Reducing Redundancy of Genetic Code

 A recent genetic discovery made by scientists in Cambridge could allow scientists to significantly cut down the amount of unneeded and repeating code that we often see in a gene. The study focuses in on one of the most studied bacteria in history, E. Coli. and its genetic code. Redundancy in a gene refers to different codons that all code for the same amino acid. For example, there are six different codons that all code for the amino acid Leucine. Because of this, we see hundreds of different combinations in each protein in different parts of the code that all code for the same amino acid. Scientists have begun to investigate this bloat, and are actively looking for ways to reduce it. In E. Coli, they started off by reducing the number of Serine codons from 6 to just 2 without it harming the bacteria. After the success of this experiment, they went even further, attempting to further build upon that reduction. However, doing this would mean they would have to remove or alter over 5 times more codons than what they removed in the original reduction. After a long period of trial and error, in which some changes destroyed the entire bacteria, scientists realized their dream, and Syn57, although extremely weak, was created.

The main benefits highlighted in the article are that Syn57 could potentially help create new drugs, useful molecules, or even combat against genetically engineered microbes released in the environment. The reason Syn57 could be useful in the fight against engineered microbes is due to the unnatural code being unreadable to the microbes, rendering their effects useless. If true, Syn57 can potentially open the door for other treatments of the same kind, thus being able to render any dangerous viruses or microbes ineffective. While still very early in this field, and any kind of real medical impact won't be anytime soon, the potential something like that holds is immeasurable and worth keeping tabs on. If we can find a way to make a gene or bacteria impossible for a foreign danger to read, there could be major positive impacts on our health as a society.

 

Probiotics: Biofilm Formulation Protects The Intestines and Brain

Necrotizing enterocolitis (NEC) is a deadly, debilitating disease that affects premature babies, causing inflamed intestinal tissue and even ischemia and necrosis of related tissue in severe cases. Children who manage to live to adulthood can face several lifelong challenges, like neurodevelopmental delays and short-gut syndrome. Oftentimes, NEC treatment involves surgical removal of the dying tissue.

Working to create a novel preventative solution, principal research investigators at Nationwide Children’s Center for Microbial Pathogenesis developed a probiotic system employing the durability of biofilm to improve probiotic administration to neonate patients. Hoping to demonstrate their model’s efficacy in an animal similar to humans, a piglet model of NEC was adapted to the study, providing the same care given to premature infants in terms of the medication and fluids, nasogastric tube feedings, and monitoring done and given. Overall, the data from the piglet model supported those of the initial rodent model, and the findings demonstrated that the Lr’s (Limosilactobacillus reuteri) biofilm protected both the brain and intestines from NEC, preventing the associated morbidity and mortality. 

Considering the severity of a child’s condition after developing NEC, it was interesting to learn about how bacterial biofilms (often having a negative connotation) could be applied to life-saving treatments to protect newborns. By using this piglet model, as well, we can better understand the safety issues associated with this biofilm formulation and provide a better foundation for researching neonatal risk for certain diseases. Potentially, a clinical trial may even be possible in the foreseeable future thanks to this model.

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Click here for the journal article for the study information

"Exercise Changes Our Gut Microbes, But How Isn’t Yet Clear?" Ashley Yeager

Sara Campbell, an assistant professorship in exercise science, at Rutgers University wondered if exercise could influence the microbes in the gut. Everyone knows all the benefits that come along with exercising, including keeping down inflammation and the enhancement of antioxidant defenses. Campbell realized the symbiosis and mutualism that goes on between the host and the microbes, which led to the beginning of the research process. After creating a research team, Campbell designed an experiment to analyze fecal samples of male mice that were fed a normal or high-fat diet for 12 weeks, while some mice were allowed to exercise and others were not(Yeager 2019). The mice that participated in physical activity generated a "unique microbiome in the guts" and also hosted, "Faecalibacterium, Clostridium, and Allobaculum"(Yeager 2019). In contrast, the mice on the high-fat diet, without any exercise, had inflammation in the gut. Exercising does boost the levels of gut microbes, which also produces butyrate. Which means, "exercise alone, without any dietary changes, is enough to change the composition of gut bacteria"(Sandoiu 2018). Overall, exercise has a larger impact on the human body than ever expected.

Moving more in depth into the research, looking at obese individuals who began to exercise had changes in their gut microbes. Although, lean individuals had different changes, "developed higher levels of Clostridiales, Lachnospira, Roseburia, and Faecalibacterium in their guts, but those microbes returned to baseline levels when the individuals stopped exercising"(Yeager 2019).the difference in changes between lean and obese individuals is still unknown, bur regardless of diet or body composition, change in the gut microbiota is still apparent. Researchers are still unsure of how exercise exactly changes the gut microbes, or if the changes are beneficial to the health, but are determined to find answers.

https://www.the-scientist.com/news-opinion/exercise-changes-our-gut-microbes--but-how-isnt-yet-clear-66281

https://www.medicalnewstoday.com/articles/323351.php

Web Meets Genomics

According to Science Daily, a DNA search engine has been made to identify microbes. Researches have combined their knowledge of bacterial genetics and web search algorithms to build a DNA search engine called BIGSI. This search engine could help researchers monitor the spread of antibiotic resistance genes and understand how viruses and bacteria adapt and evolve. The way this works is BIGSI would be able to detect any new microbial genome in the history of microbial DNA. This program is developed with a HUGE memory capacity and simply needs internet to store and search information.

The BIGSI program allows researchers to compare DNA of multiple bacterial species, and by doing so, we can understand how they are related. One of the main focuses of this project was to study the dynamics of antibiotic resistance. Most bacteria and viruses are responsible for many infectious diseases, and over the years, they have been able to evolve and "survive" the antibiotic treatment, thus becoming extremely dangerous to humans.

I believe that anything that is created in order to help us, especially preventing viruses and infections, is for a good cause. This program has been long in demand, many illnesses have taken place and most people have lost lives due to bacterial and viral infections. Being able to compare and analyze microbial DNA can lead us in preventing such outbreaks. For example, the outbreak of food poisoning, where the cause (which was found later) was a Salmonella strain, could have been evaluated earlier with a new and faster system as the BIGSI.

Microbes that can Survive Extreme Temperatures

https://www.sciencedaily.com/releases/2018/12/181205134105.htm
https://microbewiki.kenyon.edu/index.php/Sulfolobus_acidocaldarius

This Study focuses on the ability of Sulfolobus acidocaldarius to survive extreme heat to try and understand overall the ability for specific species of archaea to survive extreme temperatures. S. acidocaldarius has an unusual membrane (phospholipid bilayer). Usually, archaea typically do not generate an outer membrane but in this case, it creates a unique membrane to protect and thrive in extreme heat. It was found that a molecule called calditol is the reason the phospholipid membrane is so unique in this archaea. Through this study, this helps researchers relate and possibly find more clues about other microorganisms that can thrive in extreme temperatures. This could even develop into new medicinal or chemical practices and experiments.

Tropical Dish and their adaption to cold temperatures

According to scientist, they have discovered tropical fish can control their gut microbes allowing them to to have higher survival rates in extreme temperatures both cold and hot. Host microbe interactions can play an important role in the fitness of the host, demonstrating the concept of hologenome - in which an organism is not based as an individual but as a community. When analyzing the results of the tropical fish study, scientist noticed that the fish tend to select microbes that were more tolerant to the cold themselves which I found very interesting and also demonstrative of the idea of hologenome.







References:

https://www.sciencedaily.com/releases/2018/11/181120125843.htm

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290017/

Microbiomes in Fish Help them Adapt

https://www.sciencedaily.com/releases/2018/11/181120125843.htm
https://www.hsph.harvard.edu/nutritionsource/microbiome/

 

As the world slowly increases in temperature, stabile oceans which have specific temperatures also start to rise. This gives way to melting of the glaciers and increasing water levels while increasing temperature. This problem affects corals, fish, marine life and essentially, all life. However, researchers have found that many of the fish have small bacteria lining their innards and guts that coexist with the fish. They work in tandem to help the organism adapt to rising temperatures in the ocean rapidly. This was tested in the lab by using around 80 fish with modified microbiomes to check whether they were stressed or died under extreme temperatures. This breakthrough could mean that fish are evolving or are readily adapting to the changing environment.



Personal Bubble

           

            

           The human body is surrounded by many microscopic organisms that consist of microbes, chemicals, fungi, and microscopic animals called an "exposome". Scientists conducted research on 15 patients by using a small air-monitoring device which was a small vacuum that picked up any exposomes present around the person being monitored. Health is determined by a person’s DNA and the environment and no one has studied how biological and chemical exposures effect people on a personal level until now. By analyzing RNA and DNA the researchers chemically profiled the particles detected around the patient and created a database of over 40,000 species of all environmental exposures found. The studied showed that everyone has a unique exposome that is completely different from another person even if they live close together.

            Research studies like these are useful in order to determine if a person is allergic to certain microbes around them or if a microbe that they are allergic to is present. This device could also be used to detect if certain carcinogens are present in a particular environment and if the exposure is enough to affect a human being. If the chemicals can fit through the holes of the filter in the device, then it can reach a humans lower respiratory tract and affect the lungs. The more exposomes identified the more research can be done in order to determine how they affect our health.