夜上海论坛

The influenza virus is a quick-change artist. In a few decades, its genome can evolve as much as animal genomes can over millions of years. That means that the viral proteins, including those that alert our bodies to an infection, constantly reinvent themselves, threatening our immune systems and frustrating vaccine developers.

For Jesse Bloom, a biologist studying how evolution affects proteins, that relentless change is an opportunity. Thanks to data collected during past flu seasons, Bloom knows the exact genetic makeup of some ancestors of today’s influenza viruses. His lab group at the Fred Hutchinson Cancer Research Center in Seattle uses that information to figure out how the viruses made their immunity-dodging transformations.

Bloom and others are part of a growing group of scientists who practice “evolutionary biochemistry.” They seek to explain life’s tremendous diversity and determine exactly how that diversity emerged. Rather than focusing on how plants or animals adapted to different environments, however, these researchers consider diversity on a much smaller scale: Their work aims to explain how the small set of proteins that powered primitive life-forms evolved into the millions of specialized proteins that drive biological processes today.

Exploiting the genetic records, Bloom can assemble virus proteins that existed in bygone times, then reconstruct how they evolved, one amino acid at a time. Other researchers are analyzing modern species to resurrect the ancestral forms of biological molecules that have evolved over millions of years.

With a historical protein in hand, researchers can test how swapping out a single amino acid — as evolution might have done — changes how the protein flexes or folds and connects (or doesn’t) with other molecules. By trying out alternate versions of a protein’s history through stepwise amino acid changes, scientists can learn how a protein’s physical form has both enabled and constrained its evolution.

Ultimately, this work might answer some long-standing questions: To what extent does evolution depend on chance events? Can evolution reach the same point by traveling different paths? How does biological complexity evolve? Such experiments are also helping researchers who study modern proteins sort out how the order of amino acids relates to biological function.
That ordered series of amino acids is spelled out by the gene that holds the blueprint for a protein. Once the proper amino acids are strung together, they origami-fold into tiny structures with nooks and protrusions that determine what the protein does inside a cell. A protein’s folded shape lets it grab on to specific bits of DNA or hasten certain chemical reactions. Mutations in a gene can shift the resulting protein’s shape or alter subtle aspects of its behavior so that, over time, a protein’s function can change. But the possibilities are not endless. New proteins that fall apart, fail to fold or don’t perform as needed don’t survive the tests of natural selection.

“The physical determinants of folding, stability, solubility, function and specificity are absolutely essential aspects of the evolutionary process,” says University of Chicago biologist Joe Thornton. “That has not been widely appreciated or explicitly addressed until pretty recently.” Now, Thornton says, it’s clear that to understand molecular evolution, it’s important to study proteins as functioning, physical objects.

As they reconstruct proteins’ pasts, researchers are finding that genetic mutations sometimes remodel a molecule just enough to give a chance to other mutations that would have failed earlier. That creates opportunities for new features and functions to evolve — an idea that biologists have considered for decades but have only just begun to explore in the lab.

Bloom and colleagues, for instance, used an influenza virus protein called nucleoprotein to examine how interactions among mutations have affected the overall evolution of the virus. Understanding the combined effects of several mutations could allow researchers to anticipate the short-term effects of new genetic variation. That knowledge could help improve forecasts of which viral strains are likely to circulate in upcoming flu seasons, important information for designing effective vaccines.

Comparing nucleoprotein genes from strains of the virus isolated in 1968 and 2007, Bloom’s team mapped out the most likely steps by which the 1968 protein morphed into its newer form. Though nucleoprotein still plays the same role that it did in 1968 — aiding in the assembly of viral RNA — 33 of its 498 amino acids changed over those four decades, and a few changed more than once, the researchers reported in 2013 in eLife.

Bloom’s team built the 1968 nucleoprotein, then tested the effects of introducing each historical mutation. Some of the mutations affected parts of the protein that tip off a person’s immune cells that an invader is present — they probably helped the flu virus avoid detection. But on their own, some of those changes were bad for the virus: The nucleoprotein could no longer stay properly folded long enough to do its job.

During the course of the nucleoprotein’s evolution, some mutations boosted the protein’s stability, giving it a bit of a buffer. When later mutations occurred, allowing the virus to buck immune recognition, these earlier changes probably held the structure stable so the protein could still function.

When a mutation’s effects depend on other mutations, this interplay is called epistasis. These interactions within individual molecules have been important in shaping evolutionary trajectories, says University of Oregon biophysicist Michael Harms, who is studying how diverse functions evolved in a group of proteins called s100s. He calls epistasis “the common feature in all of evolution.”

Codependent interactions don’t occur just between pairs of mutations. They can be significantly more complex. Analyzing data from other labs, Harms has found epistatic interactions involving up to six different mutations. Such interplay means that in many cases, if genes had transformed themselves just a bit differently, evolution would have veered onto a different course.

Green light
Scientists call mutations that lay the groundwork for future change “permissive” mutations. Some protein functions came about only after permissive mutations modified an evolving molecule in highly improbable ways.

Thornton uses ancestral protein reconstruction to study how steroid hormones — which control stress responses, growth and sexual developmental in vertebrates — evolved partnerships with their receptors. Receptors are proteins that bind to specific partners to activate responses in the cell. By comparing steroid receptors in different species, Thornton can map the evolutionary relationships between the molecules and infer the likely amino acid sequence of their common ancestor. Then he introduces a DNA molecule that encodes the long-extinct protein into lab-grown cells. Those cells use the genetic instructions to manufacture a tiny piece of the deep past.

Many of Thornton’s studies begin with a 450-million-year-old receptor protein that he and colleagues reconstructed in 2006. The protein gave rise to modern receptor molecules that are activated by different hormones. One receptor, the glucocorticoid receptor, responds to the stress hormone cortisol. The other, the mineralocorticoid receptor, controls levels of salt and other electrolytes in response to the hormone aldosterone. Thornton’s team found that their reconstructed ancestor could be activated by both cortisol and mineralocorticoids.

A receptor that responded only to cortisol appeared 40 million years after the promiscuous receptor, Thornton showed. His team found a set of amino acid changes that converted the general ancestral receptor into the cortisol-specific one. But the mutations that changed the ancient receptor’s preference couldn’t have generated a functional receptor by themselves, experiments showed.

“The function-switching mutations are not tolerated on their own,” Thornton says. They destabilize parts of the receptor. Like the flu virus’s evolving nucleoprotein, the ancestral receptor’s structure had to be buttressed before it could withstand the mutations that would make the receptor choosier.

Two amino acid changes quietly readied the ancient receptor for its transformation, Thornton and colleagues reported in 2009 in Nature. Without them, the path to the function-switching mutation would have been inaccessible. “If we were to wind back the clock and set history rolling again, it’s very unlikely that those permissive mutations would occur,” he says. “We would have ended up with a very different glucocorticoid receptor and a very different endocrine system.”

Thornton and Harms, then a postdoctoral researcher in Thornton’s lab at University of Oregon in Eugene, explored whether evolution could have taken an alternate route to the same end. Harms created and screened thousands of variants of the ancestral protein, searching for alternative mutations that might have set it up for the same functional switch. He found none, the researchers reported in Nature in 2014. Evolution, it seems, had acted on a rare opportunity.

Biophysical analyses of variant receptor proteins showed why so few mutations enabled cortisol-specific binding to evolve. Although certain parts need extra support, the receptor also needs to be able to transition between two forms: an inactive conformation when no cortisol is present, and a gene-activating conformation when the hormone binds. Some mutations stabilize the active form of the receptor too much, locking it into an “always-on” configuration. Mutations also had to be compatible with the ancestral protein on their own, before the function-switching mutations were introduced.

“A mutation has to fulfill all these requirements, and that is not easy to do,” Thornton says. “That seems to be the explanation for why permissive mutations [for this functional switch] are so rare.”

But not every new function is the result of complicated epistatic interactions. In January in eLife, Thornton and Ken Prehoda of the University of Oregon described an ancient protein that gained a completely new function by way of a single amino acid change.

The team studied the origins of an animal protein that helps cells orient themselves in space before dividing. Doing so is vital for positioning new cells in the right places within a growing body. Single-celled life-forms had to get this right before multicellular organisms could evolve.
Thornton, Prehoda and colleagues focused on a segment of the protein called GK PID (for GK protein-interaction domain), which orients cells by acting as a scaffold during division. The billion-year-old ancestor of GK PID did nothing of the sort. It was an enzyme predecessor to the modern guanylate kinase, which catalyzes a chemical reaction that cells use to make some of the building blocks of DNA. Amazingly, Thornton says, one mutation was enough to transform the ancestral protein from an enzyme to a working scaffold.
That surprising result is an example of why developing general theories about the physical principles shaping evolution requires a grasp of the evolutionary histories of a broader collection of proteins.

“Every time people take [a protein] apart, they see a new feature,” Harms says. Fortunately, he says, thanks to faster computers, better software and a growing number of genomes to reference, research on ancestral protein reconstruction is on the rise.

Roads taken
While chance events can shift the landscape of evolution’s possibilities, evolving proteins also have some freedom to explore. They can take more than one path to some functions.

Douglas Theobald, a biochemist at Brandeis University in Waltham, Mass., has seen this in his own investigations of an enzyme that many cells use to produce energy without oxygen. The enzyme, lactate dehydrogenase, evolved from structurally similar enzymes not just once, but at least four times in different groups of organisms. By reconstructing the evolutionary events that transformed a similar enzyme, malate dehydrogenase, into lactate dehydrogenase, Theobald and colleagues found that two groups of single-celled parasites came by the same enzyme in different ways. The researchers reported the findings in eLife in 2014 and in Protein Science in February.

The work demonstrates that different genetic backgrounds may steer evolution along different paths in different organisms but still lead to similar outcomes, Theobald says. “Even if there is a lot of epistasis, there’s still lots of different ways to the same function.”

Biochemist Susan Marqusee of the University of California, Berkeley has also found that there’s more than one way for a protein to do something new.

Marqusee collaborated with Thornton’s team to compare how two bacteria, Escherichia coli and the heat-loving Thermus thermophilus, evolved enzymes that do the same job at very different temperatures. T. thermophilus thrives in hot springs, at temperatures that would cause most proteins to fall apart. Biochemists are eager to borrow from nature’s strategies to engineer heat-tolerant proteins but have struggled to find general principles that account for this property. By reconstructing the common ancestor of the RNA-snipping enzyme known as H1 from E. coli and T. thermophilus, Marqusee’s team found out how the bacterial protein takes the heat.

That 3-billion-year-old common ancestor was less stable than the enzyme that T. thermophilus uses today, the team reported in 2014 in PLOS Biology. As the heat-tolerant protein evolved, its stability steadily increased — not because of any one innovation, but by virtue of distinct biophysical strategies at different points in time.

“The physical chemistry doesn’t really matter as long as in the end, they add up to the right phenotype,” Marqusee says. Because evolution was able to take advantage of different amino acids to boost stability in a variety of ways, the enzyme’s growing resilience to hot environments didn’t depend on the chance occurrence of a particular set of mutations.

Foggy future
Studies of how proteins have evolved in the past are unlikely to spell out how evolution will proceed in the future. “The emerging picture is that the role of chance is so great that long-term predictions of the future evolution of any protein is a very risky enterprise,” Thornton says. But recent research does offer insights into how and why today’s proteins do what they do.
One example comes from Thornton’s work on how the DNA-binding sites on steroid receptors have evolved along with their DNA targets. The hormone-activated receptors act as transcription factors, binding to specific sections of DNA to switch on certain genes. In 2014, Thornton’s team reported in Cell that a bulky amino acid in an ancestral protein prevented the protein from binding to the stretch of DNA favored by many of today’s steroid receptors. The ancestral protein awkwardly bumped up against the DNA, unable to make enough contact to really grab on. The receptor gained its new specificity when mutations ended those obstacles and introduced new clashes that blocked its access to the former binding site.

Researchers often can’t tell which differences between two related proteins make them behave differently. But reconstructing evolutionary paths can point them in the right direction.

Using ancestral reconstruction, Theobald and Brandeis colleague Dorothee Kern studied how Abl, a growth-promoting protein linked to chronic myelogenous leukemia, diverged from the related Src protein. The researchers wanted to know why the anticancer drug Gleevec binds to and shuts off Abl without obstructing Src, even though Src has a very similar structure. Theobald, Kern and colleagues identified 15 amino acids in Abl that are crucial for Gleevec binding. The amino acids influence how the protein transitions between two different configurations (that shape-shifting is disrupted in some patients with Gleevec-resistant cancers). The finding, published last year in Science, suggests that researchers may be able to develop better drugs by considering these conformational shifts.

Some proteins, or parts of proteins, might even be inherently more able to evolve than others. Certain parts of the fast-evolving viral protein hemagglutinin are unusually tolerant of change, Bloom and Bargavi Thyagarajan, who was a postdoctoral researcher in Bloom’s lab, reported in 2014 in eLife. Antibodies against hemagglutinin are the immune system’s best defense against influenza, but the protein is adept at escaping detection.

The researchers used a relatively new method called deep mutational scanning to build and test hemagglutinin proteins with nearly every possible amino acid change — about 10,000 in all — in viruses grown in the lab. In a host, changes that disguise hemagglutinin from the immune system would be advantageous. Even though there was no immune system to hide from in the lab, viruses still survived more changes to parts of hemagglutinin that would be recognized by an immune system than they did changes to other parts of the protein. Bloom and his graduate student Michael Doud reported a more detailed view of the protein and the areas that are more and less likely to tolerate mutations online on bioRxiv.org in April.
That’s good for the virus, but bad for people. Hemagglutinin seems capable of accumulating change in the very sites that vaccine developers would like to remain the same. But the finding also suggests that flu vaccines designed to target less mutation-tolerant regions of hemagglutinin might be more likely to protect against the flu from season to season. That’s a strategy some labs are already exploring — targeting the less-evolvable stalk of hemagglutinin’s lollipop-shaped structure.

It’s not yet clear why certain parts of the hemagglutinin protein tolerate change so well; Bloom hopes that studying the mutational tolerance of other proteins will help researchers figure that out.

“We’re never going to be able to predict evolution precisely, because it’s a highly stochastic process,” Bloom says. “But I think we can make better forecasts about many of the evolutionary processes that affect us. These are really challenging problems, but I think we are getting to the point where we can use experiments and molecular understanding to help us think about these processes.”

At the end of the last Ice Age, humans undertook an epic American road trip — trekking from a northern land bridge into interior of North America. But details about the route and timing of that trip are hotly debated.

Some researchers think that humans followed a so-called “ice-free corridor” along the eastern Rocky Mountains. Studies have suggested, though, that the corridor froze over and became impassable around 21,000 years ago. Now, a bread crumb trail of fossils showing the movement of ancient bison indicates that the corridor may have reopened a few thousand years later, researchers report in the Proceedings of the National Academy of Sciences the week of June 6.

Analyzing DNA samples from 78 bison fossils unearthed in Canada, a team led by Beth Shapiro of the University of California, Santa Cruz, found that genetically distinct northern and southern populations moved north and south along the corridor by 13,000 years ago. That means humans may have also hiked along the slopes of the Rockies at the same time.

These probably weren’t the first humans to head south. Recent archaeological evidence points to early Americans trekking as far as Chile more than 15,000 years ago. But the corridor could have served as a later route, the team argues.

Kids are fascinated by fireflies. So are scientists, who, despite decades of research, are still perplexed by many of the mysteries posed by “lightning bugs.” In Silent Sparks, biologist Sara Lewis explores both the cultural and scientific fascination with these marvelous beetles.

Many creatures can manufacture their own glow, Lewis notes, but fireflies are some of the few that can readily turn their lamps on and off. Not all of the world’s nearly 2,000 firefly species light up as adults. But all of their larvae do, which suggests that the bioluminescence may have first evolved in a dinosaur-era ancestor as a “Don’t eat me! I’m toxic!” signal to predators. Only later would adults have co-opted this glimmer for the mating displays that most people are familiar with.
Some of the most impressive firefly shows involve the synchronous flashing of thousands of insects. Each mating season, these Christmas tree–like spectacles draw thousands of tourists to locales as diverse as Tennessee and Malaysia. Although researchers have a fairly good idea of how the fireflies synchronize their flashings — in some species, males continually adjust their flashing rate based on their neighbors’ activity — scientists still haven’t figured out why they do so.

Fireflies aren’t just pretty; they’re useful. For instance, food inspectors monitor food contamination by taking advantage of the chemical reactions that the insects use to signal their mates. These reactions occur only in the presence of ATP, an energy-storing chemical found in all living cells, making the glowing substances a keen detector for food-tainting bacteria such as Salmonella or E. coli.

Silent Sparks is at its best when Lewis describes her own experiences in the field, such as lying on her back on the forest floor while flickering fireflies wafted mere inches above her nose. For readers who would like their own experience, Lewis includes a field guide to the most common species found in the southeastern United States (the hot spot of North American firefly diversity).

So grab a copy of the book, along with a net, jar and kid you love, and relive fond childhood memories while inspiring a few new ones.

In the years after the animated movie Finding Nemo was released by Pixar in 2003, sales of clownfish spiked as fans, little and big, rushed to buy their own “Nemo.” So many Nemos were purchased that the sales actually depleted some wild stocks of the fish. Pressure on those wild populations has since dropped, thanks to efforts to increase captive clownfish breeding. But now there are worries that Nemo’s sequel, Finding Dory, may have a similar effect on Dory’s species, the blue tang — and an even bigger impact on the coral ecosystems in which these fish are found.

Despite concerted efforts, scientists have been unable to convince blue tangs to breed in captivity. That means that every blue tang, every Dory, sold has to be captured from the wild. And a surprisingly large number of those fish are captured with cyanide, new research shows.

Most of the 11 million fish sold in the U.S. aquarium trade come from coral reefs in the Indo-Pacific. In some places, like Hawaii and Australia, there are decent rules and enough enforcement of them that fish can be collected without too much harm to ecosystems. But in others, there aren’t enough laws or enforcers to prevent disturbing, destructive practices, such as fishing with explosives or cyanide.

For the aquarium trade, cyanide fishing is “cheap and easy to do,” says Craig Downs, executive director of the Haereticus Environmental Laboratory in Clifford, Va. A diver adds a pellet of cyanide to a bottle and squirts a bit on a target fish. Or they may use larger quantities pumped down from their boat. The poison quickly stuns the fish, which can then be captured and later sold.

But cyanide is deadly. Coral exposed to cyanide bleaches and dies. Other fish and organisms left behind can die. Even the fish that enter the aquarium trade may die within a few weeks or months of being caught. “If you survive [exposure], you’re messed up for the rest of your life,” Downs says. And while there are laws that should prevent divers from employing this fishing method — and from wholesalers in the United States from being able to purchase fish caught this way — “this practice happens all through the Indo-Pacific,” says Downs. As many as 30 million fish may be caught this way every year, and 90 percent of those may die.

There is no way for someone purchasing a fish in a pet store to tell if the animal had been exposed to cyanide. “You have to be a fish pathologist” to see the signs, Downs says. But after a fish, human or other organism is exposed to the toxin, it will excrete a cyanide metabolite, thiocyanate, in its urine. And this can be detected in the water in which a captive fish is living.

Recently, Downs and Rene Umberger, director of the nonprofit organization For the Fishes, wanted to get an idea of how many fish sold in pet stores were caught with cyanide. They purchased 89 fish from shops in California, Hawaii, Maryland, North Carolina and Virginia, collected water samples and sent them off to an independent laboratory. More than half came back positive for cyanide exposure, including many of the blue tangs. None of the fish from companies that breed fish in captivity came back positive, though. The results of this initial study will be presented later this month at the International Coral Reef Symposium in Hawaii.

A 2008 report from NOAA estimated that 90 percent of the aquarium fish imported into the United States were captured with cyanide or other illegal methods. And Downs suspects that cyanide use for the fish in his study may be higher than he and his colleague are now reporting. The fish only excrete detectable levels of thiocyanate for a short time after exposure. Plus, initial runs of a more sensitive method for detecting the chemical show that many of the negatives may really be positives for exposure, he says.

He is hoping that this method might be turned into an easy tool that can be used by consumers, citizen scientists and enforcement agencies to quickly detect fish that have been illegally caught with cyanide, which would hopefully drive down the trade.

This doesn’t mean that all saltwater fish are off limits for consumers, though. “If consumers really want to have coral reef fish, then going the cultured route is the way to go,” Downs says. There aren’t many of those fish — only 42 or so species among the more than 1,800 currently traded in the United States — but identifying them is easy. Umberger’s group has a free iOS app, Tank Watch, that lists them all. And even though the app doesn’t list every species that may be in a store, if a species isn’t on their good list, it can be assumed to be bad.

So go ahead and buy Nemo, if you must, but leave Dory and most of her fishy cousins where they belong — in the ocean.

BOSTON — New studies find a rise in drug-resistant urinary tract infections in pets, raising concerns that companion animals may serve as microbe reservoirs that could contribute to the spread of potential superbugs. About four in 10 U.S. households own dogs, which sleep with us, eat off our plates, lick our faces and leave plenty of poop to scoop. Cat ownership is nearly as prevalent.

It’s not clear whether pets are picking up the resistant microbes from their owners, or vice versa, said Cátia Marques, a veterinary medicine doctoral candidate. She presented the research, conducted by scientists from the University of Lisbon in Portugal, June 20 at a joint meeting of the American Society for Microbiology and the Interscience Conference on Antimicrobial Agents and Chemotherapy. More research is needed to answer that question, she said.
Either way, scientists worry that companion animals provide another haven for bacteria to mingle and pick up genes that give them resistance to drugs, said Michael Schmidt of the Medical University of South Carolina in Charleston, who was not involved in the new work. “It is a substantial issue,” he said.

Other research has examined human-pet sharing of bacteria, but the subject has been little explored for urinary tract infections, which are extremely common. The new research found a growing resistance in veterinary infections to antibiotics critical for treating human illness. In one study, samples of the bacterium Proteus mirabilis taken over 16 years in Portugal showed a steady climb in the prevalence of resistant strains. An example: Resistance to a class of drugs known as third-generation cephalosporins grew from 2 percent of samples in 2004 to 20 percent today. Other research found worrisome multidrug resistance in infections caused by Klebsiella. In a third study, which tested for resistance in urinary tract infections in pets across Europe, patterns of drug resistance in dogs and cats tracked that of humans, the researchers found.

In humans, doctors have watched warily as resistance to urinary tract infections has grown. In May, scientists reported the discovery of a woman with a urinary infection resistant to colistin, a rarely used drug of last resort (SN Online: 5/27/16). It’s not clear how the patient contracted the resistance, but given colistin’s role as a last-ditch drug, it raised the specter of an unstoppable microbe.

While the new research is broader, it isn’t the first study to raise concerns about the role of companion animals in difficult-to-treat urinary infections. In 2013, German researchers writing in the Journal of Antimicrobial Therapy described finding carbapenem-resistant Escherichia coli and Klebsiella urinary infections in six dogs — a discovery later called a phenomenon “of great concern” in a commentary in the same journal. E. coli and P. mirabilis are the two biggest causes of urinary tract infections. Carbapenem, which the researchers in Portugal did not test for, is also considered a drug of last resort for urinary infections.

Whether humans are giving resistant organisms to their animals or vice versa, the findings emphasize that the battle against resistance needs a global strategy that involves veterinarians along with human doctors and patients, Marques said. “We need to have a common public health approach,” she said.

Schmidt also cautioned that people who are particularly vulnerable to urinary infections, such as pregnant women, take extra care around their pets, especially when cleaning up after them. “If you do have a companion animal and you’re prone to these infections,” he said, “be very strict with your hand hygiene before you eat.”

All systems are go for the Juno spacecraft’s July 4 encounter with Jupiter.

“We couldn’t be more excited about being this close to Jupiter’s doorstep,” said Diane Brown, Juno program executive at NASA Headquarters in Washington, D.C., during a June 30 news briefing.

The scientific instruments have been shut off and the final command sequence for going into orbit around Jupiter has been uploaded to the spacecraft’s computers. On July 4, the probe will fire its main engine for 35 minutes, using it as a brake to slow down and be captured by Jupiter’s gravity. Once in orbit, Juno will spend 20 months figuring out what’s hiding beneath the thick clouds that encase the planet.

Juno has been busy during its final approach. On June 28, it got one more look at Jupiter and three of its moons. And last week Juno monitored changes in interplanetary plasma (see below) as it crossed a magnetic boundary that shields Jupiter from the stream of charged particles blowing from the sun.

Now all scientists can do is wait. “I have mixed emotions,” said mission lead Scott Bolton, a planetary scientist at the Southwest Research Institute in San Antonio. “I’m excited, but I also have tension and nervousness.” Juno has to perform a critical engine burn all on its own while passing through treacherous belts of radiation that encircle the planet. A series of radio tones from the spacecraft will let mission scientists know whether or not it worked.

“Come see us on July 4,” Bolton said.

Any traveler to the Olympics could potentially bring Zika home, but just four countries bear a substantial risk of seeing the virus spread.

Chad, Djibouti, Eritrea and Yemen all have the right ingredients to sustain mosquito-borne transmission, researchers report July 13 in a weekly report of the U.S. Centers for Disease Control and Prevention. Few people typically travel from those countries to places where Zika virus is active, but the Olympics will change that.

To gauge the risk of a single person traveling to Rio de Janeiro for the Olympics, becoming infected and then sparking an outbreak back home, CDC scientist Ardath Grills and colleagues analyzed environmental and population data for 206 countries planning to participate in the Games.

All countries risk importing Zika from Rio, the authors write, but only 19 not currently reporting Zika outbreaks have the susceptible populations and environmental conditions needed to keep local transmission going. And all but Chad, Djibouti, Eritrea and Yemen already have lots of travelers trekking back and forth from Zika-afflicted countries.

For most countries, including the United States, travel to the Olympics doesn’t add much to the risk (SN Online: 6/14/16). (Overall, the number of people planning to travel to the Games — up to an estimated 500,000 — is less than 0.25 percent of the total number of travelers in 2015 to countries with Zika, the researchers estimate.)

The new analysis is based on “worst-case scenarios,” the authors say. It does not change current public health warnings: Pregnant women should steer clear of the Games and people should take steps to avoid spreading the virus via sexual transmission when they return home.

The discovery of unknown yeasts hiding in lichens from six continents could shake up a basic idea of what makes up a lichen partnership.

For more than a century, biologists have described a lichen as a fungus growing intimately with some microbes (algae and/or cyanobacteria) that harvest solar energy. The fungus is treated as so important that its name serves as the name for the whole lichen.

Biologists have recognized that more than one fungus can show up in lichen close-ups, but their role hasn’t been clear. Now that may be on the brink of changing.
Fifty-two genera of lichens collected from around the world include a second fungus — single cells, called yeasts, of a previously unknown order now christened Cyphobasidiales. Toby Spribille of the University of Graz in Austria and colleagues report the finding online July 21 in Science.
The first example discovered illustrates why these yeasts might turn out to be more than parasites or mere hitchhikers, says study coauthor John McCutcheon of the University of Montana in Missoula. He and Spribille started the research out of curiosity. They wondered how the yellow, toxin-bearing, thready tangles of lichen called Bryoria tortuosa could have the same fungus and the same algal partner — and thus technically be the same species — as the brown, toxin-poor lichen traditionally called B. fremontii. The researchers looked to see which genes were active in each lichen in hopes that some discrepancy could explain the difference in forms. What the researchers found had nothing to do with the alga or previously known fungus. Instead, ample genetic activity of more abundant yeasts in the toxic B. tortuosa turned out to be the most striking disparity.

After five years of work, the research team now has microscope images of yeast cells embedded in the outer layer, or cortex, of B. tortuosa. Gene-activity results suggest that the yeasts could be what’s making the difference between the forms, maybe even synthesizing toxic vulpinic acid. The yeasts turning up across this widespread class of lichens might explain other mysteries, such as why researchers have largely failed to re-create lichen partnerships in the lab.
It’s a bold hypothesis, but lichenologist Robert Lücking of the Botanic Garden and Botanical Museum Berlin-Dahlem takes the idea of yeast partners seriously. “This will be a huge surprise to the lichenological and mycological community,” he says.

Mosquitoes in Miami now appear to be transmitting Zika virus.

Four cases of Zika infection in Florida were probably acquired via the bite of local mosquitoes, the state’s health department announced July 29. These are the first cases of local transmission of the virus in the continental United States.

“Zika is now here,” Tom Frieden, director of U.S. Centers for Disease Control and Prevention, said in a news briefing July 29.

No mosquitoes trapped yet have tested positive for the virus, but officials suspect Aedes aegypti mosquitoes in a several-block area in north Miami are to blame. “Everything we’ve seen so far indicates that this is mosquito-borne transmission,” Frieden said.

Florida’s small cluster of cases does not necessarily foreshadow an epidemic, he said. The four infected people probably were bitten in early July. Since then, Florida has stepped up efforts to stamp out mosquitoes — including going door-to-door to get rid of standing water and spraying insecticides by truck and by people on foot.

“We believe that widespread transmission in the continental U.S. is unlikely,” Frieden said. “But it’s not impossible.”

Two other mosquito-borne diseases, dengue and chikungunya, have spread locally in Florida in the past. But, Frieden said, those diseases generally dead-end after infecting just one person.

What had two puny arms, lived 90 million years ago and probably chowed down on other dinosaurs? (Hint: It’s not T. rex.)

A new dinosaur discovered in what is now Patagonia had the runty forelimbs of a Tyrannosaurus rex but is no cousin of the giant iconic predator, researchers report July 13 in PLOS ONE.

The new species, Gualicho shinyae, has a close relative in Africa, an analysis of fossils suggests. T. rex’s ancestors, on the other hand, came from Asia.
Gualicho is a “smaller, slimmer, trimmer version of a T. rex,” says study coauthor Peter Makovicky, a paleontologist at the Field Museum in Chicago. It probably weighed about a ton and was longer than a pickup truck.
In 2007, Makovicky’s team discovered Gualicho’s partial skeleton — including those impractical arms. The dinosaur probably caught prey with its huge head, Makovicky says. Though the researchers haven’t dug up a skull yet, tiny arms seem to be a trade-off for a big head. Finding Gualicho’s skull would help nail down that idea, he adds.

Gualicho may have fed on grazers called ornithopods, such as duck-billed dinosaurs. Or perhaps it fed on the long-necked, long-tailed sauropods, which were common in the region. But only the youngsters. Sauropod adults were gigantic, Makovicky says, definitely not prey for a (relatively) little guy like Gualicho.