers?

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On March 12, 2019

In Student Post

Woah. Pretty aggressive title, but it did grab your attention, didn’t it?

What the Heck Even Is Cas9?

Well, Cas9 is an integral part of the CRISPR-Cas9 system. The Cas9 is able to latch on to a piece of DNA (it grabs on based on a piece of guide RNA, or gRNA in the complex) and cuts it. When this happens, the cell is like, “Oh no! Broken DNA! We must fix!”.  Now I know what you’re thinking… why fix something that ain’t broke? Well, what happens is that (in science being done today) the piece of DNA already has something wrong with it that the cell isn’t aware of such as a point mutation. Breaking the DNA just brings the problem to the cell’s attention so that it can fix the DNA. This was a defense mechanism in bacteria to work against viruses and the like by ‘cataloging’ the viruses they’ve encountered and using the system to cut up the viral DNA, but scientists thought it was pretty cool so they decided to figure out a way to make it work in animals.

Alright… Why Are They Killers?

Well… what these scientists have done is that they have developed a way to basically use the CRISPR-Cas9 system as a defense mechanism for diseases prevalent in humans and plants such as cancer or the West Nile virus. Basically, how this would work is that at the end of the Cas9 researches added a little protein tail that could only be cut by a specific protein. When this protein is cut, then the Cas9 would be ‘activated’ and would do its defensive duties. Scientists could change this protein to target different things, such as adding a protein that cancer cells make enzymes for. It was also used in plants to target certain viruses. So in short, this Cas9 DNA destruction mechanism is dormant until presented with the foe it has been essentially trained to fight.

 

So Is The World Cancer-Free?

Unfortunately not, my friend. Even though this is revolutionary stuff happening, the research done is mostly for plants in order to resist infectious diseases and viruses. It has, however, offered us insight into how we can manipulate this system to serve us in a beneficial way. They also, during this whole protein-tail process, figured out that they can get the protein to still work in different configurations that make it easier to add certain protein tails. They determined that by cutting Cas9’s amino acid chain and rearranging it in certain ways, it can have easier protease recognition sites as well as attachment sites for the protein.

Do you think this system will revolutionize medicine?

Will this eventually replace vaccines?

Will the continued research into gene editing come back to haunt us in the end?

The Rice That Can Clone Itself

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On March 12, 2019

In Student Post

A team of scientists has discovered that through the use of CRISPR, they were able to create a rice plant that can asexually reproduce. The problem with previous strands of genetically modified rice plants, those bread to have a higher yield, is that their progeny did not always carry this desired trait. So farmers have to buy new genetically modified seeds every year to ensure that they will get that same yield.

Image result for rice grains

That is where the magic of CRISPR comes into the equation. The first step in the process was editing the eggs of the plant by implanting a promoter that allows the egg to start the embryo growing process without a sperm. One issue still lingered, the process of meiosis that was occurring could not produce viable offspring because it only had half of the genetic material that the progeny would need. Another team of scientists from the French National Institute for Agricultural Technology discovered that by using CRISPR to turn off three specific genes they could stop the meiosis process and allow the plant to reproduce asexually.

Image result for rice plant

This process is still only 30% efficient at this stage. However, the offspring they do produce are able to asexually produce more clones of themselves. Now the process starts to try and make this process more efficient. I think these plants could have a major impact on the agricultural industry, especially with food shortages becoming more present as the human population rapidly increases.

What do you think? Have we overstepped our bounds by editing nature? Or have we pioneered a new solution for the world hunger question on everyone’s minds?

Using CRISPR to target neurons

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On March 12, 2019

In Student Post

A rat brain stained with protein and DNA.

Researchers from the University of Alabama at Birmingham have successfully used CRISPR to target neurons. With their novel approach, the team led by Jeremy Day was able to manipulate the function of neurons in vivo.

CRISPR, a self-defense system for bacteria against viral invaders, has become a very popular gene editing tool, as it allows researchers to make very targeted changes to an organism’s DNA. Normally using CRISPR-Cas9, the process involves a piece of guide RNA guiding Cas9 to the desired gene where it cuts it, rendering the gene inexpressible.

However, Day’s team used a different CRISPR mechanism, CRISPRa, which increases the expression of the desired gene. For their CRISPRa, they used CRISPR-dCas9, a CRISPR system with a deactivated Cas9, to which they attached transcriptional effectors. This allowed the guide RNA to guide the transcriptional effectors to a particular gene so it could be up-regulated, increasing its expression. In focusing on neurons, Day’s team targeted the promoter sequence for SYN genes, a common group of genes in the brain that code for proteins that regulate neurotransmitters, and designed their guide RNA accordingly.

After injecting their effector-coupled dCas9 system into live rats using viral hosts, the desired genes were successfully up-regulated, with the researchers viewing their new protein products after the fact through fluorescent markers in cell samples. Following this achievement, Day and his team expanded their CRISPR-dCas9 system, incorporating multiple guide RNAs into a single system to target multiple sections of DNA at the same time and using it analyze the complex Bdnf gene that has multiple promoters and plays a core role in brain function and development.

This innovative approach to targeting genes in the brain has far-reaching applications, allowing for versatile gene editing in live animals, which, in the words of Vanderbilt Brain Institute researcher Erin Calipari, “is going to give us an unprecedented view of the role of gene expression in behavior”.

From psychology to physiology and beyond, there is no doubt that this discovery’s molecular insight will give us a far greater understanding of the brain.

The Cure Before Being Born

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On March 12, 2019

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lab mouse – Photo credit to Wikimedia Commons

A team of researchers from the University of Pennsylvania and Children’s hospital of Philadelphia has seen exciting results in their experiment on mice fetuses with an inherited liver disease.  The team removed the amniotic sac containing the fetus from the mother’s uterus, before injecting in a vein of thee fetus near the liver with CRISPR. This was to ensure that the genetic modification would be in the liver cells and would not affect any other vital organs. The fetus was then placed back into the uterus and the mother was thankfully unaffected by the modification, allowing for all the babies to be born without any issues.

The team used a more recently invented form of CRISPR called base editing instead of the well-known  CRISPR-CAS9.  Rather than cutting and inserting a sequence of DNA, a single nitrogenous base was replaced with another.  This newer method showed significantly less “genetic havoc”, unknown consequences for a cell that has been genetically modified with CRISPR.

The disease they targeted was a tyrosinemia type I, a mutation that effects 1 in 100,000 newborns globally, which causes causes the amino acid tyrosine to be metabolized into toxic products, which build up and cause damage to liver, and can eventually destroy it.   The scientist sought to disable the HPD gene, which creates enzymes that help to break down tyrosine.  By changing a cytosine base to thymine base, the toxic products are never produced.

Tyrosinemia type I – Photo credit to Wikimedia Commons

As the mice grew and developed, the researchers were astounded to find that despite only 15% of their liver cells having been the altered with the base edit, the genetically modified mice were surviving better and gaining more weight compared to those treated with traditional methods of drugs and monitored diet.

This is definitely a step in the right direction to eliminating genetic diseases, but base editing, especially for diseases due to multiple mutations might be more difficult, as many bases would need to be edited.  What do you think: more safe, yet possibly difficult base editing method or cut-insert method?

CRISPR Research into HIV Immunity Might Also Improve Human Cognition

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On March 12, 2019

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In the quest to genetically master human immunity to HIV, Chinese CRISPR researchers may have come across a way to control human intelligence as well.

Specifically, the trial of deleting the CCR5 gene in twin girls Lulu and Nana has lead to a scarily powerful discovery that scientists are within reach of being able to genetically modify human brain function. Scientists were initially interested in deleting the CCR5 gene because it codes for a beta chemokine receptor membrane protein which the HIV virus hijacks to enter red blood cells. However, when this alteration was tested on mice embryos in California, the resulting offspring showed evidence of improved mental capacity.

https://pixabay.com/illustrations/dna-genetic-material-helix-proteins-3539309/

After this unexpected result, scientists investigated further how the alteration would impact human function with the twins’ lives in mind. Experiments yielded evidence of improved brain recovery after a stroke and potential greater learning capacity in school. Scientists at UCLA uncovered an alternative role for the CCR5 gene in memory and suppressing the formation of new connections in the brain. The absence of this gene in the human genome would likely make memory formation easier via more efficient neural connections.

Although the mice experiment suggested that CCR5’s deletion would improve mental capacity rather than harm it, scientists cannot be sure how the alteration has impacted Lulu’s and Nana’s cognitive function. Some also fear that this discovery may have been the first Chinese attempt to genetically create superior intelligence, despite their claim to the MIT Technology Review that the true purpose of the study was to investigate HIV immunity. Although the Hong Kong scientists who engineered the twins did not publicly intend to improve human cognition, they confirmed a familiarity with UCLA’s discovered connections between CCR5 and human cognition all throughout their trial.

Are we within reach of a time when we can play with the circuit board of the human genome to raise a person’s IQ? Quite possibly. But only time and research will tell.

CRISPR Technology is Finding Its Place in the Agricultural Industry

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On March 12, 2019

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CRISPR technology is now laying a foundation in the agricultural world, trying to help corn growers improve the speed, versatility, and output of their crops. It has been difficult to implement CRISPR technology thus far, as the cells walls of plants, at a microscopic level, are particularly tough to penetrate. Fundamentally, CRISPR “…consists of enzymatic scissors called Cas9 that a guide made from RNA shuttles to an exact place in a genome.” The difficulty with plants cells is that, in comparison to animal cells, the extra-rigid cell walls make it immensely difficult for the guide RNA (gRNA) and the Cas9 to reach their destination on the genome. In response to this problem researchers have come up with what is described as an “inelegant” solution to this problem where they “…splice […] CRISPR genes into a bacterium that can breach the plant cell wall or put them on gold particles and shoot them with what’s known as a gene gun.” Unfortunately, this method doesn’t work in the crucial corn varieties where it is needed. However, a team of researchers in North Carolina, Timothy Kelliher and Quideng Que of Syngenta, in Durham, North Carolina have come up with an even more ingenious solution to deal with the stubborn plant cell walls. Haploid induction “…allows pollen to fertilize plants without permanently transferring ‘male’ genetic material to offspring. The newly created plants only have a female set of chromosomes – making them haploid instead of the traditional diploid. Haploid induction itself can lead to increased breeding efficiency and higher yielding plants.” This same method has been found to work in wheat and even Arabidopsis, “…a genus of plants related to cabbage, broccoli, kale, and cauliflower.” Yet again, sadly, CRISPR faces another drawback as scientist not that “…if it were done in the field, the changes wouldn’t spread because the male genome in the pollen – which carries the CRISPR apparatus – disappears shortly after fertilization.” However, there is still much hope for CRISPR technology, and it is without a doubt that we are making big strides into the future with gene editing technology.

CRISPR/Cas9: Controlling Genetic Inheritance in Mammals

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On March 12, 2019

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Often the subject of debate, CRISPR/Cas 9 has come to the forefront of the scientific community as its development bridges the worlds of Sci-Fi and reality. Yet while CRISPR/Cas9 has been successfully used in altering the genetic inheritance of insects, applying the same technology to mammals has proven to be significantly more complex. With the recent development of active genetics technology in mice by UC San Diego researchers, a huge stride has been made for the much contested future of gene technology.

Releasing their findings in January, the team led by Assistant Professor Kimberly Cooper engineered a copycat DNA element into the Tyrosinase gene controlling fur color. The copycat DNA results in mice that would have been black appearing white. Over two years they determined the copycat element could be copied from one chromosome to another, repairing breaks targeted by CRISPR.  Ultimately, the genotype was converted from heterozygous to homozygous.

Following the success of her lab’s single gene experiment, Cooper hopes to use the technology to control the inheritance of multiple genes and traits in mice. Her experiment, the first active genetic success in mammals, has biologists hopeful for  future development of gene drive technologies to balance biodiversity and mitigate the adverse effect of invasive species.

Hope for Duchenne Patients?

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On March 1, 2019

In Student Post

Duchenne muscular dystrophy is a genetic disorder currently without a cure. It causes progressive muscle degeneration and weakness. Duchenne Muscular Dystrophy, or DMD, is characterized by an absence of dystrophin. Dystrophin is a protein that keeps muscles intact, which when absent lead to a loss of muscle function and strength. This lack of dystrophin begins in early childhood between ages three and five mostly in males with 1 in 5,000 males inflicted and a rare

File:PBB Protein DMD image.jpg

Dystrophin Protein

occurrence in females. By later ages, individuals are forced into wheelchairs and put on respirators as their diaphragms weaken until an early death usually in their 20’s or early 30’s due to heart failure or an inability to breath.

Despite not having a cure for Duchenne Muscular Dystrophy, scientists are performing the first trials in large mammals, dogs. Many dog breeds can also be inflicted by the lack of dystrophin and thus have Duchenne Muscular Dystrophy. Four of these inflicted dogs have been chosen at only one-month-old to be treated using a harmless virus called adeno-associated virus or AAV. This harmless virus is delivering the CRISPR Cas9 protein gene-editing components to make a single strategic cut in faulty DNA to “exon 51, one of the 79 exons that comprise the dystrophin gene.”

File:MuscularDystrophy.png

Right Affected Individual        Left Unaffected Individual

These dogs were tracked and within several weeks of the CRISPR editing the missing protein was reported in muscle tissue throughout the body with as much as 92% correction in the heart and 58% correction within the diaphragm, which is the main muscle needed for breathing. While there is a clear success in the current trials with improvements greater than 15%, they are still far from human clinical trials as the question still remains if the stable levels of dystrophin do not have adverse side effects. The corrections made using CRISPR was previously noted in having successfully corrected mice and human cells only increasing the hope provided by these trials. The trial is already being called “promising” and might one day be considered “groundbreaking.”

Not only providing hope for those with DMD, but these trials also provide a significant step towards single gene editing to treat an incurable disease. While larger studies are still to be conducted, the individuals working on this study at the Royal Veterinary College in London and UT Southwestern Medical Center in the United States are eager for the study to grow. One such leader in this study, Dr.Olson from UT Southwestern has even gone as far as spawning a biotechnological company called Exonics Therapeutics Inc. with the hope of further optimizing this technology for the clinic on top of his role at the University.  

AminoKassid

CRISPR Scandal

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On January 14, 2019

In Student Post

Outrage is widespread in the scientific community, as one man’s choices may have ruined genome editing for everyone. With others calling his actions “premature,” “ethically problematic,” and “monstrous” Doctor He Jiankui remains confident in his File:He Jiankui at Second International Summit on Human Genome Editing.jpgactions. His action being creating the first genetically modified babies, twin girls born in November. “He had altered a gene in the embryos, before having them implanted in the mother’s womb, with the goal of making the babies resistant to infection with H.I.V..”

The chaos created by Dr. He’s actions are due to the fact that he failed to receive permission from an ethical board. He claims to have gotten the permission of the hospital, Shenzhen Harmonicare, but the hospital denies being involved. The hospital is even going as far as requesting a police investigation into the “fraudulent ethical review materials.” So without ethical approval, Dr. He seriously violated not only the Chinese government’s laws and regulations created by the Chinese Society for Cell Biology but also academic ethics and norms. He has risked opening the door to designer babies editing everything from eye color to I.Q and physical ability, while the CRISPR creators are attempting to limit the editing to cases of desperate unmet need where the cause cannot be prevented in any other way, unlike H.I.V. which is very easily avoidable in infants.

These twins, however, are the only known set of children to be produced from a trial of seven couples with an H.I.V. positive father and negative mother. Dr. He after deactivating the perfectly normal gene CCR₅ withFile:NHGRI-97218.jpg CRISPR-Cas9  implanted the embryos into their mothers. In deactivating the CCR₅, Dr. He made the girl’s resistant to H.I.V., but also made them more susceptible to West Nile virus and Japanese encephalitis. So while the babies were “born normally and healthy” according to Dr. He, Dr.Kiran Musunuru from the University of Pennsylvania said there was evidence of mosaicism in both twins embryos and Lulu’s placenta was also mosaic. Despite the mosaic placenta, both babies appear to be progressing well for now, but what will happen to them in the future is the unknown. While their health is positive for now, the effects will be felt in their progeny for generations to come in unknown ways as cells with CCR₅ and without are mixed.

With the unknown effects on future children, a lack of shared experimental notes/reports and ethical precautions, and a plea via youtube Dr. He only 34 years old is being shunned in the science community just days before his presentation at the Second International Summit on Human Genome Editing in Hong Kong.

AminoKassid

Click Here to Learn About the Tomato’s Fancy New Makeover

By

On January 12, 2019

In Student Post

The sun rose on a dimly light Monday morning when Adriano Nunes-Nesi, Lázaro E.P. Peres, Agustin Zsögön, Lucas de Ávila Silva, Ronan Sulpice, and Emmanuel Rezende Naves published their groundbreaking discovery that could revolutionize the cultivation of chili’s forever.   These insanely talented and well established scientists figured out how to use the CRISPR-Cas9 editing tool to turn a tomato into    a chili.

Capsaicinoids are what give peppers their heat and when these scholars of science mapped the tomato’s and chili’s genomes, they saw that the tomato has genes that, when transcribed, produce these spicy and hot capsaicinoids.

The reason why this is important is because the chili’s cultivation process is extremely tedious and requires many specific conditions, not to mention it having a small yield.  Since the yield of tomatoes is 30x that of the chili, using the CRISPR-Cas9 tool, they could change the shape and taste of the tomato to that of a chili. The price of a chili peppers, per kg, compared to tomatoes is roughly 60 cents higher. It may not seem a ton, but in bulk orders, it quickly adds up.

Lázaro E.P. Peres, who is aProfessor of Plant Physiology at the University of São Paulo and one of the scientists on the team, says, “The proof of concept here is that we can transfer the unique thing endemic to a less-produced plant into another plant that is more widely produced”.  The paper states the tomato “is highly amenable to biotechnological manipulation”. This would drive the price of the chili down which would help markets, restaurants, and Gardners worldwide.

The only issue to this is the publics opinion. For years, the already established “organic” companies having been labelling genetically modified food as unhealthy compared to non-GMO foods.  This claim is simply outright false.  “Any plant or animal product is full of DNA that our body readily digests, messing with one or two genes isn’t going to impact human health. The only way GM food could affect human health is if the modification somehow produce a protein product that was actively toxic to humans.”  This quote is from an article by the Genetic Literacy Project, which could be seen as having bias towards GMO foods, however their mission says,”is to aid the public, media and policymakers in understanding the science and societal implications of human and agricultural genetic and biotechnology research and to promote science literacy.”  All they are interested in doing is educating the public because so many people have been lied to by big organic corporations and the media to prevent customers from eating GMO products.  What would they have to gain by saying they are safe when they are not?    If the public can get passed the idea of genetically modifying foods, I believe turning a tomato into a chili pepper would save much money from hundreds of thousands of businesses– big or small.

What do you guys and gals think of GMO products?

For more information, please go check out the primary source of this article and the researchers report

 

 

Fighting the mosquito disease problems with… mosquitos?

By

On October 10, 2018

In Student Post

Since the discovery of CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), gene editing has become a highly debated topic. One of the reasons backing the use of CRISPR-cas9 is to prevent diseases. These diseases include mosquito-borne diseases such as zika, dengue fever, and malaria.  Malaria in particular kills around 3,000 children every year. Various groups of scientists have worked on genetically modifying mosquitos to stop the spread of malaria by making female offspring sterile and unable to bite, making male offspring sterile, or making mosquitos resistant to carrying diseases. A point of concern was if the modified gene would stay relative and would carry from generations. In order to make offspring, genes from both parents must be used, resulting in the offspring carrying the modified gene only half the time.  In particular cases, mutations would occur in the altered DNA, which nullified the genetic changes.  This has been solved by developing a gene drive, which makes the desired gene dominant and occur in the offspring almost 100% of time.  This entails almost the entire mosquito population could have this modified gene in as little as 11 generations.

Image by Author

Recently, the government of Burkina Faso, a small land-locked nation in west Africa, has approved for scientists to release mosquitos that are genetically modified anytime this year or next year.  The particular group of mosquitos to be released first is a group of sterile males, which would die rather quickly.  Scientists want to test the impact of releasing a genetically modified eukaryotic organism in the Africa. It is the first step in “Target Malaria” project to rid the region of malaria once and for all.

 

One of the major challenges in gaining allowance to release the genetically modified species was the approval of the residences, who lack words in the local language to describe genetics or gene editing.  Lea Pare, who leads a team of scientists modifying mosquitos, is working with linguists to answer questions the locals may have and tp help develop vocabulary to describe this complex scientific process.

What do you think about gene editing to possibly save millions?

Read the original article here.

View a video explaining how scientists can use genetic engineering to fight disease here.

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