Nerve cells not entirely 'young at heart'

Most human nerve cells last a lifetime without renewal. A trait echoed within the cells' components, some enduring as long as the organism itself. New research by Martin Hetzer, molecular biologist and president of the Institute of Science and Technology Austria (ISTA), and colleagues discovered RNA, a typical transient molecule, in the nerve cells of mice that remain stable for their entire lives. Published in Science, these findings contribute to unraveling the complexities of brain aging and associated diseases.

After two decades in the United States, Martin Hetzer returned home to Austria in 2023 to become the 2nd President of the Institute of Science and Technology Austria (ISTA). A year into his new role, the molecular biologist remains engaged in the realm of aging research.

Hetzer is fascinated by the biological puzzles surrounding the aging processes in organs like the brain, heart, and pancreas. Most cells comprising these organs are not renewed throughout a human's entire life span. Nerve cells (neurons) in the human brain, for instance, can be as old as the organism, even up to more than a century, and must function for a lifetime. This remarkable age of neurons might be a major risk factor for neurodegenerative disorders such as Alzheimer's disease. Crucial to comprehending these kinds of ailments is a deeper understanding of how nerve cells function over time and maintain control. This potentially opens doors to therapeutically counteract the aging processes of these specific cells.

The latest collaborative publication by Hetzer, Tomohisa Toda from the Friedrich-Alexander University Erlangen-Nürnberg (FAU), who is also associated with the Max Planck Center for Physics and Medicine, Erlangen, and colleagues, gives new insights into this underexplored field of intricate mechanisms. For the first time in mammals, the study shows that RNA -- an essential group of molecules important for various biological processes inside the cell -- can persist throughout life. The scientists identified specific RNAs with genome-protecting functions in the nuclei of nerve cells of mice that remain stable for two years, covering their entire lives. The findings, published in the journal Science, underpin the importance of long-lived key molecules for maintaining a cell's function.

Longevity of key molecules

The inside of cells is a very dynamic place. Some components are constantly renewed and updated; others stay the same their whole lives. It is like a city in which the old buildings blend in with the new ones. DNA found in the nucleus -- the city's heart -- for instance, is as old as the organism. "DNA in our nerve cells is identical to DNA within the developing nerve cells in our mother's womb," explains Hetzer.

Unlike stable DNA, which is constantly being repaired, RNA, especially messenger RNA (mRNA), which forms proteins upon DNA's information, is characterized by its transient nature. The cellular scope, however, extends beyond mRNA to a group of so-called non-coding RNAs. They do not turn into proteins; instead, they have specific duties to contribute to the overall organization and function of the cell. Intriguingly, their lifespan remained a mystery. Until now.

RNAs that last the whole life

Hetzer and Co. set out to decipher that secret. Therefore, RNAs were labeled, i.e. "marked," in the brains of newborn mice. "For this labeling, we used RNA analogs -- structurally similar molecules -- with little chemical hooks that click fluorescent molecules on the actual RNAs," explains Hetzer. This assured efficient tracking of the molecules and powerful microscopic snapshots at any given time point in the mice's lives.

"Surprisingly, our initial images revealed the presence of long-lived RNAs, in various cell types within the brain. We had to further dissect the data to identify the ones in the nerve cells," Hetzer explains. "Fruitful collaboration with Toda's lab enabled us to make sense of that chaos during brain mapping." Collaboratively, the researchers were able to focus solely on long-lived RNAs in neurons. They quantified the molecules' concentration throughout a mouse's life, examined their composition and analyzed their positions.

While humans have an average life expectancy of around 70 years, the typical lifespan of a mouse is 2.5 years. After one year, the concentration of long-lived RNAs was slightly reduced compared to newborns. However, even after two years, they remained detectable indicating a lifelong persistence of these molecules.

RNAs help protect the genome

Additionally, the scientists proved long-lived RNAs' prominent role in cellular longevity. They found out that long-lived RNAs in neurons consist of mRNAs and non-coding RNAs and accumulate near the heterochromatin -- the densely packed region of the genome, typically homing inactive genes. Next they further investigated the function of these long-lived RNAs.

In molecular biology, the most effective approach to achieve this is by reducing the molecule of interest and observing its subsequent effects. "As their name and our previous experiments suggest, these long-lived RNAs are extremely stable," says Hetzer. The scientists, therefore, employed an in vitro (outside a living organism) approach, using neuronal progenitor cells -- stem cells with the capacity to give rise to neural cells, including neurons. The model system allowed them to effectively intervene with these long-lived RNAs. A lower amount of long-lived RNAs caused problems in the heterochromatin architecture and stability of genetic material, eventually affecting the cells' viability. Thus, the important role of long-lived RNAs' in cellular longevity was clarified.

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Evolution in action? New study finds possibility of nitrogen-fixing organelles

Nitrogen is a nutrient essential for all life on Earth. Although nitrogen gas (N2) is plentiful, it is largely unavailable to most organisms without a process known as nitrogen fixation, which converts dinitrogen to ammonium -- a major inorganic nitrogen source.

While there are bacteria that are able to reduce dinitrogen to ammonium, researchers at the University of Rhode Island, Institut de Ciències del Mar in Barcelona, University of California at Santa Cruz and the Massachusetts Institute of Technology have discovered nitrogen-fixing symbiotic organisms exhibiting behaviors similar to organelles.

In fact, researchers posit these symbiotic organisms -- UCYN-A, a species of cyanobacteria -- may be evolving organelle-like characteristics.

Their study was recently published in the journal Cell.

UCYN-A live in a symbiotic relationship with a closely related group of marine algae, B. bigelowii, in areas of the open ocean that are often low in nutrients.

Most nitrogen-fixing bacteria have mechanisms to regulate dinitrogen use when fixed sources of nitrogen are available, alleviating the high energetic cost of this process.

However, UCYN-A have lost the genes allowing this and are able to fix nitrogen gas into ammonium even in nutrient-rich environments.

The host, in-turn, provides it with carbon fixed photosynthetically by its chloroplasts.

The study details how researchers found a size relationship between UCYN-A and their symbiotic partner cells -- consistent with the size relationships between other organelles and their hosts.

As organelles get larger, so do their host cells - eventually dividing and replicating.

Mathematical modeling revealed the metabolic trade-offs which regulate the relative cell size through nutrient acquisition and exchange.

"It requires lots of energy as well as electrons to fix nitrogen gas, to make it into something useful," said Keisuke Inomura, assistant professor of oceanography at URI's Graduate School of Oceanography and one of the study's lead authors.

"If UCYN-A are moving along the evolutionary path toward developing into nitrogen-fixing organelles and we find cells aside from B. bigelowii also have such organelles, or are evolving similarly, it could be a game-changer."

While organelles such as mitochondria and chloroplasts are much further along on the evolutionary spectrum, researchers contend that what they are seeing may be a snapshot of the evolutionary process of bacterial-derived organelles that are nitrogen-fixing.

"Our study focuses on a much more recent symbiotic relationship that emerged about 100 million years ago, allowing us to explore the evolution of organelle formation in its early stages," explained Francisco Cornejo, co-lead author and postdoc researcher in the department of marine biology and oceanography at the Institut de Ciències del Mar.

Researchers note, however, that more study is needed to demonstrate whether this is the case.

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High resolution techniques reveal clues in 3.5 billion-year-old biomass

To learn about the first organisms on our planet, researchers have to analyse the rocks of the early Earth. These can only be found in a few places on the surface of the Earth. The Pilbara Craton in Western Australia is one of these rare sites: there are rocks there that are around 3.5 billion years old containing traces of the microorganisms that lived at that time. A research team led by the University of Göttingen has now found new clues about the formation and composition of this ancient biomass, providing insights into the earliest ecosystems on Earth. The results were published in the journal Precambrian Research.

Using high-resolution techniques such as nuclear magnetic resonance spectroscopy (NMR) and near-edge X-ray Absorption Fine Structure (NEXAFS), the researchers analysed carbonaceous particles found rocks made of barium sulphate.

This enabled scientists to obtain important information about the structure of microscopically small particles and show that they are of biological origin.

It is likely that the particles were deposited as sediment in the body of water of a "caldera" -- a large cauldron-shaped hollow that forms after volcanic activity.

In addition, some of the particles must have been transported and changed by hydrothermal waters just beneath the surface of the volcano.

This indicates a turbulent history of sediment deposits. By analysing various carbon isotopes, the researchers concluded that different types of microorganisms were already living in the vicinity of the volcanic activity, similar to those found today at Icelandic geysers or at hot springs in Yellowstone National Park.

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Complex green organisms emerged a billion years ago

Of all the organisms that photosynthesize, land plants have the most complex bodies. How did this morphology emerge? A team of scientists led by the University of Göttingen has taken a deep dive into the evolutionary history of morphological complexity in streptophytes, which include land plants and many green algae. Their research allowed them to go back in time to investigate lineages that emerged long before land plants existed. Their results revise the understanding of the relationships of a group of filamentous algal land colonizers much older than land plants. Using modern gene sequencing data, researchers pinpoint the emergence of multicellularity to almost a billion years ago. The results were published in the journal Current Biology.

The study focused on Klebsormidiophyceae, a class of green algae known for its ability to colonize diverse habitats worldwide.

The team of researchers conducted extensive sampling, investigating habitats ranging from streams, rivers, and lake shores to bogs, soil, natural rocks, tree bark, acidic post-mining sites, sand dunes, urban walls, and building façades.

"It's really fascinating that these tiny robust little organisms have such a high diversity in their morphology and also are extremely well adapted to live in sometimes very harsh environments," says Dr Tatyana Darienko, University of Göttingen's Institute for Microbiology and Genetics.

This comprehensive sampling aimed to create a global distribution map for Klebsormidiophyceae, emphasizing their adaptability, ecological significance, and hidden diversity.

Based on genetic data calibrated by fossils, the researchers performed "molecular clock analyses."

While delving into the complex evolutionary history of Klebsormidiophyceae, the researchers faced challenges in resolving phylogenetic relationships using traditional markers.

To overcome this, they employed hundreds of genes obtained from the transcriptomes of 24 isolates from different continents and habitats.

"Our approach, known as phylogenomics, was to reconstruct the evolutionary history taking into account whole genomes or large fractions of genomes," explains Dr Iker Irisarri, Leibniz Institute for the Analysis of Biodiversity Change.

"This extremely powerful method can reconstruct evolutionary relationships with very high precision."

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450-million-year-old organism finds new life in Softbotics

Researchers in the Department of Mechanical Engineering at Carnegie Mellon University, in collaboration with paleontologists from Spain and Poland, used fossil evidence to engineer a soft robotic replica of pleurocystitid, a marine organism that existed nearly 450 million years ago and is believed to be one of the first echinoderms capable of movement using a muscular stem.

Published today in The Proceedings of the National Academy of Science (PNAS), the research seeks to broaden modern perspective of animal design and movement by introducing a new a field of study -- Paleobionics -- aimed at using Softbotics, robotics with flexible electronics and soft materials, to understand the biomechanical factors that drove evolution using extinct organisms.

"Softbotics is another approach to inform science using soft materials to construct flexible robot limbs and appendages. Many fundamental principles of biology and nature can only fully be explained if we look back at the evolutionary timeline of how animals evolved. We are building robot analogues to study how locomotion has changed," said Carmel Majidi, lead author and Professor of Mechanical Engineering at Carnegie Mellon University.

With humans' time on earth representing only 0.007% of the planet's history, the modern-day animal kingdom that influences understanding of evolution and inspires today's mechanical systems is only a fraction of all creatures that have existed through history.

Using fossil evidence to guide their design and a combination of 3D printed elements and polymers to mimic the flexible columnar structure of the moving appendage, the team demonstrated that pleurocystitids were likely able to move over the sea bottom by means of a muscular stem that pushed the animal forward. Despite the absence of a current day analogue (echinoderms have since evolved to include modern day starfish and sea urchins), pleurocystitids have been of interest to paleontologists due to their pivotal role in echinoderm evolution.

The team determined that wide sweeping movements were likely the most effective motion and that increasing the length of the stem significantly increased the animals' speed without forcing it to exert more energy.

"Researchers in the bio-inspired robotics community need to pick and choose important features worth adopting from organisms," explained Richard Desatnik, PhD candidate and co-first author.

"Essentially, we have to decide on good locomotion strategies to get our robots moving. For example, would a starfish robot really need to use 5 limbs for locomotion or can we find a better strategy?" added Zach Patterson, CMU alumnus and co-first author.

Now that the team has demonstrated that they can use Softbotics to engineer extinct organisms, they hope to explore other animals, like the first organism that could travel from sea to land -- something that can't be studied in the same way using conventional robot hardware.

"Bringing a new life to something that existed nearly 500 million years ago is exciting in and of itself, but what really excites us about this breakthrough is how much we will be able to learn from it," said Phil LeDuc, co-author, and Professor of Mechanical Engineering at Carnegie Mellon University. "We aren't just looking at fossils in the ground, we are trying to better understand life through working with amazing paleontologists."

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The medicine of the future could be artificial life forms

Creating artificial life is a recurring theme in both science and popular literature, where it conjures images of creeping slime creatures with malevolent intentions or super-cute designer pets. At the same time, the question arises: What role should artificial life play in our environment here on Earth, where all life forms are created by nature and have their own place and purpose?

Associate professor Chenguang Lou from the Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, together with Professor Hanbin Mao from Kent State University, is the parent of a special artificial hybrid molecule that could lead to the creation of artificial life forms. They have now published a review in the journal Cell Reports Physical Science on the state of research in the field behind their creation. The field is called "hybrid peptide-DNA nanostructures," and it is an emerging field, less than ten years old.

Lou's vision is to create viral vaccines (modified and weakened versions of a virus) and artificial life forms that can be used for diagnosing and treating diseases.

"In nature, most organisms have natural enemies, but some do not. For example, some disease-causing viruses have no natural enemy. It would be a logical step to create an artificial life form that could become an enemy to them," he says.

Similarly, he envisions such artificial life forms can act as vaccines against viral infection and can be used as nanorobots or nanomachines loaded with medication or diagnostic elements and sent into a patient's body.

"An artificial viral vaccine may be about 10 years away. An artificial cell, on the other hand, is on the horizon because it consists of many elements that need to be controlled before we can start building with them. But with the knowledge we have, there is, in principle, no hindrance to produce artificial cellular organisms in the future," he says.

What are the building blocks that Lou and his colleagues in this field will use to create viral vaccines and artificial life? DNA and peptides are some of the most important biomolecules in nature, making DNA technology and peptide technology the two most powerful molecular tools in the nanotechnological toolkit today. DNA technology provides precise control over programming, from the atomic level to the macro level, but it can only provide limited chemical functions since it only has four bases: A, C, G, and T. Peptide technology, on the other hand, can provide sufficient chemical functions on a large scale, as there are 20 amino acids to work with. Nature uses both DNA and peptides to build various protein factories found in cells, allowing them to evolve into organisms.

Recently, Hanbin Mao and Chenguang Lou have succeeded in linking designed three-stranded DNA structures with three-stranded peptide structures, thus creating an artificial hybrid molecule that combines the strengths of both. This work was published in Nature Communications in 2022.

Elsewhere in the world, other researchers are also working on connecting DNA and peptides because this connection forms a strong foundation for the development of more advanced biological entities and life forms.

At Oxford University, researchers have succeeded in building a nanomachine made of DNA and peptides that can drill through a cell membrane, creating an artificial membrane channel through which small molecules can pass. (Spruijt et al., Nat. Nanotechnol. 2018, 13, 739-745)

At Arizona State University, Nicholas Stephanopoulos and colleagues have enabled DNA and peptides to self-assemble into 2D and 3D structures. (Buchberger et al., J. Am. Chem. Soc. 2020, 142, 1406-1416)

At Northwest University, researchers have shown that microfibers can form in conjunction with DNA and peptides self-assembling. DNA and peptides operate at the nano level, so when considering the size differences, microfibers are huge. (Freeman et al., Science, 2018, 362, 808-813)

At Ben-Gurion University of the Negev, scientists have used hybrid molecules to create an onion-like spherical structure containing cancer medication, which holds promise to be used in the body to target cancerous tumors. (Chotera et al., Chem. Eur. J., 2018, 24, 10128-10135)

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Even treated wastewater affects our rivers

Effluents from wastewater treatment plants have a dual effect: Some species disappear, while others benefit. Especially certain insect orders, such as stonefly and caddisfly larvae, are decimated. Certain worms and crustaceans, by contrast, can increase in number. A team from Goethe University Frankfurt led by Daniel Enns and Dr. Jonas Jourdan has corroborated this in a comprehensive study, which has now been published in the journal Water Research. They examined 170 wastewater treatment plants in Hesse in relation to species composition.

Wastewater treatment plants are an indispensable part of our modern infrastructure; they have made a significant contribution to improving the quality of our surface waters. However, their ability to completely remove what are known as micropollutants from wastewater is mostly limited. These substances include, for example, active ingredients from pharmaceuticals and personal care products, pesticides and other synthetic substances enter waterbodies via the treated wastewater, placing an additional burden on rivers and streams. This exacerbates the challenges faced by already vulnerable insect communities and aquatic fauna. Previous studies -- which have primarily focused on single wastewater treatment plants -- have already shown that invertebrate communities downstream of such effluents are generally dominated by pollution-tolerant taxa.

Until now, however, it was unclear how ubiquitous these changes are. That is why a team of biologists from Goethe University Frankfurt has now studied extensively how wastewater from 170 wastewater treatment plants in Hesse has an impact on the species composition of invertebrates. This has prompted a change in the common conception that human-induced stressors reduce the number of species in a habitat and thus their diversity: Rather, the findings indicate that a shift in species composition can be observed. The researchers were able to identify significant shifts in the composition of the species community between sites located upstream and downstream of wastewater treatment plants. Some species were particularly affected by effluents from wastewater treatment plants -- such as stonefly and caddisfly larvae, which disappear entirely in some places. Other taxa, such as certain worms and crustaceans, by contrast, benefit and are found in greater numbers. This change can be observed especially in streams and smaller rivers. Overall, wastewater treatment plants alter conditions downstream to the advantage of pollution-tolerant taxa and to the disadvantage of sensitive ones.

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Genome analysis of 46,000-year-old roundworm from Siberian permafrost reveals novel species

Some organisms, such as tardigrades, rotifers, and nematodes, can survive harsh conditions by entering a dormant state known as "cryptobiosis." In 2018, researchers from the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia found two roundworms (nematode) species in the Siberian Permafrost. Radiocarbon dating indicated that the nematode individuals have remained in cryptobiosis since the late Pleistocene, about 46,000 years ago. Researchers from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, the Center for Systems Biology Dresden (CSBD), and the Institute of Zoology at the University of Cologne, all located in Germany, used genome sequencing, assembly, and phylogenetic analysis and found that the permafrost nematode belongs to a previously undescribed species, Panagrolaimus kolymaensis. They showed that the biochemical mechanisms employed by Panagrolaimus kolymaensis to survive desiccation and freezing under laboratory conditions are similar to those of a life-cycle stage in the important biological model Caenorhabditis elegans.

When Anastasia Shatilovich at the Institute of Physicochemical and Biological Problems in Soil Science RAS in Russia revived two frozen individual nematodes from a fossilized burrow in silt deposits in the Siberian permafrost, she and her colleagues were beyond excited. After thawing the worms in the lab, a radiocarbon analysis of plant material from the burrow revealed that these frozen deposits, 40 meters below the surface, had not thawed since the late Pleistocene, between 45,839 and 47,769 years ago. At the same time, the research group of Teymuras Kurzchalia at the MPI-CBG (Teymuras Kurzchalia is now retired) was already addressing the question of how larval stages of the nematode Caenorhabditis elegans survive extreme conditions. When the team heard about the permafrost nematodes, they immediately reached out for a collaboration with Anastasia Shatilovich.

Vamshidhar Gade, a doctoral student at that time in the research group of Teymuras Kurzchalia, started to work with the permafrost nematodes. "What molecular and metabolic pathways these cryptobiotic organisms use and how long they would be able to suspend life are not fully understood," he says. Vamshidhar is now working at the ETH in Zurich, Switzerland.

The researchers in Dresden conducted a high-quality genome assembly of one of the permafrost nematodes in collaboration with Eugene Myers, Director Emeritus and research group leader at the MPI-CBG, the DRESDEN-concept Genome Center, and the research group of Michael Hiller, research group leader at that time at the MPI-CBG and now Professor of Comparative Genomics at the LOEWE-TBG and the Senckenberg Society for Nature Research. Despite having DNA barcoding sequences and microscopic pictures, it was difficult to determine whether the permafrost worm was a new species or not. Philipp Schiffer, research group leader at the Institute of Zoology, co-lead of the incipient Biodiversity Genomics Center Cologne (BioC2) at the University of Cologne, and expert in biodiversity genomics research, joined forces with the Dresden researchers to determine the species and analyze its genome with his team. Using phylogenomic analysis, he and his team were able to define the roundworm as a novel species, and the team decided to call it "Panagrolaimus kolymaensis." In recognition of the Kolyma River region from which it originated, the nematode was given the Latin name Kolymaensis.

By comparing the genome of Panagrolaimus kolymaensis with that of the model nematode Caenorhabditis elegans, the researchers in Cologne identified genes that both species have in common and that are involved in cryptobiosis. To their surprise, most of the genes necessary for entering cryptobiosis in Caenorhabditis elegans so-called Dauer larvae were also present in Panagrolaimus kolymaensis. The research team next evaluated Panagrolaimus kolymaensis's ability to survive and discovered that mild dehydration exposure before freezing helped the worms prepare for cryptobiosis and increased survival at -80 degrees Celsius. At a biochemical level, both species produced a sugar called trehalose when mildly dehydrated in the lab, possibly enabling them to endure freezing and intense dehydration. Caenorhabditis elegans larvae also benefited from this treatment, surviving for 480 days at -80 degrees Celsius without suffering any declines in viability or reproduction following thawing.

According to Vamshidhar Gade and Temo Kurzhchalia, "Our experimental findings also show that Caenorhabditis elegans can remain viable for longer periods in a suspended state than previously documented. Overall, our research demonstrates that nematodes have developed mechanisms that allow them to preserve life for geological time periods."

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Artificial cells demonstrate that 'life finds a way'

"Listen, if there's one thing the history of evolution has taught us is that life will not be contained. Life breaks free. It expands to new territories, and it crashes through barriers painfully, maybe even dangerously, but . . . life finds a way," said Ian Malcolm, Jeff Goldblum's character in Jurassic Park, the 1993 science fiction film about a park with living dinosaurs.

You won't find any Velociraptors lurking around evolutionary biologist Jay T. Lennon's lab; however, Lennon, a professor in the College of Arts and Sciences Department of Biology at Indiana University Bloomington, and his colleagues have found that life does indeed find a way. Lennon's research team has been studying a synthetically constructed minimal cell that has been stripped of all but its essential genes. The team found that the streamlined cell can evolve just as fast as a normal cell -- demonstrating the capacity for organisms to adapt, even with an unnatural genome that would seemingly provide little flexibility.

"It appears there's something about life that's really robust," says Lennon. "We can simplify it down to just the bare essentials, but that doesn't stop evolution from going to work."

For their study, Lennon's team used the synthetic organism, Mycoplasma mycoides JCVI-syn3B -- a minimized version of the bacterium M. mycoides commonly found in the guts of goats and similar animals. Over millennia, the parasitic bacterium has naturally lost many of its genes as it evolved to depend on its host for nutrition. Researchers at the J. Craig Venter Institute in California took this one step further. In 2016, they eliminated 45 percent of the 901 genes from the natural M. mycoides genome -- reducing it to the smallest set of genes required for autonomous cellular life. At 493 genes, the minimal genome of M. mycoides JCVI-syn3B is the smallest of any known free-living organism. In comparison, many animal and plant genomes contain more than 20,000 genes.

In principle, the simplest organism would have no functional redundancies and possess only the minimum number of genes essential for life. Any mutation in such an organism could lethally disrupt one or more cellular functions, placing constraints on evolution. Organisms with streamlined genomes have fewer targets upon which positive selection can act, thus limiting opportunities for adaptation.

Although M. mycoides JCVI-syn3B could grow and divide in laboratory conditions, Lennon and colleagues wanted to know how a minimal cell would respond to the forces of evolution over time, particularly given the limited raw materials upon which natural selection could operate as well as the uncharacterized input of new mutations.

"Every single gene in its genome is essential," says Lennon in reference to M. mycoides JCVI-syn3B. "One could hypothesize that there is no wiggle room for mutations, which could constrain its potential to evolve."

The researchers established that M. mycoides JCVI-syn3B, in fact, has an exceptionally high mutation rate. They then grew it in the lab where it was allowed to evolve freely for 300 days, equivalent to 2000 bacterial generations or about 40,000 years of human evolution.

The next step was to set up experiments to determine how the minimal cells that had evolved for 300 days performed in comparison to the original, non-minimal M. mycoides as well as to a strain of minimal cells that hadn't evolved for 300 days. In the comparison tests, the researchers put equal amounts of the strains being assessed together in a test tube. The strain better suited to its environment became the more common strain.

They found that the non-minimal version of the bacterium easily outcompeted the unevolved minimal version. The minimal bacterium that had evolved for 300 days, however, did much better, effectively recovering all of the fitness that it had lost due to genome streamlining. The researchers identified the genes that changed the most during evolution. Some of these genes were involved in constructing the surface of the cell, while the functions of several others remain unknown.

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Remains of an extinct world of organisms discovered

Newly discovered biomarker signatures point to a whole range of previously unknown organisms that dominated complex life on Earth about a billion years ago. They differed from complex eukaryotic life as we know it, such as animals, plants and algae in their cell structure and likely metabolism, which was adapted to a world that had far less oxygen in the atmosphere than today. An international team of researchers, including GFZ geochemist Christian Hallmann, now reports on this breakthrough for the field of evolutionary geobiology in the journal Nature.

The previously unknown "protosteroids" were shown to be surprisingly abundant throughout Earth´s Middle Ages. The primordial molecules were produced at an earlier stage of eukaryotic complexity -- extending the current record of fossil steroids beyond 800 and up to 1,600 million years ago. Eukaryotes is the term for a kingdom of life including all animals, plants and algae and set apart from bacteria by having a complex cell structure that includes a nucleus, as well as a more complex molecular machinery. "The highlight of this finding is not just the extension of the current molecular record of eukaryotes," Hallmann says: "Given that the last common ancestor of all modern eukaryotes, including us humans, was likely capable of producing 'regular' modern sterols, chances are high that the eukaryotes responsible for these rare signatures belonged to the stem of the phylogenetic tree."

Unprecedented glimpse of a lost world

This "stem" represents the common ancestral lineage that was a precursor to all still living branches of eukaryotes. Its representatives are long extinct, yet details of their nature may shed more light on the conditions surrounding the evolution of complex life. Although more research is needed to evaluate what percentage of protosteroids may have had a rare bacterial source, the discovery of these new molecules not only reconciles the geological record of traditional fossils with that of fossil lipid molecules, but yields a rare and unprecedented glimpse of a lost world of ancient life. The competitive demise of stem group eukaryotes, marked by the first appearance of modern fossil steroids some 800 Million years ago, may reflect one of the most incisive events in the evolution of increasingly complex life.

"Almost all eukaryotes biosynthesise steroids, such as cholesterol that is produced by humans and most other animals" adds Benjamin Nettersheim from the University of Bremen, first author of the study -- "due to potentially adverse health effects of elevated cholesterol levels in humans, cholesterol doesn't have the best reputation from a medical perspective. However, these lipid molecules are integral parts of eukaryotic cell membranes where they aid in a variety of physiological functions. By searching for fossilised steroids in ancient rocks, we can trace the evolution of increasingly complex life."

What the Nobel laureate thaught impossible...

Nobel laureate Konrad Bloch had already speculated about such a biomarker in an essay almost 30 years ago. Bloch suggested that short-lived intermediates in the modern biosynthesis of steroids may not always have been intermediates. He believed that lipid biosynthesis evolved in parallel with changing environmental conditions throughout Earth history. In contrast to Bloch, who did not believe that these ancient intermediates could ever be found, Nettersheim started searching for protosteroids in ancient rocks that were deposited at a time when those intermediates could actually have been the final product.

But how to find such molecules in ancient rocks? "We employed a combination of techniques to first convert various modern steroids to their fossilised equivalent; otherwise we wouldn't have even known what to look for," says Jochen Brocks, professor at the Australian National University who shares the first-authorship of the new study with Nettersheim. Scientists had overlooked these molecules for decades because they do not conform to typical molecular search images. "Once we knew our target, we discovered that dozens of other rocks, taken from billion-year-old waterways across the world, were oozing with similar fossil molecules."

The oldest samples with the biomarker are from the Barney Creek Formation in Australia and are 1.64 billion years old. The rock record of the next 800 Million years only yields fossil molecules of primordial eukaryotes before molecular signatures of modern eukaryotes first appear in the Tonian period. According to Nettersheim "the Tonian Transformation emerges as one of the most profound ecological turning points in our planet's history." Hallmann adds that "both primordial stem groups and modern eukaryotic representatives such as red algae may have lived side by side for many hundreds of millions of years." During this time, however, the Earth's atmosphere became increasingly enriched with oxygen -- a metabolic product of cyanobacteria and of the first eukaryotic algae that would have been toxic to many other organisms. Later, global "Snowball Earth" glaciations occurred and the protosterol communities largely died out. The last common ancestor of all living eukaryotes may have lived 1.2 to 1.8 billion years ago. Its descendants were likely better able to survive heat and cold as well as UV radiation and displaced their primordial relatives.

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Earth's first animals had particular taste in real estate

Even without body parts that allowed for movement, new research shows -- for the first time -- that some of Earth's earliest animals managed to be picky about where they lived.

These creatures from the Ediacaran Period, roughly 550 million years ago, are strangely shaped soft-bodied animals that lived in the sea. Researchers have long considered them enigmatic.

"It's not like studying dinosaurs, which are related to birds that we can observe today," said Phillip C. Boan, UC Riverside paleontology graduate student and lead author of the new study. "With these animals, because they have no modern descendants, we're still working out basic questions about how they lived, such as how they reproduced and what they ate."

For this particular research project, the researchers focused on understanding where in the sea the animals spent their lives.

The ancient sea was also a largely foreign place compared to today's marine environments. It was dominated by a mat on the sea floor composed of bacteria and layers of other organic materials. In addition, predatory creatures were uncommon.

Given the alien nature of Ediacaran Earth, the researchers were surprised to find an animal that lived much the way barnacles do today. A new Paleobiology paper details how Obamus coronatus, named for the former U.S. president, opted to live on specific parts of the sea floor in the company of other Obamus.

The animal averaged about a half-inch in diameter and was "shaped like a French cruller donut with ribbons on top," Boan said. It did not move of its own accord, and likely spent its entire life embedded in its preferred spot on the sea floor.

"We think about the very oldest animals and maybe you wouldn't expect them to be so picky. But Obamus only occurs where there is a thick mat, and it's a pretty sophisticated way of making a living for something so very old," said Mary Droser, UCR distinguished professor of paleontology and study co-author.

In 2018, Droser's laboratory named the Obamus in honor of Barack Obama's passion for science. Her group discovered it at an extraordinarily well-preserved fossil site in the Australian Outback, at what is now called Nilpena Ediacara National Park.

A series of storms buried the Ediacaran sea floor at Nilpena in layers of sediment, helping preserve sandstone impressions of entire animal communities that lived together there. "This way, we're able to piece together whole ecosystems," Droser said. "Looking at them is like snorkeling around on the ancient sea floor, instead of looking at a single animal in a fish tank."

For this project, the research team selected three animals found in relatively large numbers at Nilpena, and examined how they were geographically distributed.

The other two animals, Tribrachidium and Rugoconites, are also immobile creatures with no modern descendants. "They are tri-radially symmetrical, like the Mercedes Benz logo," Boan said. "And they would have lived their entire lives embedded in the sea floor, as Obamus did."

Distribution for these other two animals was varied. Sometimes they could be found living in the company of other organisms like themselves, but not in every instance. However, Obamus displayed a clear preference.

"This is really the first example of a habitat-selective Ediacaran creature, the first example of a macroscopic animal doing this," Boan said. "But how did they get where they wanted to go? This is a question we don't yet know the answer to."

The research team theorizes that Obamus were likely motivated by the need to reproduce.

"There are a limited number of reproductive strategies, especially for animals like these," Droser said. "There are more strategies today, and they're more elaborate now. But the same ones used today were still being used 550 million years ago."

Obamus likely spread itself via selective larva that preferred locations with thick microbial mat and near other Obamus. "We don't entirely understand how Obamus offspring spread out, but we know that when they picked a place to live, it was very specific," Boan said.

A deeper understanding of how life on Earth developed over time can give researchers insight into how life could develop on another planet. For this reason, Droser's lab is funded by NASA's Exobiology program.

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Learning about what happens to ecology, evolution, and biodiversity in times of mass extinction

In times of environmental upheaval, how do communities of organisms respond? When entire species are wiped out, do surviving species move in and take over, or do new species immigrate to fill the gaps?

These are questions that Sarah Brisson, Ph.D. student in UConn's Department of Earth Sciences, set out to study. This research is published in the Proceedings of the Royal Society B.

Brisson studies a mass extinction event that happened in the Late Devonian period, around 370 million years ago, with the goal of understanding how ecosystems and the communities of organisms within them respond. For this study, Brisson focused on small, shelled, ocean-dwelling creatures called brachiopods by studying fossils collected from the Appalachian Basin in New York and Pennsylvania.

"The name 'mass extinction events' captures people's attention. These are times of major changes in the environment, and how those changes impact the organisms is relevant to understanding our current environment and environmental changes," says Brisson.

In the Late Devonian, the Appalachian Basin was a shallow sea that formed in the wake of the growing mountains. Brisson says the seafloor was likely covered with brachiopods, which were abundant in the sample set. In the water, fish were also becoming more abundant, and on land, a great greening was happening, with new plants evolving for the first time in Earth's history.

"The Devonian world was very different; there were no flowering plants for millions of years. We're just setting the stage to move into the Mesozoic -- the dinosaur era -- where we have big ferns and large, woody trees," Brisson says.

In studying these ecosystem dynamics, Brisson looks at Earth as a system, with niche changes just one aspect of the entire structure.

"A niche space is an environment where an organism lives, in this case, the level of substrate disturbance and where along the depth profile the organisms most comfortable with," says Brisson.

Two concepts to consider are niche conservatism and niche evolution. Brisson explains that with niche conservatism, organisms remain in place and retain their characteristics, whereas with niche evolution organisms change and evolve in some way into preferring the new environmental parameters through time.

"In biology, there's a lot of talk about niche dynamics, and whether we see niche evolution or niche conservatism and there are not as many researchers studying this in deep time," says Brisson.

After painstakingly identifying around 20,000 brachiopod fossils and analyzing their preferences across the depth gradient, Brisson assembled a dataset and used non-metric multi-dimensional scaling (nMDS) to see where different species were grouped across the stratigraphic range over time to interpret how the organisms responded before and after the mass extinction event. Brisson says the results were a bit of a surprise.

"I saw a lot of turnover where some species went extinct, but some species survived and remained in place, and their niches are conserved. Some scientists argue this isn't the case in a large-scale extinction event and I didn't expect that niche conservatism would be shown here."

In extinction events like this one, where an estimated 35% of marine species went extinct, Brisson explains it is expected that the opening of so many niches would encourage nearby surviving species to move in to occupy the newly free space, and the results did show this happening to some extent.

"As a rule, however, we're seeing niche conservatism in this region. In cases where you might see niche evolution in the rock record, there may have been different pressures on the organisms. I think leaving that question open is important because there are many different selective pressures and not all selective pressures can be applied to every situation."

The factors that drove the extinction pulses in the Late Devonian are still debated, says Brisson. Some work, including co-author and UConn graduate Jaleigh Pier's '18 (CLAS) research, indicated a global cooling event took place. Other evidence shows widespread anoxia which could have resulted from an influx of nutrients, much like we see today with dead zones forming in offshore marine and aquatic environments.

"Part of the reason why I love the Devonian is that there are mass extinction events that have been studied so thoroughly, especially the Mesozoic mass extinction event, but there's less certainty surrounding the Late Devonian. As you're moving back through time, it's harder to be certain because some of the proxies used in the Mesozoic don't apply to the Devonian. It's a neat and dynamic time to study."

This work represents just one chapter of Brisson's dissertation, and future analyses will look at the data further, including stable isotope analysis to understand how nitrogen may have impacted this region. Peering this far into the past may shed light on the accelerating species extinctions of today.

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Ancestral variation guides future environmental adaptations

The speed of environmental change is very challenging for wild organisms. When exposed to a new environment individual plants and animals can potentially adjust their biology to better cope with new pressures they are exposed to -- this is known as phenotypic plasticity.

Plasticity is likely to be important in the early stages of colonising new places or when exposed to toxic substances in the environment. New research published in Nature Ecology & Evolution, shows that early plasticity can influence the ability to subsequently evolve genetic adaptations to conquer new habitats.

Sea campion, a coastal wildflower from the UK and Ireland has adapted to toxic, zinc rich industrial-era mining waste which kills most other plant species. The zinc-tolerant plants have evolved from zinc-sensitive, coastal populations separately in different places, several times.

To understand the role of plasticity in rapid adaptation, a team of researchers lead by Bangor University conducted experiments on sea campion.

As zinc-tolerance has evolved several times, this gave the researchers the opportunity to investigate whether ancestral plasticity made it more likely that the same genes would be used by different populations that were exposed to the same environment.

By exposing the tolerant and sensitive plants to both benign and zinc contaminated environments and measuring changes in the expression of genes in the plant's roots, the researchers were able to see how plasticity in the coastal ancestors has paved the way for adaptation to take place very quickly.

Dr Alex Papadopulos, senior lecturer at Bangor University explained:

"Sea campion usually grow on cliffs and shingle beaches, but mining opened up a new niche for them that other plants weren't able to exploit. Our research has shown that some of the beneficial plasticity in the coastal plants has helped the mine plants to adapt so quickly."

Alex added,

"Remarkably, if a gene responds to the new environment in a beneficial way in the ancestral plants, it is much more likely that that gene will be reused in all of the lineages that are independently adapting to the new environment. Phenotypic plasticity may make it more likely that there would be the same evolutionary outcome if the tape of life were replayed. If we understand the plastic responses that species have to environmental change, we may be better equipped to predict the impacts of climate change on biodiversity."

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World's simplest animals get their place in the tree of life

The group with the world's simplest animals -- tiny blob-like life forms with no organs and just a few cell types -- finally has a fleshed-out family tree built by a research group led by the American Museum of Natural History, St. Francis College, and the University of Veterinary Medicine Hannover. The study comes more than 100 years after the discovery of these ameboid animals called placozoans and represents the first -- and potentially only -- time in the 21st century that a backbone Linnaean taxonomy is constructed for an entire animal phylum. Published today in the journal Frontiers in Ecology and Evolution, the research is based on genetic makeup -- the presence and absence of genes -- rather than outward physical appearance, which is traditionally used to classify organisms.

"Placozoans look like miniscule, shape-shifting disks -- basically, they are the pancake of the animal world," said the study's co-lead author Michael Tessler, a research associate at the Museum and an assistant professor at St. Francis College. "For a taxonomist looking through a microscope, even a powerful one, there are almost no characters to compare and differentiate them. Yet, despite most of them looking almost exactly the same, we know that on the genetic level, there are very distinct lineages."

The first placozoan species was described in 1883, and Placozoa remained a "phylum of one" until DNA-based research in the last 20 years revealed that it contains multiple lineages. Most placozoans, which generally live in tropical and subtropical waters across the globe, are about the size of a grain of sand, with hair-like structures that allow them to move. "After decades of turmoil, this most exciting phylum has finally gotten the attention it deserves," said senior author Bernd Schierwater, a professor at the University of Veterinary Medicine Hannover.

"We wanted to know the relationships within this ancient group of animals and where it sits in the tree of life," said co-lead author Johannes Neumann, a recent doctoral graduate from the Museum's Richard Gilder Graduate School. "People have been speculating about that for decades, but now, by looking at differences among placozoans on the molecular level, we're able to paint a clear picture of how these animals are related to one another."

The researchers used a method called molecular morphology -- using differences in DNA sequences and other molecular characters -- to make classifications. In doing so, they established a backbone taxonomy: two new classes, four orders, three families, one genus, and one species. Their research also suggests that placozoans are most closely related to cnidarians (a group of aquatic animals including jellyfish, corals, and sea anemones) and bilaterians (animals that have a left and right side, like insects and humans).

"I personally collected placozoans on six continents for almost 10 years, did lab work and bioinformatic work on them, but it took decades of effort from a great number of colleagues to finally get to this exciting first classification for this cryptic phylum," Neumann said. "This is why we call our newly described species Cladtertia collaboinventa, which means 'discovered in collaboration.'"

The authors suggest that this study could serve as a template to revisit systematics of other organisms that look very similar, such as bacteria, fungi, protists, and parasites. Tessler also is the lead author of a second paper out now in Frontiers in Ecology and Evolution that makes the case for molecular morphology in other groups of organisms that have few distinguishable visual features but are genetically diverse.

"Taxonomic blank slates are problematic. Without names, communication is hampered, and other scientific progress is slowed," said Tessler. "We suggest that the morphology of molecules, such as proteins -- which have distinctive structures -- should not be considered as anything less than traditional morphology."

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Animals are key to restoring the world's forests

As UN climate talks close in Egypt and biodiversity talks begin in Montreal, attention is on forest restoration as a solution to the twin evils roiling our planet. Forests soak up atmospheric carbon dioxide and simultaneously create habitat for organisms. So far, efforts to help forests bounce back from deforestation have typically focused on increasing one thing -- trees -- over anything else. But a new report uncovers a powerful, yet largely overlooked, driver of forest recovery: animals. The study by an international team from the Max Planck Institute of Animal Behavior, Yale School of the Environment, the New York Botanical Garden, and the Smithsonian Tropical Research Institute examined a series of regenerating forests in central Panama spanning 20 to 100 years post-abandonment. The unique long-term data set revealed that animals, by carrying a wide variety of seeds into deforested areas, are key to the recovery of tree species richness and abundance to old-growth levels after only 40-70 years of regrowth. The article, published in Philosophical Transactions of the Royal Society B, is part of a theme issue focused on forest landscape restoration as part of the UN Decade on Ecosystem Restoration.

"Animals are our greatest allies in reforestation," says Daisy Dent, a tropical ecologist from MPI-AB and the study's senior author. "Our study prompts a rethink of reforestation efforts to be about more than just establishing plant communities."

The report also notes that situating regenerating forests near patches of old growth, and reducing hunting, encourages animals to colonize and establish. "We show that considering the wider ecosystem, as well as features of the landscape, improves restoration efforts," says Sergio Estrada-Villegas, a biologist now at Universidad del Rosario (Bogotá, Colombia) and the study's first author.

Seed dispersal by animals is key to forest expansion. In the tropics, over 80% of tree species can be dispersed by animals, which transport seeds throughout the landscape. Despite this, forest restoration efforts continue to focus on increasing tree cover rather than reestablishing the animal-plant interactions that underpin ecosystem function. "Figuring out how animals contribute to reforestation is prohibitively hard because you need detailed information about which animals eat which plants," says Estrada-Villegas.

The forest at the Barro Colorado Nature Monument (BCNM), in the Panama Canal, offers a unique solution to this problem. In one of the best studied tropical forests in the world, generations of scientists at have documented frugivore interactions to understand which groups of animals disperse which tree species.

In the present study, the team led by Estrada-Villegas and Dent examined this unique long-term dataset to determine the proportion of plants dispersed by four groups of animals -- flightless mammals, large birds, small birds, and bats -- and how this proportion changed over a century of natural restoration.

Their results offer the most detailed data of animal seed dispersal recovery across the longest timeframe of natural restoration. "Most studies examine the first 30 years of succession, but our data spanning 100 years gives us a rare glimpse into what happens in the late phase of restoration," says Dent.

The study found that young regenerating forests were made up mostly of trees dispersed by small birds. But as the forest aged, trees dispersed by larger birds increased. Surprisingly, however, the majority of plants were dispersed by terrestrial mammals across all forest ages -- from 20 years old to old growth. "This result is quite unusual for post-agricultural regenerating forests," says Dent. "It is likely that the presence of large tracts of preserved forests near our secondary stands, coupled with low hunting, has allowed the mammal populations to thrive and to bring an influx of seeds from neighboring patches."

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Road signs for immune defense cells

Organisms are constantly invaded by pathogens such as viruses. Our immune system swings into action to combat these pathogens immediately. The innate non-specific immune response is triggered first, and the adaptive or acquired immune response follows. In this second defence reaction, specialised cytotoxic T lymphocytes known as killer T cells destroy cells in the body that have been infected and thus prevent damage from spreading. Humans possess a repertoire of some 20 million T cell clones with varying specificity to counter the multitude of infectious agents that exist. But how do the killer T cells know where danger is coming from? How do they recognise that something is wrong inside a cell in which viruses are lurking? They can't just have a quick peek inside.

At this point, antigen processing comes into play. The process can be compared to making a road sign. The molecular barcode is "processed" or assembled in the cell -- in the endoplasmic reticulum, to be exact. Special molecules are used in its making, the MHC class I molecules. They are loaded with information about the virus invader in a molecular machine, the peptide loading complex (PLC). This information consists of peptides, fragments of the protein foreign to the body. These fragments also contain epitopes, the molecular segments that elicit a specific immune response. During the loading process, an MHC I-peptide epitope complex thus forms, and this is the road sign that is then transported to the surface of the cell and presented in a readily accessible form to the killer T cells -- we could almost say that it is handed to them on a silver platter. The chaperones, special accessory proteins that assist the correct folding of proteins with complex structures in cells, also play a significant role.

The chaperones that support antigen processing are calreticulin, ERp57, and tapasin. But how do they work together? And how important are they for antigen processing? An answer has now been supplied by a study carried out by Goethe University Frankfurt and the University of Oxford and published in Nature Communications. "With this study, we have achieved a breakthrough in our understanding of cellular quality control," says Professor Robert Tampé, Director of the Institute of Biochemistry at Goethe University Frankfurt. He explains the logic underlying this quality control process as follows: "The MHC I-peptide epitope complex, the road sign, needs to be exceptionally stable, and for quite a long time, because the adaptive immune response does not start instantly. It needs 3 to 5 days to get going." So, the sign must not collapse after one day; that would be disastrous, as the immune defence cells would then fail to detect cells infected by a virus. This would mean that they would not destroy these cells and the virus would be able to continue its spread unhindered. A similar problem would arise if a cell in the body had mutated into a tumour cell: the threat would remain undetected. It is imperative, therefore, that a quality control system is in place.

As the study shows, the chaperones are central process components: they give the road sign the long-term stability it must have by making a strict selection. By rejecting the short-lived virus fragments in the mass of available material, they ensure that only MHC I molecules loaded with the best and most stable peptide epitopes in complex with MHC I are released from the peptide loading complex. The chaperones have different tasks in this selection process that is so important for the adaptive immune response, Tampé says: "Tapasin acts as a catalyst that accelerates the exchange of suboptimal peptide epitopes for optimal epitopes. Calreticulin and ERp57, in contrast, are deployed universally." This concerted approach ensures that only stable MHC I complexes with optimal peptide epitopes reach the cell surface and perform their role of guiding the killer T cells to the infected or mutated cell.

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Sponges 'sneeze' to dispose of waste

Sneezing out mucus may be one of the oldest ways for organisms to get rid of unwanted waste. A group of researchers found that sponges, one of the oldest multicellular organisms in existence, "sneeze" to unclog their internal filter systems that they use to capture nutrients from the water. Additionally, authors find that other animals who live with the sponges use their mucus as food. Their findings are publishing August 10 in the journal Current Biology.

"Our data suggest that sneezing is an adaptation that sponges evolved to keep themselves clean," says Jasper de Goeij, a marine biologist at the University of Amsterdam and the senior author of the paper.

While the field has known about this behavior for years, the authors of this paper show that these sneezes get rid of materials the sponges cannot use. "Let's be clear: sponges don't sneeze like humans do. A sponge sneeze takes about half an hour to complete. But both sponge and human sneezes exist as a waste disposal mechanism," says de Goeij.

Sponges gather food for themselves by filtering out organic matter from the water. They draw in and eject water from different openings, and sometimes the sponges will suck in particles that are too big. "These are sponges; they can't just walk to somewhere else when the water around them gets too dirty for them to handle," says de Goeij. This is when the "sneezing" mechanism comes in handy.

In videos that the authors included in the paper, you can see the water inlets slowly release mucus, and the mucus will accumulate at the surface of the sponge. Occasionally, sponge tissue will contract and push the waste-containing mucus into the surrounding water.

While the mucus may be waste to sponges, the fishes who live around them think otherwise. "We also observed fish and other animals feeding off of the sponge mucus as food," says Niklas Kornder, the first author of the study and a doctoral researcher in de Goeij's research group. "Some organic matter exists in the water surrounding the coral reef, but most of it is not concentrated enough for other animals to eat. Sponges transform this material into eatable mucus," says Kornder.

The paper recorded "sneezing" behavior in two species of sponges, the Caribbean tube sponge Aplysina archeri and another Indo-Pacific species of the genus Chelonaplysilla. "We actually think that most, if not all, sponges sneeze. I've seen mucus accumulate on different sponges while diving and in pictures taken by other scientists for other purposes," says Kornder.

"Our findings highlight opportunities to better understand material cycling in some of the most ancient Metazoans," say the authors in the paper.

There are still many aspects about sponge "sneezes" that remain open questions. "In the videos, you can see that the mucus moves along defined paths on the surface of the sponge before accumulating. I have some hypotheses, but more analysis is needed to find out what is happening," says Kornder.

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Ancient microbes may help us find extraterrestrial life forms

Using light-capturing proteins in living microbes, scientists have reconstructed what life was like for some of Earth's earliest organisms. These efforts could help us recognize signs of life on other planets, whose atmospheres may more closely resemble our pre-oxygen planet.

The earliest living things, including bacteria and single-celled organisms called archaea, inhabited a primarily oceanic planet without an ozone layer to protect them from the sun's radiation. These microbes evolved rhodopsins -- proteins with the ability to turn sunlight into energy, using them to power cellular processes.

"On early Earth, energy may have been very scarce. Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis," said UC Riverside astrobiologist Edward Schwieterman, who is co-author of a study describing the research.

Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors. They are also widely distributed among modern organisms and environments like saltern ponds, which present a rainbow of vibrant colors.

Using machine learning, the research team analyzed rhodopsin protein sequences from all over the world and tracked how they evolved over time. Then, they created a type of family tree that allowed them to reconstruct rhodopsins from 2.5 to 4 billion years ago, and the conditions that they likely faced.

Their findings are detailed in a paper published in the journal Molecular Biology and Evolution.

"Life as we know it is as much an expression of the conditions on our planet as it is of life itself. We resurrected ancient DNA sequences of one molecule, and it allowed us to link to the biology and environment of the past," said University of Wisconsin-Madison astrobiologist and study lead Betul Kacar.

"It's like taking the DNA of many grandchildren to reproduce the DNA of their grandparents. Only, it's not grandparents, but tiny things that lived billions of years ago, all over the world," Schwieterman said.

Modern rhodopsins absorb blue, green, yellow and orange light, and can appear pink, purple or red by virtue of the light they are not absorbing or complementary pigments. However, according to the team's reconstructions, ancient rhodopsins were tuned to absorb mainly blue and green light.

Since ancient Earth did not yet have the benefit of an ozone layer, the research team theorizes that billions-of-years-old microbes lived many meters down in the water column to shield themselves from intense UVB radiation at the surface.

Blue and green light best penetrates water, so it is likely that the earliest rhodopsins primarily absorbed these colors. "This could be the best combination of being shielded and still being able to absorb light for energy," Schwieterman said.

After the Great Oxidation Event, more than 2 billion years ago, Earth's atmosphere began to experience a rise in the amount of oxygen. With additional oxygen and ozone in the atmosphere, rhodopsins evolved to absorb additional colors of light.

Rhodopsins today are able to absorb colors of light that chlorophyll pigments in plants cannot. Though they represent completely unrelated and independent light capture mechanisms, they absorb complementary areas of the spectrum.

"This suggests co-evolution, in that one group of organisms is exploiting light not absorbed by the other," Schwieterman said. "This could have been because rhodopsins developed first and screened out the green light, so chlorophylls later developed to absorb the rest. Or it could have happened the other way around."

Moving forward, the team is hoping to resurrect model rhodopsins in a laboratory using synthetic biology techniques.

"We engineer the ancient DNA inside modern genomes and reprogram the bugs to behave how we believe they did millions of years ago. Rhodopsin is a great candidate for laboratory time-travel studies," Kacar said.

Ultimately, the team is pleased about the possibilities for research opened up by techniques they used for this study. Since other signs of life from the deep geologic past need to be physically preserved and only some molecules are amenable to long-term preservation, there are many aspects of life's history that have not been accessible to researchers until now.

"Our study demonstrates for the first time that the behavioral histories of enzymes are amenable to evolutionary reconstruction in ways that conventional molecular biosignatures are not," Kacar said.

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Study suggests that most of our evolutionary trees could be wrong

New research led by scientists at the Milner Centre for Evolution at the University of Bath suggests that determining evolutionary trees of organisms by comparing anatomy rather than gene sequences is misleading. The study, published in Communications Biology, shows that we often need to overturn centuries of scholarly work that classified living things according to how they look.

Since Darwin and his contemporaries in the 19th Century, biologists have been trying to reconstruct the "family trees" of animals by carefully examining differences in their anatomy and structure (morphology).

However, with the development of rapid genetic sequencing techniques, biologists are now able to use genetic (molecular) data to help piece together evolutionary relationships for species very quickly and cheaply, often proving that organisms we once thought were closely related actually belong in completely different branches of the tree.

For the first time, scientists at Bath compared evolutionary trees based on morphology with those based on molecular data, and mapped them according to geographical location.

They found that the animals grouped together by molecular trees lived more closely together geographically than the animals grouped using the morphological trees.

Matthew Wills, Professor of Evolutionary Paleobiology at the Milner Centre for Evolution at the University of Bath, said: "It turns out that we've got lots of our evolutionary trees wrong.

"For over a hundred years, we've been classifying organisms according to how they look and are put together anatomically, but molecular data often tells us a rather different story.

"Our study proves statistically that if you build an evolutionary tree of animals based on their molecular data, it often fits much better with their geographical distribution.

"Where things live -- their biogeography -- is an important source of evolutionary evidence that was familiar to Darwin and his contemporaries.

"For example, tiny elephant shrews, aardvarks, elephants, golden moles and swimming manatees have all come from the same big branch of mammal evolution -- despite the fact that they look completely different from one another (and live in very different ways).

"Molecular trees have put them all together in a group called Afrotheria, so-called because they all come from the African continent, so the group matches the biogeography."

The study found that convergent evolution -- when a characteristic evolves separately in two genetically unrelated groups of organisms -- is much more common than biologists previously thought.

Professor Wills said: "We already have lots of famous examples of convergent evolution, such as flight evolving separately in birds, bats and insects, or complex camera eyes evolving separately in squid and humans.

"But now with molecular data, we can see that convergent evolution happens all the time -- things we thought were closely related often turn out to be far apart on the tree of life.

"People who make a living as lookalikes aren't usually related to the celebrity they're impersonating, and individuals within a family don't always look similar -- it's the same with evolutionary trees too.

"It proves that evolution just keeps on re-inventing things, coming up with a similar solution each time the problem is encountered in a different branch of the evolutionary tree.

"It means that convergent evolution has been fooling us -- even the cleverest evolutionary biologists and anatomists -- for over 100 years!"

Dr Jack Oyston, Research Associate and first author of the paper, said: "The idea that biogeography can reflect evolutionary history was a large part of what prompted Darwin to develop his theory of evolution through natural selection, so it's pretty surprising that it hadn't really been considered directly as a way of testing the accuracy of evolutionary trees in this way before now.

"What's most exciting is that we find strong statistical proof of molecular trees fitting better not just in groups like Afrotheria, but across the tree of life in birds, reptiles, insects and plants too.

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Scientists reveal how Venus fly trap plants snap shut

Scientists at Scripps Research have revealed the three-dimensional structure of Flycatcher1, an aptly named protein channel that may enable Venus fly trap plants to snap shut in response to prey. The structure of Flycatcher1, published February 14 in Nature Communications, helps shed light on longstanding questions about the remarkably sensitive touch response of Venus fly traps. The structure also gives the researchers a better understanding of how similar proteins in organisms including plants and bacteria, as well as proteins in the human body with similar functions (called mechanosensitive ion channels), might operate.

"Despite how different Venus fly traps are from humans, studying the structure and function of these mechanosensitive channels gives us a broader framework for understanding the ways that cells and organisms respond to touch and pressure," says co-senior author and Scripps Research professor Andrew Ward, PhD.

"Every new mechanosensitive channel that we study helps us make progress in understanding how these proteins can sense force and translate that to action and ultimately reveal more about human biology and health," adds co-senior author Ardem Patapoutian, PhD, a Scripps Research professor who won the Nobel Prize in Physiology or Medicine for research on the mechanosensitive channels that allow the body to sense touch and temperature.

Mechanosensitive ion channels are like tunnels that span the membranes of cells. When jostled by movement, the channels open, letting charged molecules rush across. In response, cells then alter their behavior -- a neuron might signal its neighbor, for instance. The ability for cells to sense pressure and movement is important for people's senses of touch and hearing, but also for many internal body processes -- from the ability of the bladder to sense that it's full to the ability of lungs to sense how much air is being breathed.

Previously, scientists had homed in on three ion channels in Venus fly traps thought to be related to the ability of the carnivorous plant to snap its leaves shut when its sensitive trigger hairs get touched. One, Flycatcher1, caught researchers' attention because its genetic sequence looked similar to a family of mechanosensitive channels, MscS, found in bacteria.

"The fact that variants of this channel are found throughout evolution tells us that it must have some fundamental, important functions that have been maintained in different types of organisms," says co-first author Sebastian Jojoa-Cruz, a graduate student at Scripps Research.

In the new study, the researchers used cryo-electron microscopy -- a cutting-edge technique that reveals the locations of atoms within a frozen protein sample -- to analyze the precise arrangement of molecules that form the Flycatcher1 protein channel in Venus fly trap plants. They found that Flycatcher1 is, in many ways, similar to bacterial MscS proteins -- seven groups of identical helices surrounding a central channel. But, unlike other MscS channels, Flycatcher1 has an unusual linker region extending outward from each group of helices. Like a switch, each linker can be flipped up or down. When the team determined the structure of Flycatcher1, they found six linkers in the down position, and just one flipped up.

"The architecture of Flycatcher1's channel core was similar to other channels that have been studied for years, but these linker regions were surprising," says Kei Saotome, PhD, a former postdoctoral research associate at Scripps Research and co-first author of the new paper.

To help elucidate the function of these switches, the researchers altered the linker to disrupt the up position. Flycatcher1, they found, no longer functioned as usual in response to pressure; the channel remained open for a longer duration when it would normally close upon removal of pressure.

"The profound effect of this mutation tells us that the conformations of these seven linkers is likely relevant for how the channel works," says co-senior author Swetha Murthy, PhD, of Vollum Institute at Oregon Health and Science University, a former postdoctoral research associate at Scripps Research.

Now that they solved the molecular structure, the research team is planning future studies on the function of Flycatcher1 to understand how different conformations affect its function. More work is also needed to determine whether Flycatcher1 is solely responsible for the snapping shut of Venus fly trap leaves, or whether other suspected channels play complementary roles.

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