AP Biology class blog for discussing current research in Biology

Author: golgiappajackus

Microbial Tape Recorders: A new Application to CRISPR

Research in the new gene-editing technology CRISPR has raised many red flags and ethical dilemmas as its full capabilities prove to be more than what was thought previously possible. It is used by bacteria to combat viral infections, but now scientists have repurposed it to keep records of a given bacteria’s environmental conditions, which could have significant applications to accurate chronicling of biological changes. Scientific American’s article, “Bacterial ‘Tape-Recorder’ Could Keep Tabs on Bodily Function” outlines how CRISPR “is a DNA sequence that makes and keeps a genetic record of viruses the bacterium encounters, commanding it to kill any that try to reinfect the bacterium or its descendants”. This natural function of bacteria, though, can be manipulated so that instead of exclusively accounting viral encounters, any environmental abnormality can be captured by CRISPR. More specifically, the bacterial mechanism would sense a special signal from a change in its surroundings and create trigger DNA, which, according to the U.S. National Library of Medicine, is a noticeable sequence of DNA from the invaders, which could be used to identify what exactly caused the change.

Applications of this technology today are far-reaching. This technology can be theoretically used to measure contaminants in fresh water or saltwater, or the nutrient levels in topsoil, but the predicted first application will be in monitoring bodily function in humans, and other animals. Digestion problems seem likely to be the first human system monitored with this new tool. Fructose Malabsorption is a digestive disorder which results in high levels of fructose sugar remaining in the digestive system. This disorder results from damaged intestines, normally from serious infection. Sugar levels in the digestive tract can now be monitored precisely by using this application of CRISPR in Escherichia coli cells (bacteria which are naturally found in the human digestive system). The record of sugar can identify specific problems diseased patients, after the E. coli cells are recovered from a patient’s feces, and cause them no harm in the process.

This tool is not without its drawbacks. It is reported that millions of modified bacteria need to be placed in a given system to have an accurate reading of environmental surroundings, and these bacteria have to be in the region of interest for at least six hours. The magnitude and duration of this prospective tool leave much to be desired as initial costs would be enormous, and other limitations, which can only be found through proper testing, remain unknown. In all, this advanced tool still seems applicable for now on only a small scale, but it is an example of CRISPR as a tool for good, and shows much hope for the future.

Escherichia coli bacteria which can be modified with CRISPR to become a “tape-recorder” of the human digestive system

Virus VP882: Our Forgotten Spy to End our Bacteria Problem

The virus VP882, which had long ago sequenced in Taiwan as a part of a study of an outbreak of cholera, has now resurfaced and has the potential to make major waves in our addressing of the harmful bacteria. In recent years, biomagnification of harmful bacteria, in large part due to human waste, like Escherichia Coli and Vibrio Cholerae are having immediate and detrimental effects on our environment and in human health as well. For example, a significant amount of produce circulating in the United States has been contaminated with Escherichia Coli causing many to contract Shiga toxin-prducing E. coli infection (STEC) which, as according to the Centers for Diseases Control and Prevention (CDC), can causes “severe stomach cramps, diarrhea (often bloody), and vomiting”.

Our problem today is that the production of bacteria-specific responses to infection are difficult to produce and become costly as a result. Most of our anti-bacterials today target bacteria-made toxins, in order to restore affected G-Protein cell signaling function. Unfortunately, this treatment may negatively impact the integral human microbiome. An alternative way of countering bacterial infections is through use of phage therapy. This treatment is much more specific, bringing less harm to the host organism, and involves viruses to enter and reproduce in bacterial cells, eventually causing them to lyse, thus killing them. While objectively this process seems far superior than the current general treatment, too often the infective bacteria remains unknown, which as M.I.T. Professor Mark Mimee discusses in the Scientific American article on the VP882 virus, forces doctors to prescribe “a cocktails of different phages. But manufacturing cocktails and adhering to drug regulations is too expensive.” Then enters the VP882 virus.

The VP882 virus works just as most other bacteriophages: the virus uses bacteria as hosts for their reproduction, and cause them bacteria cells to lyse, after they have hijacked a given bacterium’s reproductive mechanisms. There are two things, though which make this virus special in the realm of bacteriophages. VP882 has the ability to sense bacterial cell communication and is a very simple structure, similar to a plasmid. This virus’s discovery can in part be credited to a coincidence. A student at Princeton, Justin Silpe, in his study of a molecule, DPO, which is integral in bacteria cell signaling, specifically quorum sensing, ran across this surprising virus which was sequenced in the presence of DPO. What he and his professor, Bonnie Bassler, found is that this virus, which was attacking cholera cells, was able to secretly calculate the optimal time to invade the bacteria (thus its many comparisons to a spy), by sensing a high quantity of DPO, which is a signal for when bacteria can begin their collective behavior, and possibly start a disease. What this means is that because of this ability to understand a bacteria’s quorum, they can most effectively counteract an infection.

In addition, upon further study, VP882 was found to be a very simple structure. This arguably the most important aspect of VP882. The virus is very similar to a plasmid, which can be easily modified and, thus accepted by a plethora of bacteria. This leads scientists like Bassler and Silpe to believe that VP882 can be modified to create an all-encompassing bacteriophage treatment, one which could be made cheaply and work far more effectively than general anti-bacterial treatments. Whether this is feasible still remains unknown, but in the time being, VP882 can be readily applied to neutralizing cholera in industrial wastewater without harming the natural microbiome, proving already the usefulness of this discovery.

Discharge Tube Releasing Cholera-filled Wastewater



Our Life After Death: The Postmortem Microbiome

Research in the field of the human microbiome has lead to very interesting discoveries which could revolutionize forensic science, and add to our growing knowledge of human health. Our postmortem microbiome gives us much insight into the life of the person, based on the diversity of bacteria which remain in a given person’s system. A study, presented in a Live Science article, conducted in Wayne County Medical Examiner’s office in Detroit found that different sites on the body had different populations of bacteria. These cultures of bacteria can allow us to study the health of specific parts of a person more closely. For example, the bacteria found in a person’s mouth would vary greatly from that of the person’s eye, and the diversity of certain bacteria in these areas can correlate to a high probability of infection.

Pie charts mapping diversity of bacteria in human microbiome in various areas of the body

Specifically in the realm of forensics, a major reduction in diversity of the postmortem microbiome occurs after 48 hours of the person dying, a valuable indicator of time of death to detectives, according to study co-author and forensic entomologist at Michigan State University, Eric Benbow.


Additionally, the postmortem microbiome of a given person can act as a record of one’s heart health, in particular, whether or not that person had a heart infection in their life. Researchers of the changes in the postmortem microbiome find strong links between the lack of diversity in a person’s microbiome and susceptibility to heart disease. In particular, an abundant presence of Rothia bacteria has been linked with endocarditis, an infect of the heart’s valves. The ability to have records of human heart health after has larger implications than one may realize. It is a convoluted process to track national heart health because of the sheer number of people which must be addressed, all while they are still living. A given person would only be properly diagnosed with a heart issue like endocarditis if they were alive and had issues necessitating an intense medical processes, thus making it difficult to accurate record data on a larger scale. Now with this resource of our postmortem microbiome as a record of our heart health, large scale data collection and analysis can be conducted, thus advancing our knowledge of the topic.

The Environment’s New Clothes: Biodegradable Textiles Grown from Live Organisms

Research in the field of biodegradable materials shows promise to revolutionize the current fashion world. The dominant practice of immediately turning runway prototypes to intensely manufacture goods is an extreme threat to our environment’s future. The concept, commonly known as “fast fashion“, is one which requires vast quantities of clothing to be made for commercial purchase as quick as possible. This forces overproduction, where large corporations shoot individual purchase prices way down to tempt the consumer to buy clothes based on how little they cost. Making enormous quantities of clothes is necessary to make each trend profitable, but it is very destructive. Overproducing clothes requires huge amounts of energy, which uses fossil fuels and water, and results in a massive increase in land-fill waste, once the cheap clothes are out of style or can no longer serve their use. Today nine percent of the municipal solid waste in our landfills are clothing material according Scientific American. This issue of a rapid influx of new waste to landfills is compounded because the cheap materials used to make the clothes, traditionally plastic-based acrylics, are not biodegradable.

Clothing Production in Japanese Factory

New research has proven that it is possible to bioengineer materials from organisms such as bacteria, yeast, algae animal cells, and fungi, which leads us to believe there is a hopeful solution to the multitude of issues caused by “fast fashion’s” need for rapid overproduction. One professor’s work from the Fashion Institute of Technology,  Theanne Schiros is described in great detailed. She mainly works with algae for the production of her material. Her award-winning team, AlgalKit, has created a yarn-like substance by removing alginate, a polysaccharide in kelp, and making a water based gel, which is then died by non-chemical pigments, and is then dried to produce a colored fibrous material which is then woven into fabric. One of the large benefits from this process, as professor Schiros elaborates, is that these gels can be grown to fit molds, ultimately eliminating the massive amount of unused waste material that results from the hasty overproduction in today’s textile factories. Schiros also explains that her material is strong and flexible, which are two major criteria in choosing material to be mass-produced. In addition Schiros has looked into the possibility of synthesizing dyes for the material from bioengineered bacteria, which could supplant the use of toxic dyes normally tested on animals. Addressing both the issues of wasted resources, like energy, water, and material, and the growing problem of clogged landfills with non-biodegradable materials, algal-based fabrics in clothing shows great promise in changing the fashion industry for the betterment of our environment.

Kelp Forest used for Harvesting Alginate

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