Sea level changes shaped early life on Earth, fossil study reveals

A newly developed timeline of early animal fossils reveals a link between sea levels, changes in marine oxygen, and the appearance of the earliest ancestors of present-day animals.

The study reveals clues into the forces that drove the evolution of the earliest organisms, from which all major animal groups descended.

A team from the University of Edinburgh studied a compilation of rocks and fossils from the so-called Ediacaran-Cambrian interval -- a slice of time 580-510 million years ago. This period witnessed an explosion of biodiversity according to fossil records, the causes of which have baffled scientists since Charles Darwin.

The early animals found from this era were all sea-dwellers, at a time when oxygen levels in the air and ocean were much lower than today.

While the very first lifeforms before this time were mostly single-cell, and simple multi-celled organisms, creatures in the Ediacaran Period started to become more complex, with multiple cells organised into body plans that allowed them to feed, reproduce, and move across the ocean floor.

This era also marked the emergence of so-called bilaterian animals -- which display symmetrical body plans, in common with most present-day species including humans.

By compiling data from different sources -- including radioactive dating and geochemical information about the layers of rock in which fossils were found -- the team mapped all major fossil finds and various environmental datasets onto a single timeline.

The new chronology allowed the team to study trends in biodiversity for the period in question with more detail than before.

They combined these insights with further chemical clues from the geological record -- confirming a link between major changes in global sea levels, intervals when shallow marine environments gained more oxygen, and the appearance and diversification of early animal groups.

This dynamic set the stage for several significant bursts in biological diversity, known as the Avalon, White Sea, and Cambrian assemblages, each marking the arrival of new animal groups and the decline of others.

By reconstructing environmental conditions in deepest time, the study unlocks new insights into the ancient forces and pressures that shaped the earliest life on our planet.

The team also identified gaps in the fossil record, suggesting that current knowledge about early animals is biased by the clusters of sites worldwide where fossils have been found and studied.

Dr Fred Bowyer of the University of Edinburgh's School of Geosciences, said: "Constructing a timescale of early animal evolution using the rock record is a daunting task, only made possible through international and interdisciplinary research. But an integrated global approach is crucial. It exposes biases in our records, while also revealing patterns in fossil appearances, sea level cycles, and environmental oxygen."

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Scientists untangle interactions between the Earth's early life forms and the environment over 500 million years

The atmosphere, the ocean and life on Earth interacted over the past 500-plus million years in ways that improved conditions for early organisms to thrive. Now, an interdisciplinary team of scientists has produced a perspective article of this co-evolutionary history published in multidisciplinary open-access journal National Science Review.

"One of our tasks was to summarize the most important discoveries about carbon dioxide and oxygen in the atmosphere and ocean over the past 500 million years," says Syracuse University geochemistry professor Zunli Lu, lead author on the paper. "We reviewed how those physical changes affected the evolution of life in the ocean. But it's a two-way street. The evolution of life also impacted the chemical environment. It is not a trivial task to understand how to build a habitable Earth over long time scales"

The team from Syracuse University, Oxford University and Stanford University explored the intricate feedbacks among ancient life forms, including plants and animals, and the chemical environment in the current Phanerozoic Eon, which began approximately 540 million years ago.

At the start of the Phanerozoic, carbon dioxide levels in the atmosphere were high, and oxygen levels were low. Such a condition would be difficult for many modern organisms to thrive. But ocean algae changed that. They absorbed carbon dioxide from the atmosphere, locked it into organic matter and produced oxygen through photosynthesis.

The ability of animals to live in an ocean environment was affected by oxygen levels. Lu is studying where and when ocean oxygen levels may have risen or fallen during the Phanerozoic using geochemical proxies and model simulations. Co-author Jonathan Payne, professor of Earth and planetary sciences at Stanford University, compares an ancient animal's estimated metabolic requirements to places where it survived or disappeared in the fossil record.

As photosynthetic algae removed atmospheric carbon into sedimentary rocks to lower carbon dioxide and raise oxygen levels, the algae's enzymes became less efficient in fixing carbon. Therefore, algae had to figure out more complicated ways of doing photosynthesis at lower carbon dioxide and higher oxygen levels. It accomplished this by creating internal compartments for photosynthesis with control over the chemistry.

"For algae, it is changes in the environmental ratio of O2/CO2 that seems to be key to driving improved photosynthetic efficiency," says co-author Rosalind Rickaby, who is a professor of geology at Oxford. "What is really intriguing is that these improvements in photosynthetic efficiency may have expanded the chemical envelope of habitability for many forms of life."

Ancient photosynthesizers had to adapt to changes in the physical environment that they themselves had created, notes Lu. "The first part of the history of the Phanerozoic is increasing habitability for life, and then the second part is adaptation."

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Venus had Earth-like plate tectonics billions of years ago, study suggests

Venus, a scorching wasteland of a planet according to scientists, may have once had tectonic plate movements similar to those believed to have occurred on early Earth, a new study found. The finding sets up tantalizing scenarios regarding the possibility of early life on Venus, its evolutionary past and the history of the solar system.

Writing in Nature Astronomy, a team of scientists led by Brown University researchers describes using atmospheric data from Venus and computer modeling to show that the composition of the planet's current atmosphere and surface pressure would only have been possible as a result of an early form of plate tectonics, a process critical to life that involves multiple continental plates pushing, pulling and sliding beneath one another.

On Earth, this process intensified over billions of years, forming new continents and mountains, and leading to chemical reactions that stabilized the planet's surface temperature, resulting in an environment more conducive to the development of life.

Venus, on the other hand, Earth's nearest neighbor and sister planet, went in the opposite direction and today has surface temperatures hot enough to melt lead. One explanation is that the planet has always been thought to have what's known as a "stagnant lid," meaning its surface has only a single plate with minimal amounts of give, movement and gasses being released into the atmosphere.

The new paper posits that this wasn't always the case. To account for the abundance of nitrogen and carbon dioxide present in Venus' atmosphere, the researchers conclude that Venus must have had plate tectonics sometime after the planet formed, about 4.5 billion to 3.5 billion years ago. The paper suggests that this early tectonic movement, like on Earth, would have been limited in terms of the number of plates moving and in how much they shifted. It also would have been happening on Earth and Venus simultaneously.

"One of the big picture takeaways is that we very likely had two planets at the same time in the same solar system operating in a plate tectonic regime -- the same mode of tectonics that allowed for the life that we see on Earth today," said Matt Weller, the study's lead author who completed the work while he was a postdoctoral researcher at Brown and is now at the Lunar and Planetary Institute in Houston.

This bolsters the possibility of microbial life on ancient Venus and shows that at one point the two planets -- which are in the same solar neighborhood, are about the same size, and have the same mass, density and volume -- were more alike than previously thought before diverging.

The work also highlights the possibility that plate tectonics on planets might just come down to timing -- and therefore, so may life itself.

"We've so far thought about tectonic state in terms of a binary: it's either true or it's false, and it's either true or false for the duration of the planet," said study co-author Alexander Evans, an assistant professor of Earth, environmental and planetary sciences at Brown. "This shows that planets may transition in and out of different tectonic states and that this may actually be fairly common. Earth may be the outlier. This also means we might have planets that transition in and out of habitability rather than just being continuously habitable."

That concept will be important to consider as scientists look to understand nearby moons -- like Jupiter's Europa, which has shown proof of having Earth-like plate tectonics -- and distant exoplanets, according to the paper.

The researchers initially started the work as a way to show that the atmospheres of far-off exoplanets can be powerful markers of their early histories, before deciding to investigate that point closer to home.

They used current data on Venus' atmosphere as the endpoint for their models and started by assuming Venus has had a stagnant lid through its entire existence. Quickly, they were able to see that simulations recreating the planet's current atmosphere didn't match up with where the planet is now in terms of the amount nitrogen and carbon dioxide present in the current atmosphere and its resulting surface pressure.

The researchers then simulated what would have had to happen on the planet to get to where it is today. They eventually matched the numbers almost exactly when they accounted for limited tectonic movement early in Venus' history followed by the stagnant lid model that exists today.

Overall, the team believes the work serves as a proof of concept regarding atmospheres and their ability to provide insights into the past.

"We're still in this paradigm where we use the surfaces of planets to understand their history," Evans said. "We really show for the first time that the atmosphere may actually be the best way to understand some of the very ancient history of planets that is often not preserved on the surface."

Upcoming NASA DAVINCI missions, which will measure gasses in the Venusian atmosphere, may help solidify the study's findings. In the meantime, the researchers plan to delve deep into a key question the paper raises: What happened to plate tectonics on Venus? The theory in the paper suggests that the planet ultimately became too hot and its atmosphere too thick, drying up the necessary ingredients for tectonic movement.

"Venus basically ran out of juice to some extent, and that put the brakes on the process," said Daniel Ibarra, a professor in Brown's Department of Earth, Environmental and Planetary Sciences and co-author on the paper.

The researchers say the details of how this happened may hold important implications for Earth.

"That's going to be the next critical step in understanding Venus, its evolution and ultimately the fate of the Earth," Weller said. "What conditions will force us to move in a Venus-like trajectory, and what conditions could allow the Earth to remain habitable?"

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Bizarre new fossils shed light on ancient plankton

A scientist from the University of Leicester has discovered a new type of fossil that reveals life in the oceans half a billion years ago.

The tiny organisms, detailed in a new study in the journal Proceedings of the Royal Society B, resemble modern-day algae and might also give scientists an insight into the climate changes that affected our oceans.

The fossils are microscopic and look like spiny balls connected together. The study's author Dr Tom Harvey, from the University of Leicester School of Geography, Geology and the Environment, said: "When I first saw them, I had no idea what they were. I wondered if they could be animal eggs, or some new type of organism. There's nothing quite like them, living or extinct."

But as further specimens came to light, Dr Harvey identified similarities with modern green algae that live floating in the plankton of ponds and lakes. He explains: "The fossils have the same sort of colonial structure as the modern algae, with cells linking together, explaining their neat, geometric arrangements. Surprisingly, though, the fossil examples lived in the sea, giving a rare glimpse of the early marine plankton."

The importance of the fossils lies in their immense age. They lived around the time when animals were first evolving, during the Cambrian 'explosion' of life -- and this is probably no coincidence. In today's world, phytoplankton provides the fundamental food source for almost all life in the oceans. However, the modern groups of phytoplankton evolved relatively recently, and we do not know which groups inhabited the Cambrian oceans.

Dr Harvey explains: "When we look at modern plankton, we see that algae develop colonies when animals are trying to eat them. It's a defence mechanism. So, the existence of colonial algae in the Cambrian Period suggests that early animals were evolving to feed in the plankton, starting a predator-prey relationship that has continued ever since.

"Considering that the plankton underpins life in the oceans, and fossil plankton helps us build ancient climate models, these small fossils have a big role in telling the history of life on Earth."

The new discovery will prompt a re-think on other early microfossils. For years, scientists have thought that the spiny balls found individually were the dormant cysts of single-celled life.

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Fossil site is 'Rosetta Stone' for understanding early life

Leading edge technology has uncovered secrets about a world-renowned fossil hoard that could offer vital clues about early life on earth.

Researchers who analysed the 400 million-year-old-cache, found in rural north-east Scotland, say their findings reveal better preservation of the fossils at a molecular level than was previously anticipated.

Fresh scrutiny of the exquisitely preserved treasure trove from Aberdeenshire has enabled scientists to identify the chemical fingerprints of the various organisms within it.

Just as the Rosetta Stone helped Egyptologists translate hieroglyphics, the team hopes these chemical codes can help them decipher more about the identity of the life forms, that other more ambiguous fossils represent.

The spectacular fossil ecosystem near the Aberdeenshire village of Rhynie was discovered in 1912, mineralised and encased by chert -- hard rock composed of silica.Known as the Rhynie chert, it originates from the Early Devonian period -- about 407 million years ago -- and has a significant role to play in scientists understanding of life on earth.

Researchers combined the latest non-destructive imaging with data analysis and machine learning to analyse fossils from collections held by National Museums Scotland and the Universities of Aberdeen and Oxford.Scientists from the University of Edinburgh were able to probe deeper than has previously been possible, which they say could reveal new insights about less well-preserved samples.

Employing a technique known as FTIR spectroscopy -- in which infrared light is used to collect high-resolution data -- researchers found impressive preservation of molecular information within the cells, tissues and organisms in the rock.

Since they already knew which organisms most of the fossils represented, the team was able to discover molecular fingerprints that reliably discriminate between fungi, bacteria and other groups.

These fingerprints were then used to identify some of the more mysterious members of the Rhynie ecosystem, including two specimens of an enigmatic tubular "nematophyte."

These strange organisms, which are found in Devonian -- and later Silurian -- sediments have both algal and fungal characteristics and were previously hard to place in either category. The new findings indicate that they were unlikely to have been either lichens or fungi.

Dr Sean McMahon, Chancellor's Fellow from the University of Edinburgh's School of Physics and Astronomy and School of GeoSciences, said: "We have shown how a quick, non-invasive method can be used to discriminate between different lifeforms, and this opens a unique window on the diversity of early life on Earth."

The team fed their data into a machine learning algorithm that was able to classify the different organisms, providing the potential for sorting other datasets from other fossil-bearing rocks.

The study, published in Nature Communications, was funded by The Royal Society, Wallonia-Brussels International and the National Council of Science and Technology of Mexico.

Dr Corentin Loron, Royal Society Newton International Fellow from the University of Edinburgh's School of Physics and Astronomy said the study shows the value of bridging palaeontology with physics and chemistry to create new insights into early life.

"Our work highlights the unique scientific importance of some of Scotland's spectacular natural heritage and provides us with a tool for studying life in trickier, more ambiguous remnants," Dr Loron said.

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The beginning of life: The early embryo is in the driver's seat

One often thinks that the early embryo is fragile and needs support. However, at the earliest stages of development, it has the power to feed the future placenta and instructs the uterus so that it can nest. Using 'blastoids', in vitro embryo models formed with stem cells, the Lab of Nicolas Rivron at IMBA showed that the earliest molecular signals that induce placental development and prepare the uterus come from the embryo itself. The findings, now published in Cell Stem Cell, could contribute to a better understanding of human fertility.

Who takes care of whom at the onset of life? The placenta and the uterus nurture and shelter the fetus. But the situation at the very early stage of development, when the blastocyst still floats in the uterus, was unclear so far. Now, the research group of Nicolas Rivron at IMBA (Institute of Molecular Biotechnology of the Austrian Academy of Sciences) uncovered basic principles of early development using blastoids.

Blastoids are in vitro models of the blastocyst, the mammalian embryo in the first few days following fertilization. These embryo models were first developed by the Rivron lab from mouse stem cells (Nature, 2018) and then from human stem cells (Nature, 2021). Blastoids provide an ethical alternative to the use of embryos for research and, importantly, enable multiple discoveries.

Now, blastoids settled a "chicken or egg" dilemma. Using mouse blastoids, the researchers found that the early embryonic part (~10 cells) instructs the future placental part (~100 cells) to form, and the uterine tissues to change. "By doing this, the embryo invests in its own future: it promotes the formation of the tissues that will soon take care of its development. The embryo is in control, instructing the creation of a supporting surrounding," states Nicolas Rivron.

Indeed, the team discovered several molecules secreted by the few cells from which the fetus develops, the epiblasts. They observed that these molecules tell other cells, the trophoblasts that later form the placenta, to self-renew and proliferate, two stem cell properties that are essential for the placenta to grow.

The team also found that these molecules induce the trophoblasts to secrete two other molecules, WNT6 and WNT7B. WNT6 and WNT7B tell the uterus to wrap around the blastocyst. "Other researchers had previously seen that WNT molecules are involved in the uterine reaction. Now we show that these signals are WNT6/7B and that they are produced by the blastocyst trophoblasts to notify the uterus to react. The relevance could be high because we have verified that these two molecules are also expressed by the trophoblasts of the human blastocyst," states Nicolas Rivron.

The team made their findings partly by examining the extent of implantation of the mouse blastoids in an in vivo implantation mouse model. "I was very surprised by the efficiency at which our blastoids implanted into the uterus. And by changing the properties of the trophoblasts within blastoids, including the secretion levels of WNT6/7B, we could clearly change the size of the uterine cocoon," says co-first author Jinwoo Seong, a postdoctoral fellow in the Rivron lab, who performed these experiments.

Because implantation is the bottleneck in human pregnancies -- around 50 percent of pregnancies fail at that time -- and WNT6 and WNT7B are also present in human blastocysts, these findings might explain why, sometimes, things go wrong. "We are currently repeating these experiments with human blastoids and uterine cells, all in a dish, to estimate the conservation of such basic principles of development. These discoveries might ultimately contribute to improving IVF procedures, developing fertility drugs, and contraceptives" says Nicolas Rivron.

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Supermountains controlled the evolution of life on Earth

Giant mountain ranges at least as high as the Himalayas and stretching up to 8,000 kilometres across entire supercontinents played a crucial role in the evolution of early life on Earth, according to a new study by researchers at The Australian National University (ANU).

The researchers tracked the formation of these supermountains throughout Earth's history using traces of zircon with low lutetium content -- a combination of mineral and rare earth element only found in the roots of high mountains where they form under intense pressure.

The study found the most giant of these supermountains only formed twice in Earth's history -- the first between 2,000 and 1,800 million years ago and the second between 650 and 500 million years ago. Both mountain ranges rose during periods of supercontinent formation.

Lead author, ANU PhD candidate Ziyi Zhu, said there are links between these two instances of supermountains and the two most important periods of evolution in Earth's history.

"There's nothing like these two supermountains today. It's not just their height -- if you can imagine the 2,400 km long Himalayas repeated three or four times you get an idea of the scale," she said.

"We call the first example the Nuna Supermountain. It coincides with the likely appearance of eukaryotes, organisms that later gave rise to plants and animals.

"The second, known as the Transgondwanan Supermountain, coincides with the appearance of the first large animals 575 million years ago and the Cambrian explosion 45 million years later, when most animal groups appeared in the fossil record."

Co-author Professor Jochen Brocks said: "What's stunning is the entire record of mountain building through time is so clear. It shows these two huge spikes: one is linked to the emergence of animals and the other to the emergence of complex big cells."

When the mountains eroded they provided essential nutrients like phosphorus and iron to the oceans, supercharging biological cycles and driving evolution to greater complexity.

The supermountains may also have boosted oxygen levels in the atmosphere, needed for complex life to breathe.

"The early Earth's atmosphere contained almost no oxygen. Atmospheric oxygen levels are thought to have increased in a series of steps, two of which coincide with the supermountains," Ms Zhu said.

"The increase in atmospheric oxygen associated with the erosion of the Transgondwanan Supermountain is the largest in Earth's history and was an essential prerequisite for the appearance of animals."

There is no evidence of other supermountains forming at any stage between these two events, making them even more significant.

"The time interval between 1,800 and 800 million years ago is known as the Boring Billion, because there was little or no advance in evolution," co-author Professor Ian Campbell said.

"The slowing of evolution is attributed to the absence of supermountains during that period, reducing the supply of nutrients to the oceans.

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Some of the world’s oldest rubies linked to early life

While analyzing some of the world's oldest coloured gemstones, researchers from the University of Waterloo discovered carbon residue that was once ancient life, encased in a 2.5 billion-year-old ruby.

The research team, led by Chris Yakymchuk, professor of Earth and Environmental Sciences at Waterloo, set out to study the geology of rubies to better understand the conditions necessary for ruby formation. During this research in Greenland, which contains the oldest known deposits of rubies in the world, the team found a ruby sample that contained graphite, a mineral made of pure carbon. Analysis of this carbon indicates that it is a remnant of early life.

"The graphite inside this ruby is really unique. It's the first time we've seen evidence of ancient life in ruby-bearing rocks," says Yakymchuk. "The presence of graphite also gives us more clues to determine how rubies formed at this location, something that is impossible to do directly based on a ruby's colour and chemical composition."

The presence of the graphite allowed the researchers to analyze a property called isotopic composition of the carbon atoms, which measures the relative amounts of different carbon atoms. More than 98 per cent of all carbon atoms have a mass of 12 atomic mass units, but a few carbon atoms are heavier, with a mass of 13 or 14 atomic mass units.

"Living matter preferentially consists of the lighter carbon atoms because they take less energy to incorporate into cells," said Yakymchuk. "Based on the increased amount of carbon-12 in this graphite, we concluded that the carbon atoms were once ancient life, most likely dead microorganisms such as cyanobacteria."

The graphite is found in rocks older than 2.5 billion years ago, a time on the planet when oxygen was not abundant in the atmosphere, and life existed only in microorganisms and algae films.

During this study, Yakymchuk's team discovered that this graphite not only links the gemstone to ancient life but was also likely necessary for this ruby to exist at all. The graphite changed the chemistry of the surrounding rocks to create favourable conditions for ruby growth. Without it, the team's models showed that it would not have been possible to form rubies in this location.

From Science Daily

Origin of life: The chicken-and-the-egg problem

 A Ludwig-Maximilians-Universitaet (LMU) in Munich team has shown that slight alterations in transfer-RNA molecules (tRNAs) allow them to self-assemble into a functional unit that can replicate information exponentially. tRNAs are key elements in the evolution of early life-forms.

Life as we know it is based on a complex network of interactions, which take place at microscopic scales in biological cells, and involve thousands of distinct molecular species. In our bodies, one fundamental process is repeated countless times every day. In an operation known as replication, proteins duplicate the genetic information encoded in the DNA molecules stored in the cell nucleus -- before distributing them equally to the two daughter cells during cell division. The information is then selectively copied ('transcribed') into what are called messenger RNA molecules (mRNAs), which direct the synthesis of the many different proteins required by the cell type concerned. A second type of RNA -- transfer RNA (tRNA) -- plays a central role in the 'translation' of mRNAs into proteins. Transfer RNAs act as intermediaries between mRNAs and proteins: they ensure that the amino-acid subunits of which each particular protein consists are put together in the sequence specified by the corresponding mRNA.

How could such a complex interplay between DNA replication and the translation of mRNAs into proteins have arisen when living systems first evolved on the early Earth? We have here a classical example of the chicken-and-the-egg problem: Proteins are required for transcription of the genetic information, but their synthesis itself depends on transcription.

LMU physicists led by Professor Dieter Braun have now demonstrated how this conundrum could have been resolved. They have shown that minor modifications in the structures of modern tRNA molecules permit them to autonomously interact to form a kind of replication module, which is capable of exponentially replicating information. This finding implies that tRNAs -- the key intermediaries between transcription and translation in modern cells -- could also have been the crucial link between replication and translation in the earliest living systems. It could therefore provide a neat solution to the question of which came first -- genetic information or proteins?

Strikingly, in terms of their sequences and overall structure, tRNAs are highly conserved in all three domains of life, i.e. the unicellular Archaea and Bacteria (which lack a cell nucleus) and the Eukaryota (organisms whose cells contain a true nucleus). This fact in itself suggests that tRNAs are among the most ancient molecules in the biosphere.

Like the later steps in the evolution of life, the evolution of replication and translation -- and the complex relationship between them -- was not the result of a sudden single step. It is better understood as the culmination of an evolutionary journey. "Fundamental phenomena such as self-replication, autocatalysis, self-organization and compartmentalization are likely to have played important roles in these developments," says Dieter Braun. "And on a more general note, such physical and chemical processes are wholly dependent on the availability of environments that provide non-equilibrium conditions."

In their experiments, Braun and his colleagues used a set of reciprocally complementary DNA strands modeled on the characteristic form of modern tRNAs. Each was made up of two 'hairpins' (so called because each strand could partially pair with itself and form an elongated loop structure), separated by an informational sequence in the middle. Eight such strands can interact via complementary base-pairing to form a complex. Depending on the pairing patterns dictated by the central informational regions, this complex was able to encode a 4-digit binary code.

Each experiment began with a template -- an informational structure made up of two types of the central informational sequences that define a binary sequence. This sequence dictated the form of the complementary molecule with which it can interact in the pool of available strands. The researchers went on to demonstrate that the templated binary structure can be repeatedly copied, i.e. amplified, by applying a repeating sequence of temperature fluctuations between warm and cold. "It is therefore conceivable that such a replication mechanism could have taken place on a hydrothermal microsystem on the early Earth," says Braun. In particular, aqueous solutions trapped in porous rocks on the seafloor would have provided a favorable environment for such reaction cycles, since natural temperature oscillations, generated by convection currents, are known to occur in such settings.

During the copying process, complementary strands (drawn from the pool of molecules) pair up with the informational segment of the template strands. In the course of time, the adjacent hairpins of these strands also pair up to form a stable backbone, and temperature oscillations continue to drive the amplification process. If the temperature is increased for a brief period, the template strands are separated from the newly formed replicate, and both can then serve as template strands in the next round of replication.

The team was able to show that the system is capable of exponential replication. This is an important finding, as it shows that the replication mechanism is particularly resistant to collapse owing to the accumulation of errors. The fact that the structure of the replicator complex itself resembles that of modern tRNAs suggests that early forms of tRNA could have participated in molecular replication processes, before tRNA molecules assumed their modern role in the translation of messenger RNA sequences into proteins. "This link between replication and translation in an early evolutionary scenario could provide a solution to the chicken-and-the-egg problem," says Alexandra Kühnlein. It could also account for the characteristic form of proto-tRNAs, and elucidate the role of tRNAs before they were co-opted for use in translation.

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Living in an anoxic world: Microbes using arsenic are a link to early life

 Much of life on planet Earth today relies on oxygen to exist, but before oxygen was present on our blue planet, lifeforms likely used arsenic instead. These findings are detailed in research published today in Communications Earth and Environment.

A key component of the oxygen cycle is where plants and some types of bacteria essentially take sunlight, water and CO2 and convert them to carbohydrates and oxygen which are then cycled and used by other organisms that breathe oxygen. This oxygen serves as a vehicle for electrons, gaining and donating electrons as it powers through the metabolic processes. However, for half of the time life has existed on Earth, there was no oxygen present and for the first 1.5 billion years we really do not know how these systems worked, says lead author of the study and UConn Professor of Marine Sciences and Geosciences Pieter Visscher.

Light-driven, photosynthetic organisms appear in the fossil record as layered carbonate rocks called stromatolites dating to around 3.7 billion years ago, says Visscher. Stromatolite mats are deposited over the eons by microbial ecosystems, with each layer holding clues about life at that time. There are contemporary examples of microbes that photosynthesize in the absence of oxygen using a variety of elements to complete the process, however it is not clear how this happened in the earliest life forms.

Theories as to how life's processes functioned in the absence of oxygen have mostly relied on hydrogen, sulfur, or iron as the elements that ferried electrons around to fulfill the metabolic needs of organisms.

Visscher explains these theories are contested, for example photosynthesis is possible with iron but researchers do not find evidence of that in the fossil record before oxygen appeared some 2.4 billion years ago. Hydrogen is mentioned yet the energetics and competition for hydrogen between different microbes shows it is highly unfeasible.

Arsenic is another theoretical possibility, and evidence for that was found in 2008. Visscher says the link with arsenic was strengthened in 2014 when he and colleagues found evidence of arsenic-based photosynthesis in deep time. To further support their theory, the researchers needed to find a modern analog to study the biogeochemistry and element cycling.

Finding an analog to the conditions on early Earth is a challenge for a number of reasons, besides the fact that oxygen is abundant on modern earth. For instance, the evidence shows early microbes captured atmospheric carbon and produced organic matter at a time when volcanic eruptions were frequent, UV light was intense in the absence of the ozone layer, and oceans were essentially a toxic soup.

Another challenging aspect of working within the fossil record, especially those as ancient as some stromatolites, is that there are few left due to the cycling of rock as continents move and time marches on. However, a breakthrough happened when the team discovered an active microbial mat, currently existing in the harsh conditions in Laguna La Brava in the Atacama Desert in Chile.

The mats have not been studied previously but present an otherworldly set of conditions, like those of early Earth. The mats are in a unique environment which leaves them in a permanent oxygen-free state at high altitude where they are exposed to wild, daily temperature swings, and high UV conditions. The mats serve as powerful and informative tools for truly understanding life in the conditions of early Earth.

Visscher explains, "We started working in Chile, where I found a blood red river. The red sediments are made up by anoxogenic photosynthetic bacteria. The water is very high in arsenic as well. The water that flows over the mats contains hydrogen sulfide that is volcanic in origin and it flows very rapidly over these mats. There is absolutely no oxygen."

The team also showed that the mats were making carbonate deposits and creating a new generation of stromatolites. The carbonate materials also showed evidence for arsenic cycling -- that arsenic is serving as a vehicle for electrons -- proving that the microbes are actively metabolizing arsenic much like oxygen in modern systems. Visscher says that these findings, along with the fossil evidence gives a strong indication of what was seen on early earth.

"Arsenic-based life has been a question in terms of does it have biological role or is it just a toxic compound?" says Visscher. That question appears to be answered, "I have been working with microbial mats for about 35 years or so. This is the only system on Earth where I could find a microbial mat that worked absolutely in the absence of oxygen."

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Scientists reveal solar system's oldest molecular fluids could hold the key to early life

The oldest molecular fluids in the solar system could have supported the rapid formation and evolution of the building blocks of life, new research in the journal Proceedings of the National Academy of Sciences reveals.

An international group of scientists, led by researchers from the Royal Ontario Museum (ROM) and co-authors from McMaster University and York University, used state-of-the-art techniques to map individual atoms in minerals formed in fluids on an asteroid over 4.5 billion years ago.

Studying the ROM's iconic Tagish Lake meteorite, scientists used atom-probe tomography, a technique capable of imaging atoms in 3D, to target molecules along boundaries and pores between magnetite grains that likely formed on the asteroid's crust. There, they discovered water precipitates left in the grain boundaries on which they conducted their ground-breaking research.

"We know water was abundant in the early solar system," explains lead author Dr. Lee White, Hatch postdoctoral fellow at the ROM, "but there is very little direct evidence of the chemistry or acidity of these liquids, even though they would have been critical to the early formation and evolution of amino acids and, eventually, microbial life."

This new atomic-scale research provides the first evidence of the sodium-rich (and alkaline) fluids in which the magnetite framboids formed. These fluid conditions are preferential for the synthesis of amino acids, opening the door for microbial life to form as early as 4.5 billion years ago.

"Amino acids are essential building blocks of life on Earth, yet we still have a lot to learn about how they first formed in our solar system," says Beth Lymer, a PhD student at York University and co-author of the study. "The more variables that we can constrain, such as temperature and pH, allows us to better understand the synthesis and evolution of these very important molecules into what we now know as biotic life on Earth."

The Tagish Lake carbonaceous chondrite was retrieved from an ice sheet in B.C.'s Tagish Lake in 2000, and later acquired by the ROM, where it is now considered to be one of the museums iconic objects. This history means that the sample used by the team has never been above room temperature or exposed to liquid water, allowing the scientists to confidently link the measured fluids to the parent asteroid.

By using new techniques, such as atom probe tomography, the scientists hope to develop analytical methods for planetary materials returned to Earth by space craft, such as by NASA's OSIRIS-REx mission or a planned sample-return mission to Mars in the near future.

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Scientists have discovered the origins of the building blocks of life

Rutgers researchers have discovered the origins of the protein structures responsible for metabolism: simple molecules that powered early life on Earth and serve as chemical signals that NASA could use to search for life on other planets.

Their study, which predicts what the earliest proteins looked like 3.5 billion to 2.5 billion years ago, is published in the journal Proceedings of the National Academy of Sciences.

The scientists retraced, like a many thousand piece puzzle, the evolution of enzymes (proteins) from the present to the deep past. The solution to the puzzle required two missing pieces, and life on Earth could not exist without them. By constructing a network connected by their roles in metabolism, this team discovered the missing pieces.

"We know very little about how life started on our planet. This work allowed us to glimpse deep in time and propose the earliest metabolic proteins," said co-author Vikas Nanda, a professor of Biochemistry and Molecular Biology at Rutgers Robert Wood Johnson Medical School and a resident faculty member at the Center for Advanced Biotechnology and Medicine. "Our predictions will be tested in the laboratory to better understand the origins of life on Earth and to inform how life may originate elsewhere. We are building models of proteins in the lab and testing whether they can trigger reactions critical for early metabolism."

A Rutgers-led team of scientists called ENIGMA (Evolution of Nanomachines in Geospheres and Microbial Ancestors) is conducting the research with a NASA grant and via membership in the NASA Astrobiology Program. The ENIGMA project seeks to reveal the role of the simplest proteins that catalyzed the earliest stages of life.

"We think life was built from very small building blocks and emerged like a Lego set to make cells and more complex organisms like us," said senior author Paul G. Falkowski, ENIGMA principal investigator and a distinguished professor at Rutgers University-New Brunswick who leads the Environmental Biophysics and Molecular Ecology Laboratory. "We think we have found the building blocks of life -- the Lego set that led, ultimately, to the evolution of cells, animals and plants."

The Rutgers team focused on two protein "folds" that are likely the first structures in early metabolism. They are a ferredoxin fold that binds iron-sulfur compounds, and a "Rossmann" fold, which binds nucleotides (the building blocks of DNA and RNA). These are two pieces of the puzzle that must fit in the evolution of life.

Proteins are chains of amino acids and a chain's 3D path in space is called a fold. Ferredoxins are metals found in modern proteins and shuttle electrons around cells to promote metabolism. Electrons flow through solids, liquids and gases and power living systems, and the same electrical force must be present in any other planetary system with a chance to support life.

There is evidence the two folds may have shared a common ancestor and, if true, the ancestor may have been the first metabolic enzyme of life.

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Early life experiences biologically and functionally mature the brain

Experiences early in life have an impact on the brain's biological and functional development, shows a new study by a team of neuroscientists. Its findings, which centered on changes in mice and rats, reveal how learning and memory abilities may vary, depending on the nature of individual experiences in early life.

"The implications of this are many, including environmental influences on mental health, the role of education, the significance of poverty, and the impact of social settings," says Cristina Alberini, a professor in New York University's Center for Neural Science and the senior author of the paper, which appears in the journal Nature Communications.

"These results also offer promise for potential therapeutic interventions," add Alberini and Benjamin Bessieres, an NYU postdoctoral researcher and the paper's co-lead author. "By identifying critical time periods for brain development, they provide an indicator of when pharmaceutical, behavioral or other type of interventions may be most beneficial."

In general, very little is known about the mechanisms that underlie the development of learning and memory abilities. The Nature Communications study sought to shed new light on this process studying the biological elements linked to episodic memories -- those of specific events or experiences -- in infants by using rats and mice.

In their experiments, the scientists tested whether and how different types of experiences mature learning and memory abilities.

In one experience, infant mice and rats were placed in a small compartment -- a procedure paired with a mild foot shock (a commonly used method to test memory for a context). Their memory was tested by placing them back in these compartments; if they revealed a hesitation, it indicated that they had formed a memory of previously being in the compartment.

In a different type of experience, the infant mice and rats were exposed to novel objects in a given spatial configuration. Here, rodents that have a memory for this experience show more exploration toward a novel object location when presented with a combination of new and old locations, simply because they have a natural tendency to explore more new object locations. This reveals a memory of object location. Both types of experiences, context and object location, are stored by the same memory system.

The authors then asked two questions.

The first was: Does learning mature memory abilities?

The results showed that it does as both context and object location experiences matured the brain at both biological and functional levels. Overall, in fact, researchers found that the episodic experiences of the young mice and rats led to unique biological changes, specifically indicating maturation in the hippocampus -- a region critical for episodic memory formation. However, they did not find the same changes in older mice and rats.

Furthermore, they saw that with each type of learning, context or object location, the infant animal matured its performance and became capable of remembering long-term, more like an older animal does.

The team's second question was: Does the maturation produced by one type of experience develop the entire memory system and all its abilities? Or is the maturation selective for the type of experience that the animal had?

They found that the maturation produced by one type of experience (context) did not transfer to the other learning (object location) and vice versa, leading them to conclude that the maturation of learning and memory abilities is selective for the type of experiences encountered early in life.

"Because the biological maturation changes no longer occurred with episodic learning at later ages, it's clear that the infant brain employs distinct biological mechanisms to form and store episodic memories," write Alberini and Bessieres. "We found that this biological maturation is paralleled by and required for the functional maturation of memory -- that is, the ability to express memory long-term."

"Our results indicate that specific experiences during the infantile developmental period make a major contribution to individual differences in learning and memory abilities," they add. "Although all individuals are exposed to general learning of facts, people, things, time, and spaces, and therefore must develop a wide range of abilities and competences processed by the hippocampal memory system, our data suggest that the individual history shapes the maturation of selective abilities."

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Earth's oldest animals could take trips

New UC Riverside-led research settles a longstanding debate about whether the most ancient animal communities were deliberately mobile. It turns out they were, because they were hungry.

"This is the first time in the fossil record we see an animal moving to get food," said study lead Scott Evans, a UCR paleontology doctoral candidate.

Evans' team demonstrated that the 550-million-year-old ocean-dwelling creatures moved on their own rather than being pushed around by waves or weather. The research answers questions about when, why and how animals first developed mobility.

The team searched for evidence of movement in more than 1,300 fossils of Dickinsonia, dinner-plate-shaped creatures up to a meter long that lived and fed on a layer of ocean slime.

Details of the team's analysis were published this month in the journal Geobiology. It found that Dickinsonia move like worms, constricting and relaxing their muscles to go after their next meal of microorganisms.

Dickinsonia were first discovered in the 1940s and since then, scientists have debated whether the fossils showed evidence of self-directed movement. To test this, it was crucial that Evans be able to analyze how multiple creatures living in the same area behaved relative to one another.

Evans and study co-author Mary Droser, a UCR professor of paleontology, reasoned that if Dickinsonia were riding waves or caught in storms, then all the individuals in the same area would have been moved in the same direction. However, that isn't what the evidence shows.

"Multiple fossils within the same community showed random movement not at all consistent with water currents," Evans said.

Critically, Evans was able to use fossil communities in the Australian outback unearthed by Droser and paper co-author James Gehling of the South Australian Museum. The duo systematically excavated large bed surfaces containing as many as 200 Dickinsonia fossils, allowing Evans to test whether the groups of the animals moved in the same or different directions, Evans said.

The team also analyzed the directions traveled by individual Dickinsonia.

"Something being transported by current should flip over or be somewhat aimless," Evans said. "These movement patterns clearly show directionality based on the animals' biology, and that they preferred to move forward."

Future studies at UCR will try to determine what Dickinsonia bodies were made of. "The tissues of the animals are not preserved, so it's not possible to directly analyze their body composition," he said. "But we will look at other clues they left behind."

Understanding Dickinsonia's capabilities offers insight not only into the evolution of animal life on Earth, but also about the Earth itself and possibly about life on other planets.

"If we want to search for complex life on other planets, we need to know how and why complex life evolved here," Evans said. "Knowing the conditions that enabled large mobile organisms to move during the Ediacaran era, 550 million years ago, gives us a clue about the habitable zone elsewhere."

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Origin of life: A prebiotic route to DNA

How were the building-blocks of life first formed on the early Earth?

DNA, the hereditary material, may have appeared on Earth earlier than has been assumed hitherto. Ludwig-Maximilians-Universitaet (LMU) in Munich chemists led by Oliver Trapp show that a simple reaction pathway could have given rise to DNA subunits on the early Earth.

How were the building-blocks of life first formed on the early Earth? As yet, only partially satisfactory answers to this question are available. However, one thing is clear: The process of biological evolution that has given rise to the diversity of life on our planet must have been preceded by a phase of chemical evolution. During this 'prebiotic' stage, the first polymeric molecules capable of storing information and reproducing themselves were randomly assembled from organic precursors that were available on the early Earth. The most efficient replicators subsequently evolved into the macromolecular informational nucleic acids -- DNA and RNA -- that became the basis for all forms of life on our planet.

For billions of years, DNA has been the primary carrier of hereditary information in biological organisms. DNA strands are made up of four types of chemical subunits, and the genetic information it contains is encoded in the linear sequence of these 'nucleosides'. Moreover, the four subunits comprise two complementary pairs. Interactions between two strands with complementary sequences are responsible for the formation of the famous double helix, and play a crucial role in DNA replication. RNA also has vital functions in the replication of DNA and in the translation of nucleotide sequences into proteins.

Which of these two types of nucleic acid came first? The unanimous answer to that question up to now was RNA. Plausible models that explain how RNA molecules could have been synthesized from precursor compounds in prebiotic settings were first proposed decades ago, and have since received substantial experimental support. Moreover, its conformational versatility allows RNA both to store information and to act as a catalyst. These insights have led to the idea of an 'RNA world' that preceded the emergence of DNA, which is now well established among specialists. How then were the first DNA subunits synthesized? The generally accepted view is that this process was catalyzed by an enzyme -- a comparatively complex biomolecule whose emergence would have required millions of years of evolution.

But now a team of chemists led by LMU's Professor Oliver Trapp has proposed a much more direct mechanism for the synthesis of DNA subunits from organic compounds that would have been present in a prebiotic environment. "The reaction pathway is relatively simple," says Trapp, which suggests it could well have been realized in a prebiotic setting. For example, it does not require variations in reaction parameters, such as temperature. In Trapp's experiments, the necessary ingredients are water, a mildly alkaline pH and temperatures of between 40 and 70°C. Under such conditions, adequately high reaction rates and product yields are achieved, with high selectivity and correct stereochemistry.

Each of the nucleoside subunits found in DNA is made up of a nitrogen-containing base and a sugar called deoxyribose. Up to now, it was thought that deoxynucleosides could only be synthesized under prebiotic conditions by directly coupling these two -- preformed -- components together. But no plausible non-enzymatic mechanism for such a step had ever been proposed. The essential feature of the new pathway, as Trapp explains, is that the sugar is not linked to the base in a single step. Instead, it is built up on the preformed base by a short sequence of reaction steps involving simple organic molecules such as acetaldehyde and glyceraldehyde. In addition, the LMU researchers have identified a second family of possible precursors of DNA in which the deoxyribose moiety is replaced by a different sugar.

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Ammonium fertilized early life on Earth

Early Earth concept.

A team of international scientists -- including researchers at the University of St. Andrews, Syracuse University and Royal Holloway, University of London -- has demonstrated a new source of food for early life on the planet.

Life on Earth relies on the availability of critical elements such as nitrogen and phosphorus. These nutrient elements are ubiquitous to all life, as they are required for the formation of DNA, the blueprints of life, and proteins, the machinery. They are originally sourced from rocks and the atmosphere, so their availability to life has fluctuated alongside significant changes in the chemistry of Earth's surface environments over geologic time.

The research, published in Nature Geoscience, reveals how the supply of these elements directly impacted the growth of Earth's oxygen-rich atmosphere and were key to the evolution of early life on Earth.

The most dramatic change in Earth history followed the evolution of oxygenic photosynthesis, which fundamentally transformed the planet by providing a source of carbon to the biosphere and a source of oxygen to the atmosphere, the latter culminating in the Great Oxidation Event (GOE) some 2.3 billion years ago.

Despite the critical importance of nutrients to life, the availability of nitrogen and phosphorus in pre-GOE oceans is not well understood, particularly how the supply of these elements drove and/or responded to planetary oxygenation.

Using samples of exceptionally well-preserved rocks that have been associated with early evidence for oxygenic photosynthesis 2.7 billion year ago, the team of researchers examined Earth's early nitrogen cycle to decipher feedbacks associated with the initial stages of planetary oxygenation.

"There is precious little rock available from this time interval that is suitable for the type of analyses we performed. Most rocks that are this old have been deformed and heated during 2.7 billion years of plate tectonic activity, rendering the original signals of life lost," says Christopher Junium, associate professor of Earth sciences in the College of Arts and Sciences.

The rock samples showed the first direct evidence of the build-up of a large pool of ammonium in the pre-GOE oceans. This ammonium would have provided an ample source of nitrogen to fuel the early biosphere and associated oxygen production.

Research team leader Aubrey Zerkle, reader in the School of Earth and Environmental Sciences at the University of St Andrews, says: "Today we think of ammonium as the unpleasant odor in our cleaning supplies, but it would've served as an all-you-can-eat buffet for the first oxygen-generating organisms, a significant improvement on the dumpster scraps they relied on earlier in Earth's history."

As well as helping scientists better understand the role of the nitrogen cycle in global oxygenation, the new findings also provide context for other nutrient feedbacks during early planetary evolution.

"It is becoming ever more clear that the game of nutrient limitation has tipped back and forth through Earth's history as life has evolved and as conditions have changed," Junium says.

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Earliest life may have arisen in ponds, not oceans

Did life originate in shallow ponds?

Primitive ponds may have provided a suitable environment for brewing up Earth's first life forms, more so than oceans, a new MIT study finds.

Researchers report that shallow bodies of water, on the order of 10 centimeters deep, could have held high concentrations of what many scientists believe to be a key ingredient for jump-starting life on Earth: nitrogen.

In shallow ponds, nitrogen, in the form of nitrogenous oxides, would have had a good chance of accumulating enough to react with other compounds and give rise to the first living organisms. In much deeper oceans, nitrogen would have had a harder time establishing a significant, life-catalyzing presence, the researchers say.

"Our overall message is, if you think the origin of life required fixed nitrogen, as many people do, then it's tough to have the origin of life happen in the ocean," says lead author Sukrit Ranjan, a postdoc in MIT's Department of Earth, Atmospheric and Planetary Sciences (EAPS). "It's much easier to have that happen in a pond."

Ranjan and his colleagues have published their results today in the journal Geochemistry, Geophysics, Geosystems. The paper's co-authors are Andrew Babbin, the Doherty Assistant Professor in Ocean Utilization in EAPS, along with Zoe Todd and Dimitar Sasselov of Harvard University, and Paul Rimmer at Cambridge University.

Breaking a bond

If primitive life indeed sprang from a key reaction involving nitrogen, there are two ways in which scientists believe this could have happened. The first hypothesis involves the deep ocean, where nitrogen, in the form of nitrogenous oxides, could have reacted with carbon dioxide bubbling forth from hydrothermal vents, to form life's first molecular building blocks.

The second nitrogen-based hypothesis for the origin of life involves RNA -- ribonucleic acid, a molecule that today helps encode our genetic information. In its primitive form, RNA was likely a free-floating molecule. When in contact with nitrogenous oxides, some scientists believe, RNA could have been chemically induced to form the first molecular chains of life. This process of RNA formation could have occurred in either the oceans or in shallow lakes and ponds.

Nitrogenous oxides were likely deposited in bodies of water, including oceans and ponds, as remnants of the breakdown of nitrogen in Earth's atmosphere. Atmospheric nitrogen consists of two nitrogen molecules, linked via a strong triple bond, that can only be broken by an extremely energetic event -- namely, lightning.

"Lightning is like a really intense bomb going off," Ranjan says. "It produces enough energy that it breaks that triple bond in our atmospheric nitrogen gas, to produce nitrogenous oxides that can then rain down into water bodies."

Scientists believe that there could have been enough lightning crackling through the early atmosphere to produce an abundance of nitrogenous oxides to fuel the origin of life in the ocean. Ranjan says scientists have assumed that this supply of lightning-generated nitrogenous oxides was relatively stable once the compounds entered the oceans.

However, in this new study, he identifies two significant "sinks," or effects that could have destroyed a significant portion of nitrogenous oxides, particularly in the oceans. He and his colleagues looked through the scientific literature and found that nitrogenous oxides in water can be broken down via interactions with the sun's ultraviolet light, and also with dissolved iron sloughed off from primitive oceanic rocks.

Ranjan says both ultraviolet light and dissolved iron could have destroyed a significant portion of nitrogenous oxides in the ocean, sending the compounds back into the atmosphere as gaseous nitrogen.

"We showed that if you include these two new sinks that people hadn't thought about before, that suppresses the concentrations of nitrogenous oxides in the ocean by a factor of 1,000, relative to what people calculated before," Ranjan says.

"Building a cathedral"

In the ocean, ultraviolet light and dissolved iron would have made nitrogenous oxides far less available for synthesizing living organisms. In shallow ponds, however, life would have had a better chance to take hold. That's mainly because ponds have much less volume over which compounds can be diluted. As a result, nitrogenous oxides would have built up to much higher concentrations in ponds. Any "sinks," such as UV light and dissolved iron, would have had less of an effect on the compound's overall concentrations.

Ranjan says the more shallow the pond, the greater the chance nitrogenous oxides would have had to interact with other molecules, and particularly RNA, to catalyze the first living organisms.

"These ponds could have been from 10 to 100 centimeters deep, with a surface area of tens of square meters or larger," Ranjan says. "They would have been similar to Don Juan Pond in Antarctica today, which has a summer seasonal depth of about 10 centimeters."

That may not seem like a significant body of water, but he says that's precisely the point: In environments any deeper or larger, nitrogenous oxides would simply have been too diluted, precluding any participation in origin-of-life chemistry. Other groups have estimated that, around 3.9 billion years ago, just before the first signs of life appeared on Earth, there may have been about 500 square kilometers of shallow ponds and lakes worldwide.

"That's utterly tiny, compared to the amount of lake area we have today," Ranjan says. "However, relative to the amount of surface area prebiotic chemists postulate is required to get life started, it's quite adequate."

The debate over whether life originated in ponds versus oceans is not quite resolved, but Ranjan says the new study provides one convincing piece of evidence for the former.

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Secrets of early life revealed from less than half a teaspoon of blood

A global team of scientists have mapped the developmental pathway of a newborn's life for the first time. The research, published in Nature Communications, could transform our understanding of health and disease in babies.

Co-led by the MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, the new study included lifting the lid on what genes are turned on, what proteins are being made and what metabolites are changing in the first seven days of human life.

Newborn babies are the most vulnerable population when it comes to infectious disease. Establishing key pathways in early development could help measure the impact of factors such as diet, disease and maternal health, as well as key interventions like vaccines.

The study was conducted by the Expanded Program on Immunization Consortium (EPIC) research team, which includes MRC Unit The Gambia at the London School of Hygiene & Tropical Medicine, Boston Children's Hospital, the University of British Columbia, and the Papua New Guinea Institute of Medical Research.

The first week of a newborn's life is a time of rapid biological change as the baby adapts to living outside the womb, suddenly exposed to new bacteria and viruses, yet surprisingly little is known about these early changes. One of the biggest challenges in gathering data on newborn development has been sourcing a large enough blood sample for comprehensive profiling from a tiny newborn. The team overcame this with pioneering laboratory techniques applied on less than half a teaspoon of blood.

By using sophisticated software and new approaches they integrated different kinds of measurements to interpret the complex data derived from the precious samples. Thousands of changes over the first week of life were found including in gene expression and components involved in immunity.

Senior author Beate Kampmann, Professor of Paediatric Infection and Immunity from the London School of Hygiene & Tropical Medicine and Director of its Vaccine Centre, said: "Up to two thirds of newborn deaths can be prevented if effective health measures are provided at birth and during the first week of life. Of the 5.4 million under-five child deaths per year, about half occur during the neonatal period, i.e. the first month of life.

"Knowledge about key developmental processes during our earliest days remains sparse, but this study plugs some of those crucial gaps. This work is particularly important for vaccine research. Newborns have very limited protection from infection in early life and there is an urgent need to optimise protective measures, including vaccines, used in this age group."

Working closely with local communities, the research team recruited newborns in a health centre in The Gambia, West Africa. They took blood samples from the babies on the day of birth, and then again either on day one, three or seven.

The samples were processed in the collaborating laboratories in Africa and North America, where the researchers discovered dramatic molecular changes driven by development. The findings were then validated in a second group of Australasian newborns. The two independent cohorts were found to have common, highly dynamic developmental trajectories, suggesting that the changes do not occur at random, but instead follow an age-specific pathway.

Prof Kampmann said: "The MRC Unit in The Gambia has carried out important studies in newborns for a long time in order to optimize the use of vaccines. Given our excellent community relations and infrastructure, we were ready to partner with our collaborators to apply the new tools of systems biology to very small blood samples. We wanted to establish this work in a real world situation in order to gain insight into immune development in a setting where new interventions can have the biggest impact on newborn survival."

Ofer Levy, Director of the Precision Vaccines Program at Boston Children's Hospital and a senior author on the paper, said: "Most infections in the world occur early in life, and newborns have the greatest susceptibility and the worst outcomes. This work provides a valuable window into health and disease in the first week of life. Our exciting findings allows us to ask bigger questions about the differences between different populations and the impact of biomedical interventions such as vaccines on development.

"Currently, most vaccines are developed by trial and error. We seek deep molecular insight into vaccine function in early life so we can better develop infant vaccines for the future. We demonstrated that it's possible to recruit newborns in a resource-poor setting, obtain small amounts of their blood, process it, ship it, conduct systems biology assays and integrate the results -- turning big data into knowledge."

Going forward, the EPIC team is currently investigating the impact of different vaccines on this early developmental trajectory in a larger cohort in The Gambia and Papua New Guinea.

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Unusual microbes hold clues to early life

Scientists use the deep-diving robot Jason to collect water samples from oceanic crust at a subseafloor observatory off the coast of Washington. A recent study found that a group of unusual microbes living below the seafloor provides clues to the evolution of life on Earth, and potentially other planets.

A new study has revealed how a group of deep-sea microbes provides clues to the evolution of life on Earth, according to a recent paper in The ISME Journal. Researchers used cutting-edge molecular methods to study these microbes, which thrive in the hot, oxygen-free fluids that flow through Earth's crust.

Called Hydrothermarchaeota, this group of microbes lives in such an extreme environment that they have never been cultivated in a laboratory for study. A research team from Bigelow Laboratory for Ocean Sciences, the University of Hawai'i at Manoa, and the Department of Energy Joint Genome Institute bypassed the problem of cultivation with genetic sequencing methods called genomics, a suite of novel techniques used to sequence large groups of genetic information. They found that Hydrothermarchaeota may obtain energy by processing carbon monoxide and sulfate, which is an overlooked metabolic strategy. The microbes use energy from this process to grow as a form of chemosynthesis.

"The majority of life on Earth is microbial, and most microbes have never been cultivated," said Beth Orcutt, a senior research scientist at Bigelow Laboratory and one of the study's senior authors. "These findings emphasize why single cell genomics are such important tools for discovering how a huge proportion of life functions."

Analyzing Hydrothermarchaeota genomes revealed that these microbes belong to the group of single-celled life known as archaea and evolved early in the history of life on Earth -- as did their unusual metabolic processes. These observations suggest that the subsurface ocean crust is an important habitat for understanding how life evolved on Earth, and potentially other planets.

The researchers also found genetic evidence that Hydrothermarchaeota have the ability to move on their own. Motility offers a valuable survival strategy for the extreme environment they call home, which has a limited supply of nutrients essential to life.

"Studying these unique microbes can give us insights into both the history of Earth and the potential strategies of life on other planets," said Stephanie Carr, first author on the paper and a former postdoctoral researcher with Orcutt who is now an assistant professor at Hartwick College. "Their survival strategies make them incredibly versatile, and they play an important, overlooked role in the subsurface environments where they live."

In 2011, Orcutt and other project scientists sailed to the flank of the Juan de Fuca Ridge, a mid-ocean ridge off the coast of Washington where two ocean plates are separating and generating new oceanic crust. They used Woods Hole Oceanographic Institution's deep-diving robot Jason to travel 2.6 km to the seafloor and collect samples of the fluid that flows through the deep crust.

These crustal fluids contained microbes that had never before been studied. Working in partnership with the Department of Energy Joint Genome Institute, the researchers sorted and analyzed the microbes in the Single Cell Genomics Center at Bigelow Laboratory. This cutting-edge research facility is directed by Ramunas Stepanauskas, a senior research scientist and study author. The project team also analyzed the microbes using metagenomics, a technique that extracts genomic information directly from environmental samples. These analyses yielded insights into the genetic blueprints of Hydrothermarchaeota, their relationship to other archaea, and the strategies they have evolved to survive in the subseafloor.

The researchers will build upon this discovery when they return to the Juan de Fuca Ridge in May 2019 to continue investigating the extreme microbes thriving below the seafloor. Orcutt will lead a cruise using ROV Jason with this team of researchers to further explore the subseafloor environment, leveraging funding from the National Science Foundation and NASA.

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Membraneless protocells could provide clues to formation of early life

Membraneless protocells -- called complex coacervates -- can bring together molecules of RNA allowing the RNAs to perform certain reactions, an important step in the origin of life on Earth. The Image shows droplets of complex coacervates as seen under a microscope. The inset shows RNA molecules (cyan) are highly concentrated inside the droplets compared to the surrounding (dark). At roughly 2-5 micrometers in diameter, the droplets are about 14-35 times thinner than human hair.

Membraneless assemblies of positively- and negatively-charged molecules can bring together RNA molecules in dense liquid droplets, allowing the RNAs to participate in fundamental chemical reactions. These assemblies, called "complex coacervates," also enhance the ability of some RNA molecules themselves to act as enzymes -- molecules that drive chemical reactions. They do this by concentrating the RNA enzymes, their substrates, and other molecules required for the reaction. The results of testing and observation of these coacervates provide clues to reconstructing some of the early steps required for the origin of life on Earth in what is referred to as the prebiotic "RNA world." A paper describing the research, by scientists at Penn State, appears January 30, 2019 in the journal Nature Communications.

"We're interested in how you go from a world with no life to one with life," said Philip C. Bevilacqua, Distinguished Professor of Chemistry and of Biochemistry and Molecular Biology at Penn State and one of the senior authors of the paper. "One can imagine a lot of steps in this process, but we are not looking at the most elemental steps. We are interested in a slightly later step, to see how RNA molecules could form from their basic building blocks and if those RNA molecules could drive the reactions needed for life in the absence of proteins."

Life as we know it today generally requires genetic material -- DNA, which is first transcribed into RNA. These two molecules carry information for the production of proteins, which are in turn required for most functional aspects of life, including the production of new genetic material. This sets up a "chicken and the egg" dilemma for the origins of life on early Earth. DNA is required to produce proteins, but proteins are required to produce DNA.

"RNA -- or something similar -- has been thought of as a key to solving this dilemma," said Raghav R. Poudyal, Simons Origins of Life Postdoctoral Fellow at Penn State and first author of the paper. "RNA molecules carry genetic information, but they can also function as enzymes to catalyze the chemical reactions needed for early life. This fact has led to the notion that life on Earth went through a stage where RNA played an active role in facilitating chemical reactions -- "the RNA World" -- where self-replicating RNA molecules both carried the genetic information and performed functions that are now generally carried out by proteins."

Another common feature of life on Earth is that it is compartmentalized in cells, often with an outer membrane, or in smaller compartments inside cells. These compartments ensure that all the components for the chemical reactions of life are in easy reach, but in the prebiotic world the building blocks for RNA -- or the RNA enzymes needed to drive the chemical reactions that could lead to life -- would probably have been scarce, floating around in the primordial soup.

"You can think of these RNA enzymes like a car being produced in an assembly line," said Poudyal. "If you don't have the parts in the right place in the factory, the assembly line doesn't work. Without coacervates, the parts needed for chemical reactions are too dilute and are unlikely to find each other, but inside the coacervates, all the parts that the enzyme needs to work are nearby."

The researchers therefore looked at a variety of materials that may have existed in the pre-life Earth that can form coacervates -- membraneless protocells -- and then allowed critical functions like sequestering the building blocks of RNA and bringing together RNA enzymes and their targets.

"It was previously known that RNA molecules can assemble and elongate in solutions with high concentrations of magnesium," said Poudyal. "Our work shows that coacervates made from certain materials allow this non-enzymatic template-mediated RNA assembly to occur even in the absence of magnesium."

The coacervates are composed of positively charged molecules called polyamines and negatively charged polymers which cluster together to form membraneless compartments in a solution. Negatively charged RNA molecules are also attracted to the polyamines in the coacervates. Within the coacervates the RNA molecules are as much as 4000 times more concentrated than in the surrounding solution. By concentrating the RNA molecules in the coacervates, RNA enzymes are more likely to find their targets to drive chemical reactions.

"Although all the polyamines we tested were able to participate in formation of RNA-rich droplets, they differed in their ability to support RNA elongation," said Christine Keating, professor of chemistry at Penn State and a senior author on the paper. "These observations help us understand how the chemical environment within different membraneless compartments can impact RNA reactions."

"Although we can't look back to see the exact steps taken to form the first life on Earth, coacervates like the ones we can create in the laboratory may have helped by facilitating chemical reactions that otherwise would not have been possible," said Poudyal.

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