BioQuakes

AP Biology class blog for discussing current research in Biology

Author: burrology

CRISPR Defends Bacteria, and Helps Scientists Discover New Bacterial Defenses

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On March 12, 2018

In Student Post

Although CRISPR is known for being a gene-editing tool, it can be used in other areas, such as a defense mechanisms in bacteria. This discovery “Probably doubles the number of immune systems known in bacteria,” according to a microbiologist at the University of California. Bacteria have to defend themselves against Phages, which take control over bacteria’s genetic machinery and force them to produce viral DNA. Bacteria use CRISPR to defend themselves against Phages because it stores a piece of past invaders DNA so bacteria can recognize and fight of those future viruses.

 

Photo By J LEVIN W (Own work) [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons

the researchers found that nine groups of bacterial genes were defense systems, and one system protected against plasmids. The data revealed a possible shared origin between bacterial defense systems and defense systems in more complex organisms. Some of the genes contained DNA fragments that are also  important parts of the immune system in plants, mammals, and invertebrates. The discovery of more bacterial defense systems poses the question of wether they will also be useful biotechnology tools like CRISPR is.Only 40% of bacteria have CRISPR, so scientists searched for other bacterial defense mechanisms. To do this, they looked at genetic information from 45,000 microbes, flagging genes with unknown functions located near defense genes, because defense-related genes cluster together in the genome. The researchers then used genomic data to synthesize the DNA and  inserted them into Escherichia coli and Bacillus subtilis, which can both be grown and studied in the lab. They then studied how well bacteria defended themselves during phage attacks with various genes detected. If eliminating certain genes deterred the bacteria’s defense, that determined that those specific genes were a defense system.

 

For more information, click here. For more information on CRISPR’s role in bacteria, click here.

280 Million Year Old Trees in Antarctica

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On January 18, 2018

In Student Post

Geologists have discovered 280 million year old tree fossils, which could be evidence of the oldest polar forest in Antarctica. The scientists had previously found 260 million year old tree fossil fragments, and returned to find out how a forest could have flourished there.

Credit: Erik Gulbranson

Professor Gulbranson, one of the geologists on the expedition, believes the trees must have been an extremely hearty species to survive, and “The trees could turn their growing cycles on and off like a light switch. We know the winter shut off happened right away, but we don’t know how active they were during the summertime and if they could force themselves into dormancy while it was still light out.” The polar forest grew at a latitude (geographic coordinate– location) where plants can no longer grow today, and they grew in nearly half a year of darkness and five months of continuous light. They were able to grow in these conditions because they grew during the Permian Period, where Antarctica was much warmer than today and part of Gondwana (A supercontinent which was part of Pangea).

One of the biggest challenges for the team was dating the trees. The trees could be 20 million years older or younger than their dated age of 280 million years because of the margin of error. They are still researching why polar ecosystems changed during the mass extinction at the end of the Permian period, but their current theory is that 90% of all species were wiped out because of higher global temperatures and ocean acidification. Professor Gulbranson believes his work could help understand the effects of contemporary climate change.

For more information click here.

Smile, it makes your dog happy!

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On December 10, 2017

In Student Post

Looking at your dog can bring a smile to your face, and looking at you can actually make your dog smile too!  A new study shows that dogs have an emotional response to our facial expressions; dogs like smiling faces, and don’t like angry faces. This is linked to the hormone oxytocin, which influences what and how a dog emotionally experiences what it sees. Oxytocin is a neurotransmitter, dubbed the “love hormone,” so an increase in oxytocin yields a positive reaction.

University of Helsinki researchers studied 43 domestic dogs. The dogs were presented with pictures of unfamiliar faces with happy or angry expressions. Each dog was tested twice; once under the influence of oxytocin, and once without oxytocin. The dogs reactions were determined by their gaze and pupil size, because emotions and attentiveness regulate these reactions (for more information on the relationship between pupil size and emotions, click here). According to the authors, “dogs typically focus on the most remarkable aspect of each situation, such as threatening stimuli in a frightening situation.” Therefore in the trial, dogs will focus on the most remarkable face, either the happy or angry one.

The dogs under the influence of oxytocin were more interested in the smiling faces, and the oxytocin influenced their emotional state, as indicated by their pupil size. They had a larger emotional response to smiling faces under oxytocin, because their pupils were wider. When the dogs weren’t under the influence of oxytocin, their pupils were wider when looking at angry faces, so they were more focused on and had a larger emotional response to the angry faces. The researchers concluded that oxytocin made the angry faces seem less threatening, and the happy faces seem more appealing. This is why the dogs focused on happy faces with oxytocin, and angry faces without oxytocin.

This photo is credited to Max Pixel.

To further the studies, the scientists said that more studies are needed to determine wether the results are only for domestic dogs or if the same reaction occurs with other animals. More studies should also be conducted on dogs with familiar faces, to see if familiarity would change the results of oxytocin on emotional face processing. They also added that in future studies, account of the dog breed, sex, and personality traits should be taken into account because oxytocin does not have uniform effects.

For more information, click here. For the research, click here.

Could a new bacterial test reduce the chances of new superbugs emerging?

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On October 11, 2017

In Student Post

We’ve all suffered from a nasty bacterial infection of some sort, like strep or a sinus infection. Usually, we go to the doctor and are prescribed antibiotics, and are cured in a few days. The problem with this is that bacteria are becoming multi-drug resistant and skipping over weaker antibiotics and immediately using stronger ones to increase the effectiveness. This is because to test out if an infection is resistant to antibiotics, a doctor would have to send a sample to a lab and wait 2-3 days for the results (Fore more information on standard bacterial lab tests, click here). The more antibiotics that are overused and misused, the more super-bugs (multi-drug resistant bacteria) will emerge.

Luckily, there is a new advancement in testing bacterias resistance to antibiotics. A new test has been developed at Caltech that can identify antibiotics resistant bacteria in as little as thirty minutes. The test was focused on UTI’s; they took a sample of infected urine and divided into two groups. One group was incubated, and the other was exposed to antibiotics for fifteen minutes. The bacteria were then lysed, or broken down, to release their cellular contents. The contents are then run through a process combining d-LAMP and Slip chips. This process replicates specific DNA markers which are imaged and counted as fluorescent spots on the chip.

This Photo is credited to Wikipedia

The logic behind this test is that antibiotics affects the DNA replication of bacteria, so there will be less fluorescent spots on the chip for bacteria that is not resistant to bacteria. If the DNA are resistant to bacteria, the DNA replication, fluorescent spots, will be the same in both groups. The tests had a 95% match with the standard two day test, (hyperlink info about standard test) and was tested on 54 subjects with UTI’s caused by the same bacteria, Escherischia Coli.

The creators of this test, Ismagilov, Schoepp, and Travis Schlappi, are continuing to test other bacterial infections, and hope to modify the test to be able to test blood infections. Blood infections are more difficult to test because the presence of bacteria in blood is significantly less than in urine. Having a test like this, for many types of different bacteria, which could be performed in one doctors visit would help reduce the overuse and misuse of bacteria, thus decreasing the chance of new superbugs emerging.

For more information and visuals click here.

 

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