BioQuakes

AP Biology class blog for discussing current research in Biology

Author: lukewarm

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

In Student Post

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

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

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

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

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

Interested in Reusable Energy? This New Advancement may Transform the way we Store our Energy.

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On March 17, 2023

In Student Post

One of the biggest struggles with modern reusable energy sources is the unreliability of the systems. Solar is dependent on sunlight and has no
functionality at night. Wind power is dependent on pressure systems
building wind strength, and solar uses “photovoltaic cells” that “must have
sunlight to create electricity”. Additionally, enough wind farms, which can be produced do to a lack of ability to store their energy, can have an effect on our weather patterns and impact “major hurricanes” by “removing energy from the air”. While these emerging reusable energy sources are great when working, how do we harness the excess energy produced to then use when the sun isn’t shining or the wind isn’t blowing?

According to a research team out of the Department of Energy’s Pacific
Northwest National Laboratory, they may have created a new battery
enhancement using “low cost metals” such as sodium and aluminum to
provide “safer and more scalable stationary energy storage system”.
The development is in the speed at which the battery can charge and
discharge energy. The new development of molten salt batteries seem to
absorb energy “much faster” than conventional high-temperature sodium
batteries. According to a resaercher in the group, Li Guosheng, they also “operate at a lower temperature” and have “excellent energy storage capacity”. Additionally,
these molten salt batteries use raw materials that are much more
abundant than those found in conventional sodium batteries and lithium ion batteries.

Wileyfox Swift – Li-ion battery SWB0115

When comparing the new molten salt battery to a conventual lithium-ion
battery that can be found in your cell phone or electric vehicle, it is
important to note how it reaches a similar capacity while being much
cheaper and simpler to produce. These new batteries have a two stage
mechanical chemical reaction that is acidic. The addition of a seccond
reaction increases the overall capacity, allowing the battery to retain “82.8
percent” of peak charge capacity. The researchers wanted to apply this molten technology to the grid in order to maximize our conservation of energy storage from reusable sources. They used the molten salt technology in a flat cell solid state design that allowed for electrical discharge for over 28.2 hours under laboratory conditions. Compare this to our current lithium ion technology that can handle 10-12 hours and this will be able to drastically increase our ability to harness excess renewable energy and discharge it during nigh-time.

Lastly, when looking at the cost of this new battery technology, the researchers estimate $7.02 per kWh for the active materials. Compare this to “$151 per kWh” for our current lithium ion system makes the advancement even more important. Overall, while this technology is still in “coin cell testing phase” it makes promising enhancements to our current battery technology and sets the stage for future investment in renewable energy sources.

In AP Biology, we have learned about genetic diversity, adaptation and different genotypes within organisms. We see how dominant and recessive traits are passed from parents to offspring and the ways in which these traits appear physically, either in co-dominance or incomplete dominance. Our rapidly changing climate plays a key role in determining natural selection, and controlling the genotypes that aid offspring in survival. Take the Atlantic Killfish for example, a fish that has evolved genetically in order to tolerate high levels of toxins in polluted waters, which is a key adaptation of the environmental stressors it faces. Researchers have identified specific genes that are involved in this tolerance, including genes that code for proteins involved in the detoxification of pollutants, such as cytochrome P450 enzymes. The possible alleles for this gene are passed down through each generation of Atlantic Killfish, and will only become more common as climate change and pollutants continue to increase. Overall, AP Biology looks at the genetics and individuals genetic makeup which can help predict certain offsprings traits. With our changing climate, it is vital to understand what traits are necessary to keep organisms alive and realize the dangers of any single natural factor in an ecosystem changing too quickly.

Try to eat just one potato chip – it probably won’t happen.

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On January 16, 2023

In Student Post

Potato Chips or any junk food for that matter can be very addicting after just the first bite. The high concentrations of carbohydrates, sugars, and fats commonly found in these processed foods contribute to one of America’s greatest health risks, adult obesity. Today, over 40% of America’s adult population is considered obese and in the last 20 years, the prevalence of severe obesity has almost doubled to 9.2%. A single bag of Lay’s Potato Chips contains 15g of carbohydrates and around 170mg of sodium which could take around 15 mins of very intense workout to burn off. We have learned in AP Bio that consuming many carbohydrates without burning them off through exercise results in carbs converting into fatty acids during cellular respiration. So, when looking into obesity, researchers from Osaka Metropolitan University wanted to understand why “High-calorie foods — high in fat, oil, and sugar” tend to be overeaten.

Walmart Wenatchee 2

The researchers investigated the specific gene behind overeating and linked it to one named “CREB-Regulated Transcription Coactivator 1 (CRTC1).” In the past, trials on mice have indicated that when the CRTC1 gene is removed, they become more obese indicating that it “suppresses obesity”. But, it is now known that CRTC1 is found in all neurons around the brain so, they wanted to dive deeper and find the specific mechanism or neuron within this gene that reduced obesity.
First, Associate Professor Shigenobu Matsumura, who lead the research, hypothesized that “CRTC1 expression in MC4R-expressing neurons suppressed obesity because mutations in the MC4R gene are known to cause obesity.” So, they conducted trials on mice, manipulating the MC4R-expressing neurons to test their theory. It turns out that when on a standard diet, the original mouse and the one with the manipulated MC4R gene remained the same weight. But, when put on a high-fat diet, or one more resembling junk food, the mouse that was deficient with the CRTC1 MC4R neuron became “significantly more obese than the control mice and developed diabetes.” Reflecting on this outcome, the researchers have concluded that the CRTC1 gene plays a role in controlling our portions. Looking forward, the researchers hope this will lead to a better understanding of what causes people to overeat.

Mouse Brain Cross-Section

In our current AP Biology unit, we have been learning about cell respiration and the way our body consumes both O2 and food to create ATP energy. Our body can break down glucose through glycolysis, convert it into two Pyruvate, and then Acetyl CoA, to then create NADH and FADH2 through the Citric Acid Cycle to produce about 28 ATP energy molecules through Oxidative Phosphorylation. Other nutrients we consume like fats and proteins are also converted to ATP energy when needed but, when no energy deficit is created through activity, these nutrients along with excess glycogen are bound to insulin to create fat around the body. Looking forward, it is important to understand how addictive these unhealthy foods can be on a neurological and biological level, warning us of the dangers of overconsumption.

Ever wonder if you were exposed to COVID-19? This new device may be able to help.

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On December 8, 2022

In Student Post

Riding a public train. Traveling on an airplane. Or just shopping in a public mall. These are all ways someone may contract COVID-19 without realizing that a stranger around them is infected. Traveling via public transport can expose you to unwanted germs, especially when travel times exceed 15 minutes resulting in longer exposure to a possible carrier of the virus. According to the CDC, being exposed to someone with COVID-19 for more than 15 mins results in a “Higher Risk” scenario of contracting the virus. According to Johns Hopkins Coronavirus Resource Center, there have been over 600 million cases of COVID-19 across the globe. What if you could detect COVID-19 particles around you and then change your seat accordingly to reduce exposure?

Well, scientists out of Tohoku University have created a battery-less device which can detect COVID-19 particles in the air, causing a signal response on the device telling you of the virus’s presence. The device generates power via “alternative magnetization caused by vibration” which can detect “bending vibration energy” and transmit the detection wirelessly. The scientists first objective was to modify a “0.2mm thick Fe-Co/Ni plate with a rectifier/storage circuit”. This unit can detect substances that adhere to the clad plate through the change in vibration and resonance frequency. The ability to use this device without power as well as the ability to adjust triggers for its response are the key reasons it was chosen. 

The next task for the scientists was to adjust the transmission device to detect type “229E (HCoV-229E)”, one of seven strains of human coronavirus. Coating the clad surface of the plate using targeted proteins, in this case a CD13 protein caused the resonance frequency or vibrations of the device to decrease when exposed to this certain COVID-19 strain. Through repeated tests, they were able to verify that these coated plates could transmit the detection of the type “229E (HCoV-229E)”virus without needing an external power source, “something not capable with current biosensors“.

Proteins stimulating responses in our cells when fighting a virus like COVID-19 occur during the Cell Signaling process that we are studying in AP Biology. Through the process of an Immune Response to a virus, after the virus is broken down inside a macrophage, a MHC2 protein will bring part of that virus to the outside of the macrophage to signal a helper cell. The Helper T Cell then has a protein of its own called a CD4 protein which will pair with the MHC2 protein to identify the shape of the virus. In this part of the Immune response to a virus, we see a protein transferring information to a helper t cell, similarly we see a protein on the surface of these coated clads identify a strain of COVID-19 and then send a signal.

As the scientists continue their research on batteryless biomedical devices, they hope to further “develop our device and see if it applies to other viruses, such as MERS, SARS and COVID-19“.

Know Someone addicted to Opioids or Painkiller? This Biomedical Advancement May Be Able to Help.

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On October 24, 2022

In Student Post

First and foremost, the opioid crisis effects Americans nationwide. The United States is facing a major health crisis that rarely is even mentioned on the news. In the last 20 years(1999-2020) National overdose deaths involving any opioid have risen by more than a factor of six. Nearly 70,000 Americans died in 2020 rising by over 44% since just 2017. Whether given after a major surgery or sports injury, the addictive nature of opioids combined with the difficult side effects have left researchers looking for a better solution.

The general goal for this research was to target different receptors in the cell to do away with the harmful side effects of opioids. An international team of researchers led by the Chair of Pharmaceutical Chemistry at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) are “focusing particularly on the molecular structures of the receptors that dock onto the pharmaceutical substances”. In short, they are looking to activate adrenaline receptors instead of opioid receptors.

Researchers looked at the central nervous system to discover receptors in cells that lacked the sedative effect. While many of these adrenaline receptors are involved in pain processing, few have been cleared for use in therapies. This is where a team of researchers from Erlangen, China turned their attention to the adrenaline producing alpha 2A adrenergic receptor. One problem is that the analgesics that target the alpha 2A receptor produce a strong sedative effect. Gmeiner, one of the researchers, quotes “Dexmedetomidine(an analgesic) relieves pain, but has a strong sedative effect, which means its use is restricted to intensive care in hospital settings and is not suitable for broader patient groups”.

The goal for the researchers was to separate the sedative effect from the adrenaline receptors to ensure that this therapy could be used on a wider scale. Through the use of extremely high-resolution cryo-electron microscopic imaging, researchers were able to develop agonists that like Dexmedetomidine send large amounts of adrenaline to the brain thus, revealing  the sensation of pain very well. But, the real development was the “fact that none of the new compounds caused sedation, even at considerably higher doses than those that would be required for pain relief.”

In AP Biology, we have looked at the active transport of molecules through the phospholipid bilayer of the cell. Using ATP energy, cells in your body are able to move particles from a high concentration outside the cell to a lower concentration inside the cell. One process cells use to move these particles is Receptor Mediated Endocytosis. Specific ligands (ions, small molecules, or proteins) bind to a coated pit in the receptor while the receptor matches the ligands shape. Next, the ligands pass through the phospholipid bilayer and are put into a coated vesicle to be transported around the cell. A similar process takes place when receptors receive pain relieving drugs.

The prospect of removing the addictive and violent side effects of opioid use through the use of adrenaline receptors sounds promising, but it is important to keep in mind that this is still just research in the lab. With enough funding and time, the possibility of saving thousands of lives by developing non-opioid pain medication is a very exciting advancement and worth the investment.

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