AP Biology class blog for discussing current research in Biology

Tag: E Coli

Cracking the Code of Shigella

In the article titled, Scientists discover the possible triggers for bacterial pathogens, opening the door for new treatment strategies, the reporter discusses how Alexander Fleming’s unintentional discovery represented a crucial turning point in medical history and sparked the creation of several additional antibiotics, saving countless lives in the process. This famous Scottish pharmacist discovered penicillin, the first antibiotic, in 1928 and since then many others have followed in his footsteps. Additionally, his discoveries led to the idea that “extraordinary appearances” should not be ignored. His famous sentiments hold true to multiple scientific discoveries, including a group of scientists at UNLV who are studying shigella.

Shigella stool

Shigella is a harmful bacteria that can cause many issues in the human body such as stomach cramps, fever, diarrhea (which is frequently bloody), and can also be fatal. Shigella infection is an intestinal ailment caused by a family of bacteria called shigellosis. Shigella spreads quickly. When individuals come into touch with and ingest quantities of germs from an infected person’s feces, they get infected with shigella. 

Initially I was not engaged with this topic because I had no idea how it could be relevant to my life. However, my recent work as an EMS volunteer has proved me wrong. Although I have not seen a patient who had shigella, I have observed many other patients who experienced similar bacterial diseases and am eager to find the best way to treat them. 

Moreover, these  scientists are focused on the proteins in shigella that are called VirB. VirB proteins act as a switch in the bacteria and bind to Shigella by interacting with Shigella’s DNA. This interaction between VirB and Shigella’s DNA is a key step in the process that activates the bacterium’s virulence genes. Essentially, the DNA is what causes disease in people. Researchers found that by interfering with the way VirB bonds to the shigella, they can minimize the effects it has on humans. 

Furthermore, this research is largely important to the understanding of how proteins such as VirB are able to turn harmless bacteria into deathly ones. Moreover, this insight is also helpful in the development of treatments for other diseases such as Campylobacteriosis, E coli, and Cholera which are caused by similar proteins in different bacterias.

After studying Organic Compounds in my AP Biology class, I was able to make connections to the material we have learned such as the different protein structures which heightened my interest in this topic even more. The reason that similar proteins are able to cause so many different diseases is because of the altercation in protein shape as well as body response. All proteins have specific shapes and structures that determine how the protein will interact with the human body. Additionally, there are four main protein structures including primary, secondary, tertiary, and quaternary which all play a role in how proteins behave. Moreover, all proteins have side chains which provide characteristics and make them different from one another. The side chains in proteins give amino acids characteristics and by changing one small detail you will change the structure (shape) of the protein and thus how it interacts with the human body.

To continue, E coli is a type of bacteria frequently discovered in both the human and animal intestines. Since it aids in digestion and the creation of several vitamins, it is often safe and even advantageous. However, some E. coli strains have the potential to be dangerous and contagious.

1999 Escherichia-coli

However, the most important factor in this research is a molecule known as CPT, which is short for Camptothecin. Camptothecin was first identified as a topoisomerase inhibitor in 1966. Topoisomerases are nuclear enzymes involved in DNA replication (and more). To understand its role, you can think of Camptothecin as a key part in a puzzle involving Shigella. VirB acts as a switch to turn on the bacterium’s ability to cause disease in the human body. For this switch to work correctly, it needs Camptothecin. Camptothecin is the key that enables VirB to bind to Shigella’s DNA, which then activates the disease-causing process.

In all, the researchers are interested in interfering with this binding process. By doing so, they aim to prevent Shigella and many more diseases from making people sick.

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


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.


Great Pine Tree In Vozdvizensky Forrest

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”

Xylem Stained

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.

Escherichia coli electron microscopy

E.coli Electron Microscopy


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

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. 

Genetic Engineering on Gut Bacteria!?

E. coli on MAC – Photo credit to VeeDunn on flickr under Creative Commons License

Researchers at the Wyss Institute at Harvard University has successfully tested a genetically engineered signaling bacteria within a mouse’s gut. Having known that the many types of bacteria in the human gut can communicate through “quorum sensing” , researchers set to observe a particular type of quorum sensing, acyl-homoserine lactone sensing, which has not been observed in the mammalian gut. They wanted to test if using that particular type of signaling could create a genetically engineered bacterial information transfer system.

Using a strain of E. coli bacteria, they created two different colonies, each with a different genetic change: one was the “signaler”, it contained a copy of the luxl gene which produces a quorum-sensing molecule when activated, and the other was the “responder”, which contained a “cro” gene turning on a “memory element” in the responder.  This “memory element” expressed another copy the the pro gene, which allowed for the loop to continue, and the LacZ gene, which made the bacteria turn blue!

LacZ gene expression – Photo credit to Viraltonic on Wikimedia Commons under Creative Commons License

The researchers analyzed fecal samples of mice given signaler and responder E.coli and they were happy to see the signal transmission, blue coloring, was evident in the samples. This result meant that they had created a functional communication bacteria system in the mouse’s gut.

The researchers then repeated their experiment with a different type of bacteria, S. Typhimurium, as the “signaler” and E. coli as the “responder”, and they were pleased to see similar successful results.  They were able to successfully confirm that is possible to genetically engineer these communication circuits between different species of bacteria in the mammalian gut microbiome.

These tests are merely stepping stones for the bigger goal of creating genetically modified bacteria that will help humans in various different ways: detecting and or curing diseases, improving digestion, and so on. Isn’t it cool that something we barely realize is inside us has such a developed communication system that we might soon be able to cultivate more benefits from? What do you think would be some other benefits to be being able to genetically modify our gut microbiomes?



Have No Fear, Gut Microbes Are Here!

Ever dream about being a real life Captain America? Well, with the help of microbes, we are one step closer to achieving a “super soldier.” Microbes might not make a soldier muscular, but they can help with soldiers’ health and versatility. Scientist Jeff Tabor is working on engineering a probiotic organism that can help humans easily fight diseases, prevent obesity, and change their body’s ability to adapt to certain environments.

The gut bacteria affects many functions of the human body. The digestive system, immune system, and nervous system are all influenced by gut bacteria. Disrupting these microorganisms can cause indigestion, a weak immune system, depression, insomnia, and affect other cognitive abilities. Tabor’s goal is simply to create a microbe that can be consumed to prevent these problems.

Gut Microbe

Gut Microbe

Initially, Tabor wanted to use these microbes to target obesity because scientists have abundant knowledge of obesity at the molecular level. He recently succeeded in genetically modifying E.Coli to detect chemicals in the body that carry disease in mice guts. He hopes to use this modified E.Coli to sense chemicals in the gut that are connected to obesity and then use other molecules to prevent this obesity. The creation of a microbe that can control weight can be extremely helpful for the U.S. armed forces. For example, soldiers going from sea level to the top of a mountain way above sea level experience changes in temperature and pressure. Using this engineered gut microbe, the soldiers can put on weight to help them keep warm on top of the mountain and then lose weight to keep cool at sea level.

Another military benefit that these microbes can provide is to help soldiers operate effectively on little to no sleep or to help soldiers adapt to changes in their circadian rhythms, either from time change or going below sea level in a submarine. Scientists are interested in experimenting with the gut microbe to be able to achieve these goals in the future.

Some people might be afraid of the possible affects that these genetically modified bacteria might have on the human body. However, Tabor’s goal is for the bacteria to stay in the gut for about six hours to do its job and then self-destruct or die naturally to prevent the bacteria for staying in the body too long. There are other concerning issues about creating a microbe that can help prevent obesity. The creation would take away any incentive for humans to eat healthy and focus on their diets because they could just use the microbe to prevent gaining weight. Any new scientific experiment comes with its pros and cons, but using gut microbes for human health, especially for the military, can be a big step in the right direction.

Source Article

Bringing the Human Gut Microbiome into the Light

The human gut microbiome is an incredible system of symbiotic organisms. These micro-organisms that provide us with vitamins and amino acids as well as break down toxins and protect us from harmful invaders. We could not live without them and they could not survive without their host, us. We carry over 3 pounds of these little helpers in our body and outnumber our cells. Although this system is so important to our survival, it has been hard to study for long periods of time, until now. Judah Folkman, professor of Vascular Biology at Harvard Medical School states, “”Until now, use of traditional culture methods and even more sophisticated organoid cultures have prevented the microbiome from being studied beyond one or two days. With our human gut-on-a-chip, we can not only culture the normal gut microbiome for extended times.”

 Escherichia coli

E. Coli 10000x magnified

The human gut-on-a-chip is constructed from a clear, flexible polymer roughly the size of the a flash drive. This chip simulates the environment of our gut so well that cultures can last up to weeks. This extended period of time can allow for major breakthroughs in the study of the microbiome and what happens when things do not go as planned. Judah Folkman adds, “we can also analyze contributions of pathogens, immune cells, and vascular and lymphatic endothelium, as well as model specific diseases to understand complex pathophysiological responses of the intestinal tract.”


The Wyss team thinks that this new technology can help treat patients by eventually culturing there own cells and microbiome on the human gut-on-a-chip to test different treatments. This new technology, although not directly discovering anything about the human gut microbiome, will lead to major discoveries down the line.


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Bacteria become ‘genomic tape recorders’, recording chemical exposures in their DNA


MIT Engineers have developed a way to create genomic tape recorders out of the Bacteria E. Coli. Timothy Lu, an engineering professor at the university describes the method by which they altered the bacterial DNA in order to allow it to store information. The researchers engineered the cells to produce a recombinase enzyme which can insert a certain sequence of Nucleotides into the genome. However, the trait is useful because the enzyme is activated by specific stimuli. In order to retrieve the information the researchers can either sequence the genome and look for the specific code or look for the trait expressed by the targeted gene by using antibiotics. This process will be useful in the future because of its ability to store long term biological memory. Also, this process transcends previous limitations of genome storage as it is now able to indiscriminately store data as opposed to previous methods that were only able to identify a specific stimulus.

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