BioQuakes

AP Biology class blog for discussing current research in Biology

Category: Student Post (Page 1 of 75)

Ants Play Dead?

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On May 30, 2023

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Ants are known for their amazing survival strategies, from building complex colonies to working together to gather food. However, researchers have discovered a new survival strategy used by ants on Kangaroo Island in Australia: playing dead. In a recent study, published in the journal Ecology, researchers found that ants on Kangaroo Island would freeze and stop moving when they sensed a predator nearby, effectively playing dead to avoid being attacked. This strategy, known as thanatosis or “playing dead,” has been observed in other insects, but this is the first time it has been documented in ants. The researchers studied two species of ants on Kangaroo Island: the meat ant (Iridomyrmex purpureus) and the bull ant (Myrmecia pyriformis). They found that when the ants were exposed to potential predators, such as spiders or lizards, they would freeze and remain motionless for up to 15 minutes. This behavior appeared to be a successful defense mechanism, as the predators did not attack the ants while they were in this state. The researchers also discovered that the ants used chemical signals to communicate with one another during this process. When a predator was detected, the ants would release a chemical signal that alerted other ants to play dead as well. This allowed the entire colony to effectively avoid being attacked by predators. This discovery sheds light on the complex and sophisticated survival strategies of ants, and raises questions about how other species may have evolved similar behaviors to avoid being preyed upon.

Portrait of an ant, profile view

While the behavior of “playing dead” may be new to ants, it is not uncommon in other species. Many animals have evolved this strategy as a way to avoid predators. Here are a few examples: Opossums are well-known for their ability to play dead. When they sense danger, they will fall to the ground and remain motionless, with their tongue hanging out and their eyes closed. This behavior can last for several minutes, fooling predators into thinking they are dead and leaving them alone.  Some species of snakes, such as the hognose snake, will play dead when threatened. They will roll onto their back, open their mouth, and emit a foul-smelling odor. This behavior can deter predators from attacking them. Some species of fish, such as the threespine stickleback, will “play dead” by floating upside down when they sense danger. This can make them appear unappetizing to predators, and increase their chances of survival. Species may evolve to play dead as a survival strategy to avoid being preyed upon by predators. By appearing lifeless, an animal may fool a predator into thinking that it is not worth attacking, or that it has already been killed. This can provide the animal with an opportunity to escape, or to wait until the predator moves on before resuming its normal activities. Playing dead can be particularly effective when an animal is confronted by a predator that relies on movement or other cues to detect prey. By remaining still and appearing lifeless, the animal may be able to avoid being detected altogether. In addition, playing dead can be a low-cost defense mechanism that does not require the animal to expend a lot of energy or risk injury in a fight with a predator. The evolution of the “playing dead” strategy is likely a response to the pressure of predation and has allowed many species to survive in environments where they might otherwise be vulnerable to attack.

The discovery of ants “playing dead” on Kangaroo Island is a fascinating insight into the survival strategies of these insects. It highlights the complexity and sophistication of ant behavior and raises questions about how other species may have evolved similar strategies to avoid predators. As we continue to study the behavior of animals, we may uncover even more surprising and innovative survival strategies.

Gene Editing Used to Eliminate Invasive Rodent Species’ on Islands

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On May 26, 2023

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Species of Invasive House Mice have been not just a nuisance, but potentially dangerous and damaging on islands for hundreds of years. These house mice can be dangerous, as they have the potential to spread diseases by getting into food stores or biting humans, to cause asthma or allergy flare ups, and to bring unwanted insects such as fleas, ticks, or  lice into a home. Scientists have been looking for a way to remove these invasive pests from homes throughout time, and to no avail. Now, they have found a new way to eliminate entire populations of these pests at a time in a mere 25 years. 

Mouse white background

With the emergence of DNA editing technology, scientists have found  a way to edit the mice’ DNA so that a certain chunk of the edited DNA is inherited way more often than the average trait. This lab-created trait is called a gene drive, which had in the past been used to successfully reduce many pesky populations of insects before, but had not been proven effective in mammals. To fix this issue, scientists decided that they most discover more about the haplotypes, which are “naturally occurring group(s) of genes that gets passed on as a unit during replication” within house mice. They discovered that the t-haplotype within house mice get passed on to offspring 95% of the time, instead of the usual percentage of 50%. The editing of this t-haplotype was found to be very favorable. This haplotype evolved naturally within these house mice, meaning that will continue to be present in the wild, and there is no projection of resistance to this haploytpe being found anytime soon. Another reason why the editing of this gene sequence is favorable is that it is only present in the invasive species of house mice, meaning that it will not effect other noninvasive species

 

Now the only question is, how will scientists change this haplotype? Well, as CRISPR technology is emerging and evolving, it has been found as the obvious tool to use to edit this gene. Molecular Biologists have used CRISPR to edit the mice’ DNA to add the CRISPR tool into the t-haplotype. There are two affects of this change, when male mice with a heterozygous genotype of the edited gene mate, the CRISPR genes inserted will cause any baby female mice created to be infertile. The other effect of this genetic change is that males with the homozygous genotype of the edited gene will be sterile.

CRISPR logo

Now you might be asking, “has this format gene editing to eliminate the population of the invasive house mice actually been proven effective in any way?” Well, the answer to that is complicated, as scientists have not yet properly tried it out on any island populations. They have used computer simulations to test their hypothesis, finding that in the simulation that after adding 256 mice with the altered gene into the population, the island population of this mouse would go extinct within 25 years. Scientists have still only tested the changing of the t-haplotype within these mice in labs, and have not yet tested the use of CRISPR to effectively damage genes needed for fertility in the house mice. More testing must be done to effectively ensure that this method of eliminating the species is effective, and so we might have to wait some years to begin the overall mission. Overall, scientists are hoping to find a way to eliminate populations of invasive species such as the house mouse in timelines smaller than 25 years,  and many are looking to the future of CRISPR technology as the true way to achieve this goal.

A New Approach to Wound Care

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On May 7, 2023

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Researchers at Linköping University in Sweden have made an incredible contribution to the field of medicine, specifically in wound care and infection detection that does not interfere with the patient’s healing process.

In medicine, wounds are typically treated with a dressing, which is changed often to avoid infection. In order to detect infection, healthcare providers have to frequently open the wound’s covering, which can be painful and can potentially disrupt the healing process. Additionally, each time the wound is opened, the risk of infection is increased. The researchers were alarmed by this issue, and developed a wound dressing comprised of nanocellulose that has the ability to display early signs of infection without further tampering with the wound or lifting the dressing. Daniel Aili, a professor involved in the study, has confidently stated that “being able to see instantly whether a wound has become infected, without having to lift the dressing, opens up for a new type of wound care that can lead to more efficient care and improve life for patients with hard-to-heal wounds. It can also reduce unnecessary use of antibiotics.”

The new wound dressing is made of a tight mesh nanocellulose material, which prevents bacteria and other harmful microbes from entering the wound. However, the mesh-like material allows airflow in, which is critical in the wound healing process. However, if the wound does become infected, the nanocellulose dressing will display a shift in color, notifying healthcare providers that the wound needs care. pH also plays a major role in this creation. Wounds that are not infected maintain a pH value of about 5.5. If an infection occurs, the wound starts to become basic and can increase to a pH value of 8, or higher. The increase in pH occurs because the wound’s bacteria shift their pH to properly fit their optimal growth environment. As we learned in AP Biology class, bacteria and enzymes have an optimal pH level to grow and function. If this level is not maintained, they cannot function properly. So, the bacteria increase their pH in response to infection if the optimal level is compromised. This elevated pH level in the wound can be detected by the nanocellulose dressing before any physical signs of infection.

pH Value Scale

In order to make the nanocellulose display infection with an elevated pH value, the researchers used bromthymol blue, a dye that reacts to a change in pH value. The bromthymol blue shifts from yellow to blue if the pH value increases past 7. The material of the bromthymol was then able to be combined with the dressing material without ruining the nanocellulose. As a result, the researchers successfully developed a safe-to-use, noninvasive wound dressing that will display a blue color if an infection occurs.

Bromothymol blue colors at different pH levels

 

Ethical and Scientific Limitations of CRISPR Gene Editing

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On May 7, 2023

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The Third International Summit on Human Genome Editing issued a closing statement a few weeks ago calling for a pause on human genome editing – not permanently as some activists had hoped on ethical grounds, but instead for the near future because the technology is not currently sufficiently advanced as to ensure success. Gene editing involves editing embryos outside the womb and then implanting them to establish pregnancy. In addition to the numerous ethical concerns, such as a pathway to eugenics that the technology might lead to, the summit decided that the risks are simply too great at the present time.

CAS 4qyzThis is because the edits made can result in unintended – and sometimes dangerous – consequences for the embryo that traditional DNA screenings may not pick up on. Gene editing works by unraveling the double helix with helicase (just like in DNA replication), cutting the DNA strand with an enzyme, and then having the cell’s own mechanisms, such as primase and DNA polymerase, combined with the new “blueprint” for DNA,  tell the cell the order the nucleotides are placed in and complete the double helix again to form a complete, but modified, DNA strand. However, sections of DNA can be permanently lost or mistranscribed in the process, resulting in genetic disorders or cell malfunction, including cancers. These are similar to the risks that occur during DNA replication and the general life of the cell, but are significantly more likely to occur. Furthermore, mosaicism, often seen on small levels like calico cats (where different cells receive different activated genes than others), can occur on a massive scale, where some cells receive edits and others don’t, leading to health problems down the road for the embryo, if it survives at all.

As a result, the summit, composed of the world’s leading experts in CRISPR technology and research, decided to enact a pause on human genome editing for now. As the technology advances and is made safer, however, they claim that they will reconsider it. Until then, the use of CRISPR is limited to other organisms, such as plants and lab animals.

Are Fish Mind Readers?

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On April 30, 2023

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Several inherited behavioral mechanisms in humans and animals are deeply rooted in prehistoric animals. Some of these mechanisms, for example, fear, as well as the ability to fall in or out of love, humans have possessed for thousands of years and are found in our ancient genetic pathways. Although scientists are hesitant to attribute human-like feelings to animals, it has been proven that many animals, including fish, have moods. A recent study published in the journal; Science, demonstrated that fish can identify fear in other fish. This ability is regulated by the hormone oxytocin. This is the same “brain chemical” that controls the feeling of empathy in humans. The researchers discovered that fish could detect fear in other fish by deleting genes linked to producing and absorbing oxytocin. These fish became fearful as well.

Zebrafisch

Deleting genes involves various techniques, which is specific to the organism and the purpose for the deletion. Generally, there are two main approaches for deleting genes: Targeted Deletion and Random Deletion. In Targeted Deletion, very specific regions of the DNA sequence are removed or replaced to eliminate the gene of interest. Random Deletion occurs when large sections of the DNA sequence are randomly deleted in the hope of removing the gene of interest. The research focused on zebrafish brains; a small tropical fish often used for such research. The fish used in this experiment became practically antisocial and failed to change their behavior and could no longer detect when other fish were anxious. Scientists then injected oxytocin into some of the altered fish, and the fish’s ability to sense and react to the feelings of other fish was re-established. Fish behave just like humans in that they respond to other individuals being frightened. During this experiment, fish were seen paying considerably more attention to previously stressed or frightened fish.

Oxytocin is a hormone that plays a key role in social bonding and emotional communication in mammals, including humans. It is produced in the hypothalamus and released into the bloodstream by the pituitary gland. One of the primary functions of oxytocin is to produce social bonding between individuals. It has been shown to increase trust and cooperation between people, and it is often referred to as the love hormone because of its role in promoting feelings of love and intimacy.

Oxytocin with labels

Hans Hofmann, an evolutionary neuroscientist at the University of Texas at Austin, said that it’s less of a “love hormone” and more of a “scale” that helps fish recognize the most noticeable social situation. This recognition activates neural circuits that may make one run from danger or engage in behavior that results in mating. This ability is essential to certain species of fish survival.

CRISPR-Cas9 – The Human Editor

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On April 30, 2023

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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.

Can We Alter Mammals Social Behavior Using CRISPR Gene Editing Mechanisms?

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On April 30, 2023

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At Georgia State University a team of researchers led by professor H. Elliott Albers and Professor Kim Huhman put gene editing mechanisms to the test to determine if it was possible to alter hamsters behaviors. The hamsters that were utilized in this experiment were Syrian hamsters. These hamsters have been extremelGolden hamster front 1y important in many scientific experiments that look into social behaviors, aggression and communication. Furthermore, hamsters are widely used in scientific research due to the fact that their social skills resemble most similarly to humans.

 

In this experiment, professor H. Elliott Albers and Professor Kim Huhman utilized CRISPR-Cas9 technology to deactivate neurochemical signaling pathways that play a major part in controlling mammalian social behaviors. The regulators of the social phenomena that controls pair bonding, cooperation, social communication, dominance and aggression are the hormone vasopressin and the receptor it acts on, Avpr1a. VasopressinSek

After the gene editing and the observation of the hamsters were complete, the researchers were shocked by their unexpected results. As stated by Professor H. Elliott Albers,  he “anticipated that if we eliminated vasopressin activity, we would reduce both aggression and social communication. But the opposite happened.”

Instead of reducing the hamsters’ aggression and social communication, the absence of the receptor that activates the vasopressin led the hamsters to demonstrate increased levels of social communication behaviors than when observed prior to the gene editing. Furthermore, it was observed that the differences in opposite sex aggression were removed. Both the male and female hamsters showed aggression towards other same-sex hamsters.  

This shocking finding led the researchers to a different conclusion than foreseen. Because it is known that vasopressin correlates with the increase of social behaviors, it can be concluded that the Avpr1a receptor is inhibitory. 

Moreover, confirming this study done at Georgia State University, another study published in the Proceedings of the National Academy of Sciences, finds that that eliminating the Avpr1a receptor in hamsters windes up deactivating the vasopressin’s action on the receptor, therefore changing the social behavior of the hamsters drastically in ways one would not expect.

Overall, Professor H. Elliott Albers contends that this study is of extreme value as it helps researchers understand the“neurocircuitry involved in human social behavior and our model has translational relevance for human health. Understanding the role of vasopressin in behavior is necessary to help identify potential new and more effective treatment strategies for a diverse group of neuropsychiatric disorders ranging from autism to depression.”

Connection to AP Biology 😀

This study is connected to our AP biology class as we have learned about regulation of gene expression. Without the presence of the Avpr1a receptor, the vasopressin has no way to be mediated, thus enhancing its social behavioral effects. And with the presence of the Avpr1a receptor, the vasopressin is still active, however, muted. 

Do Eating Times Lesson Your Chances of Developing Type 2 Diabetes?

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On April 30, 2023

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On April 6th, 2023 an experiment  to test how we can reduce the chances of developing type 2 diabetes was conducted by the University of Adelaide and published on Science direct.  This experiment  compared  two different eating habits, one was an intermittent fasting diet and the second was a lessened-calorie diet. The purpose was to see which diet was more effective in limiting the chances of type 2 diabetes in people who are more likely to develop it.

 

Type 2 diabetes occurs when a body’s cells doest effectively use and make insulin. Type 2 diabetes also effects people’s blood glucose levels. In biology class, we have learned the importance of insulin. Insulin is an essential hormone in our bodies. It helps our bodies turn food into energy and controls our blood sugar levels. Without insulin, our blood glucose levels can become dangerously high. About 60 percent of type 2 diabetes cases could be helped with changes to diet and lifestyle.

Insulin glucose metabolism

It was discovered that people who followed the intermittent fasting diet, eating between 8am and 12pm for three days had a higher tolerance to glucose after 6 months and had lower chances of developing type 2 diabetes than those on a low calorie diet. It was also revealed that participants who were intermittent fasting had more sensitivity to insulin and had decreased blood lipids compared to those on a low calorie diet. As we learned in biology class high insulin sensitivity allows the cells of the body to use blood glucose more effectively, reducing blood sugar.

 

The conclusion of this study implies that meal timing and fasting have many health benefits to reduce the chance of type 2 diabetes and other health issues. This is very intriguing to me because I have heard many mixed opinions from friends and family if eating times do have any type of effect on our health!



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

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On April 30, 2023

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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?

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On April 30, 2023

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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.

From Bacteria to Biotech: The Surprising Similarities in Immune Systems

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On April 30, 2023

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Bacteria have always been considered harmful and something to be avoided, but according to a recent study by the University of Colorado Boulder, bacteria might just hold the key to unlocking novel approaches to treating various human diseases. The research reveals that bacteria and human cells possess the same core machinery required to switch immune pathways on and off, meaning that studying bacterial processes could provide valuable insights into the human body’s workings. Moreover, researchers found that bacteria use ubiquitin transferases – a cluster of enzymes – to help cGAS (cyclic GMP-AMP synthase) defend the cell from viral attack. Understanding and reprogramming this machine could pave the way for treating various human diseases such as Parkinson’s and autoimmune disorders.

CRISPR, a gene-editing tool, won the Nobel Prize in 2020 for repurposing an obscure system bacteria used to fight off their own viruses. This system’s buzz reignited scientific interest in the role proteins and enzymes play in anti-phage immune response. Aaron Whiteley, senior author and assistant professor in the Department of Biochemistry, said that the potential of this discovery is much bigger than CRISPR. The team discovered two key components, Cap2 and Cap3 (CD-NTase-associated protein 2 and 3), which serve as on and off switches for the cGAS response. Understanding how this machine works and identifying specific components could allow scientists to program the off switch to edit out problem proteins and treat diseases in humans.

CAS 4qyz

This discovery opens new avenues of research as bacteria are easier to genetically manipulate and study than human cells. Whiteley said that the more scientists understand about ubiquitin transferases and how they evolved, the better equipped the scientific community is to target these proteins therapeutically. The study provides clear evidence that the machines in the human body that are important for just maintaining the cell started out in bacteria, doing some really exciting things. The ubiquitin transferases in bacteria are a missing link in our understanding of the evolutionary history of these proteins. Thus, this research shows the importance of studying evolutionary biology, and how it can provide valuable insights into human health.

The study highlights the similarities between bacteria and human cells in terms of their immune response, specifically, describing how cGAS (cyclic GMP-AMP synthase), a protein critical for mounting a downstream defense when the cell senses a viral invader, is present in both bacteria and humans. This similarity suggests that portions of the human immune system may have originated in bacteria, a concept explored in the evolutionary biology unit. In this past unit, we discussed the origins of life, and how all life originated from a simple bacteria cell. This bacteria cell, though many many many repeated cycles of evolution and natural selection allowed for variation within its species and the formation of new species through the processes of speciation.

Exploring Multicellularity on Planet Earth

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On April 30, 2023

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Billions of years ago, it is believed that some event—whether it be a meteor crash-landing on planet Earth, or a lightning strike creating amino acids and proteins—sparked the origin of life. From there, single celled organisms, like bacteria, made their home on our planet; and eventually, unicellularity became multicellularity. The reason behind this phenomenon, though, is what continues to be unknown. What really is the point of the majority of organisms being compiled of millions of cells, and not just one? 

Scientists at Lund University strive to answer this question. In order to do this, green algae from Swedish lakes were taken into their lab, as this specific botanic organism is extremely suitable for the goals of this experiment. For one, it is a eukaryote, which will allow researchers to gain insight on the evolution of all eukaryotes, in general. They are widely studied in the study of evolution because of their very apparent evolutionary process. There is a great amount of data to reveal that all eukaryotes have common ancestry, including the presence of double membranes, circular genomes, ribosomes, linear chromosomes, and more in all eukaryotic organisms. 

Another reason as to why green algae is such an appropriate fit for an experiment exploring the evolutionary characteristics of unicellular and multicellular organisms is that it is sometimes unicellular, other times starts off this way but then becomes multicellular, and the remaining types are always multicellular. This makes green algae the perfect candidate for an experiment such as this. Data from the environments of all these different cellularly-dense types of algae was collected and compared to one another. While doing this, scientists looked out for the adaptations promoted by the environments the algae were in, what conditions exactly promoted unicellularity or multicellularity, and why the form of life it encouraged was beneficial to the organism. 

Previously, it had been theorized by evolutionary biologists that multicellularity benefited organisms that utilized it, but the Lund University research team was shocked at the results they found from analyzing the environmental data of the algae: there were no benefits of living multicellularly for these organisms. A member of the study, Charlie Cornwallis, made the following comment on the experiment’s outcomes: “I was surprised that there were no benefits or costs to living in multicellular groups. The conditions that individual cells experience can be extremely different when swimming around on their own, to being stuck to other cells and having to coordinate activities. Imagine you were physically tied to your family members, I think it would have quite an effect on you.” 

At the conclusion of the study, Charlie Cornwallis made one final statement: “The results of this study contribute to our understanding of how complex life on Earth has evolved….The next time you walk along the shores of a lake rich in nitrogen just imagine that this fosters the evolution of multicellular life.”

Green algae under a microscope

Green algae under a microscope.

Maternal Stress During Pregnancy

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On April 30, 2023

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According to researchers at the University of Cincinnati, maternal stress during pregnancy has a harmful effect on the neurodevelopment of babies. A methyl group gets added to DNA, which is called DNA methylation. This likely plays a role in it. The findings could provide new insight into how the fetal environment potentially influences neurodevelopment, metabolism, and immunologic functions. 

DNA methylation

More than 5,500 people took part in this study, which broke down into 12 different groups. The research examines financial stress, conflict with a partner, conflict with a family member or friend, abuse, and death of a friend or relative. Plus, there is a cumulative score that combines all these categories. 

Two young people demonstrating combat

They found that mothers experienced a great amount of stress during pregnancy. There was an association with DNA methylation in the umbilical cord blood, which is an epigenetic modification in the baby’s development. They found five specific locations of DNA methylation with three different maternal stressors. The three different maternal stressors were conflict with a friend or family, abuse, and death of a close friend or relative.  

Epigenetics modifications

In AP Biology, we have learned that DNA methylation causes nucleosomes to pack tightly together, which prevents transcription factors from binding to the DNA. Gene expression is the process of turning on a gene to produce protein and RNA. 

The researchers plan to further investigate and do some functional analyses to see how the genes work and how the DNA methylation affects their expression. 

 

Glow in the dark proteins???

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On April 30, 2023

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Recently scientists have discovered Glow in the dark proteins that could help diagnose viral diseases. Scientist rely on a chemical reaction using the luciferase protein, which “catalyze the oxidation of the substrate in a reaction that results in the emission of a photon”, which then causes the glow in the dark effect. The luciferase protien is then put into sensors that show a light when they find their target. Although these sensors are simple and would make point-of-care testing much easier, scientists have “lacked the sensitivity required of a clinical diagnostic test”. The gene editing tool CRISPR could provide this for them but requires many steps. According to MedlinePlus gene editing is a “a group of technologies that give scientists the ability to change an organism’s DNA“. A well known type of gene editing is called CRISPR, it is supposed to be more efficient and accurate than other genome editing methods. Scientist Maarten Merk decided to use CRIPSR related proteins and combine them with a bioluminescence technique whose signal could be detected. During testing scientists discovered that if a specific viral genome that was being tested for was present, the two CRISPR proteins would bind to the specific nucleic acid sequences and come close to each other, this would then cause the luciferase protein to shine a blue light.

AP Bio Connection

Exons are the coding regions of a gene that are translated into functional proteins. These contain the information needed for the synthesis of a specific protein. Introns are the non-coding regions of a gene that do not code for proteins. Introns are transcribed into RNA along with the exons, but they are removed from the final RNA transcript. Gene editing techniques, such as CRISPR-Cas9, rely on specific recognition of DNA sequences by the Cas9 enzyme. To achieve targeted gene editing, the Cas9 enzyme needs to be guided to a specific site in the genome using RNA molecules called guide gRNAs. gRNAs are designed to bind to a specific sequence in the genome, typically located in an exon, which is then split by the Cas9 enzyme.CRISPR logo

Genetic Variation the Savior

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On April 30, 2023

In Student Post

In the article “Genetic variation in the SARS-CoV-2 receptor ACE2 among different populations and its implications for COVID-19,” published in Nature Communications, the authors explore the genetic variation in the ACE2 receptor across different populations and its potential impact on COVID-19 susceptibility and severity. The ACE2 receptor is a key entry point for the SARS-CoV-2 virus into human cells. Its expression level and genetic variants may affect the virus’s ability to infect and replicate within the host. Therefore, understanding the genetic variation in ACE2 among different populations can provide insights into the different susceptibilities and severity of COVID-19 seen across the world. The authors analyzed genetic data from various global populations and found that there is significant genetic variation in ACE2 between populations. Specifically, they identified several ACE2 variants that are more prevalent in certain populations, including a “variant that is more common in East Asian populations” and may affect the receptor’s expression level.

Microorganisms-08-01259-g001

The authors also conducted in vitro experiments – medical procedures, tests, and experiments that researchers perform outside of a living organism – to investigate the impact of these ACE2 variants on SARS-CoV-2 infection. They found that some variants, such as the one more prevalent in East Asian populations, led to reduced viral entry and replication, while others did not significantly affect viral infection. These findings suggest that genetic variation in ACE2 may contribute to the different COVID-19 outcomes observed across different populations. For instance, the higher prevalence of the ACE2 variant in East Asian populations may explain why these populations had a lower incidence of severe COVID-19 despite being initially hit hard by the pandemic. Furthermore, the author highlights the importance of considering genetic variation when developing COVID-19 treatments and vaccines. For instance, vaccines that were designed based on the original strain of SARS-CoV-2 may be less effective against strains that have evolved to better utilize ACE2 variants prevalent in certain populations. Overall, the article sheds light on the genetic variation in ACE2 among different populations and its implications for COVID-19 susceptibility and severity. The authors’ findings show the importance of taking genetic diversity into account when studying diseases and developing treatments and vaccines, particularly in the context of a global pandemic. In our recent DNA unit in class genetic variation was one of the topics of discussion, genetic variation is extremely important for the survival of a population as there is an easier chance that the species will be able to adapt and survive in different situations. Without genetic variation, many species can die out and therefore including the topic of genetic variation in viruses like covid-19 is extremely detrimental to the survival of humans when fighting this illness.

Fighting Cancer with CRISPR

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On April 27, 2023

In Student Post

For many years the treatment of cancer has remained difficult and uncertain. Though there are many treatment methods such as chemotherapy and bone marrow transplants, these methods are never guaranteed to work. However, a teenage girl named Alyssa diagnosed with T-cell acute lymphoblastic leukemia (T-ALL) has been successfully treated with a new experimental treatment. T-ALL is a type of cancer where cancerous T-cells overpopulate healthy T-cells, leaving the patient susceptible to disease. In this form of cancer, T-cells also mistake each other as threats. CRISPR illustration gif animation 1Due to the nature of this cancer, in order for treatment to be effective, T-cells would have to appear foreign to the patient’s immune system. This is made possible through the gene editing system, CRISPR. For Alyssa’s treatment, doctors utilized and altered donated T-cells. Using CRISPR, the donated T-cells were stripped of CD7 protein, a common T-cell protein, and CD52 protein, a protein recognized by cancer treatment.  Additionally, donated T-cells received a receptor that gave them the ability to target cancerous and healthy T-cells by having the ability to recognize CD7. All of these changes were made through a process called base editing with CRISPR. During base editing, individual letters, or bases, in the T-cells’ DNA code were altered. These minor alterations have the ability to change the nature of the cell. Thanks to this new treatment, Alyssa’s cancer is now undetectable.

 

I found T-ALL cancer and its destructive nature relatable to the way that viruses take over human body cells, however, our adaptive immunity uses antigens to recognize an intruder. T-cells contain specific proteins which make them recognizable to other T-cells, including cancerous ones. T-ALL destroys the body’s own T-cells which is why this specific treatment needed to use altered T-cells that did not contain recognizable proteins. WheT Lymphocyte (16760110354)n the body is infected by a virus, memory T and B cells use antibodies, a little piece of the virus, to remember and recognize the virus if it were to enter the body again. 

 

CRISPR gene editing: The Benefits and the risks

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On April 27, 2023

In Student Post

CRISPR gene editing is a precise technique that uses the Cas9 enzyme and gRNA to modify DNA sequences in an organism’s genome. This method is inspired by a natural bacterial mechanism that protects against viruses. It can change existing genes, introduce new genetic material, and revolutionize fields such as industry, agriculture, and medicine.

CRISPR gene editing was first invented in 1987 by Ishino Etal. Scientists first hypothesized that prokaryotic cells use this method as part of their adaptive immune systems. However, this method was not elucidated until 2007. This gene-editing technique uses RNA molecules to direct the Cas9 enzyme to the precise location where the DNA strands are being cut, thus allowing genetic materials to be modified or added. To be more specific, this system relies on the enzyme’s ability to cleave DNA double helix strands at a particular location, allowing scientists to modify the DNA sequence. This technique is especially beneficial to the medicinal fields due to its specificity; it can potentially treat genetic diseases such as cystic fibrosis, Alzheimer’s, Huntington’s, Parkinson’s, or cancer by modifying the immune cells and directing them to target and kill cancer cells.

CRISPR-Cas9 Editing of the Genome (26453307604)

Despite the benefits, CRISPR also contains some serious risks. A specific protein called p53, also known as the “guardian of the genome,” helps to detect any damage in the DNA and thus; heads the cells to stop diving to prevent any mistakes. The CRISPR technique might trigger a p53 response, in which edited cells can be “tagged” as damaged and eliminated, thus reducing the efficiency of the gene editing process. However, recent research also indicates that CRISPR can lead to cell toxicity and genome instability. In addition, CRISPR may disrupt normal cell functioning, which leads to cells being unable to detect any DNA damage or extra cell division, thus increasing the risk of further mutations.

Nonetheless, CRISPR still goes deep down into our biology field as it contains molecular biology, where it goes deep down into the cells and modifies DNA sequence. However, changing an organism’s DNA sequence using CRISPR gene-editing technology could have unintended consequences such as off-target effects, incomplete editing, and unknown long-term effects such as cancer or DNA mutation if the matching went wrong.

In First, Scientists Use CRISPR for Personalized Cancer Treatment

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On April 27, 2023

In Student Post

Behold, have researchers found a groundbreaking method to fight tumors? Could genome-edited immune cells finally provide a way to defeat cancer?

In a recent clinical trial, immune cells were modified by CRISPR gene editing to recognize mutated proteins specific to tumors. When released into the body, the cells could target and kill the specific tumor cells. This cancer research utilized gene editing and T-cell engineering.

CAS 4qyz

Link to Picture

The trial involved 16 individuals who suffered from solid tumors (including breast and colon cancer). The results were published in Nature by Heidi Ledford and then presented on November 10, 2022 in Boston, Massachusetts at The Society for Immunotherapy of Cancer conference. The findings were later released in Scientific American.

According to Antoni Ribas, a co-author of the study and a cancer researcher and physician at the University of California, Los Angeles, ” It is probably the most complicated therapy ever attempted in the clinic.” He describes the process as “trying to make an army out of a participant’s own T cells.”

To begin the study, Ribas and his colleagues ran DNA sequencing on each patient’s blood sample and tumor biopsies. The goal was to identify unique mutations of the timer, but not present in the blood. Ribas notes that these mutations differ across different types of cancer, with only a few being shared. Then using algorithms, Ribas’s team predicted which mutations were the most likely to initiate a response from the T cells(a type of white blood cell that functions to notice and destroy irregular cells); however, immune systems rarely destroy cancerous tumors. With that being said, the team used CRISPR gene editing to insert designated t-cell receptors that recognized the tumor. Patients were given medication to reduce normal immune cells before the researchers infused the engineered cell.

Joseph Fraietta, who specializes in designing T-cell cancer therapies at the University of Pennsylvania in Philadelphia, describes the process as “tremendously complicated”, for some cases could take more than a year to complete in certain cases.

Each individual in the study received T cells engineered to target up to three sites, and after some time, the concentration of the engineered T cells was higher than the average T cells in the bloodstream near the tumors. A month after the treatment, five participants’ tumors had not progressed, and only 2 showed evidence of T-cell activity.

While the treatment’s effectiveness was limited, Ribas notes that a small dose of T cells was used at first and stronger doses would be proven more effective. Fraietta feels “The technology will get better and better.”

Although engineered T cells, also known as CAR T cells, were approved to treat certain blood and lymphatic cancers, CAR T cells only target proteins that are present on the surface of tumor cells, and According to Fraietta, no surface proteins have been discovered in solid tumors. Additionally, tumor cells may suppress immune responses by releasing immune-suppressing chemical signals and consuming local nutrient supplies to promote their rapid growth.

Red White Blood cells

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Researchers are hopeful to engineer T cells to not only recognize cancer mutations but also to become more active in the vicinity of the tumor. Potential techniques include ” removing the receptors that respond to immunosuppressive signals, or by tweaking their metabolism so that they can more easily find an energy source in the tumor environment,” as Heidi Ledford, writes in her article. With advances in CRISPR technology, researchers anticipate revolutionary ways of engineering immune cells in the next ten years.

In AP Biology this year, we learn about the Immune system. This topic is specifically related to the adaptive, or pathogen-specific, Immune response. T Lymphocytes, or T cells for short, are a part of the cell-mediated immune response where T-cells can identify, and kill infected or cancerous cells, while also preventing reinfecting.

The Blood Brain Barrier Can’t Block This!

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On April 23, 2023

In Student Post

University of Wisconsin-Madison Professor, Shaoqin “Sarah” Gong is ready to take on finding cures for brain disease such as Alzheimer’s and Parkinson’s disease. Gong and her colleagues strive to enable a “noninvasive, safe and efficient delivery of CRISPR genome editors” that can be used as forms of therapy for these diseases. According to MedlinePlus, there are many forms of brain disease, some caused by tumor, injury, genetics; however, Gong’s research focuses on degenerative nerve diseases. Degenerative nerve diseases can affect balance, movement, talking, breathing and heart function. The reason cures for degenerative nerve disease are difficult to create is because of the blood brain barrier. According to the American Society for MicroBiology, the blood brain barrier is a feature of the brain and central nervous system blocking the entrance of “microorganisms, such as bacteria, fungi, viruses or parasites, that may be circulating in the bloodstream”. Unfortunately, the barrier block is a very selective site that won’t let vaccines and therapies through. Fortunately, Gong’s nano-capsules with CRISPR’s genome editors point toward brain disease therapy and a cure.

 

Alzheimer's disease brain comparison

Gong’s study proposes dissolvable nano sized capsules that can carry CRISPR genome editing tools into organs. According to CRISPR Therapeutics, CRISPR technology meaning Clustered Regularly Interspaced Short Palindromic Repeats is an “efficient and versatile gene-editing technology we can harness to modify, delete or correct precise regions of our DNA”. CRISPR edits genes by “precisely cutting DNA and then letting natural DNA repair processes take over.” CRISPR targets mutated segments of DNA that can produce abnormal protein causing diseases such as degenerative nerve disease.  CRISPR works with the help of a guide RNA and Cas9. Together the complex can recognize and bind to a site next to a specific target sequence of DNA that would lead to the production of an abnormal protein. CAS9 can cut the DNA and remove a segment. As a result natural DNA pathways occur and RNA polymerase will return to rebuild and correct the mutated segment. 

via GIPHY

Consequently with the addition of glucose and amino acids the nano-capsules containing CRISPR Technology can pass through the blood brain barrier to conduct gene editing to target the gene for the amyloid precursor protein that is associated with Alzheimer’s. The topic of gene editing coincides with the Gene Expression portion of the AP Biology curriculum. In the topic of gene expressions 2 processes are emphasized: transcription (the process of making an RNA copy of DNA) and translation ( the process of making proteins using genetic information from RNA). In the CRISPR technology the editing of genes closely relates to the process of transcription. Transcription mistakes can be made which can lead to mutations, these mutations can potentially cause nonsense, missense or deletions of nucleotides ultimately producing wrong codons that would code for incorrect/abnormal proteins. However, the CRISPR technology would be able to correct these mutations in the DNA, replacing the incorrect nucleotides to correct ones and preventing the production of abnormal proteins. Fortunately, Gong’s unique nano-capsules have successfully been tested on mice, giving scientists hope that treatments and therapy for these brain diseases are coming soon and can help many.

CRISPR May Be the Cure!

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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.

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