How a little fern called Azolla drastically cooled down the earth 50 million years ago.

As I said a couples of posts ago, we have started Ecology in Biology IB. Today in our lesson, we talked about climate change. more particularly, about how the CO2 levels affect to the global temperature and they both increase and decrease together at the same rate.  

(Photo credit: Bioknlowledgy)

This afternoon I was watching a couple of videos from SciShow (https://www.youtube.com/channel/UCZYTClx2T1of7BRZ86-8fow) and I was really surprised when I realized that yesterday they posted a video about this exact same thing!

Link to the video:

https://www.youtube.com/watch?v=LUnpHax9EwA

What the video is talking about is one of the main hypothesis about how the earth’s temperature drastically decreased 50 million years ago. And this reason is a Fern called Azolla, a small fern that lives over fresh water which flourished around 50 million years ago in the northern arctic sea, covering millions of square kilometers and almost lowering the CO2 levels in the atmosphere by half. By doing this, as CO2 is a gas which contributes to the greenhouse effect, the temperature was reduced drastically, leading to a new glacial period.

A lot of research is being done at the moment about Azolla, and one of the main questions that the researchers want to solve is… Would Azolla be able to cool down the earth AGAIN under the right conditions?

But this is just a little summary, in the video they explain it much deeply and better, so, go check it out!

DNA profiling.

We are finishing genetics in our Biology lessons, and one of the main experiments we performed was DNA profiling. For this experiment, we used gel electrophoresis. An important step before we start is to put gloves on, so we don’t put any pieces of our own DNA into the sample and contaminate the results.

We placed four identical copies of the same DNA strand into four containers. The first container was empty, but the other three had different restriction enzymes. Each of this restriction enzymes cut the DNA strand after different sequences. These enzymes were EcoRl, BamHl sonf HindIII.

After placing the DNA in the different containers, we placed the containers into a hot water bath (About 36º C but I’m not completely sure) for the enzyme to work correctly and a bit faster. while we wait for the enzyme to cut the entire pieces of DNA, we poured agarose gel into the electrophoresis tank and and let it there a couple of minutes so it solidifies.

While the gel in the electrophoresis tank is solidifying, we mixed the samples (each of them separately) with ink. When the gel is solidified we placed two carbon fibre tissues on each side of the electrophoresis tank. Then we put some TBE buffer on top of it. After that we pour the samples of DNA already mixed with the ink carefully into the wholes of the gel with a micro syringe through the buffer. 

As the DNA is negatively charged, it would be attracted to a positive pole of electricity, but it would be more difficult to attract the big strands of DNA than the smaller ones so if we let the magnets attract the different samples through the gel for a couple of hours, we will be able to appreciate different strands of DNA placed through the gel, the ones that are nearer to the opposite site of the tank would have to be smaller and the ones that are nearer to the other site of the tank should be bigger. by doing this, we can compare the result to another sample and get conclusions like if they are the same person or even if they are related. 

For doing this, we connected two wires to each site of the tank, attaching them to the carbon fibre, creating therefore an electric attraction that is able to move the gel. After being connected for two hours, we disconnect the electricity and analyze the results in the gel.

(Photo credits: Oliver Ferres)

Pellet Dissection!

A couple of days ago (before the easter holiday started) we did an experimental work in Biology which didn't seem really appealing at first, but ended up being fun and interesting. We are still in the topic of ecology, so the experimental work wanted to show us how the loss of biomass in the different trophic levels is actually expressed in nature.

The experimental work consisted in dissecting Owl Pellet. Pellet is the mass from the food that can’t be digested and is regurgitated by some species of carnivorous birds such as Hawks and owls. This mass can present indigested feathers, hair, insect exoskeletons and even bones from small vertebrates such as rats or mice. 

What we tried to do in the experiment consisted in dig into the pellet with the aim of finding bones from this type of small mammals, and I have to say even if it looked a bit nasty at first, it ended up being pretty addictive and exciting to even being able to find skulls, jaws, legs or even full skeletons of rats.

Synthetic bacteria shows us the essential genes for life

This morning I was watching this youtube video from Scishow I found it amazingly interesting:

https://www.youtube.com/watch?v=nsYwNZxIuKs

During the first part of the video it explains us how a group of scientists and researchers from “Celera Genomics” lead by the president founder of the company Craig Venter have been able to create a synthetic bacteria with the minimum amount of genes necessary for the organism to survive. 

                            (Photo credit: Tom Deerinck & Mark Ellisman/NCMIR/University of California at San Diego)

For achieving this, they carried out the following experiment during the last years: They started with the genome of the bacteria “JCVI-syn1.0”, commonly known as “Synthia”, a Genetically engineered  bacteria created by the same team in 2010 witch is considered as the world first synthetic organism. They started up with the original 901 genes from Synthia and then started deleting with restriction enzymes the genes which they didn't consider “essential” for the bacteria to live, and then testing if the new organism was able to survive after cutting down that gene.

After testing this for years, they ended up with an organism which the called JCVI-syn3.0 which presented ONLY 473 genes! a really small amount of genes considering that the smallest genome from a bacteria known in nature is 525 genes and Humans present from 20000 to 25000 genes. This experiment is not only important because it created a living organism with the smallest possible genome, but also because it showed us which genes in an organism are actually essential for it to be “alive”, considering to be alive to be able to process organic matter into energy allowing it to grow and therefore reproduce by replicating itself.

What is more interesting about these experiment is that inside of these genome there are 149 genes which scientist don’t actually know what they code for! This is 31% of the genome of the bacteria and we don’t have any idea of what it does, but we know they are completely essential for the bacteria for being able to live. This is like saying that we don’t know one third of essential biology, and shows us how much we still have to research for achieving full knowledge in this field.

On the other hand, this experiment is part of our first steps in creating synthetic life, and it carries some ethical issues with it  which consist in what some people refer to as “playing god”. There’s an article on The New Scientist about this, and it tell us that we’re far from “playing god” yet. This is the link to the article.

https://www.newscientist.com/article/mg23030672-700-breakthrough-in-synthetic-biology-is-far-from-playing-god/

New species of Octopus found in record depth

The NOAA expedition project is a three year long project which started in 2015. It’s aim is to carry out a couple of expeditions in the deep waters near Hawaii for finding out more wildlife in this part of the world. (further information: http://oceanexplorer.noaa.gov/okeanos/explorations/ex1603/background/plan/welcome.html)

What is interesting about this deep waters in Hawaii is that they keep a huge ecosystem in a really unusual depth. It appears twice as deep as the ones that were considered the deepest "big ecosystems" until a couple of years. This ecosystem is founded at 4000m of depth, and during the eight previous dives that the team has performed this last months they have been able to contribute with a lot of information to scientists about life habits of rare species that science didn't know a lot about.

It was only matter of time that a new species were discovered and this has been the case. A new type of “ghost” octopus species found at 4290m deep in the seas surrounding Hawaii, which you can see in the following link:

https://www.youtube.com/watch?v=zWHvekDCAo4

Animals which sense the magnetic field

Animals like pigeons, lobsters, moles, even fruit flies can use the magnetic field for orientating themselves in the globe. This has been known since a couple of decades, but why do we know so little about it even if there’s loads of experiments and research going on with this topic? 

https://www.newscientist.com/article/2080998-animal-superpowers-how-were-homing-in-on-their-magnetic-satnav/

I was reading an article on the new scientist about this and I found it really interesting. Basically, even there are a lot of animals with some kind of ability for feeling the magnetic field, none of them show a real organ or region in their body that is designed for this. As the article says “There is no nose or ear for feeling the magnetic field that we can appreciate”, and also, if this different “organ” even exist, it doesn’t necessarily have to be in the same place for all animals which sense the magnetic field.

Lately one of the substances that has been studied is Cryptochrome, a type of protein found in the eyes of some animals. It produces radicals (A type of chemical compound) depending on the magnetic field, and it’s used by fruit flies for sensing the magnetic field, for example. For proving that this substance had something to do with magnetic orientation, a team of scientists from the University of Oxford genetically modified a group of fruit flies cutting down the gene which produced this substance. This engineered flies that didn’t present Cryptochrome, weren’t able to orientate using the magnetic field. Unfortunately, we cannot say that all animals which sense the magnetic changes base that perception on this substance, because humans also contain Cryptochrome and we don’t sense the magnetic field. 

Animals with the ability to feel the magnetic field are still a mystery for us, so there’s still a lot of research to be done in this topic, but if we get to find what is the real root of all this, It could have great benefits for us.

My Own Mesocosm!

A Mesocosm is an experiment carried out for studying the development of nature under controlled conditions. It is really useful for testing the changes that organism will undergo under certain circumstances.

Last week in Biology we created our own mesocosm. It was simple, we picked up a bottle, added some small rocks, some sand, some compost, some water and the plant that we wanted to. I chose to put germinating peas into it. Then we sealed the bottle with some tape. As we studied in Photosynthesis, the plants would get Water, CO2 and sunlight to form glucose, creating Oxygen and water vapour as byproducts. Then, the bacteria from the compost would use the oxygen and produce CO2, which will be used by the plants, completing then the cycle. Then, even if the small ecosystem was isolated, it should be able to survive. The only element that should be getting in and out would be energy in the form of sunlight getting into the bottle and kinetic energy in form of 

heat.   

In theory this works, but in practice this is not so simple. The plants could die due to many reasons: Too much water, not enough CO2, not enough compost and therefore bacteria for producing oxygen… Etc. So I wasn’t really sure if my plants were going to survive.

I have to say I got really excited when one of the germinating peas started to root. That was three days ago, now a couple of germinating peas have already grown up. It may seem like a kind of childish experiment but if you think about it’s really interesting and it has so many applications. Now everyday the first thing I do in the mornings is check how my plants are, even knowing that I wouldn't be able to do anything about it because is completely sealed, but still it makes me feel really excited.