BioQuakes

AP Biology class blog for discussing current research in Biology

Author: linbicdendrite

CRISPR Inhibited by Nucleosomes

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On April 13, 2016

In Student Post

CRISPR/Cas9 is currently being researched as a method to alter genes by editing or silencing them. This enzyme is derived from bacteria and archaea that use it to protect themselves from viruses. Researchers are currently finding more practical applications for this discovery. However, it has been recently been found that nucleosomes may play a large effect on CRISPR.

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Structure of a Nucleosome

At UC Berkeley, researchers have been studying the interaction of these prokaryotic enzymes with eukaryotic cells. They have found that nucleosomes may inhibit CRISPR/Cas9. Because bacteria likely do not use this enzyme to explore eukaryotic chromatin structures, their enzymes are not adapted to these types of structures. This is seen by many of the researchers’ experiments where stretches of DNA with low concentrations of nucleosomes had higher activity of CRISPR while others stretches with high concentrations of nucleosomes had lower activity. Scientists have also added chromatin remodeling enzymes while using CRISPR and found higher activity.

This has a few implications on the usage of the enzyme. While gene editing may be less influenced because only one cut is needed to introduce a sequence, scientists should take nucleosome concentration into account in gene silencing and epigenetic editing. CRISPR/Cas9 is an amazing discovery for genetics but we still have much to learn about how it works and how we can use it.

Original Article

Invasive Troubles

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On March 10, 2016

In Student Post

In the 2000’s a container ship carrying Asian toads arrived in Madagascar. Invasive species have a reputation have a reputation for causing an imbalance in local ecosystems. However, what has happened with the Asian toads in Madagascar since then?

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Photograph of Asian Toad taken in Thailand

A new report says that the eradication of the species from Madagascar is “not currently feasible.” Estimates place their current population at around 4 million. Each female toad can lay an average of 20,000 eggs each year. Although most don’t survive, their population is not going down anytime soon. Scientists estimate that keeping the population stable would require 1.5 million toads killed each year while eradicating the population would require 2.5 million toads killed per year. It wouldn’t be very expensive, but no one knows where to look for these toads, let alone kill over 60% of its population.

As a result of being a new introduction into the ecosystem, predators do not have any way of dealing with this toad. Since the Asian toad is also poisonous, predator populations can decline. This can have profound effects on the ecosystem, one of which the further decline of the snake population. Snakes are also predators for rodents. If their population is allowed to skyrocket, diseases can run rampant. Industries and commercial items can be overrun. Toads can also directly affect the human population if humans decide to try and eat them.

If nothing is done, which is probably the most likely case, the toad population will go past the point of recovery similar to the case of the introduction of cane toads to Australia. Madagascar’s only choice is to attempt to adapt to this invasion.

Original Article

Dysbiosis: Does Imbalance Help?

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On January 9, 2016

In Student Post

The gut microbiome is a very large collection of mutualistic relationships between microorganisms and an animal. In our case, these microorganisms control very much of the digestive tract and have influences throughout the body. Crohn’s disease is something that can happen due to imbalance in this microbiome or “dysbiosis“. Usually marked by inflammation in the digestive tract, this disease is a result of an autoimmune response against possibly microbial antigens. Although there is no cure, scientists have determined the best course of action is to relieve the symptoms. This results in disruptions to the gut microbiome.

Inflammation of the colon due to Crohn’s disease

Scientists studying responses in the gut microbiome have found that treatment for Crohn’s disease have caused various responses in the people in the experiment. Antibiotics have been found to decrease bacterial growth in the tract while allowing fungus to grow more freely. Formula diets relieved inflammation and other symptoms but didn’t repair bacterial balance in the microbiome. Immunosuppressants decreased inflammation and bacterial dysbiosis at the expense of increasing fungal dysbiosis. All these methods don’t seem to work out.

But what if the microbiome does not need to be restored to remain healthy? Formula diets caused more dysbiosis but were able to alleviate symptoms. Suddenly, the microbiome does not seem to be as necessary as previous studies suggest. However, this experiment only measures a few variables. Results beneficial to treatments for Crohn’s disease may cause something bad to happen elsewhere in the microbiome. Replacing the gut microbiome would definitely have massive side effects.

Perhaps one day, we could find some way to substitute parts of our mutualistic relationship with the bacteria inhabiting our gut. However, that day seems far off. For now, we should probably stick with what we have.

Original Article

Degenerative Evolution?

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On November 18, 2015

In Student Post

Myxozoa are tiny parasites that infect fish stock and other aquatic life. Once thought to be unicellular, these multi-celled organisms have recently been analyzed more closely. Containing more than 1300 different species, these highly unusual microorganisms had their DNA sequenced by researchers at the University of Kansas.

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Triactinomyxon stage of Myxobolus cerebralis

Myxozoa show many similarities to cnidarians, a phylum that contains jellyfish, corals, and sea anemones. One of the key similarities is the presence of the nematocyst, a weapon or defense mechanism that members of the cnidaria phylum possess. This and other traits were once attributed to convergent evolution. However, this theory was debunked by their gene sequences. On further inspection, these microorganisms are actually tiny jellyfish living on other organisms.

The average cnidarian contains 300 million base pairs. However, Myxozoa have been stripped down to about 20 million base pairs, 15 times less. Despite this reduction in genome size, Myxozoa still contain the genes to express the creation of a nematocyst. These microscopic organisms have one of the smallest animal genomes reported.

The categorization of these organisms is shaking up the foundation of what we can call an “animal.” In the past, animals were classified by whether they had certain genes instrumental in their development such as Hox genes, genes that influence body structure. Myxozoa have no such gene. Since organisms are also classified based on their ancestors, this fumbles the system.

Because of this discovery, scientists are questioning whether this type of backwards evolution from a macro-organism to microorganism is more common than we think. Other microscopic organisms could potentially become “animals” as a result.

This also opens a gate to greater understanding of the organisms in our aquaculture. Many fish are affected by the parasitic nature of Myxozoa.

Next time you eat salmon, notice that you could also unknowingly be eating tiny parasitic jellyfish.

Original Article

Portabella Batteries

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On October 18, 2015

In Student Post

People are always complaining that their cellphone batteries are inefficient. Our current industries use a lithium ion battery in many consumer products. In these batteries, synthetic graphite is used as the anode in the chemical reaction that supplies power to our devices. However, the production of these anodes is very cost inefficient and harmful to the environment.

Diagram of Lithium Ion Battery

Researchers at the University of California Riverside Bourns School of Engineering have found an alternative anode in the form of Portabella mushrooms. Using the mushrooms’ initial ribbon-like structure, researchers heat the samples up to 500 and 1100 degrees Celsius to create strips of porous carbon. These strips have a very high surface area as a result of these pores and are very useful for the storage of energy.

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A Portabella Mushroom

Portabella mushrooms have the potential to be better batteries than our current graphite anode counterparts. When the graphite anodes are mass produced, massive amounts of sulfuric acid and hydrofluoric acid are needed which creates hazardous waste. On the other hand, the Portabella mushroom is an easily grown biomass and has little to no impact on the environment.

In terms of energy efficiency, users usually complain about the decreasing capacity of current batteries with graphite anodes. Portabella mushroom batteries may feature capacities that increase over time. Mushrooms have a high concentration of potassium ions. As these batteries are used, more pores can activate creating an anode with increasing electrolytes.

Now, it is up to the researchers to introduce this product to the world. They are currently filing for patents and will hopefully bring a more environmentally friendly solution to our energy storage troubles.

Original Article

You can find the abstract and published research here: http://www.nature.com/articles/srep14575

 

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