Still changing after all these years

Richard Lenski is MSU's Hannah Professor of Microbiology and Molecular Genetics. Science magazine called him "the man who bottled evolution."

If Paul Simon were to write a song about the bacteria in Richard Lenski's long-term evolution experiment, or LTEE, it could be titled, "Still Changing After All These Years."

In a paper published in the current issue of Nature, the Michigan State University John Hannah Distinguished Professor of Microbiology and Molecular Genetics and an international team of researchers used cutting-edge technology to study tens of thousands of generations of E. coli bacteria. They sequenced the entire genomes, or genetic code, of the bacteria to pinpoint the genes with beneficial mutations that gave the bacteria a competitive edge over their ancestors.

The bacteria from different generations of the LTEE have been stored in freezers for nearly 30 years, but they were brought back to life to look for the changes in their DNA. Being able to go back into the freezer to study samples from years ago is one of the reasons Lenski calls the LTEE "the experiment that keeps on giving."

"One of the nice things about such a long-term experiment is that new technologies come along that didn't exist when I started the LTEE in 1988," said Lenski, who's part of MSU's BEACON Center for the Study of Evolution in Action. "The first bacterial genome was not sequenced until 1995, and now, in this single paper, we've sequenced 264 complete genomes from this one experiment."

The team sequenced hundreds of E. coli genomes to examine how the bacteria had changed in their DNA over 50,000 generations. The researchers found more than 14,000 changes across the LTEE's 12 populations. Each population changed in different ways, but there were some important commonalities as well.

Most significant, and most simply, the mutations were concentrated in a subset of the genes -- those where mutations gave the bacteria a competitive edge. One of the striking differences that arose between populations is that half of them evolved to mutate at much higher rates than the other populations, even though they all started from the same ancestral strain that had a low mutation rate.

"Even in the simplest microcosm we can imagine to study evolution -- a single bacterium kept in the laboratory under monotonous conditions for years -- we are learning new things about the rates and processes of evolution," said Jeffrey Barrick, an assistant professor of molecular biosciences at the University of Texas at Austin. "This quantitative information is important for human health, as it improves our ability to predict how bacteria evolve, particularly in chronic infections and in our microbiome."

This paper is the product of several wonderful collaborations, Lenski said. Noah Ribeck, MSU postdoctoral researcher, developed some of the mathematical theory used to interpret the data. Barrick, a former MSU postdoc in Lenski's lab, created software for analyzing the genomes.

Read more at Science Daily

No, Asteroid Bennu Won't Destroy Earth

There is indeed a chance that the 1,650-foot-wide (500 meters) asteroid Bennu — the target of NASA's OSIRIS-REx spacecraft, which is scheduled to launch next month — could hit Earth late in the 22nd century.

But, mission officials stressed, that chance is slim, and the space rock is not nearly big enough to pose an existential threat to the planet, despite what some media reports claimed over the weekend.

"We're not talking about an asteroid that could destroy the Earth," OSIRIS-REx principal investigator Dante Lauretta, of the Lunar and Planetary Laboratory at the University of Arizona, told Space.com. "We're not anywhere near that kind of energy for an impact."

Sampling an Asteroid

If all goes according to plan, the $800 million OSIRIS-REx (Origins, Spectral Interpretation, Resource Identification, Security, Regolith Explorer) mission will lift off atop a United Launch Alliance Atlas V rocket from Florida's Cape Canaveral Air Force Station on Sept. 8.

The spacecraft will spend two years chasing Bennu down, finally rendezvousing with the near-Earth asteroid in August 2018. OSIRIS-REx will then study the space rock from orbit for another two years before grabbing at least 2.1 ounces (60 grams) of surface material in July 2020.

In 2023, this relatively hefty sample should make it back to Earth, where researchers in laboratories around the globe will analyze the material in a number of ways.

The mission team is chiefly interested in learning the role that asteroids like Bennu — dark, primitive and apparently carbon-rich objects — may have played in helping life get a foothold on Earth, Lauretta said.

"Did these kinds of bodies deliver organic material and water, in the form of hydrated minerals like clays, to the surface of our planet that created the habitability and the environments that may have led to the origin of life?" Lauretta said.

"That's the prime mission," to investigate that question, he added.

There are secondary objectives as well, including learning more about the valuable resources that Bennu-like asteroids may harbor, Lauretta said. And then there's the planetary-defense angle, which has gotten a lot of attention in the last few days.

A Potentially Hazardous Asteroid

Bennu is officially classified as a potentially dangerous asteroid. In fact, there's an 0.037 percent (or 1-in-2,700) chance that it will strike Earth in the last quarter of the 22nd century, NASA scientists have calculated.

Specifically, that's the probability that, during an Earthy flyby in 2135, Bennu will hit a special orbit-altering "keyhole" that will send it on a collision course with the planet later in the century.

OSIRIS-REx will help scientists refine those odds, by refining their understanding of Bennu's orbit. (That orbit, by the way, is already the best-known of any asteroid, Lauretta said; thanks to extensive observations since Bennu's 1999 discovery, astronomers have nailed the space rock's orbital radius down to within 20 feet, or 6 m.)

"Our uncertainties will shrink, so that will allow us to recalculate the impact probability," Lauretta said. "We don't know which direction it'll go. It could go down, because we just eliminated a bunch of possible keyholes that Bennu may hit. Or it may go up, because in the area that's left we have a higher concentration of keyholes compared to the overall area of the uncertainty plane."

OSIRIS-REx's work will also help researchers better understand the Yarkovsky effect, which describes how absorbed sunlight, when radiated away as heat, affects an object's trajectory. Such information will improve knowledge not only of where Bennu is headed, but where it came from, Lauretta said.

But to focus on where it's headed — what if Bennu does hit one of those keyholes in 2135, and the space rock squares Earth up for an impact in 2185 or thereabouts? What should humanity expect?

Read more at Discovery News

Look Up! Perseid Meteors Could be Supercharged

The Perseids are here: The dazzling meteor shower's peak of activity is Aug. 12, but you can already see its streaks of light peppering the sky.

Skywatchers are particularly excited about this year's Perseids. Though the meteor shower is an annual event, the Perseids are in outburst this year. That means that rather than 80 meteors per hour, we might see 150 to 200 per hour, according to NASA meteor expert Bill Cooke.

"Next, we move into the August Perseids, which is perhaps the most popular meteor shower of all," Cooke told Space.com in our summer meteor shower guide. "This year, they will be in what we call 'outburst' — their rates will double, because we're running into more material left behind by Comet Swift-Tuttle." [Perseid Meteor Shower 2016: When & How to See It]

The Perseid meteor shower occurs when Earth moves through the trail of dust and debris left by Comet Swift-Tuttle as it orbits the sun; the debris hits Earth's atmosphere and burns up, creating the white-hot streaks we see in the sky. Most of the pieces of debris, which move at 37 miles per second (59 kilometers per second), are about the size of a grain of sand, NASA has said.

Earth is passing through a particularly dense clump of debris this year — the source of the outburst — caused by the influence of Jupiter's gravity on Swift-Tuttle's trail. The number of meteors is increasing as Earth penetrates the heart of the debris, and it will diminish again once it passes through (after the peak).

The moon will be full six days after the meteor shower's peak, which might wash out the vivid streaks across the sky. So it might be a good idea to look earlier on, before the peak, to see the brightest streaks and fireballs, and to go to the darkest location you can, Cooke said. All of the meteors will appear to stream away from the constellation Perseus — that apparent source is called the shower's radiant — but will materialize all across the sky.

You don't need a telescope to see the meteors. In fact, because telescopes narrow your field of view, it's much easier to watch a meteor shower with the naked eye, just looking up at the entire sky. It will take around 30 minutes in the dark night for your eyes to adjust, and Cooke suggested to plan for a few hours outdoors, taking in the views. The Perseids will appear most clearly in the Northern Hemisphere after 10 p.m. local time, and the meteor rate will increase each night all the way until dawn.

Read more at Discovery News

Origins of the female orgasm explained

Female orgasm seems to be a happy afterthought of our evolutionary past when it helped stimulate ovulation, a new study of mammals shows.

The role of female orgasm, which plays no obvious role in human reproduction, has intrigued scholars as far back as Aristotle. Numerous theories have tried to explain the origins of the trait, but most have concentrated on its role in human and primate biology.

Now scientists at Yale and the Cincinnati Children's Hospital have provided fresh insights on the subject by examining the evolving trait across different species. Their study appears Aug. 1 in the journal JEZ-Molecular and Developmental Evolution.

"Prior studies have tended to focus on evidence from human biology and the modification of a trait rather than its evolutionary origin," said Gunter Wagner, the Alison Richard Professor of Ecology and Evolutionary biology, and a member of Yale's Systems Biology Institute.

Instead, Wagner and Mihaela Pavličev of the Center for Prevention of Preterm Birth at Cincinnati Children's Hospital propose that the trait that evolved into human female orgasm had an ancestral function in inducing ovulation.

Since there is no apparent association between orgasm and number of offspring or successful reproduction in humans, the scientists focused on a specific physiological trait that accompanies human female orgasm -- the neuro-endocrine discharge of prolactin and oxytocin -- and looked for this activity in other placental mammals. They found that in many mammals this reflex plays a role in ovulation.

In spite of the enormous diversity of mammalian reproductive biology, some core characteristics can be traced throughout mammalian evolution, note the researchers. The female ovarian cycle in humans, for instance, is not dependent upon sexual activity. However, in other mammalian species ovulation is induced by males. The scientists' analysis shows male-induced ovulation evolved first and that cyclical or spontaneous ovulation is a derived trait that evolved later.

The scientists suggest that female orgasm may have evolved as an adaptation for a direct reproductive role -- the reflex that, ancestrally, induced ovulation. This reflex became superfluous for reproduction later in evolution, freeing female orgasm for secondary roles.

A comparative study of female genitalia also revealed that, coincidental with the evolution of spontaneous ovulation, the clitoris was relocated from its ancestral position inside the copulatory canal. This anatomical change made it less likely that the clitoris receives adequate stimulation during intercourse to lead to the neuro-endocrine reflex known in humans as orgasm.

Read more at Science Daily

New areas of the brain identified where ALS gene is active

The dentate gyrus of the mouse hippocampal formation which contributes to the formation of new episodic memories stained for neurons (green) and stem cells (red).

For the first time novel expression sites in the brain have been identified for a gene which is associated with Motor Neuron Disease and Frontotemporal Dementia.

Many people who develop Motor Neuron Disease, also called Amyotropic Lateral Sclerosis (ALS), and/or Frontotemporal Dementia (FTD) have abnormal repeats of nucleotides within a gene called C9orf72 which causes neurons to die.

A team from the Department of Biology & Biochemistry at the University of Bath discovered for the first time that the C9orf72 gene is strongly expressed in the hippocampus of the mouse brain- a region where adult stem cells reside and which is known to be important for memory.

C9orf72 is also expressed at the olfactory bulb, involved in the sense of smell. Loss of smell is sometimes a symptom in FTD.

They also found that the C9orf72 protein changes from being concentrated in the cytoplasm of cells to both the cytoplasm and nucleus as the brain cortex develops, and during the development of neurons.

Dr Vasanta Subramanian, who led the study, said: "By uncovering novel sites of expression in the brain our findings provide an important resource for researchers studying animal models of C9orf72 mediated ALS and FTD.

"It is essential to know in which cell types in the nervous system the C9orf72 gene is expressed and where within the cell the C9orf72 protein is present.

"Our hope is that by researching accurate animal models of these diseases scientists can eventually develop new treatments and eventually cures for these devastating degenerative diseases."

The researchers, Ross Ferguson, Eleni Serafeimidou- Pouliou and Vasanta Subramanian, were working to map expression of C9orf72 in developing and adult mouse brains to help characterise reliable animal models to study the gene and its effects in both kinds of neurodegenerative diseases, for which there are currently no cures.

Dr Brian Dickie, Director of Research Development at the Motor Neurone Disease Association, said: "It is unclear why people who carry an abnormality in genes like c9orf72 don't usually develop symptoms of these diseases until several decades after birth, but it is possible that the activity of the gene early in life somehow 'primes' certain types of neuron to degenerate later in life.

"This detailed study provides a platform for future research to understand the role of this important gene in health and disease."

Read more at Science Daily

Scientists grow mini human brains

A midbrain organoid in a petri dish. The black pigment is neuromelanin, a hallmark of the human midbrain.

Scientists in Singapore have made a big leap on research on the 'mini-brain'. These advanced mini versions of the human midbrain will help researchers develop treatments and conduct other studies into Parkinson's Disease (PD) and aging-related brain diseases.

These mini midbrain versions are three-dimensional miniature tissues that are grown in the laboratory and they have certain properties of specific parts of the human brains. This is the first time that the black pigment neuromelanin has been detected in an organoid model. The study also revealed functionally active dopaminergic neurons.

The human midbrain, which is the information superhighway, controls auditory, eye movements, vision and body movements. It contains special dopaminergic neurons that produce dopamine -- which carries out significant roles in executive functions, motor control, motivation, reinforcement, and reward. High levels of dopamine elevate motor activity and impulsive behaviour, whereas low levels of dopamine lead to slowed reactions and disorders like PD, which is characterised by stiffness and difficulties in initiating movements.

Also causing PD is the dramatic reduction in neuromelanin production, leading to the degenerative condition of patients, which includes tremors and impaired motor skills. This creation is a key breakthrough for studies in PD, which affects an estimated seven to 10 million people worldwide. Furthermore, there are people who are affected by other causes of parkinsonism. Researchers now have access to the material that is affected in the disease itself, and different types of studies can be conducted in the laboratory instead of through simulations or on animals. Using stem cells, scientists have grown pieces of tissue, known as brain organoids, measuring about 2 to 3 mm long. These organoids contain the necessary hallmarks of the human midbrain, which are dopaminergic neurons and neuromelanin.

Jointly led by Prof Ng Huck Hui from A*STAR's Genome Institute of Singapore (GIS) and Assistant Prof Shawn Je from Duke-NUS Medical School, this collaborative research between GIS, Duke-NUS, and the National Neuroscience Institute (NNI) is funded by the National Medical Research Council's Translational Clinical Research (TCR) Programme In Parkinson's disease (PD) and A*STAR. Other collaborators are from the Lieber Institute for Brain Development, the Johns Hopkins University School of Medicine, and the Nanyang Technological University.

Assistant Prof Shawn Je from Duke-NUS Medical School's Neuroscience & Behavioural Disorders Programme said, "It is remarkable that our midbrain organoids mimic human midbrain development. The cells divide, cluster together in layers, and become electrically and chemically active in three-dimensional environment like our brain. Now we can really test how these mini brains react to existing or newly developed drugs before treating patients, which will be a game changer for drug development."

Prof Tan Eng King, Research Director and Senior Consultant, Department of Neurology at NNI and Lead PI of the TCR Programme in PD, remarked, "The human brain is arguably the most complex organ and chronic brain diseases pose considerable challenges to doctors and patients. This achievement by our Singapore team represents an initial but momentous scientific landmark as we continue to strive for better therapies for our patients."

Read more at Science Daily

Is Earthly life premature from a cosmic perspective?

This artist's conception shows a red dwarf star orbited by a pair of habitable planets. Because red dwarf stars live so long, the probability of cosmic life grows over time. As a result, Earthly life might be considered "premature."

The universe is 13.8 billion years old, while our planet formed just 4.5 billion years ago. Some scientists think this time gap means that life on other planets could be billions of years older than ours. However, new theoretical work suggests that present-day life is actually premature from a cosmic perspective.

"If you ask, 'When is life most likely to emerge?' you might naively say, 'Now,'" says lead author Avi Loeb of the Harvard-Smithsonian Center for Astrophysics. "But we find that the chance of life grows much higher in the distant future."

Life as we know it first became possible about 30 million years after the Big Bang, when the first stars seeded the cosmos with the necessary elements like carbon and oxygen. Life will end 10 trillion years from now when the last stars fade away and die. Loeb and his colleagues considered the relative likelihood of life between those two boundaries.

The dominant factor proved to be the lifetimes of stars. The higher a star's mass, the shorter its lifetime. Stars larger than about three times the sun's mass will expire before life has a chance to evolve.

Conversely, the smallest stars weigh less than 10 percent as much as the Sun. They will glow for 10 trillion years, giving life ample time to emerge on any planets they host. As a result, the probability of life grows over time. In fact, chances of life are 1000 times higher in the distant future than now.

"So then you may ask, why aren't we living in the future next to a low-mass star?" says Loeb.

"One possibility is we're premature. Another possibility is that the environment around a low-mass star is hazardous to life."

Although low-mass, red dwarf stars live for a long time, they also pose unique threats. In their youth they emit strong flares and ultraviolet radiation that could strip the atmosphere from any rocky world in the habitable zone.

To determine which possibility is correct -- our premature existence or the hazard of low-mass stars -- Loeb recommends studying nearby red dwarf stars and their planets for signs of habitability. Future space missions like the Transiting Exoplanet Survey Satellite and James Webb Space Telescope should help to answer these questions.

From Science Daily

Lack of Water Doomed Alaska Island Woolly Mammoths

About 5,600 years ago, on what is now Alaska's St. Paul Island, an isolated population of woolly mammoths gradually disappeared, and now scientists think they know why.

Decreased water levels in the island's lakes, along with decreased quality of the water likely doomed the mammoths, according to a new study by University of Alaska Fairbanks researchers.

"Freshwater resources look like the smoking gun for what pushed them into this untenable situation," said study co-author Matthew Wooller, in a statement.

Woolly mammoths became isolated on the island after the Bering Sea land bridge was covered by water during a period of rising sea levels. The island gradually became smaller, hampering the mammoths' chances to find new places with ample water.

Wooller and his colleagues extracted core samples from the bed of a freshwater lake on St. Paul Island, testing the remains of aquatic insects preserved in the sediment. Key chemical signatures retained by the insect remains allowed the scientists to assess the lake's water level and quality before, during, and after the time of the mammoths.

The analysis of the core told the researchers that water abundance and quality had indeed both diminished.

Meanwhile, chemical analyses of mammoth bones and teeth indicated that the island had grown progressively drier in the run-up to the animals' die-off.

The drier conditions and decreased lake levels "paints a dire picture of the situation for these mammoths," said Wooller.

Woolly mammoths disappeared from mainland sites some 10,000 years ago. About the size of today's African elephants, the last among them died out about 4,000 years ago on Russia's Wrangel Island, north of Siberia in the Arctic Ocean, an island also cut off by the submerged Bering Sea land bridge.

The St. Paul Island mammoths would have enjoyed the vegetation of the time, which was much as it is today, Wooller said in 2014. There's no evidence humans occupied the land at the same time as the mammoths.

Wooller and his team have published their findings in the journal Proceedings of the National Academy of Sciences.

From Discovery News

Novel 'repair system' discovered in algae may yield new tools for biotechnology

This is a TEM image of the algae C. reinhardtii.

A new way of fixing inactive proteins has been discovered in an algae, which uses chloroplast extracts and light to release an interrupting sequence from a protein.

Research specialist Stephen Campbell and Professor David Stern at the Boyce Thompson Institute report the discovery in the July 29 issue of the Journal of Biological Chemistry. This repair system may have applications in agriculture and biotechnology because it could potentially be harnessed to enable proteins to become active only in the light.

Many proteins contain extra sequences, called insertions, that can disrupt their function. The current paper demonstrates that the algae Chlamydomonas reinhardtii has the necessary toolkit to repair proteins by removing these insertions.

Campbell discovered this new repair system while purifying a protein from the chloroplasts of C. reinhardtii that can cut RNA. Upon sequencing the protein, he identified it as RB47, a protein that was not known to have any RNA-cleaving ability. Campbell noticed that the middle of the protein was missing. When he compared the protein sequence to its corresponding gene sequence, the protein was much shorter than expected.

Upon further study, Campbell found that he could detect a long version of the protein that contained an insertion and a short version that didn't. The cells make both versions when grown in the light or the dark, but only the short version can cleave RNA. The long version of the protein could be converted into the short one by mixing it in a test tube with chloroplasts from cells grown in the light and by illuminating the reaction. This process removed the interrupting insertion and restored the RNA-cutting activity of the protein. It is likely that the chloroplast maintains the machinery necessary to remove the sequence so that it can restore functionality to the protein.

This new type of repair system provides intriguing possibilities for biotech applications.

Because the insertion can be placed so that it interrupts a protein's function, the insertion and repair system may be useful for producing certain pharmaceuticals or protein products -- such as cancer drugs -- in culture, which would otherwise kill the cell. After purification, the inactive products could be treated with chloroplast factors and light to remove the insertion and activate the proteins.

In future work, the researchers plan to investigate exactly how the insertion becomes spliced out of the protein and which plant factors facilitate its removal. They also aim to understand the purpose of the insertion, and whether the algae can control the splicing to respond to changes in the environment.

Read more at Science Daily

Chorus of black holes radiates X-rays

The blue dots in this field of galaxies, known as the COSMOS field, show galaxies that contain supermassive black holes emitting high-energy X-rays. They were detected by NASA's Nuclear Spectroscopic Array, or NuSTAR, which spotted 32 such black holes in this field and has observed hundreds across the whole sky so far. The other colored dots are galaxies that host black holes emitting lower-energy X-rays, and were spotted by NASA's Chandra X-ray Observatory. Chandra data show X-rays with energies between 0.5 to 7 kiloelectron volts, while NuSTAR data show X-rays between 8 to 24 kiloelectron volts.

Supermassive black holes do not give off any of their own light, hence the word "black" in their name. However, many black holes pull in, or accrete, surrounding material, and emit powerful bursts of X-rays. Collectively, these active black holes throughout the sky can be thought of a cosmic choir, singing in the language of X-rays. Their "song" is what astronomers call the cosmic X-ray background.

To date, NASA's Chandra mission has managed to pinpoint many of the individual black holes contributing to the X-ray background, but the ones that let out high-energy X-rays--those with the highest-pitched "voices"--have remained elusive.

New data from NASA's Nuclear Spectroscopic Telescope Array, or NuSTAR, has, for the first time, begun to pinpoint large numbers of the black holes sending out the high-energy X-rays. More technically, NuSTAR has made significant progress in resolving the high-energy X-ray background.

"We've gone from resolving just 2 percent of the high-energy X-ray background to 35 percent," says Fiona Harrison, Benjamin M. Rosen Professor of Physics and Astronomy at Caltech, the principal investigator of NuSTAR, and lead author of a new study describing the findings in an upcoming issue of The Astrophysical Journal. "We can see the most obscured black holes, hidden in thick gas and dust."

The results will ultimately help astronomers understand how the growth patterns of supermassive black holes change over time--a key factor in the development of black holes and the galaxies that host them. For instance, the supermassive black hole at the center of our Milky Way galaxy is dormant now, but at some point in the past, it would have siphoned gas and bulked up in size.

As black holes grow, their intense gravity pulls matter toward them. The matter heats up to extremely high temperatures and particles get boosted to close to the speed of light. Together, these processes make the black hole surroundings glow with X-rays. A supermassive black hole with an ample supply of fuel, or gas, will give off more high-energy X-rays.

NuSTAR is the first telescope capable of focusing these high-energy X-rays into sharp pictures.

"Before NuSTAR, the X-ray background in high-energies was just one blur with no resolved sources," says Harrison. "To untangle what's going on, you have to pinpoint and count up the individual sources of the X-rays."

"We knew this cosmic choir had a strong high-pitched component, but we still don't know if it comes from a lot of smaller, quiet singers, or a few with loud voices," says coauthor Daniel Stern, the project scientist for NuSTAR at JPL. "Now, thanks to NuSTAR, we're gaining a better understanding of the black holes and starting to address these questions."

High-energy X-rays can reveal what lies around the most obscured supermassive black holes, which are otherwise hard to see. In the same way that medical X-rays can travel through your skin to reveal pictures of bones, NuSTAR can see through the gas and dust around black holes, to get a deeper view of what is going on inside.

With NuSTAR's more complete picture of supermassive black hole populations, astronomers can begin to puzzle together how these objects evolve and change over time. When did they start and stop growing? What is the distribution of the gas and dust that both feed and hide the black holes?

The team expects that over time, NuSTAR will be able to resolve more of the high-energy X-ray background--and better decipher the X-ray song of the universe's black holes.

From Science Daily