Sunday, November 15, 2015

ConCiencia - Logro Nivel Estatal - Felicidades

Felicidades a los miembros de lab biorem: Elena, Miriam, Maria Jose y Isaac para haber ganado primer lugar de nivel Estatal en el reto del Medio Ambiente. También a Marleny, Yadira, Karen y Adrian para haber ganado mención honorifica del reto en Energia.
Mejores deseos al equipo de Elena en nivel Nacional.

Tuesday, November 3, 2015

Scientist from Harvard Sugest Diamond Dust as an Alternative to Climate Change

Injecting solid dust in the stratosphere could be a feasible "geoengineering" to counter the climate changes.

Geoengineering has been defined as an approach to the climate change problem. The Royal Society defines geoengineering as "deliberate large-scale manipulation of the planetary environment to counteract anthropogenic climate change". It is dividen into two basic categories:
  1. Carbon Dioxide Removal techniques.
  2. Solar Radiation Management techniques, which reflect a small percentage of the sun's light and heat back into the space.
Climate scientists have thought up plenty of futuristic ways to cool the planet, but a recent study suggest a new idea: spraying diamond dust in the stratosphere. Solid aerosol particles have been proposed as an alternative to sulfate aerosols for solar geoengineering. A team of scientist from Harvard University in Cambridge, Massachusetts, in their paper published in Atmospheric Chemistry and Physics suggest that nanoparticles of diamond and aluminum oxide could be more effective and less environmentally damaging than sulphate due to in atmosphere, sulphate can produce sulphuric acid, which is a problem to the ozone layer, also, by absorption of certain wavelengths, they heat up the lower stratosphere, it could affect air-circulation patterns and climate. This problem isn't present when alumina and diamond are used, it is because they don't produce sulfuric acid and absorb particular wavelengths of light in a different way. Alumina dust would achieve a similar cooling effect to that sulphate sprays, but diamond dust would be at least 50% more effective.
There are different problems with the application of this project, one of the most important is the cost of diamond dust, this is less expensive than cut gemstones, but the cost still being high (less than US$100 per kilogram), however, according to the results of the paper, the amount of human-emitted greenhouse gases would take hundreds of thousands of tonnes of dust annually.
In another paper, David Keith says that by 2065 the population of the planet will be among 10 billion people, and the cost might be of $5 per person to pump up 450,000 tons of dust.
In spite of the disadvantages of sulphate, it is well studied and understood, however, the risk of both alumina and diamond nanoparticles are unknown, although the Harvard researchers are doing la test to remedy that. 
Recent studies suggest that solid dust could significantly lower some of the risks associated with sulphates.

  • Weisenstein, D. K., & Keith, D. W. (2015). Solar geoengineering using solid aerosol in the stratosphere. Atmospheric Chemistry and Physics Discussions, 15(8), 11799-11851.


Friday, September 25, 2015

MicroRNAs act as transcriptomic modifiers of the preimplantation embryo even if the embryo is donated.

Endometrial fluid is a viscous fluid secreted by endometrial glands into the uterine cavity and its function is the nutrition of the embryo and gives an environment in which the first communication between the maternal endometrium and the embryo occurs during the window of implantation. This endometrial fluid contains different molecules such as proteins, glycodelin, lipids and cytokines, which are employed by the embryo for its development, but they can also create an impact in its physiology. A clear example are microRNAs from endometrial fluid (small, 19-22 nucleotide sequences of non-coding RNA), which can regulate the gene expression of endogenous genome (embryo). 
This study says that the mother can change the genetic information even when the egg has been donated. The finding shows an exchange between endometrial fluid and embryo, it had been though because of the physical similarity between mother and children of ovodonation, as well as disease incidence in children related with maternal pathologies during gestation, such as obesity and smoking (fig. 1).

Figure 1. Analysis of microRNAs content in endometrial fluid and evaluation of its biological function.
Transmission of molecules occurs during the window of implantation, it is because after fecundation, the embryo takes 5 days to move from fallopian tubes to the uterine cavity, and then are necessary around 24-36 hours to the implantation. In this period the embryo takes the genetic information of endometrial fluid and it can modify its development. These microRNAs prepare the embryo for implantation with specific protein expression (fig. 2). That communication can inhibit specific functions or on the other hand can express new functions.
With this information, researchers can employ the knowledge in future to avoid diseases such as obesity.
Figure 2. Endometrial fluid from the maternal endometrium modify the embryo transcriptome.
Vilella, F., Moreno-Moya, J. M., Balaguer, N., Grasso, A., Herrero, M., Martínez, S., ... & Simón, C. (2015). Hsa-miR-30d, secreted by the human endometrium, is taken up by the pre-implantation embryo and might modify its transcriptome. Development, 142(18), 3210-3221.

Wednesday, August 26, 2015

Producing opiates from sugar

For several years, synthetic research teams have modified pathways into microorganisms to produce benzylisoquinoline alkaloids which are used in pharmacology. If it were possible, the analgesic production would be cheaper, safer and more effective. In recent years, synthetic biologists have engineered yeast strains to make morphine (belonging to opiates, naturally produced from the opium poppy Papaver somniferum) from sugar.
Going from glucose to morphine is a complex pathway which is carried out in 18 stages. Vicent Martin and his collages at Concordia University in Montreal, Canada, created yeast that can go to R-reticuline to morphine. R-reticuline is an intermediate compound in this pathway. To go from glucose to S-reticuline (an intermediate compound before R-reticuline), John Deuber's team at University of California, Berkeley carried out their research. Both groups worked together to found the enzyme needed to transform S-reticuline to R-reticuline and have the complete pathway, but this could take many years. 

Stages known of glucose-morphine pathway. (Oye et al., 2015)

The last week, a research team by Cristina Smolkey, a synthetic biologist at Standford Universty in Palo Alto, California, published in Science that they had achieved to turn sugar into thebaine, a key opiate precursor to morphine, by a Saccharomyces cerevisiae strain. This biosynthesis required the expression of 21 genes from a rat, a bacterium and several plants. This research presents the most complete pathway of glucose to morphine, because thebaine is the last intermediate in this pathway, but is still the first piece of the project. Is necessary to increase the yield to each cell 100, 000 times to accomplish that the process scales up, be economically feasible and can compete with the oppium poppy production in pharmacology.


- Galanie, S., Thodey, K., Trenchard, I. J., Interrante, M. F., & Smolke, C. D. (2015). Complete biosynthesis of opioids in yeast. Science, aac9373.

- Oye, K. A., Lawson, J. C., & Bubela, T. (2015). Drugs: Regulate'home-brew'opiates. Nature,521(7552), 281.

Saturday, August 15, 2015

Felicidades Nayeli

Me da mucho gusto compartir la noticia que la M.C. Nayeli Ortiz Silos, compañera de Biorem y egresada como Ingeniera Bioquímica de nuestra Facultad, ha sido nombrada como Secretaria de la Facultad de Ciencias Químicas de la Universidad Veracruzana. Muchas Felicidades Nayeli y mejores deseos para muchas éxitos en su camino profesional y nivel personal.

M.C. Nayelo Ortiz Silos

Wednesday, August 12, 2015

Study of Effects of Pollution in Health Through Mouse Embryonic Stem Cells

During our life we are exposed to several substances due to industrial processes. These compounds tend to accumulate in the environment, thus, we are at risk of several health effects caused by them, even if we don't have a direct contact with the pollutants. Stem cell toxicology is a favorable alternative to animal tests or in vitro assays because it allows the develope of a pollutant of interest, quickly, thoroughly, and cost-effectively. Embryonic stem cells (ESCs) have several advantages such as the ability of be cultived indefinitely in dishes, can be employed in developmental toxicity assays, and they can virtually differentiate specifically into any type of cell of an adult organism.
One of the most studied pollutants is Bisphenol A (BPA) that is employed to make polycarbonate plastics in different products, and is recognized by the effects in health such as fertility problems, behavioral abnormalities, heart disease, diabetes, and obesity. 
The researchers used a combination of biochemical and cell-based assays to examine the gene expression during the differentiation of mouse embryonic stem cells upon treatment with BPA.
Previous reports have employed many in vivo and in vitro systems, but almost none utilized stem cells and when BPA was used in mouse ESCs, the effects were not toxic or not detected. In this study the effects of the toxicant BPA on mouse ESCs were tested with the stem cell toxicology system., resulting in a contradiction to previous reports, because the stem cell toxicology system was able to detect BPA toxicity in vitro, particularly towards the neural ectoderm specification.
"Our stem cell toxicology system proved to be very sensitive and reflective of the physiological toxic effects of BPA", said Francesco Faiola, Professor at the State Key Laboratory of Environmental Chemistry and Ecotoxicology. "What's even more valuable is the fact that this system can be applied to assess numerous other pollutants for their toxicity and/or lethality without the expenses of time-consuming animal models.

If you want to know more visit:

Monday, July 27, 2015

Tiny little lasers

Injectins cells with a luminiscent dye and droplets of oil turns the cells in tiny little lasers that can be used in diagnosting diseases and like a label for a cell.
An optical fibre is shown activating tiny lasers created within pig skin cells.

Scientists turned cells in lasers at injecting oil or fat mixed with a luminiscent dye an activating it with short pulses of light.
This finding could be used for diagnosis and for medical treatment and was divised by Seon Hyuk Yun and Matjaz Humar, optical physicists from Harvard Medical School in Cambridge, Massachussets and uses oil droplets or fat to reflect and amplify the light to generate a laser.
The lipid droplet (orange) within a fat cell can be used as a natural laser.

Luminiscent probes, which includes proteins and fluorescent dyes, had a broad emission spectra around 30 to 100 nanometers. With this broad bands its limits the number of probes, because its difficult to distinguish the sources of light.
This could change because the spectra from this source of light is narrow - around 500 to 800 nanometers, making it easy to label cells. Also, Yan and Humar reported that can vary the wavelenght and can tag individual cells using polystirene beads with different diameter rather than inject oil or fat. And also reports that in theory usind differents dyes with different spectral properties and different polystirene bends they can tag every cell in the human body. 

Saturday, June 6, 2015

Sun + Water + Microorganisms= Renewable energy

Photovoltaic cells have considerable potential to satisfy future renewable-energy needs, but efficient and scalable methods of storing the intermittent electricity they produce are required for the large-scale implementation of solar energy.

Renewable-fuels generation has emphasized water splitting to produce hydrogen and oxygen. For accelerated technology adoption, bridging hydrogen to liquid fuels is critical to the translation of solar-driven water splitting to current energy infrastructures. One approach to establishing this connection is to use the hydrogen from water splitting to reduce carbon dioxide to generate liquid fuels via a biocatalyst. 

Fig.1 Schematic diagram of bioelectrochemical cell (Torella et al., 2015)

An alternative approach to the direct reduction of CO2 to liquid solar fuels is to engineer fuel production in organisms that naturally use light energy to fix CO2 to biomass. Notwithstanding, photosynthetic organisms suffer inefficiencies arising from nonideal light-harvesting properties that are not likely to be addressed in the near term.  As a result, the observed solar-to-biomass efficiency by plants typically approach only 1% of the thermodynamic maximum annually or between 1.4% and 2.0% over the growing season when calculated on the basis of total solar radiation.

This way providing a foundation for the development of new biological, H2-based CO2 reduction strategies to produce liquid and solid fuels.

For more information about the article you could click on the link:

Tuesday, May 26, 2015

Sleeping Beauty, the forgotten publications

In science, sleeping beauty refers to several papers whose importance isn't recognized in the moment when they are published, however, after several years have an impact in the science world.
According to new analysis of 22 million studies that had been published over more than a century,  it was found that the "sleeping beauty" phenomenon is very common.
"We followed the history of these papers from the moment they were published to the moment they received maximum citations in other papers," said Alessandro Flammini, one of the study's authors and professor of informatics and computing at Indiana University .
Maybe the most famous example of the sleeping beauty is a paper published in 1935 by Albert Einstein, Boris Podolsky and Nathan Rosen, wich rested unloved for decades, until it started being citated by other researchers in 1994.
Albert Einstein wrote a paper in 1935 that wasn't widely cited until 1994.
Radicchi and his colleagues established  the term "beauty coefficient", a value based on the number of citations and how long after the publication acquired them.
The most known "sleeping beauty" are listed in the following table.
Top 15 sleeping beauty.
Therefore,if you have published something and it haven't been cited, you still can hope about it being cited in the future. However, Radicchi warns about not to hold out too much hope that all publications with not citations are sleeping beauties."I expect, if you look at a paper that is 10 years old (and not cited) my guess is it will continue to have zero citations forever" said Radicchi.

Saturday, May 2, 2015

The zombies exist!

A new research publicated the last week in Scientific Reports in Nature showed that when bacteria are exposed to a solution of silver, can absorbe the silver particles and die, after this dead-bacteria can kill a viable culture of the same bacterium. 

The silver was used since 1893 as antimicrobial for Karl Wilhelm Von Nageli showed the silver's properties as the capacity for permeability of the membrane and once inside the cell, altering its enzymatic system, inhibiting its metabolism and energy production and modifying its genetic material, losing the ability to grow and replication, for this has been employed in the elimination of pathogenic microorganisms. 
But the zombie effect has been recognized to now. This mechanism was show with Pseudomonas aeruginosa (viable bacterial population of ca. 108 CFU/ml) wich was killed when was added nitrate silver solution to different concentrations (1, 2, 5, 15 and 20 ppm) then, this tubes were centrifugated and filtrated and the supernatat was mixed with viable culture of the same bacteria (108 CFU/ml) for 6 hours, then were counted the viable cells. 

P. aureginosa before to treatment with silver (Wakshlak et al., 2015).
P. aeruginosa after to treatment with silver; the white granules represent silver deposition which account for the ‘‘zombies’’ biocidal action (Wakshlak et al., 2015). 

The results showed that at all concentrations the dead-bacterias act as biocidal agents, they achieved to kill the 99.999% of viable cells and this elimination increased with the silver concentration. 
This is due to the dead-bacteria serve as reservoir of silver and the metallic cations are released which are lethal for the live bacteria, the explanation of this phenomenon is given by the principle of Le-Chatelier wich says that if in a equilibrium system is modificated some factor (pressure, temperature, concentration, ..) the system evolves in the direction that tends to oppose this modification. It is said that the equilibrium is shifted to the right (if increases products concentration and decreases the reactive to the initial equilibrium), or left (if increases the reactants concentration and the product concentration decrease).

In this experiment the principle was demonstrated when the silver cations were transferred to dead-bacteria and the viable bacteria because they acted as new unoccupied adsorption sites for silver, and the equilibrium of silver between the reservoir and the liquid, is shifted. 

This investigation proposed a new biocidal agent for microbial infection when the silver concentration adequate is added. Although exist diverse factors involved that can be reviewed in future researches.

Sunday, April 12, 2015

Reaction map suggest meteorite chemistry route to life.
The scientists believe their reaction network could explain the rapid emergence of many different chemicals needed for life.

UK chemist showed a network chain reaction that could explain the rapid emergence of life, but it could be wrong and right in a certain way. The mapped reactions produces 3 sugars, amino acids, ribonucleotides and glycerol. These substances form part of proteins, and could  become ribonucleic acid (RNA) molecules. The map shows how these products were form on Earth's surface with just hydrogen cyanide, hydrogen sulfide and ultraviolet light from the sun. 

This model gain insight because tries to answer where the RNA molecules were from, and that's for the content of the meteorite that crashed on the Earth, that contents that reacted with the nitrogen on the atmosphere, creating cyanide, indispensable for the model, also the meteorite contents iron sulfide. 

Under this condition, it can produce 11 types of amino acids, glycerol, also synthetised molecules cytidine and uridin ribonucleotides and small sugars. This condition yielded 60%-70% of the products while in the experiment of Miller origins of life experiments that zapped electricity through a mixture of methane, ammonia, hydrogen and water only produced 1% of the products.

This method was carried out by adding one substrate after another instead of mixing them all. This would done with a slope formed for the water in the layers of the Earth, carrying the substrates on streams and pools. But this was geological improbable because it needs high concentrations of cyanide but there isn't proof to back up this idea (yet).

This teach us that with an open mind, knowledge and logic you could assemble great and innovative ideas.

For more information about the article you could click on the link:

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!