BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: RNA (Page 1 of 2)

CRISPR Mini | New Territory Unlocked

For over a million years, DNA has centered itself as the building block of life. On one hand, DNA (and the genes DNA makes up) shapes organisms with regard to physical appearance or ways one perceives the world through such senses as vision. However, DNA may also prove problematic, causing sickness/disease either through inherited traits or mutations. For many years, scientists have focused on remedies that indirectly target these harmful mutations. For example, a mutation that causes cancer may be treated through chemotherapy or radiation, where both good and bad cells are killed to stop unchecked cell replication. However, a new area of research, CRISPR, approaches such problems with a new perspective.

The treatment CRISPR arose to answer the question: what if scientists could edit DNA? This technology involves two key components – a guide RNA and a CAS9 protein. Scientists design a guide RNA that locates a specific target area on a strand of DNA. This guide RNA is attached to a CAS9 protein, a molecular scissor that removes the desired DNA nucleotides upon locating them. Thus, this method unlocks the door to edit and replace sequences in DNA and, subsequently, the ways such coding physically manifests itself. Moreover, researchers at Stanford University believe they have further broadened CRISPR’s horizon with their discovery of a way to engineer a smaller and more accessible CRISPR technology.

This study aimed to fix one of CRISPR’s major flaws – it is too large to function in smaller cells, tissues, and organisms. Specifically, the focus of the study was finding a smaller Cas protein that was still effective in mammalian cells. The CRISPR system generally uses a Cas9 protein, which is made of 1000-1500 amino acids. However, researchers experimented with a Cas12f protein which contained only 400-700 amino acids. Here, the new CasMINI only had 529 amino acids. Still, the researchers needed to figure out if this simple protein, which had only existed in Archaea, could be effective in mammals that had more complicated DNA.

To determine whether Cas12f could function in mammals, researchers located mutations in the protein that seemed promising for CRISPR. The goal was for a variant to activate a protein in a cell, turning it green, as this signaled a working variant. After heavy bioengineering, almost all the cells turned green under a microscope. Thus, put together with a guide RNA, CasMINI has been found to work in lab experiments with editing human cells. Indeed, the system was effective throughout the vast majority of tests. While there are still pushes to shrink the mini CRISPR further through a focus on creating a smaller guide RNA, this new technology has already opened the door to a variety of opportunities. I am hopeful that this new system will better the general well-being as a widespread cure to sickness and disease. Though CRISPR, and especially its mini version, are new tools in need of much experimentation, their early findings hint at a future where humans can pave a new path forward in science.

What do you think? Does this small CRISPR technology unlock a new realm of possibility or does it merely shed light on scientists’ lack of control over the world around us?

CRISPR Causes Cancer, Sort Of

          Scientific researchers are always looking for ways to improve modern science and help create new treatments. Currently, CRISPR, “a powerful tool for editing genomes,” holds the ability to help advance medicine, specifically gene editing, so long as the kinks in this specific method are worked out. One of these problems is the DNA damage caused by CRISPR “activates the protein p53,” which tries to protect the damaged DNA. This raises not one, but two concerns as present p53 can diminish the effectiveness of this technique, however when there is no p53 at all cells grow rapidly and become cancerous. As we learned in AP Biology class, typical cells communicate through chemical signals sent by cyclins that ensure the cell is dividing the right amount. Cancer cells, however, contain genetic mutations that prevent them from being able to receive these signals and stop growing when they should. “Researchers at Karolinska Institute” have discovered that “cells with inactivating mutations of the p53 gene” have a higher survival rate when contingent on CRISPR. To further their research, they discovered genes with mutations similar to those of the p53, and also “transient inhibition” of the gene could help prevent “the enrichment of cells” that are similar. Although seeming antithetical, these researchers proved that inhibiting p53 actually makes CRISPR work better and prevent enrichment of mutated p53 and other similar genes. 

CRISPR logoDNA animation

           These results give crucial information, helping advance CRISPR and make it more usable in current medicine. Additionally, the researchers have uncovered the possibility that the damage CRISPR causes to DNA might be key in creating a better RNA sequence (the RNA sequence tells us the “total cellular content of RNAs”) guide, showing where DNA should be changed. In future tests, these researchers want to try and get a better idea of when the enhancement of mutated p53 cells from CRISPR becomes a problem.    

Redesigned Cas9 protein provides safer gene editing than ever before!

Gene editing is a group of technologies that give scientists the ability to change an organism’s DNA. These technologies allow genetic material to be added, removed, or altered at particular locations in the genome. Several approaches to genome editing have been developed. A recent one is known as CRISPR-Cas9, which is short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. The CRISPR-Cas9 system has generated a lot of excitement in the scientific community because it is faster, cheaper, more accurate, and more efficient than other existing genome editing methods.

One of the challenges that come using CRISPR-based gene editing within humans is that the molecular machinery may sometimes make edits to the wrong section of a host’s genome. This is problematic because it creates the possibility that an attempt to repair a genetic mutation in one location in the genome could accidentally create a dangerous new mutation in another spot. Scientists at The University of Texas at Austin have redesigned a key component of a widely used CRISPR-based gene-editing tool, called Cas9, to be thousands of times less likely to target the wrong stretch of DNA while remaining just as efficient as the original version, making it potentially much safer.

The CRISPR-Cas9 system works similarly in the lab. Researchers create a small piece of RNA with a short ‘guide’ sequence that binds to a specific target sequence of DNA in a genome. The RNA also binds to the Cas9 enzyme. As in bacteria, the modified RNA is used to recognize the DNA sequence, and the Cas9 enzyme cuts the DNA at the targeted location. Although Cas9 is the enzyme that is used most often, other enzymes can also be used. 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.

Other labs have redesigned Cas9 to reduce off-target interactions, but so far, all these versions improve accuracy by sacrificing speed. SuperFi-Cas9, as this new version has been named, is 4,000 times less likely to cut off-target sites but just as fast as naturally occurring Cas9. Scientists say you can think of the different lab-generated versions of Cas9 as different models of self-driving cars. Most models are really safe, but they have a top speed of 10 miles per hour.

In my opinion, setting aside any and all ethical concerns, genome editing is of great interest in the prevention and treatment of human diseases. Currently, most research on genome editing is done to understand diseases using cells and animal models. Scientists are still working to determine whether this approach is safe and effective for use in people. It is being explored in research on a wide variety of diseases, including single-gene disorders such as cystic fibrosis, hemophilia, and sickle cell disease. It also holds promise for the treatment and prevention of more complex diseases, such as cancer, heart disease, mental illness, and human immunodeficiency virus (HIV) infection.

Is CRISPR the COVID-19 Cure?

New Developments In CRISPR Gene Editing Technology Show Promising Advances In Possible COVID-19 Antiviral Pill

CRISPR Gene Editing. If you have never heard of it, don’t worry, I hadn’t either. When google searching CRISPR Gene editing, I went straight to Wikipedia for the simple answer that it is a procedure done in molecular biology, in which the genomes of a living organism can be modified with extremely high precision. One of its many applications is the treating and prevention of disease, enabling researchers to edit DNA and use the natural defense system of bacteria to target and destroy the genetic material of viruses. In a new study from this summer, Dr. Sharon Lewin and her team of researchers at the Peter Doherty Institute for Infection and Immunity at the University of Melbourne believe they may have harnessed CRISPR’s gene editing abilities to block the replication of COVID-19. 

Very similar to the replication of DNA, RNA replication begins with a single strand of “Template” RNA. In DNA, because it can only be replicated in one direction (5’-3′), and the strands run antiparallel, each strand is built in opposite directions creating one leading strand and one lagging strand. However, RNA only needs one strand made because it is single-stranded instead of a double. In SARS-CoV-2, an enzyme called RNA-Dependent RNA Polymerase adds nucleotides in the 5’-3′ direction, replicating the template RNA. Because humans have DNA, we don’t copy RNA; instead, we transcribe it to make proteins. Therefore this RNA replication process does not occur in humans and only in viruses.

Lewins’ team designed the gene editing to target single strands of RNA, like those found in COVID-19. CRISPR is most commonly associated with Cas9, an RNA-guided enzyme that cleaves foreign nucleic acids. However, Lewin and her team used a different enzyme, Cas13b, which could cleave RNA instead. Targeting specific sites on the RNA strands of SARS-CoV-2, Cas13b binds to the RNA and destroys the part of the virus needed to replicate, “Once the virus is recognized, the CRISPR enzyme is activated and chops up the virus,” said Lewin. She continues to explain that although the COVID-19 vaccines are highly effective, there is still a clear and urgent need for treatment once the disease is contracted. The ideal treatment would be an antiviral drug that could be taken shortly after the patients tested positive for COVID-19, “That’s what we hope to achieve one day with this gene scissors approach.” 

CRISPR Cas9 technology

Having written in previous blog posts about my mother’s struggles with COVID-19, my dad also had a very different yet real struggle. Like most people, my dad, having somehow not contracted COVID from my mom at the beginning of quarantine, was very fearful of getting sick himself. Fortunately, my dad has still never had COVID (knock on wood). This is great because he has remained healthy; however, it also had downsides. For my brother and me, being both kids and relatively healthy, when we contracted COVID in mid-August, it was nothing more than a rough cold. A cold that, after ten days, not only was gone but enabled me to feel some sense of temporary immunity to the virus and allowed me to feel comfortable going out with friends and returning to some level of normalcy. My dad never got this. Because he never contracted COVID, he lived a completely secluded life until this past February (when he gave up and began going out in public). If my family and I went to a mall, he would wait in the car. If we ate out, he would wear a mask the whole time and not eat until we got home. The fear for my dad was not specifically getting covid but not having some antiviral drug to take once he contracted the virus. A solution like Dr. Lewins would have been and still would be a life-changer for many families who still live in fear of getting sick from COVID-19.  

Although this breakthrough in RNA CRISPR technology is remarkable, the study was performed in lab dishes and is still waiting for testing on animals or humans. Additionally, CRISPR technology medicines have not been approved to treat any diseases. Unfortunately, we are probably a couple of years away from a widely available treatment. 

How Gene-edited Strawberries are Safe and Beneficial to the Consumer

Over one-third of purchased strawberries end up getting thrown in the trash due to bruising, mold, or mushy texture. However, The J.R. Simplot Company and Plant Sciences Inc. hope to change this outcome. The pair of companies plan to modify the DNA of strawberries with the help of CRISPR-Cas9 and sell them on a commercial scale— and don’t worry! Recently published research suggests that it is safer than other alternatives.

These gene modifications aim to extend strawberry shelf life, prolong its growing season, and reduce consumer waste. This essentially means that farmers can efficiently grow more quality fruit for longer portions of the year.

CRISPR-Cas9 is a tool derived from the immune defense system in Streptococcus Pyogenes bacteria and is currently repurposed to edit sections of DNA sequences. CRISPR-Cas9 or the CRISPR/Cas9 system is primarily made up of the Cas9 protein, crRNA, and tracrRNA (or, more simply, guide RNA). 

As we have learned in AP Biology, RNA is a single-stranded molecule crucial to the processes of coding, decoding, regulation, and expression of genes. Our initial understanding of RNA holds to be true as the human-engineered guide RNA from the CRISPR/Cas9 system dictates exactly where the protein to cuts in the sequence. After the targeted section is cut, the Cas9 protein removes the particular section of DNA. Then, Host DNA can be placed in the removed portion of the DNA sequence and elicit a desired trait in the gene. For a deeper explanation of how CRISPR-Cas9 functions, I recommend watching Paul Andersen’s YouTube video on the subject.

This is exactly how The J.R. Simplot Company and Plant Sciences Inc. plan to genetically modify the genes within the strawberry.

This technology is far more efficient than the cumbersome process of selective crop breeding. To boot, Plants modified by the CRISPR/Cas9 system were found to be nearly identical to plants bred using traditional methods. The CRISPR/Cas9 system has also been found to have been thousands of times less likely to target the wrong stretch of DNA, making it potentially much safer than alternative methods of gene editing.

In the near future, The Simplot and Plant Sciences Inc. team plan to sell the strawberries after they identify the key genomes that determine shelf life and edit the plants for ideal crops. 

Strawberries picked

Do you think this is exciting news? Would you try a gene-edited strawberry? Why or why not?

Optimus Prime, Megatron, Proteins? The New Transformer Vaccine Candidate!

Amid the global outbreak of COVID-19, with no end in sight after nearly two years, the future wellbeing of humans is in danger. Coughs, fevers, and shortness of breath have lent way to millions of deaths across the globe. As thousands of researchers relentlessly work to find solutions to this virus, multiple vaccine candidates have emerged. Specifically, in the United States, millions of Americans have received doses of the Pfizer-BioNTech, Moderna, and Johnson & Johnson’s Janssen vaccines. However, scientists at Scripps Research recently recognized a new, self-assembling COVID-19 vaccine as a potentially more efficient and effective way to fight this worldwide battle.

 

Primarily, it is critical to understand how vaccines function as they help protect the immune system. The COVID-19 vaccines currently in effect are mRNA-based; in other words, the messenger RNA signals one’s body to produce a harmless viral protein that resembles the structure of a spike protein. The body, with the help of T-Helper cells, recognizes this structure as a foreign invader as B cells bind to and identify the antigen. The T-Helper cells will then signal these B cells to form B-Plasma cells and B-Memory cells. When getting the vaccine, the B-Memory cells are especially important as they prevent reinfection. This is a process known as adaptive immunity. Here, in the event of future infection with the spike-protein COVID-19, the memory cells would help carry out the same response more quickly and efficiently. Essentially, this process acts as the body’s training in case of any future infections.

 

While the Scripps Research COVID-19 vaccine would evoke a similar immune response to that described above, it differs from other candidates in how it assembles in the human body; this new vaccine would be comprised of proteins that are able to self-assemble. On their own, these nanoparticle proteins would transform into a sphere protein structure surrounded by smaller proteins, mimicking the coronavirus’s shape. Here, the self-assembled spike proteins are more sturdy and stable than in an mRNA-produced structure. Thus, it more accurately prepares the body for future infection with COVID-19. In fact, multiple tests found that mice who were given the experimental vaccine were able to fight off not only SARS-CoV-2 but also SARS-CoV1 along with the alpha, beta and gamma variants.

 

Nonetheless, influencing the public to get a newer vaccine instead of the well-trusted vaccines already in production requires proof of the candidate’s benefits. Primarily, as mentioned, early results find that this new candidate would perform well with many different strains of COVID-19. Additionally, researchers assert that this vaccine would be relatively simple to produce on a mass scale. Lastly, scientists found that this vaccine may well be more protective and long-lasting than current vaccine candidates. Although the process of vaccine approval is lengthy and often difficult, I am hopeful for the future of the Scripps Research vaccine if it is put into production. Moreover, I believe that such experimentation with self-assembling nanoparticle proteins transcends the current pandemic. The benefits of this field present a wide array of opportunities, and I look forward to seeing what its future may hold.

 

What do you think? Are these transformer-like self-assembling particles a gateway to the future of medicine or an unnecessary distraction from effective treatments already in circulation?

The COVID-19 Vaccine: How, What, and Why

We have all seen the news lately – COVID, COVID, and more COVID! Should people get the vaccine? What about the booster shot? Are vaccines more harmful than COVID-19? Will my child have birth-defects? This blog post will (hopefully) answer most of your questions and clear up a very confusing topic of discussion!

Discovery of monoclonal antibodies that inhibit new coronavirus(Wuhan virus)

First off, what are some potential effects of COVID-19? They include, but are certainly not limited to, shortness of breath, joint pain, chest pain, loss of taste, fever, organ damage, blood clots, blood vessel problems, memory loss, hearing loss tinnitus, anosmia, attention disorder, and the list goes on. So, our next question naturally is: what are the common effects of the COVID-19 Vaccine? On the arm that an individual receives the vaccine the symptoms include pain, redness, and swelling. Throughout the body, tiredness, a headache, muscle pain, chills, fever, and nausea can be experienced. To me, these effects seem much less severe than COVID-19’s!

COVID-19 immunizations begin

Now that we have covered effects, you are probably wondering what exactly the COVID-19 Vaccine does – will it make it impossible for me to get COVID-19? Will I have superpowers? Well, you may not get superpowers, but your cells will certainly have a new weapon, which we will discuss in the next paragraph! The COVID-19 Vaccine reduces “the risk of COVID-19, including severe illness by 90 percent or more among people who are fully vaccinated,” reduces the overall spread of disease, and can “also provide protection against COVID-19 infections without symptoms” (asymptomatic cases) (Covid-19 Vaccines Work).

So, how does the vaccine work? Many people think that all vaccines send a small part of the disease into us so our cells learn how to fight it at a smaller scale. However, this is not the case with the COVID-19 vaccine! As we learned in biology class, COVID-19 Vaccines are mRNA vaccines which use mRNA (genetic material that tells our cells to produce proteins) wrapped in a layer of fat to attach to cells. This bubble of fat wrapped mRNA enters a dendritic cell through phagocytosis. Once inside of the cell, the fat falls off the mRNA and the strand is read by ribosomes (a protein maker) in the cytoplasm. A dendritic cell is a special part of the immune system because it is able to display epitopes on MHC proteins on its surface.

Corona-Virus

After being made by the ribosomes, pieces of the viral surface protein are displayed on the surface of the dendritic cell (specifically the MHC protein), and the cell travels to lymph nodes to show this surface protein. At the lymph nodes, it shows the epitope to other cells of the immune system including T-Helper Cells. The T-Helper Cells see what they’re dealing with and create an individualized response which they relay to T-Killer cells that attack and kill virus-infected cells. This individualized response is also stored in T-Memory cells so that if you do end up getting COVID-19, your body will already know how to fight it! The T-Helper Cells additionally gather B-Plasma cells to make antibodies that will keep COVID-19 from ever entering your cells. T-Helper Cells are amazing! As you can see, the vaccine never enters your nucleus, so it cannot effect your DNA! No birth-defects are possible!

You are now equipped with so much information and able to disregard many common misconceptions about the COVID-19 vaccine! Additionally, you can make an educated decision about whether or not you should get the vaccine. I think yes! If you have any questions, please feel free to comment them and I will answer. Thanks for reading!

 

The Potential End To COVID-19: How An Antiviral Pill Could Decrease Death Rates

When will the world return back to normal? In recent years, people have questioned the longevity of the COVID-19 outbreak. While concentrating on vaccine delivery and vaccination capabilities, a pill has been developed in the hopes of preventing future COVID variations. Hopefully, the pill will eventually be administered to patients; this would make it the first oral treatment for the virus.

A current study on molnupiravir, an antiviral pill, has published data demonstrating that the medicine has the ability to lower hospitalization and fatality rates as a result of COVID-19. The study dealt with two groups of people. One group of 377 people were given a placebo, and the other group of 385 people were given molnupiravir to examine how the antiviral affected patients with COVID-19. The findings were substantial. Within 29 days of starting the trial, 14.1 percent of the group given the placebo were hospitalized. Fortunately, of the individuals who were given molnupiravir, only 7.3 percent of them were hospitalized.

Molnupiravir is a prodrug of N4-hydroxycytidine (NHC), a nucleoside analog (meaning that it contains a sugar and a nitrogenous base). Molnupiravir metabolism

Molnupiravir is similar to the genetic coding of the coronavirus’s RNA, as is remdesivir (a FDA-approved medication). By interfering with the polymerase enzyme, the “fake” basic elements impair the coronavirus’s RNA synthesis, preventing the virus from replicating. Despite the fact that the two medications serve the same goal, they serve different actions. Remdesivir penetrates a growing RNA strand, slowing and ultimately blocking the polymerase enzyme. Unlike the COVID-19 vaccine, the structure of molnupiravir gives it the ability to target the polymerase enzyme instead of the virus’s spike protein. Molnupiravir enters the cell and is transformed into RNA-like building components. The active medication binds to the genome of RNA viruses, setting off a chain of mutations; this process is known as viral error catastrophe. In simpler terms, it disrupts how the virus replicates RNA.

Molnupiravir could theoretically be administered as soon as a patient receives a positive COVID-19 test, thereby preventing floods of COVID-19 patients from overburdening medical systems while the highly infectious delta variant continues to spread. Although the side effects of the drug remain unknown, it has been reported that the side effects of COVID-19 are much worse than those of molnupiravir. The antiviral drug has the potential to save lives, but the primary concern is about the long-term repercussions. When contemplating molnupiravir, the fear of birth abnormalities or cancer comes into play because it is a mutagenic medication. In response, the drug’s creator, Merck, stated that there is no indication of the possibility for mutagenicity. Although the manufacturer is confident in the treatment and believes that the long-term consequences are insignificant, it is logical that parents might have concerns about molnupiravir.

Ultimately, if patients receive the vaccination that targets the spike protein and are also able to take molnupiravir, hospitalization and mortality rates may dramatically reduce.

Mutation in the Nation

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.

 

LION: The King Of The COVID Vaccines

As the SARS-CoV-2 virus (also known as COVID-19) continues to rage across the world killing millions, more time, effort, and money is being put into researching the best vaccines to help bring the world back to a state of normalcy.  One such vaccine is being developed at the University of Washington using replicating RNA is called LION (Lipid InOrganic Nanoparticle). In its animal trials in July, the vaccine already found some success inducing “coronavirus-neutralizing antibodies” in mice young and old which has given researchers a lot of hope for the future of the vaccine.

 

One might wonder, why do we need a vaccine at all? Vaccines are used to expose your body to small doses of a virus or in this case by mRNA, which teaches your body to produce the antibodies needed to fight the virus and makes memory cells. The next time you are exposed to the virus, your body will be able to produce the necessary antibodies to a much larger degree, much quicker, for longer so you will be protected from becoming sick.

One of the lead researchers on LION, Professor Deborah Fuller of the University of Washington School of Medicine qualified the goals of a successful COVID-19 vaccine saying it, “will ideally induce protective immunity after only a single immunization, avoid immune responses that could exacerbate virus-induced pathology, be amenable to rapid and cost-effective scale-up and manufacturing, and be capable of inducing immunity in all populations including the elderly who typically respond poorly to vaccines.” This is quite a lot to accomplish but LION lends itself very well to these goals, conquering most of the problems a typical DNA vaccine would have. DNA vaccines work by coding for the antigens which are then exposed to the immune system to create memory cells so the body can treat the virus later. The downsides of a DNA vaccine is sometimes those antigens fail to create an immune response or can even cause the cell to become cancerous when the DNA joins the host cells DNA, disrupting it. There is far less risk with RNA vaccines which occupy the cytoplasm and only interact with ribosomes.

Shown above us a basic drawing of what SARS-CoV-2 virus looks like.

LION is a replicating RNA vaccine, but how does replicating RNA work? RNA codes for spike proteins and ribosomes in the body make the necessary proteins. Replicating RNA allows for more spike proteins and ribosomes to be coded at a greater rate, which produces a greater number of proteins continuously while triggering “a virus-sensing stress response that encourages other immune activation.” For the vaccine the RNA replicates proteins that tell the body to reject the SARS-CoV-2 and attack them “with antibodies and T cells”  which stop the protein spikes on the virus from interfering with the cell. The development of B cells, which remember how to make the antibodies to fight the virus when infected again, as well as T cells is especially critical for the vaccine as they can develop immunity to the SARS-CoV-2 antigens. What makes the LION vaccine special is the nanoparticle it is named after which “enhances the vaccine’s ability to provoke the desired immune reaction, and also its stability.” This makes it more valuable than other vaccines of the same kind as it can achieve effective results with a longer shelf life. It can also be mixed simply using a two vial method as the mRNA component is made separately from the main vaccine formulation. For all these reasons, the scientists are optimistic as the vaccine goes into the next stages of testing that this vaccine could help provide a long term solution to the COVID-19 pandemic.

As COVID-19 vaccines start becoming available to essential workers in the coming weeks and my father prepares to take one, it can be quite unnerving to think about all the potential negative side effects of the vaccine. These vaccines have been developed without the typical ten years of testing, so knowing more about the research behind the vaccines serves as a comfort me and many others. Our future is in these vaccines and research so knowing which we should invest our time and money in is always a good idea.

How Reliable Are Covid-19 Tests and What Are The Different Types of Tests?

For my study of research, I’ve decided to learn more about Covid-19 testing and its effectiveness. In this article, How Accurate Are COVID-19 Tests? Many Factors Can Affect Sensitivity, Specificity of Test Results, it discusses several methods of testing, along with how accurate the results are. The article also goes into detail about what factors can affect the tests accuracy. 

Sensitive tests, which are positive results, are less likely to produce a false-positive outcome, and a specific test, negative results, are less likely to produce a false-negative outcome. Labs can provide the analytics of sensitivity and specificity for a test, which is concluded from confirmed specimens of positive and negative results. These results, however, come from when someone either had a great exposure, or none, so they are true under ideal conditions. Since there is so much variability between patients, the numbers are often lower when they are under real life conditions. 

There are two main types of testing for the novel Coronavirus. The first type of test detects RNA from the virus by using methods such as, polymerase chain reaction (PCR). I have never heard of this process before, so I decided to find a source explaining what it is. PCR is used to amplify, which is making many copies of a gene or DNA. Using this process, many copies can be created, just from a small part of the DNA taken for the sample. This process can help to identify a pathogen when trying to detect a virus, such as the novel Coronavirus. This past week in class, we learned about the immune system and about the characteristics of viruses. We learned that a virus has spike proteins on the outside, and it has RNA strands in the inside of the cell. This connects to what we learned about RNA and viruses, because this test actually tests for RNA to see if a patient has the virus. they are more accurate because they are from the genetic sequence from the virus itself, which is unique to it. If a test comes back positive, it is most likely accurate. The second type of test is molecular testing. The nasopharynx is said to have the largest concentration of a virus. Since using NP swab samples, nasopharyngeal swabs, are hard to get, the sensitivity of a test can be altered or tampered. This can create a false-negative result in a patient, who really could have it. Testing with saliva and blood has more of a likeliness to reduce the sensitivity. The article also mentions that swabbing the patient in the oropharynx or nose can also have a lower sensitivity. 

Antibody testing is through drawing blood from a vein, and it can detect whether or not someone was infected by Covid-19. The test uses enzyme immunoassays and rapid lateral flow immunoassays. By day 14 following symptoms appearing, most patients did have the IgG antibodies. I wasn’t exactly sure what an IgG antibody was, so I found a source to explain that in some more detail. It is an immunoglobulin and is found in all fluids within the body. They are the most common and small antibodies that are in the body. These antibodies help to fight bacterial infections and viruses. These antibodies are actually the only ones that can help protect a woman’s fetus, which is very interesting. As time goes on, it is less likely that the antibodies will be detected. There is some evidence, not confirmed yet, that suggests that children and asymptomatic or mild-symptom patients could be less likely to have detected antibodies. 

I found this article to be very fascinating because it went into detail about each test and its effectiveness. I didn’t know that children and asymptomatic or mild-symptom patients were less likely to have detectable antibodies. I am excited to research more as I continue to further my studies in Covid-19 testing. 

 

Inhale RNA, Exhale Your Worries

The focus of a recent study is inhalation genetic therapy to give patients with Cystic Fibrosis relief when they breathe. A defective gene in people with Cystic Fibrosis causes a mucus build-up in specific organs. The respiratory complications due to mucus build-up in the lungs are which infections, clogged airways, inflammation, and respiratory failure.

Recently, scientists developed a study that involves mice inhaling messenger RNA. The messenger ribonucleic acid is genetically manipulated so that it contains an oxidative enzyme called “luciferase”, which is known for causing bioluminescence. Scientists manipulated the mRNA by “packaging” or combining the enzyme with a polymer that would be inhaled into the lungs of the mice. The inhaled polymer would then travel through the respiratory system and be taken in by the lungs, where it would eventually be broken down by cells within the lungs. Scientists were able to distinguish if the experiment was successful as the light from the luciferase combined with the mRNA could be detected from within a lung cell.

Another experiment was conducted with similar circumstances in that it tested genetically modified mice cells that glowed red from the cell’s reception of mRNA. This offered the scientists the opportunity to test a range of mRNA-polymer dosages to quantify or count the resulting “red” mice cells.

As we continue this road down modern medicine, mRNA can be evolutionary for patients with Cystic Fibrosis because the messenger RNA can recreate functional copies of itself to produce CFTR protein (cystic fibrosis transmembrane conductance regulator protein), which is the protein that codes and determines the functionality of the CFTR gene. Could mRNA polymers possibly be a treatment for milder respiratory issues like asthma? This experiment might just be a breakthrough in the world of medicine, as strands of ribonucleic acid could be the answer to ending compromising respiratory complications.

i-motif: A new form of DNA discovered

Australian researchers have discovered a new structure of DNA called i-motif. This form of DNA is in the shape of a twisted knot, vastly different from the conventional double helix model. i-motif basically looks like a four-stranded knot of DNA. In the i-motif form, the C bases on the same strand of DNA bind to each other instead of their complementary pairs.

File:G-quadruplex.gif

(Photo: Wikimedia Commons)

How did scientists discover i-motif?

i-motif previously haven’t been seen before, apart from in in-vitro (which means under laboratory conditions and not in the natural world) To detect i-motif, scientists used a tool made up of a fragment of an antibody molecule. This antibody could recognize and attach to i-motifs. Researchers showed that the i-motif structures mostly formed at the G1 phase -when mRNA is synthesized- in a cells life cycle. The i-motifs show up in promoter regions and in telomeres in the chromosome.

While scientists aren’t really sure the actual reason for their existence, some researchers suggest that they are there to help switch genes on and off and affect whether or not a gene is actively read.

Whatever the reason for their existence, they have potential to play an important role in how and when DNA is read. Prof Marcel Dinger at the Garvan Institute for Medical Research says, “It’s exciting to uncover a whole new form of DNA in cells — and these findings will set the stage for a whole new push to understand what this new DNA shape is really for, and whether it will impact on health and disease.”

Closer to Reality: Gene Editing Technology

In August of 2017, scientists in the United States were successful in genetically modifying human embryos, becoming the first to use CRISPR-cas9 to fix a disease causing DNA replication error in early stage human embryos. This latest test was the largest scale to take place and proved that scientists were able to correct a mutation that caused a genetic heart condition called hypertrophic cardiomyopathy.

CRISPR-cas9 is a genome editing tool that is faster and more economical than othe r DNA editing techniques. CRISPR-cas9 consists of two molecules, an enzyme called cas9 cuts strands of DNA so pieces of DNA can be inserted in specific areas. RNA called gRNA or guide RNA guide the cas9 enzyme to the locations where impacted regions will be edited.

(Source: Wikipedia Commons)

 

Further tests following the first large-scale embryo trial will attempt to solidify CRISPR’s track record and bring it closer to clinical trials. During the clinical trials, scientists would use humans- implanting the modified embryos in volunteers and tracking births and progress of the children.

Gene editing has not emerged without controversy. While many argue that this technology can be used to engineer the human race to create genetically enhanced future generations, it cannot be overlooked that CRISPR technology is fundamentally for helping to repair genetic defects before birth. While genetic discrimination and homogeneity are possible risks, the rewards from the eradication of many genetic disorders are too important to dismiss gene editing technology from existing.

 

What does the future hold for CRISPR-Cas9?

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?

CRISPRainbow

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)and CRISPR-associated protein 9 complex has become one of the biggest technological advances in science. This genome editing technology has taken multiple advances toward closer research into studies of embryonic development to cancer. CRISPRainbow, a modification to CRISPR where the Cas9 is mutated, allows researchers to label up to seven different genomic locations in live cells.
CRISPR has been used for editing genomes, however, research specialist Hanhui Ma and his team has used it to label DNA and track the movement of DNA in live cells. With this new research, we can find the precise genomic location in order to understand the movement of chromosomes. This is important because the genes that create our biological make-up and control our health do so by their location in the 3-D space.
Currently, with CRISPR, we can only label three genomic locations at a time in each cell. It has extremely challenged scientists to label more sites because it would require cells to be mixed in formaldehyde, which would kill them, making it impossible to observe the chromosome’s structure when stimulated by a response.
The new Cas9 mutation causes the nuclease to deactivate, so it only binds to DNA and doesn’t cut the genome. Then, the CRISPRainbow is docked into location by the guide RNA which can be programmed technologically. Research specialist, Hanhui Ma was able to figure out a way to implement computational coloring. Each guide RNA would include one of the three primary fluorescent proteins: red, green or blue which then can be observed in real time under a microscope. Pretty cool, right? Well, guess what? It doesn’t stop here. Ma decided to go even further in his research and attach a second fluorescent protein to the guide RNA. Ma could then combine the three primary colors to generate three additional labels: cyan, magenta, and yellow. From the primary colors, he was able to achieve white as the seventh color.
CRISPRainbow can track the challenging and dynamic movement of genomes that may lead to biological consequences. Research Scientist, Hanhui Ma, states “With this technology, we can visualize different chromosome loci at different points in time.” We can observe the structural changes in chromosomes overtime with help us understand their relation to health and disease. So why do you think they called is CRISPRainbow? What kind of diseases can we track with this new technology? What more can CRISPRainbow do in the near future?

Questioning one of the most widely-held beliefs about the origins of life!

Two scientists, Dr. Charles Carter, of University of North Carolina at Chapel Hill, and Peter Wills, a physics professor at the University of Auckland, are challenging one of the most widely-held beliefs in the world of science.

A widely accepted hypothesis of the origin of life is called the “RNA-world” hypothesis, which states that life began from nucleic acids and only evolved later into proteins. However, in two recent studies, scientists Carter and Wills have found that this hypothesis is false, and have named their findings the “peptide-RNA” hypothesis. They believe their findings are much more probable and realistic. They argue that RNA could not be the source of biological life on earth because it lacks an important characteristic, called “reflexivity”. This means RNA lacks the ability to form the feedback loop that is necessary to lead to eventual life forms.

Source: https://pixabay.com/en/dna-string-biology-3d-1811955/

At the core of their “peptide-RNA” hypothesis is that the remnants of ancient enzymes are still found in all living organisms today. These ancient enzymes are called aminoacyl-tRNA-synthetases (aaRSs). These 20 aaRSs enzymes are broken into 2 structurally distinct families which each are exact opposites of each other. Being that these enzymes are so simple in structure, Cater and Wills believe they are the basis of biological life.

So, which theory do you believe, the “RNA-world” hypothesis or the “peptide-RNA” hypothesis?

Original Article: https://www.sciencedaily.com/releases/2017/11/171101160756.htm

A Second Theory: Is the RNA World Hypothesis Wrong?

Introduction

Prior to recent research, scientists strongly supported the “RNA world” hypothesis, a theory that claims that DNA derived from RNA, and that RNA therefore provided the basis for life as we know it. The evidence of this new study under scientists at The Scripps Research Institute leads to an alternate theory that challenges this previous mode of thinking. This study is intriguing not only because it challenges what has mostly been accepted as factual truth by most scientists, but also because it attempts to solve the question of where and how first life developed.

Background: The “RNA world” hypothesis

The “RNA world” hypothesis dates back to over 30 years ago. Proposed independently by Carl Woese, Francis Crick, and Leslie Orgel, it essentially is a theory that states that RNA existed before modern cells, and stored genetic information and catalyzed chemical reactions within earlier cells. This theory further claims that DNA came later and only then contained the genetic material. It also infers that proteins served as a catalyst much later, only fulfilling this role once RNA evolved. The evidence that supports this theory lies with the chemical differences that distinguish RNA from DNA. RNA can be formed from formaldehyde (HCHO) which is chemically simple, especially in comparison to the much more complicated sugar deoxyribose. In a reaction catalyzed by a specific enzyme, deoxyribose is produced from ribose which also indicates the possibility that DNA comes directly after the structurally more simple and single helix RNA.

Recent Studies

Researchers believe that if this theory is correct, RNA nucleotides and DNA backbones would have mixed to create “heterogeneous” (or a product resulting from differing “parents” with unique charateristics) strands. The resulting “chimeras” (an organism composed of cells from different zygotes leading to subtle variations in form) would be an intermediate step in the transition to RNA if stable, however the study shows a decrease in stability (specifically in thermal stability or the ability to function at high temperatures) when the backbone is shared between the two nucleic acids. The researchers attribute this instability to a slight difference between the sugar in RNA and the sugar in DNA. As a result, if the RNA theory had been true, the chimeras would have died off. This proves that evolution has lead to a system where enzymes have developed to maintain the system of “homogenous” molecules, keeping RNA and DNA separate since they function much better separate from one another. Since these enzymes are fairly “new” in terms of the span of the existence of DNA and RNA, it is highly unlikely that RNA was able to transition to newly developed DNA. Without any mechanisms to keep DNA and RNA separate, it is logical to conclude that RNA does not predicate DNA. This concept is reminiscent of the endosymbiont theory that discusses the possible reason for the unique qualities of mitochondria and chloroplasts in that both theories rely on existing knowledge about these unique structures and how each component might contribute to a different function. Similar to the endosymbiont theory, there is no exact answer as to whether this theory is correct, however through challenging the theory and conducting experiments, we can further develop our understanding of certain biological phenomena.

Conclusion

This alternate theory, on the other hand, proposes a different view that RNA and DNA have coexisted and that one therefore did not develop from the other. While this theory is not completely new, these recent findings regarding instability for a backbone shared between the two nucleic acids provide more evidence for this secondary theory (to the RNA world theory). If this theory is accurate, DNA could have developed its homogenous system much earlier than scientists have predicted up until this point. According to this second theory, after RNA first interacted with DNA it still could have evolved to create DNA. Although scientists will never be able to discover life’s exact origin, these findings can provide insights for biology overall.

images

https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-7-23

http://www.sciencemag.org/news/2016/05/rna-world-inches-closer-explaining-origins-life

https://www.sciencedaily.com/releases/2016/09/160928153357.htm

http://www.medicinenet.com/script/main/art.asp?articlekey=8905

XRN1: The Virus Hitman

When I think of the words killer and assassin, my mind drifts to shady men in all black equipped with sniper rifles. However, recent research conducted by the University of Idaho and the University of Colorado Boulder has indicated that I should expand that mental list to include XRN1, a gene in saccharomyces cerevisiae which, according to a recent study, kills viruses within the yeast. Upon stumbling onto this subject, I was intrigued because it was a fairly simple procedure that led to a huge discovery. To grasp the significance of such a discovery, one must understand it on a molecular level. XRN1’s duty in yeasts is to create a protein which breaks down old RNA. The image below shows the generic process of the creation of a new protein through gene regulation.

Wikipedia- Regulation of Gene Expression

Wikipedia- Regulation of Gene Expression

Yeasts also contain viral RNA since practically all yeasts are infected by viruses. When scientists removed XRN1 from the yeasts, the viruses within yeasts replicated much faster, and when they expressed high amounts of XRN1, the virus was completely eradicated. This is because the XRN1 gene was inadvertently breaking down the viral RNA, mistakenly taking it for the yeast’s RNA. Scientists continued the research by using XRN1 from other saccharomyces yeast species. The virus continued replicating rapidly but the XRN1 did continue its job of breaking down the yeast’s RNA. This shows that the XRN1 from each yeast species evolves to attack the specific viruses that occur in its host while still maintaining their basic role as the RNA eaters. Scientists are hopeful about this study’s human health implications. Viruses such as Polio and Hepatitis C work by degrading XRN1 and not allowing it to break down RNA, respectively. Dengue Fever also occurs when XRN1 is unable to perform its function of RNA breakdown. These studies on Dengue Fever and Hepatitis C elaborate on the implications of XRN1 not breaking down RNA. Scientists hope that this discovery could lead to the triumph of XRN1 over these viruses. Could this really be the discovery that leads to the first ever Hepatitis C vaccine? Do you think that XRN1’s success against virus in yeasts guarantees eventual success against viruses in humans?

 

Original Article: http://phys.org/news/2016-10-yeast-gene-rapidly-evolves-viruses.html

 

CRISPR-Cas9 Can Now Be Applied to Not Only DNA But RNA

Anyone who has seen the movie Gattaca knows that the plot is set in a futuristic society that is able to edit the human genome. Of course, there’s a reason that it’s set in the future. Scientists of today couldn’t possibly dream of being able to edit genes in our DNA…right?

Well, wrong. Say hello to CRISPR-Cas9. CRISPER-Cas9 is, in short, a highly effective and popular DNA-editing technique that scientists started to use to sequence and edit human genes.

However, thanks to scientists at University of California-San Diego, CRISPR-Cas9 is not only limited to editing DNA. By altering only a few key features, this mechanism can now also be used with RNA, another highly important and fundamental molecule in the human body. CRISPR-Cas9 as of now can be used to track RNA in its movement, such as its many essential roles in protein synthesis. Below is a picture that briefly shows the importance of mRNA and tRNA:

 

Screen Shot 2016-04-11 at 12.01.31 AM

(Source: http://www.proteinsynthesis.org/protein-synthesis-steps/)

It’s an exciting development in that certain diseases, such as cancer and autism, are linked to mutations in RNA. By using CRISPR-Cas9 to their advantage, scientists could study the movement of RNA in the cell—and how and when it gets there—to track any defective RNA that can potentially lead to such diseases and then hopefully develop treatments. Gene Yeo, PhD, an associate professor of cellular and molecular medicine at UC-San Diego, expresses hope that “future developments could enable researchers to measure other RNA features or advance therapeutic approaches to correct disease-causing RNA behaviors”.

Intrigued? Confused? Please leave any comments or questions below!

 

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