Detailed image of the human retina

What cell types are found in which human tissue, and where? Which genes are active in the individual cells, and which proteins are found there? Answers to these questions and more are to be provided by a specialised atlas -- in particular how the different tissues form during embryonic development and what causes diseases. In creating this atlas, researchers aim to map not only tissue directly isolated from humans, but also structures called organoids. These are three-dimensional clumps of tissue that are cultivated in the laboratory and develop in a way similar to human organs, but on a small scale.

"The advantage of organoids is that we can intervene in their development and test active substances on them, which allows us to learn more about healthy tissue as well as diseases," explains Barbara Treutlein, Professor of Quantitative Developmental Biology at the Department of Biosystems Science and Engineering at ETH Zurich in Basel.

To help produce such an atlas, Treutlein, together with researchers from the Universities of Zurich and Basel, has now developed an approach to gather and compile a great deal of information about organoids and their development. The research team applied this approach to the organoids of the human retina, which they derived from stem cells.

Many proteins visible simultaneously

At the heart of the methods the scientists used for their approach was the 4i technology: iterative indirect immunofluorescence imaging. This new imaging technique can visualise several dozen proteins in a thin tissue section at high resolution using fluorescence microscopy. The 4i technology was developed a few years ago by Lucas Pelkmans, a professor at the University of Zurich and coauthor of the study that has just been published in the scientific journal Nature Biotechnology. It is in this study that the researchers applied this method to organoids for the first time.

Typically, researchers use fluorescence microscopy to highlight three proteins in a tissue, each with a different fluorescent dye. For technical reasons, it is not possible to stain more than five proteins at a time. In 4i technology, three dyes are used, but these are washed from the tissue sample after measurements have been taken, and three new proteins are stained. This step was performed 18 times, by a robot, and the process took a total of 18 days. Lastly, a computer merges the individual images into a single microscopy image on which 53 different proteins are visible. They provide information on the function of the individual cell types that make up the retina; for example, rods, cones, and ganglion cells.

The researchers have supplemented this visual information of retinal proteins with information on which genes are read in the individual cells.

High spatial and temporal resolution

The scientists performed all these analyses on organoids that were of different ages and thus at different stages of development. In this way, they were able to create a time series of images and genetic information that describes the entire 39-week development of retinal organoids. "We can use this time series to show how the organoid tissue slowly builds up, where which cell types proliferate and when, and where the synapses are located. The processes are comparable to those of retinal formation during embryonic development," says Gray Camp, a professor at the University of Basel and a senior author of this study.

The researchers published their image information and more findings on retinal development on a publicly accessible website: EyeSee4is.

Further tissue types planned

So far, the scientists have been studying how a healthy retina develops, but in the future, they hope to deliberately disrupt development in retinal organoids with drugs or genetic modifications. "This will give us new insights into diseases such as retinitis pigmentosa, a hereditary condition that causes the retina's light-sensitive receptors to gradually degenerate and ultimately leads to blindness," Camp says. The researchers want to find out when this process begins and how it can be stopped.

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Atmospheric research provides clear evidence of human-caused climate change signal associated with CO2 increases

New research provides clear evidence of a human "fingerprint" on climate change and shows that specific signals from human activities have altered the temperature structure of Earth's atmosphere.

Differences between tropospheric and lower stratospheric temperature trends have long been recognized as a fingerprint of human effects on climate. This fingerprint, however, neglected information from the mid to upper stratosphere, 25 to 50 kilometers above the Earth's surface.

"Including this information improves the detectability of a human fingerprint by a factor of five. Enhanced detectability occurs because the mid to upper stratosphere has a large cooling signal from human-caused CO2 increases, small noise levels of natural internal variability, and differing signal and noise patterns," according to the journal article, "Exceptional stratospheric contribution to human fingerprints on atmospheric temperature," published in the Proceedings of the National Academy of Sciences (PNAS). Noise in the troposphere can include day-to-day weather, interannual variability arising from El Niños and La Niñas, and longer-term natural fluctuations in climate. In the upper stratosphere, the noise of variability is smaller, and the human-caused climate change signal is larger, so the signal can be much more easily distinguished.

"Extending fingerprinting to the upper stratosphere with long temperature records and improved climate models means that it is now virtually impossible for natural causes to explain satellite-measured trends in the thermal structure of the Earth's atmosphere," the paper states.

"This is the clearest evidence there is of a human-caused climate change signal associated with CO2 increases," according to lead author Benjamin Santer, an adjunct scientist in the Physical Oceanography Department at the Woods Hole Oceanographic Institute (WHOI) in Massachusetts.

"This research undercuts and rebuts claims that recent atmospheric and surface temperature changes are natural, whether due to the Sun or due to internal cycles in the climate system. A natural explanation is virtually impossible in terms of what we are looking at here: changes in the temperature structure of the atmosphere," added Santer, who has worked on climate fingerprinting for more than 30 years. "This research puts to rest incorrect claims that we don't need to treat climate change seriously because it is all natural."

The research was motivated by earlier work by Suki Manabe and Richard Wetherald, who in 1967 used a simple climate model to study how CO2 from fossil fuel burning might change atmospheric temperature. Their modeling found a very distinctive feature: an increase in CO2 levels led to more trapping of heat in the troposphere (the lowest layer of Earth's atmosphere) and less heat escaping higher up into the stratosphere (the layer above the troposphere), thus warming the troposphere and cooling the stratosphere. This prediction of tropospheric warming and stratospheric cooling in response to increasing CO2 has been confirmed many times by more complex models and verified by comparing model results with global-mean atmospheric temperature observations from weather balloons and satellites.

Although these earlier studies considered global-mean temperature changes in the middle and upper stratosphere, roughly 25 to 50 kilometers above Earth's surface, they did not look at detailed patterns of climate change in this layer. This region can be better studied now because of improved simulations and satellite data. The new research is the first to search for human-caused climate change patterns -- also called "fingerprints" -- in the middle and upper stratosphere.

"The human fingerprints in temperature changes in the mid to upper stratosphere due to CO2 increases are truly exceptional because they are so large and so different from temperature changes there due to internal variability and natural external forcing. These unique fingerprints make it possible to detect the human impact on climate change due to CO2 in a short period of time (~10 -- 15 years) with high confidence," stated co-author Qiang Fu, a professor in the Department of Atmospheric Sciences at the University of Washington.

"The world has been reeling under climate change, so being as confident as possible of the role of carbon dioxide is critical," said co-author Susan Solomon, Martin Professor of Environmental Studies at the Massachusetts Institute of Technology. "The fact that observations show not only a warming troposphere but also a strongly cooling upper stratosphere is unique tell-tale evidence that nails the dominant role of carbon dioxide in climate change and greatly increases confidence."

Santer said that although it is intellectually gratifying to be able to extend fingerprinting higher up into the atmosphere to test the prediction by Manabe and Wetherald, it is also deeply concerning.

"As someone who tries to understand the kind of world that future generations are going to inhabit, these results make me very worried. We are fundamentally changing the thermal structure of Earth's atmosphere, and there is no joy in recognizing that," Santer said.

"This study shows that the real world has changed in a way that simply cannot be explained by natural causes," Santer added. "We now face important decisions, in the United States and globally, on what to do about climate change. I hope those decisions are based on our best scientific understanding of the reality and seriousness of human effects on climate."

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Viruses could reshuffle the carbon cycle in a warming world

Microbes play important roles in ecosystems, and these roles are changing with global warming. Scientists also now know that most types of microbes are infected by viruses, but they know relatively little about how these viral infections could change how microbes react to warming. In this study, scientists describe many different ways that increasing temperatures could affect viruses and their microbial hosts. These changes could ultimately affect the responses of whole ecosystems to warming. The work exposes several important gaps in researchers' current knowledge about the connections between viruses, warming, and ecosystem functioning. Filling these gaps is crucial for understanding and predicting the effects of climate change on ecosystems.

This study creates a roadmap for understanding the many different ways that viruses could modify the effects of warming on communities of microbes. Viruses likely have strong effects on processes with microbes and the ways ecosystems function. Incorporating these previously ignored effects into ecosystem models will help scientists improve their predictions of how ecosystems could respond to climate change.

Microorganisms play integral roles in ecosystems by controlling the flow of energy and matter through processes like photosynthesis (carbon uptake), respiration (carbon release), and decomposition (carbon recycling). Climate change is currently altering how ecosystems function by changing how organisms operate within microbial food webs. Scientists know that viruses can have strong impacts on microbial processes, but they have less knowledge of how these impacts will change with future warming.

In this study, scientists from Duke University, the University of Tennessee Knoxville, the Netherlands Institute of Ecology, and Oak Ridge National Laboratory reviewed the potential impacts of warming on viruses and how these might alter scientific understanding of ecosystem responses to climate change. Warming likely affects several different stages of the viral infection cycle, as well as virus-host dynamics. However, there are still many gaps in our understanding about these effects. Because viruses are ubiquitous across all habitats and have strong effects on microbial functioning, filling these gaps is critical to understanding how warming will affect the flow of energy and matter within ecosystems. The researchers' preliminary models show that viruses could potentially tip the scales on natural carbon balances, causing some ecosystems to switch from being net carbon sources (releasing more carbon than they store) to being net carbon sinks (absorbing carbon). This study shows how incorporating viruses into predictive models can lead to new and unexpected effects on ecosystems in response to climate change.

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Researchers discover that the ice cap is teeming with microorganisms

There are no plants, and only very few animals: people rarely come here. The large glaciers in Greenland have long been perceived as ice deserts. Gigantic ice sheets where conditions for life are extremely harsh.

But now, it seems, we have been wrong. There is much more life on the glaciers than we thought.

Headed by Professor Alexandre Anesio, a group of researchers from the Department of Environmental Science at Aarhus University have discovered that the glaciers are teeming with life. Microbes that have adapted to life on the ice. And not just one or two species. Several thousand different species.

"A small puddle of melt-water on a glacier can easily have 4,000 different species living in it. They live on bacteria, algae, viruses and microscopic fungi. It's a whole ecosystem that we never knew existed until recently," says Alexandre Anesio.

What do the microbes live on?

Over the past 50 years, researchers have repeatedly been surprised by the hardiness of life. Life has been found several kilometres underground -- where there is neither sun nor oxygen. Billions of microorganisms "eat" minerals in the bedrock and so can survive.

Researchers have shown that life can even survive in space. In 2007, European researchers placed a colony of more than 3,000 microscopic water bears (tardigrades) outside a satellite and sent them into orbit around the Earth. The orbit lasted 10 days, after which the satellite returned to Earth. No less than 68 per cent of the microbes survived the vacuum of space and the lethal radiation.

Therefore, it might not come as a surprise that life also thrives on the glaciers. After all there is sun, oxygen and water. Nevertheless, until recently, researchers believed that the ice had too little nourishment to sustain life. But they were wrong.

There is nourishment. Just in incredibly small quantities, explains Alexandre Anesio.

Black algae

One of the microorganisms on the ice that the researchers spent most time investigating is a small black algae. The algae grows on top of the ice and tinges it black. There is a reason why the black algae so interesting for the researchers.

"When the ice darkens, it becomes more difficult to reflect sunlight. Instead, heat from the sun's rays is absorbed by the ice, which starts to melt. The more the ice melts, the warmer the temperature on Earth. The algae therefore play an important role in global warming," says Alexandre Anesio.

In recent years, larger and larger areas of the ice have become stained by the algae, making the ice melt even faster. Alexandre Anesio has calculated that the algae are increasing the ice melt by about 20 per cent.

The algae on the ice also existed before people kicked off global warming through industrialisation. However, climate change means spring arrives ever earlier to the Arctic and as a result the algae have a longer season to grow and spread.

"The algae spread a little more every year. When I travel to Greenland, I now see vast areas where the ice is completely dark because of the algae," he says.

Looking for an algaecide

Alexandre Anesio and his colleagues are spending a lot of time on the black algae because they are trying to find out whether the algae growth can be slowed down in some way or another.

The is a balance In most ecosystems -- a kind of equilibrium -- because the various organisms keep each other in check. So Alexandre Anesio wants to learn more about the relationship between the different microbes.

"The various microorganisms on the ice affect each other. Some leave nutrition that others live off. Small viral particles attack and consume bacteria. We believe that some of the fungal spores could eat the black algae. This is what we're looking for," he says.

However, he stresses that, even if they do find a way to curb algae growth, this will not solve climate change. Although it could slow it down.

Algae growth is a consequence of our releasing too many greenhouse gases into the atmosphere. And this is where the problem must be solved. We need to focus on slowing down our emissions.

The same pigment as in black tea

Algae is found virtually everywhere. In the sea, in lakes, on trees and rocks, and even as small spores in the air. Most algae are greenish. Like plants and trees, they are green because of chlorophyll. A molecule that enables them to photosynthesise.

But it's different for the black algae.

"Because the algae live on the ice, they're bombarded with sunlight and radiation. To protect themselves, they produce a lot of black pigment. It's actually the same pigment as in black tea. The pigment forms a protective layer outside the algae and protects the chlorophyll molecules against the dangerous radiation," says Alexandre Anesio. When the pigment absorbs the sun's rays, it generates heat. This heat makes the ice around the algae melt. And this actually benefits the algae. They need both water and micronutrients from the ice to live.

And they can only use the water when it is liquid.

NASA also has an eye on his research

Alexandre Anesio's research into life on the ice is important for a better understanding of climate change. However, NASA is also following his research results closely. The results may be crucial in the hunt for life in space.

"NASA has approached us several times because we're working with life that lives in one of the most inhospitable places on Earth. If life thrives on and under the ice, there's a probability that we'll also find life in the ice on Mars or Jupiter's and Saturn's ice moons, for example," he says.

Before NASA sent their Perseverance rover to Mars, they even invited Alexandre Anesio to a meeting.

"They were afraid that the rover would take with it microbes from Earth. Microbes that may be able to survive on Mars and pollute the samples they were going to take from Mars. So, they wanted to know what conditions life can survive in. What are the boundaries for life?"

Can give an indication of what they should look for

NASA is so interested in the research of life in the ice because we haven't found liquid water on any other planets in the solar system. Not yet, anyway. But we've found plenty of ice.

However, there is evidence to suggest that there are liquid oceans beneath the frozen surface of Saturn's moon, Enceladus and Jupiter's moon, Europa -- and one of the necessities of life, as we know it, is liquid water.

Therefore, NASA and other space agencies are very interested in learning more about the type of life that can live on and under the ice. Because organisms that resemble those in Greenland are probably those they'll be looking for on the ice moons.

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The evolution of honey bee brains

Researchers have proposed a new model for the evolution of higher brain functions and behaviors in the Hymenoptera order of insects. The team compared the Kenyon cells, a type of neuronal cell, in the mushroom bodies (a part of the insect brain involved in learning, memory and sensory integration) of "primitive" sawflies and sophisticated honey bees. They found that three diverse, specialized Kenyon cell subtypes in honey bee brains appear to have evolved from a single, multifunctional Kenyon cell-subtype ancestor. In the future, this research could help us better understand the evolution of some of our own higher brain functions and behaviors.

Are you "busy as a bee," a "social butterfly" or a "fly on the wall"? There are many ways we compare our behavior to that of insects, and as it turns out there may be more to it than just fun idioms. Studying insects could help us understand not only how their behavior has evolved, but also the behavior of highly evolved animals, including ourselves. Mammalian brains are big and complex, so it is difficult to identify which behaviors and neural and genetic changes have co-developed over time. By comparison, insect brains are much smaller and simpler, making them useful models for study.

"In 2017, we reported that the complexity of Kenyon cell (KC) subtypes in mushroom bodies in insect brains increases with the behavioral diversification in Hymenoptera (a large and varied order of insects)" explained Professor Takeo Kubo from the Graduate School of Science at the University of Tokyo and co-author of the current study. "In other words, the more KC subtypes an insect has, the more complex its brain and the behaviors it may exhibit. But we didn't know how these different subtypes evolved. That was the stimulus for this new study."

The team from the University of Tokyo and Japan's National Agriculture and Food Research Organization (NARO) chose two Hymenoptera species as representatives for different behaviors: the solitary turnip sawfly (which has a single KC subtype) and the sophisticated, social honey bee (which has three KC subtypes). As the sawfly has a more "primitive" brain, it is thought to contain some ancestral properties of the honey bee brain. To uncover the potential evolutionary pathways between them, the researchers used transcriptome analysis to identify the gene expression profiles (the genetic activity) of the various KC subtypes and speculate their functions.

"I was surprised that each of the three KC subtypes in the honey bee showed comparable similarity to the single KC type in the sawfly," said Assistant Professor Hiroki Kohno, co-author from the Graduate School of Science. "Based on our initial comparative analysis of several genes, we had previously supposed that additional KC subtypes had been added one by one. However, they appear to have been separated from a multifunctional ancestral type, through functional segregation and specialization." As the number of KC subtypes increased, each subtype almost equally inherited some distinct properties from an ancestral KC. These then modified in different ways, resulting in their varied present-day functions.

The researchers wanted a specific behavioral example of how ancestral KC functions are present in both the sawfly and the honey bee. So, they trained sawflies to engage in a common honey bee behavior test, where they learn to associate an odor stimulus with a reward. Although challenging at first, the team was eventually able to engage the sawflies in the memory task. The researchers then manipulated a gene called CaMKII in sawfly larvae, which in honey bees is associated with forming long-term memory, a KC function. When the larvae became adults, their long-term memory was impaired, indicating that the gene plays a similar role in both sawflies and honey bees. Although CaMKII was expressed (i.e., was active) across the entire single KC subtype in sawflies, in honey bees, it was preferentially expressed in only one KC subtype. This suggests that the role of CaMKII in long-term memory was passed down to the specific KC subtype in the honey bee.

Despite differences in the size and complexity of insect and mammalian brains, there are commonalities in terms of function and the basic architecture of the nervous system. That is why the model proposed in this study for the evolution and diversification of KC subtypes may help towards better understanding the evolution of our own behavior. Next, the team is interested in studying KC types acquired in parallel with social behaviors, such as the honey bee's "waggle dance."

Read more at Science Daily

Researchers develop model for how the brain acquires essential omega-3 fatty acids

Researchers at the UCLA David Geffen School of Medicine, the Howard Hughes Medical Institute at UCLA and the National Institutes of Health have developed a zebrafish model that provides new insight into how the brain acquires essential omega-3 fatty acids, including docosahexaenoic acid (DHA) and linolenic acid (ALA). Their findings, published in Nature Communications,have the potential to improve understanding of lipid transport across the blood-brain barrier and of disruptions in this process that can lead to birth defects or neurological conditions. The model may also enable researchers to design drug molecules that are capable of directly reaching the brain.

Omega-3 fatty acids are considered essential because the body cannot make them and must obtain them through foods, such as fish, nuts and seeds. DHA levels are especially high in the brain and important for a healthy nervous system. Infants obtain DHA from breastmilk or formula, and deficiencies of this fatty acid have been linked to problems with learning and memory. To get to the brain, omega-3 fatty acids must pass through the blood-brain barrier via the lipid transporter Mfsd2a, which is essential for normal brain development. Despite its importance, scientists did not know precisely how Mfsd2a transports DHA and other omega-3 fatty acids.

In the study, the research team provides images of the structure of zebrafish Mfsd2a, which is similar to its human counterpart. The snapshots are the first to detail precisely how fatty acids move across the cell membrane. The study team also identified three compartments in Mfsd2a that suggest distinct steps required to move and flip fatty acids through the transporter, as opposed to movement through a linear tunnel or along the surface of the protein complex. The findings provide key information on how Mfsd2a transports omega-3 fatty acids into the brain and may enable researchers to optimize drug delivery via this route. The study also provides foundational knowledge on how other members of this transporter family, called the major facilitator superfamily (MFS), regulate important cellular functions.

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Tiny microbes could brew big benefits for green biomanufacturing

A research team led by Lawrence Berkeley National Laboratory (Berkeley Lab) and UC Berkeley has engineered bacteria to produce new-to-nature carbon products that could provide a powerful route to sustainable biochemicals.

The advance -- which was recently announced in the journal Nature -- uses bacteria to combine natural enzymatic reactions with a new-to-nature reaction called the "carbene transfer reaction." This work could also one day help reduce industrial emissions because it offers sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels.

"What we showed in this paper is that we can synthesize everything in this reaction -- from natural enzymes to carbenes -- inside the bacterial cell. All you need to add is sugar and the cells do the rest," said Jay Keasling, a principal investigator of the study and CEO of the Department of Energy's Joint BioEnergy Institute (JBEI).

Carbenes are highly reactive carbon-based chemicals that can be used in many different types of reactions. For decades, scientists have wanted to use carbene reactions in the manufacturing of fuels and chemicals, and in drug discovery and synthesis.

But these carbene processes could only be carried out in small batches via test tubes and required expensive chemical substances to drive the reaction.

In the new study, the researchers replaced expensive chemical reactants with natural products that can be produced by an engineered strain of the bacteria Streptomyces. Because the bacteria use sugar to produce chemical products through cellular metabolism, "this work enables us to perform the carbene chemistry without toxic solvents or toxic gases typically used in chemical synthesis," said first author Jing Huang, a Berkeley Lab postdoctoral researcher in the Keasling Lab. "This biological process is much more environmentally friendly than the way chemicals are synthesized today," Huang said.

During experiments at JBEI, the researchers observed the engineered bacterium as it metabolized and converted sugars into the carbene precursor and the alkene substrate. The bacterium also expressed an evolved P450 enzyme that used those chemicals to produce cyclopropanes, high-energy molecules that could potentially be used in the sustainable production of novel bioactive compounds and advanced biofuels. "We can now perform these interesting reactions inside the bacterial cell. The cells produce all of the reagents and the cofactors, which means that you can scale this reaction to very large scales" for mass manufacturing, Keasling said.

Recruiting bacteria to synthesize chemicals could also play an integral role in reducing carbon emissions, Huang said. According to other Berkeley Lab researchers, close to 50% of greenhouse gas emissions come from the production of chemicals, iron and steel, and cement. Limiting global warming to 1.5 degrees Celsius above pre-industrial levels will require severely cutting greenhouse gas emissions in half by 2030, says a recent report by the Intergovernmental Panel on Climate Change.

Huang said that while this fully integrated system can be envisioned for a large number of carbene donor molecules and alkene substrates, it is not yet ready for commercialization.

"For every new advance, someone needs to take the first step. And in science, it can take years before you succeed. But you have to keep trying -- we can't afford to give up. I hope our work will inspire others to continue searching for greener, sustainable biomanufacturing solutions," Huang said.

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Scientists present evidence for a billion-years arms race between viruses and their hosts

Researchers have proposed a new evolutionary model for the origin of a kingdom of viruses called Bamfordvirae, suggesting a billion-years evolutionary arms race between two groups within this kingdom and their hosts.

Their study, published today as a Reviewed Preprint in eLife, provides what the editors say are convincing analyses that advance our understanding of the deep evolutionary history of viruses, the interaction between viruses and the first eukaryotes (organisms with cells that include a nucleus), and the diversification of viral lineages.

Viruses in the kingdom Bamfordvirae make up one of the most diverse groups that infect living organisms. They include the Nucleocytoplasmic Large DNA viruses (NCLDVs; the largest viruses characterised to date), virophages (viral parasites of other viruses), adenoviruses (common viruses that cause cold and flu-like symptoms), and Mavericks and Polinton-like viruses (both virus-like mobile genetic elements that colonise the genomes of their hosts).

There are two main hypotheses for the origins of these viruses: the 'nuclear-escape' and 'virophage-first' hypotheses. The nuclear-escape hypothesis says that a Maverick-like ancestor originated with hosts (endogenous), escaped from the host cell nucleus and gave rise to adenoviruses and NCLDVs. In contrast, the virophage-first hypothesis suggests that NCLDVs co-evolved with early virophages. Mavericks then evolved from virophages that became endogenous, with adenoviruses escaping from the host nucleus at a later stage.

"Despite these proposed scenarios, the diversification of viruses in the Bamfordvirae kingdom remains a major open question in virus evolution. To gain a better understanding of their history, we wanted to test the predictions made by both the nuclear-escape and virophage-first models, and consider alternative scenarios regarding the origin of different lineages," says José Gabriel Niño Barreat, Postdoctoral Research Assistant at the University of Oxford, UK. Barreat is a co-author of the study alongside Aris Katzourakis, Professor of Evolution and Genomics at the University of Oxford's Department of Biology.

Barreat and Katzourakis used two hypothesis-testing methods (maximum-likelihood and Bayesian frameworks) to compare the plausibility of the nuclear-escape versus alternative evolutionary scenarios. They focused on four key proteins shared by viruses in this lineage which are involved in the formation of viral capsids: major and minor capsid proteins, DNA-packaging ATPase, and protease. They applied another two methods that use genetic data to estimate rooted phylogenies, to infer the evolutionary trajectory of the different lineages. Then, they assessed whether adenoviruses and NCLDVs descended from a common ancestor, as predicted by the nuclear-escape scenario.

Their analyses revealed strong evidence against a sister relationship between adenoviruses and NCLDVs, as suggested by the nuclear-escape hypothesis. Instead, the findings suggest that adenoviruses descended from a common ancestor with Mavericks, to the exclusion of NCLDVs. At odds with a virophage-first scenario, the researchers found that the most recent common ancestor of Mavericks and adenoviruses was not a virophage. However, their work does not rule out the virophage-first hypothesis completely, making it the one best supported by current phylogenetic analyses.

Additionally, their work provides support for the positioning of the Bamfordvirae ancestral root between virophages and the other viral lineages. This positioning pointed the team towards a new model for the evolutionary origins of these viruses.

"The model proposes that the Bamfordvirae ancestor did not originate from an invasion of the eukaryotic cell nucleus, and that it was a non-virophage DNA virus with a small genome," says co-author Aris Katzourakis. "The lifestyle of virophages would have evolved at a later stage as these became specialised parasites of the ancestral NCLDVs." Katzourakis adds that the relative timing of events suggests the most recent common ancestor of the Bamfordvirae kingdom existed more than a billion years ago, extending to the initial stages of eukaryotic life. However, an absolute timescale for the precise dating of these events is not currently available.

Another limitation of the study is that the phylogenetic signal in the protein data analysed may have been obscured by the deep divergences and extreme diversity in this lineage. However, the authors were able to robustly distinguish between alternative scenarios, and the focus on the origin and development of the viral capsid provides a simple way to explain the available data.

"This work contributes to our knowledge on how viruses evolve different evolutionary strategies, for example to become parasites of other viruses like virophages, or viral giants like NCLDVs," Barreat says. "As well as playing important roles in Earth's ecosystems, it is becoming increasingly clear that viruses may have contributed to major evolutionary transitions during the history of life. Therefore, understanding the deep evolutionary history of viruses provides more context for these ancient interactions and the actors involved."

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Vanishing glaciers threaten alpine biodiversity

With glaciers melting at unprecedented rates due to climate change, invertebrates that live in the cold meltwater rivers of the European Alps will face widespread habitat loss, warn researchers.

Many of the species are likely to become restricted to cold habitats that will only persist higher in the mountains, and these areas are also likely to see pressures from the skiing and tourism industries or from the development of hydroelectric plants.

The research study -- led jointly by the University of Leeds and University of Essex -- calls on conservationists to consider new measures to protect aquatic biodiversity.

Invertebrates -- key role in ecosystems

The invertebrates, which include stoneflies, midges and flatworms, play a key role in nutrient cycling and organic matter transfer to fish, amphibians, birds and mammals in the wider Alpine ecosystem.

Using glacier, landscape and biodiversity mapping data collected across the Alps, scientists from across Europe simulated how key invertebrate populations across the mountain range are likely to change between now and 2100 because of climate change.

As the climate warms, the modelling predicted the invertebrate species would seek out colder conditions in the highest parts of the mountain range. In the future, these colder areas are also likely to be prioritised for skiing or tourism or the development of hydropower plants.

Lee Brown, Professor of Aquatic Science at the University of Leeds who co-led the research, said: "Conservationists need to be thinking about how protected area designations must evolve to take into account the effects of climate change.

"It may be that some species will have to be moved to refuge areas if we want to safeguard their survival as many of them are not strong fliers so they cannot disperse easily through the mountains."

Alpine climate is changing rapidly

The research, involving a collaboration between nine European research institutions, brought together data on invertebrate species distribution in the Alps, an area that covers more than 34,000 square kilometres, and mapped it alongside expected changes to glaciers and river flows.

There was sufficient data to model what was likely to happen to 19 invertebrate species, mainly aquatic insects, that live in the cold-water regions of the Alps.

Dr Jonathan Carrivick, from the School of Geography at Leeds who co-led the research, said: "We have quantified that as glaciers melt and retreat, the rivers running through the Alps will experience major changes in their water source contributions.

"In the short term, some will carry more water and some new tributary rivers will form, but over several decades from now -- most rivers will become drier, flow slower and become more stable, and there could even have periods in a year when there is no water flow. Additionally, most water in Alpine rivers will also be warmer in the future."

Losers and winners

By the turn of the century, the modelling predicts that most of the species would have experienced "consistent losses" of habitat.

Those hardest hit are expected to be the non-biting midges, Diamesa latitarsis grp., D. steinboecki, and D. bertrami; the stonefly, Rhabdiopteryx alpina; and mayfly, Rhithrogena nivata.

However, several species are expected to benefit from the habitat changes, including the flatworm, Crenobia alpina and the flat headed may fly, Rhithrogena loyolaea.

Other species would find refuge in new locations. The scientists predict the stonefly Dictyogenus alpinus and the caddisfly Drusus discolor will be able to survive in the Rhone valley in southeast France while other species will be lost from the rivers that flow into the Danube basin.

Conservation

Writing in the paper, the researchers describe the "substantial work" that is necessary to protect the biodiversity in rivers that are being fed by retreating glaciers. The locations where glaciers still exist late in the 21st century are likely to be prioritised for hydropower dam construction and ski resort development.

Dr Martin Wilkes, from the University of Essex and who co-led the research, said: "The losses we predict for Alpine biodiversity by the end of this century relate to just one of several possible climate change scenarios.

"Decisive action by world leaders to reduce greenhouse gas emissions could limit the losses. On the other hand, inaction could mean that the losses happen sooner than we predict."

Understanding how invertebrate populations respond to climate changes is key to understanding how biodiversity in high mountainous areas can be affected, and the techniques developed in the study could be applied to other mountain environments.

Read more at Science Daily

Scientist uncovers roots of antibiotic resistance

Bacteria naturally adapt to various environmental stimuli and as they mutate, these changes can make them resistant to drugs that would kill or slow their growth.

In a recent article published in PLoS Genetics, UCF College of Medicine microbiologist Dr. Salvador Almagro-Moreno uncovers the evolutionary origins of antimicrobial resistance (AMR) in bacteria. His studies on the bacterium that causes cholera, Vibrio cholerae, provide insight into deciphering what conditions must occur for infectious agents to become resistant.

"How AMR occurs in bacterial populations and the pathways leading to these new traits are still poorly understood," he said. "This poses a major public health threat as antimicrobial resistance is on the rise."

Dr. Almagro-Moreno studied genetic variants of a protein found in bacterial membranes called OmpU. Using computational and molecular approaches, his team found that several OmpU mutations in the cholera bacteria led to resistance to numerous antimicrobial agents. This resistance included antimicrobial peptides that act as defenses in the human gut. The researchers found that other OmpU variants did not provide these properties, making the protein an ideal system for deciphering the specific processes that occur to make some bacteria resistant to antimicrobials.

By comparing resistant and antibiotic sensitive variants, the researchers were able to identify specific parts of OmpU associated with the emergence of antibiotic resistance. They also discovered that the genetic material encoding these variants, along with associated traits, can be passed between bacterial cells, increasing therisk of spreading AMR in populations under antibiotic pressure.

By understanding how mutations occur, researchers can better understand and develop therapeutics to combat resistant infections. Dr. Almagro-Moreno is also looking at environmental factors such as pollution and warming of the oceans, as possible causes of resistant bacteria. "We are studying the genetic diversity ofenvironmental populations, including coastal Florida isolates, to develop a new approach to understandinghow antimicrobial resistance evolves," he explained.

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