BioQuakes

AP Biology class blog for discussing current research in Biology

Author: maxillary

CRISPR Gene “Editors” Are Making “Typos” in DNA

Two recently published studies cited two types of CRISPR gene editors that change individual bases in the DNA of mouse embryos and rice plants. While one of these worked as normal, the other introduced unintended mutations, making edits in the wrong places.

If one doesn’t already know what it is, CRISPR is a gene editing tool that can alter DNA sequences and modify gene functions. These “genetic scissors” are easy to use and are more efficient than than the previous genome-editor, TALENS. In particular, the CAS 9 enzyme allows for CRISPR to work the way it does. Recently, scientists demonstrated that CRISPR can be used to fix human genetic defects such as cystic fibrosis and cataracts in animal models.

Back to the topic at the hand, the study created an experiment to test how many accidental edits were made by three different CRISPR editors. After injecting one of the two mouse early-stage embryo cells with a CRISPR editor, the researchers used a genetic trick that made all cells that received the editor glow the color red. They separated the edited cells and the unedited cells before deciphering both of the groups.

Two of the gene editors, the CRISPR CAS9 as well as a base editor that changes adenine to cytosine, didn’t cause any more mutations than unedited cells. For the CRISPR CAS9 editor, this means that that the CAS9 enzyme were making cuts as intended. However, the base editor that changes cytosine to thymine caused 20 times more mutations than that of unedited cells. According to David Liu, a chemical biologist whose team created the two base editors, the cytosine changing enzyme can “grab single-stranded DNA that it gets close and make edits on its own.” The tighter these cytosine base enzymes bind to the DNA, the more likely the editor can introduce mistakes into the DNA.

Obviously, these editors need revising and improvement. “The community needs these worst-case scenario pressure tests so we can make sure there’s a good margin of safety when these agents do enter clinical trials,” says David Liu. He then assures that “newer versions of the cytosine base editors don’t bind to DNA as tightly” and that “more recent versions will produce fewer typos.”

Bears Are Adapting To Our Unbearable Drones

A recent paper by Mark A Ditmer’s researchers offers some insight that suggests that American black bears are adapting to the exposure of unmanned drones.

An American Black Bear
Photo Credit: Stephan Oachs

These drones are used mainly for conservation purposes to gather data in various environments. Yet, animals are known to be disturbed by low flying drones, displaying changes in animal behavior when drones are near. In fact, many animals display behavioral signs of fear towards a low flying drone.

However, most recently, Ditmer’s group of researchers discovered American black bears are adapting to the presence of drones after repeated exposure. The researchers performed used drones previously before not using them for 118 days. Afterwards, they began drone tests again. Immediately, using cardiac biologgers, the researchers saw signs of increased tolerance from American black bears to drone presence.

Something to note is that this tolerance to drone exposure is probably species dependent. In particular, more social animals that interact with humans frequently are assumed to have higher tolerance drones. This implies that the American black bear has evolved and habituated to human exposure and, as a result, have increased tolerance after repeated exposure to unique stimuli.

Despite this discovery, Ditmer warns that “close-proximity drones near wildlife should [still] be avoided.” However, he expresses that this new discovery “can provide benefits without long-term high-stress consequences” for drones with conservation purposes.

 

Cellular Roadblocks for Immigrants: The Loss of Gut Microbe Diversity

Recent evidence from the University of Minnesota in conjunction with the Somali, Latino, and Hmong Partnership for Health and Wellness suggested that immigrants and refugees moving to the United States were likely to experience a rapid change in their gut microbes. Described as “westernizing” to their environment, immigrants tended to lose their diverse, native microbes in favor of microbes that are common to European Americans.

The participants of this study originated from Southeast Asia, specifically the ethnic minorities of Hmong and Karen from China, Burma, and Thailand. The study used ethnic minority communities from both Southeast Asia as well as those living in Minnesota as a comparison, analyzing the gut microbes in these participants and using Caucasian American people as controls. The researchers also looked into the first generation children of these immigrants. Additionally, the study was able to follow a group of nineteen Karen refugees, tracking the changes in their gut microbes as they traveled to the United States.

The study discovered that the gut microbes in these participants changed rapidly. Particularly, in the group of Karen refugees, the Western strain of Bacteriodes replaced the non-Western strain of Prevotella in the matter of less than a year. Furthermore, the overall gut microbe diversity continued to decrease in all participants in the United States in relation to the length of their stay. Likewise, the children of immigrants had a more profound decrease in diversity. Researchers in this study suggested that this decrease in microbe diversity may have been a result of a Western diet, or for the children, growing up in the United States.

Image result for bacteroides

Closeup of Bacteroides biacutis(Image Credit: CDC/Dr. V.R. Dowell)

 

So why does this matter? Well, the study established a correlation: the greater the “westernization” of gut microbes, the greater obesity in immigrants. This obesity problem appeared to be more prevalent in immigrants, and the study had discovered a key piece of evidence for why.

“When you move to a new country, you pick up a new microbiome.” Dan Knights, one of the key authors of the study as well as a quantitative biologist at the University of Minnesota, says. “…What enzymes they carry…may affect the kinds of food you can digest and how your diet affects your health. This may not be a bad thing, but we do see that Westernization of the microbiome is associated with obesity in immigrants.”

 

A Fintastic Discovery

Sharks have interesting biological features: a cartilage skeleton, highly developed senses, dermal denticles, and an oil-storing liver. However, these traits are difficult to identify within the huge genomes of sharks.

 

Previously, the genomes for sharks were larger than many other organisms, making it difficult for scientists to decode and understand the genetic background behind the lifestyle of sharks. However, the Japanese team at RIKEN Center for Biosystems Dynamics Research managed to decode whole genomes of two species of shark: the brown banded bamboo shark and the cloudy catshark. They also improved the genome sequences of the whale shark.

Image result for whale shark of sharks

Whale shark Photo Credit: Zac Wolf

Whale Shark

According to the RIKEN team, the large genomes in many shark species was a result of huge, repetitive insertions within the genome. Additionally, it was discovered that these shark genomes have been evolving at a slow rate, suggesting that sharks have kept some characteristics that were similar to distant ancestors.

 

Already, particular parts of the shark genome revealed certain characteristics of sharks. Using the DNA from the shark genomes, researchers discovered that the rhodopsin pigments in a whale shark can sense short wavelengths, allowing them to see at 2000 meters below the water level when they aren’t hunting on the surface. Furthermore, the team determined that there were too few olfactory genes in the shark genomes, meaning that the highly developed navigation system is not done through smell.

 

These results help fill the gaps in the genetic background in sharks while understanding the way sharks live. Keiichi Sato, deputy director of Okinawa Churaumi Aquarium, says, “Such understanding should contribute to the marine environments as well as to sustainable husbandry and exhibitions at aquariums that allow everyone to experience biodiversity up close.”

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