Meet !Gubi, the tribal elder of a group of Bushmen (or Khoisan), one of the oldest known human lineages. He lives the life of a hunter-gatherer in the Namibian part of the Kalahari Desert. But he also has a strange connection to James Watson, the British American scientist who helped to discover the structure of DNA. For a start, they’re both around 80 years old. But more importantly, they are two of just 11 humans to have their entire genomes sequenced.

Along with Archbishop Desmond Tutu, !Gubi is one of two southern Africans, whose full genomes have been sequenced by Stephan Schuster and an international team of scientists . Schuster’s team also analysed the genes of three other Bushmen – G/aq’o, D#kgao and !Aıˆ (see footnote for pronunciation guide) – focusing on the parts of their genome that codes for proteins. Like, !Gubi, these men are tribal elders and all are around 80 years old. Despite the fact that the four Bushmen come from neighbouring parts of the Kalahari, their genetic diversity is astounding. Pick any two and peer into their genomes and you’d see more variety than you would between a European and an Asian. 

This diversity reveals just how important it is to include African people in genome sequencing projects. Until now, the nine complete human genomes have included just one African – a Yoruban man from Nigeria. The rest have hailed from Europe, America, China, Korea and, most recently, Greenland circa 4,000 years ago. This is a major oversight. Africa is the birthplace of humanity and its people are the most genetically diverse on the planet. To understand human genetics without understanding Africa is like trying to learn a language by only looking at words starting with z.

The Bushmen certainly provide a glimpse into this diversity. Desmond Tutu was also selected because his ancestry covers the two largest of southern Africa’s Bantu groups – the Tswama and the Nguni – making him an excellent representative for many southern Africans. Vanessa Hayes, who worked on the study, says, “This work is very expensive so we wanted to maximise the amount of diversity we could get in one individual.” The team had other reasons for sequencing the bishop.”He’s a voice for southern Africans and for his people. He’s a chairman of the Global Elders. He provides a genome with a lot of medical history behind it, having survived prostate cancer, polio and Tb, diseases that affect many southern Africans.” But most importantly, Hayes says, “He wanted to participate. He himself wanted to study medicine so this for him was a personal endeavour.”

The researchers hope that their new data will allow medical research to become more inclusive. Vanessa Hayes, who led the study, says that she found HIV research in South Africa to be very difficult because most genetic databases are severely Eurocentric, which rules out a lot of Africans from medical research. Without this knowledge, for example, we have no way of knowing if a drug that was developed and tested in Western patients will have the same benefits and risks in African ones.

(more…)

According to Sitemeter, Not Exactly Rocket Science passed 2,000,000 page views today!!! Virtual hugs, high-fives and fist-bumps all round.

As near as I can make out, the hit that did it came from Israel and was directed to yesterday’s autism post via Stumbleupon.

A quick retrospective calculation tells me that it took the first 35 months of NERS to get the first million hits and the last 7 to get the second million. I really am constantly delighted and humbled by the fact that people are actually reading this and that more seem to do so. Thanks to all of you for reading.

All of our cells are staffed by armies of executioners. They are usually restrained but when unleashed, they can set off a fatal chain reaction that kills the cell. This suicide squad does away with billions of cells every day. It helps to balance the production of new cells with the loss of old ones, to sculpt growing tissues and to destroy potential cancer cells.

But a new study suggests that the executioners aren’t always lethal. In fact, they’re essential for life. Through the unorthodox method of damaging our DNA, they can actually activate important genes. This technique for switching genes on is new to science but it’s apparently vital for allowing some types of stem cell to produce new types of tissue.

Stem cells are bundles of untapped potential, with the ability to produce hundreds of specialist cells across the body. This process is called differentiation. Its details vary depending on which type of cell is being produced, but scientists have recently found that some aspects are apparently common to all tissues, be they muscle, blood or bone. Surprisingly, one of these is the recruitment of executioner proteins – caspases.

Caspases cut up other proteins and in doing so, some of them produce yet more caspases. The result is a growing army of death, hacking and slashing its way through the cell. But one of these killers – caspase-3 – is a necessary part of differentiation. Get rid of it and, suddenly, stem cells can’t produce their specialised daughters. Now, thanks to Brian Larsen from the Sprott Centre for Stem Cell Research, we know why. 

(more…)

The social interactions that come naturally to most people are difficult for people with autism and Asperger syndrome. Simple matters like making eye contact, reading expressions and working out what someone else is thinking can be big challenges, even for “high-functioning” and intelligent individuals. Now, a preliminary study of 13 people suggests that some of these social difficulties could be temporarily relieved by inhaling a hormone called oxytocin.

The participants, who either had Asperger or high-functioning autism, experienced stronger feelings of trust, showed stronger social interactions in a simulated game, and paid more attention to socially important cues like someone else’s eyes. These results will need to be confirmed in larger studies in real-world situations, but for the moment, they’re promising.  

Oxytocin is involved a myriad of emotions and social behaviours including trust, social interactions, sexual arousal, the bond between mother and child (see SciCurious’s epic oxytocin series for more). It has been linked to autism before. Autistic children have lower levels of the hormone coursing through their blood and what little there is appears to be made in an abnormal way. Some researchers are testing oxytocin as a treatment for some symptoms of autism, including repetitive behaviours, but the new results are some of the most interesting yet.

(more…)

Millions of people in Latin America have been invade by a parasite – a trypanosome called Trypanosome cruzi. They are passed on through the bite of the blood-sucking assassin bug and they cause Chagas disease, a potentially fatal illness that affects the heart and digestive system. The infections are long-lasting; it can take decades for symptoms to show and a third of infected people eventually die from the disease. But T.cruzi does much more than invade our flesh and blood; it also infiltrates our genomes.

T.cruzi is unusual in that a massive proportion of its DNA, around 15-30%, lies outside of its main genome. These accessory sequences are stored in the form of thousands of interlinked DNA rings. In the parasite, these sequences are found in the mitochrondria – small structures that provide it with energy – but they have found a way to spread much further.

According to new research from Mariana Hecht and a team of Brazilian scientists, T.cruzi has the ability to inveigle its DNA rings into the genomes of those it infects. Once inside, the parasite genes can hop around, hitchhiking from one chromosome to another and leaving genetic chaos in their wake. They can even be passed on from one generation to the next. Hitching a ride aboard sperm and eggs, they can add themselves to the genomes of children, who’ve never been in direct contact with trypanosomes.

Hecht’s discovery suggests that T.cruzi is an unexpected source of genetic diversity in our species. It’s certainly not the only parasite to do this. Viruses have been infiltrating our genes since time immemorial and a massive part of our genome has a viral origin. These events, where viruses joined our family tree, provided raw material for natural selection. Some viral genes wreaked havoc by disrupting important genes, while others were eventually domesticated to act as helpful, even necessary, parts of our genome.

But T.cruzi is a different story. Despite its microscopic, single-celled nature, it’s a vastly complex creature compared to a simple virus. And it continues to breach our DNA today. Now that we’re getting technically better at detecting such “horizontal gene transfers“, we may find that many other parasites are also smuggling their genes into ours. In Hecht’s words, the “human population may be a patchwork of all the organisms to which it has ever been exposed.”

(more…)

Bees can communicate with each other using the famous “waggle dance”. With special figure-of-eight gyrations, they can accurately tell other hive-mates about the location of nectar sources. Karl von Frisch translated the waggle dance decades ago but it’s just a small part of bee communication. As well as signals that tell their sisters where to find food, bees have a stop signal that silences dancers who are advertising dangerous locations. 

The signal is a brief vibration at a frequency of 380 Hz (roughly middle G), that lasts just 150 milliseconds. It’s not delivered very gracefully. Occasionally, the signalling bee will use a honeycomb to carry her good vibrations, but more often than not, she’ll climb on top of another bee first or use a friendly headbutt. The signal is made when bees have just travelled back from a food source where they were attacked by rivals or ambush predators. And they always aim their buzzes at waggle dancers. The meaning is clear; it says, “Don’t go there.”

These signals were identified decades ago, but scientists originally interpreted them as a begging call, intended to cadge some food of another worker.  It seems like a strange conclusion, when you consider that the signals never actually prompt workers to exchange food. Their true nature became clearer when scientists showed that playing them through speakers could stop dancers from waggling.

(more…)

Meet “Inuk”. He is the ninth human to have their entire genome sequenced but unlike the previous eight, he has been dead for some 4,000 years old. Even so, DNA samples from a tuft of his frozen hair have revealed much about his appearance and his ancestry.

Inuk had brown eyes and brown skin. His blood type was A+. His hair was thick and dark but had he lived, he might not have kept it – his genes reveal a high risk of baldness. Inuk may well have died quite young. Like many Asians and Native Americans, his front teeth were “shovel-graded”, meaning that their back faces had ridged sides and concave middles. We even know about his earwax – it was dry, again like many Asians and Native Americans, rather than the wet wax that dominates other ethnic groups.

Inuk is the singular of Inuit and it means “man”. He was one of the Saqqaq people, one of the first cultures to settle in the frozen north of the New World. Few of their remains have been found – all we have are four small tufts of hair and four small pieces of bone. So Inuk’s genome is a treasure trove of knowledge about this extinct Eskimo culture. His remains were discovered in Greenland in the 1980s and his genome has just been sequenced by a large team of scientists from 8 countries, led by Morten Rasmussen, Yingrui Li and Stinus Lindgreen.

This isn’t the first time that scientists have tried to sequence the genes of an ancient human (or related species). So far, the most successful result was a first draft of the Neanderthal genome based on bone and tooth samples. It comprises just 63% of the total genome, but even getting this much was a struggle. Ancient genomes aren’t easy to decipher. Even if enough tissue is preserved, it is often riddled with the DNA of fungi and bacteria. The very act of extracting the tissues often adds human DNA to the list of contaminants.

Scientists have developed ingenious workarounds to this problem, but Rasmussen’s team solved it by working with a well-frozen specimen and focusing on his hair. Hair is a rich source of DNA and it protects genomes from both damaging elements and contaminating microbes. It allowed scientists to sequence the genome of the woolly mammoth and it has now done the same for Inuk. Around 80% of the DNA recovered from a tuft was Inuk’s hair was human, with no evidence of modern contamination. After all, all the scientists who handled the samples were European and there weren’t any traces of European sequences in the deciphered genome.

Rasmussen’s group used next-generation sequencing technology to analyse the recovered DNA. These powerful techniques allowed them to sequence around 80% of the genome around 20 times. With such extensive coverage, they could be incredibly confident about exactly which sequences lay in each location. Eske Willerslev who headed the group says, “It’s comparable to a modern human genome in terms of quality.” For comparison, the Human Genome Project’s gold standard required that the entire genome should be sequenced just 10 times.

(more…)

Mothers can teach their children much about the world, but some mothers can do it without ever meeting their young. Take the field cricket Gryllus pennsylvanicus. A female cricket isn’t exactly a caring mother. Once she lays her eggs, she abandons them to their fate. But amazingly, she can also forewarn her young of the dangers they might face. If a pregnant female is exposed to a wolf spider, her experiences affect her unborn young. When they hatch, the baby crickets are more likely to freeze when they smell wolf spiders nearby.

If mothers sense a threat in their environment, there are clear advantages in being able to prepare her young to face those threats. Over the last decade or so, scientists have discovered that many animal and plant mothers do exactly this, even before their young are born. If pregnant water fleas are exposed to the smell of a predatory midge, they produce young that are armed with larger “crowns-of-thorn”, defensive spiky helmets that make them difficult mouthfuls. In the same way, aphids produce more winged offspring if they sense danger. Even the humble radish can generate a generation with sharp, spiky hairs.

In all of these examples, the adaptations are physical ones. The case of the crickets, documented by Jonathan Storm and Steven Lima at Indiana State University, is the clearest example yet of mothers preparing their young for life by influencing their behaviour. Physical defences wouldn’t do much good here, for even the largest of crickets are easy pickings for spiders.

Storm and Lima bred crickets that had never seen a wolf spider before. They placed pregnant females in cages with wolf spiders whose killing fangs had been disabled with wax. After a while, the females were removed and allowed to lay their eggs. Storm and Lima collected the hatchlings and placed them in plastic arenas lined in paper saturated with the faeces and silk lines of wolf spiders.

(more…)

The English language is full of metaphors linking moral purity to both physical cleanliness and brightness. We speak of “clean consciences”, “pure thoughts” and “dirty thieves”. We’re suspicious of “shady behaviour” and we use light and darkness to symbolise good and evil. But there is more to these metaphors than we might imagine. The mere scent of a clean-smelling room can take people down a virtuous road, compelling them to choose generosity over greed and charity over apathy. Meanwhile, the darkness of a dimmed room or a pair of sunglasses can compel people towards selfishness and cheating.

These new results are the latest from psychologist Chen-Bo Zhong. Back in 2006, he showed that people who brought back memories of past wrong-doings were more likely to think of words related to cleaning, or to physically crave cleaning products. He called this the “Lady Macbeth effect”. Subsequently, another group found that it works the other way too. People judge moral transgressions more leniently if they had previously washed their hands or if they had been primed with words related to cleanliness, like ‘pure’ or ‘immaculate’.

Now, Zhong, together with Katie Liljenquist and Adam Galinsky, have expanded on these studies by showing that clean smells can make people behave more virtuously. They ushered 28 volunteers into a room that was either unscented or that had been lightly sprayed with a citrus air freshener. In either case, they had to play a trust game, where a “sender” has a pot of money and chooses how much they want to invest with a “receiver”. The investment is tripled and the receiver decides how much to give back.

The volunteers were all told that they had been randomly chosen as receivers. Their anonymous partner had invested their entire $4 pot with them, which had been tripled to $12. Their job was to decide how much to give back. On average, they returned a measly $2.81in the unscented rooms but a more equitable $5.33 in the scented ones. The single spray of citrus nearly doubled their tendency to reciprocate.

In a second experiment, the trio again ushered 99 students into either a scented or unscented room. They were given a pack of miscellaneous tasks, including a flyer requesting volunteers for a charity called Habitat for Humanity. Those in the citrus-scented rooms were more likely to be interested in volunteering, and almost four times more willing to donate money to the cause.

(more…)

These are rock hyraxes or dassies. They may look like guinea pigs, but they’re in an entirely different order of mammals. It’s sometimes said that they are the closest living relatives of elephants. However, some scientists would dispute that sirenians – the manatees and dugongs – are more closely related still, with the hyraxes as a more distant outgroup.
They’re nimble animals, scuttling comfortably across rocky terrain and even climbing trees with relative ease. They can often be spotted basking in the sun to raise their body temperature, not unlike a reptile would. We found this pair in Tsitsikamma National Park.