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2016

Climate Change and the Case of the Shrinking Red Knots
New York Times, May 12, 2016
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Animal migrations combine staggering endurance and exquisite timing.

Consider the odyssey of a bird known as the red knot. Each spring, flocks of the intrepid shorebirds fly up to 9,300 miles from the tropics to the Arctic. As the snow melts, they mate and produce a new generation of chicks. The chicks gorge themselves on insects, and then all the red knots head back south.

“They are there less than two months,” said Jan A. van Gils, an ecologist at the Royal Netherlands Institute for Sea Research. “It’s a very tight schedule.”

It is also a vulnerable one. The precipitous decline of the red knots that winter in West Africa may provide a small but telling parable of the perils of climate change.

Bacteria-Infected Mosquitoes Could Slow Spread of Zika Virus
New York Times, May 4, 2016
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If there is ever a contest for Least Appreciated Creature on Earth, first prize should go to a microbe called Wolbachia.

The bacterium infects millions of invertebrate species, including spiders, shrimps and parasitic worms, as well as 60 percent of all insect species. Once in residence, Wolbachia co-opts its hosts’ reproductive machinery and often greedily shields them from a variety of competing infections.

Ever since the Zika outbreak began in Brazil last year, scientists have suspected that Wolbachia might protect mosquitoes from the virus. Now, researchers have confirmed this hunch, providing the first solid evidence that releasing Wolbachia-infected mosquitoes into the wild could help quell the epidemic.

Foxes That Endure Despite a Lack of Genetic Diversity
New York Times, April 21, 2016
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The Channel Islands, off the coast of Southern California, are a natural laboratory for a particularly adorable experiment in evolution.

A unique species called the island fox has lived there for several thousand years, their bodies shrinking over the generations until now each is smaller than a house cat. Adult island foxes weigh as little as 2.35 pounds.

Now a team of scientists has discovered another way in which island foxes are extraordinary: Genetically, they are nearly identical to one another. In fact, a fox community on one island has set a record for the least genetic variation in a sexually reproducing species.

Oliver A. Ryder, the director of genetics at the San Diego Zoo Institute for Conservation Research, said the new research posed a biological puzzle.

Scientists Unveil New ‘Tree of Life’
New York Times, April 11, 2016
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A team of scientists unveiled a new tree of life on Monday, a diagram outlining the evolution of all living things. The researchers found that bacteria make up most of life’s branches. And they found that much of that diversity has been waiting in plain sight to be discovered, dwelling in river mud and meadow soils.

“It is a momentous discovery — an entire continent of life-forms,” said Eugene V. Koonin of the National Center for Biotechnology Information, who was not involved in the study.

The study was published in the journal Nature Microbiology.

In his 1859 book “On the Origin of Species,” Charles Darwin envisioned evolution like a branching tree. The “great Tree of Life,” he said, “fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

Fathered by the Mailman? It’s Mostly an Urban Legend
New York Times, April 8, 2016
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Five days a week, you can tune into “Paternity Court,” a television show featuring couples embroiled in disputes over fatherhood. It’s entertainment with a very old theme: Uncertainty over paternity goes back a long way in literature. Even Shakespeare and Chaucer cracked wise about cuckolds, who were often depicted wearing horns.

But in a number of recent studies, researchers have found that our obsession with cuckolded fathers is seriously overblown. A number of recent genetic studies challenge the notion that mistaken paternity is commonplace.

“It’s absolutely ridiculous,” said Maarten H.D. Larmuseau, a geneticist at the University of Leuven in Belgium who has led much of this new research.

The term cuckold traditionally refers to the husband of an adulteress, but Dr. Larmuseau and other researchers focus on those cases that produce a child, which scientists politely call “extra-pair paternity.”

Tapeworms and Other Parasites Can Make Good Guests
New York Times, March 31, 2016
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The kakapo, a large flightless parrot that can live 95 years and perhaps longer, is dangerously close to extinction. Once found throughout New Zealand, the population has dwindled to fewer than 150.

Conservation biologists are doing everything they can to keep the kakapo from vanishing. And so, when they discovered a few years ago that a pair of captive kakapos were infected with tapeworms, they did the obvious thing: They dewormed the birds.

Hamish G. Spencer, a geneticist at the University of Otago in New Zealand, thinks that was unwise. If endangered species are going to escape extinction, he argues, they may need parasites to survive.

“Some of these parasites may turn out to be quite good for their hosts,” Dr. Spencer said.

Researchers Find Fish That Walks the Way Land Vertebrates Do
New York Times, March 24, 2016
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It’s one of the most famous chapters in evolution, so familiar that it regularly inspires New Yorker cartoons: Some 375 million years ago, our ancestors emerged from the sea, evolving from swimming fish to vertebrates that walked on land.

Scientists still puzzle over exactly how the transition from sea to land took place. For the most part, they’ve had to rely on information gleaned from fossils of some of the intermediate species.

But now a team of researchers has found a remarkable parallel to one of evolution’s signature events. In a cave in Thailand, they’ve discovered that a blind fish walks the way land vertebrates do.

The waterfall-climbing cave fish, Cryptotora thamicola, has even evolved many of the skeletal features that our ancestors did for walking, including a full-blown pelvis.

Ancestors of Modern Humans Interbred With Extinct Hominins, Study Finds
New York Times, March 17, 2016
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The ancestors of modern humans interbred with Neanderthals and another extinct line of humans known as the Denisovans at least four times in the course of prehistory, according to an analysis of global genomes published Thursday in the journal Science.

The interbreeding may have given modern humans genes that bolstered immunity to pathogens, the authors concluded.

“This is yet another genetic nail in the coffin of our oversimplistic models of human evolution,” said Carles Lalueza-Fox, a research scientist at the Institute of Evolutionary Biology in Barcelona, Spain, who was not involved in the study.

Unappetizing Experiment Explores Tools’ Role in Humans’ Bigger Brains
New York Times, March 9, 2016
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Scientists recently turned Harvard’s Skeletal Biology Laboratory into a pop-up restaurant. It would have fared very badly on Yelp.

Katherine D. Zink, then a graduate student, acted as chef and waitress. First, she attached electrodes to the jaws of diners to record the activity in the muscles they use to chew food. Then she brought out the victuals.

Some volunteers received a three-course vegetarian meal of carrots, yams or beets. In one course, the vegetables were cooked; in the second, they were raw and sliced; in the last course, Dr. Zink simply served raw chunks of plant matter.

Study Finds Surprising Benefit of Viral DNA: Fighting Other Viruses
New York Times, March 3, 2016
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What could be more alien than a virus? It’s a nanobiological weapon — a microscopic protein shell holding a few genes that hijack a cell’s internal machinery, forcing it to make new viruses. The battles we fight with these alien enemies brings malaise, scars and even death.

Yet as foreign as viruses may seem, the boundary between us and them is turning out to be remarkably blurry. We use DNA from viruses to do things that are essential to our own survival, scientists are finding. Somehow, we have managed to domesticate some of these invaders.

A number of viruses replicate by inserting their DNA into our own genes. On rare occasions, their genes get passed down to future generations.

Inside the secret defense systems of giant viruses
STAT, February 29, 2016
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The strangest life forms on Earth just got a lot stranger.

In 2003, Didier Raoult of Aix-Marseille University in France and his colleagues discovered a new kind of virus lurking inside single-celled protozoans. Like other viruses, it couldn’t grow on its own, lacking the biochemical machinery to build proteins and genes. Instead, it had to infect host cells and use their material to produce new viruses.

But this new virus was enormous, measuring hundreds of times bigger than any previously known virus. What’s more, it was far more complex. Typical viruses may have just a few genes. The new virus had over 900 — more than many species of bacteria.

DNA Under the Scope, and a Forensic Tool Under a Cloud
New York Times, February 26, 2016
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Marina Stajic worked for nearly three decades as director of the forensic toxicology lab at the medical examiner’s office in New York City. Last week Dr.. Stajic, 66, filed a lawsuit against the city, claiming she had been forced into retirement last year in part because of a disagreement with her superiors over the accuracy of certain DNA tests.

There is more at stake here than Dr. Stajic’s retirement. The cutting-edge technique at the center of this legal dispute, called low copy number DNA analysis, has transformed not just police work, but also a range of scientific fields including cancer biology, in vitro fertilization, archaeology and evolutionary biology. Yet some of the technique’s applications have triggered scientific controversy.

The medical examiner’s office has become a strong advocate for the technique. It is the only public lab in the United States that uses low copy number DNA to develop profiles for use in criminal cases. But experts have long warned that investigators must take particular care in interpreting these tests: analyzing so few DNA molecules can lead to errors.

In Neanderthals’ DNA, Ancient Humans May Have Left Genetic Mark
New York Times, February 17, 2016
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In 1997, scientists found the first scrap of Neanderthal DNA in a fossil. Since then, they have recovered genetic material, even entire genomes, from a number of Neanderthal bones, and their investigations have yielded a remarkable surprise: Today, 1 to 2 percent of the DNA in non-African people comes from Neanderthals.

That genetic legacy is the result of interbreeding roughly 50,000 years ago between Neanderthals and the common ancestors of Europeans and Asians. Recent studies suggest that Neanderthal genes even influence human health today, contributing to conditions from allergies to depression.

Now scientists have found that the genes flowed both ways. In a study published on Wednesday in Nature, a team of scientists reports that another instance of interbreeding left Neanderthals in Siberia with chunks of human DNA.

A Parasite, Leopards, and a Primate’s Fear and Survival
New York Times, February 11, 2016
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Many of our primate ancestors probably ended up in the bellies of big cats. How else to explain bite marks on the bones of ancient hominins, the apparent gnawing of leopards or other African felines?

Big cats still pose a threat to primates. In one study of chimpanzees in Ivory Coast, for example, scientists estimated that each chimp ran a 30 percent risk of being attacked by a leopard every year.

A new study suggests that the big cats may be getting some tiny help on the hunt. A parasite infecting the brains of some primates, including perhaps our forebears, may make them less wary.

Scientists Investigate How Viruses Like Zika Cause Birth Defects
New York Times, February 8, 2016
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The Zika virus has quickly gained Ebola-level notoriety as it has spread through the Western Hemisphere in recent months. Researchers in Brazil, where it was first detected in May, have linked infections in pregnant women to a condition known as microcephaly: infants born with undersize heads.

Where birth defects are concerned, however, the Zika virus is far from unique. A number of other viruses, such as rubella and cytomegalovirus, pose a serious risk during pregnancy. Researchers have uncovered some important clues about how those pathogens injure fetuses — findings that are now helping to guide research into the potential link between Zika and microcephaly.

“I think we’ll discover a lot of parallels,” said Dr. Mark R. Schleiss, the director of pediatric infectious diseases and immunology at the University of Minnesota Medical School.

DNA Study of First Ancient African Genome Flawed, Researchers Report
New York Times, February 4, 2016
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When scientists first started to figure out how to extract DNA from ancient skeletons, their success was met with astonishment. One minute, scientists were fishing Richard III’s genes from his royal bones, and the next they were showing off DNA retrieved from 5,00-year-old Incan mummies.

The idea that DNA could survive for thousands of years — let alone be reassembled into an entire genome — seemed little short of miraculous.

Despite the field’s rapid advances in recent years, though, ancient DNA is still hard to find and hard to make sense of. Potential errors lurk around every corner. Even little oversights can cause big headaches.

Tribes’ Win in Fight for La Jolla Bones Clouds Hopes for DNA Studies
New York Times, January 29, 2016
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The San Diego Archaeology Center holds a pair of extraordinary skeletons. Dating back about 9,500 years, they are among the oldest human remains ever found in the Americas.

A number of scientists would love to study the bones, using powerful new techniques to extract any surviving DNA.

“These skeletons of such antiquity are so important for helping us understand what happened in the past in North America,” said Brian Kemp, a molecular anthropologist at Washington State University.

Telling Jewels From Junk in DNA
New York Times, January 21, 2016
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When you learned about genes in high school, chances are it went something like this:

Our DNA holds about 20,000 protein-coding genes. To make a protein, a cell makes a copy of the corresponding gene, in the form of a single-stranded molecule called RNA. The cell uses the RNA molecule as a template to make the protein. And then the protein floats off to do its job.

That’s certainly true. But there’s more to the story.

Some of our genes don’t encode proteins; instead, they create long RNA molecules that don’t serve as protein templates. They have different jobs.

Obama’s big bet on science
STAT, January 18, 2016
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To anyone who follows science, President Barack Obama’s announcement of a “moonshot” to cure cancer last week brought on a strong sense of déjà vu. It was, in fact, the third time in less than three years that he has launched a high-profile effort to solve a complex biomedical problem.

A year ago, in his 2015 State of the Union address, Obama announced the Precision Medicine Initiative, which is intended to usher in what he called “a new era of medicine — one that delivers the right treatment at the right time.”

And in an April 2013 speech at the White House, Obama unveiled the BRAIN Initiative, which he described as “the next great American project,” designed to help figure out how the brain works.

“Think about what we could do once we do crack this code,” Obama said. “Imagine if no family had to feel helpless watching a loved one disappear behind the mask of Parkinson’s or struggle in the grip of epilepsy. Imagine if we could reverse traumatic brain injury or PTSD for our veterans who are coming home.”

Searching for Cancer Maps in Free-Floating DNA
New York Times, January 14, 2016
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Loose pieces of DNA course through our veins. As cells in our body die, they cast off fragments of genes, some of which end up in the bloodstream, saliva and urine.

Cell-free DNA is like a message in a bottle, delivering secrets about what’s happening inside our bodies. Pregnant women, for example, carry cell-free DNA from their fetuses. A test that analyzes fetal DNA has proved to be more accurate in screening for Down syndrome than standard blood tests.

In 2012, Jay Shendure, a geneticist at the University of Washington, and his colleagues were able to reconstruct the entire genome of a fetus from cell-free DNA in a pregnant woman’s saliva. A team of Stanford University researchers collected DNA fragments from the blood of patients who had received heart transplants and managed to find DNA from their donated hearts. (Tellingly, levels were highest in patients who were rejecting their hearts.)

U.S. Restricts Movement of Salamanders, for Their Own Good
New York Times, January 12, 2016
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The Fish and Wildlife Service is barring the door against 201 species of salamanders, making it illegal to import them or move them across state lines, the agency announced on Tuesday. Scientists hope the ban will help prevent a devastating outbreak from driving native salamander species extinct.

In 2013, scientists in the Netherlands discovered a species of fungus infecting native fire salamanders. Later research revealed that the fungus, called Batrachochytrium salamandrivorans, or Bsal, was carried by Asian salamanders that were imported into Europe as pets. While the fungus was harmless to the Asian amphibians, it was lethal to the Dutch ones.

Although Bsal has continued to spread in Europe, there is no sign that it has taken hold in the United States. But if the vigorous pet trade goes unchecked, scientists fear that it is only a matter of time before Bsal threatens some of the 190 salamander species that live in the United States. The Fish and Wildlife Service estimated that from 2004 to 2014, nearly 2.5 million live salamanders, representing 59 species, were imported into the United States.

Genetic Flip Helped Organisms Go From One Cell to Many
New York Times, January 12, 2016
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Narwhals and newts, eagles and eagle rays — the diversity of animal forms never ceases to amaze. At the root of this spectacular diversity is the fact that all animals are made up of many cells — in our case, about 37 trillion of them. As an animal develops from a fertilized egg, its cells may diversify into a seemingly limitless range of types and tissues, from tusks to feathers to brains.

The transition from our single-celled ancestors to the first multicellular animals occurred about 800 million years ago, but scientists aren’t sure how it happened. In a study published in the journal eLife, a team of researchers tackles this mystery in a new way.

The researchers resurrected ancient molecules that once helped single-celled organisms thrive, then recreated the mutations that helped them build multicellular bodies.

Scientists unearth bacteria from stomach of 5,300-year-old iceman
STAT, January 7, 2016
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In 1991, a German couple hiking in the Alps came across the body of a middle-aged man lying face down in a snowfield. It took days for a recovery team to hack him out of the ice and haul him by helicopter and truck to a lab in Austria. There, scientists determined the man had died 5,300 years ago.

Ötzi, as the man was nicknamed (after the nearby Ötztal Valley), has kept scientists very busy for the past 24 years. They’ve even built an entire research center — the Institute for Mummies and the Iceman in Bolzano, Italy — to house Ötzi and study him. They’ve slowly extracted one clue after another about how Ötzi died and, more importantly, how he lived.

But Ötzi still has much left to tell us. On Thursday, researchers reported in the journal Science that they have reconstructed the entire genome of a species of bacteria that lived in his stomach. Now Ötzi may be able to tell us not just about ancient humans. He can tell us about ancient microbiomes, too.

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