AP Biology class blog for discussing current research in Biology

Author: ethanols

Using CRISPR to Treat Cancer Causers

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology’s origin stems from a 1987 discovery of specific genetic sequences inside the genome of Escherichia Coli; however, it wasn’t until 2007 which introduced practical usages of CRISPR. While CRISPR is seemingly a natural phenomenon, scientists quickly acknowledged its potential and began researching practical usages of it. Scientists discovered that certain bacteria, such as E. Coli, use CRISPR as an antiviral mechanism. CRISPR’s capabilities intrigue scientists because it offers a differentCRISPR illustration gif animation 1 approach that is more precise, quicker, and cheaper for altering an organism’s genome to better suit it for survival. Whether CRISPR is being used to treat genetic mutations that lead to cancer or drought-resistant plants, CRISPR’s applications can be applied nearly anywhere on the genetic level. CRISPR-Cas9 works by combining a protein that can snip DNA strands with a molecule that guides it to the site of concern. “When bacteria survive a viral attack, they incorporate snippets of the virus’s DNA into their genomes. Those stolen segments are called ‘CRISPR.’ If the virus attacks again, the bacteria use those CRISPR segments as a template to create strands of RNA that home in on the corresponding sequence in the virus’s genome. The CRISPR RNA carries along a protein called Cas9 to the target location on the DNA. The protein disarms the virus by cutting its DNA at that spot” (c&

One particular area of concern where CRISPR technology may provide some aid is the p53 and associated genes. According to, the “p53 gene makes a protein found inside the nucleus of cells and plays a key role in controlling cell division and cell death. Mutations (changes) in the p53 gene may cause cancer cells to grow and spread in the body” ( P53 pathwaysCells that have this mutated p53 gene lack the ability to control cell division and death. We’ve learned in AP Biology that the interphase cells go through before undergoing mitosis, and cytokinesis is extremely important to ensure that they divide and grow properly. But if something goes wrong during G1, S, or G2, that could lead to uncontrolled cell growth and division and cancer. Targeting p53 using CRISPR technology has some limitations, though. CRISPR is much less effective against p53 that is active, but both inactivated and mutated p53 allow for uncontrolled growth, leading to cancer. So, the scientists at Karolinska Institute propose that p53 inhibition is the most effective way to manipulate p53 to be better suited for CRISPR treatments. Preventing further mutation of p53 became the key concern because this leads to extra complexities and danger to associated genes.

Preventing similar genes from DNA damage is key to preventing uncontrolled cell growth. The researchers “identified a network of linked genes with mutations that have a similar effect to p53 mutations, and shown that the transient inhibition of p53 is a possible pharmaceutical strategy for preventing the enrichment of cells with such mutations” (Karolinska Institute). Furthermore, the scientists studied the DNA damage response as a possible answer in developing a more accurate guide to RNA sequences, which are used to guide CRISPR where a DNA sequence requires editing. The scientists claim that “We believe that the up-regulation of genes involved in the DNA damage response can be a sensitive marker for how much unspecific (‘off-target’) activity a guide RNA has, and can thus help in the selection of ‘safer’ guide RNAs.”

Cancer has been a seemingly unsolvable problem for generations. Any step taken to further our capabilities for handling cancer is a good step, and eventually, we will reach a point where cancer is hopefully a disease of the past. Utilizing CRISPR to its fullest potential will take time, but scientists are hopeful that it will be an absolute game-changer in the fight against cancer and other genetic diseases.

Our Circadian Rhythm Could Affect Alzheimer’s Disease

The National Institute of General Medical Sciences defines the circadian rhythm by our behavioral changes that follow a twenty-four-hour cycle heavily influenced by light and dark periods (NHS.GOV). Whether these changes are physical, mental, or behavioral, our circadian rhythm is critical for our survival as a species. The most important way of maintaining an efficient circadian rhythm pattern is by having a consistent sleep schedule, as explained by the scientists at Rensselaer Polytechnic Institute. Your body can adequately enter Delta (slow-wave) sleep by having a consistent sleep schedule. This sleep cycle is the most crucial out of them all, for it is when your body achieves maximum restoration and when your mind can sufficiently rest.Circadian rhythm in a human

But what else does our body’s circadian rhythm do for us? Well, scientists at the Rensselaer Polytechnic Institute have uncovered a possible correlation between Alzheimer’s disease symptoms and our circadian rhythm. Essentially, they have discovered that “the circadian system is composed of a core set of clock proteins that anticipate the day/night cycle by causing daily oscillations in the levels of enzymes and hormones, ultimately affecting physiological parameters such as the immune response” (RPI). Furthermore, diseases such as Alzheimer’s and diabetes become far more prevalent when the circadian rhythm is interrupted.

Microscopic signs of Alzheimer'sSo then, what exactly happens on the molecular level? How does disruption of the circadian rhythm influence diseases such as Alzheimer’s? As we’ve learned through the Immune System unit, macrophages engulf unwanted foreign invaders, which is one of the most critical aspects of our immune system. In the case of Alzheimer’s, one telltale is the formation of extracellular clumps of AB42, the 42 amino acid form of amyloid-β, around the brain which macrophages would typically engulf through phagocytosis (NIH.GOV). Further, “the researchers noticed oscillations in enzymes that help to make two proteins on the macrophage cell surface — heparan sulfate proteoglycan and chondroitin sulfate proteoglycan- both of which are known to play a role in regulating clearance of AB42” (RPI). As explained in the previous paragraph, if a disruption of the circadian rhythm affects our body’s immune response, this indeed entails that a disease like Alzheimer’s would only worsen over time, assuming that no regulation of the circadian rhythm would take place.

The findings seem promising, especially for a disease like Alzheimer’s which has no known cure yet. Only medicines that reduce symptoms are currently in circulation which just isn’t sufficient especially since Alzheimer’s is a prominent issue within older citizens. If scientists are able to further utilize this knowledge to help prevent Alzheimer’s from reaching high severity, then hopefully the lives of many will be improved and Alzheimer’s can be a disease of the past!

Amoeba Cells May Offer Treatment to Combat Lung Disease

Whenever attempting to (solve) complicated biological issues, especially those relating to disease treatment, typically referring back to the core principles of the biology of cells is an excellent place to start. One instance where tracing our steps back to the basics of cell biology may be the critical step scientists need to make more significant strides would be treating chronic obstructive pulmonary disease (COPD). According to Johns Hopkins Medicine, “COPD is the fourth leading cause of death in the U.S., affecting more the 15 million adults.” (Johns Hopkins Medicine). X-ray of COPD exacerbation - anteroposterior viewTreating COPD has had scientists stumped left and right at numerous roadblocks. Patients who experience COPD are constrained to one choice, living with it and treating the symptoms. No actual treatment exists to cure or effectively remove the disease from bodies. COPD isn’t necessarily much of a concern for non-smokers; however, smokers make up colossal numbers of our population, therefore discovering new methods to treat or cure COPD remains high.

Filamentous amoeba digesting two unsuspecting diatomsOften, obscure and unsuspected treatment methods offer the most ideal-even the best results. For COPD, scientists at the Johns Hopkins Medicine School took a different approach than traditional ways- utilizing far simpler cells compared to human cells to better understand the biological structure of the disease and genes that protect against the harmful chemicals of cigarette smoke.

For this experiment, the scientists utilized the Dictyostelium discoideum amoeba, which is commonly studied to better understand cell movement and communication. Briefly describing the experiment, the scientists pumped cigarette smoke into a chamber filled with the specific amoeba cells. Then, engineered amoebas were deployed to identify any genes that influence the effect of cigarette smoke. Fortunately, one family of genes did spark interest in countering the impact of COPD, the adenine nucleotide translocase (ANT) family. This gene is located on the surface of the mitochondria, which, as we’ve learned, produces Adenosine Triphosphate, or simply cell energy. When the ANT gene is highly active, “cells get better at making fuel [ATP], protecting them from the smoke”( Johns Hopkins Medicine). Not only does the ANT gene assist with protecting the amoeba from the smoke, but it also helps them overcome the damaging effects and symptoms caused by cigarette smoke.

Symptoms of COPDWhile discovering the effects of the ANT gene family on amoeba cells is highly beneficial for our overall understanding, the human application is what ultimately matters. How can we use this newfound knowledge to treat COPD in humans? Well, according to the Johns Hopkins scientists, “To better understand how ANT genes behave in humans, tissue samples of cells lining the lungs were taken from 28 people with COPD who were treated at the University of Pittsburgh and compared the lung cells’ genetic activity with cells from 20 people with normal lung function” (Johns Hopkins Medicine). The scientists learned that COPD patients experienced roughly 20% less of the ANT2 gene’s genetic expression than those with healthy/unaffected lungs. The lead scientist believes that while further research is necessary, producing medicine that increases the amount of the ANT2 gene in COPD patients may be a key component in treating the disease. Hopefully, the damage cigarette smoke has on people’s lungs becomes reversible in the future, and COPD becomes a disease of the past.








Protein Responsible for Increasing the Severity of COVID-19

The CDC reported that the first human COVID-19 case, originating in Wuhan, China, to enter the United States was on January 20th, 2020 via DNA samples. Present-day, COVID-19 has affected nearly three hundred million people worldwide according to the New York Times. Now, one would assume that this virus would have the same effects from person to person, yet it actually produces drastically different effects depending on the victim’s body composition. Some people “develop mild or no symptoms upon infection,” whereas others, “develop severe, life-threatening disease” (University Of Kent). But what exactly causes this alteration of symptoms from patient to patient? Well, researchers at the University of Kent have scrutinized through their resources to determine a possible source for this predominant world health issue.

Protein CD47 PDB 2JJS

As we’ve learned throughout units two and three, protein structure is pivotal for determining the protein’s function, and proteins as a whole are what viruses, for example, SARS-CoV-2, consist of on the molecular level. SARS-CoV-2 transmits itself through our body by binding its spike proteins to our healthy cell’s receptors, which then emits a signal to the cell, ultimately altering the genetic code of the cell, changing its function. One protein synthesized from our cells is called ‘CD47,’ a cellular surface protein, which, in broad terms, “tells circulating immune cells called macrophages not to eat these cells” (  Once SARS-CoV-2 cells begin to synthesize this surface protein, the cells become ‘protected’ from our immune system, enabling the cells to continuously reproduce and flood the body without any interference from the macrophage and other immune system anti-virus functions. Virus-synthesized CD47 on the surface of SARS-CoV-2 cells allows for the production of higher volume of virus, ultimately resulting in a more severe disease infection.

Viruses-08-00106-g001According to the researchers at the University of Kent, CD47 is far more prevalent among older people, which may provide a reasonable explanation as to why they typically exhibit severer symptoms compared to those of younger people. One condition that high levels of CD47 typically produce is high blood pressure, which forces the body to deviate by over 1o mm Hg systolic and 10 mm Hg diastolic, according to the American Heart Association. High blood pressure, specifically caused by CD47, puts people ” [at] a large risk factor for COVID-19 complications such as heart attack, stroke, and kidney disease”(University of Kent). The researcher’s data demonstrates that both age and virus-synthesized CD47 greatly contributes to more severe COVID-19 by blocking a fully functioning immune response which increases tissue and organ damage.

COVID-19 vaccines (2021) AThis finding should provoke optimism within the scientific community, understanding what causes differing symptoms-severe or less severe- is incredibly useful for combatting both the virus’s spread and severity from person to person. Hopefully, scientists will be able to further utilize CD47 research to save lives of people who are at higher risk of experiencing more severe COVID-19 symptoms.



Advancements in Molecular Imaging May Further Human Knowledge

As we’ve learned throughout unit one, protein shape and structure are pivotal for deciding the protein’s function inside of the cell. Some proteins serve as enzymes to speed up chemical processes, while others serve as antibodies to protect against infectious diseases. Some are hormones, others provide structural support. What all of these proteins have in common is their amine group and carboxyl group which are both bonded to the central carbon, or alpha carbon; consisting of hydrogen, carbon, nitrogen, and oxygen, all proteins seemingly possess the same traits. But not all proteins are the same, in fact, there are twenty different amino acids which all pay tribute to the variable R group. Yet proteins are far more complex than just their variable R group. Proteins are able to reshape and undergo complex transformations that drastically alter their function inside the cell. These complexities, along with outdated technology, have created a substantial lapse of knowledge in this field, and scientists are in dire of a better understanding of the intricacies of protein structure.

Amino Acid Structure

Taking on the challenge of creating cutting-edge technology, a group of scientists stationed at the University of North Carolina Medical School discovered a new methodology to capture live-time imagery of unique protein shape and structure. This technologically advanced technique is being coined the ‘Binder Tag,’ which, “allows researchers to pinpoint and track proteins that are in the desired shape or “conformation,” and to do so in real-time inside living cells” (UNC Health Care).

The group of scientists, led by Ph.D. Klaus Hahn and Ph.D. Timothy Elston understood that they would be attacking a “fundamental challenge” of molecular imagery; this being that working molecules inside of cells are unable to be photographed because light from standard microscopes bends irregularly around particles inside the cell, creating a nearly impossible image to render. The ‘Binder Tag’ method avoids these limitations by inserting a molecule that has received a ‘tag’ into a protein, and then a separate molecule binds to the tag once the protein undergoes some type of formation alteration. Assuming the process is done correctly, researches are able to effectively image the precise location of tagged molecules over time, documenting real-time changes in the protein shapes.

Main protein structure levels en Furthermore, “a technique called FRET (Förster resonant energy transfer), which relies upon exotic quantum effects, embeds pairs of such beacons in target proteins in such a way that their light changes as the protein’s conformation changes” (UNC Health Care). However, FRET has its own limitations, such as the fluorescent beacon may be too weak to track live protein dynamics.

Hopefully, this method can be further experimented within the scientific community so we are able to better understand the complex, dynamic world of protein structure.




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