BioQuakes

AP Biology class blog for discussing current research in Biology

Category: Student Post (Page 1 of 66)

Neuralink: Science Fiction or Reality?

Throughout centuries of scientific discoveries, most of the human body has been discovered and fully understood. Now this would be completely true if it wasn’t for one organ in our body: the brain. The brain is a humans most complex organ, but it is something that we only understand about 10% of how it works. There is a common misconception that we only use 10% of our brain, but “it’s not that we use 10 percent of our brains, merely that we only understand about 10 percent of how it functions.” This is both scary and interesting as the organ that runs our body is hardly understood. While we only understand 10% of its function, there have still been many advancements in technology: one more notable one in the future being Elon Musks’ Neura Link          

The name Neura Link might not ring a bell, and that’s okay because it is something that if fairly new and still in somewhat of a developmental stage. For those who do not know, Neura Link is a device that “place electrodes near neurons in order to detect action potentials. Recording from many neurons allows us to decode the information represented by those cells. In the movement-related areas of the brain, for example, neurons represent intended movements. There are neurons in the brain that carry information about everything we see, feel, touch, or think.” In summary, this is a device that interprets your neurons signals, records it, decodes it, and can then represent the intended message.

All this might sound like some fancy new technology with its only purpose being to interpret what the brain is saying, and that is basically what Neura Link does. However, the implications of this can be very helpful in the world of modern treatments. One thing that is very promising about Neura Link is that the procedure is preformed by robot, so the risk of human error is out of the equation, and it can be done for cheaper than it might have been if a human doctor was preforming the surgery. They are actively trying to make it affordable for the average person that needs it. It is hypothesized that Nuera Link can help bring back motor function to paralyzed people by being an intermediary between damaged neurons. In Neura Links own words, their device could “help people who are paralyzed with spinal or brain injuries, by giving them the ability to control computerized devices with their minds. This would provide paraplegics, quadriplegics and stroke victims the liberating experience of doing things by themselves again.

One thing we have learned in this bio class this year is how there are many processes for many parts of the body. These processes (such as cellular respiration) require many resources as well as a lot of moving parts, and have to be executed very well. There are processes like these for the healing process of certain parts of the body as well. One thing, however, is that neurons and certain nerves, when damaged, can not be recovered or reproduced. There is no system in the body to heal these damaged neurons or nerves. With the absence of a system in place to recovery these damaged parts of the body, they are left there damaged. One thing that is very interesting is that many scientists have tried to find ways to repair this tissue, but Neura Link, instead of trying to repair it, is almost trying to replace it.

While the idea of placing technology inside your brain may seem a little creepy, it might just be the solution to many seemingly unsolvable issues in the body. I think that if these ambitions of the Neura Link team are met with reality (through thorough rigorous testing and safety protocols) that there should be no limit to what it can help with. Since the brain plays a pivotal roll all over the body, there is no telling what Neura Link could do decades from now.

Genetically Engineering the Food We Eat to Increase Consumer Desire

Solanaceae is an order of classification for a group of plants known as nightshades. The Solanaceae are a family of plants that ranges from annual and perennial herbs to vines, shrubs, and trees. Included in this family of variety are also a number of agricultural crops like tomatoes, medicinal plants like jimson weed, spices, weeds, and ornamentals. This group of plants are given the term “nightshade” because some of these plants prefer to grow in shady areas, and some flowers at night.Solanum americanum, fruits

The Solanaceae is one of humankind’s most utilized and important families. It contains some of the world’s most important vegetables as well as some of the most deadly toxic plants. Foods like potato, tomato, peppers, ground cherries, and eggplant all hail from this incredible plant. With the benefits of this plant family also comes the dangerous variety of plants. The belladonna, mandrake, Jimson weed, and tobacco also come from this family. Solanum trilobatum flowersNot only does this family of plants produce important vegetables and deadly plants, various chemicals and drugs can be harvested. Some of these include nicotine, solanine, capsaicin, atropine, scopolamine, and hyoscyamine.

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a gene editing tool that can be used to edit DNA in cells. It used a specific enzyme called Cas9, which stands for CRISPR associated nuclease 9, and a specific RNA guide to either disrupt host genes or insert sequences of interest. CRISPR was initially used in bacteria as an adaptive immunity response but is now being used as an alternative in genome engineering.CRISPR illustration gif animation 1

In the agricultural world, plant breeding has always been the way to improve the traits wanted in a plant. With technological improvements, increased production has been vastly upgraded. Recent advances in gene editing have revolutionized the field of plant breeding. The process of genetic engineering has allowed people to target specific genes to improve rather than continuous breeding to produce the desired trait. 

Consumers choose the type of foods they want to eat by the traits of the fruit/vegetable, and in response, it leads the path to ensure that plant breeding will produce that trait again. In the horticulture industry, fruits are an important food that many people buy. Fruits are known to have a crucial source of energy, vitamins, fibers, and mineral components. The larger the fruit, the less sour and more nutrients it tends to store, influencing consumers to buy fruits that are bigger in size and shape. As a plant family with various crops, Solanaceae crops have a variety of fruit sizes and shape features. With advancing gene editing technology, Solanaceae fruit crops have been on the receiving end of being genetically modified to increase desirable traits of fruit size, fruit weight, fruit quality, and plant architecture.Maduración del tomate (Solanum lycopersicum)

Many of the vegetables and fruits we eat today are slowly being improved with CRISPR. For instance, in tomatoes, the ARGONAUTE7 (SlAGO7) gene function in leaf shape development was one of the first edits done with CRISPR Cas9. Tomatoes have been at the forefront of CRISPR Cas9 gene editing on plants because it is a model crop that is able to grow variability. Many more plants of the Solanaceae family, like the goji berry and groundcherry, have been engineered to produce the best product and CRISPR gene editing will continue to enhance the fruit and plant.

This CRISPR gene editing research on the order of Solanaceae plants is relevant to AP Biology because of gene editing. In the first year of biology, we learned about the taxonomy of species and the order of specificity. The order of Solanaceae plants indicates that it isn’t a particular family of plants that includes the different genus and species. Instead, it is a broader classification. We didn’t specifically learn about CRISPR gene editing in class this year, but we learned about DNA and RNA and their replication process. In a way, we learned about CRISPR because it relies on a strand of RNA with the preferred traits that is then transcribed into DNA.

Novel Nanobody Treatment Could be Used to Treat Animals Infected with SARS-CoV-2

As we have learned in AP Biology class, the spike protein, or S protein, is located on the surface of SARS-CoV-2 is linked to transmissibility and cell entry. Located on the S protein is the receptor-binding domain (RBD) which is a key factor that allows the virus to dock to body receptors and invade host cells. Effective antibody therapeutics target S proteins.

Fimmu-11-579250-g001

Due to their small size and ability to penetrate into lung tissue, nanobodies have been speculated to be an excellent source for novel COVID-19 antibody therapeutics. A recent study measured these proposed capabilities for potential usage as a treatment. The proposed therapeutics would be used in veterinary medicine and aim to directly prevent SARS-CoV-2 pseudoviruses from compromising host cells.

The researchers screened and sequenced specific nanobodies, then, they were produced and amplified. The study validated the speculation by observing the carefully selected nanobodies bind to the SARS-CoV-2 S protein and RBD protein simultaneously. 85% of pseudoviruses were observed to be inhibited in a solution with 100mg of nanobody concentration.

What makes nanobodies even more attractive for usage in veterinary medicine is that its inexpensive to produce and can be made in large amounts. Given these beneficial qualities of nanobodies, they seem to be a plausible and favorable COVID-19 treatment.

Can Technology Ketchup To These Super Tomatoes?

Sicilian Rouge tomatoes are one of the first foods made with CRISPR-Cas9 technology to be sold to the public. An article by Emily Waltz, of Scientific American, goes in depth on how these tomatoes are taking Japan by storm. Sanatech Seed, a company based in Tokyo, has edited the tomatoes to have a large amount of GABA(γ-aminobutyric acid).  According to the company, GABA supposedly lowers blood pressure and promotes relaxation when ingested orally.

In Japan, GABA is a popular addition to many foods, drinks and other products such as chocolates. Hiroshi Ezra works as both the chief technology officer at Sanatech and a plant molecular biologist at the University of Tsukuba. He says that “GABA is a famous health-promoting compound in Japan. It’s like vitamin C…That’s why we chose this as our first target for our genome editing technology. “

 

CRISPR has been used in a myriad of ways by plant bioengineers. Non-browning mushrooms and drought-tolerant soybeans are just a few examples of this. However, Sanatech’s Sicilian Rouge tomato was the first CRISPR-edited food known to be commercialized.

 

But what is CRISPR and why has it become so popular? Yourgenome.org effectively explains what the different parts of the CRISPR-Cas9 technology do. The system is made of two parts: the enzyme and RNA. The enzyme is called Cas9 and its role in gene editing is to ‘cut’ the specific genome in strand of DNA so that the mutation can be made. The RNA acts as a guide for the enzyme, which is why it is called gRNA. The piece of RNA is made of an approximately 20 base sequence that is a part of the longer RNA ‘scaffold’. When the strand binds to the DNA the 20 base sequence guides the Cas9 to the part of the genome that is meant to be cut. The scaffold is able to find the correct genome because its bases are made to be specifically complementary to the target genome. Once the genome is cut the cell recognizes the cut in the DNA and repairs it. It is when this repair takes place that the changes/mutations to the genome occur. 

4.3. The CRISPR Cas 9 system III

The processes of CRISPR are similar to what we learned about in biology too. During DNA replication, small complementary strands of RNA act as primers so that DNA polymerase can add to anc continue the chain. DNA polymerase also ‘proofreads’ strands of DNA for any mistakes which it would cut out and replace with the correct nucleotides. The Ligase then reforms the phosphodiester bonds which hold the nucleotides together. This process of error correction is what takes place once the Cas9 cuts the genomes.

 

Another type of DNA editing is called TALENs or transcription activator-like effector nucleases. A company called Calyxt commercialized TALENs through their genetically edited soybean oil that is free of trans fats. Gene editing hasn’t only been bound to plants, but also animals too. In October of last year Japan approved CRISPR two gene-edited fish. One was an edited tiger puffer which “exhibits depressed appetite suppression”. The other was a Red Sea bream which was edited to have “increased muscle growth”.

 

From super-crops to super-fish, it appears as though there are no limits for CRISPR in our daily lives. It’s amazing how precise technology has allowed us to alter the nutrition of the food we eat. I wonder what other possibilities lie in the future of CRISPR and how they will affect our society.

Can CRISPR Gene Editing Cause Problems in the Embryos it is Meant to Customize?

Researchers from around the Tri-State area came together in 2020 to examine the effectiveness of the Crispr-Cas9 double stranded DNA break (DSB) induction on human embryos to repair a chromosomal mutation. The study, which was published in Cell, began with sperm from a mutated male patient at the EYS locus, which causes retinitis pigmentosa blindness. The researchers then attempted to use CRISPR-Cas9 technology to repair the blindness gene in a number of fertilized embryonic stem cells that carried the EYS mutation.  The results showed that about half of the breaks in the experiment went unrepaired, which resulted in an undetectable paternal allele. After mitosis, the loss of one or both the chromosomal arms was also common. This study shows that using CRISPR-Cas9 technology is still in its early days, and needs to be further vetted before it is used to treat patients.

CRISPR Cas9 technology

Instead of correctly and consistently editing the genome of the embryos, the Crispr-Cas9 wreaked havoc, leaving behind chromosomal trauma. The data shows that the embryos started to tear apart and get rid of big pieces of the chromosome that had the EYS mutation, some losing the entire chromosome. The promise of Crispr technology is about changing one gene, but how can that be done when a larger, untargeted part of the genome is also being altered? Dr. Egli, the paper’s main author, brought up a more likely use for the Crispr editing: deploying it as a form of “moleculure bomb”, sent in to shred unwanted chromosomes. An important part of using gene editing is the ability to consistently predict the outcome, However, the resulting “mosaicism prevents inferring the genotype of the fetus from a biopsy and is thus incompatible for clinical use”, according to the Cell authors.

There were many rarities that appeared in the alleles of the embryos used. With a small sample size, due to the difficulty to acquire human embryos, there was no ability to rule out rare events. Although there were combinations of maternal and paternal alleles that showed interhomolog events, they occurred after the two-cell-stage injections, all mosaic. A single Cas9-induced break can result in outcomes in the human embryo that suggest species-specific differences in repair. In on-target sequencing of the cells, the detection of only a wild-type maternal allele might have been because of the unrepaired breaks and the loss of the chromosomal arm or the loss of the entire chromosome. This study shines light on the dangers of Crispr gene editing. The quotes from researchers, doctors, and genealogists all echo the same risk, we must walk before we can run. Testing and ensuring the safety of using Crispr on an embryo before the first round of DNA replication happens is crucial to the ultimate promise of gene repair. If it can’t be done safely with no off target effects, then Crispr “would be deeply unethical”, according to Dr Faraheny from Duke University.

Cas9/10

Gene editing sounds to most like an intriguing opportunity at the very least, if not a groundbreaking advancement in human development, however it does not come without any flaw. We are not living in “Gattaca”quite yet to say the least. One of the most common gene editing processes, CRISPR, is equipped with a relatively predictable flaw in particular; an error taking place at the molecular level that results in the wrong genome being altered than what had been intended, therefore leading to potentially dangerous or life altering mutations in said gene. A team of specialized professionals at the University of Texas at Austin decided to revamp a significant component used for the CRISPR gene editing process. Their new version of Cas9 reduces the chances of the wrong genome being manipulated by thousands.  This is a figurative unicorn of scientific discovery,  it is groundbreaking on top of groundbreaking, it is cloth cut from the fabric of similar discoveries that have changed the course of human history and still – it is only the beginning.

When there is an error in the way the genomes are adjusted, it is a rather simple explanation as to how, and even simpler when describing how the new version of Cas9 can fix it. When the letters making up the DNA’s structure are incorrectly assembled or mismatched, causing a lack of stability in the structure of the DNA itself. Due to this, Cas9 is not capable of making the necessary adjustments to the DNA in order to properly execute the procedure. The new version of Cas9 is far more capable and strong, meaning that it can in fact execute the procedure.

Although this new Cas9 is an answer to a previously inherent setback to gene editing, it doesn’t come without its own respective setbacks. A primary caveat to the increased accuracy of this Cas9 is that it works at a much slower pace than Cas9 that is naturally occurring.

There is a self awareness that seeps through this accomplishment to the people that set it in motion. Kenneth Johnson, a professor at the University of Texas at Austin and co-author of the study even says that this newfound tool “could really be a game changer” when it comes to further use of gene editing among the public. It is truly a tremendous feat conquered by this group of experts in the field of genetic engineering.

Ultimately, further advancements in genetic editing could very well change the human race and the world as we know it so long as quality time and effort is put into it, as seen with this study. With the incentive of the potential advancement of human kind as a whole, its anyone’s guess as to what could one day be possible.

Can we make Jurassic Park real?

CRISPR technology has already demonstrated its potential to revolutionize modern biology. Summarized, CRISPR is a gene editing technology. It has the ability to change the sequence of DNA in living cells, therefore changing their traits. However, the applications of CRISPR extend far beyond simple fun with gene editing. CRISPR can be used to modify the foods we eat, making them easier to grow and more resistant to harsh climate. CRISPR has even been theorized to have implications for treating human genetic diseases. However, how far does this technology go?

Dino Park

A group of scientests have been focusing on a much more radical side of CRISPR: they are attempting the revival of an extinct species. The Christmas Island Rat went extinct over 100 years ago in 1903. Thankfully, some DNA of the rat has been maintained, allowing scientists to sequence the genome. Through analysis, they have found that the Christmas island rat is very closely related to the brown rat. In fact, the genomes have a 95% similarity between them. This similarity begs the question, can we CRISPR a Brown Rat into a Christmas Island Rat?

Because of the highly similar genomes, scientists believe that they can use the gene editing technology in CRISPR to recreate the Christmas Island Rats from the brown rat. While they have not yet achieved their goals, they are confident in their ability to produce results. Although modifying a rat to bring back a close relative is a long way off from bringing back dinosaurs from nothing, this amazing experiment may pave the way for future scientists to make the movies real life. As science progresses, we may be able to transform more complex and distantly related species, we will just need to wait and see.

Will Microscopic Worms Replace Dogs in Sniffing Out Cancer?

It is very rare that doctors are able to find cancer at its early stages, however, on the rare occasion that they do there is a much higher chance that the patients survive. You may be asking yourself: Why isn’t there a way to find this cancer earlier inorder to save more lives? A recent study shows that microscopic worms are able to sniff out cancer as early as stage 1. While dogs are also able to smell cancer from human breath, urine, and blood, keeping cancer sniffing dogs in a lab is not practical. These tiny worms create a more practical solution to this problem. 

Specifically, lung cancer is found by doing a biopsy or different kinds of imaging tests. However, these kinds of tests are not able to detect lung cancer until it is in its later stages and more severe. As we learned in AP Biology, cancer is caused by cells that uncontrollably divide. In normally dividing cells there are checkpoints the cell must pass in order to divide. These checkpoints are at the G1, S, and G2 phases. If the cell needs to divide there will be an influx of cyclin concentration and MPF activity. Cyclins are proteins that control the progression of the cell through its checkpoints by activating cyclin-dependent kinases. MPF, or maturation promoting factors, promotes the cell’s entrance into the M phase from the G2 phase. In cancer cells there is a genetic mutation, sometimes it is hereditary, however it can also be caused by caused by tobacco smoking, radiation, etc. This genetic mutation causes these proteins to not work properly. Because of the malfunction of these proteins, cells do not know when to stop dividing and continue to divide. 

A team of scientists from Myongji University in Korea found a type of worm called C. elegans that is attracted to the floral scent of lung cancer cells. 

Caenorhabditis elegans hermaphrodite adult-en

During their experiment, scientists placed the worms in a center chamber. On each side of the chamber was a petri dish, one with lung cancer cells and one with normal cells. The scientist found that these worms were more likely to move towards the lung cancer cells than the regular cells. Now, researchers hope to increase the accuracy of the worm’s attraction to the lung cancer cells and use these worms to detect lung cancer during its early stages. Worms that have already been exposed to the lung cancer cells will be used to detect cancer in patients urine, saliva, and even their breath. These researchers will continue to work with doctors to test their theory and see if these microscopic worms will replace dogs in sniffing out cancer.

 

Harnessing the Power of Photosynthesis for Environmental Gain

Human use of fossil fuel as a form of energy to sustain industry and modern lifestyle has had a detrimental effect on environmental efficiency. Nature’s ecosystems are dying and the atmosphere is polluted, causing climate change that further negatively impacts the ecosystems. With fossil fuel sources being depleted, humans must find new energy sources to sustain their current way of living while minimizing the potential harmful effects on the environment. Perhaps, surprisingly, a solution to these problems may be found in the untapped power of plants to sustain themselves through use of sunlight and water in a process called photosynthesis.

Sun shining

Photosynthesis is the process by which photons of light (coming from the rays of the sun) and water molecules are converted, through a complex, multi-step process, into glucose, a form of stored energy. Today, scientists are working on various ways to mimic the natural process of photosynthesis through artificial photosynthesis. Their goal is to find clean, affordable, efficient and sustainable ways to create energy that would allow humans to subsist as they do. 

 

Harnessing the power of the sun is full of potential because the sun’s energy is so great that the amount of sunlight hitting the earth in one hour can satisfy the energy needs of all humans for one year. 

 

Currently, the process most similar to artificial photosynthesis is photovoltaic technology which allows a solar cell to convert the sun’s energy into electricity. A small PV cell usually produces between 1 and 2 watts of power when sandwiched between protective materials like glass and plastics. In order to harness maximum energy, these PV cells, which are composed of semiconductor materials, are often chained into arrays that have the capacity to be bound to a larger electrical grid.  However, this process is inefficient because it harnesses only 20% of the sun’s energy, in part because the semiconductors in solar panels have limited ability to absorb and store sunlight energy.

 

By contrast, photosynthesis can store 60% of sunlight as chemical energy in biomolecules. In her research, Yulia Pukshar, a biophysicist at Purdue University, has been replicating the photosynthesis process by creating an analog that collects sunlight then splits water molecules to create hydrogen. Hydrogen is useful as a fuel to be used in fuel cells or as a fuel to be combined with other fuels (like natural gas) to provide power to homes, cars, electronic devices, etc. Much of Pushkar’s research has focused on determining which combinations of catalysts and photosystem II proteins work best to generate hydrogen from water molecules. She seeks to use chemicals and compounds that are abundant, easily accessible, inexpensive and non-toxic. Artificial photosynthesis is being developed with “nontoxic, easily available elements” which sets it apart from preexisting forms of “clean” energy. 

 

Currently, researchers have determined that the most durable oxygen evolving complexes (the portion of photosystem II that promotes photo-oxidation of water during photosynthesis) are those composed of cobalt-oxide based water oxidation catalysts. The use of such catalysts, that most closely resemble the true catalyst present in photosystem II, is highly costly and impractical when applied at a large scale. What seems to be a breakthrough in man-made, photosynthetic technology is merely in its infancy. If human civilization is to ever make a dent in this environmental crisis, new sources of sustainable energy must be implemented globally.  

 

Ever since I moved to Brookville from New York City, I developed a greater appreciation for the beauty and peacefulness of nature in my surroundings. My understanding of the process of photosynthesis has reinforced my sentiments as I now fully comprehend the value of plants to human life. As my family plants more trees on our property, I recognize that such plantings are helping the environment by absorbing CO2 and providing vital oxygen to the atmosphere. For this reason, among others, I support reforestation initiatives around the world as well as the Forest Program at FA.

Environmental Cues Can Trigger Planned Movement and Advance Studies of Motor Disorders

A group of scientists from different universities, including Dr. Hidehiko Inagaki, Dr. Susu Chen, and Dr. Karel Svoboda, came together to understand how cues in our environment can trigger planned movement. Neurons in the human brain are active with diverse patterns and timing. The Motor cortex is responsible for the control of movement. The patterns of the motor cortex differ in the phases of movement. The transitions between these phases is a critical part of movement. The brain areas controlling these transitions were a mystery.

To identify the parts of the brain controlling these transitions the group of scientists performed their research on mice.They recorded the activity of neurons in a mouse’s brain when doing a triggered movement task. Researchers found brain activity taking place directly after the go cue and between the stages of movement. This brain activity came from a circuit of neurons in the midbrain, thalamus, and cortex. To determine whether this circuit was a conductor or not the scientists used optogenetics. Through the use of optogenetics Dr. Inagaki and his colleagues were able to identify a neural circuit critical for triggering movement in response to environmental cues. Dr Inagaki says that “We have found a circuit that can change the activity of the motor cortex from motor planning to execution at the appropriate time. This gives us insight into how the brain orchestrates neuronal activity to produce complex behavior.

Figure-1

Not only is this important for the use of knowing more about the brain but it also helps to advance studies of motor disorders, such as Parkinson’s disease. By adding environmental cues to trigger movements it could drastically change the mobility of patients.

In Ap Biology class we learned about cell communication. Neurons communicate with each other by releasing specific molecules in the gap between them, called the synapses. The sending neuron passes on messages through neurotransmitters that are picked up by the receptors of the receiving neuron.

CRISPR Quits Coronavirus Replication

The gene-editing CRISPR has now been utilized by scientists to prevent the replication of Coronavirus in human cells, which can ultimately become a new treatment for the contagious virus. However, since these studies were performed on lab dishes, this treatment can be years away from now.

Firstly, CRISPR is a genome-editing tool that is faster, cheaper, and more accurate than past DNA editing techniques whilst having a much broader range of use. The system works by using two molecules: Cas9 and guide RNA (gRNA). Cas9 is an enzyme that acts as “molecular scissors” that cuts two strands of DNA at a specific location. gRNA binds to DNA and guides Cas9 to the right location of the genome and ultimately makes sure that Cas9 cuts at the right point.

 

CRISPR'S Cas9 enzyme in action

CRISPR’S Cas9 enzyme in action

In this instance, CRISPR is used to allow the microbes to target and destroy the genetic material of viruses. However, they target and destroy the RNA rather than the DNA. The specific enzyme they use for this is Cas13b, which cleaves the single strands of RNA, similar to those that are seen in SARS-CoV-2. Once the enzyme Cas13b binds to the RNA, it destroys the part of the RNA that the virus needs to replicate. This method has been found to even work on new mutations of the SARS-CoV-2 genome, including the alpha variant.

COVID-19 vaccines are being distributed around the world, but an effective and immediate treatment for the virus is necessary. There are many fears that the virus will be able to escape the vaccines and become a bigger threat. Although this treatment is a step in the right direction for effective treatment of COVID-19, this technique will ultimately take a long time for the treatment to be publicly available.

CRISPR is greatly relevant to AP Bio, as seen through its use of enzymes in DNA replication. CRISPR utilizes Cas9, an enzyme that is similar to helicase. In DNA replication, the helicase untwists the DNA at the replication fork, which after the DNA strands are replicated in both directions. 

This article is fairly outdated since there have now been immediate treatments created for COVID-19. But, what do you think about the use of CRISPR for future viruses and pandemics? Personally, I believe that CRISPR will ultimately become a historical achievement in science due to its various uses. Thank you for reading and let me know what you think in the comments! 

 

CRISPR can help in the detection of Kidney Rejection sooner than you thought

 

 

Kidney Transplant

Diagram of a Transplanted Kidney

As of now, the only way to diagnose acute rejection is through a biopsy. This procedure can only detect problems when they are in a late stage. Doctors would be able to begin anti-rejection medication sooner if there was a way to non-invasively diagnose kidney rejection at an early stage. Well, there might be now….

 

Researchers have found an early warning sign of rejection in the urine of kidney transplant patients, a cytokine protein called CXCL9. Currently, the method used for measuring the protein (an enzyme-linked immunosorbent assay, or ELISA)  has been unsuccessful. However, Jonathan Dordick and colleagues have been working to develop a better technique. 

 

Kidney Transplant

How CRISPR works

They have based their new detection method on a gene-editing technology called  CRISPR/Cas12a. The CRISPR/Cas12a enzyme cuts a probe to produce a fluorescent signal when in the presence of the CXCL9 protein. Then by attaching a DNA barcode that aggregates a large number of CRISPR/Cas12a molecules, they were able to boost the fluorescent signal. This then led to an antibody that recognizes CXCL9. 

 

Another essential thing to note is that, unlike different CRISPR-based detection methods, the use of PCR amplification is not required. This makes it easier to modify to a device that could be used in more accessible ways, like in a doctor’s office or at home. When tested, the new system accurately measured CXCL9 levels for 11 kidney transplant patients. Since the immuno-CRISPR system is about 7 times more sensitive than an ELISA, kidney rejection can now be detected early. 

Can Cancer Cell’s Medication Immunity Be Stripped?

Cancer is one of the hardest diseased to fight. If a tumor begins to grow inside of a patient, they may be given drugs to fight off the corrupt cells. The problem with this is that the cancer cells could become immune to these drugs. Through the use of CRISPR. In Novel Crispr imaging technology reveals genes controlling tumor immunity, a new way of fighting cancer is revealed. Instead of targeting the whole tumor, Perturb-map marks cancer cells and the cells around cancer cells. Once this is completed, it is able to identify genes controlling cancer’s ability to become immune to certain drugs.

Mitosis appearances in breast cancer

To fight cancer cells, scientists use thousands of CRISPRs at the same time. This identifies every gene in a sequence and allows them to be studied. Through Perturb-map, scientists can now dive deeper and find where the cell immunity to drugs originates. A certain pathway in the cell is controlled by the cytokine interferon gamma or IFNg, and a second is by the tumor growth factor-beta receptor or TGFbR. When the cell had a gene with TGFbR2 or SOCS1, the latter of which regulates IFNg, tumor cells grew. When the cell lacked one of these, it shrunk. Moreover, it was discovered that tumors with SOCS1 were susceptible to attacks by T cells, but TGFbR cells had immunity against them. This stayed true even when both types of cells lived in the same environment. With findings like these emerging more and more, the future of cancer treatment is looking brighter than ever.

Chromosome DNA Gene unannotated

Could Overproducing A Gene Prevent Parkinson’s Disease?

A team from the University of Geneva (UNIGE) discovered a gene that, when overexpressed, prevents the development of Parkinson’s disease in fruit flies and mice. Parkinson’s disease is a movement disorder caused by a brain disorder. Parkinson’s disease symptoms typically appear gradually and worsen over time. Men are affected by the disease at a rate that is roughly half that of women. A combination of genetic and environmental factors contributes to the disease’s underlying cause.

Emi Nagoshi, Professor in the Department of Genetics and Evolution at the UNIGE Faculty of Science, studies the mechanisms of dopaminergic neuron degeneration using the fruit fly. The midbrain dopaminergic neurons are the primary source of dopamine in the central nervous system. Their absence is linked to Parkinson’s disease. Emi’s test connects to the Fer2 gene, whose human homolog encodes a protein that regulates the expression of many other genes and whose mutation may lead to Parkinson’s disease through unknown mechanisms. 

The absence of Fer2 causes Parkinson’s disease-like symptoms, the researchers investigated whether increasing the amount of Fer2 in the cells could provide protection. When flies are exposed to free radicals in their environment, such as toxins, their cells undergo oxidative stress, which leads to the degradation of dopaminergic neurons. By creating mutants of the Fer2 Homolog in mouse dopaminergic neurons, the scientists were able to show that oxidative stress has no negative effect on the flies if they overproduce Fer2, confirming the hypothesis of its protective role. They discovered abnormalities of these neurons, as well as defects in movement patterns in aged mice, just as they did in the flies.

Alleles on gene

Genes can have alleles, which give different traits to different people.

In comparison with our unit, the Fer2 provides the understanding of how the molecules that make up cells determine the behavior of in this case mice and fruit flies. Each is made up of nucleotides that are arranged in a linear fashion that resides in a specific location on a chromosome. Most genes encode for a specific protein or protein segment that results in a specific characteristic or function, such as providing a protective barrier towards Parkinson’s disease.

 

 

 

Can We Genetically Modify Humans to Live on Mars?

CRISPR is a gene-editing technique that modifies the genomes of living organisms. They do this by searching for a strand of DNA and “when the target DNA is found, Cas9 – one of the enzymes produced by the CRISPR system – binds to the DNA and cuts it, shutting the targeted gene off.” CRISPR has been used to cure people of genetic diseases. Crispr

Humans have always dreamed of being able to live freely on another planet other than earth. It has been the topic of many pop culture movies throughout history. However with the use of gene editing theoretically this is possible. In a research paper written in 2016, they state that the main problems of living in other worlds would be radiation. With the use of gene-editing they’ve found that the protein named “Dsup prevented the animal’s DNA from breaking under the stress of radiation and desiccation“. It was also able to block X-ray damage by almost 40%. Lisa Nip a scientist at MIT state that “using genetic editing tools like CRISPR to actually transform our own DNA and make ourselves more able to survive in space.” This relates to our AP Bio class as we learned about genes as well as how the genes shape our traits as human. The idea of changing our genes is incredible as we always believed that it’s just how we were born and our parent’s chromosomes determined how we are, but now with CRISPR gene-editing, they can alter our DNA structure. Then through Mitosis, we are able to multiply our DNA, and eventually, all our genes are the edited version.DNA replication cy

CRISPR is rapidly advancing our research of gene-editing as it is the easiest and most reliable way to review gene-editing meaning that people are able to study it easily. This also means that scientist have easy access to it and are able to run many trials on DNA editing. Finally, there is a moral question to ask. Is it ethical to edit a person’s genes even if it helps them? Should we tamper with our human genetics? These questions aren’t very pressing as of now because we are still in the primary stages of gene-editing, however, some day these are going to be upon us. Thank You For reading let me know what you think about gene-editing down below.

A Vision For a Better Future

CRISPR is a world changing technology that is essentially used to edit genes. The discovery of CRISPR took place in the University of Alicante, Spain. Reported in 1993, Francisco Mojica was the first to characterize CRISPR locus. Throughout the 90s and early 2000s, Mojica realized that what was once reported as unique sets of repeat sequences actually shared common features, which are known to be hallmarks of CRISPR sequences. Through this finding, Mojica was able to correctly hypothesize that CRISPR is an adaptive immune system. In the year 2013, Feng Zhang, was the first scientist to successfully adapt CRISPR-Cas9 for genome editing in Eukaryotic Cells. Zhang was able to engineer two different Cas9 orthologs and he then demonstrated targeted genome cleavage in both human and mouse cells. They discovered that this system could then be used to target multiple genomic loci and could also drive homology directed repair.

CRISPR-Cas9 mode of action.png

How Does it Work?

“Clustered regularly interspaced short palindromic repeats,” also known as CRISPR, are repeats found in bacteria’s DNA. CRISPR-Cas9 was adapted by scientists from a naturally occurring genome editing system in bacteria. This bacteria captures parts of DNA from invading viruses and it uses them to create DNA segments known as CRISPR arrays. This DNA allows the bacteria to recognize and remember the virus’s. If the same virus, or a similar one, attacks again, the bacteria will consequently RNA segments in order to target the viruses DNA. After, the bacteria uses the enzyme Cas9 in order to cut the DNA apart, thus disabling the virus. Scientists in a lab will create small pieces of RNA that attach to a specific target sequence of DNA and also the Cas9 enzyme. In this process, the RNA is used to recognize DNA and the Cas9 will cut the targeted DNA. Once cut, researchers will utilize the cell’s ability to repair DNA in order to add or remove pieces of genetic material. It can also replace existing DNA with custom DNA in order to make changes.

How is it used?

CRISPR is a tool that can be used to fight cancer among other known diseases. The therapy involves making four modifications to T-cells. T-cells are cells that help fight cancer. CRISPR adds a synthetic gene that gives the T-cells a claw-like receptor. This receptor can locate NY-ESO-1 molecules on cancer cells. CRISPR is then used to remove three genes. Two of the removed genes can interfere with the NY-ESO-1 receptor and the third limits a cell’s cancer killing abilities.

Another way CRISPR is used is against Leber’s Congenital Amaurosis(LCA). LCA is a family of congenital retinal dystrophies that results in vision loss. Patients tend to show nystagmus, sluggish pupillary responses, decreased visual acuity and photophobia. The CRISPR trial focuses on one gene mutation that causes a severe form of degeneration. It is said that this mutation creates somewhat of a “stop sign,” and RNAs will target sequences on either part of the stop sign. The Cas9 enzyme will then cut them out, allowing the DNA to then repair itself.

iDNA

DNA is often referred to as “storing genetic code” or “data”. Information of sorts. While this is true, it is a bit different from data when referring to it in layman’s terms; data is often associated with the internet and computers. However, the line creating this barrier of difference is becoming very blurred. A study at the Beckman Institute of Science and Technology claims that DNA and its double helical structure can be used to store anything; including virtual media.

Though DNA is microscopic in size, its ability to store information is colossal. According to Kasra Tabatabaei, a researcher who helped conduct the study, “Only one gram of DNA would be sufficient” to store the several petabytes of data that are created from the internet each day. To say that this is staggering would be terribly understated. Furthermore, DNA is quite durable. It has a longevity to it that is rivaled by few other mechanisms on the planet. The material can last for thousands of years without severe damage to its ability to store information as it’s supposed to. There is also little competition with DNA when it comes to abundance. Due to the fact that there is DNA present within each living thing, there is quite a lot, to say the least. This makes it a very sustainable source of storage, as the odds that there will be a shortage is extremely unlikely.

Of course DNA has a large capacity but it seems almost necessary to expand upon it in order for the material to truly be able to slay the informational beast that is the internet. DNA already has 4 naturally occurring chemicals; Adenine,Guanine, cytosine and Thymine, that allow for it to have such capacity. To allow for its capabilities to transcend adequacy, the researchers added seven artificial nucleases. To find which would work, they experimented with “77 different combinations of the 11 nucleotides”. This change expands DNA’s capabilities tremendously, as it opens doors for a much larger range of data that can be stored.

The internet is boundless. Where technology takes the human race next is still largely unknown. However, none of it can be done without data, and the future of data storage may be exactly where it started.

 

 

CRISPR Tomatoes Help You De-Stress

Tomato jeFor the first time, genome-edited food is being sold on the open market. A recent article published on December 14th, 2021 outlines how CRISPR-Cas9 technology has been used to create genome-edited food. Consumers in Japan have been able to purchase genetically edited Sicilian Rouge tomatoes through the Tokyo-based company, Sanatech Seed. These genetically edited tomatoes have been altered to have high amounts of y-aminobutyric, aka GABA. 

In Japan, consuming GABA is very popular. It is supposed to lower blood pressure and promote relaxation. It does so through reducing the excitement of neurons in the nervous system. GABA is an inhibition neurotransmitter in the nervous system.

To test its audience, in May 2021 Sanatech first sent seedlings for genome-edited tomatoes to 4,200 home gardeners in Japan. Because of the positive feedback and high demand, Sanatech started selling tomatoes to the general public.

The tomatoes are altered through CRISPR-Cas9 genome editing. CRISPR has successfully been used to alter foods, such as making mushrooms that don’t brown, or soybeans that are tolerant to drought. Although many foods have been regulated, these tomatoes by Sanatech are the first to be commercialized.

CRISPR Cas9 technologyCRISPR is a technology that can be used to edit the genes of prokaryotic organisms like archea and bacteria. CRISPR is a way of finding a specific sequence of DNA in a cell, and then altering that DNA. CRISPR-Cas9 (pictured to the right) is the enzyme which finds and binds with specific DNA strands complementary to the CRISPR sequence.

DNA simple2DNA is a polymer which carries the genetic instructions for an organism. It is made up of two strands of bases (two polynucleotide chains) which compliment each other. Each base in a strand of bases can be one of four nucleotides, adenine, thymine, guanine, and cytosine. One nucleotide, or base, on one side of the DNA double helix matches with the corresponding base on the other side of the DNA to form a base pair. Adenine nucleotides must match with thymine, and guanine must match with cytosine.

GRNA-Cas9Sanatech increased GABA in the tomatoes by altering GABA’s metabolic pathway, aka the GABA shunt. They first inserted a strand of guide RNA along with the enzyme CRISPR-Cas9. This guide RNA is a strand that compliments the part of the DNA strand Sanatech wishes to disable: the gene that encodes CaMBD (calmodulin binding dominant). The RNA strand attaches, and the enzyme CRISPR-Cas9 cuts the DNA sequence Sanatech wishes to remove out. Disabling the gene that encodes CaMBD increases the enzyme glutamic acid decarboxylase’s activity. This enzyme catalyzes the decarboxylation of glutamate to GABA, raising GABA levels.

Increasing GABA levels is said to be a healthy way to decrease stress and lower blood pressure, and people around the world love being able to do so through eating everyday foods, such as tomatoes. People are also more accepting of these genome altered tomatoes because they have been edited specifically by CRISPR, which is a pretty trusted and well known form of gene editing technology. CRISPR technology has, and will, change the world by giving humans the power to alter and change DNA.

Instead of Bringing Back Dinosaurs, These Scientists are Bringing Back the Extinct Christmas Island Rat

Majestic dinosaurs and mammoths on our planet both underwent extinction millions and millions of years ago. The Christmas Island rat? In 1908. De-extinction techniques, also known as resurrection biology, garnered popularity within the science world in the 1990s. The Encyclopedia Britannica defines it as, “the process of resurrecting species that have died out or gone extinct.” Here is how these scientists are attempting to bring back a rat species that you have probably never heard of, and what that can mean for the future.

De-extinction using CRISPR gene-editing

 

File:MaclearsRat-PLoSOne.png - Wikimedia Commons

path of extinction of the Christmas Island rat

The process of de-extinction with the Christmas Island rat is driven by the method of CRISPR gene-editing, which allows for the genome of organisms to be modified, or edited, meaning that an organism’s DNA can be changed by us humans. This allows for genetic material to be added, removed, or modified at specific locations said genome. The idea behind the de-extinction of an animal through CRISPR gene-editing is to take surviving DNA of an extinct species and compare it to the genome of a closely-related modern species, then use CRISPR to edit the modern species’ genome in the places where it differs from the extinct one. The edited cells can then be used to create an embryo implanted in a surrogate host.

CRISPR thought to be “genetic scissors”

Thomas Gilbert, one of the scientists on the team of this project, says old DNA is like a “book that has gone through a shredder”, while the genome of a modern species is like an intact “reference book” that can be used to piece together the fragments of its degraded counterpart.

What is the difference between a genome and a gene?

File:Human genome to genes.png

Gene depicted within genome

Genes, a word you are most likely familiar with, carry the information which determines our traits, or features/characteristics that are passed on to us from our parents. Like chromosomes, genes come in pairs. Each of your parents has two alleles of each of their genes, and each parent passes along just one to make up the genes you have. Genes that are passed on to you determine many of your traits, such as your hair color and skin color. Known dominant traits are dark hair and brown eyes, while known recessive traits are blonde hair and blue or green eyes. If the two alleles that you receive from your parents are the same, you are homozygous for that gene. If the alleles are different, you are heterozygous, but you only express the dominant gene.

Each cell in the human body contains about 25,000 to 35,000 genes, and genes exist in animals and plants as well. Each gene is a small section of DNA within our genomes. That is the link between them, and they are not the same.

Is this possible? Can we really bring back the dead?

Reconstructed image of the extinct woolly mammoth

See, CRISPR gene-editing itself is of great interest for having shown promising results in terms of human disease prevention and treatment for diseases and single-gene disorders such as cystic fibrosishemophilia, and sickle cell disease, and shows promise for more complicated illnesses such as cancer, HIV infection, and mental illness–not so much with de-extinction. Here’s a simple diagram displaying the process.

File:Crispr.png

In this scenario, it is not looking very likely that these rats can come back. Gilbert and his team of 11 other scientists, through extensive processes and attention to small-detail, have in total reconstructed 95% of the Christmas Island rat genome. While 95% may be an A on a test, in regards to genomes, that 5% is crucial. In this case, the missing 5% is linked to the control of smell and immunity, meaning that if we were to bring this animal back, it would lose key functionality. Gilbert says 100% accuracy in genome reconstructing of this species is “never” going to happen.

The success of de-extinction is quite controversial in itself. Restoring extinct species can mean an increase in biodiversity and helping out our ecosystems which are suffering greatly from climate change.  However, research also suggests it can result in biodiversity loss through possibly creating invasive species (yes, I wrote this) or for other reasons.

While the science is interesting, the reality of the unlikeliness of de-extinction becoming a normal and official process is kind of dream-crushing. Who knows, maybe as technology advances, hopefully, we can make all of this happen without harmful side effects, aid our ailing ecosystems, and visit some mammoths on a safari vacation!

Away With Treadmills and Low Carb Diets: Is CRISPR the New Hack For Fat Loss?

Are you sick and tired of spending all of your time running on the treadmill and eating restrictive diets? Are you looking for a way to hack fat loss without ruining your way-of-life? Look no further than CRISPR gene-editing!

In humans, stubborn body fat can be attributed to either white or brown fat. Brown fat, specifically, is used in humans primarily for insulation, and can be tapped into when we are cold or need to ramp up our metabolism to generate heat. This fat is caused by a caloric surplus in humans, and is burned off by engaging in caloric deficit. However, in mice studies conducted by Steven Romanelli, Ormand MacDougald, and colleagues, CRISPR gene-editing offers promising results regarding the topic of brown fat loss in humans. CRISPR-Cas9 Editing of the Genome (26453307604)

But what exactly is CRISPR gene-editing? CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeat, gene-editing entails organizing short, palindromic DNA sequences of bacteria. These DNA sequences are surprisingly important in the immune function of these bacteria and other microorganisms, making CRISPR an incredibly promising and innovative tool in science research. 

Bacteria have short sequences of variable DNA called “spacers” in between CRISPR DNA sequences. This DNA helps protect the bacterium from reinfection from viruses. If any virus were to attack the bacterium, the CRISPR DNA sequences would cut up that viral DNA matching any spacer within the genetic code of the bacterium, preventing it from reinfection. 

CRISPR gene-editing works by processing invading viral DNA into short fragments that are inserted into the CRISPR DNA as spacers. Then, CRISPR replicates and spacers in the DNA of the bacterium experience transcription, in which DNA becomes RNA and CRISPR RNAs. These CRISPR RNAs help bacteria kill viruses, as they match the exact DNA as the viral DNA attacking the bacterium. 

In mice experiments conducted by Romanelli, MacDougald, and colleagues, has used CRISPR gene-editing to have an enzyme named Cas9 break strands of DNA and a single piece of RNA to be packed into a harmless virus cell that will be delivered into cells in the study, which are brown fat cells in this case. This process has shown to delete several genes, namely the UCP1 gene in mice, that allows brown fat to exist and create heat. However, the mice in the study did not die when exposed to cold environments. They were able to survive despite a huge loss in brown fat. 

Accordingly, using CRISPR gene-editing as a tool for brown fat loss in humans provides incredibly promising results. It is certain that, once CRISPR gene-editing becomes available for use in the reduction of brown fat in humans, I will no longer be using the treadmill as my mode of fat-burning and shift toward this method instead.

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