Tag: genome

Pocket Science – lessons from spongy genomes, and a deadly bat-killing disease

By Ed Yong | August 6, 2010 9:00 am

Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Sponge

Spongebob’s genome reveals the secrets of building an animal

Sponges are animals but, outside of children’s cartoons, they’re about as different from humans as you can imagine. These immobile creatures lie on the very earliest branch on the animal family tree. They have no tissues or organs – their bodies are made of just two layers of cells, twisted and folded into simple shapes. But despite this simplicity, the first complete sponge genome tells us a lot about what it takes to build an animal.

The genome was sequenced from an Australian species called Amphimedon queenslandica by a large team of scientists led by Mansi Strivastava from the University of California, Berkeley. It tells us that sponges share a ‘genetic toolkit’ with humans and all other animals. This includes 4,670 families of genes that are universal to all animals, 1,286 of which separate us from our closest single-celled relatives, the choanoflagellates. Within these families lie the keys to a multicellular existence.

This shared toolkit controls all the fundamental processes that allow individual cells to cooperate as part of a single creature, including how to divide, die, grow together, stick to one another, send signals to one another, take up different functions, and tell the difference between each other and outsiders. They also include many genes that are implicated in cancer, a disease where individual cells go rogue and multiply out of control at the expense of the collective. The presence of cancer-related genes in the sponge genome tells us that as long as cells have been cooperating within a single body, they have needed to guard against the threat of cancer.

Srivastava estimates that the foundations of multicellular life were laid between 600 and 800 million years ago. More than a quarter of the big genetic changes that separate humans from the single-celled choanoflagellates took place during this window, before sponges split off from the ancestors of all other animals. The last common ancestor of all animals emerged during this period and it was a creature of remarkable complexity – a multicellular species that could sense, react to and exploit its environment.

Read more from Adam Mann at Nature, Bob Holmes at New Scientist and an earlier post from me on how sponges provide clues to origin of nervous system

Reference: Nature http://dx.doi.org/10.1038/nature09201; Image by Adamska et al

Bat_extinction

Holy extinction, Batman! One of America’s most common bats could be wiped out in 16 years by new disease

The little brown bat is one of the most common bats in North America but in 16 years, people on the East Coast will be lucky to see any. The bat is being massacred and the culprit is a new disease known as white-nose syndrome caused by the ominously named fungus Geomyces destructans. The fungus grows on the wings, ears and muzzles of hibernating bats, rousing them too early from their deep sleep, sapping their fat reserves and causing strange behaviour.

White-nose syndrome was first identified in a New York cave in February 2006, but it spreads fast. In the last four years, it has covered over 1200 km and contaminated wintering roosts throughout the north-eastern US and its neighbouring Canadian provinces. In infected areas, the fungus is slaughtering bats at a rate of around 45% a year. Cave floors are littered with carcasses.

Five years ago, the little brown bat was thriving, thanks to the installation of bat boxes, conservation efforts and a reduction in pesticide use. The eastern seaboard alone was home to 6.5 million of them. But all of that good is being undone by a single disease. Using a mathematical model, Winifred Frick from Boston University calculated a 99% chance that the species will become locally extinct within 16 years. Even if the current death rate slows to just 5% a year – a highly optimistic target– the population will still collapse to around 65,000 individuals. These last survivors would be just 1% of the previous total, with a 60% chance of dying off by the end of the century. At this stage, the question isn’t if the little brown bat will go locally extinct, but when.

This is just the tip of the iceberg. White-nose syndrome is spreading across North American and at least six other bat species are affected. These animals eat such a large volume of insects that their disappearance would have severe economic and ecological consequences. There’s a desperate need for more research to understand the disease, to keep a track of it, to find ways of fighting it, and to ensure that something like it doesn’t happen again. Frick thinks that white-nose syndrome spread so quickly with such devastating results that it must have been introduced from another part of the world, hitting species whose immune systems were totally unprepared for it. This problem of “pathogen pollution” is a neglected issue in conservation – perhaps the demise of the little brown bat will provide the impetus to take it seriously.

Read more from Brandon Keim at Wired and more from me on bats and how wind turbines burst their lungs

Reference: Science http://dx.doi.org/10.1126/science.1188594

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Scientists create first ever synthetic bacterium that looks like Craig Venter

By Ed Yong | May 20, 2010 3:33 pm

Venter_mycoplasma

In a move that’s been hailed as one of the greatest scientific breakthroughs of the century, a group of scientists have created a synthetic bacterium that looks like Craig Venter.

The team artificially synthesised a genome in the lab and inserted it into an empty bacterial cell, which promptly remodelled its outer wall into a picture of Venter’s face.

“Before today, there had only been one genome in the world with the right sequence of nucleotides to encode my face,” said Venter, speaking from his secret volcano lair. “Now there are two, and I can’t help but think that things have greatly improved.

“Of course, the ultimate goal is to build a creature with 100 heads, not unlike the mythical hydra, but where every head is my head.

“Or, er, something about biofuels,” he added.

Other scientists warned that the ethical debates sparked by the discovery had only begun. Andrew McQueen from New York University said, “Imagine going for a walk in the park only to find that every bird in the trees has Craig’s face on it and they’re all looking at you.”

“They’re not smiling either,” he added before curling up on the floor and crying quietly.

While the research was widely reported as a major breakthrough, other newspapers were more critical, with one spokesperson saying, “He’s basically just taken information from an existing source, copied it and reprinted it in another place. That’s our f**king job!”

Meanwhile, it transpired that Venter has coded a line from a James Joyce novel into his synthetic genome, a move that drew condemnation from America’s creationist groups, who didn’t understand what a novel was.

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CATEGORIZED UNDER: Not Exactly Rocket Satire
MORE ABOUT: genome, synthetic, venter

Pocket Science – geneticist hunts down the cause of his own genetic disorder, and male moths freeze females by mimicking bats

By Ed Yong | March 11, 2010 2:53 pm

Not Exactly Pocket Science is a set of shorter write-ups on new stories with links to more detailed takes by the world’s best journalists and bloggers. It is meant to complement the usual fare of detailed pieces that are typical for this blog.

Geneticist sequences own genome, finds genetic cause of his disease

If you’ve got an inherited disease and you want to find the genetic faults responsible, it certainly helps if you’re a prominent geneticist. James Lupski (right) from the Baylor College of Medicine suffers from an incurable condition called Charcot-Marie-Tooth (CMT) disease, which affects nerve cells and leads to muscle loss and weakness.

Lupski scoured his entire genome for the foundations of his disease. He found 3.4 million placed where his genome differed from the reference sequence by a single DNA letter (SNPs) and around 9,000 of these could actually affect the structure of a protein. Lupski narrowed down this list of candidates to two SNPs that both affect the SH3TC2 gene, which has been previously linked to CMT. One of the mutations came from his father and the other from his mother. Their unison in a single genome was the cause of not just Lipson’s disease but that of four of his siblings too.

It’s a great example of how powerful new sequencing technologies can pinpoint genetic variations that underlie diseases, which might otherwise have gone unnoticed. The entire project cost $50,000 – not exactly cheap, but far more so than the sequencing efforts of old. The time when such approaches will be affordable and commonplace is coming soon. But in this case, Lupski’s job was easier because SH3TC2 had already been linked to CMT. A second paper tells a more difficult story.

Jared Roach and David Gallas sequenced the genomes of two children who have two inherited disorders – Miller syndrome and primary ciliary dyskinesia – and their two unaffected parents. We don’t know the genetic causes of Miller syndrome and while the four family genomes narrow down the search to four possible culprits, they don’t close the case.

For great takes on these stories and their wider significance, I strongly recommend you to read Daniel Macarthur’s post on Genetic Future, Mark Henderson’s piece in the Times and Nick Wade’s take in the NYT (even if he does flub a well-known concept). Meanwhile, Ivan Oranksy has an interesting insight into the political manoeuvres that go into publicising two papers from separate journals.  And check out this previous story I wrote about how genome sequencing was used to reverse the wrong diagnosis of a genetic disorder.

Reference: http://dx.doi.org/10.1056/NEJMoa0908094  and http://dx.doi/org/10.1126/science.1186802

Male moths freeze females by mimicking bats

Flying through the night sky, a moth hears the sound of danger – the ultrasonic squeak of a hunting bat. She freezes to make herself harder to spot, as she always does when she hears these telltale calls. But the source of the squeak is not a bat at all – it’s a male moth.  He is a trickster. By mimicking the sound of a bat, he fooled the female into keeping still, making her easier to mate with.

The evolutionary arms race between bats and moths has raged for millennia. Many moths have evolved to listen out for the sounds of hunting bats and some jam those calls with their own ultrasonic clicks, produced by organs called tymbals. In the armyworm moth, only the males have these organs and they never click when bats are near. Their tymbals are used for deceptive seductions, rather than defence.

Ryo Nakano found that the male’s clicks are identical to those of bats. When the males sung to females, Nakano found that virtually all of them mated successfully. If he muffled them by removing the tymbals, they only got lucky 50% of the time. And if he helped out the muted males by playing either tymbal sounds or bat calls through speakers, their success shot back up to 100%. Nakano says that this is a great example of an animal evolving a signal to exploit the sensory biases of a receiver.

More on bats vs. moths from me

Reference: Biology Letters http://dx.doi.org/10.1098/rsbl.2010.0058

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Africa's genetic diversity revealed by full genomes of a Bushman and a Tutu

By Ed Yong | February 17, 2010 1:00 pm

Bushmen.jpg

!Gubi.jpgMeet !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.

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Meet Inuk – full genome of ancient human tells us about his hair, eyes, skin, teeth, ancestry and earwax

By Ed Yong | February 10, 2010 1:00 pm

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.

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Meet your viral ancestors – how bornaviruses have been infiltrating our genomes for 40 million years

By Ed Yong | January 6, 2010 4:00 pm

Cast your mind back 40 million years and think about your ancestors. You’re probably picturing creatures that looked like a bit like today’s monkeys, but they’re only part of your family tree. To see your other ancestors, you’d have to whip out an imaginary microscope. Meet your great-great-great-etc-grandviruses.


The human genome is littered with the remains of viruses that, in ages past, integrated their genes into the DNA of our ancestors. They became a permanent fixture, passed down from parent to child. Today, these “endogenous retroviruses“, or ERVs, make up around 8% of our genome. They’re a living fossil record of prehistoric plagues.

Until recently, scientists thought that the only viruses to have left such a legacy were the retroviruses, a group that includes modern members such as HIV and hepatitis B. But they are no longer alone. Masayuki Horie and Tomoyuki Honda from Osaka University have found that another viral dynasty, the bornaviruses, have repeatedly inveigled their way into the genomes of mammals. They’re found in humans, the great apes, elephants, rodents and many more. Those that lurk amid our genes have been our partners in evolution for at least 40 million years.

Almost all of these hidden sequences match the N gene of the most famous bornavirus – BDV or Borna disease virus. As a result, Horie and Honda christened their newfound sequences as EBLNs (or “endogenous Borna-like N” elements). We carry four such sequences but many others exist. A scan of over 234 genomes revealed that EBLNs are found in all manner of mammals, including chimps, gorillas, orang-utans, macaques, lemurs, bushbabies, African elephants, hyraxes, ground squirrels, mice, rats, guinea pigs, bats and opossums.

Most of these EBLNs are the result of independent invasions, at different points in the history of mammal evolution. Squirrels have only carried their EBLNs for less than 10 million years but our own genetic passengers have been riding and co-evolving with us for over 40 million years.

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CATEGORIZED UNDER: Evolution, Genetics, Viruses
MORE ABOUT: bornavirus, EBLN, erv, genome

Robots evolve to deceive one another

By Ed Yong | August 17, 2009 3:00 pm

Blogging on Peer-Reviewed ResearchIn a Swiss laboratory, a group of ten robots is competing for food. Prowling around a small arena, the machines are part of an innovative study looking at the evolution of communication, from engineers Sara Mitri and Dario Floreano and evolutionary biologist Laurent Keller.

They programmed robots with the task of finding a “food source” indicated by a light-coloured ring at one end of the arena, which they could “see” at close range with downward-facing sensors. The other end of the arena, labelled with a darker ring was “poisoned”. The bots get points based on how much time they spend near food or poison, which indicates how successful they are at their artificial lives.

They can also talk to one another. Each can produce a blue light that others can detect with cameras and that can give away the position of the food because of the flashing robots congregating nearby. In short, the blue light carries information, and after a few generations, the robots quickly evolved the ability to conceal that information and deceive one another.

Their evolution was made possible because each one was powered by an artificial neural network controlled by a binary “genome”. The network consisted of 11 neurons that were connected to the robot’s sensors and 3 that controlled its two tracks and its blue light. The neurons were linked via 33 connections – synpases – and the strength of these connections was each controlled by a single 8-bit gene. In total, each robot’s 264-bit genome determines how it reacts to information gleaned from its senses.

In the experiment, each round consisted of 100 groups of 10 robots, each competing for food in a separate arena. The 200 robots with the highest scores – the fittest of the population – “survived” to the next round. Their 33 genes were randomly mutated (with a 1 in 100 chance that any bit with change) and the robots were “mated” with each other to shuffle their genomes. The result was a new generation of robots, whose behaviour was inherited from the most successful representatives of the previous cohort.

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Dinosaurs provide clues about the shrunken genomes of birds

By Ed Yong | June 21, 2009 8:30 am

Revisitedbanner.jpg

Blogging on Peer-Reviewed ResearchThere is a reason why there are no dinosaur geneticists – their careers would quickly become as extinct as the ‘terrible lizards’ themselves. Bones may fossilise, but soft tissues and molecules like DNA do not. Outside of the fictional world of Jurassic Park, dinosaurs have left no genetic traces for eager scientists to study.

Tyrannosaurus had a genome half the size of a house mouseNonetheless, that is exactly what Chris Organ and Scott Edwards from Harvard University have managed to do. And it all started with a simple riddle: which came first, the chicken or the genome?

Like almost all birds, a chicken’s genome – its full complement of DNA – is remarkably small. DNA is made up of millions of units called ‘base pairs’, just like a book contains millions of letters. A typical bird genome is made up of about 1.5 billion of these base pairs, just half the number of the comparatively flabby human genome. Like their bodies, bird genomes are feather-weight and streamlined.

Some scientists have suggested that, over the course of evolution, birds shrunk their genetic packages to help them fly. Smaller genomes involve less DNA, which in turn can be housed in smaller cells. And smaller cells are more energy-efficient than larger ones, in the same way that a Mini is more efficient than a gas-guzzling SUV.

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How the common cold evolves – full genomes of all known human rhinoviruses

By Ed Yong | February 12, 2009 6:00 pm

This is the eighth of eight posts on evolutionary research to celebrate Darwin’s bicentennial.

Blogging on Peer-Reviewed ResearchIn Virginia, USA, sits a facility called the American Type Culture Collection. Within its four walls lie hundreds of freezers containing a variety of frozen biological samples and among these, are 99 strains of the common cold. These 99 samples represent all the known strains of the human rhinoviruses that cause colds. And all of their genomes have just been laid bare.

Ann Palmenberg from the University of Wisconsin and David Spiro from the J. Craig Venter Institute have cracked the genomes of all 99 strains, and used them to build a family tree that shows the relationships between them. Already, it has started to plug the holes in our understanding of this most common of infections. It reveals how different strains are related and how new strains evolve. It tells us which features are shared by all strains and which are the more unique traits that making rhinoviruses such slippery targets.

This extra knowledge may go some way to remedying the slightly baffling situation we find ourselves in, where all the vaunted progress of modern medicine has failed to produce a single approved treatment for an infection that most of us get at least twice a year.

The 99 historical strains of human rhinovirus fall into two separate species – HRV-A and HRV-B. More recently, a possible third species – HRV-C – has been identified in patients hospitalised with severe, flu-like illnesses. To build their family tree, Palmenberg and Spiro analysed the complete genomes of all 99 strains from the Virginia facility, seven samples of HRV-C, and 10 fresh samples collected from patients just a few years ago.

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