Wednesday, February 28, 2018

Plants, Sounds, Art!

Trees are sanctuaries. Whoever knows how to speak to them, whoever knows how to listen to them, can learn the truth. They do not preach learning and precepts, they preach undeterred by particulars, the ancient law of life.
An excerpt from “Wanderings” by Hermann Hesse (1877–1962)  (Monica Gagliano; The flowering of plant bioacoustics: how and why, Behavioral Ecology, Volume 24, Issue 4, 1 July 2013, Pages 800–801, https://doi.org/10.1093/beheco/art021

In the realm of behavioral ecology, plants have evolved to respond to sound waves and vibrations, and will change their behavior accordingly; acoustic signaling. Check out this paper that elaborates on this awesome phenomena better than I could!
Also, this 'sonic artist' has found a way to harness these bioacoustics and present them in a beautiful performance art as well as a didactic tool. Sonic Artist- Watch the video!

Watch Nerve Cells Form in a Mouse Brain for the First Time

Hey! Unrelated to what we have been learning in class, but a couple weeks ago scientists at the University of Zurich recorded for the first time the growth of radial stem cells in live mice. The researchers took pictures every 12-24 hours for two months to create this video, it was possible by removing the layers of tissue that cover the hippocampus and marking 63 of the cells. Attached is a link with a short explanation and with the Youtube video...pretty cool so I wanted to share!

https://www.sciencenews.org/article/watch-nerve-cells-being-born-brains-living-mice

Tuesday, February 27, 2018

Viruses Are the Kings of Life

       So, in class, we touched a little bit on viruses when we were defining what constitutes life. I think we eventually came to the conclusion that viruses are not alive, but that got me thinking: if viruses aren't alive, where did they even come from?
        After a little research, I found that there are three main theories as to how viruses came to be the infectious, flu-inducing, fun little friends we know today: the Virus-First Theory, the Reduction Theory, and the Escape Theory. 
         The Escape Theory hypothesizes that viruses evolved directly from cells. Supporters of this theory imagine a vesicle enclosing a small part of a cell's genome and "escaping" the cell, forming a membrane-bound body of genetic material. This would account for the similarities we see amongst viruses and their host genomes.
         The Reduction Theory finds the birth of viruses in a primordial, parasitic cell that lived its life buried inside another cell, sucking away resources as parasites do. Scientists think this parasitic cell eventually left its host, losing some of its cellular machinery in the process, and thus, became permanently dependent on a host, like viruses we see today. However, one would expect to see strong genomic similarities between viruses and some of the smaller parasitic cells of today, but this is not what we see.
          Finally, the Virus-First Theory (which I am rather biased towards) makes WAY more sense! This proposes that before life even evolved, viruses were the reigning leaders of the primordial soup. It's not hard to imagine these somewhat simple, protein-bound containers of genetic material are ancestors of the complex cells that we see today. Some support for this theory includes the fact that viruses are the most physically abundant and genetically group on Earth, which would make sense if they've been evolving for even longer than cells. Also, while many parts of the cellular genome are conserved in viruses, there are many parts of the viral genome that are NOT conserved in cells. Where would viruses have gotten these virus-exclusive parts of their genome if the evolved from cells?? Also also, it would explain why viruses remain universally compatible and can infect across all three domains of life if viruses were the predecessors of all three domains of life.
          Many people refute the Virus-First Theory because it violates the fundamental definition of viruses in that they rely on a host to survive. How could viruses have survived if they came before the cells, whose machinery they need to live, you may ask? Well, my friend, who says a viral host has to be a cell? The primordial soup that these viruses would have evolved in would have been ridden with complex molecules, including proteins. It is quite possible that viruses could have used the extra-cellularviral environment as machinery for manufacturing a capsid coat, especially considering that viruses have been co-evolving with cells for a long time; the machinery they use now is probably very different from the machinery they used back then.
           Welp, this has been a long, drawn-out rant about why viruses are the king. Comments/discussion/you're-totally-wrong-Shay are all welcome. :)

Monday, February 26, 2018

Obese Mice

In class a few weeks ago we discussed intestinal microflora and how it plays a role in obesity, of course for research to be done around this topic scientists must have performed experiments with obese mice. And I still cannot shake the image of a lab full of adorable round chunky mice, albeit mutants made to be obese.

While I spent an unreasonable amount of time looking at images of fat mice, I also read an article in Scientific American concerning why obese mice are more sedentary. A dopamine receptor in the mice's brains, DR2, has a lower activity level in obese mice that are gaining weight, which causes less movement. When obese mice have DR2 restored they move more and have the same activity level of non-obese mice. When non-obese mice have the DR2 removed, they move less and become more sedentary. So obese mice are not just lazy and adorable. They have impaired brain function and are adorable. Please enjoy these pictures of fat mice.
Image result for obese mice
Image result for obese mice
Related image
Related image


Article:
https://www.scientificamerican.com/article/obese-mice-can-move-but-they-dont/

Also here's the actual scientific journal paper the article references:
http://www.cell.com/cell-metabolism/fulltext/S1550-4131(16)30596-4

This week I decided to further read about coastal redwoods and the upper limit of tree growth. According to an article in Live Science (below), the upper limit of tree growth is between 400 and 426 feet. The tallest known tree, a coastal redwood, is 379 feet; and, according to the article, there were taller redwood trees in the past that have since been felled by logging.

 I was still interested in the way that redwoods could grow this tall and since we talked about the role of fog in class I decided to look into that as well. In Science Daily there is an article that talked about the decline of fog in old growth redwood forests due to changing temperatures, which disrupt the "conveyer belt" of nutrient rich fog from the ocean to the forest. This article also described the process in which redwoods can use fog to supplement their water intake.

 Finally, I took a quick look at the US Forest service website to see what information they had on Redwoods. They described much of what I had already read, adding some tree anatomy and information about the redwood's fellow forest inhabitants. The most interesting part of that website was this image:

 
This, along with learning that the oldest living organism (a tree!), was cut down made me want to go hug and/or chain myself to a tree.

https://www.livescience.com/14667-tall-trees-grow.html
https://www.scientificamerican.com/article/fog-that-nourishes-california-redwoods-declining/
https://www.nps.gov/redw/learn/nature/about-the-trees.htm

Thursday, February 22, 2018

CRISPR in Plants!

     CRISPR is a system of proteins originally used for viral immunity in bacteria that has become a valuable genome editing tool.  In humans, CRISPR is used to delete/insert specific alleles in hopes of curing genetic diseases.  Similarly, researchers are beginning to use CRISPR in plants to create more desirable specimens.
    CRISPR is able to create "synthetic epigenomes" by altering DNA methylation.  In plants, this is useful in producing certain nutrients and creating a more diverse population.  CRISPR is also used to create a plant that is ideal for human use.  Essentially, we can select for phenotypes by changing the genome with CRISPR to make a plant that is larger, has more seeds/ fruit etc.  For example, in the rice DEP1, an early stop codon in an essential protein causes there to be more rice grains on the plant.  Cas9 proteins can be used to introduce a stop codon into the gene, creating more plants with the beneficial mutations.  Hopefully this technology will be used to make all our apples CRISPR :)

Article: https://www.sciencedirect.com/science/article/pii/S001216061730760Image result for mutant plants
-Kenna Sherman

Monday, February 19, 2018

Rotifers and reproduction

While sexual reproduction has the benefit of generating genetic diversity, asexual reproduction has its merits as well. At least, in theory. Certain animals have a variety of reproductive techniques that help them adapt to their environment, for example, corals can reproduce both sexually and asexually. For corals, sexual reproduction produces larvae that can travel a far distance; however, these larvae are free-floating and very vulnerable because they don't have a protective outer membrane. A lot of them die before they have a chance to settle. Asexual reproduction on the other hand disperses offspring within a short distance, which is better for guaranteeing survival and development. A species of rotifer, Brachionus calyciflorus, also normally reproduces both sexually and asexually. But these guys can be restricted to just asexual reproduction by being homozygous for a certain recessive allele! Simple Mendelian inheritance!

Rotifers are funky little dudes. They're microscopic aquatic animals and they remind me of rodents for some reason... if rodents looked more bacteria-like. They can also engage in horizontal gene transfer at a low rate, which is still pretty cool since that's mostly seen in prokaryotes.

Wednesday, February 7, 2018

WE MUST CELEBRATE DARWIN DAY

Charles Darwin was born on February 12th in 1809, which means that this Monday he is turning 209 years old! Even more importantly on Tuesday he will be turning 209 years and 1 day old, and I feel as though we must find some way to celebrate in our class. This could entail delicious treats or singing to the student or professor who looks most like Darwin (probably John, everyone else would require a fake beard). Let's make something happen to celebrate this wonderful man with many odd habits such as eating owls, riding tortoises, and being a backgammon fiend! Also make sure to save the date for Erasmus's birthday on December 12th.
If you wanna learn about how people around the United States celebrate Darwin Day read this: https://thehumanist.com/news/aha_news/celebrate-darwin-day-2018
and if you want some more interesting facts about the "Father of Evolution" look at this: http://thefactfile.org/charles-darwin-facts/

Thursday, February 1, 2018

Did Arabic Scholars Discover Evolution in the Ninth Century?

I can't find the book I was thinking of but here are two articles in popular media with all the names you will need to explore further in this field:
Did Arabic Scholars Discover Evolution in the Ninth Century?
and more generally:
Science: Islam's forgotten geniuses