BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: DNA (Page 1 of 7)

Pink Pineapples???

By

On October 31, 2023

In Student Post

Most days at school, I eat a snack that consists of pineapples — typical, yellow pineapples. However, it has come upon me that my favorite fruit can also be pink?! With the addition of a singular gene, genetically-modified (GMO) pineapples have their yellow inner color turn into bright pink.

Pineapple

In order to add the gene that causes a color change, scientists use a bacterium called Agrobacterium tumefaciens. They use this bacterium since it treats host cells like a virus does and transfers its DNA to the host cell. Thus, by adding Agrobacterium tumefaciens bacteria cells holding the color-changing gene to pineapples, the new gene’s DNA is able to transfer to the genome of a pineapple. I found this DNA transfer process interesting since it illustrates how prokaryotes can work differently:

In the Endosymbiotic Theory that I learned in AP Bio class, it is said that mitochondria and chloroplasts came into eukaryotic cells by being engulfed by them long ago as prokaryotic cells. All prokaryotes have their own DNA, but, different from Agrobacterium tumefaciens, these prokaryotes must have not been able to transfer their DNA to the host cell because the Endosymbiotic Theory is used to explain why mitochondria and chloroplasts have their own DNA separate from the cell, among other features.

Once in the pineapple’s genome, the DNA transcribes RNA, also as I learned in AP Bio class. However, rather than telling a ribosome what protein(s) to make, the RNA here purposefully interferes with the mRNA that pineapples naturally have that tells ribsomes to create an enzyme called lycopene beta-cyclase. This is in order to stop the prodcution of lycopene beta-cyclase, the enzyme which breaks down pineapple’s naturally-occuring pigment of lycopene into beta-carotene and makes pineapples yellow.

With the lycopene beta-cyclase enzyme no longer being synthesized, these GMO pineapples now have a surplus of lycopene; pineapples’ naturally-occuring lycopene is no longer being broken down. Lycopene is the compound that gives many red and pink fruits and vegetables, such as watermelons and grapefruits, their color. Hence, why pineapples high in lycopene concentration shine pink on the inside.

Lastly, if you ever buy one of these pretty pineapples, it came from the company Del Monte in Costa Rica, who patented the GMO pineapples and is therefore the only company allowed to grow them. Fortunately for Del Monte and rightfully so in my opinion, in Costa Rica these pineapples are higher in demand than supply.

Do you want to see more pink pineapples in the world?

Breakthrough at MIT: Cutting and Replacing DNA Through Eukaryotes

By

On October 23, 2023

In Student Post

File:Researchers in laboratory.jpg

Scientists working at the Massachusetts Institute of Technology’s (MIT) McGovern Institute for Brain Research have found thousands of groundbreaking enzymes called Fanzors. Fanzors – produced in snails, amoeba, and algae – are RNA-guided enzymes. These enzymes combine enzymatic activity with programmable nucleic acid recognition, allowing a single protein or protein complex to aim at several sites. These enzymes were previously found in prokaryotes, like bacteria. 

An example of one of these enzymes is CRISPR, which instead of coming from Eukaryotes like the new Fanzors, “CRISPR technology was adapted from the natural defense mechanisms of bacteria and archaea, a domain of relatively simple single-celled microorganisms”, according to LiveScience. Similar to Fanzors, these enzymes could alter genetic information and how the cell functions. 

File:CAS 4qyz.png

Orange ssDNA target bound to a type-I CRISPR RNA-guided surveillance complex (Cas, blue).

Although similar enzymes to Fanzors have existed, McGovern Fellow Jonathan Gootenberg says, “Eukaryotic systems are really just a whole new kind of playground to work in.” Eukaryotic cells carry membrane bound organelles, such as a nucleus, which holds genetic information, and a mitochondrion, which produces energy, but neither are found in prokaryotic cells, which have no membrane bound organelles. Eukaryotes are also the basis for both unicellular and multicellular organisms, while prokaryotic cells have no membrane bound organelles, and are solely the basis of unicellular organisms. Eukaryotes are found in animal cells, just like ours, while prokaryotic cells are found in bacteria and archaea. Furthermore, TechnologyNetwork says that prokaryotic cells are much smaller than eukaryotic cells “measuring around 0.1-5 μm in diameter”, while, “eukaryotic cells are large (around 10-100 μm) and complex”. 

Eukaryotic cell and its organelles (left) and a prokaryotic cell and its flagella, or tails (right) [NDLA]

As Gootenberg said, all these differences prove that a brand new pathway to further developments has been unlocked. Research has shown that these eukaryotic cells carrying the enzyme have developed the gene cutting enzyme over many years, separate from the development of bacterial enzymes. It is believed that this makes them far more efficient and precise than past enzymes. Fanzors are found to cut targeted DNA sequences with 10-20% efficiency, while other programmable RNA guided enzymes found trouble targeting a single sequence and often attacked others. Ultimately, this discovery is a major breakthrough and will lead to further developments in the process of cutting and replacing DNA. 

How do you expect or want this new discovery to be utilized? Are you excited for the  new avenues for research Fanzors can create? Let me know in the comments!

PGx DNA Test Kits Can Conveniently Predict How We Respond to Certain Drugs – But Do They Always Work and What Are the Limitations?

By

On October 23, 2023

In Student Post

At-home pharmacogenomic testing, or PGx, is at the forefront of personalized medicine, providing patients with a convenient way to understand how their genes influence their response to medications. This allows pharmacists to determine the right strength of the dose to prescribe to their patients, facilitating the prescription process by making prescription doses more precise. 

 

In our biology class, we learned that DNAs encode the specific instructions for carrying out DNA synthesis. In the nucleus, DNAs are transcribed into mRNAs, which are then exported from the nucleus to serve as a template for protein synthesis in ribosomes (or “protein factories” as we learned in class). Therefore any variation in DNA segments also would alter the protein that the DNA segment codes for. 

 

This is the fundamental concept that is necessary for understanding how PGx testing works. PGx testing looks for variation in DNA genes to predict drug response. For example, the presence of a certain genetic variant, a change in the DNA sequence that makes up the genes, is very significant. These variants could be either hereditary and present in virtually every cell of the body, or non-inherited variants that are present in only certain cells. Detection of these genetic variants using PGx testing could thus indicate that the protein it codes for has weaker abilities to break down a certain drug. This would lead to the effect of having a larger amount of the medication in your body and therefore leading to potential harms that could be caused to the body. 

medic

Although convenient, there are also many limitations to these at-home PGx testing kits. One limitation is that most PGx tests do not look for every possible variant of every human gene. This means that PGx results may predict certain responses your body produces for a medication, but not all the side effects. Another limitation is that there is a lack of diversity in the study participants that the PGx tests are based on, placing restrictions on the applicability of PGx test results. This lack of diversity in study trials is not unique to just PGx testing trials, but to many other clinical trials conducted for other medical studies as well across to the US. In the past, studies have shown that this limitation has cost the US billions of dollars due to underrepresentation in clinical research, therefore indicating the significance of increasing diversity in medical trials. 

 

Despite the limitations, the good news is that due to the widespread accessibility and direct-to-consumer nature of PGx tests, patients can actively manage their health. By having access to their genetic information, patients can make more informed decisions about their healthcare and treatment options. In my opinion, democratization of genetic information is crucial in healthcare as patients are then able to understand how their information are used and allows them to make personalized decisions based on their personal values and circumstances. In addition, it also promotes health literacy as it encourages individuals to learn about genetics, understand the medications they are prescribed, as well as the potential impacts of the medications on their personal health. 

 

Reflecting on my experiences with healthcare professionals, I realize that as patients, we often lack in-depth knowledge or understanding of the medications we are prescribed  beyond a general sense of their purpose and a brief overview of potential side effects. Therefore I believe that the democratization of genetic information that PGx provides is a significant value that will help many patients working with healthcare professionals as they learn in-depth information about not only their own genetics, but the medications that they are prescribed as well. After reading this article, given the increasing accessibility of at-home pharmacogenomic testing, what are your thoughts on the balance between the benefits that PGx testing provides to patients and the potential challenges associated with limited diversity in the study populations that underpin these genetic tests?

 

Unlocking Our Ancient Past: Exploring the Genetic Legacy of Extinct Cousins DNA

By

On October 21, 2023

In Student Post

Have you ever wondered where we came from? Who we were? What genes truly lie within us, our mothers, fathers? According to a recent research article from ScienceDaily, Neanderthal genetics is one of them, and the genes still affect human life today. In this research article, the researchers from multi-institution teams, including Cornell University, have shown that Neanderthal genes comprise about 1 to 4% of the genome of present-day humans, mostly of those whose ancestors migrated out of Africa. These genomes are not surprising to the scientific community, but their effect on today’s society in human bodies is remarkable. Through a new plethora of computational genetic tools, researchers found the genetic effects of interbreeding between humans of non-African ancestry and Neanderthals that took place 50,000 years ago, as well as the effects on present-day human life. 

Close up of a Neanderthal in a museum

 In a study published in eLife, researchers reported that some Neanderthal genes are essential for specific traits in modern humans. Using an extensive dataset from the UK Biobank consisting of hereditary and trait information of nearly 300,000 Brits, the researchers examined more than 235,000 genetic variants likely to have originated from Neanderthals. They found that 4,303 of those differences in DNA play a vital role in modern humans and influence 47 distinct genetic traits. These genetic traits can include how fast someone can burn calories or a person’s natural immune resistance to certain diseases. Isn’t that unbelievable? How did something from so many years ago affect such a critical part of our lives? Even though they lived thousands of years ago, we all have a part of the Neanderthals in our genetics.

In another article by U.S.News, the idea of immune resistance through our body’s fight against COVID-19 is displayed. The results show that some people who have increased genes from their Neanderthal ancestors may have an increased likelihood of suffering severe forms of COVID-19. These genes, haplotype, increase the risks of hospitalization and not recovering from the virus, showing that having these traits while being able to burn calories fast may cause harm to us as well. As appealing as it might sound, I know it does to me that Neanderthal genes can help in various ways; it is also quite scary. The risk factors of diabetes, heart problems, and obesity can lead to death when mixed with the virus and the gene itself lingering within us. Since these genes are a part of our fundamental hereditary units and will continue to pass down from generation to generation, with all of these effects, this investigation commenced and evolved into an important and crucial step toward understanding where we came from and who we are. Therefore, these traits affect the lives of humans every day in COVID as well as provide multiple factors of traits that we live with every day, not even knowing where they came from.

Hospital HallwayNovel Coronavirus SARS-CoV-2

As an AP Bio student, in Unit 1, we talked about the parts of the cell along with the DNA that is within the cell. These cells are deeply related to what this topic is about, as the process in which genes work revolves around the cell that it is in. First, it starts with transcription, which is the process in which the genetic material is stored in DNA and replicated into a molecule of messenger RNA. The information goes from the DNA in the nucleus to the cytoplasm to carry out protein synthesis. In the cytoplasm, ribosomes make the proteins that create these specific effects mentioned above. Each gene carries instructions for the proteins that determine your features, such as eye color, hair color, height, and, in this case, immune resistance. These two must connect with each other to fully understand how these genes are still here thousands of years later. The answer is that the genetic material has been carried down for this time through each and every ancestor we have had. It’s pretty scary, if you ask me.

Diagram of a gene on a chromosome CRUK 020

I am not the only one who believes that these causes of our ancestral genes are threatening. If you are like me and want to continue learning about this, reach out! As well as anyone with first-hand knowledge of the research or possible medical intervention, please comment! Share your knowledge with me. The custom software discussed in the ScienceDaily link from UCLA is available for free download and use by anyone interested in further research. So, if you are an AP Bio student like I am or just interested in the genes defining us, even though they are from thousands of years ago, join the conversation. These traits and genes are just being figured out, as most of the work started in September 2023. No matter what fears you may have, to leave you with a sense of comfort after a long list of possible effects, modern human genes are prevailing over successive generations. Therefore, this research, although evolving with us, must continue.

CRISPR-Cas9 – The Human Editor

By

On April 30, 2023

In Student Post

What is CRISPR-Cas9? CRISPR-Cas9 (Clustered, Regularly Interspaced Short Palindromic Repeats) is a powerful technology that allows geneticists to modify or “edit” parts of the target genome by adding or removing whole sections of the DNA sequence. Currently, CRISPR is the most versatile and accurate DNA modification tool globally. This tool allows scientists to fix flaws in most organisms’ DNA and has minimal risk of off-target damage.

Cas9 cleavage position

CRISPR-Cas9 has two main molecules that carry out the change in DNA, an enzyme called Cas9, and a piece of RNA called guide RNA (gRNA). The Cas9 enzyme locates the target area and can cut the DNA in a specific location in the genome so that small pieces of DNA can either be added or removed. The gRNA is made of a small piece of a lab-designed RNA sequence, roughly 20 bases long, located within the RNA scaffold. To ensure that the Cas9 enzyme cuts at the right point in the genome, the scaffold binds to the DNA, and the lab-designed sequence pilots the Cas9 enzyme to the correct location. The gRNA has RNA bases that match those of the target DNA sequence in the genome. The Cas9 enzyme follows the gRNA to the specific area and makes a precise cut across both strands of the DNA. During this stage, the cell recognizes that the DNA has been damaged and will try to repair itself. Scientists use this DNA repair system to add or remove changes in one or multiple genes. This technology is consistent with our most recent AP Biology Unit, DNA Replication, and Gene Expression/Replication.

In my opinion, CRISPR-Cas9 is an incredible technology as it has so many practical applications. The future of this technology has potential in many diverse fields such as genetic engineering, bioengineering, and molecular biology, among other areas of study.

The technology has been tested on dogs with Duchenne Muscular Dystrophy, a gene mutation adversely affecting muscle proteins. In this case, a CRISPR gene-editing treatment demonstrated promising signs of permanently fixing the genetic mutation responsible for this disease, which in humans, affects approximately 1 in 3,500 male births worldwide. The mutation prevents an organism from producing an appropriate level of functioning dystrophin which causes muscles to be weak and not respond efficiently. Researchers at the University of Texas Southwestern found that gene editing restored the functioning dystrophin levels in the dog’s muscles and heart tissue. The increase in the dystrophin levels would need to be more significant for it to work in humans, but researchers have been making substantial progress in advancing this developing CRISPR-Cas9 technology.

Have you ever been caught with a viral disease and been misdiagnosed by your doctor? New CRISPR technology may eliminate this from happening.

By

On April 30, 2023

In Student Post

So first, what even are viral diseases and how can they affect your health?  Well, some common viral diseases include HIV, herpesvirus, COVID-19, or even the common cold. Any disease classified under viral can enter your body through breathing air, touching something with viruses on it, intercourse, close contact, or getting bitten by a bug “such as a mosquito or tick”. Viruses typically infect one type of cell in your body and this is why the “common cold typically infects only cells in your nose, mouth, and throat”. 

In a study by PubMed Central (PMC) their goal was to identify the most common errors in diagnosing infectious diseases and their causes using physicians’ reports. In their concluding results, “the most common infectious diseases affected by diagnostic errors were upper respiratory tract infections (URTIs) (n = 69, 14.8%), tuberculosis (TB) (n = 66, 14.1%), pleuro-pulmonary infections (n = 54, 11.6%)”. This data was taken from a sample of 465 patient cases and the researchers concluded that, “a substantial proportion of errors in diagnosing infectious diseases moderately or seriously affect patients’ outcomes”. So when diagnosing viral infectious diseases, steps need to be taken to improve our testing process.

Researchers from the American Chemical Society are looking at using “glow in the dark” proteins to help diagnose viral diseases. Fireflies, anglerfish, and phytoplankton all create a glowing effect using bioluminescence, which is caused by a chemical reaction involving luciferase protein. This protein has been used in sensors for point-of-care testing, but lacks the high sensitivity needed for clinical diagnostic tests. Researchers wanted to combine CRISPR-related proteins with a bioluminescence technique to improve sensitivity. They developed a new technique called LUNAS, which uses recombinase polymerase amplification (RPA) to amplify RNA or DNA samples. Two CRISPR/Cas9 proteins bind to targeted nucleic acid sequences and form the complete luciferase protein, causing blue light to shine in the presence of a chemical substrate. This new technique successfully detected SARS-CoV-2 RNA in clinical samples within “20 minutes, even at low concentrations“. The researchers believe this technique could be used to detect many other viruses effectively and easily.

In relation to AP Biology, we have learned about the process of gene expression where RNA and proteins are produced due to a specific gene being activated. The regulation of gene expression conserves energy and allows organisms to turn on and off genes only when they are required. The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) gene which are found in prokaryotes cut DNA phages and plasmids to prevent damage to the prokaryote itself. It is used as a rudimentary immune response system. The CRISPR can be associated with other proteins to create an associated complex which allows for the excision and insertion of genes along the length of the genome. Using this process, viral diseases can be identified when combined with the bioluminescence mentioned above.

Looking into the future, researchers are searching for ways to apply CRISPR proteins to detect a greater range of viral diseases so that all patients can get the proper care that they need.

Can Gene Editing Prevent Disease in the future?

By

On April 30, 2023

In Student Post

There is very exciting news in the world of biology right now. For the first time ever, according to the University of California San Francisco‘s chancellor,  Sam Hawgood, CRISPR gene editing will be delivered to a human in an attempt to study how gene editing can help with asthma.

CRISPR-Cas9 Editing of the Genome (26453307604)

CRISPR-Cas 9 was adapted from a naturally occurring genome that allows bacteria to fight off viruses. When a bacteria was infected with a virus, it would use this genome to take pieces of the DNA from the virus and add them to its own DNA to create a pattern known as a ‘CRISPR array.’ The ‘CRISPR array’ allows the bacteria to remember the virus and cut the DNA of the virus apart.

In 2021, Peter Turnbaugh administered CRISPR into mice in order to target a specific gene and edit it out of the mouses gut. It was this work that inspired the scientists at UCSF to experiment with adding the CRISPR to a human microbiome.

Asthma is the perfect place to start because there is a clear microbial target to attack. There is a molecule that is produced by bacteria in the human gut that can trigger asthma in childhood. The scientists goal is to stop the microbes from producing that molecule, rather than remove the microbe altogether, as that microbe plays other beneficial roles in the human body. By taking a small piece of sgRNA, the scientists would be able to attach that to the target sequence in the DNA of the bacteria that produces that molecule, and ultimately stop the bacteria from producing the molecule that causes asthma.

This can be related to the topic of DNA and Genes that I learned about in AP bio. While reading the UCSF article, I couldn’t help but think about DNA replication, and what implications gene editing would have on DNA replication.

As we learned in AP bio, DNA replication is the process by which a cell copies its DNA before cell division, ensuring that each daughter cell receives a complete set of genetic instructions. During replication, the double-stranded DNA molecule is unwound and separated into two strands, each of which serves as a template for the synthesis of a new complementary strand. The result is two identical copies of the original DNA molecule.

If the scientists at UCSF were able to edit the genes to properly stop the microbes from producing the molecule that causes asthma, would that trait now be passed on to the new complementary strands? Would this gene editing get passed on through DNA replication, and even further would it be passed on to gametes? If both parents were to get this gene edited, would their zygotes now also be immune to asthma, and if so it is almost as if this gene editing is affecting natural selection and evolution.

All of this was very interesting to me and it seems that if/when this becomes a regular part of society, it will have major implications on the way our species sees diseases in the future.

CRISPR May Be the Cure!

By

On April 23, 2023

In Student Post

There are still many disorders and diseases in this world that cannot be cured, and Huntington’s disease (HD) is one of them.

HD is a neurological disorder that causes individuals to lose control of movement, coordination, and cognitive function. HD occurs because of a mutation in the Huntingtin (HTT) gene where a specific codon sequence repeats, creating a long, repetitive sequence that turns into a toxic, expanded protein clump. These clumps form in a part of the brain that regulates movement called the striatum and prevent the neurons in the striatum from functioning properly. As of now, HD still has no cure, but CRISPR gene editing (Clustered Regularly Interspaced Short Palindromic Repeats) might just be the solution.

Dr. Gene Yeo of UC San Diego School of Medicine, along with his team and colleagues from UC Irvine and Johns Hopkins University, researched RNA-targeting CRISPR/Cas13d technology as a way to possibly eliminate HD and its negative effects on the brain. CRISPR gene editing, as its name suggests, enables scientists to “edit” – add, remove, or alter – existing genetic material. The group desired to see if RNA-targeting CRISPR would be able to prevent the creation of the protein clumps that damage the function of the striatum. As we learned in AP Biology, the addition, removal, or substitution of a base of a codon can drastically change the structure and function of a protein. Each codon codes for a specific amino acid, and if multiple codons have changed due to a mutation, it is likely that the protein will fold differently than it is supposed to and will lose its function.

Yeo and his team desired to develop an effective therapy for HD, hoping to stop the formation of toxic protein clumps and alter the course of the disease. However, they did not want to create permanent changes in the human genome as a precaution. The team instead engineered a therapy that alters the RNA that turns into the protein clumps.  They conducted testing on mice and found that RNA-targeting CRISPR therapy reduced toxic protein levels in a mouse with HD, improving motor coordination. In connection with the molecular genetics unit in AP Biology, since the RNA that causes HD is altered, the protein that is translated will change since different amino acids correspond to different codons.

Transcription and Translation

Further testing will be necessary to confirm the benefits of this therapeutic strategy, but CRISPR does look like a promising medical treatment for HD and many other diseases in the future.

CRISPR Tool PASTEs in New Genes

By

On April 23, 2023

In Student Post

Researchers at Massachusetts Institute of Technology developed a revolutionary new gene editing tool. The tool is called PASTE, and it is a new CRISPR-Cas9 based genome editing tool. It combines traditional CRISPR and integrases, enzymes that can insert or remove DNA sequences, to cut out certain DNA segments and “paste” in other DNA segments. This new method removes the necessity for double-stranded DNA breaks, which can lead to mutations in the DNA sequence. CRISPR logo

PASTE combines CRISPR-Cas9 nickase, which cuts out a singular DNA strand, with serine integrase, an enzyme that can insert a lot of DNA, and reverse transcriptase, an enzyme that allows PASTE to add a single strand of DNA each time while preventing double-stranded DNA breaks. PASTE produces less indels than CRISPR-Cas9 alone. Indels(insertions or deletions are genetic mutations that often occur when a gene is edited. They can alter the function of genes, thus affecting the organism’s overall health or specific traits (New Atlas).

Additionally, PASTE researchers believe that PASTE could possibly treat genetic diseases by replacing “bad” genes with “good” genes. This is because PASTE is great at “pasting” genes into various parts of an organism’s genome. PASTE researchers tested PASTE against homology-independent targeted insertion and homology-directed repair, discovering that paste had higher insertion effectiveness than homology-independent target insertion, but lower insertion effectiveness than homology-directed repair. PASTE, however, produced less “inaccuracies” than homology-directed repair. These inaccuracies occur when the tool inserts DNA into the wrong part of an organism’s genome, effectively risking unwanted effects (Genome Web).

While PASTE is still in its infancy, it is already revolutionizing the gene editing industry. It not only reduces the risk of undesired mutations, but also increases the efficiency of gene insertion. It is pioneering treatment of genetic diseases. 

AP Bio Side Note 🙂

This technology relates to AP Bio because of its use of introns and exons. PASTE can remove or replace introns and exons, depending on what causes the genetic mutation. This is interesting because although introns are noncoding sequences of DNA, mutations in them can still cause negative effects in people. Additionally, while more intuitive, it is also revolutionary that technology is able to replace exons. I am excited to see what the future for Crispr tools holds. Please leave a comment if you found this post interesting!

Medicine of the Future

By

On April 23, 2023

In Student Post

According to researchers at Karolinska Institutet in Sweden, there are many challenges when it comes to using CRISPR gene editing as a part of medicine of the future. One challenge is how cells behave when subjected to DNA damage. 

TopBP1 Activation of ATR in DNA Damage ResponseDamage to cells activates the protein p53. The technique is less effective when p53 is activated, but a lack of p53 allows cells to grow rapidly and become cancerous. The p53 protein gene is a tumor suppressor gene. If a person inherits only one copy of the p53 gene from their parents, they are predisposed to cancer and usually develop numerous tumors, Other linked genes with mutations can have a similar effect to p53 mutations. The transient inhibition of p53 is a strategy for preventing the advancement of mutated cells. The DNA damage response can potentially be a marker in development of more precise guide RNA sequences. 

P53

We have learned thus far in AP Biology that mutations are changes that occur in the DNA sequence of an organism or a change in a genetic sequence. Mutations can be caused by mistakes during cell division. They can be harmful, beneficial or have no effect. 

The researchers plan to further conduct clinic-centered tests in order to understand how pertinent these mechanisms are. This study is largely focused on CRISPR screening experiments on isolated cells and analysis of the DepMap database. 

CAST is in the past, it’s time for HELIX

By

On April 23, 2023

In Student Post

CRISPR stands for clustered regularly interspaced short palindromic repeats.’ The term references a series of repetitive patterns in the DNA of bacteria discovered in the 90s. 20 years later, Jennifer Doudna and Emmanuelle Charpentier discovered that CRISPR-Cas9 could be used to cut any desired DNA sequence by just providing it with the right template, meaning it could be used as a gene-editing tool. To add a desired DNA sequence, one needs an upgraded version of CRISPR editing called CAST, CRISPR-associated transposases. Unfortunately,  CASTs suboptimally insert more DNA sequences than wanted and have a relatively high rate of unwanted off-target integration at unintended sites in the genome. This leads to mutations, the three being, silent mutations, missense mutations, and nonsense mutations. A silent mutation is an insertion or deletion of a nucleotide that doesn’t change the amino acid sequence. A missense mutation is an insertion or deletion of a nucleotide that changes one or more of the amino acids. Lastly, a nonsense mutation leads to an early stop signal.

4.2. The CRISPR Cas 9 system II

Luckily, new research published in Nature Biotechnology tells the reader that an improved CAST system called HELIX now exists. Helix stands for Homing Endonuclease-assisted Large-sequence Integrating CAST-compleX. This mouthful dramatically increased the efficiency of correct DNA insertions, reducing insertions at unwanted off-target sites. HELIX has over a 46% increase in on-target integration compared to that of the CAST system. This discovery is one of many that will continue to help us understand the complexity of our genes.

If You Give A Mouse…Sight!

By

On April 23, 2023

In Student Post

In a recent study published in the Journal Of Experimental Medicine, researchers in China successfully used CRISPR Gene-Editing technology to restore sight to mice with retinitis pigmentosa.

That’s a lot of vocabulary all at once, so let’s establish some definitions first and foremost.  According to the National Eye Institute, retinitis pigmentosa is a “genetic disease that people [and animals] are born with…that [affects] the retina (the light-sensitive layer of tissue in the back of the eye)”. As for CRISPR Gene-Editing technology, YG Topics defines it as, “a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence”.

Most inherent forms of blindness and loss-of-vision stem from genetic mutations, and thus retinitis pigmentosa is one of many forms of genetically caused blindness.  However, through CRISPR technology, the researchers in the study successfully edited the DNA of mice who had the mutation to eliminate retinitis pigmentosa and give them the ability to see.  The results of the study are very promising, as not only does retinitis pigmentosa affect mice, but human beings.  Thus, there is evidence that CRISPR could be used to cure blindness among everyday people.  Kai Yao, a professor from the Wuhan University of Science and Technology who contributed to the study said, “The ability to edit the genome of neural retinal cells, particularly unhealthy or dying photoreceptors, would provide much more convincing evidence for the potential applications of these genome-editing tools in treating diseases such as retinitis pigmentosa”.

In AP Biology, we discussed how DNA factors into the traits of a living being.  DNA is made up of 3 base codons that form up to 20 different amino acids.  These amino acids code for specific proteins.  Through a process of DNA transcription and translation, the DNA uses various forms of RNA to code for proteins, which help tell the cell what to do.  Thus, the way the cell acts is largely determined by its DNA.  Essentially, DNA codes certain traits through various amino acid sequences.  Mutations and alternations to amino acid sequences cause different traits, such as red hair, blue eyes, or blindness.

Thus, successfully altering the DNA of mice has huge implications for the human race.  CRISPR could potentially be used to edit the DNA of humans, and thus help limit and prevent certain genetic conditions.  Many diseases are based on genetic mutations, and if CRISPR Gene Editing technology is proven successful, we could potentially eliminate genetic diseases in a few decades.  While “much work still needs to be done to establish both the safety and efficacy” of CRISPR technology, some groundbreaking scientific treatments could be coming sooner than you think (Neuroscience News).

Мышь 2

The “Most Complicated” Cancer Treatment EVER

By

On April 23, 2023

In Student Post

There are many approaches to treating cancer, ranging from invasive surgeries to extremely damaging radiation and chemotherapy.  The teeny-tiniest clinical trial ever began at UCLA in yet another attempt to find another way to eradicate cancer.  With only 16 participants, this trial combined two areas of research: gene editing and T-cell engineering.   The reason for the miniscule sample size is the intensely customized nature of the treatment.  Each patient’s tumor had completely unique mutations, so each patient needed equally unique T-cell engineering through gene editing.  

One reason cancer is so hard to treat is because they have adapted to be resistant to the body’s own immune response.  The patients that have cancers, especially ones in the later stages, have lost the battle against their cancer with their own immune system, so a new super-immune system must now be built.  This army of new T-cells (white blood cells, which identify and kill bad cells, seen below) will need “training” for its difficult battle ahead.  First, however, the researchers must determine how to train these cells so they will actually be successful.  They used algorithms to find identifiable mutations in the tumor, something that the T-cell can seek out to differentiate the cancerous cells from the normal cells.  Healthy Human T Cell

After testing to make sure that the T-cells can actually identify these mutations, T-cell receptors are designed specifically to their tumor.  Then, each patient’s blood is taken so that the DNA code for the new receptors can be inserted using CRISPR,  a genome editing technology at the cutting edge of genetic medical research.  The DNA code is transcribed to mRNA, which is then used in the ribosome to build polypeptides, in this case, the receptor proteins for the T-cells.  In order to ensure that these new T-cells (with the special receptors) are received, the patients had to take medication that suppressed the number of immune cells, so that the ones they are given can take hold.  

One month into treatment, 5 of the patients’ tumors stopped growing, and only 2 of the participants had associated side effects.  Although only 5 patients had the desired results, Dr. Ribas, one of the researchers, says that they “need to hit it stronger the next time” because they were limited to a small dosage of T-cells to start in order to establish safety.  Additionally, the technology will only get better and better as the research progresses and the T-cells can have more and more mutation targets to look for in a tumor.  

We Live In a Time Where We Can Hack and Edit The DNA In Diseases, and We Have Only Just Begun…

By

On April 23, 2023

In Student Post

CRISPR gene editing, (Clustered Regularly Interspaced Short Palindromic Repeats), is a relatively new biological technology that allows scientists to fix unimaginable flaws with an unprecedented minimal risk of off-target effects. This advanced technology aligns perfectly with our current unit of DNA replication and Gene expression/replication, so it should be a good review to keep reading.

CRISPR gene editing has two main components; the Cas9 protein and a guide RNA (gRNA). The Cas9 protein acts as the Helicase, cutting and unzipping the DNA strand. The gRNA is designed to recognize a specific sequence in the DNA of a cell. Once the DNA is cut, the cell uses a homologous DNA template to repair the break in the DNA molecule. The template DNA, Homology Directed Repair (HDR), is designed to carry the desired genetic modification and incorporate it into the DNA through the natural DNA repair mechanisms. This process alters or even adds new genetic information to the organism. For example, researchers from UT Southwestern Medical Center used CRISPR to treat Duchenne muscular dystrophy (DMD). A genetic disease that causes muscle degeneration and weakness. The team used CRISPR to delete the gene responsible for producing a toxic protein that causes DMD. They then replaced the missing gene with a shorter, functional version, which allowed the muscles to regenerate and become stronger.

CRISPR illustration gif animation 1

This advanced technology has been used to increase crop yield from various crops. In California it was used to create more drought resistant rice. In another state, it was used to eliminate browning of red apples. This process is becoming increasingly useful and popular because of its safety. The gRNA can be designed to target a very specific sequence of DNA, which means that scientists can modify genes with precision and accuracy. This specificity also reduces unintended genes, which remains to be a large concern for other gene-editing processes. This technology has enormous potential in the science world and can safely guide us into disease treatments, agricultural efficiency, and advanced biological research.

DCas SAM system

Is Nobel Prize-Winning CRISPR Technology as Sound as Scientists Say?

By

On April 23, 2023

In Student Post

CRISPR—short for ‘clustered regularly interspaced short palindromic repeats’—is a nobel-prize winning scientific advancement in genetic modification technology. It was initially developed by Dr. Jennifer Doudna of Harvard University, and is based on the naturally occurring gene-editing system found in bacteria. Researchers now use this new method to modify the DNA of various organisms, potentially being able to make advancements in disease treatment, improving resilience of crops, correcting genetic defects, and more. 

CRISPR-Cas9 Editing of the Genome (26453307604)

To make an understatement, the introduction of CRISPR into the scientific community has been nothing short of groundbreaking, but researchers from Rice University have raised their own doubts about this seemingly miraculous technology, and whether or not it is as fool-proof as it’s presented to be. In response to this question, they have begun to lead an effort with a goal “to reveal potential threats to the efficacy and safety of therapies based on CRISPR-Cas9…even when it seems to be working as planned.” 

CRISPR-Cas9 was designed to treat sickle-cell anemia. In order to combat this disease, the technology works to edit large sequences in a patient’s DNA, therefore aiming to change their DNA and erase the aspect of it that makes them suffer from the illness. However, researchers have begun to fear that taking such a large step as this (erasing large portions of one’s DNA) is presumptuous, and could possibly yield dangerous, long-term effects, since this genetic modification CRISPR allows will only further spread throughout the patient’s body through stem cell division/differentiation. 

These fears mainly stem from the fact that scientists are not sure how DNA strands are able to rejoin after so many of their sequences have been cut out, and therefore, separated. However, bioengineer Gang Bao of Rice University has other concerns, as well: “large deletions (LDs) can reach to nearby genes and disrupt the expression of both the target gene and nearby genes.’”

Gene expression is a very complex process that occurs in the cells of all organisms, but which can be broken down into two major steps: transcription—”synthesis of RNA using information from DNA”—and translation—”synthesis of a polypeptide or protein using information in the mRNA.”  This process running smoothly is extremely important, as the ‘information from the DNA,’ or amino acid bases, need to be copied exactly without any mistakes, duplicates of bases, etc.. 

Bao also expresses another concern about CRISPR-Cas9: “‘you could also have proteins that misfold, or or proteins with an extra domain because of large insertions. All kinds of things could happen, and the cells could die or have abnormal functions.’”

With so many hypotheses at play, Bao and his research team knew they had to somehow figure out answers: they developed a technique called SMRT—’single molecule, real time’—that utilizes molecular identifiers to seek out and find accidental LDs, long insertions, and chromosomal rearrangements that are located at a Cas9 cutting site. To do this, a machine was used called the ‘LongAmp-seq’ (long-amplicon sequencing) to emphasize the presence of particular DNA molecules. This allows for the quantification of LDs and large insertions on a DNA strand. 

Researchers used streptococcus pyogenes as a medium. With this bacteria, they edited enhancers such as beta-globin (HBB), gamma-globin (HBG), and B-cell lymphoma/leukemia 11A (BCL11A), and genes such as PD-1 gene in T-cells of sickle-cell anemia patients. 

In testing these, they found incredible results: across the 3 enhancers and 1 T-cell gene, the average frequency of several thousand large DNA deletions averaged a whopping 20.025%. 

While it is unclear at this time whether Bao’s team’s discoveries will unveil consequences of genes modification by CRISPR technology, they state that they will work to “determine the biological consequences of gene modifications due to Cas9-induced double-strand breaks,” and look forward to testing if “‘these large deletions and insertions persist after the gene-edited HSPCs are [transplanted] into mice and patients.’

New CRISPR Technique can Potentially be a Treatment for Leukemia

By

On April 23, 2023

In Student Post

An article published on December 11, 2022 on newscientist, shares fascinating information on a 13 year old patient with leukemia, having no detectable cancer cells after being the first person to receive a new type of CRISPR treatment, to attack cancer.  

The 13-year-old leukemia patient, Alyssa, has had many treatments that have been unsuccessful in helping her condition. Leukemia is caused by immune cells in the bone marrow dividing and growing rapidly. This relates to what we learned about in Biology class in how cancer cells become cancerous by cells dividing uncontrollably. It is also related to how cancer is caused by changes to the DNA (mutations) that alter important genes and change the behavior of them. Leukemia is also caused by the mutations in DNA.

Normal and cancer cells structure

The most common treatments for leukemia are known as killing all bone marrow cells with chemotherapy and then replacing it with a transplant. If this treatment is unsuccessful, an approach known as CAR-T therapy is used. This involves adding a gene to a type of immune cell known as a T cell that causes it to destroy cancerous cells. This also relates back to how in biology class we learned about the functions of T- cells being vital because they protect us from infection. The modified cells are called CAR-T cells. Alyssa’s leukemia was caused by T cells so if they used this technique to modify CAR-T cells to attack other T cells, it would lead to these cells killing each other. Wasseem Quasim at the University College London Great Ormond Street Institute of Child Health, has discovered many drawbacks with this treatment. Due to the many problems conventional gene editing can cause, Qasim and his team used a modified form of the CRISPR gene-editing protein, and Alyssa is the first person ever to be treated with. Alyssa received a dose of immune cells from a donor that had been altered to attack the cancer, and tests revealed 28 days later she had no signs of cancer cells. CRISPR is technology that can be used to edit genes. It finds specific DNA inside a cell and then changes that piece of DNA. It has also been discovered that CRISPR can be an effective tool for cancer  treatment. This new approach to CRISPR treatments could be hugely beneficial  to cancer patients and Many other treatments involving CRISPR base editing are being developed.  

 

 

 

 



New Generation of Coral!

By

On March 17, 2023

In Student Post

As global warming continues to increase the temperature of the atmosphere and water column across our planet, the coral populations in our oceans are decreasing. Normally, to survive, coral hosts microscopic algae in its structure, which provides the coral with the energy it needs to grow. The algae produce glucose through photosynthesis, which the corals use to survive and to build their skeletons. This coral then releases oxygen that the algae takes back in. The stability of this symbiotic relationship is critical to corals’ survival. When a coral loses these symbiotic algae due to increases in water temperature, it causes the coral to turn white, as the coral struggles to meet its energy needs, which can often prove fatal. This phenomenon is called “bleaching.”

Bleached Staghorn Coral
Scientists studying coral bleaching have found evidence that some species of coral appear to be adapting to climate change and increasing their tolerance to warming ocean waters by changing the symbiotic algae communities they host. This allows the photosynthetic process to continue and provides them with the energy they need to live. This more resilient species of coral have been found in eastern tropical Pacific places such as Costa Rica, Mexico, and Colombia. These locations are projected to have higher coral cover through 2060. Pocillopora is one such species of coral and is an important genus found within the shallow coral reefs in the eastern tropical Pacific Ocean and the Indian Ocean.
I selected this article for my blog as it embodies several key biological concepts that we have studied and discussed in detail in class this year. These include the photosynthetic process and its important energy-producing biochemical reactions, the various types of successful symbiotic relationships between different organisms, and the role that DNA and genetics play in the evolutionary process of advancing successful biological adaptation.

DNA Structure+Key+Labelled.pn NoBB
Consistent with Darwin’s theory of evolution, it appears that Mother Nature, once again, may have found a way to overcome climate change, at least in this specific instance, and we may be witnessing it firsthand!

Researchers Discover Hacking Enzymes as New Cancer Treatment

By

On March 15, 2023

In Student Post

We all know that mutations occurring in the synthesis of our cells lead to cancer, whether that be via ultraviolet light radiation, the inhalation of cigarette smoke over a long period of time, or otherwise. But how do these mutations actually occur, and if modern science knows that much, why can’t scientists step in before the mutation occurs in the cell and stop the creation of a cancerous one altogether? While the answer to this is evidently easier said than done, researchers such as Szymon Barcawz, Rahul Bhomick, Malgorzata Clausen, Marisa Dinis, Masato Kanemaki, Ying Liu, Katrine Lundgaard, and Wei Wu have found a way to limit the success of cancer-yielding cell mutations. 

In this study titled, ‘Mitotic DNA Synthesis in Response to Replication Stress Requires Sequential Action of DNA Polymerases Zeta and Delta in Human Cells,’ researchers studied the replication process of cells, also known as mitosis, in human body cells (all human cells except gametes, sex cells). In order to understand the study fully, a few biological concepts should be covered first; For starters, the activation of the oncogene in relation to developing cancer. ‘Oncogene’ is simply a term for a mutated cell which turns cancerous. The activation of such creates disorder to cells going through mitosis called DNA replication stress, the name of which essentially reveals its effect: when genetic material is being synthesized under these conditions, it is extremely difficult for the mitotic cell to correctly replicate, causing faulty, under-replicated DNA regions (UDRs) to be built. Since DNA replication is completed in the S phase of interphase, which technically is before the commencement of mitosis in a cell; enough genetic material needs to be available for the cell to split in order for it to be replicated. Therefore, if UDRs are going to occur in a cell, they are created during this time. 

However, our cells have developed clever adaptations to attempt to fight this type of cellular mistake. The strategy includes performing “‘unscheduled’ DNA synthesis in mitosis (termed MiDAS) that serves to rescue under-replicated” genetic material (Barcawz et al.). In studying this cellular defense mechanism, these researchers have discovered how exactly cells make up for a faulty S phase (the phase which copies DNA during mitosis) utilizing DNA gap-filling mechanisms (REV1 and Pol ζ) and DNA polymerases (group of enzymes) whose sole purpose is to replicate unfinished genomes (Pol δ). The study’s main goal, however, was to reveal which of these polymerases was the most crucial in the “rescuing” of under-developed genetic material, which were not, and which were not really necessary at all. 

The researchers were most interested in studying POLDI (a subunit of  Pol δ), REV 1, and REV 3 / REV 7 (both subunits of Pol ζ).  These are all different polymerases whose main job is to “[promote] the bypass of damaged DNA sites” (Barcawz et al.). Each one works to solve a different issue within DNA replication that could lead to a mutation. For example, a TLS polymerase called Pol ζ4 is better at “bypassing bulky regions” of genetic material than the others (Barcawz et al.); this can be defined as Pol ζ4’s ‘role.’  

A crucial realization in this study was that the polymerases Pol ζ and Pol δ may actually be switching roles at some point within the rescuing process by switching their subunits, which we defined earlier as POLDI, and REV3 / REV 7. But, this still doesn’t answer the question of whether or not all the aforementioned polymerases are essential in the process of fixing mutations in the copying of genetic material during mitosis. 

The study at hand was successful at answering this question. It found that POLDI, REV1, and REV 3 are crucial to MiDAS, while REV7 is not at all. Additionally, it was discovered that POLDI and REV1 colocalize with another substance (FANCD2) in mitosis, which reveals how they both indeed play a role in the ‘rescue’ of under-replicated regions” (Barcawz et al.).

However, something unexpected about REV1 was also discovered. While it was found to be useful in mending UDRs in conjunction with POLDI and FANCD2, it actually does more harm than good: When REV1 was removed from the rescuing process in a situation where all the cell’s defense mechanisms failed at stopping the synthesis of a cancer cell, cancer cells were much less likely to survive in the human body. This suggests that it is very possible for a new and effective way to treat cancer to be the inhibition of the presence of REV1 polymerase. 

In the coming years, if the inhibition of REV1 is found to be possible and turns out to be a promising way of preventing cancer cells from surviving in the body, we could be looking at a groundbreaking advancement to modern medicine and the world of cancer treatment as we know it changing forever.

Cancer cells

Real image of cancer cell under a microscope.

A View into Life Millions of Years Ago

By

On January 19, 2023

In Student Post

In an obscure geological valley at the very northern tip of Greenland’s large ice sheet, investigators have uncovered scientifically derived evidence of the existence of a lush, ancient ecosystem that was functioning over 2 million years ago. The clues to this ecosystem come from the oldest DNA ever recovered, bits and pieces of genetic material, carefully and tediously extracted from buried sediments representing more than 100 kinds of animals and plants. The investigators painstakingly extracted and “sequenced” the DNA strands and compared them to libraries of existing DNA “reads” from living species today.

DNA double helix horizontal
This is an incredibly impressive example of the power of environmental DNA (eDNA), as it is genetic material collected from the ambient environment and not individual organisms. The investigative team aimed to collect hundreds of samples from different locations within the ancient valley and reconstruct what this ecosystem looked like before the ice age. They found many different types of conifers, including poplars, thujas, and species like black geese and horseshoe crabs, that are now common further south of Greenland, but most of which are no longer found in the Arctic at all.
There are many reasons that I believe this discovery is important, not the least of which is that it may give scientists clues as to how some species were able to adapt to climate change in the past and give us some insight into climate change and evolution as we advance. It may also turn the time-honored discipline of paleontology on its head by driving it from its almost all fieldwork mode into the molecular biology laboratory.

The DNA/RNA biochemical process plays a very important role within the nucleus of each cell which defines the existence and evolutionary success of living plants and animals on the planet. The article which I selected from “Nature” discussed above, really emphasizes importance of these chemical structures regardless of whether we are investigating the past, looking into possible future biological scenarios, or looking to “improve”, correct or modify existing biological systems. Understanding both the future and historic past of the biology of the planet is no longer simply relegated to the desktop microscope, but more appropriately is a function of understanding the complex biochemical reactions at the molecular level, not just the cellular level. The extraction of biological (environmental DNA) material from historic sediments thousands of years old underscores the important changes taking place in this exciting new field and emphasized to me that the study of DNA/RNA biochemistry is very relevant to understanding all living systems, past, present and likely into the future.

 

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

By

On January 8, 2023

In Student Post

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

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

Ácido desoxirribonucleico (DNA)

 

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

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

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

Obesity-waist circumference

 

 

Page 1 of 7

Next →

Archives

Powered by WordPress & Theme by Anders Norén

Skip to toolbar