Sunday, March 29, 2015

"They reveal Nitrogen compounds on the surface of the planet Mars"

The latest data from NASA's Curiosity rover reveal, for the first time, nitrogen compounds on the surface of Mars. This discovery brings new tracks of that the planet red could have hosted life in some moment of their history before return is dry and sterile.

Previously identified nitrogen compounds in the atmosphere of Mars, but never before found nitrates on the surface, but now with this finding was found in both surface dust samples and sediments Gale Crater.

Fig. 1. Sedimentary rocks of the Gale crater (Grotzinger et al., 2014).

Nitrogen in the form of N2 makes up approximately 2% of the Martian atmosphere, is now shown that the concentration of nitrogen in the surface of Mars is of 20-250 nanomoles in the form of nitric oxide or nitrogen monoxide, but little is known about other potential reservoirs of N on Mars, including those which may contain fixed forms of N (i.e. NH3, NH4+ and NO3) in the mantle, crust and sediments.

There is a concentration of nitrogen in the surface of Mars, it suggests that "the existence of a source of biochemically accessible nitrogen on Mars seems a fundamental prerequisite for the possible habitability of the planet", an example of this is the terrestrial life that requires a form fixed nitrogen for incorporation in biomolecules as nucleobases and amino acids that are the building blocks for DNA, RNA and proteins

Thus the presence of N fixed on Mars suggests that, at some point, was established the first half of the nitrogen cycle. On Earth, the N in your cycle returns to the atmosphere by denitrification by biological activity, but on Mars, the likely absence of life near the surface would result in fixed N accumulated as nitrate in the geological surface of Mars.

If you want to know more:

Monday, March 16, 2015

Global CO2 emissions stall without an economic crisis in 2014

Greenhouse gas emissions may finally be decoupling from economic growth
Until 2013 CO2 emissions had shown an increase due to two main origins: natural and anthropogenic, being the anthropogenic the most striking the last years.
However, 2014 was different, during this year the result showed that CO2 emissions were maintained and in the absence of an economy crisis.

Information from the International Energy Agency (IEA) indicate that global emission of Carbon Dioxide stood at 32 gigatonnes in 2014, unchanged from the preceding year. It means that sustainable alternatives may be having a positive impact keeping the same levels in emissions.
In the last 40 years, the IEA has been collecting data about this emission, and there have only been three times in which emission have still or fallen compared to the previous year, but when this happened, all were associated with global downturns:
1.       1980: US recession
2.       1992: Collapse of the former Soviet Union
3.       2009: Global financial crisis

In 2014, however, the global economy grew 3%.
"For the next time, greenhouse gas emissions are decoupling from economic growth". Explained IEA Chief Economist Fatih Birol, who was just named the next IEA executive director.
Nowadays China is the biggest investor in renewable energy
In China, 2014 saw greater generation of electricity from renewable sources, such as hydropower, solar and wind, and less burning of coal. In OECD economies, recent efforts to promote more sustainable growth – including greater energy efficiency and more renewable energy – are producing the desired effect of decoupling economic growth from greenhouse gas emissions.
The objective for 2020s and 2030s is to limit the increase of the average global surface temperature to no more than 2 ºC to avoid climate change employing renewable energy.

Credit: IEA, Financial Times

Sunday, March 8, 2015

Is it possible to recreate your face only with your DNA?

Maybe for the forensic scientists could soon be possible. Scientists can already decode hair and eye color with reasonable accuracy using as little as 0.05 nanograms of extracted DNA. Will be possible to predict the color of skin, freckles, baldness, curly hair, tooth shape and age. 

This is possible thanks to The Snapshot DNA Phenotyping Service snapshots which reads tens of thousands of genetic variants from a DNA sample and uses this information to predict what an unknown person looks like, this technology was development by Parabon NanoLabs and was based partly on the work of Mark D. Shriver, a professor of anthropology and genetics at Penn State University, he development a mathematical method based on the 3D coordinates of more than 7,000 points on the face so he adjust that face based on 24 genetic variants in 20 genes involved in facial variation.

Fig. 1. Snapshot DNA Phenotyping. Parabon Nanolabs.

But, is this really complex?

The eye and hair color is relatively easy for its determination, because a single gene has a large influence on these traits. Neither predict the age, ‘cause it can analyze markers that shut off certain genes as people grow older, said Manfred Kayser, a professor of forensic molecular biology at Erasmus.

The problem here is that they want to implement for obtain traits of crimes suspects. How safe it is to use this technology in forensic science? It sounds like a science fiction novel. 

Fig. 2. Individuals' faces compared with Snapshot DNA Phenotyping.
The New York Times.

Some scientists question their accuracy because not all features are uniquely determined by DNA, also influenced by environmental factors. For this, the program presents a measure of confidence, which reflects the degree to be affected by epigenetics. For example traits such as eye color, which are highly hereditable are predicted with higher accuracy and confidence. But, it would not be a problem with the shared traits among relatives? Some scientists question the accuracy of the technology and they say use of these techniques could exacerbate racial profiling among law enforcement agencies and infringe on privacy. 

What do you think about this? Do you believe that is possible? 

If you want to know more you can read: Building a face, and a Case, on DNA.

Monday, March 2, 2015

Human DNA enlarges mouse brains and xenoxed gene trace the way of the human brain.

Fig. 1. The blue stains in these developing mice embryos show that the human DNA inserted into the rodents turns on sooner and is more widespread (right) than the chimp version of the same DNA, promoting a bigger brain.

The researches show the size of the brain of a mice has increased at inserting a piece of human DNA that controls the gene activity; "The DNA could be an important component in how the human brain was expanded" said Mary Ann Raghanti, a biologist anthropologist at Kent State University in Ohio who did not participate in the experiment.

The biologists have wondered what makes the humans humans, and now they can start to tag the molecules of our brain that allow bipedalism, varied diet, and what makes us so sucessful. En 2008, almost two dozens of comparisons of genes on humans and apes were isolated, and they produced hundreds of pieces of DNA that could be important.  But rarely the researchers have given the next step to probe that a piece of DNA has made a difference in human evolution.

Greg Wray is interested in the segments of DNA called enhacers, which control the activities of genes nearby. He and Lomax Boyd have scanned and compared different enhacers between apes and humans and in important genes nearby  for the development of the brain. With over a hundred candidates, the team  and the neurobiologist Debra Silver proved half dozen of these genes. First they inserted an enhacer in the mice embryo to observe how the genes changed. Then they inserted HARE5, the most active enhacer in cortex brain and made minigenes from the version of the gen of either apes or humans from an enhacer attached to a "reporter" gen, which turned the enhacer blue when there was an activity from the enhacer on the genes. The mice brain turned blue sooner and reported that HARE5 controls a gen called Frizzled 8, which form part of a pathway of brain development. The studies reported that the enhacer caused a great amount of stem cells  that will be part of the cortex. The mice brain with human HARE5 increased 12% more than the mice brain with the ape enhace. Now it will be proved if this increase in the brain size has made the mice smarter.

Fig. 2. The folding on the right side of this mouse embryo’s cortex reflects the increased growth stimulated by the insertion of a duplicated human gene into that side of the brain.

With this research, another team has taken this investigation furthermore, and has discovered certain gen that not only made the mice brain increase,  but also gave it distintive folds found in the brains of apes.

The new study started when Wieland Huttner, a developmental neurobiologist at the  Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, began to examinate aborted human fetal tissue and embryonic mice. “We specifically wanted to figure out which genes are active during the development of the cortex, the part of the brain that is greatly expanded in humans and other primates compared to rodents,” said Marta Florio, graduated student of Huttner who carried out the main part of the experiment.
This was more difficult. Building the cortex requieres various types of stem cells.  The stem cells divide themselves in various "intemediates" stem cells which will divide and will form neurons that will constitute the brain tissue. To learn which genes are active, the team had to separate various types of cortical stem cells.

After months of work, they resolved how to separate them.  They added fluorescent tags attached to stem cells and whereas they isolated each type of cortical cell and after  measuring the activity in genes of each stem cell, the team discovered 56 genes in human tissue that mice tissue lacks of. One of the most active genes in division of stem cells of human tissue was  ARHGAP11B, which is also under suspect of aiding human evolution.

Years ago, a group of researchers found out that the gen ARHGAP11B arose after ancestral gen made an incomplete copy of itself. While humans have an aditional version of this gen, chimps do not. They concluded duplication occurs after humans and chimp lineages splitted off. Neither mice nor apes have the gen ARHGAP11B, but modern humans and their ancestors, the Denosivans and Neanderthals do.

The team decided to put ARHGAP11B in developmental mice. The number of stem cells on cortex doubled and their brains sometimes developed folds. These folds are not seen on mice but they are in apes.  Researches found that the gen introduced caused the stem cells  became intermediate stem cells more frequently than in animals, and that these cells duplicated more frequently before turning on a neuron. These various effects increased the size of the brain.

The result “emphasizes the likelihood that this gene is indeed important during mammalian evolution for the design of a new brain, bigger and more complex,” Borrell Franco said.
This could be an important approach in how we evolutionated and  where we come from.

How much energy do you need for ATP synthesis? part I

The other day I was trying to write my thesis when I started to divagate about something I’ll probably talk later in another post. Anyway, a paper took me to others papers and I ended up reading two papers about bioenergetics in archaea and bacteria that are really interesting if you are interested in such things. Also they help you to understand certain things about biodigesters!

So, I’m sharing some things I learned from them with you because I think it is important for us to know at least the basics of bioenergetics and also because I’m lonely here and I don’t have anyone to discuss about bioenergetics in anaerobes.

Ok, let’s start!

The paper I liked the most was “Adaptations of anaerobic archaea to life under extreme energy limitation” from Florian Mayer and Volker Müller, which explains about mechanisms for energy conservation in 4 different anaerobic archaea, and of course they discuss about methanogens. It has been about three years since it was confirmed that hydrogenotrophic pathways is actually cyclic but new things have been discovered and actually hydrogenotrophic methanogens are more versatile than we thought. But the reason of why I liked this review is not because of methanogens.

The interesting part is the introduction of some basic concepts of bioenergetics and also the description of the structure and functioning of the ATP synthase from archaea, which allows you to understand how this enzyme translocates H+ or Na+ and also how many of these are needed for the synthesis of ATP.

Anyway, what do you have to know to understand?

First, how much energy do you need for the synthesis of ATP from ADP and Pi?
According to Thauer et al. (1977) (Another review you should read):

So, for phosphorylation of ADP at standard conditions you need approximately +32 kJ/mol of energy. Now, where do you get such energy?

For that, two mechanisms of ATP synthesis are known: substrate level phosphorylation and che­miosmotic ion gradient-driven phosphorylation.

In the case of substrate level phosphorylation, there must be a highly exergonic reaction, which liberates enough energy to drive phosphorylation. In other words, the free energy (AG) of such reaction must be higher than -32 kJ/mol. The number of reactions that are that exergonic is limited, and some of them are listed in the review. The first three are the ones that are usually employed by fermentative organisms and they are reactions mediated by the enzymes acetate kinase, phosphoglycerate kinase and pyruvate kinase.

If you pay attention to those reactions, you will notice that there is something else they share besides their high free energies at standard conditions.

Anyway, for an anaerobic chemoorganotrophic organism fermenting hexoses to acetate, the maximum ATP gain is:

Yes, just 4 ATP. But the important thing you have to know from this is that for the gain of that number of ATP, the fermentative organism needs to produce hydrogen in order to recycle the reducing equivalents produced during fermentation (NADH, NADPH or ferredoxin). What would happen if, by any reason, they don’t get to produce the 4 molecules of hydrogen? I leave that question to you.

Now that it is clear that there are reactions whose free energies are high enough to drive ADP phosphorylation, let’s move on in to the second mechanism for ATP production: che­miosmotic ion gradient-driven phosphorylation.

We know that in this mechanism, ADP is phosphorylated by the activity of the ATP synthase and this reaction is driven by the ion gradient across the membrane (more outside, few inside). To maintain the ion gradient, the cell, mitochondria and chloroplasts must translocate ions across the membrane. And this, of course, requires energy. So, an exergonic reaction, which involves integral enzymes, is needed to couple ion translocation.

Electron transfer along integral enzymes/cytochromes (aka. the respiratory chain) is the classic example of exergonic reactions coupled to ion translocation. But of course, not all living organisms have respiratory chains. For this matter, such organisms must employ another type of reactions in order to obtain energy for ion translocation and a principal requisite is that those reactions must take place in the membrane.

The reaction of the CH3-H4M(S)PT:CH3-CoM Methyl-tranferase in the methanogenic pathways along with hydrogen production by reduced ferredoxin are examples of reactions that couple ion translocation in organisms that don’t have cytochromes.

Now, this leads us to one of the most important questions: how much energy is needed in order to translocate one ion across the membrane?

This section is full of equations that explain how are you supposed to calculate the minimum amount of energy for the translocation of one ion across the membrane. Personally, I think that when you have to lead with equations, you are supposed to understand what those equations mean instead of memorizing them. So I’m not going to write any more equations (for that you can read the paper), instead, I’m going to try explaining them so that at least you can understand how the minimum energy for ion translocation is calculated.

In order to avoid any confusion, by using the word “ion” I’m referring to either H+ or Na+. Although H+ translocation is more common, organisms living under energy limitation use Na+. You’ll discover later in the paper why this information is important (specially you, Isco!).

Let’s start this long explanation by reminding you (again) that there must be an electrochemical ion gradient across the membrane and that this is possible thanks to exergonic reactions that keep pumping ions in order to maintain such gradient.

The electrochemical ion gradient is the one that defines the minimum of energy required.

Why? It’s really simple. Every system tries to reach the equilibrium. Since maintaining high concentrations of ions outside the membrane is going against such equilibrium, it obviously involves the input of energy. So imagine that you start with an “x” quantity of ions outside the membrane, which is higher than the one you find inside the membrane. For that quantity, you have to invest some “y” amount of energy in order keep translocating ions. After some time (and assuming ions are not returning to the inside of the membrane), you will have a greater amount of ions than the “x” initial quantity, which means you are far from reaching the equilibrium, so the energy required from ion translocation must be higher than the initial “y”. So the electrochemical ion gradient is just the difference of ion concentration across the membrane.

What I wrote above it’s what first equation of the article tries to explain with the appropriate concepts of thermodynamics. What do you need to know in order to calculate the electrochemical ion gradient? Well, first, the membrane potential. You can measure it directly or calculate its theoric value. Second, you need to know the concentrations of the ion outside and inside of the cell. Having at least that information will help you to determine the ion gradient.

As the article points it out, this value has been determined in just a few organisms and is about -180 to -200 mV. Now, you can calculate the minimum amount of energy required for translocation of only one ion, using the equation from the review:

In which:
, Represents the electrochemical ion gradient (-180 to -200 mV)
F, the Faraday constant (96. 485 KJ V-1mol-1)
n, the number of ions translocated (just 1)

If you substitute the values from above in the equation you’ll see that you need about -17 to -21 KJ/mol of energy in order to translocate just one ion across the membrane. However, the minimum energy could be lower if the electrochemical ion gradient is lower too. This is important because microorganisms that live under extreme energy limitations might use such strategy for their survival.

Now that we know the energy for the translocation of one ion across the membrane, the next question we have to answer is… how many ions do the cell need for the synthesis of ATP?

I’ll leave that question to you for now, because if I keep going with this post, it will be getting longer and longer and you will lose the interest.

I’ll try to write part two this week but meanwhile you can read the whole paper and try to answer that question. If you want to discuss something, you can ask me here or you can send me an email.

So, see you soon!