BioQuakes

AP Biology class blog for discussing current research in Biology

Author: rokhsarscov2

The Redesigning of CRISPR

Cas9, a key component of a widely used CRISPR-based gene-editing tool has been redesigned by scientists at The University of Texas at Austin to be thousands of times less likely to target the wrong stretch of DNA while remaining just as efficient as the original version. This could potentially make gene replication safer and more abundant for medical use.

The CRISPR-Cas9 system consists of an enzyme that introduces a change or mutation into DNA. Cas9 enzymes can cut strands of DNA at a specific location in the genome so parts of the DNA can then be added or removed. CRISPR-based gene-editing tools are adapted from naturally occurring systems in bacteria. In nature, Cas9 proteins search for DNA with a very specific sequence of 20 letters. When most of the letters are correct, Cas9 could still change these DNA fragments. This is called a mismatch, and it can have disastrous consequences in gene editing.

The challenge with using CRISPR-based gene editing on humans is that the molecular machinery occasionally makes changes to the wrong section of a host’s genome. This could possibly repair a genetic mutation in one spot in the genome but may accidentallyDna, Analysis, Research, Genetic Material, Helix create a dangerous new mutation in another.

SuperFi-Cas9 is the name of the new version of Cas9 which has been studied and proven to be 4,000 times less likely to unnecessarily cut off-DNA sites but operates just as fast as naturally occurring Cas9. In the Sauer Structural Biology Lab, scientists were surprised to discover that when Cas9 encounters a type of mismatch, there is a “finger-like structure” that swoops in and holds on to the DNA, making it act like the correct sequence. Usually, a mismatch leaves the DNA unorganized since this “finger-like structure” is mainly used to stabilize the DNA. Based on this insight, scientists redesigned the extra “finger” on Cas9 so that instead of stabilizing the part of the DNA containing the mismatch, the finger is stored away which prevents Cas9 from continuing the process of cutting and editing the DNA. This result in SuperFi-Cas9, a protein that cuts the right target just as readily as naturally occurring Cas9, but is much less likely to cut the wrong target.

This applies to our unit on mitosis when cells are replicating DNA in the S-phase. When chromosomes are duplicated, gene replication occurs. Sometimes gene replication could result in mutations which could lead to a cell not functioning properly. A cancerous cell is an example of cell not performing normally since it rapidly performs mitosis causing the cell to duplicate uncontrollably. This results from an abnormality in gene replication where CRISPR technology can locate this mutation and restore the cell back to normalcy.

Do Mitochondria contribute to neurological and psychiatric disorders?

Mitochondria have had a deep history through the evolution of eukaryotic cells. A primitive bacterium was engulfed by another free floating prokaryotic cell. Many think that this was originally how eukaryotic cells were formed and why mitochondria have their own DNA different from a their cells nucleus. Endosymbiotic theory has been used to understand the intricacies of Mitochondria and leaves many clues as to how their relationship with their cell affects its overall performance  The mutually beneficial relationship between both has lasted for over two billion years by fueling the processes for everyday life.

Mitochondria are membrane-bound cell organelles which generate majority of the chemical energy needed to power a cell’s biochemical reactions. Cell, Mitochondria, Biology, Organelle, ScientificChemical energy produced by the mitochondria is stored in a small molecule called adenosine triphosphate or ATP. This is only one of the many essential jobs mitochondrion hold as an organelles in our cells.

Since mitochondria have their own set of DNA different from their cells, it makes it both a critical element of our cells and a potential source of problems. Mitochondrial DNA can harbor mutations similarly to ones in our nuclei. These can either be detrimental to their function powering our bodies or have little to no effect whatsoever. Age, stress and other factors may disrupt mitochondria’s many functions. On top of that, mitochondrial injury can release molecules that, due to their similarities to those made by bacteria, can be mistaken by our immune system as foreign invaders, triggering a harmful inflammatory response against our own cells.

One of our most important organs, the brain, needs mitochondria the most for its power driven functions. “The more energetically demanding a cell is, the more mitochondria they have, and the more critical that mitochondria health is — so there’s more potential for things to go wrong,” says Andrew Moehlman, postdoctoral researcher who studies neurodegeneration at the US National Institute of Neurological Disorders and Stroke (NINDS). Some estimates assume that each neuron can have up to two million mitochondria meanwhile there are eighty-six billion neurons in our brain.

Researchers have then linked dozens of disorders to alterations in mitochondrial DNA and nuclear DNA related to mitochondrial function. The majority of these are either neurological in nature or have some effect on the brain because of how dominant mitochondria is in the brain. According to Douglas Wallace, a doctoral student at Yale University, despite making up only 2 percent of a human’s body weight, the brain uses roughly a fifth of the body’s energy. These small reductions in mitochondrial function can have large effects on the brain, Wallace explains.

ATP gives us the energy we need for our body to function as we learned through our cellular respiration unit. Without this form of energy, our body simply cannot function which is why mitochondria play a key role in brain function. Mutations which affect the flow of ATP synthase seem most detrimental to cell function and as we know is where ADP and a Phosphorus join together to create ATP. Mitochondria’s own set of DNA makes it difficult to pinpoint a mutation and leaves animals vulnerable to neurological disorders.

Understanding Merck’s Molnupiravir

Since the beginning of the pandemic, research of antiviral medicines and drugs have only become more specific with combating the Coronavirus. Merck’s new drug, Molnupiravir, was a result of pharmaceuticals amplifying research on Covid. The foreshadowing of this drug shows a bright future and an end to Covid-19 once and for all.

Merck applied for authorization first in October and many praised the new drug as a potential game-changer. Pfizer submitted their version of medication called Paxlovid in November. The Food and Drug Administration has provided emergency use authorizations for pills from both Merck and Pfizer while scientists continue to study the real-world effectiveness of both. Molnupiravir is administered as four 200 milligram capsules taken orally every 12 hours for five days, for a total of 40 capsules. It is not authorized for use for longer than five consecutive days where its use seems to be feasible to all users.

Molnupiravir works by introducing errors into the SARS-CoV-2 virus’ genetic code where it prevents the virus from further replicating. Dr. Shaw, a Yale Medicine infectious diseases specialist, explains when the drug enters your bloodstream, it blocks the ability of the SARS-CoV-2 virus to replicate, a Yale Medicine infectious diseases specialist, Dr. Shaw explains. The coronavirus uses RNA as its genetic material. The structure of Molnupiravir resembles the nucleosides (or chemical building blocks) used to make the virus’s RNA. The drug works by incorporating itself into the RNA as it’s being synthesized where it “results in many mutations, or changes in the RNA genetic code, introduced into the viral RNA,” says Dr. Shaw. “And when this RNA is translated into viral proteins, these proteins contain too many mutations for the virus to function.” If this disables replication and RNA’s ability to infect our cells, we will not be as sick from Covid no longer.

An early report showed the Merck drug cut the risk of hospitalization and death to 50% in patients who had mild-to-moderate cases. Results from the Molnupiravir clinical trial, conducted in the U.S. and other countries, suggested the drug would be effective against CDC “variants of concern,” including the Delta, Gamma, and Mu mutations. Scientists are still studying how well the drug works to treat Omicron and are optimistic since its application is the same with Omicron’s RNA.

While this is exciting news, the vaccine many researchers, scientist, and doctors say is still our first line of defense. Some are even concerned that the attention on Molnupiravir will “draw attention away from vaccination,” says Dr. Meyer. “Some people might say, ‘I’m not getting vaccinated because I’ll have access to these medications’—to this pill or to remdesivir or other treatments. But you can’t trade one for the other. If you haven’t done so already, the most important thing is still to get the vaccine.”

Changing Composition of SARS-CoV-2/Understanding the Alpha Variant in England

Since its emergence in the Fall of 2020, the original SARS-CoV-2 variant of concern (VOC) rapidly became the dominant lineage across much of Europe. Although, simultaneously, several other variants of concern were identified globally. Like B.1.1.7 or the Alpha Variant (first mutation of SARS-CoV-2 found to be more transmissible), these VOCs possess mutations thought to create only partial immunity.

Researchers are understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant. This is where scientists in the UK examined trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spanned from January 31st of 2021 to May 15th of 2021.

Through this data, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label of Delta) spread rapidly, becoming the dominant variant in England by late May, similarly to the Alpha Variant.

Shown by many mutations in the spike protein receptor (RBD), studies suggest B.1.1.7 is 50–80% more transmissible with greater severity than previously circulating Covid Variants. B.1.1.7 rose rapidly, from near 0% to over 50% in under two months, and soon made up greater than 98% of sequenced samples in England. Its rapid spread necessitated a third lockdown in England during last January. Subsequent spread in Europe and North America has highlighted the threat this variant poses to a continued alteration of the Coronavirus.

The 69–70 deletion in B.1.1.7′s Spike gene causes PCR tests to return negative results for that gene target which is a major problem when identifying and testing for Covid. One of the most important changes in lineage of B.1.1.7 seems to be a spike protein substitution of N501Y, a change from asparagine to tyrosine in amino-acid position, that enhances transmission. These alterations can change antibody recognition while also affecting ACE2’s (receptor protein) binding specificity which can then lead to the virus becoming more infectious. We are seeing a pattern of the same type of mutation in Covid consistently.

An example of a similar mutation that has been recent is the new Omicron variant out of South Africa. Omicron is similar in which their has been a specific change in the spike protein where antibody recognition is limited and it is highly transmissible between any living organism. Our class has understood and studied the importance of our body being able to identify and create an antibody for the specific antigen being displayed by a pathogen.  These mutations within the spike protein allow another immune response to happen which a different antibody has to be created to mark the different antigen being displayed. Unfortunately, this will be a continuing problem without vaccine mandates since it gives the virus more time to mutate where outbreaks like in South Africa will continue to transpire around the world.

Muscle Regeneration and the Rebuilding of Tissue

Using a combination of molecular compounds that are commonly used in stem-cell research called Yamanaka factors, researchers found the regeneration of muscle tissue was prevalent among mice.  Yamanaka factors are a group of proteins which play a vital role in the creation of induced pluripotent stem cells (cells that have the ability to become any cell in the body), often called iPSCs. They control how DNA is copied for translation into other proteins and are used to convert specialized cells, like skin cells, into more stem-cell-like cells that are pluripotent.

Myogenic progenitor cells, also known as satellite cells or myoblasts, possess the ability to differentiate into large multinucleated myotubes (muscle fibers) to provide a cell culture model of mature skeletal myofibers. “Loss of these progenitors has been connected to age-related muscle degeneration,” says Salk Professor.

The primary role of these progenitor cells is to replace dead or damaged cells. In this way, progenitor cells are necessary for repair after injury and as part of ongoing tissue maintenance. Using the combination of Yamanaka factors to create these special muscle building tissues will allow for muscle repair to be quicker, easier, and available to everyone.  This will allow any cell to be turned into a muscle repair cell. Protein Synthesis Elongation

In the study, researchers found that adding the Yamanaka factors accelerated muscle regeneration in mice by also reducing the levels of a protein called Wnt4, which then activated the satellite cells to be turned into muscle repair cells. We could potentially use this technology to either directly reduce Wnt4 levels in skeletal muscle or to block the communication between Wnt4 and muscle stem cells.

In our class, we have learned about the different jobs of proteins and how some some of these functions are positive (such as the creation of collagen) and negative to cells. WNT4 in this case researchers analyzed are bad for muscle development in creating structure of muscles but can be stopped with the help of Yamanaka factors. Similar to chaperonins, Yamanaka factors allow for the replication of proteins to be easier by controlling how DNA is copied in these myogenic progenitor cells.

 

Powered by WordPress & Theme by Anders Norén

Skip to toolbar