BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: DNA sequence

173 Species of Gut Bacteria Newly Sequenced!

The health of our gut is essential to the everyday function of our body — our gut focuses on the breaking down, transfer and excretion of the food we eat. As such, the balance of bacteria within our gut especially when it comes to breaking down molecules. In particular, the bacteria in the lumen of our colons “ferment the carbohydrates to short chain fatty acids, which are absorbed to provide a second energy source” (Warell, Cox and Firth). Due to the importance of bacteria within the gut, research and advancement in the gut weighs heavily on our ability to interact with problems involving digestion — obesity being a prominent one.

At the Wellcome Trust Sanger Institute, 173 species of bacteria were sequenced for the first time, including 105 species that were isolated for the first time as well. It’s incredible that so many species were identified and isolated for the first time all in one institution. To those who don’t know, DNA sequencing is a process that determines the genetic details of a DNA section: in this case, the DNA sequencing helps scientists determine the genetic information of gut bacteria. This genetic information is highly useful in determining the effects of bacteria — as DNA directly affects the production of proteins, like enzymes in the gut.

While research on the gut relied on mixed-samples of gut bacteria, this new research frees scientists to better identify and isolate each component species. The very foundation of bacteria research has shifted with so many species of bacteria finally open to more specific experimentation, and I’m so excited to see that even the basics of gut research has completely advanced. Not only does this show us the ever-changing advancement of how scientists conduct research and create experiments, but this also holds so much hope for the future: our gut holds importance within our day to day well being, and the ability to conduct much more specific experiments will open up our ability to treat different gastrointestinal disorders.

CRISPR/Cas9: A New Means to Alter Genes

Biologists can now control genetic inheritance in mammals with a CRISPR/Cas9-based approach, which allows geneticists to alter parts of the genome by removing, adding or altering sections of the DNA sequence.  Scientists have sought a way to make precise changes to the genome of living cells for a long time, and now they actually can. You may ask, what are CRISPR and CAS9? Why are they important? Simply put, “The functions of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and CRISPR-associated (Cas) genes are essential in adaptive immunity in select bacteria and archaea, enabling the organisms to respond to and eliminate invading genetic material.”  Thus, this recent discovery has created the groundwork for developing new ways to fight diseases. UC San Diego researchers are responsible for this breakthrough. First, they injected a mouse with an engineered active genetic “CopyCat” DNA element into a Tyroisinase gene. The Tyroisinase gene determines fur color. The CopyCat element “disrupts” both copies of the Tyroisinase gene, causing the mouse to have white fur instead of black. The CopyCat element, however, could not spread through a population by itself, unlike the CRISPR/Cas9 systems, which could. This approach, though, was effective only in female mice, not in male ones, likely because of timing differences in meiosis – “a process that normally pairs chromosomes to shuffle the genome and may assist this engineered copying event.” The findings are nonetheless a success. Scientists are optimistic they will be able to alter multiple genes and traits using the same techniques in the near future. Cooper, one of the researches, summed up their achievement nicely: “We’ve shown that we can convert one genotype from heterozygous to homozygous. Now we want to see if we can efficiently control the inheritance of three genes in an animal. If this can be implemented for multiple genes at once, it could revolutionize mouse genetics,” said Cooper. More importantly, these findings continue to speed up research into diseases like cancer and mental illness.

Related image

CRISPR-CAS9 — “How the genome editor works”

Diesel Exhaust Causes Changes Within

Diesel Exhaust

Two hours of exposure to diesel exhaust fumes has proven to show fundamental health-related changes in biology by switching some genes on and others off.

A study put volunteers in a polycarbonate-enclosed booth and had them breath diluted and aged exhaust fumes. These fumes were about equal to the air quality along a Beijing highway. The researchers examined how the exposure affected the chemical coating that attaches to many parts of a person’s DNA. The coating they were referring to is carbon-hydrogen coating, also known as methylation. The coating can silence or dampen a gene and prevent it from producing a protein. Methylation is a mechanism for controlling gene expression.

The study found that diesel exhaust caused changes in methylation located at about 2,800 different places along a person’s DNA, which affects about 400 genes. Some places led to more methylation. How these changes affect health is the next topic of research. However, the AstraZeneca Chair in Occupational and Environmental Lung Disease claims that the fact that DNA methylation was affected from only two hours of exposure is a positive implication; when something happens that quickly, it usually means you can reverse it through either therapy, change in environment, or change in diet.

This article is very similar to what we are learning about methylation and epigenetics. It discusses how the environment can affect someone’s genes and their gene expression as opposed to solely being their DNA sequence. I found this interesting because diesel exhaust is something people are exposed to everyday and it is important to know the affects it can have other than just respiratory issues.

Source:

http://www.eurekalert.org/pub_releases/2015-01/uobc-bid010715.php

http://aqicn.org/city/beijing/

http://www.whatisepigenetics.com/dna-methylation/

http://commons.wikimedia.org/wiki/File:Diesel-smoke.jpg

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