“Some Chimpanzees Have Entered Stone Age.” Scientists On 3 Continents Make Surprising Discovery.
In the rainforests of west Africa, the woodlands of Brazil and the beaches of Thailand, archaeologists have stumbled upon some fascinating stone tools.
What sets them apart is not the workmanship or their antiquity: they belong to the same age as the Egyptian pyramids.
The tools are crude. A chimpanzee or monkey stone hammer is hardly a work of art to rival the beauty of an ancient human hand axe. But that’s not the point. These primates have developed a culture that makes routine use of a stone-based technology. That means they have entered the Stone Age.
The chimpanzees of west Africa had used these tools in a cruder way, to crack open nuts for example.
A few years ago, biologists believed only humans could make extensive use of tools. However, recent discovery falsifies this claim.Our closest living relatives might be similar to us, more than we could have ever imagined. An article published in Oxford journals suggests monkeys and chimpanzees have a flair for reading each other’s facial expressions. This certainly calls for a re-assessment of primates.
Countries like New Zealand and the United Kingdom consider experiments on apes, illegal. Spain for example, allots them some human rights. In the U.S. too, there are reforms taking place in this area. A trial pending in New York courts wants chimpanzees to be granted full human rights.
If nothing else, we should certainly be compassionate and sympathetic to our primate cousins.
NIH/National Institute of Allergy and Infectious Diseases
Summary:
To determine how long Ebola virus could remain infectious in a body after death, scientists sampled deceased Ebola-infected monkeys and discovered the virus remained viable for at least seven days. They also detected non-infectious viral RNA for up to 70 days post-mortem.
Abstract
The ongoing Ebola virus outbreak in West Africa has highlighted questions regarding stability of the virus and detection of RNA from corpses. We used Ebola virus–infected macaques to model humans who died of Ebola virus disease. Viable virus was isolated 7 days posteuthanasia; viral RNA was detectable for 10 weeks.
Joseph Prescott, Trenton Bushmaker, Robert Fischer, Kerri Miazgowicz, Seth Judson, and Vincent J. Munster
Author affiliations: National Institutes of Health, Hamilton, Montana, USA
Research:
The ongoing outbreak of Ebola virus (EBOV) infection in West Africa highlights several questions, including fundamental questions surrounding human-to-human transmission and stability of the virus. More than 20,000 cases of EBOV disease (EVD) have been reported, and >8,000 deaths have been documented (1). Human-to-human transmission is the principal feature in EBOV outbreaks; virus is transmitted from symptomatic persons or contaminated corpses or by contact with objects acting as fomites (2). Contact with corpses during mourning and funeral practices, which can include bathing the body and rinsing family members with the water, or during the removal and transportation of bodies by burial teams has resulted in numerous infections (3).
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Assessing the stability of corpse-associated virus and determining the most efficient sampling methods for diagnostics will clarify the safest practices for handling bodies and the best methods for determining whether a person has died of EVD and presents a risk for transmission. To facilitate diagnostic efforts, we studied nonhuman primates who died of EVD to examine stability of the virus within tissues and on body surfaces to determine the potential for transmission, and the presence of viral RNA associated with corpses.
The Study
We studied 5 cynomolgus macaques previously included in EBOV pathogenesis studies and euthanized because of signs of EVD and viremia. Two animals were infected with EBOV-Mayinga and 3 with a current outbreak isolate (Makona-WPGC07) (4).
Immediately after euthanasia, multiple samples were collected: oral, nasal, ocular, urogenital, rectal, skin, and blood (pooled in the body cavity) swab samples and tissue biopsy specimens: from the liver, spleen, lung, and muscle. Swabs were placed in 1 mL of culture medium and tissue samples were placed in 500 μL of RNAlater (QIAGEN, Valencia, CA, USA), or an empty vial for titration, before freezing at −80°C. Carcasses were placed in vented plastic containers in an environmental chamber at 27°C and 80% relative humidity throughout the study to mimic conditions in West Africa (5). At the indicated time points (<9 days for 2 animals and 10 weeks for 3 animals), swab and tissue samples were obtained and used for EBOV titration on Vero E6 cells to quantify virus or for quantitative reverse transcription PCR (qRT-PCR) (40 cycles) to measure viral RNA, as reported (6,7).
Viral RNA was detectible in all swab samples and tissue biopsy specimens at multiple time points (Figure 1). For swab samples (Figure 1, panel A), the highest amount of viral RNA was in oral, nasal, and blood samples; oral and blood swab specimens consistently showed positive results for all animals until week 4 for oral specimens and week 3 for blood, when 1 animal was negative for each specimen type. Furthermore, oral swab specimens had the highest amount of viral RNA after the first 2 weeks of sampling, although after the 4-week sampling time point, some samples from individual animals were negative.
In all samples, RNA was detectable sporadically for the entire 10-week period, except for blood, which had positive results for <9 weeks. Tissue samples were more consistently positive within the first few weeks after euthanasia (Figure 1, panel B). All samples from the liver and lung were positive for the first 3 weeks, and spleen samples were positive for the first 4 weeks, at which time lung and spleen samples were no longer tested because of decay and scarcity of tissue. Muscle sample results were sporadic: a sample from 1 animal was negative at the 1-day time point and at several times throughout sampling.
Figure 1. Presence and stability of Ebola virus RNA in deceased cynomolgus macaques. Swab (A) and tissue (B) specimen samples were obtained at the indicated time points, and viral RNA was isolated and used in a 1-step quantitative reverse transcription PCR with a primer/probe set specific for the nucleoprotein gene and standards consisting of known nucleoprotein gene copy numbers. Line plots show means of positive samples from 5 animals up to the 7 day time point and from 3 animals thereafter. Error bars indicate SD, and - indicates time points at which ≥1 animal had undetectable levels of viral RNA at that time point. Absence of a hyphen indicates that all animals had detectible levels of viral RNA.
Figure 2. Efficiency of Ebola virus isolation from deceased cynomolgus macaques. Swab (A) and tissue (B) specimen samples were obtained at the indicated time points, and virus isolation was attempted on Vero E6 cells. Cells were inoculated in triplicate with serial dilutions of inoculum from swab specimens placed in 1 mL of medium or tissues homogenized in 1 mL of medium. The 50% tissue culture infectious dose (TCID50) was calculated by using the Spearman-Karber method (8). Line plots show means of positive samples from 5 animals to the day 9 time point. Error bars indicate SD.
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Viable EBOV was variably isolated from swab from all sampling sites. Among blood samples, those from the body cavity had the highest virus titer (2 × 105 50% tissue culture infectious doses/mL) and longest-lasting isolatable virus (7 days posteuthanasia) (Figure 2, panel A). Consistent with the qRT-PCR results, for swab samples, oral and nasal sample titers were highest, followed by those for blood samples, and relatively high titers were observed <4 days posteuthanasia (Figure 2, panel B). Similar to the qRT-PCR experiments, virus titers were higher in tissue samples than in swab samples but were not as sustained; all tissue samples were positive at day 3 posteuthanasia but negative by day 4.
Conclusions
The efficiency of detecting EBOV from corpse samples has not been systematically studied; this information is needed for interpreting results for diagnostic samples for epidemiologic efforts during outbreaks. We showed that viral RNA is readily detectable from oral and blood swab specimens for <3 weeks postmortem from a monkey carcass that was viremic at the time of death, in environmental conditions similar to those during current outbreak (5).
The stability of the target RNA used for RT-PCR is more robust than that of viable virus because degradation of any part of the genome (or proteins and lipids) would compromise the ability of the virus to replicate. Thus, the ability to isolate replicating virus in cell culture from postmortem materials was much less sensitive than detection of viral RNA by qRT-PCR. The sensitivity for quantitating infectious virus is probably lowered because of limitations in isolation efficiency on cell culture and necessary dilutions of tissues for homogenization for titration. Nonetheless, we detected viable virus <7 days posteuthanasia in swab specimens and 3 days in tissues, and showed that infectious virus is present at least until these times. Because virus titers decreased relatively sharply, despite sensitivity issues, it is unlikely that viable virus persists for times longer than we measured.
Humans who die of EVD typically have high levels of viremia, suggesting that most fresh corpses contain high levels of infectious virus, similar to the macaques in this study (9). Furthermore, family members exposed to EVD patients during late stages of disease or who had contact with deceased patients have a high risk for infection (2). The presence of viable EBOV and viral RNA in body fluids of EVD patients has been studied, and oral swabbing has been shown to be effective for diagnosis of EVD by RT-PCR compared with testing of serum samples from the same persons (10,11). However, detection limits for diagnostic swab samples are unknown for early phases of EVD, and blood sampling is probably more sensitive and reliable for antemortem diagnostics and should be used whenever possible, which has also been shown with closely related Marburg virus (12).
Although these studies included data from outbreak situations, they are limited in their sampling numbers, swabbing surfaces, and time course, and it is unknown how predictive they are for samples collected postmortem. It is essential to stress that swab samples should be obtained by vigorous sampling to acquire sufficient biologic material for testing, and development of a quality-control PCR target (housekeeping gene target) would be beneficial for sample integrity assessment, which is a limitation of this study.
In summary, we present postmortem serial sampling data for EBOV-infected animals in a controlled environment. Our results show that the EBOV RT-PCR RNA target is highly stable, swabbing upper respiratory mucosa is efficient for obtaining samples for diagnostics, and tissue biopsies are no more effective than simple swabbing for virus detection. These results will directly aid interpretation of epidemiologic data collected for human corpses by determining whether a person had EVD at the time of death and whether contact tracing should be initiated. Furthermore, viable virus can persist for >7 days on surfaces of bodies, confirming that transmission from deceased persons is possible for an extended period after death. These data are also applicable for interpreting samples collected from remains of wildlife infected with EBOV, especially nonhuman primates, and to assess risks for handling these carcasses.
Dr. Prescott is a research fellow in the Virus Ecology Unit at Rocky Mountain Laboratories, Hamilton, Montana. He is currently involved in the Ebola virus outbreak at the combined Centers for Disease Control and Prevention/National Institutes of Health diagnostic laboratory, Monrovia, Liberia. His research interests include the immune response, transmission, and modeling of viral hemorrhagic fevers.
Acknowledgments
We thank Darryl Falzarano and Andrea Marzi for use of animal carcasses upon completion of their studies and Anita Mora for providing assistance with graphics.
This study was supported by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health.
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Suggested citation for this article: Prescott J, Bushmaker T, Fischer R, Miazgowicz K, Judson S, Munster VJ. Postmortem stability of Ebola virus. Emerg Infect Dis. 2015 May [date cited]. http://dx.doi.org/10.3201/eid2105.150041
You'll probably hear the parrotfish before you see them. The animals chomp through solid rock and coral with fused beaks. When you're snorkeling on one of Hawaii's reefs, the noise is unmistakable. Crunch, crunch, crunch.
To watch the grazers at work, it would be easy to mistake parrotfish for the bad guys. Their chompers scar the reef with deep gouges and reduce what was once hard stone into nothing more than a cloud of sand, squirted unceremoniously out the fish's backsides.
Where does it all come from? In Hawaii, where beaches are constantly ranked the best in the world, a significant portion of that pristine, white, beautiful sand is actually poop.
Yep, poop.
Parrotfishes, or uhu in Hawaiian, are key players in regulating algae and reef life. Their parrot-like beaks and fused-together teeth are used for scraping and biting dead coral, while additional teeth in their throats help to break it all down into sand. Snorkelers can actually hear them chomping or see the bite marks they leave on rocks.
Because parrotfishes don’t have stomachs, their meals pass straight through the long intestine, exploding in a cloud of sand out the backdoor. Larger parrotfish are like sand factories, producing as much as 700 pounds of sand per year. For Oahu’s snorkeling hot spot, Hanauma Bay (where a few hundred parrotfish graze), that means hundreds of tons of fish-made sand per year.
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Worms, sponges, and oysters also produce Pacific ocean sand, but no animal is as proficient as the parrotfish, a badge of honor it has held for centuries. According to the Maui Ocean Center, the native Hawaiian name for the female redlip parrotfish translates to “loose bowels.”
But according to Darla White, a marine scientist with Hawaii's Division of Aquatic Resources (DAR), parrotfish are actually integral to both the reefs' day-to-day health and long-term resiliency.
"It's all about real estate on the reef," says White. "Every living thing is just looking for space, and each bite the parrotfish takes opens up an opportunity for coral larvae to settle in."
Those bites are more valuable now than ever. Coral reefs thrive on clean, clear, low-nutrient water. But runoff from the islands contains fertilizers from farms and lawn care, and these excess nutrients cause both naturally occurring and invasive algae to go haywire. Before you know it, all the available real estate is shellacked with fast-growing algae, and the extremely slow-growing coral can't colonize these surfaces. Parrotfish keep these blooms in check by beak-biting straight down to the substrate.
(Jeffrey L. Rotman/Corbis)
Unfortunately for the reefs, parrotfish are freaking delicious. They are also beautiful. And that means the fish are a prized target of both subsistence-, sport-, and even some commercial-fisherman. Most herbivores don't take a hook, but spearfishing and nets work well enough. Add to this the unfortunate fact that many species of parrotfish are also really heavy sleepers, and you can see there's a problem. At night, they secrete a layer of mucous across their body that's thought to protect them from parasites and perhaps keep predators from sniffing them out. But it does nothing to prevent unscrupulous night divers from plucking the fishies from the reef like cooling pies off the proverbial windowsill.
To combat these pressures, White and her colleagues at the DAR designated part of the reef along West Maui's coast as the Kahekili Herbivore Fisheries Management Area in 2009. This made it illegal to kill or injure several species of herbivorous fish, including parrotfish, surgeonfish, and sea chubs, as well as sea urchins anywhere in the preserve. After several years of watching and waiting, they analyzed the results in 2012 and reported that parrotfish biomass had actually doubled. What's more, they found a strong positive relationship between total parrotfish biomass and the amount of coral growing on the reef.
Problem is, White says only 1 percent of Hawaii's coral reefs are under this kind of protection — which means most of the region's parrotfish are getting picked off before they can even reach full size. And this is a problem, because when it comes to parrotfish reproduction, size matters.
Hawaii's parrotfish live in harems — one guy to half a dozen or more gals — but every fish begins its life as a female. If the harem's male gets speared by a diver or otherwise decides to go out for a pack of smokes, the most dominant female can, over time, turn herself into a male.
You can tell when a female is going through this miraculous transformation because she will start to change from a dull gray to the more striking blues, greens, and purples of parrotfish males. And because the change doesn't just simply happen overnight, it's not uncommon to see a parrotfish swimming around that's half gray (female) and half green (male).
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Before the color change is complete, some species of parrotfish use their half-and-half status as camouflage, deftly sneaking into harems that still have a super-male and fertilizing the females' eggs before the alpha fish knows what's up. (Note: This is known as "streaking" (through the Quad), and it's a good way to get your ass beat. Parrotfish are highly territorial.)
It should come as no surprise then that the biggest, beefiest, most flamboyantly colored parrotfish — which you now know to be exclusively male — are at the highest risk of human predation. This makes repopulating the reefs with algae-eaters all the more difficult, since males aren't simply hatched — they're built, over time and circumstance.
"It's human nature to try to fix something once it's broken," says White, regarding the state of Hawaii's reefs. "But to try to fix an entire ecosystem, especially one that's in the water? It's not easy."
But that won't stop them from trying. The DAR has partnered up with organizations like the Coral Reef Alliance and local businesses like The Snorkel Store to educate policymakers and actually get them in the water to see what's at stake. They've worked with hotels and landscapers to raise awareness about runoff. And the Coral Reef Alliance established something called the Fish-Friendly Business Alliance, which promotes businesses that don't sell fish food — because if grazers are eating pellets out of the hands of tourists, they don't have to eat as much algae.
Whether it's reducing algae and pollution or giving parrotfish populations a chance to rebound, the goal is to return Hawaii's reefs back to some semblance of balance — or lokahi, as the locals might say. Here on the mainland, I think that translates to, "You break it, you bought it."
For all their virtual accomplishments, gamers aren't feted for their real-world usefulness. But that perception might be about to change, thanks to a new wave of games that let players with little or no scientific knowledge tackle some of science's biggest problems. And gamers are already proving their worth
In 2011, people playingFoldit, an online puzzle game about protein folding,resolved the structure of an enzyme that causes an Aids-like disease in monkeys. Researchers had been working on the problem for 13 years. The gamers solved it in three weeks.
A year later, people playing an astronomy game called Planet Hunters found a curious planet with four stars in its system, and to date, they've discovered 40 planets that could potentially support life, all of which had been previously missed by professional astronomers.
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On paper, gamers and scientists make a bizarre union. But in reality, their two worlds aren't leagues apart: both involve solving problems within a given set of rules. Genetic analysis, for instance, is about finding sequences and patterns among seemingly random clusters of data. Frame the analysis as a pattern-spotting game that looks like Candy Crush, and, while aligning patterns and scoring points, players can also be hunting for mutations that cause cancer, Alzheimer's disease or diabetes.
"Our brains are geared up to recognise patterns," says Erinma Ochu, a neuroscientist and Wellcome Trust Engagement Fellow at the University of Manchester, explaining why scientists are turning to gamers for help, "and we do it better than computers. This is a new way of working for scientists, but as long as they learn how to trust games developers to do what they do best – make great games – then they can have thousands of people from all around the world working on their data."
The potential is huge. As a planet we spend 3bn hours a week playing online games, and if even a fraction of that time can be harnessed for science, laboratories around the world would have access to some rather impressive cognitive machinery. The trick, though, is to make the games as playable and addictive as possible – the more plays a game gets, the larger the dataset generated and the more robust the findings.
Zoran Popovic is the director of the Centre for Game Science at the University of Washington and is the co-creator of Foldit. He explains that while successfully entertaining the masses, these games are meeting a very pressing need: science needs more people.
"No matter what academic process we go through," he says, "we end up whittling down a huge population of middle schoolers interested in science to some small percentage that actually survive the PhD process and end up doing science. Considering how many open scientific problems there are, and how few scientists there are, it's clear that we're stymied in the progress of science simply by the number of able and interested people out there."
Through Foldit alone he estimates that the number of people working on protein folding around the world has increased by four times in the past two and a half years. Zooniverse, a website that offers a wide range of online citizen-science projects including Planet Hunters, estimates that, together, their volunteers give them a virtual office block of 600 people working around the clock on scientific questions.
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If you want to join in and become a fully fledged citizen scientist, or if you just want to contribute to science on your way to work, here are 10 of the best games around. But be careful, because they're all pretty addictive. But that shouldn't be a surprise… they've been designed, by scientists, to be so.
It's tough to know what to like more about Phylo, the colourful puzzles or the jazzy music. Either way, their combination makes the complicated world of bioinformatics, or more specifically multiple sequence alignment optimisation, incredibly accessible. By pushing around coloured blocks into patterns, you're actually aligning DNA from different animal species, helping research into genetic diseases by identifying disease-associated or mutated genes. Beat algorithms and other players by aligning the patterns and minimising gaps as much as possible.
A bewitchingly addictive puzzle game. Use shakes, tweaks, wiggles and rubber bands to twist and contort your protein into its most stable and thus highest-scoring shape. Each puzzle is a bit like a Rubik's cube in that there is only one perfect solution to each structure, but there are various intermediate or less stable ones in between. Work your way up the high scores tables by joining groups and sharing puzzle solutions with other players. En route, you'll help researchers discover more about the rules that govern the shape, and therefore function, of proteins, helping the fight against cancer, Alzheimer's disease and HIV/Aids.
If you loved Monkey Island, this game, a visually beautiful point-and-click adventure game with a compelling narrative, is for you. You're a scientist with a secret past, trapped on a mysterious island where an explosion has destroyed the biology lab. Photographs of organisms are strewn across the island. Collect and answer questions about the photos to earn game money, which you spend on tools to help you progress and hopefully get off the island. Your classification of these real-life photos from around the world will help biologists to study the effects of urban sprawl on local ecosystems or to detect evidence of regional or global climactic shifts.
Think Candy Crush but with coloured leaves. To play this Facebook game, align different patterns with a reference pattern: the better the alignment, the higher the score. Tussle for ownership of a given pattern by beating other players' scores. In sorting the patterns to increasingly higher accuracy, you'll actually be helping to detect genetic variants that can protect Europe's ash trees (Fraxinus excelsior) from a deadly fungal disease. Each pattern represents actual DNA lengths from the trees and the fungus, from which scientists hope to identify genetic variants that either confer resistance or increase susceptibility.
A similar concept to Foldit (it was made by some of the same people), but this time you're trying to get RNA into a target shape. RNAs, which have an important role in building proteins and regulating genes, are made up of four different types of nucleotide bases. Switch these to alter the RNA's configuration, increase its stability, and up your score. Target shapes get increasingly more complicated as you progress to becoming a puzzle architect or, in the lab mode, compete for the chance to have your own RNA designs synthesised and assessed by scientists at Stanford University.
Not released until later this year, but well worth keeping an eye out for. You'll be charged with taking care of a plot of New Zealand forest and protecting it from ravenous Australian bushtail possums. Set traps, create sanctuaries or fly aerial operations to sow toxic bait to save your pixelated forest. Researchers will then take the best strategies and apply them in real New Zealand forests, where native plants and animals are under threat from these invading possums. To help raise money for the game, Ora's developers have released Possum Stomp, a mini game app available on iOS or Android.
Zooniverse's flagship project. Sift through pictures of millions of galaxies and help classify their shapes to unravel their history. A galaxy's shape tells you whether it's collided with another galaxy, if it's formed stars, and how it's interacted with its environment. Like all Zooniverse projects, Galaxy Zoo offers an authentic experience of science, so you'll not get points. However, if seeing far-flung corners of the universe before any other human eye isn't enough for you, keep a look out for weird and wonderful objects and they might be named after you, such as Hanny's Voorwerp, a galaxy-sized gas cloud named after one player.
Help scientists figure out how the brain is wired, starting with nerves in the back of the eye. You're given a cube of tangled nerves from which you have to tease out the shape of individual nerves and, slice by slice, build up their three-dimensional structure. It's little wonder this game is so pleasing: it taps into two things you probably forgot that you love – colouring in and treasure hunts. Score points by tracing well and unearthing new neurons. The timed events really ramp up the heat, and might have you sitting at your computer all night. Be warned.
Whale FM: help marine biologists find out more about whales.
Listen to whales, help marine biologists
Another authentic experience from Zooniverse. This time be a marine biologist (no scuba diving, sadly) and study whale song. Listen to recordings of killer whales and pilot whales from around the world and link them with a list of potential matches. Find a match and it'll be stored for further analysis. Your work will help biologists determine the size of these animals' repertoire and whether they have accents, indicators of intelligence or a culture. If you've noticed neither animal is a whale but instead a type of dolphin, this game is probably for you.
By 2050 there will be 10 billion of us on the planet. That's a lot of hungry mouths that we'll struggle to feed with the current agricultural setup. Trawl through satellite images of the Earth and look for arable land to help develop the first-ever global crop map, which will help plan for global food security, identify yield gaps and monitor crops affected by droughts. The more land you identify, the higher your score and the better your chances of winning great weekly prizes, such as an Amazon Kindle, a smartphone, or a tablet. But hurry: the competitions stop in April.
(Jeffrey L. Rotman/Corbis)
