BioQuakes – Page 2 – AP Biology class blog for discussing current research in Biology

Would you ever think that straightening your hair could risk your health? It turns out that the use of chemical hair straighteners, such as relaxers, may lead to an increase in uterine cancer in women. Until recent research, researchers believed that only ovarian and breast cancer could result from the application of chemical hair straighteners. But a recent study conducted by the National Cancer Institute proves otherwise. Many people question how these harmful chemicals are allowed in hair care products and why the FDA does not ban their use. In response to that question, hair care products are not regulated by the Food and Drug Administration. Therefore the FDA is not responsible for the safety of customers who become victims of these harmful chemicals found in their products. In addition, these products are mainly bought and used by black women, who permanently want to straighten their hair. In comparison to other women within the study, 60% of women who did use these products identified as black. As a black woman, I believe that information about what is in our hair care products needs to be studied and the research needs to be shared. With the hope that more black women can avoid harmful products such as relaxers to prioritize their health.

A study was conducted for a decade on 34,000 women to see if hair straightening products led to uterine cancer. The study did not prove a cause-and-effect relationship between products and uterine cancer. However, there was 2.41% difference between the risk factor of women who did use chemical straightening products and women who did not use chemical straightening products.

Parabens, bisphenol, formaldehyde, and metals play a key role in the increase of uterine cancer because of their reputation for disrupting the endocrine system. The endocrine system is the organ system responsible for controlling and regulating the body’s hormones. The organ system, compiled of multiple glands placed throughout the body, releases hormones into the bloodstream to control factors such as insulin, the function of reproductive organs, body growth, and energy development.

When these hormones are called upon by a cell’s receptors, which send out signals asking for specific hormones, they come in contact with the targeted cells. This process would not be possible without the cell membrane. The cell membrane is a layer that encompasses all the cell’s internal parts called organelles. In addition, the membrane serves as a barrier between what is inside and outside the cell. The importance of the cell membrane and how it transports and brings materials into the cell is emphasized in the AP Biology curriculum. At this point within the cell, the cell takes on the process of receptor-mediated endocytosis. The hormone whose need is triggered by the cell docks with a receptor. The cell membrane then engulfs the needed hormone.

In all, research about the harmful effects of chemicals in hair straightening products is alarming for women everywhere. Specifically, for the black community who’s women depend on these products more often for hair maintenance and care.

Advancing Towards a Cure for Mucolipidosis Type II

By avahesion

On October 24, 2022

Mucolipidosis type II—also known as “I-cell disease”—is a rare life-threatening condition in which the heart and abdomens become swollen, bones deform, and the patient typically does not make it past the age of 7. This lysosomal storage disease is heritable and currently incurable.

Inclusion cells are non-living substances located in the cell that are not membrane-bound. These non-living substances include glycogen, lipids, and pigments. In mucolipidosis, inclusion cells in growing fibroblasts occupy the cytoplasmic space aside the Golgi apparatus—hence the name “I-cell disease.”

Recent research reveals a new gene, TMEM251, that is defective in humans with symptoms of mucolipidosis type II. TMEM251 is crucial in enabling lysosomes to function appropriately. In AP Biology class, we covered how lysosomes are essential to various cell processes, such as digesting food and breaking down old cell parts enclosed in vesicles. Without the lysosome’s function, this waste will build up, unable to be broken down.

Several enzymes inside lysosomes digest worn-out cell parts (proteins, carbohydrates, lipids, and nucleic acids) of which the lysosome recycles. These enzymes require a signal called the mannose-6-phosphate biosynthetic pathway (M6P) in order to enter the lysosome. TMEM251 activates the M6P. When TMEM251 is defective, there is no M6P to allow the enzymes into the lysosome, thus creating an inability for the lysosomes to function

Researchers tested the link between defective TMEM251 and type II mucolipidosis symptoms by knocking this gene out in zebrafish, ultimately yielding defects in the zebrafish’s abdomen, heart, and skeletal development. These symptoms align with those of mucolipidosis type II in humans, concluding the existence of a relationship between TMEM251 and the disease.

To treat children with mucolipidosis type II, the researchers propose the idea of “enzyme replacement therapy.” They hypothesize that by supplying enzymes containing M6P modification to TMEM251-deficient cells, the enzymes will be able to filter into the cell through endocytosis, delivering them to the malfunctioning lysosomes. Isn’t that neat? In AP Biology class, we learned that endocytosis occurs when the substances surrounding the cell membrane are transported into the cell. Through the process of receptor-mediated endocytosis, specific ligands (i.e. enzymes) bind to receptors that match their shape.

I believe that enzyme replacement therapy would efficiently treat mucolipidosis in humans, and encourage further study in this area to seek treatment for this deadly disease that robs young children of their bright futures. Would you support further research in this area? Please feel free to share your thoughts in the comments!

Why is it That I Tend to Get More Mosquito Bites Than All Of My Friends?

By avzuckerbrot

On October 21, 2022

Have you ever wondered why some people get more mosquito bites than others? To your surprise it is not because they have “sweet blood,” there is actually an odor that our body produces, some more than others, that attracts mosquitoes. Jason Arunn Murugesuu, a reporter for the New Scientist, recently published an article regarding research conducted by Maria Elena De Obaldia at Rockefeller University in New York. In this study, they posed the question of whether body odor affects mosquitos’ attractiveness to an individual.

In this experiment, there were two boxes that contained nylon fabric swatches that were worn by two different individuals, and in each box lay the fabrics. The third box held female Aedes aegypti mosquitoes. The researchers tested which box most attracted the Aedes aegypti. After numerous trials, it was found that their results stayed persistent.

It was determined that nylon fabrics that most attract mosquitoes were worn by individuals that happened to have a higher concentration of carboxylic acids present in their body odor. The bacteria on our skin produce carboxylic acids, which are a result of sebum, a substance composed of lipids that lie on the skin’s surface as a protective barrier.

Sadly, one cannot necessarily prevent the amount of carboxylic acids our body produces to limit the number of mosquito bites. According to De Obaldia, our body’s odor comes down to our genetics, skin microbiome and diet. It is unlikely for body odor to be altered based on mild changes, such as a temporary change in diet. Skin bacteria live deep down in our pores, so it is unlikely that they can be removed, which is why they are a significant factor in our body odor.

Moreover, De Obaldia repeated the study but replaced the Aedes aegypti mosquitoes with genetically modified mosquitoes that have a weakened ability to sense acids. After this experiment was conducted, the researchers found that some of the mosquitoes had a lessened preference for nylon fabrics that contained a higher concentration of carboxylic acids.

This study concludes that mosquitoes do, in fact, have a preference as to who they are choosing to bite. Scientists now have a reasonable solution to decrease mosquitoes’ preference for humans and spread diseases, which is to genetically modify the mosquitoes.

Now, after reading this, if you notice that you are getting more mosquito bites than all of your friends, it is possible that you have a higher amount of carboxylic acids present in your body odor.

Are Skittles Toxic from Titanium Dioxide?

A lawsuit came out in recent months that made claims of the chemical titanium dioxide, a toxin known to scientists being found in a popular candy, Skittles. A consumer filed a suit against Skittles manufacturer, Mars, for titanium dioxide is now a banned chemical a ccording to the European Union. However, in many countries, such as the United States and Canada, titanium dioxide is still considered to be safe to consume. There still needs to be regulations put about the amount of the chemical that can be found in food, but in limited amounts, many think it is relatively harmless in small doses. Toxicologists who are studying the chemical found research indicating that using chemicals. Agnes Oomen, a senior scientist at the Netherlands’ National Institute for Public Health and the Environment, told Scientific American that saying we’re not certain that it’s safe is very different from saying it’s unsafe.” When the European Union placed the ban on titanium dioxide, they were just being overly cautious.

What is Titanium dioxide? It is a white powder that is used as a pigment in many candies and other consumer items, such as makeup and paints. Titanium dioxide is good at scattering visible light. This causes products that contain the chemical a brighter and more vibrant color. What raised skepticism for consumers was the fact that Titanium dioxide is also used in many sunscreens because it is an efficient barrier to ultraviolet light.

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The United States Food and Drug Administration had deemed the chemical safe in food, but it still must be a regulated amount of not being able to be more than 1% by weight of the product. In contrast, Europe is going through a period of “great detox”, for the European Food Safety Authority (EFSA), an organization that researches the risks of foods, is banning many chemicals previously found in products. In 2021, EFSA found in a report that titanium dioxide can be genotoxic. That means the drug could alter genetic materials such as DNA. This possibility is what causes the EFSA to ban the use of titanium dioxide in products. Oomen participated in making the report about titanium dioxide saying the decision “is on the cautious side.” The European Union’s decision to ban the chemical was based on a slight possibility that titanium dioxide is harmful, for there has been no evidence so far that proves it could cause people any significant dangers.

Saji George, from McGill University, said researchers are “ missing other big parts of the picture. There are so many other things that could be happening with small, consistent amounts of titanium dioxide in a diet over a long period of time.” Along with his colleagues, they recently discovered that the chemical could amplify allergies to some proteins in foods, making titanium dioxide still a concern. George also mentioned that the studies done on titanium dioxide were done mainly on rates, not humans. “We don’t know how titanium dioxide could enhance certain diseases—for example, inflammatory bowel disease in people with preexisting conditions,” he states. This just goes to show there is still a lot we don’t know about the drug.

Oomen agrees with the European Union’s decision to ban the use of titanium dioxide because researchers have not made any conclusive findings that confirm if the drug is safe or could be harmful. She feels there needs to be a more suitable method to study the chemical. Norb Kaminski, director of the Institute for Integrative Toxicology at Michigan State University said “I think that titanium dioxide in the amount that it’s used in Skittles and food products is of no toxicological concern or health concern to the public. There’s just not the evidence to support that currently.”

This topic relates to our most recent unit in Biology because one of the concerns regarding titanium dioxide involved the alteration of DNA. We learned about DNA in this unit when we learned about organic compounds. DNA is one of the nucleic acids we learned about when we studied different organic compounds. DNA functions to store all our hereditary information, and it plays an essential role in our cells. Also, that titanium dioxide had the potential to cause allergies to proteins found in certain foods. We learned about protein being another organic compound vital to the cell. We learned about all the different functions of proteins that are crucial for all cells to function properly.

Geneticist Svante Pääbo is the first person to extract DNA from extinct human species.

By blakelement

On October 21, 2022

Various forms of the human species have been alive for hundreds of thousands of years before us. For the longest time, it was concluded that DNA breaks down over time and cannot be excreted from ancient fossils…until Svante Pääbo joined the research.

Pääbo, the leader of his research team, was able to extract fragments of DNA from the bones of Neanderthals and Denisovans. By extracting mitochondria outside the cell nuclei, Pääbo’s team was able to place the genetic information into the appropriate chromosome locations “by matching each fragment to similar sequences in human DNA” (Bower). As we learned in class, mitochondria contain circular chromosomes of DNA. Pääbo’s team was able to extract the mitochondria from the cell and then analyze the mtDNA in comparison to modern-day humans. With this process, he concluded that humans diverged from Neanderthals about 516,000 years ago.

Another way they were able to identify common genetic information in the present-day Homo sapiens was by putting DNA into a certain bacteria, which would then make copies of DNA fragments. With this effort, they were able to recover 29 out of the 35 genes that they were targeting.

These new techniques brought research teams to conclude that modern-day humans share similar genes to Denisovans such as ones that regulate brain size, help us adapt to altitude, or even make covid-19 more severe in some cases. The evidence around the commonalities of certain genes encourages the theory that at some point there was interbreeding between Homo lineage.

Pääbo’s findings have paved the way for groundbreaking research, identifying commonalities in evolution, and have helped us understand what makes humans so unique. This new state-of-the-art process can hopefully one day expand to multiple labs, research teams, and even countries. This would allow us to learn even more about our sophisticated past and maybe even some things about our future!

Next Time You Think Losing An Hour Or Two Of Sleep Won’t Hurt… Think Again.

By isatonic

On October 21, 2022

We’ve all been there. It’s a busy week, it’s getting late, and you’re tired, but you still have a lot to do for tomorrow.

You convince yourself that if you sacrifice your sleep during the week and make it up on the weekend everything will be okay. Right? Well, unfortunately, according to the Mount Sinai School of Medicine, quite the opposite is true.

Research completed by Mount Sinai Hospital demonstrates that reducing the amount of sleep you get each night can lead to an increased risk of inflammatory disorders and heart disease. The researchers monitored 14 healthy adults that normally sleep 8 hours a night and had them sleep 6-7 hours for 6 weeks. They then drew and analyzed their blood, finding an increased number of immune cells, many of which did not function properly to protect against infections. An increased number of immune cells may seem beneficial, but in reality, if the number gets too high, immune cells can overreact and create inflammation. The DNA structure of the cells was also altered, which provides evidence for their decreased ability to defend against illnesses.

The researchers continued the study with testing on mice and found that even after having sleep recovery time, the mice still had changes in their immune system. The mice’s immune cells were rewired and reprogrammed to function under the stresses of having disrupted sleep, producing more white blood cells, which put the mice at a greater risk of having inflammation or a disease. These results serve as evidence to prove that sleep recovery cannot reverse the effects of lack of sleep.

The cells experience this change due to limited time to repair injured cells. As we sleep, our bodies turn their attention to our immune system, repair damaged cells, and release growth hormones. When we have disrupted or limited sleep, our bodies are not able to carry out these functions, causing greater susceptibility to health problems. It is important that our cells are able to complete their tasks, and it’s even more important that we can remove and replace cells that cannot. As we learned in AP Biology, the lysosome plays a major role in helping damaged cells perform apoptosis (programmed cell death). If our bodies are not given the time to carry out apoptosis and replace old damaged cells with new immune cells, our bodies are at greater risk for metabolic abnormalities and replication errors, connecting sleep deprivation to disease risk. So the next time you’re thinking of sacrificing sleep to do work, I hope you remember the health consequences and reconsider your decision 🙂

Can this Protein Cause Alzheimer’s?

By shaminoacid

What causes Alzheimer’s? Initially, one might think that it is a result of age-related changes in the brain or environmental and lifestyle changes. One may also think that it is caused by a genetic predisposition to the disease. Personally, I thought Alzheimer’s was a result of poor health as one got older. Although these all may be true, a new study has found that Alzheimer’s Disease can be caused by a certain protein, or rather, a protein mutation. These new findings provide scientists with a way to detect and treat the disease in the long run. Using multiple methods to analyze mitochondrial DNA, researchers found a mitochondria microprotein that is associated with Alzheimer’s Disease. This protein, known as SHMOOSE is seen to have a role in the neurodegeneration of people, thus giving them an increased chance of Alzheimer’s Disease. Furthermore, the researchers found that the microprotein is found in over a quarter of Europeans. The researchers of The Cohen Laboratory at the University of Southern California published their findings in the journal of Molecular Psychiatry. The journal states that the microprotein, SHMOOSE was discovered through the use of neuroimaging, mass spectrometry, and transcriptomic. All of these are methods of looking into the mitochondrial DNA and locating the mutated protein. According to the study, a mutation of the SHMOOSE microprotein has a connection to a higher risk for Alzheimer’s Disease. They also discovered that 25% of individuals with European ancestry have the mutated version of the protein. Dr. Pinchas Cohen says that the SHMOOSE mutation is a result of a single nucleotide polymorphism or SNP. An SNP is essentially a change or alteration within a single nucleotide, in this case, the change resulted in the mutated SHMOOSE protein. Additionally, he states that the variant can guide ways to identify who is affected while also forming new medical treatments and preventative measures. In class, we learned about how proteins are created and coded for, and we also learned about how protein structure directly affects their function. Both of these concepts are directly seen in this study. Firstly, DNA is what codes for proteins, if the DNA or even the nucleotide is incorrect or altered, the protein would in turn also be incorrect or altered. This is seen directly through the SNP, the single change in the nucleotide entirely changed the protein creating the SHMOOSE protein. Next, the structure of the protein, the sequence of the amino acids, or just the overall composition of the protein entirely plays a role in the function and actions of the protein. For example, if the structure of a protein is compromised, so is the function. This is also directly seen in the study because the structure of the SHMOOSE protein was altered due to the SNP, its function was also altered. The altered function is that it would put people at a higher risk for Alzheimer’s Disease. Another article speaks on the silver lining of the SHMOOSE protein. Because the protein is the approximate size of an insulin peptide, it could easily be administered into the human body for a positive effect. This means that the mutated protein could be used for treating Alzheimer’s Disease and increasing its therapeutic value. This idea is just one of many that venture into the field of precision-based medicine. In the case of Alzheimer’s the mutated SHMOOSE would be focused upon as a target area rather than the disease as a whole. I think that the use of SHMOOSE in a medical or therapeutic way would be risky at first in that it would likely be difficult for scientists to specifically target the way to treat it. What may be a safer option for those with the mutation could be to continue with tried and tested Alzheimer’s Disease treatments rather than immediately opting for something new. The new precision-based medicine method should undergo severe trials, examinations, and successes before it is widely implemented.

How Do Ancient Viruses Still Impact Humans?

By angenetic

When one thinks of the similarities between modern and ancient humans, one will probably think of the basic genetic material that determines our physical structure. However, what is not so obvious are the viruses that infected them yet remain in our genes. It is known that DNA containing these ancient viruses make up about eight percent of the human genome (Ancient Viruses). These viruses have previously been believed to be insignificant, however, recent research has disproved this theory.

The viruses that have been genetically passed down are known as retroviruses. Retroviruses spread by making copies of themselves through the production of RNA which contains instructions for its DNA and replication. This reproduction process, called transcription, is similar to that which is done in the nucleus of eukaryotic cells. However, in this case, the synthesized DNA is then placed in the DNA of the cell it occupies. With that in mind, For the genes containing these viruses (or any gene) to be activated, they must contain specialized RNA with the information for its reproduction and it must be revealed by a protein called the transcription factor.

Using data from the Genotype-Tissue and Expression project, scientists Aidan Burn, Farrah Roy, Michael Freeman, and John M. Coffin searched for these active virus genomes in healthy tissue. They specifically sought out HML-2 which is a relatively new virus. They also looked for the RNA which would indicate its activation. This virus was found in all of the tissue they examined and they found the highest activity of it in the cerebellum.

Though they were once harmful to humans, these viruses found within healthy cells and tissues no longer serve as functioning viruses. They are now known as Endogenous Retroviruses (ERV). They cannot infect, but rather they serve us in our immune system. Their activation has been shown to have a vital role in embryonic development and aid in the detection of cancer.

I found the origination of ERV in human genomes to be similar to that of mitochondria and chloroplasts’ origin in eukaryotic cells. It is likely that mitochondria and Chloroplasts were engulfed by bacteria cells and are now able to carry out their functions (reproduction) within them while also benefiting the cell (providing it with ATP). Similarly, at some point during human evolution, the virus entered humans and was then able to utilize its environment (the host cell) to reproduce. I would also describe the relationship between ERV and modern-day humans as symbiotic due to the recent research which has revealed their benefits.

Can Eating Late Increase the Obesity Risk in Humans?

By nescleus

Are you frustrated that, despite your healthy diet, you constantly feel like you are lacking energy, gaining weight, frequently hungry, and fatigued? Did you know that adjusting the time you consume meals could resolve this? Let me enlighten you on why you might be facing these symptoms!

A recent study by Brigham’s women’s hospital orchestrated experiments to answer the following question “Does the time that we eat matter when everything else is kept consistent?”. In the experiment, 16 patients with a BMI (body mass index) that indicated they were overweight, were examined closely. The 16 patients were on strict schedules so that their behavioral and environmental factors wouldn’t disrupt their results. They all had the same amount of sleep, the same diets, the same amount of physical activity, and the same wake up time. The only thing manipulated was the times each of them ate their meals. Each patient recorded the times they felt an increase in appetite, had their body temperature and energy levels measured and gave blood samples. The conductors of this experiment performed biopsies of adipose tissue from the patients, to evaluate how their eating times affected how the body stores fat.

The test results showed that the participants that were on a later eating schedule had a decrease in a hormone called leptin, which is a hormone that regulates your appetite and energy level. The patients with a later eating scheduled were caused to feel more hungry than the group that consumed food earlier due to their body’s decrease in leptin. Eating later also had an effect on Ghrelin which is a hormone that increases your appetite.

The experiment discovered evidence that the group eating later was more at risk of obesity. The adipose tissue gene expression revealed the pathways involved with lipid metabolism, receptor tyrosine kinases, and autophagy was altered in a way that decreased lipolysis and increased adipogenesis. Lipolysis is the process of breaking down lipids. In our biology class, we learned how hydrolysis is the process where water is added to a molecule, which results in the molecule breaking into smaller molecules. In lipolysis, hydrolysis breaks down triacylglycerols into glycerol and free fatty acids. In biology class, we learned that lipids provide us with mass amounts of energy when they are broken down and if they aren’t being properly broken down in our body it can lead to damage in our cells and tissues. We also learned in biology class that autophagy allows your body to break down and reuse old cell parts so that our bodies won’t work as efficiently.

Overall, the time of our eating has many effects on our appetite, body temperature, weight fluctuation, number of calories we burn, energy level, and risk of obesity, and can even cause molecular changes in our fat tissue. In the future, Brigham and Women’s Hospital, hope to perform more related experiments to discover further information about this topic and specifically the relationship between meal time and bedtime on energy balance.

I have always tried to be the healthiest version of myself, which will make me feel like my best self. I remember telling my brother that I was feeling sick because I ate really late at night and he laughed at me and said I was being dramatic. It is really interesting to learn the science behind eating late at night and how it can affect how you look and feel. I especially liked gaining a better understanding of this topic because now I know the factors that cause my body to not feel as great when I eat later than usual!

HABs – The Tiny Killers

By walkabuffalo

Harmful Algal Blooms (HABs) occur when algae, which can range from microscopic, single-celled organisms to large seaweed, produce harmful toxins that grow in extremely high numbers and are in dense concentrations at the surface of lakes and in marine environments. These HABs are killing fish, mammals, and birds and may cause human illness or even death in extreme cases. In some instances, the algae blooms can be nontoxic but, in any event, consume all the oxygen in the water as they die off and decay, which can clog the gills of fish and invertebrates or smother corals. They are becoming a growing concern because they affect the health of humans, freshwater, and marine ecosystems. One research study indicates that the economic loss resulting from algal blooms, including regular phytoplankton algal blooms and what is now referred to as “harmful algal blooms or “HABs” formed by cyanobacteria, is on the order of approximately $4 billion annually.

In October 2019, a research article was published in the prestigious scientific journal; Nature, which documented a significant increase in phytoplankton (algal) blooms worldwide since the 1980s. This was reported by a detailed study of worldwide LANDSAT satellite photography utilizing three decades of satellite imagery. Using these satellites, 71 large lakes throughout the world were studied.

These phytoplankton populations form the basis of the food chain and contribute or are engaged in numerous biological, chemical, and biochemical processes that are important to everyday life on our planet. Many of these blooms can be caused by cyanobacteria which are prokaryotic cells that still can generate oxygen via photosynthesis, much like the eukaryotic microscopic plant cells, better known as phytoplankton. Some cyanobacteria can “fix” atmospheric nitrogen as well. Several cyanobacteria species also produce toxins as a bi-product of their metabolism that can adversely affect the liver, kidney, and nervous systems in humans and animals.

NOAA is at the forefront of HAB research to better understand how and why these blooms form and to improve the detection and forecasting of these seasonal events. The causes of this significant increase in algal blooms are somewhat unclear; however, it seems to be linked to precipitation, trends in fertilizer use, changing weather patterns, nitrogen concentrations, phosphorus concentrations, and perhaps climate change; as increases in temperature worldwide are occurring, but this data is inconclusive. Humans may also impact how frequently they occur and their intensity. Increased pollution, food web alterations, introduced species, water flow modifications, and climate change are all human activities that may play a role in creating these blooms.

These blooms concern me because, for the first time in many years, I have observed several algal blooms where I spend my summers on Upper Saranac lake, a freshwater lake in the Adirondack Park. While these are not HABs (harmful algal blooms) produced by cyanobacteria, they indicate changes in the lake’s biochemical, chemical, and perhaps physical parameters. The lake is monitored 24/7 via a telemetric sampling station that runs typical water quality parameters, which are being studied as we speak by local researchers. I feel we must continue to research the causes and effects of this situation to better manage algal blooms in the future. Can you think of any methods to reduce the likelihood of these Harmful Algal Blooms from forming?

AlphaFold: Is Artificial Intelligence Taking Over?

By Joshmosis

In this news article by Tina Hesman Saey, she talks about a new deep-learning artificial intelligence system called AlphaFold. The purpose of this new technology is to predict the 3-D shapes of proteins by recognizing patterns in structures. At its first release in 2021, the AlphaFold included predictions for most known human proteins, with predictions of over 350,000 protein structures. Since its initial release, the AlphaFold database has increased the number of protein structure predictions to over 200 million.

As you can see by the model, some parts of the prediction are more or less accurate than others. One of the main issues with AlphaFold is the fact that these are only predictions. Scientists cannot use this information with full confidence and require further experiments to be able to be confident in the findings. Even with this issue, scientists and researchers have been able to develop potential new vaccines, improve their understanding of diseases, and gain insight into human evolution with this new artificial intelligence system.

As you may remember from your AP Biology class, protein structures are extremely important in allowing the protein to perform its job. Proteins are extremely integral in your body’s ability to function. Enzymes are used to speed up reactions, antibodies protect our body from diseases, hormones send signals to the body, etc. By knowing the structure of the protein, scientists gain a better understanding of how proteins and all of these processes work. Just by changing one amino acid, the whole structure changes which can cause diseases such as Sickle Cell Anemia. If you would like to learn more about other important purposes of protein structure, this article goes into more in-depth on the applications of protein structure and modeling.

Now onto the topic of artificial intelligence as a whole. While artificial intelligence can reduce human error, take risks instead of humans, create unbiased decisions, and automate repetitive actions, it also has several downsides(besides the possibility of it becoming sentient and taking over the world like in movies). Some of these are having high costs, increasing the amount of unemployment, being emotionless, having no morals, and making humans lazier. Artificial intelligence has the potential to completely change society as a whole. I believe that as long as we are able to keep artificial intelligence under control and not let it get into the wrong hands, it will be a great benefit to society through important breakthroughs, such as AlphaFold, and new ideas that would have never been thought of without the use of this technology.

Do you believe artificial intelligence will be the salvation for humanity or will it be its downfall?

Omicron: The Most Infectious COVID Variant Yet

By rnase

Omicron has become the most infectious variant of COVID yet, even managing to re-infect people who already had COVID. According to researchers in Botswana and Africa, omicron’s ability to spread so easily is due to its 60 genetic mutations, which include 42 changes to its spike proteins.

In class, we learned about a form of endocytosis called receptor-mediated endocytosis. Receptor-mediated endocytosis occurs when ligand bind to receptor proteins on the cell membrane that match their shape. This process triggers the cell to let in the virus in a coated vesicle. In this case, the ligands are the COVID spike proteins are the receptor proteins are called ACE2. The omicron spike protein is shaped like a claw machine. Most antibodies attack the claw fingers, however, omicron keeps its “knuckles” bent to hide the parts the antibodies target. Omicron can also stick out one positively charged finger to grab onto the negatively charged receptor. This electrical attraction in omicron is three to five times greater than that of the delta variant, greatly contributing to its ability to infect the cell.

Researchers also suspect that omicron uses a mechanism unlike previous variants to enter the cell. They believe that omicron uses a backdoor compartment called an endosomes, sorting organelles part of the endomembrane system, and a protein called cathepsin L to drop its genetic material. We discussed in class that the endomembrane system also included vesicles, nuclear envelope, the Golgi body, plasma membrane, and the ER. Through this method, omicron is able to enter the cell without killing it. This is particularly significant as the virus can use the host cell to create even more of the virus to spread. Another mutation that aids the virus is a sugar molecule on the spike protein. This modification makes it difficult for antibodies to attack the virus. For these reasons, omicron has managed to evade very effective vaccines. In one case, it was found that two doses of the Moderna vaccine was only 44% effective at preventing omicron infection between 14-90 days after getting the vaccine, and only 23.5% effective between 3-6 months after getting the vaccine.

I was interested in this topic because I’ve noticed that many of my classmates have gotten infected with COVID recently, even after receiving multiple vaccines or having already being infected with COVID. We can only hope that the next mutations will not lead to a more virulent form of the virus.

TMEM251: A Gene Come True?

By deukaryota

Have you ever finished a painfully long math problem, only to realize you made a mistake in the very first step? Although you probably panicked because your final answer was embarrassingly far away from the correct one, fixing your one small mistake may have actually revealed that the mess was not truly all that complicated. Identifying the root of a seemingly drastic problem quite frequently uncovers the underlying simplicity of the matter, but who would have thought that this basic concept could save generations of victims of a viciously lethal disease?

Mucolipidosis type II is an extremely rare inherited disease that causes physical, mental, and visual deformities and usually claims its victims before they turn seven years old (oftentimes much sooner). What causes Mucolipidosis type II? Simply put, it is when lysosomes do not receive the enzymes necessary to digest materials, making them not only ineffective, but also dangerous. When lysosomes are unable to perform the necessary recycling functions that you have learned about in AP Biology, materials are instead stored in the cell, causing Mucolipidosis type II and its seemingly infinite list of tragic symptoms such as scoliosis, neurological disabilities, ectrodactyly, enlargement of the heart, and more.

In fully functional cells, mannose-6-phosphate biosynthetic pathway, or M6P, signals the transport of hydrolytic enzymes into the lysosomes. Inversely, when M6P is either not functional or not present, the hydrolytic enzymes do not make it to the lysosomes, causing Mucolipidosis type II. Now that we know what happens when M6P is dysfunctional, let’s take one more step back. What causes M6P to stop working in the first place? Well, it turns out that a team of scientists at the University of Michigan had the same question.

Using CRISPR technology, the team tested individual genes’ effects on cellular functions, and they found the answer to our previous question: TMEM251. This gene is responsible for creating an enzyme called GNPT, which signals M6P to transport the enzymes to the lysosomes, and when this one singular gene fails to work, it causes the lifelong adversities of Mucolipidosis type II. Also, TMEM251 is located in the Golgi apparatus, and you (hopefully) already learned in AP Biology that lysosomes are created from this organelle. Therefore, this fact further supports the validity of the new finding.

The disease currently has a 100% fatality rate because scientists have not yet discovered a cure. Or have they? Now that scientists have identified the root of the problem, non-functional TMEM251 genes, they are experimenting with enzyme replacement therapy- the supplementing of missing lysosomal enzymes into the cell through endocytosis– to rehabilitate the cells to their proper, functional forms. It may be too early to place bets, but this groundbreaking discovery could turn out to be the hope that scientists around the globe have been searching for.

The Failure Of The Endangered Species Act

By wrightor mortis

In a recent study, biologists at the Columbia Climate School have determined why the Endangered Species Act fails to protect endangered species throughout America. The Endangered Species Act (ESA), passed in 1973, provides programs and guidelines for protecting and rehabilitating endangered plants and animals throughout the country.

On October 12th, the Columbia Climate School posted a study (led by Environmental biologist Erich Eberhard) that broke down why the ESA has been unsuccessful. However, in the 39 years since the act was passed, it has failed to recover a single endangered species to the point where it no longer needs protection. While eleven species have been delisted from endangerment status, biologists claim none of them are due to the ESA, and rather due to natural recovery or due to displacement on the list, as they were never endangered. According to Competitive Enterprise Institute Research Associate Brian Seasholes, “The ESA has failed to recover a single species, not one.”

The Columbia Climate School’s recent study claims that the ESA fails because it does not provide protection until a species population is precariously small, limiting any chance of recovery. Eberhard writes, “small population sizes at time of listing, coupled with delayed protection and insufficient funding, continue to undermine one of the world’s strongest laws for protecting biodiversity.” Since small populations are drastically more vulnerable to environmental, genetic, and human threats, by the time the ESA gets involved, the species in question is already doomed.

Moreover, the ESA has had issues with the declining water quality nationwide. Clean water is very important to endangered species, as water allows for life to exist through its various properties. Internally, the cohesion and adhesion of water helps transport water molecules around the body, and helps support bodily functions that depend on water. Externally, water helps moderate the climate of nearby environments. For example, water’s high specific heat allows it to absorb heat generated by the sun, cooling the temperature in costal regions. Thus, water regulates the temperate and environment that organisms in costal reasons have adapted to. When the external temperate dips below freezing level, bodies of water do not freeze throughout, as ice floats on top of water. The hydrogen bonds of water stop moving when frozen, and due to the spaces in between them, ice is less dense than liquid water with rapidly moving water particles, in which hydrogen bonds form and break easily.

The lack of clean water prevents these properties to happen, which worsens the habitat of already endangered species, pushing them further to extinction. The Environmental Protection Agency has increased efforts to control water by partnering the efforts of the ESA and The Clean Water Act (CWA), they have once again had limited success.

The authors hope that “leaders in the U.S. and across the world will learn from these lessons to better protect and conserve imperiled species across the globe.” The ESA has undoubtedly failed to protect endangered species in America.

Xylem Filters Engineered to Remove E. Coli: A Possible Solution to the Deadly Bacteria?

By itsalive

Overview

Novel research has proven that filters made from xylem in trees can be used to remove bacteria and pathogens from drinking water, leading to a possible solution for the worldwide E.coli crisis.

Intro

Pine Tree

Nonflowering trees, such as pine and ginkgo, contain sapwood lined with straw-like conduits known as xylem. Xylem is a vascular tissue found in plants that provides structural integrity and carries water and minerals from the roots to the rest of the plant. Xylem tissue is made of specialized cells which are water-conducting, allowing for the water molecules to adhere to its tissue as it is being pulled up the plant. Water passes through Xylem’s conduits which are interconnected via thin membranes that act as natural sieves, filtering out bubbles from water and sap. Inspired by this natural phenomenon, a study published by the Massachusetts Institute of Technology engineered a filter made of xylem that successfully removes E. coli from drinking water.

“Two Birds With One Stone”

Stained Xylem Cross-Section

One major problem that the engineers ran into was dryness and its effect on the xylem’s permeance: as the wood dried, the branches’ sieve-like membranes began to stick to the walls, reducing the filter’s permeance, or ability to allow water to flow through. Another problem found was that the filters would erode and degrade with use, causing a build-up of woody matter which clogged its passageways. The engineers were able to solve both of these problems by cutting the xylem into small cross-sections, soaking them in hot water and then in ethanol, and letting them dry. Now, the filters were ready to be used.

In Action

The engineers quickly sprang into action and brought their invention to India for testing; India holds the highest mortality rate due to water-borne disease in the world, where safe and reliable drinking water is inaccessible to more than 160 million people. Their trials in India provided them with beneficial feedback regarding replacement frequency and the comfortability of the product being natural and recognizable. With this criticism and assurance in mind, they crafted a new prototype and are now hoping to produce these on a massive scale so that all can have access to clean water.

E.coli Electron Microscopy

Urgency

A study published by the International Journal of Environmental Research and Public Health concluded that safe drinking water for all is one of the major challenges of the 21st century and that microbiological control of drinking water should be the norm everywhere. E. coli infections cause approximately 265,000 illnesses and about 100 deaths in the US and greater than 300 million illnesses and nearly 200,000 deaths are caused by diarrheagenic E. coli globally each year worldwide. It is imperative that this filter be mass-produced and utilized nationally in order to prevent further deaths and guarantee clean water to everyone across the globe.

Transpiration of Water in Xylem

Relation to AP Bio

This topic is closely related to the adhesive and cohesive properties of water. In plants, water adheres to the xylem as it is brought up from the roots and dispersed throughout the plant. Water also coheres to itself, allowing for more than one molecule to move up at a time and therefore causing a cascade of molecules to follow in one’s path. If it were not for this property of water, plants would not have evolved xylem and therefore this filtration innovation would not exist.

Tired of Listening to Mom? Here’s why teens grow to explore unfamiliar voices instead of the familiar

By riwang

On April 28th, 2022, Lauren Sanders, a neuroscientist and senior writer, published an article regarding the internal neurological development of kids to teens. Sanders’s primary inquiry surrounded a research article about how the development of what individuals perceive benefits them influences what voices they interact with. Specifically, Sanders’s scope of inference is based on Daniel Abrams’s study where the brain activity of a group of individuals aged seven through 16 was observed to see their responses to the voices of a mother and to unfamiliar voices too.

Abrams posed the idea that the brain activity of teens is piqued by the possibility and mystery of reward when engaging with unfamiliar voices. The biologist and anthropologist Leslie Seltzer continues this conversation by juxtaposing this idea with how kids have more increased brain activity when hearing the voice of their mother. She introduces the theory that our maturity connects to how we are less dependent on a mother figure and more dependent on our peers. Moreover, she extends this research on how powerful the voices of maternal figures have in the reduction of stress hormones.

In an age where communicating messages can be sent over text, Seltzer claims that there exists a power of voice over text where emotions and neurological signals greatly increase by hearing the authentic/emotional message in person. Further research can be conducted on the difference between voice and text, which could provide even more insight into how the increase technology use in teens could influence how teens respond to voices.

These differences in brain activities reminded me of the functions of membrane proteins. One of the significant functions of membrane proteins is signal transduction, where proteins act as receptors for hormone signals and neurotransmitters. On a more micro level, this biological lens informed me of how we humans react and respond to these voices from cell to cell.

I feel that it’s quite early to make full conclusions about causation, especially since the scope of the study is small. It’s hard to draw these connections when there are confounding variables like socioeconomic status and stability in the household, especially if these factors can simply disrupt the fluidity of communication between parental figures and children.

Can Reactive Oxygen Species Maintain Stem Cell Function and Prevent Inflammation?

By avacuole

Have you ever wondered what “gut health” really means? What keeps your gut microbiome functioning properly, maintaining homeostasis, and preventing inflammation? Originating from oxygen, reactive oxygen species (ROS) that are highly reactive function as central indicators of cellular flaws and issues in the body, such as inflammation. Nai-Yun Hsu of Mount Sinai has stated that “Reactive oxygen species released by stem cells are critical in maintaining a heathy gut via maintaining proper balance of intestine barrier cell types.”

A team of researchers from the Ichan School of Medicine at Mount Sinai have gone in depth about the importance of these oxygen species for stem cell function, avoiding inflammation, and repairing wounds in a recent study. Using mice as models, the researchers were also able to conclude that microfold cells, called “m cells” regulate an organism’s gut immune response, and emerged from a loss of ROS in mice and humans.

The experiment was conducted in vino and in vitro conditions with the mice cells, and ex vivo conditions with human intestinal biopsies post-colonoscopy. Both the human intestinal biopsies and mouse cells were utilized to determine the amount of ROS in the body to support a finding. In addition to determining the amount of the oxygen species, the biopsies and mice were used to analyze the “gene expression profile” of barrier cells in intestines of mice and humans that are diagnosed with a “subtype of IBD known as ulcerative colitis.”

A decrease in these oxygen species can lead to TNF’s emergence in the body, which is a substance that attempts to maintain homeostasis in the body and avoid inflammatory diseases, like IBD and ulcerative colitis. They have concluded that losing species like NOX1, a protein that creates these species, is directly linked with inflammatory diseases like Inflammatory Bowel Disease (IBD). Judy H. Cho, MD, has stated that the study is a breakthrough “in defining the key role of oxygen species in maintaining a healthy epithelial barrier for IBD.” These reactive oxygen species are relevant to AP Bio considering the information we have learned about general biological systems and cells, which function to maintain homeostasis in the body. The mitochondria, which is an organelle of the cell covered in AP Bio, receives signals from gut bacteria that reveals inflammation. While the mitochondria is typically known as the site of cell respiration and performing reactions, new evidence has shown a relationship between the gut microbiota and mitochondria to trigger immune responses and activate barrier cell function. These processes relate to changes to the mitochondria that occur from gut-related issues in IBD patients, meaning that there is a connection to ROS.

Gut Microbiota

As a conclusion to proving the direct link between the highly reactive oxygen species and treating inflammation, these researchers encourage and plan to conduct further study on this topic, but for using “oxygen species-stem cell modulation therapy” to potentially treat IBD patients.

Neuralink: Science Fiction or Reality?

By photosamthesis

On May 4, 2022

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

Drawing of Human Brain

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.

Human Neuron Diagram

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.”

Neura Link Robot

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

By charlottersmosis

On April 26, 2022