A solar panel made of bacteria

"Water splitting–biosynthetic system with CO2 reduction efficiencies exceeding photosynthesis"

Science Vol. 352, Issue 6290, pp. 1210-1213

"Among renewable energy resources, solar energy is by far the largest exploitable resource, providing more energy in 1 hour to the earth than all of the energy consumed by humans in an entire year."  

Nathan Lewis & Daniel Nocera, PNAS

Sun gods: Splitting a water molecule

The sun is the source of most of the energy that powers life on Earth. Through the process of photosynthesis - the chemical reaction used by plants to generate sugar from carbon dioxide, water and sunlight - the energy from the sun is converted into biological life.

Electron microscope image of crystals
 of the photosynthesis reaction center

The leaves of plants; seaweed; algae; moss; tiny blue-green bacteria - all these things have a greenish tint because they contain the molecule chlorophyll, a green colored organic molecule. 

Chlorophyll absorbs energy from the rays of the sun, and directs this energy to an intricate molecular structure called the photosynthetic reaction center, made of several different proteins and other molecules. 

Each photosynthetic reaction center is a tiny, minuscule thing - much smaller than a single cell, which can contain hundreds of individual reaction centers.

Yet despite their minuscule size, something remarkable and miraculous occurs inside them. Inside the reaction center, the energy absorbed from sunlight is used to split water molecules into hydrogen and oxygen. 

The chemical bonds in a water molecule are extremely strong compared to the bonds in organic molecules like sugars and proteins. Using sunlight to break these bonds releases a lot of energy, which the cell is able to store as chemical energy in the form of the molecules ATP and NADPH. 

All organisms throughout the kingdoms of life use these two molecules as a universal store of energy - ATP molecules are sometimes called the 'energy currency' of the cell.

The plants then use the ATP and NADPH generated by splitting water molecules to convert carbon dioxide to sugar in a complex series of biochemical reactions known as the light-independent reactions of photosynthesis (also known as the Calvin Cycle).

The sugar created this way provides the material for the plant to grow and reproduce. Animals and other organisms feed on the plants. Other animals eat the plant eaters, and when all these things die bacteria and fungi feed on their corpses. But all of the energy and matter that makes this entire cycle has a single source - sugar produced by plants from sunlight, water and air. 

In this way, the Sun makes nearly all life on Earth possible. Most ancient cultures have a central role for sun gods, because they understood that in some mysterious way this big ball of fire in the sky made it possible for their crops to grow. It is only through the insights of very recent science that we have begun to probe the nanoscale structures of the reaction centers that make this miracle possible.

Photosynthesis is the source for all human food, and thus for the energy that we have always relied on to sustain ourselves. For most of human history, agriculture has been the engine that drove human societies and civilizations. 

But the human capacity for invention eventually allowed our species to tap into much larger reservoirs of energy.

Buried sunshine: The fossil fuel revolution

The technologies of industrialization allowed us to burn fossil fuels like coal and oil to generate motion for transport and large-scale industrial automation. The invention of electricity allowed us to transmit and utilize this energy in completely novel ways, leading to light-bulbs, electronic appliances and the entire computing revolution.

From the earliest days of industrialization, we have understood the utility of digging deep in the ground to extract oil and coal. We learnt that these are incredibly dense stores of energy, and we utilized them on a vast scale to create modern, industrialized human societies.

Fossil fuels store ancient photosynthetic energy

Where does the energy inside these fossil fuels come from? Fossil fuels are made from the decomposition and fossilization of ancient plants and animals that died millions of years ago. The bodies of these organisms contain chemical energy in the form of the chemical bonds in their sugars, fats and proteins. These chemical bonds were able to exist because ancient plants converted air, water and sunlight into sugar.

Fossil fuels store the energy from ancient water-splitting reactions in the form of coal, oil and natural gas. When we dig them up, we can burn them to release this energy for our own use - obtaining far more energy than would be possible from all the living plants in the world.

We can tap into the stored energy of thousands of years of combined photosynthesis when we extract and burn fossil fuels. The amount of energy contained in these deposits vastly exceeds that which can be produced by living plants, because the dead always outnumber the living.

To this day, fossil fuels account for the vast majority of the energy produced by human beings. But this is becoming a problem. Fossil fuels have been stored in the ground for millions of years, but humans are now burning them on a large scale in a very short period of time. This is resulting in much greater amounts of carbon dioxide being released in the air, and is the cause of the ongoing and potentially catastrophic problems of climate change and global warming.

There is a pressing need, therefore, to find carbon-neutral energy sources. 

Carbon-neutral energy sources do not increase the amount of carbon dioxide on the planet when they produce power. One example is nuclear power - nuclear power does not rely on carbon atoms at any point to generate energy, relying instead in the process of nuclear fission in heavy radioactive metals like uranium. Thus, nuclear power will never generate carbon dioxide and contribute to global warming. However it has severe shortcomings - the storage of nuclear waste and the risk of a devastating nuclear meltdown high among them.

Renewable energy sources like wind and solar are currently too expensive and inefficient to become a realistic alternative to fossil fuels, but there are many well-funded and plausible research projects that could make cost-effective renewable energy a reality in the recent future.

A solar tower

In solar power generation, solar panels constructed of special materials are exposed to sunlight to generate energy. This can be done in a number of ways. In photovoltaic panels, solar energy is converted directly into electric current using special semiconducting materials. In solar thermal collection, sunlight is converted to heat, which can be used directly or turned into electricity.

However, both these forms of solar power generation suffer from a severe shortcoming - there is no easy way to store the energy generated by them. Because the planet has day/night cycles, it is difficult for these forms of solar power to generate all our energy needs because they would only work during daylight hours and clear skies.

Photosynthesis does find a way to easily store the energy from sunlight - it stores it in the form of chemical bonds in sugar and other organic molecules. This form of storage is incredibly stable and effective - just look at the fossil fuels that provide most of our energy needs

This biological example has inspired some scientists to try and create systems for artificial photosynthesis.


Daniel Nocera is a chemist whose group has been trying to make inorganic catalysts that can mimic the organic reaction centers that split water molecules in photosynthesis. Whereas plants use a complex of proteins and other organic molecules to use sunlight to split water into hydrogen and oxygen, Nocera's group is trying to create inorganic complexes of metals that can carry out the same reaction.


An artificial leaf

Schematic diagram of the artificial leaf:

Co-OEC - water splitting cobalt catalyst;

3jn-a-Si - silicon absorbs sunlight energy';

NiMoZn - catalyst for hydrogen formation
(source)

In a breakthrough study in 2008, the group discovered a cheap catalyst made of cobalt and phosphate that could catalyze the water splitting reaction, analogous to the reaction center in photosynthesis.

Just as the reaction center in a leaf cannot capture solar energy without chlorophyll, the cobalt catalyst requires a separate component to do this. The group went on to combine this water splitting cobalt catalyst with a silicon semiconductor that mimics the action of chlorophyll, creating an 'artifical leaf'.

This artificial leaf takes sunlight and water, and produces hydrogen and oxygen. The hydrogen produced can be burnt to produce energy. Thus, this artificial leaf allows for the direct conversion of water and sunlight into a usable fuel - hydrogen.




A solar panel made of bacteria

The artificial leaf is combined with living bacteria -
R. eutropha can extract energy from hydrogen
and use this to produce chemicals like petrol (source)

In order for hydrogen to be used widely as a fuel, we would have to invest a vast amount of money developing the infrastructure to store and transport hydrogen in order to create a functioning hydrogen economy.

Without a working hydrogen economy, the artificial leaf created by Nocera's team cannot be a viable source of carbon-neutral energy.

Nocera's team overcame this problem by combining the artificial leaf with a living bacteria that can extract energy from hydrogen, and use this energy to create organic chemicals, including fuels like petrol.



Nocera collaborated with noted synthetic biologist Pamela Silver to create the hybrid device. They chose to use the bacteria Ralstonia eutropha. R. eutropha is a lithotroph - unlike most organisms, lithotrophs are able to extract energy from inorganic chemicals like minerals and rocks.

R. eutropha has the rare ability to extract energy from hydrogen and use this energy to convert carbon dioxide into sugars and other organic chemicals. Although wild R. eutropha does not naturally produce hydrocarbon fuels, it can be genetically engineered to synthesize these chemicals in large amounts.

By combining the artificial leaf with genetically engineered bacteria, the team were able to create a single device that could transform solar energy into easily usable organic fuels.

But their initial efforts had a drawback - the metals used generate toxic compounds called reactive oxygen species during the water splitting reaction, and these begin to kill the bacteria after some time.

The new biocompatible artificial leaf
only uses cobalt and phosphorus as catalysts
(source)

In their most recent paper, the collaborative groups overcame this hurdle by developing a new artificial leaf for the water splitting reaction.

They replaced some of the metals used with a new cobalt-phosphorus alloy that does not produce toxic reactive oxygen species, creating a system that supports bacterial life and is 'bio-compatible'.


The new artificial leaf is 'bio-compatible', allowing for full integration with biological components like genetically engineered bacteria. This bio-compatible, hybrid system is able to take in sunlight, air and water, and convert it directly to carbon-neutral fuels.

Although it will take many years for this breakthrough technology to be commercialized, it has the potential to one day provide a source of cheap, renewable energy and completely transform human society.

The genetic control of wing pattern variation in moths and butterflies

"The gene cortex controls mimicry and crypsis in butterflies and moths"

Nature 534, 106–110

"The industrial melanism mutation in British peppered moths is a transposable element"

Nature 534, 102–105

Electron microscope image of
butterfly wing scales

Moths and butterflies belong to an order of insects called Lepidoptera. One of the main distinguishing features of this order is that they have tiny scales on their wings and other parts of their bodies. Other groups of insects do not have these scales.

These tiny scales can serve a number of functions in moths and butterflies, but one of the most important functions is their role in creating the vivid and unique patterns that these insects have on their wings.

We are all familiar with the beautiful patterns of color and shape that moths and butterflies carry on their wings. These diverse wing patterns are a stunning example of biological variation.

Examples of wing pattern variation
in moths and butterflies

What is variation? Simply put, it refers to groups of items that are 'similar but different'
The wing patterns of moths and butterflies are an example of variation:

• they are similar: all the wing patterns share many basic features, e.g. on the microscopic level they are constructed from similar tiny scales;
• but they are different: individual moths and butterflies have wing patterns that are different in shape and colour from other moths and butterflies

Biological variation is the main object of study in the science of genetics. Geneticists are interested in discovering the "genetic component of biological variation".

What does this mean? Biological variation arises from two sources:

• Environmental variation: differences in organisms caused by differences in environment, e.g. Sam is shorter than Xi because Sam did not have enough food growing up
• Genetic variation: differences in organisms caused by differences in their genes, e.g. Sam is shorter than Xi because Sam's parents are shorter than Xi's parents.

This is commonly referred to as the "nature versus nurture" debate, but there is not so much debate about this in biology. All organisms have a genetic code that determines what it looks like and how it behaves - there will always be a genetic component to all biological phenomena.

Most examples of biological variation involve both nature and nurture - the more correct question is "how much nature versus how much nurture".

By analyzing the DNA sequence of subjects and measuring different traits, geneticists can try and find correlations between differences in DNA and differences in traits. These experiments allow them to answer two questions:

1. How much variation is controlled by genes versus the environment (nature vs. nurture)?
2. What are the DNA mutations causing the genetic variation?

It is only recently, with the invention of genome sequencing technologies and powerful computational methods to analyze genetic data, that scientists have been able to answer the second question. Being able to identify the individual mutations that drive biological variations has huge implications for science and human life. We are just beginning to identify these mutations, and much work remains to be done.

A living histogram of human height variation

An example of this kind of genetic science can be found in a recent large study on the genetic factors controlling variation in human height.

Human height is a classic example of complex intraspecific variation - across human society people can be short, or tall, or somewhere in between.

The authors of this study measured height and analyzed DNA mutations in 253,288 subjects. This kind of experiment is called a genome-wide association study (or GWAS), and it requires very large study populations for the statistical precision needed to draw reliable inferences. 

This study identified 697 different mutations that account for about 1/5th of the observed variation in height among the subjects. What is the significance of this finding? Traits that are controlled by such a large number of genes are known as complex or quantitative traits. 

Because height is a complex trait, we cannot look at a single mutation in a baby and use it to accurately predict someone's adult height. We would have to identify all the known mutations that influence human height, and even then we would obtain an imperfect prediction of adult height as there still so many unknown factors controlling human height.

The opposite of a complex trait is called a Mendelian trait. In Mendelian traits, nearly all of the observed biological variation is controlled by mutations in a single gene. A classic example of this is sickle cell anemia, a genetic blood disease caused by mutations in a single gene: hemoglobin. By identifying whether a baby has the sickle cell mutant form of hemoglobin, we can perfectly predict whether they will have sickle cell anemia.

Scientists have recently begun to study the genetic mutations controlling wing pattern variation in different species of moths and butterflies. These studies have revealed that multiple mutations in a single gene called cortex can control wing pattern variations across many different species of Lepidoptera. 

In a 2009 paper, geneticists from Chris Jiggins' group at the University of Edinburgh studied the genetic basis of intraspecific wing pattern variation in three separate species of Heliconius butterflies.

Intraspecific wing pattern variation in 4 Heliconius species (source)

As you can see, each species contains individuals with different wing patterns. This is an example of intraspecific variation, similar to human height.

The authors determined the genetic component controlling wing pattern variation in three separate species, using a separate set experiments for each species. In order to do this, they used an experimental technique called linkage mapping.

The breeding scheme used to map
mutations causing wing pattern variation (source)

Similar to a GWAS, linkage mapping involves analyzing DNA mutations and measuring wing patterns in a large number of individual butterflies. But while a GWAS analyzes large natural populations, linkage mapping involves breeding animals in the lab and genetically analyzing their children.

In this study, male and female butterflies with different wing patterns were bred to each other, resulting in a number of children with different wing patterns.

Each butterfly child has its wing pattern measured and its DNA analyzed for mutations. By looking at correlations between different mutations and wing patterns, the scientists showed that in each species a single locus (or region of DNA) controlled the difference in wing pattern.

Further analysis showed that not only was a single locus responsible in each case, but that all three of the loci identified were homologous to each other - i.e. the same sequence of DNA appeared to control wing patterns in all 3 species!

However, there is a limitation to their study. Most linkage mapping experiments do not discover a single gene or mutation that is responsible, but rather a large sequence of DNA that contains multiple possible mutations.

In order to precisely narrow down the exact mutation responsible, scientists have to use a technique called fine-mapping. This traditionally means carrying out more breeding experiments and linkage analysis - the increased sample size gives greater statistical precision, allowing us to narrow down the sequence to a single gene.

A recent paper from the Jiggins lab used a newer, GWAS-based approach to fine-map the gene responsible for this pattern of variation in some Heliconius butterflies. By combining the results from the previous linkage analysis with a large GWAS of wing pattern variation in wild butterflies, the authors were able to pinpoint all the mutations to a single gene called cortex.

From the paper: In situ hybridization shows the
location of cortex in pupal wings (below in blue)
matches location of dark spots in adult wings (above in color)

It is currently not known how the cortex gene influences wing patterning. The authors hypothesize that it controls the formation of the scale cells that create the pattern. Using a technique called in situ hybridization, the authors were able to visualize the anatomical locations where the cortex gene is expressed.

They find that the patterns in which the cortex gene is expressed in the developing larval wing of the butterfly closely match the location and shape of colored spots and stripes in the adult wing. This kind of very specific, restricted gene expression suggests that the cortex gene is specifically turned on in groups of cells that give rise to adult wing patterns.


The same issue of Nature with this Heliconius paper contains a second study on a completely different example of Lepidopteran wing pattern - industrial melanism in moths. Industrial melanism occurs when insects like moths evolve a dark black color in response to increased air pollution from industrialization.

An example of industrial melanism in moths.
The moth on the right has evolved industrial melanism.

Although these moths are a very distant species from Heliconius butterflies, the authors find that a single mutation in the same gene - cortex - leads to the evolution of industrial melanism in British peppered moths.

So we find that many different mutations in a single gene - cortex - control intraspecific differences in a single trait - wing patterning - across multiple species in the order Lepidoptera. The figure below shows all the known Lepidoptera species for which mutations in cortex completely control the observed variations in wing pattern. It is likely that there are many more moths and butterflies for which this will also be true.

Known Lepidopteran species where cortex mutations control wing pattern variation (source)

Some Heliconius butterflies have an alternative
'multi-locus' control of wing pattern variation

But, despite these remarkable findings, cortex is not the only gene that controls wing pattern variation in moths and butterflies. Studies on other species of Heliconius butterflies have demonstrated that they use an alternative system where multiple genes interact to control wing pattern variation.

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Rare mutation can reduce heart disease risk by 34%

"Variant ASGR1 Associated with a Reduced Risk of Coronary Artery Disease"

N Engl J Med 374;22

It is only very recently in human history that we have had the power to begin to explore human genetics. Without the technology to cheaply sequence DNA, without the powerful computers and sophisticated statistical methods needed to analyze huge amounts of genetic data, it was impossible for us to even begin to ask fundamental questions about the genetic factors that contribute to human life and disease.

The invention of these technologies has lead to an explosion of studies on human genetics, particularly through the use of a type of study called genome-wide association studies (or GWAS).

An example of a genetic difference, or variation

In these studies the DNA of large numbers of people is sequenced and compared to the sequences of other people. 

Most of our DNA is identical, as we all belong to the same species, but there are many places where two or more people have 'differences' in their DNA sequence.

These differences can be called many things - mutations, polymorphisms, variants - but all these words simply refer to a difference in DNA sequence that exists in two or more individuals.

Scientists can test if the presence or absence of different DNA variants associates strongly with different 'traits' like height, smoking behavior and risk for inflammatory bowel disease. This requires conducting very large case-control trials that can involve collecting DNA and clinical information from hundreds of thousands of subjects.

Imagine that you had a study where 30,000 subjects had a rare mutation and 150,000 controls didn't have that mutation. Because the sample population is so large and diverse, if you observe that the group with the mutation differs consistently from the control group in some trait, you can conclude that is quite likely that the mutation is responsible for this difference. This is the basis of a GWAS study.

A recent paper from Kári Stefánsson's group at deCODE genetics has identified a rare genetic mutation that is associated with a reduced risk for heart disease.

They identified a rare mutation in a gene called asialoglycoprotein receptor 1 (ASGR1) - in their study population, 1 in a 120 people were heterozygous for this rare mutation. In a large analysis involving 42,524 cases with heart disease and 249,414 controls, the team showed that carrying the rare ASGR1 mutation can reduce the risk of heart disease by up to 34%. 

Survival curves comparing morality between
carriers and noncarriers of the ASGR1 mutation
(from the paper)

So how can a mutation in this gene protect someone from heart disease? This is an important question - cardiovascular disease is the leading cause of death across the globe. More people will die annually from cardiovascular disease than any other cause.

A single mutation that can reduce the risk of heart disease by such a large amount has enormous implications for medicine. Scientists can now study the function of the non-mutant ASGR1 gene in cardiovascular physiology, and try and understand how a mutation in this gene can protect from heart disease.

The mutation identified in this study is a 12 base-pair long deletion in an intron of the ASGR1 gene. It leads to a frameshift mutation in the gene, so that the protein that it encodes is truncated. The mutant protein is not stable - because it is a truncated mutant that could harm the cell, it is targeted by the proteasome, a cell organelle that is used to destroy mutant and waste proteins. Thus, the mutation leads to a total absence of the gene from the organism.

The study did not identify people who were homozygotes for the mutation, presumably because a human being that totally lacked this essential gene would die. Instead, the study identified heterozygotes who have one functioning copy and one broken mutant. These individuals are haploinsufficient for ASGR1 - they have lower amounts of ASGR1 protein in their cells than most of the population.

At this point we do not fully understand how the mutation protects people from heart disease - future studies combining genetics and cardiac physiology in mouse models of human disease are needed to fully answer this question.

Individuals with the mutation were also found to have lower levels of non-HDL cholesterol (or "bad" cholesterol) in their blood. While this probably explains part of the protective effect of the mutation, it is unlikely to be the complete story. It is also not yet understood how this mutation leads to lowered levels of bad cholesterol.

The figure below from the paper compares the effects of different rare mutations (using data collected across multiple large studies) on bad cholesterol levels (x-axis) and heart disease risk (y-axis) in human populations.

Each point represents a single mutation. Mutations in the upper half of the dotted axes increase the risk of heart disease, while those in the lower half reduce this risk. ASGR1, the gene identified in this study, is highlighted in blue.





Previous to this study, other mutations in genes such as APOC3 had already been identified that reduce the levels of bad cholesterol and reduce heart disease risk. But the ASGR1 mutation identified in this study is different - it leads to a greater reduction in heart disease risk than any other previously identified mutation, but it leads to a milder reduction in bad cholesterol levels.

So reduced bad cholesterol levels can't be the entire story - there are other unknown mechanisms by which the mutation protects from heart disease.

Understanding these mechanisms could lead to new therapies and interventions for cardiovascular disease, the leading cause of death across the globe.

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Legumes use calcium signaling to coordinate growth of symbiotic nodules

"Nuclear-localized cyclic nucleotide–gated channels mediate symbiotic calcium oscillations"

SCIENCE 27 MAY 2016 • VOL 352 ISSUE 6289

Animals acquire nitrogen by eating other animals or plants, but this is not a viable option for plants that have to rely on photosynthesis for their food (although insect eating plants like the Venus fly trap remind us that evolution can always find a loophole).

Plants can acquire nitrogen in the form of ammonia from the soil. This ammonia can either be present naturally, or added by humans as fertilizer.

The Haber process allowed production of ammonia on an industrial scale, revolutionizing global agriculture. Chemical ammonia remains one of the most widely used crop fertilizers in the world.

But many wild plants grow in nitrogen-poor soil and it has been known for a long time that certain plants, particularly legumes, can replenish the nitrogen content of the soil after it has been exhausted by other crops.

How is this possible? Certain soil bacteria can take gaseous nitrogen from the air and chemically convert it to ammonia, which can be used by plants for growth. This process is called nitrogen fixation.

Some plants, particularly legumes, are able to form symbiotic associations with these soil bacteria. The soil bacteria recognize the roots of the plant, and infect them. The bacteria extend tiny 'infection threads' into the body of the root. The plant and the bacteria together make a small, swollen structure on the root that is called a nodule.

Symbiotic bacteria invade a plant root and trigger nodule formation (from)

The nodules act as sites of exchange between the plant and nitrogen-fixing soil bacteria. The bacteria take nitrogen gas from the air and turn it into ammonia, which helps the plant grow. In exchange the bacteria receive carbon from the plant in the form of sugar.

How does the plant know how to respond correctly to the nitrogen-fixing bacteria? Plant roots will encounter many parasitic bacteria and fungi in the soil - if they responded to all of them by letting them infect their roots, the plant would not be able to survive. Therefore, both the plant and the symbiotic bacteria need signaling systems to (1) recognize each other, and (2) respond to each other by forming root nodules.

Biology is full of such signaling systems: the mating songs of birds are signals to attract potential mates. The fragrant aroma of flowers comes from the chemicals synthesized by the plant to attract insect pollinators. The smell of a flower may give us joy, but for the plant it acts more like a job posting in a newspaper.

A similar signaling system exists to help legumes and other plants attract the good nitrogen-fixing bacteria, and avoid the bad parasites. To attract good bacteria, plants release a number of chemicals (known as strigolactones and flavenoids) into the soil. The bacteria respond to these chemicals by moving towards the root and secreting a number of chemicals called 'nodulation factors'. These nodulation factors are recognized by the plant, and this triggers the beginning of nodule formation.

The nodulation factors trigger a series of transformations in the cells of the root. They have to change their shape and physiology in a precise manner to give rise to a root nodule. This process is similar to the kind of transformations that occur when a caterpillar transforms into a butterfly, or the body changes that occur when a human child goes through puberty. Just as hormones like estrogen and testosterone tell the tissues of our body to mature into their adult forms, the nodulation factors released by nitrogen-fixing bacteria tell the cells of the plant root to form nodules.

How does the plant know how to respond correctly to the nodulation factors? It is not that the nodulation factors simply cause the roots to swell - they lead to very precise and ordered changes in the cells of the root.

How can the plant perform such complex, organized behavior in response to such a simple chemical signal? In order for this to be possible, the cells of the root must have biological signal transduction systems. 

Most processes in biology rely on some kind of signal transduction systems. Biology is all about ordered responses to changing environments. Living things of all shapes and sizes are constantly absorbing information from the outside world, and they are also constantly responding to this information by changing their behavior - think of a mouse hiding in fear at the sight of an owl's shadow, or a flower bud that blooms only when the season is right.

In all these cases an input signal is received by the organism and converted into some kind of behavioral output. But how?

When you drop a letter into a mailbox your only goal is for it to reach the address you have written down. But this is only possible because of an intricate system of mailmen, post offices, postal codes, systems for sorting mail, etc. that ensure that your letter reaches the correct address. This complex arrangement of people is a kind of signal transduction system: the postal system reads the address you wrote on the envelope and converts this information into a sequence of actions that ends with the delivery of your letter.

Similarly when the nitrogen-fixing bacteria secrete nodulation factors, their only goal is for the plant to start forming root nodules - but for this to be possible the plant must have an appropriate signal transduction system. But instead of mailmen and post offices, the plant cell uses a molecular signaling system composed of things like proteins, sugars, hormones. And calcium ions.

Most of us think of calcium as a structural component of our bones, as a mineral that imparts structural strength rather than as something that has a complex biological function like DNA or estrogen.

But in reality the use of calcium ions as a signaling molecule is widespread throughout biology. Cells often keep reservoirs of calcium ions in special compartments. The correct signal leads to the rapid release of these charged ions, causing a wave of calcium ions to flood the cytoplasm. This free calcium can then interact with other proteins and signal transduction systems to instruct the cell to carry out certain behaviors. 

Alfalfa roots injected with calcium indicator dye;
The dye glows after nodulation factors are added (from here)

Scientists can study calcium signaling in cells by using calcium-sensitive indicator dyes that change colour in the presence of free calcium. By injecting tissues of interest with the appropriate dye, scientists can test if calcium signaling is involved in the response to a particular signal.

In a paper from 1996, the authors injected calcium-sensitive dyes into the root hairs of an alfalfa plant. When they applied nodulation factors to the root hair, the dye changed color to show that the root cells respond to the nodulation factor with a sudden spiking oscillation in their calcium levels.

Calcium imaging of alfalfa root
after applying nodulation factors (from here)

This seemed to suggest that the cells were releasing stores of calcium in response to the nodulation factor, but the precise mechanisms by which this calcium release occurs are not fully understood. 

A recent paper from Giles Oldroyd's lab has filled in some of the missing pieces. By studying specific genetic mutants in a small clover species called Medicago trunculata, the authors were able to identify specific genes that lead to abnormal patterns of calcium oscillations. These genes turn out to be members of a group of genes called ion channels, tiny molecular pores that control the flow of ions between compartments.

Mutations in specific ion channels
cause abnormal calcium signaling (from)

Mutations in three specific calcium channels in Medicago trunculata cause it to have abnormal calcium signaling in response to nodulation factors. Without these three functioning genes, the plant cannot form nodules in response to nitrogen-fixing bacteria.

This paper shows that gated calcium ion channels play a key role in the formation of root nodules by legumes and nitrogen-fixing bacteria. Understanding the biological mechanisms by which nitrogen fixing nodules are formed could help the design of technologies that reduce the use of chemical fertilizers.

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Capsaspora and the evolution of animals

"The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity"

Cell 165, 1224–1237, May 19, 2016

All animals - which includes, but is not limited to, insects, worms, fish, birds, mice, coral, jellyfish - have a single common ancestor in evolutionary history, a single proto-animal cell that floated in the oceans of our planet hundreds of millions of years ago. This single proto-animal evolved into several different early animals with distinct anatomies. These early animals gave rise to distinct "lineages", and over a period spanning hundreds of millions of years, these lineages grew and grew, giving rise to all the animals that have ever existed: bony fish, land vertebrates, insects, dinosaurs, mammals, birds and many, many more. 

Early animal life

Fossils have helped us understand some of the earliest events in animal evolution, particularly fossil deposits like the Burgess Shale Formation. The Burgess Shale fossils are over 500 million years old and give us some of our clearest glimpses into the form of early animal life.

All animals are multicellular - unlike bacteria and single-celled eukaryotes like yeast or amoeba. They are composed of many cooperating cells that form tissues and organs. All of these tissues and organs arise from a single fertilized egg cell that grows into a multicellular adult through a process called animal development. 

The common ancestor of animals and their closest single-celled cousins must have been single-celled, because all life began with single cells. 

How does a single cell become multicellular? This is one of the big questions in evolutionary biology, and to a large extent it remains a mystery. There are many multicellular organisms that are not animals - plants and fungi for instance. It seems that there are many independent genetic and evolutionary paths that lead to multicellularity. 

How did animals become multicellular? This is a more specific, tractable question. As all animals existing today have a single common unicellular ancestor, we can use comparative biology to understand the manner in which animals became multicellular.

The Evolutionary Tree of Animals

Comparative approaches have long been a powerful tool in evolutionary biology. Key organisms occupy very special positions in the evolutionary history of animals. Consider the extinct dinosaur Archaeopteryx - a transitional intermediate between ancient dinosaurs and modern, feathered birds. 

By comparing the anatomy of Archaeopteryx fossils to both their dinosaur ancestors and their bird descendants, scientists can infer the evolutionary steps that lead to the evolution of structures like feathers and wings. 

The invention of genome sequencing technologies has allowed biologists to extend these comparative approaches to the molecular scale, comparing DNA sequences instead of skeletal anatomy.

Every organism contains a trace of all its ancestors within its DNA, because every genome arises from the evolution of a pre-existing genome. The science of comparative genomics tries to reconstruct the evolutionary and genetic history of organisms by comparing their genome sequences. For example, studies have compared the genome sequences of human beings to chimpanzees, our closest living relatives. Although human and chimpanzee genomes are extremely similar, there are some DNA sequences that are very different in humans. Presumably, these sequences played a key role in the evolution of Homo sapiens from our ape-like ancestors.

So how did animals genetically evolve to become multicellular? Two hypotheses can be put forward:

1. New Genes: animal ancestors evolved completely new genes 
2. New Regulation: animal ancestors evolved new ways to control existing genes

Scanning EM image of Capsaspora owczarzaki
(taken from PNAS)

In order to address this question, a group of scientists studied Capsaspora owczarzaki - an organism that is one of the closest unicellular relatives to the entire animal lineage. 

Iñaki Ruiz-Trillo's group at the Institut de Biologia Evolutiva in Barcelona has published a number of comparative genomic studies on Capsaspora to try and answer some fundamental questions about the evolution of animal multicellularity.

In previous work from the group, the entire Capsaspora genome was sequenced and compared to known animal genomes. Many of the complex genes previously thought to be unique to animals turned out to be present in this simple, unicellular relative. But there are still a large number of genes that appear to be unique to the animal lineage, particularly those involved in communication between cells, a process that is extremely important during animal development.

In their most recent paper, the group applied some new genomic methods to study the Capsaspora genome. While traditional genome sequencing gives a static readout of the DNA sequence, newer methods can provide dynamic snapshots of the genome in action. 

Every gene has associated DNA control elements that limit where and when the gene is turned on - acting as 'switches' and 'regulators'. The processes by which the expression of genes is controlled across space and time are called gene regulation.

All organisms have control elements in their DNA called 'promoters' that are always located close to the genes that they regulate. Some organisms have a second set of control elements called 'enhancers' - these can occupy very distant locations from the genes they control and are thought to expand an organism's capacity for complex gene regulation.

New technologies allow us to visualize the organization of these control elements in different organisms. This paper provides our first view of the organization of gene regulation in Capsaspora, and thus provides a view into what elements of gene regulation are unique to the multicellular animal lineage.

The study finds that although Capsaspora gene regulation has many elements in common with animals, it completely lacks the distant 'enhancer' control elements that are present in all animals. This suggests that the evolution of this mode of gene regulation was absent before the evolution of early animal ancestors, and could have been one of the key genetic innovations that lead to the evolution of animal multicellularity.

So did animal multicellularity require the invention of new genes or new regulation of old genes? As with many things in biology, it was a bit of both.

A new resolution limit for protein imaging with cryo-electron microscopy

"Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery"

Cell 165, 1–10, June 16, 2016

Single cells are tiny things. So tiny that 200 red blood cells could fit across the width of a single human hair. 

Yet a single cell is packed with thousands of even tinier proteins. Even though each protein molecule is so tiny that hundreds of them could fill a single cell, each of them is an incredibly complex, uniquely specific, dynamic thing. There are thousands of uniquely shaped proteins across the kingdoms of life. The diversity of forms is staggering in its scale.

Each of these proteins is a complex nanomachine - some act as motors, others as structural scaffolding. Many are enzymes - catalysts for the chemical reactions that give rise to life. And many are completely unkown and remain to be understood.

Some examples of protein structures 

Each protein is composed of distinct physical parts that have different functions. Some have little "battery packs" that power the activity of the protein. Many have moving parts - hinges that swing, pores that open and shut. 

Each protein has a physical form. You can think of it as a very small shape made of atoms, an incredibly intricate kind of molecular origami. Biologists call this shape a 'structure'. Biologists who study the structures of proteins are called 'structural biologists'.

Understanding the structures of proteins has enormous potential for drug discovery. Drugs like antibiotics target specific bacterial proteins and disable them, killing dangerous bacteria. Knowing the structure of target proteins in disease could guide the design of drugs to target them.

X-ray crystallography

Studying an object as small as a protein is very technically challenging. Historically, one of the main methods for doing this has been a technique called X-ray crystallography. In this method, scientists must first make large amounts of the protein they are studying, and then coax these fickle, fragile molecules into forming well-ordered solid crystals. This is very difficult, and can consume years of a scientist's life.

Once the crystals are made they are treated with chemicals and zapped with powerful X-rays inside giant particle accelerators, creating a pattern of dots that can be 'read' to determine the positions and orientations of the atoms in the protein molecule. This is the 'structure' - the location and orientation of all the individual atoms that make up a protein.

Although X-ray crystallography is an incredibly powerful technique that has lead to multiple Nobel Prizes, it has a very serious limitation - proteins can only be studied after being made into solid crystals, but proteins do not form these kinds of crystals inside the cells where they live and work. There is always a worry that the 'crystal' structure being studied is very different from the 'native' structure of the protein inside a living cell. 

Scanning EM image of a fly's head

A more recent method for studying protein structures that is gaining popularity is called cryo-electron microscopy. Electron microscopy (EM) is a form of microscopy that replaces a beam of photons with a beam of electrons, giving rise to much higher resolution magnification. Electron microscopes have been used to take stunningly detailed images of cells and insects, but until recently technical limitations have prevented it from being used to study structures as small as individual proteins.

Technical advancements in cryo-EM have the potential to bring in a new era of structural biology, allowing scientists to get atomic resolution structures of individual proteins in a more 'native' form, although it carries its own set of limitations.

Cryo-EM image of glutamate dehydrogenase,
taken from the paper

A recent paper from Sriram Subramaniam's lab at the NIH in Bethesda, Maryland has broken the previous resolution barriers to cryo-EM. Whereas previously cryo-EM was limited to studying very large protein complexes like entire virus particles or the ribosome, the authors in this study overcome these technical barriers to obtain atomic scale structures of two small protein enzymes (lactate dehydrogenase and glutamate dehydrogenase) that have been implicated in cancer. 

Excitingly, the authors were also able to image physical interactions of the proteins with drug molecules. This kind of analysis has the potential to guide the design of newer, more effective medicines targeting specific proteins implicated in human disease.