BioQuakes

AP Biology class blog for discussing current research in Biology

Author: bunsenbyrner

Using CRISPR and AAV gene insertion to cure disease

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On April 7, 2025

In Student Post

What is CRISPR?

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) are genes that quickly repeat DNA base sequences that are mechanically edited using a protein called Cas9. This system is based on the Cas9 protein’s ability to splice a given DNA sequence by being given a matching RNA code.  This is incredibly similar to how alternative RNA splicing works in gene regulation for eukaryotic organisms.  In the same way that alternative RNA splicing removes sequences of RNA code during the RNA processing stage of gene expression to create a variety of different proteins, the Cas9 protein removes sequences of code from DNA to synthesize unique proteins. When given a specific RNA sequence, the Cas9 protein will match that RNA sequence to a sequence of DNA, commencing the splicing of the DNA at that location. This process was discovered by Emmanuel Charpentier et al. in bacteria that use the Cas9 protein to target harmful DNA code inserted into the bacterial cytoplasm by viral organisms. Using the Cas9 protein, genetic engineers are able to remove DNA sequences in organisms to cause them to create different proteins and show a wanted phenotypic trait.

DNA alternative splicing

What is AAV?

AAV is a method of inserting DNA into a non-embryonic organism through structures similar to that of viruses.  However, instead of containing harmful virus DNA, these vessels contain modified DNA using CRISPR to force a desired gene expression at a given location in the human body.  AAV-based delivery systems are able to change a person’s genome during their lifetimes, potentially reducing the harm of/eliminating genetic diseases.

Experimentation

Dr. Peace Chinonyerem Ike et al. ran an experiment this year on pediatric males to test the effectiveness of using CRISPR editing through AAV to alter the genomes of certain cells. The diseases they chose are those that have been linked to the X-linked chromosome, meaning that men are more likely to get these diseases such as hemophilia and DMD. This is because X-linked traits in men come exclusively from the mother making it statistically more likely that they will express the phenotype of that gene. After experimentation over five years with treating patients, they saw that using CRISPR was significantly more effective than previous methods for reducing symptoms in these x-linked traits (such experiments include ZFNS).

What Does This Mean

After concluding that CRISPR can be used to treat genetic diseases on the X chromosome we may be able to expand its capabilities to more genetic illnesses such as Cystic Fibrosis that are autosomal. Using CRISPR, we can move medicine away from preventing side effects to outright curing illnesses at the level of the genome. This is a huge feat in the field of medicine and may predict a wave of new treatment strategies involving DNA modification in the future. I believe that, although this possible form of treatment is monumental, we must be incredibly cautious about using AAV-based systems as they may cause harmful mutations in the person’s genome. If we do not make sure that this treatment is safe we may cause multiple people to undergo harmful gene mutations and, for example, develop cancer. So you think that we will see the application of this treatment form in practice? If so, what do you think the ethical and moral ramifications are when using gene editing on a developed person?

iPSCs and Synthesizing Heart Muscle Tissue

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On March 20, 2025

In Student Post

Jyotsna Joshi’s Study

In order to determine the practicality of iPSCs in medicinal research, Jyotsna Joshi and her associates began experimentation as to how effectively iPSCs can create heart muscle tissue (cardiomyocytes) for the purpose of treatment research for arrhythmia.  Dr. Joshi and her colleagues were able to determine that the iPSCs were able to create tissue suitable for experimentation and that would react similarly to that of cardiomyocytes.  Jyotsna concludes her research by stating the potential harms of iPSCs and by explaining the benefits that iPSCs can give to research in arrhythmia.

What are hPSCs and iPSCs?

A human Pluripotent Stem Cell (hPSC) is a cell capable of not only copying itself through mitosis but also synthesizing cells that are different from the original Stem Cell. For example, an hPSC is capable of dividing and one of the sister cells could be a skin cell, an epithelial cell, or any other cell that the body requires.  hPSCs are mostly present during the pre-embryonic stage of human development where the developing organism is a blastocyst.  These cells are responsible for creating cellular variation in the fetus that is necessary for early growth but becomes less essential to humans as they grow in size as the cells derived from hPSCs can undergo mitosis.  This leads to many hPSCs being discarded as the human grows into adulthood with very few remaining as Adult Stem Cells (ASCs).  An induced Pluripotent Stem Cell (iPSC) is a somatic cell that has been genetically re-engineered (likely using CRISPR technology) to have the same attributes as an hPSC.  This is done by reintroducing pluripotent associated genes into a skin or blood cell, making it able to perform the same functions that an hPSC is capable of.

Stem cell differentiation into various tissue types

What is the Problem?

For scientific research in cardiovascular tissue scientists often need cardiomyocytes to undergo experimentation.  However, any cells in the adult human body are incapable of undergoing mitosis including muscle tissue.  This can be due to a multitude of reasons such as nerve cells being incapable of undergoing mitosis due to the unique shape of the cells with their long axons preventing telophase from being able to occur.  In the case of muscle tissue, such as that in the heart/cardiovascular system, they are incapable of undergoing cell division due to how highly specialized their function is as a cell and as a mass of tissue.  Simply put, a muscle cell is incapable of undergoing mitosis because its contractile nature makes the process incapable of occurring.  In muscle tissue, to prevent mitosis from occurring, these cells do not pass through the G1 DNA checkpoint and are perpetually stuck in the G0 phase. This means that grown adults who do not have the ASCs required to rebuild cardiovascular tissue will receive permanent damage if cardiomyocytes were to become damaged in some way (such as alterations in the genomes of the cells).  This makes extracting this tissue via biopsies for research purposes very dangerous and very limiting in the amount of tissue that can be taken.

The Problems with Modern Stem Cell Experimentation:

The potential methods by which scientists can get a hold of heart muscle cells (Cardiomyocytes/CMs) are either through direct extraction or synthesizing tissue using laboratory stem cells. As stated before hPSCs are only abundant in the human body during the pre-embryonic faze of human development and are scarce as humans reach adulthood.  Therefore the main component in stem cell transplants (such as in the case of fixing chronic arrhythmia), those being the stem cells themselves, are incredibly difficult to come across.  Scientists have proposed multiple different answers to this problem, but most of them are unsatisfactory.  For example, it is an option to extract embryonic hPSCs from a mother’s umbilical cord and store those hPSCs for the future use of the offspring.  Another option is to extract ASCs from a patient (or a donor with similar DNA to a sibling) and replicate them in a lab through mitosis and reintegrate the new and previous stem cells back into the patient.  The problem with these systems is that as time goes on stem cells in laboratories have tendencies to behave similarly to cancer cells in that their behavior and replication become more sporadic than when it was inside the body.    Therefore, such stem cells are often wastefully discarded.  Another major flaw of stem cell transplants is the limited number of them in the adult human body to be extracted and genetically modified.  This drastically decreases the practicality of stem cells. The process is also very expensive as extraction and genetic modification are both very difficult and require a lot of resources to pull off.

The introduction of iPSCs in treatment is able to mitigate these problems in modern stem cell transplants.  For starters, iPSCs are not ASCs being extracted from the body and being modified, but rather blood and skin cells that have undergone genetic engineering.  This means that doctors are no longer restricted to procedurally removing ASCs from the body to create useful stem cells which will reduce overall cost and patient safety in that aspect.  The potential abundance of iPSCs also alleviates the need for long-term stem cell storage.

iPSCs in Treating Chronic Heart Arrhythmia:

Arrhythmia occurs when a person’s heartbeat behaves abnormally.  This disease can be caused by the cardiomyocytes responding incorrectly to a signal from associated neurons.  Chronic Heart Arrhythmia causes significant pain in the patient, greatly increases the likelihood of heart attacks, can affect blood pressure, and increases the likelihood of stroke.  To treat this disorder, researchers must have heart tissue to determine what treatment options work most effectively at correcting the patient’s heartbeat. iPSCs provide cardiomyocytes in mass quantities as iPSCs can perform mitosis and become factories for these cells and only require blood or skin cells for reprogramming.  This heavily speeds up research for more effective treatments for arrhythmia as more resources are readily available and easy to produce.  iPSCs are a pathway to more effective treatments for the future and more efficient and available experimentation in cellular biology.

What Does This Mean?

I believe that iPSCs’ potential is not limited to just heart arrhythmia, but can be applied to any cell that is difficult to acquire naturally (i.e. neurons).  iPSCs, especially as scientists begin to maximize their similarities to hPSCs, are going to pave a path to the future of biological experimentation in a similar way that HeLa cells did for cancer research; By providing cells in mass that can represent tissue matter scientists wish to experiment on, iPSCs are going to be able to make experimentation much cheaper, simpler, safer, and practical.  We still have to inquire further about the negative consequences of iPSCs, as the technology to create them and their existence is still very recent (first developed around 2007).  Looking further into the future still, there is a potential that these iPSCs can functionally replace stem cells, however, this is still a point of contention among scientists as to its plausibility.  Do you think iPSCs could potentially be used in practical medicine beyond research?  If this is the case, would you trust iPSCs to function as a normal PSC would be able to?

How We Prevent COVID-19 Beyond Vaccinations.

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On January 9, 2025

In Student Post

SARS-CoV-2 without background

In 2023, Chinese researchers conducted a study to determine the genetic diversity of COVID-19 before and after nationwide policies were instituted to prevent the virus’s further spread.  A specific focus was placed on measuring the development of the more recent Omicron variant in terms of genetic diversity.  This study was carried out from September 2022 to January 2023 and researchers gathered genomic data and concluded that, after the implementation of international global health policies focused on prevention and control (promoting the coronavirus vaccine for example), there were no particularly genetically unique Omicron variants across all samples (over 21,000 genomic sequences with 1,897 of those being from outside of China) that provide any new harm to human health and safety.

The immense genetic diversity of Coronavirus is primarily due to it being an RNA-based virus.  A typical DNA based virus functions in a similar way that steroids cause gene expression in cells because they enter the cell (through endocytosis rather than simple diffusion for steroids) and then head to the cell nucleus to add and virus genes into the cell and cause them to be expressed.  However, RNA0based viruses virus types only contain RNA in their genome, releasing RNA directly into the cell (bypassing the transcription phase in gene expression) and immediately interacting with the cell’s ribosomes to create more viruses.  Not having DNA means that fewer regulatory processes take place to regulate genomic adaptation, causing more variations to occur among virus particles.  This makes it very difficult for modern medicine to keep up with SARS-CoV-2 as antibodies manufactured through vaccines become less effective to newer, more differentiated strands of the virus with different targetable spike proteins.  This process is also very beneficial to the replicative abilities of the virus, as RNA viruses are known to replicate at an increased rate than their DNA-centered counterparts.  This is due to the fact that eliminating the need for DNA transcription makes the creation of new virus particles much more rapid, making such species typically more volatile.  However, Chinese health policies have counteracted the danger presented by viruses such as COVID-19 by enforcing strict policies regarding the spread of the virus and vaccination policies in order to reduce the number of infected hosts and therefore limit the opportunities that these viruses have to mutate beyond our control.  This has proven successful as no significantly dangerous strands have appeared since policies to spread vaccination and limit the COVID epidemic in China were implemented.

This study has proven the value that can be derived from taking preventative measures against viruses and that limiting the mutability of pathogenic viruses can lead to long-term health.  Vaccinations are an incredibly valuable tool in our fight against diseases and their future usefulness is dependant on our ability to limit the spread and mutation of the pathogen the vaccine targets for.  In order to keep ourselves and our neighbors safe, it is our responsibility to take preventative measures against contracting diseases to make sure that vaccines continue to keep us all immune.

This does add to the notion of the potential ineffectiveness of vaccinations given certain circumstances occurring within the virus genome and may show that medicine is overly reliant on the development of vaccinations rather than enforcing more strict prevention measures.  The COVID-19 pandemic has shown the extreme unpreparedness that humanity has for the elimination of viruses.  The results of this study beg the question if we focus less on the development of new vaccine models and more on limiting virus mutation or would this ultimately be detrimental to human health with minimal benefit?  Due to the negative mental impacts that quarantine has had on humans globally, would people even prefer this strategy of prevention?

 

Treating Cerebral Palsy In Kids Through VR

By

On November 4, 2024

In Student Post


Child discovering the applications of immersive technology through a virtual reality headset

In order to determine more effective treatments for Cerebral Palsy – an early developmental condition that causes the brain to improperly stimulate muscle cells –  a 2023 neurological study was conducted with the purpose of measuring the amount of benefit that Virtual Reality technology could provide to children with CP when it implemented alongside traditional therapeutic practices.  The study involved a random selection of kids ages 18 and younger, providing them with a one-hour-long VR experience three times a week for 4 weeks.  Each of the children was provided a simulation of a small toy which they could interact with through their VR headset (paired with sound stimuli).  After the study was concluded, the researchers found significant evidence that using VR technology with standard physical therapy caused a significant increase in kinesthetic performance for these children.  The benefits of VR are likely due to the fact that the repetition of a singular physical activity significantly increases the efficiency by which the nervous and musculoskeletal systems are able to work in tandem.  This useful information is able to be enhanced through the use of VR because VR provides endless possible simulations for training.  This helps kids place themselves in useful training environments based on their needs.

VR is able to help train neurons in the Peripheral Nervous System because, as stated before, sending a similar signal from the brain over and over again through the same neuron allows the dendrites to adapt to that signal and, over time, learn to respond accordingly.  This training may not just benefit the dendrites of the cell, but also the sodium-potassium pumps in the axon of the cell which can become more effective at carrying signals with repeated use.  VR is also able to benefit the neurons that are sending stimuli to the brain, as VR allows for both cognitive and sensory stimuli to be sent to the brain, allowing for the neurons to experience many different neurotransmitters associated with different stimuli.

I believe that the implementation of Virtual Reality can be an incredibly useful tool in order to personalize the physical therapy experience for children who are already having a difficult and frustrating experience navigating the world through their bodies.  Life is already very difficult for kids with CP and these early stages of development are crucial for their development as functional adults in their lifetimes.  Virtual Reality can not only help these children with their condition but also make the experience more fun and enjoyable along the way.

This does raise the question of how VR can treat other illnesses that are not necessarily musculoskeletal.  Due to the cognitive benefits of VR, could it help to heal mental illnesses?  Could it possibly have a positive affect on cognitive function, but the dissociation from the world could have an overall negative effect on the mental health of children?  I invite you to consider these possibilities when observing the affects of Virtual Reality on mentally ill children.

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