AP Biology class blog for discussing current research in Biology

Author: ryzouak

From Bacteria to Biotech: The Surprising Similarities in Immune Systems

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.

Biomaterial Breakthrough: A New Hope for Heart Attack Patients

In the world of science and medicine, new breakthroughs are always being made. In very recent news, a team of researchers from the University of California San Diego has created a game-changing biomaterial that could be the answer to treating tissue damage caused by heart attacks. This new discovery is not only exciting for those suffering from heart conditions, but it also showcases the importance of understanding cell and tissue repair in AP Biology.

Here’s how it works: the biomaterial, which can be injected intravenously or infused into a coronary artery in the heart, is made from a hydrogel derived from the extracellular matrix (ECM) of cardiac muscle tissue. The hydrogel forms a scaffold in damaged areas of the heart, promoting cell growth and repair. In previous studies, the team had already proven the effectiveness of the hydrogel when injected directly into the heart muscle. However, this method could only be used a week or more after a heart attack, as injecting sooner could cause damage during the procedure.

But this new biomaterial takes things to the next level. It’s put through a centrifuge to sift out larger particles, leaving only nano-sized particles, and then undergoes dialysis and sterile filtering before being freeze-dried. Adding sterile water to the final powder results in a material that can be infused into a blood vessel in the heart or injected intravenously, allowing for immediate treatment after a heart attack.Depiction of a person suffering from a heart attack (Myocardial Infarction)

And that’s not all! The biomaterial was tested on rodent and porcine models of heart attacks, and researchers found that not only did it pass through blood vessels and into the tissue, but it also bound to cells and closed gaps in the blood vessels, reducing inflammation and accelerating healing. In addition, the team tested the hypothesis that the same biomaterial could help target inflammation in rat models of traumatic brain injury and pulmonary arterial hypertension.

So, why is this important from an AP Biology perspective? Well, in the course, we’ve learned about the body’s ability to repair and regenerate cells and tissues. By mimicking the B blood cells’ ability to reduce inflammation and react to an infection, this new biomaterial is a prime example of how that knowledge can be applied in the real world to help improve human health. It’s a new approach to regenerative engineering, and the possibilities of treating other difficult-to-access organs and tissues are endless.


The researchers, along with Ventrix Bio, Inc., a startup co-founded by lead researcher Karen Christman, are hoping to receive FDA authorization to conduct a study in humans within the next one to two years. This is exciting news for those affected by heart conditions, and we can’t wait to see what the future holds for this groundbreaking biomaterial.

Are Rats Really Interacting With Reef Fish???

A new study has found that the presence of invasive rats on tropical islands is affecting the territorial behavior of fish on surrounding coral reefs. The rats, which arrived on the islands as stowaways on ships in the 1700s, change the behavior of jewel damselfish, a herbivorous species of tropical reef fish that “farm” algae in the branches of corals.Microspathodon chrysurus

The study, which was led by scientists from Lancaster University in the UK and involving researchers from Lakehead University in Canada, was published in Nature Ecology and Evolution and compared five rat-infested and five rat-free islands in a remote archipelago in the Indian Ocean. The rats disrupt an important nutrient cycle by attacking and eating small resident seabirds and their eggs, leading to a drop-off of nutrients in the seas surrounding rat-infested islands. This results in a lower nutrient content of seaweed for herbivorous fish, such as the damselfish. The damselfish around rat-infested islands behave less aggressively and need to have larger territories due to the lower nutrient content of the algae.

Seabirds travel out into the open ocean to feed and return to nest on islands. The seabirds then deposit nutrients, through their droppings, onto the islands, and many of these nutrients are subsequently washed into the seas, fertilizing the surrounding coral reef ecosystems. On islands with invasive rats, the rodent populations decimate the seabirds, leading to seabird densities that are up to 720 times smaller on rat-infested islands. This results in much less nitrogen flowing onto the coral reefs around these islands.

Seabirds LC0141

Around islands with intact seabird populations, the farming damselfish aggressively defend their small patch, typically less than half a square meter, of the reef to protect their food source – turf algae. However, the scientists observed that farming damselfish on reefs adjacent to rat-infested islands were much more likely to have larger territories and were five times more likely to behave less aggressively than those who lived on reefs adjacent to islands without rats. The damselfish around rat-infested islands need to have larger territories because the algae around rat-infested islands is less nutrient-rich due to the missing seabird-derived nutrients.

NSW seabed 1

This behavior change in the damselfish could potentially have wider implications for the spread of different species of coral, the distribution of other reef fish, and the resilience of damselfish over generations due to changes in hereditary traits. Changes in behavior are often the first response of animals to environmental change and can scale up to affect how and when species can live alongside one another. This study is the first to show that invasive rats can change the behavior of coral reef fish in this way and highlights the importance of understanding and managing the impacts of invasive species on ecosystems.

Students in our AP Biology class are likely to be familiar with these concepts of nutrient cycling and the importance of nutrients in supporting the growth and productivity of an ecosystem. The study highlights how the nutrient cycle on coral reefs is disrupted by the presence of invasive rats, leading to a drop-off in nutrients in the surrounding seas and a lower nutrient content of seaweed for herbivorous fish. This can have consequences for the growth and productivity of the coral reefs and the overall health of the ecosystem.

SARS-CoV-2 Is Making My Heart Ache??

New research from the University of Maryland School of Medicine’s (UMSOM) Center for Precision Disease Modeling identifies the specific protein in SARS-CoV-2, the virus responsible for COVID-19, that causes damage to heart tissue.

Protein Structure Gif

Some experiments they did were performed on fruit fly hearts. When Nsp6 is present in a fruit fly heart, the heart shows structural defects compared to a normal heart without the viral protein. However, when fruit fly hearts with the viral Nsp6 protein are treated with the drug 2DG, the hearts begin to resemble normal hearts more closely.

In their latest study, researchers found that the Nsp6 protein is the most toxic SARS-CoV-2 protein in the fruit fly heart. They also discovered that the Nsp6 protein hijacks the fruit fly’s heart cells, activating the glycolysis process and disrupting the mitochondria, which produce energy from sugar metabolism. When they blocked sugar metabolism in fruit fly and mouse heart cells using the drug 2DG, they found that it reduced the heart and mitochondria damage caused by the Nsp6 viral protein.

Dr. Han, the lead researcher, says this about the protein : “We know that some viruses hijack the infected animal’s cell machinery to change its metabolism to steal the cell’s energy source, so we suspect SARS-CoV-2 does something similar. The viruses can also use the byproducts of sugar metabolism as building blocks to make more viruses,”


Drosophila melanogaster under microscope

Thus, the University of Maryland School of Medicine’s research identified the specific protein in SARS-CoV-2 that causes damage to heart tissue and has found a potential treatment for it. The protein, called Nsp6, activates the glycolysis process in heart cells and disrupts the mitochondria, which are responsible for producing energy through glycolysis and oxidative phosphorylation. By blocking the processes  with the drug 2DG, the researchers were able to reduce the heart and mitochondria damage caused by Nsp6. This discovery aligns with the topic of glycolysis and ATP generation in AP Biology as it highlights the importance of proper metabolism in the functioning of cells and the potential consequences of disruptions to this process.


Would You Have Survived the Black Death?!?!

New research from McMaster University, the University of Chicago, the Pasteur Institute, and other organizations suggests that during the Black Death, 700 years ago, there were select individuals whose genes actually PROTECTED them from the devastating population-crushing Bubonic Plague.

Model of bubonic plague bacteria - Smithsonian Museum of Natural History - 2012-05-17

The Bubonic Plague, later nicknamed the Black Death after many realised people would develop blackened tissue on their body postmortem, due gangrene(the death of tissue due to lack of blood flow). “It remains the single greatest human mortality event in recorded history, killing upwards of 50 per cent of the people in what were then some of the most densely populated parts of the world.” (

The team researching this genetic phenomena collected DNA from the deceased 100 years before, during and after the Black Death. They collected samples from the greater London area, as well as some parts of Denmark to accurately represent Upon searching for evidence of genetic adaptation, they found 4 different genes prevalent in the pandemic survivors, all of which are protein-making genes that are used in our immune systems, and found that versions of those genes, called alleles, either protected or rendered one susceptible to plague. We in AP Biology will soon learn more about alleles in higher depth, for they are imperative in the genetics of almost every DNA-carrying organism’s survival.

People with two identical copies of a gene named ERAP2 were able to survive the Black Plague at significantly higher rates than those who lacked that specific gene. “When a pandemic of this nature …  occurs, there is bound to be selection for protective alleles in humans … Even a slight advantage means the difference between surviving or passing. Of course, those survivors who are of breeding age will pass on their genes”.- evolutionary geneticist Hendrik Poinar. Mr. Poinar’s analysis of this research poses a unique and interesting question. Does the natural selection that occurred during the Bubonic Plague mean that you and I have a higher chance of having this gene in our DNA? If another plague with a similar biological makeup to the Black Death, would our bodies be better suited to find it?

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