Unlocking Pandora’s Virus

By most standards, viruses aren’t alive. They have genetic material, yes, and they reproduce, but a true living organism must have some form of metabolism – it must be able to build up and break down chemicals on its own. Viruses have no metabolism. They don’t make their own proteins, and they can only reproduce by enslaving host cells into manufacturing copies of themselves, and then forcing the host cell to self-destruct and unleash the new viruses. However, researchers Nadége Philippe and colleagues have recently discovered massive, bacteria-sized viruses with genomes larger than those of any viruses known heretofore, and this discovery could change our understanding not only of viruses, but of the tree of life.

These newly discovered viruses are the largest found to date, but they are not the first giant viruses ever found. A decade ago, researchers Bernard La Scola and colleagues discovered the Mimivirus, which has a genome of 1.18 million bases. Since then, researchers have found similar “megaviruses,” which seem to share certain structural and functional peculiarities. Now, Philippe and colleagues have found two huge viruses, so very unique that they have been dubbed the “Pandoraviruses.”

“It’s like finding a sasquatch.” – Elodie Ghedin, virologist at University of Pittsburg, PA1

Pandoravirus salinus and Pandoravirus dulcis weigh in at 2.47 and 1.91 million base pairs long, respectively, and P. salinus is 1 micron long – one hundred times the size of most viruses! So, if these viruses are so large, why haven’t researchers seen them before now? Actually, they may have done so unknowingly. The discoverers suspect that people have seen Pandoraviruses before, but assumed that they were bacteria, since they were much larger than any known viruses. In fact, Pandoraviruses may be quite common – the researchers found one in Chile and one in Australia, and they could well exist in many other places.

Pandoraviruses are viruses, without a doubt: they do not produce their own proteins, they depend on living cells for replication, and they share some genes with other large viruses. Morphologically and genetically, however, Pandoraviruses are unique. Unlike most large viruses, they require activities in the host cell’s nucleus, lack many core viral genes, and have relatively few introns (pieces of a gene that are spliced out of the final gene product) in their genomes.

As the researchers stated in their paper, “93% of Pandoraviruses genes resemble nothing known, [and] their origin cannot be traced back to any known cellular lineage.”2 Their almost alien genome, coupled with the huge size of the genome, may even suggest the existence of a fourth domain of life, in addition to Bacteria, Archaea, and Eukaryota. Perhaps, the researchers suggest, early life was extraordinarily diverse, consisting of many different domains that evolved, existed, and eventually died out, leaving only the three that we know today – and maybe a fourth that we are just on the frontier of discovering.


References:

1Pennisi, Elizabeth. “Ever-Bigger Viruses Shake Tree of Life.” Science Vol. 341, Issue 6143, pp. 226-227 (2013). DOI: 10.1126/science.341.6143.226. http://www.sciencemag.org/content/341/6143/226

2Philippe, Nadége, Matthieu Legendre, Gabriel Doutre, Yohann Couté, Olivier Poirot, Magali Lescot, Defne Arslan, Virginie Seltzer, Lionel Bertaux, Christophe Bruley, Jérome Garin, Jean-Michel Claverie, Chantal Abergel. “Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes.” Science Vol. 341, Issue 6143, pp. 281-286 (2013). DOI: 10.1126/science.1239181. http://www.sciencemag.org/content/341/6143/281

Advertisements

The Seeds of Plant Domestication

Humans have been cultivating domesticated plants for food for thousands of years, but when and where did agriculture begin? According to archaeological findings scattered across much of the Middle East, ancient people actually developed plant domestication in several places at once.

A recent Science article by Riehl, et al. describes archaeological findings at a site called Chogha Golan, which was occupied from about 12,000 to 9,800 years ago. Located in the foothills of Iran’s Zagros Mountains, Chogha Golan is one of a number of contemporaneous sites throughout the “Fertile Crescent” region. Many of these sites show signs of plant cultivation emerging about 10,500 to 11,500 years ago.

Researchers at the Chogha Golan site studied the contents of successive layers of strata, including the remnants of ancient plants, to determine biological change over time. The plant remains buried at Chogha Golan clearly document the process of domestication, from collection of wild-growing seeds to the cultivation of morphologically distinct, domesticated grains.

Domestication – plant or animal – is a gradual process. According to the archaeological record, humans started out by gathering wild plants, like the seeds of wild barley, wheat, or lentils, for food. Over time, people began to practice plant “management” – not quite agriculture, but a step beyond simple gathering – while selecting for those plants that have the most advantageous characteristics. Over hundreds of years of selective cultivation of the plants with the biggest seeds, stronger resilience, or whatever other characteristic people preferred, these cultivated varieties became distinct from their wild counterparts.

Interestingly, the archaeological evidence shows different varieties of domesticated plants emerging at different sites. Groups of ancient people probably developed their own local crops, domesticated from various species of wild plants, which created a wide variety of distinct, locally-developed domesticated plants.

The domestication of plants was a harbinger of huge changes to come for ancient humans. Chogha Golan shows an excellent record of this development – and it looks like it was only one of several agricultural origin points.

References:

Riehl, Simone, Mohsen Zeidi, Nicholas J. Conard. “Emergence of Agriculture in the Foothills of the Zagros Mountains of Iran.” Science Vol. 341, Issue 6141, pp. 65-67. http://www.sciencemag.org/content/341/6141/65.

Willcox, George. “The Roots of Cultivation in Southwestern Asia.” Science Vol. 341, Issue 6141, pp. 39-40. http://www.sciencemag.org/content/341/6141/39.

Cheetahs on the Run

Cheetahs have been making the rounds of science news lately. Famous for their speed, they have in the past been clocked at 29 meters per second (nearly 65 miles per hour), making them the fastest animals on land – but that’s old news. A new study by A.M. Wilson and colleagues delved deep into the mechanics of the hunt with five wild cheetahs in Botswana, and their findings were a little surprising.

The cheetah still holds onto its place as the fastest land animal – the researchers recorded an impressive top speed of 25.9 m/s, or about 58 mph – but it turns out that the cheetah’s dexterity and maneuverability, not its phenomenal speed, hold the secret to its hunting success.

Wilson, et al. outfitted five wild cheetahs with GPS tracking collars that also contained accelerometers, to capture and transmit data on the cheetahs’ movements. The researchers used the data to reconstruct the speed, acceleration, and maneuvering in each of 367 runs over the course of 17 months; they also tracked the terrain of each hunting attempt by overlaying the GPS data onto Google Earth.

When most people think of a running cheetah, they probably envision a high-speed chase through open grasslands. In reality, about half of the runs recorded in this experiment took place among shrubs or dense vegetation, and cheetahs hunted about as successfully in these environments as they did on open ground. Although each of the five cheetahs reached speeds of 20 m/s (about 45 mph) or higher at least once during the 17 month study, during most hunts they only got up to a leisurely 14.9 m/s (about 33 mph) – although that would still leave Olympic sprinters in the dust.

According to this study, a cheetah on the chase only runs at top speed for a second or two; once it pulls near its quarry, the cheetah decelerates, and this is where the chase reaches its critical moments. At a slower speed, the cheetah can employ its maneuvering prowess, using large claws, high-traction footpads, and a low posture to grip the ground and make sharp, fast turns, in order to subdue its agile prey. The deceleration phase of the chase is the most important – paradoxically, the researchers found that greater deceleration was correlated with greater likelihood of catching the prey in the end. Maneuverability is more important than speed in the final moments of a chase.

Cheetahs are undeniably powerful runners. The fibers in the running muscles of wild cheetahs shorten faster than fibers in similar-sized muscles in other running animals – the researchers mention racing greyhounds and horses, for comparison – giving cheetahs extraordinary power of acceleration. But in the end, the key to the cheetah’s chase isn’t in sheer power. It’s all in the control.

Recent Research: Biodiversity

These days, biodiversity loss is one of the primary hot-button issues in conservation, and loss of biodiversity has been an issue of concern for quite some time. So, today I’m going to talk about it a little bit, in light of a recent research article published in Ecology Letters.

Biodiversity is important. It’s a major indicator of the health of an ecosystem, and it’s also an important contributor to the ecosystem’s well-being. Ecosystems with low biodiversity – either inhabited by only a small number of species, or dominated by a few species, with other species being relegated to marginal roles – tend to be more susceptible to other environmental threats, like pollution and temperature changes. Ecosystems that lose biodiversity become less stable and less resilient against further damage.

When trying to understand the current state of biodiversity and gauge the effectiveness of current conservation efforts, it’s important to know how things have been in the past, and what changes have taken place over the long term. To that end, researchers Carvalheiro, et al. conducted a broad analysis of insect and plant biodiversity, using data collected over the course of six decades.

Carvalheiro, et al. looked at data on the biodiversity of plants and flower-visiting insects (bees, hoverflies, and butterflies) in Great Britain, the Netherlands, and Belgium, from 1950 to 2009. The study examined biodiversity over a large spectrum of spatial ranges, from 10 x 10 kilometer chunks at the smallest to entire countries at the large end of the scale. This allowed the researchers to compare patterns of change at local, regional, and nation-wide levels.

Great Britain, the Netherlands, and Belgium have instituted fairly rigorous conservation efforts in the past few decades, and the findings in this study reflect positively on those efforts. They indicate that biodiversity fell most precipitously from about 1950 to 1990, coinciding with a period of rapid habitat loss. However, since about 1990, an upturn in public awareness and the institution of good conservation measures slowed the loss of biodiversity in these countries. That’s not to say that biodiversity isn’t still declining – it is – but this analysis tells us that careful conservation efforts can be successful in slowing the loss of biodiversity.

Results aside, the methods used for analysis in this study were pretty interesting in and of themselves. The researchers didn’t go out and collect data themselves. Instead, they collated a huge tangle of existing data – gathered with a variety of different methods, sample sizes, and areas of interest – and performed a variety of statistical tests to decipher patterns of change over 20-year chunks of time 1950 to the present. Despite the challenges of working with non-standardized data, the researchers were able to glean some meaningful and highly robust patterns. Nevertheless, they do note that consistent data collection over time is important for long-term ecological study.

The researchers conclude on a note of hope. Biodiversity loss has become less severe in response to well-managed conservation efforts in Great Britain, the Netherlands, and Belgium. Conservation efforts are valuable, worthwhile endeavors; instituting them in other countries, and continuing them where they already exist, could further help counteract today’s rapid biodiversity loss.

Carvalheiro, Luisa Gigante, William E. Kunin, Petr Keil, Jesus Aguirre-Gutiérrez, William Nicolaas Ellis, Richard Fox, Quentin Groom, Stephan Hennekens, Wouter Van Landuyt, Dirk Maes, Frank Van de Meutter, Denis Michez, Pierre Rasmont, Baudewijn Ode, Simon Geoffrey Potts, Menno Reemer, Stuart Paul Masson Roberts, Joop Shaminée, Michiel F. WallisDeVries, Jacobus Christiaan Biesmeijer. “Species richness declines and biotic homogenization have slowed down for NW-European pollinators and plants.” Ecology Letters. Published online May 21, 2013. Doi: 10.1111/ele.12121

Recent Research: Why Do Dogs Yawn?

First things first – I would like to note that I could not read this research article without yawning (though my dog seemed entirely unaffected).

To all dog owners out there – researchers have long been aware of how closely attuned domestic dogs are to human moods. Is it possible that this extraordinary connection, developed over thousands of years of dog-human co-evolution, extends to the phenomenon of contagious yawning?

In humans, yawning appears to have a social component; more empathetic humans tend to be more susceptible to yawn contagion, and contagious yawning emerges alongside the capacity for empathy and a theory of mind in early human development. However, contagious yawning isn’t unique to humans – researchers have observed it in many nonhuman primates and dogs as well, to varying extents. But do animals exhibit contagious yawning for the same reasons humans do? In a recent study published in Animal Cognition, researchers Buttner and Strasser set out to determine the impetus behind this phenomenon in dogs.

When they began their research, Buttner and Strasser had two possibilities in mind. One, dogs might indeed exhibit contagious yawning as a form of social interaction with humans. On the other hand, contagious yawning might actually be a form of stress yawning. Many animals, including dogs, yawn in response to stressful or uncomfortable situations. We humans can easily mistake a stress yawn for a sleepy yawn, and maybe that works the other way as well: dogs might mistake a sleepy human for a stressed one, then get stressed, and yawn in response.

The researchers used 60 shelter dogs in an experiment to determine whether each would yawn in response to a human yawning, in comparison with a control trial in which a researcher simply opened and closed her mouth. The researchers also evaluated the social-cognitive prowess of each dog – they presented each dog with a choice of two containers (one with a treat, one empty) and then gestured and looked pointedly at the treat-containing box. Dogs more closely attuned to human signals would choose the correct container more frequently, thus giving an indication of the dog’s social-cognitive ability. The researchers also estimated each dog’s stress level by measuring the levels of cortisol, a stress hormone, in a sample of each dog’s saliva. This experimental setup would, ideally, allow the researchers to determine possible links between social cognition, stress levels, and contagious yawning.

As it turned out, the results weren’t so simple to interpret. Only 12 dogs seemed to exhibit contagious yawning (that is, they yawned in response to a yawning human, but did not yawn in the control trial), and there was no overall trend of contagious yawning. These dogs did not score any better on the social-cognitive test than the other dogs, but they did have elevated cortisol levels following the experiment (but not beforehand.) From this information, Buttner and Strasser concluded that apparent contagious yawning in dogs was probably a result of stress, not empathetic social interaction. The 12 dogs that showed contagious yawning probably perceived the human yawning as a sign of stress, thus increasing their own stress levels and causing them to yawn in response.

So, next time I see my own (very spoiled) mutt yawn, perhaps I should give her a tummy rub.

Relaxed dog lying on couch.

I wouldn’t want her to get too stressed out.

References:

Buttner, Alicia, and Rosemary Strasser. “Contagious yawning, social cognition, and arousal: an investigation of the processes underlying shelter dogs’ responses to human yawns.” Animal Cognition, May 2013 (published online). DOI 10.1007/s10071-013-0641-z.