Posts tagged genetics
Articles and news from the latest research reports.
Method offers DNA blueprint of a single human cell
Humans, strawberries, honeybees, chickens and rats are among the many organisms to have their DNA sequenced. But although sequencing an individual species is challenging, it is much harder to sequence the DNA of a single cell.
To get enough DNA for sequencing, thousands or even millions of cells are usually required. And finding out which mutations are in which cells is almost impossible, and mutations present in only a few cells (like early cancerous cells) are hidden altogether.
But a technique reported today in Science provides a way to copy DNA so that more than 90% of the genome of a single cell can be sequenced. The method also makes it easier to detect minor DNA sequence variations in single cells and, so, to find genetic differences between individual cells. Such differences can help to explain how cancer becomes more malignant, how reproductive cells emerge and even how individual neurons differ.
Sunney Xie, a chemical biologist at Harvard University in Cambridge, Massachusetts, and his colleagues have developed a technique, called multiple annealing and looping-based amplification cycles (MALBAC), that allows them to sequence 93% of the genome of a human cell. In MALBAC, DNA from a single cell is isolated, then short DNA molecules called primers are added. These are complementary to random parts of the DNA, which makes them stick to the strands and act as starting points for DNA replication.
The primers consist of two parts - a sticky eight-nucleotide portion that varies and binds to the DNA, plus a common sequence of 27 nucleotides. This common sequence stops the DNA from being copied too many times and massively cuts down the amplification bias. It does this by incorporating itself into the newly copied strands so that they loop back on themselves, which prevents over-copying.
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“MALBAC opens a door to many critical questions,” says Bing Ren, who studies gene regulation at the University of California, San Diego. For example, it can be used to examine how quickly mutations accumulate, and to find variations in gene-copy number and chromosomal abnormalities across a population of cells. It also helps to detects variants across more of the genome than other sequencing methods.
“I think people are going to start using it right away,” agrees James Eberwine, who works on single-cell genetics at the Perelman School of Medicine at the University of Pennsylvania in Philadelphia. He adds that researchers may have to tweak conditions — such as the ratio of primers to genomic DNA — to get experiments to work.
But although MALBAC covers the genome more thoroughly than other techniques, it is not perfect. It still misses perhaps one-third of single-nucleotide variations. Also, the enzyme that copies the DNA is error prone, so the copying process itself can introduce variants that were not present in the cell.
Xie was able to weed out all false positives, but only by comparing individually sequenced genomes from three closely related cells. That will increase costs, and could prove impossible for certain tissue samples, says Nicholas Navin at the MD Anderson Cancer Center in Houston, Texas, who has developed his own techniques for single-cell sequencing.
They came from the sea: the gene behind limb evolution
In the late Devonian period, roughly 365 million years ago, fish-like creatures started venturing from shallow waters onto land.
Among the various adaptations associated with the switch to land life was the conversion of fins into limbs. This transition allowed animals to both navigate aquatic habitats and walk on land.
We already know that fins and limbs share the same genetic program for their induction and early development. But due to their divergent morphological traits (form and structure), it was unknown how a fin could evolve into a limb.
But now, a paper published in the journal Developmental Cell by Renata Freitas and colleagues from the University of Andalusia (Seville, Spain), suggests the key to fin-to-limb transition lies in the regulation of the homeotic (responsible for the formation of body parts) gene hoxd13.
(Source: theconversation.edu.au)
Sheep Help Scientists Fight Huntington’s Disease
When University of Cambridge neurobiologist Jenny Morton began working with sheep five years ago, she anticipated docile, dull creatures. Instead she discovered that sheep are complex and curious. Morton, who studies neurodegenerative diseases such as Huntington’s, is helping evaluate sheep as new large animal models for human brain diseases.
Huntington’s is a fatal, hereditary illness that causes a cascade of cell death in the brain’s basal ganglia region. The idea to use sheep to study this disease arose in 1993 in New Zealand, a country where sheep outnumber humans seven to one. Researchers had already identified disorders shared by humans and sheep, but University of Auckland neuroscientist Richard Faull and geneticist Russell Snell had a more ambitious notion. They decided to develop a line of sheep carrying Huntington’s, which is brought on by repeats within the gene IT15, in the hopes of studying the condition’s progression and developing a treatment. They accomplished their goal in 2006 after extensive efforts.
Why sheep? For one, they have big brains—comparable to macaques, which are the only other large animals currently used to study this disease—with developed, cortical folding like our own. Also, sheep can be kept in large paddocks with their fellows and monitored remotely via data-logger backpacks, allowing scientists to study these creatures in a natural setting with fewer ethical concerns than studying caged primates. What is more, these long-lived, social animals are active and expressive, recognize faces, and have long memories. They also learn quickly and engage in experiments readily. This has allowed Morton to develop cognitive tests similar to those given to humans. The researchers can study the full progression of Huntington’s—which in humans is associated with gradual mental and motor decline—and compare the changes with the normal functioning of healthy individuals.
This spring Faull, Snell, Morton and their colleagues will begin monitoring two flocks of Huntington’s sheep in Australia. One flock will be inoculated with one of the most promising therapies yet devised—a virus that silences IT15’s mutations—and the other will serve as the control. Currently no cure exists for any human brain disease. The researchers believe these studies could be a milestone. “The tragedy of this disease is enormous. It’s a curse on the family,” Faull says. “Maybe we can lift that curse.”
Resistance to cocaine addiction may be passed down from father to son
Research from the Perelman School of Medicine at the University of Pennsylvania and Massachusetts General Hospital (MGH) reveals that sons of male rats exposed to cocaine are resistant to the rewarding effects of the drug, suggesting that cocaine-induced changes in physiology are passed down from father to son. The findings are published in the latest edition of Nature Neuroscience.
"We know that genetic factors contribute significantly to the risk of cocaine abuse, but the potential role of epigenetic influences – how the expression of certain genes related to addiction is controlled – is still relatively unknown," said senior author R. Christopher Pierce, PhD, associate professor of Neuroscience in Psychiatry at Penn. "This study is the first to show that the chemical effects of cocaine use can be passed down to future generations to cause a resistance to addictive behavior, indicating that paternal exposure to toxins such as cocaine can have profound effects on gene expression and behavior in their offspring."
In the current study, the team used an animal model to study inherited effects of cocaine abuse. Male rats self-administered cocaine for 60 days, while controls were administered saline. The male rats were mated with females that had never been exposed to the drug. To eliminate any influence that the males’ behavior would have on the pregnant females, they were separated directly after they mated.
The rats’ offspring were monitored to see whether they would begin to self-administer cocaine when it was offered to them. The researchers discovered that male offspring of rats exposed to the drug, but not the female offspring, acquired cocaine self-administration more slowly and had decreased levels of cocaine intake relative to controls. Moreover, control animals were willing to work significantly harder for a single cocaine dose than the offspring of cocaine-addicted rats, suggesting that the rewarding effect of cocaine was decreased.
In collaboration with Ghazaleh Sadri-Vakili, MS, PhD, from MGH, the researchers subsequently examined the animals’ brains and found that male offspring of the cocaine-addicted rats had increased levels of a protein in the prefrontal cortex called brain-derived neurotrophic factor (BDNF), which is known to blunt the behavioral effects of cocaine.
"We were quite surprised that the male offspring of sires that used cocaine didn’t like cocaine as much," said Pierce. "While we identified one change in the brain that appears to underlie this cocaine resistance effect, there are undoubtedly other physiological changes as well and we are currently performing more broad experiments to identify them. We also are eager to perform similar studies with more widely used drugs of abuse such as nicotine and alcohol."
The findings suggest that cocaine use causes epigenetic changes in sperm, thereby reprogramming the information transmitted between generations. The researchers don’t know exactly why only the male offspring received the cocaine-resistant trait from their fathers, but speculate that sex hormones such as testosterone, estrogen and/or progesterone may play a role.
(Source: eurekalert.org)
Faulty gene linked to condition in infants
Researchers at King’s College London have for the first time identified a defective gene at the root of Vici syndrome, a rare inherited disorder which affects infants from birth, leading to impaired development of the brain, eyes and skin, and progressive failure of the heart, skeletal muscles and the immune system.
Published in the journal Nature Genetics, the study identified a defect in the EPG-5 gene, indicating a genetic cause of the condition which was previously unknown. Researchers at King’s and Guy’s & St Thomas’ NHS Foundation Trust, part of King’s Health Partners, analysed the DNA of 18 infants with Vici syndrome and identified the inactivity of EPG-5 as a major cause of the condition.
Infants born with Vici syndrome inherit two copies of the defective gene, one from each parent. Although there are only around 50 known cases of the disorder across the world, researchers believe the precise incidence is unknown due to lack of awareness of this condition. Dr Heinz Jungbluth, from the Children’s Neuroscience Centre at St Thomas’ Hospital, who led the study along with Professor Mathias Gautel from the Cardiovascular Division at King’s, said: ‘Vici syndrome is likely to be under-diagnosed as there is potential for misdiagnosis, particularly when you consider the many different organ systems affected by Vici and the significant overlap with other, more common disorders.’
The study also highlighted the ‘autophagy’ process and the role of EPG-5 in causing this mechanism to fail. Autophagy is a highly regulated cellular process that removes damaged or unwanted components, which is crucial for the health of all cell types, including those involved in muscles, the immune system and brain development. Abnormalities in this process have been implicated previously in neurodegenerative conditions, but defects causing disorders of normal development such as Vici syndrome have rarely been reported. The researchers suggest that autophagy could play a key role in causing a range of disorders, offering the potential for treatment of other conditions. Dr Jungbluth said: ‘Although the condition is very rare, it is likely that insights provided by research into Vici syndrome will also be transferable to the diagnosis and therapy of neurodegenerative and neurodevelopmental disorders, and a wider range of primary muscle conditions.’
Professor Gautel added: ‘Having identified where this genetic defect occurs we are now able to explore potential interventions. For instance, there is the possibility of enhancing other pathways unaffected by the EPG-5 gene, or by preventing use of the defective pathway in the first place.’
As the defective gene is inherited from both the mother and father, there is also the possibility of screening families with a known history of Vici syndrome. Professor Gautel said: ‘Mothers could be offered preimplantation diagnosis, which involves removing a cell from an embryo when it is around three days old and testing it for genetic disorders, so that an unaffected embryo can be implanted into the mother’s womb, if necessary.’
(Source: kcl.ac.uk)
A Key Gene for Brain Development
About one in ten thousand babies is born with an abnormally small head. The cause for this disorder – which is known as microcephaly – is a defect in the develoment of the embryonic brain. Children with microcephaly are severely retarded and their life expectancy is low. Certain cases of autism and schizophrenia are also associated with the dysregulation of brain size.
The causes underlying impaired brain development can be environmental stress (such as alcohol abuse or radiation) or viral infections (such as rubella) during pregnancy. In many cases, however, a mutant gene causes the problem.
David Keays, a group leader at the IMP, has now found a new gene which is responsible for Microcephaly. Together with his PhD-student Martin Breuss, he was able to identify TUBB5 as the culprit. The gene is responsible for making tubulins, the building blocks of the cell’s internal skeleton. Whenever a cell moves or divides, it relies on guidance from this internal structure, acting like a scaffold.
The IMP-researchers, together with collaborators at Monash University (Victoria, Australia), were able to interfere with the function of the TUBB5 in the brains of unborn mice. This led to massive disturbances in the stem cell population and impaired the migration of nerve cells. Both, the generation of large numbers of neurons from the stem cell reservoir and their correct positioning in the cortex, are essential for the development of the mammalian brain.
To determine whether the findings are also relevant in humans, David Keays collaborates with clinicians from the Paris-Sorbonne University. The French team led by Jamel Chelly, examined 120 patients with pathological brain structures and severe disabilities. Three of the children were found to have a mutated TUBB5-gene.
This information will prove vital to doctors treating children with brain disease. It will allow the development of new genetic tests which will form the basis of genetic counseling, helping parents plan for the future. By understanding how different genes cause brain disorders, it is hoped that one day scientists will be able to create new drugs and therapies to treat them.
The new findings by the IMP-researchers are published in the current issue of the journal “Cell Reports”. For David Keays, understanding the function of TUBB5 is the key to understanding brain development. “Our project shows how research in the lab can help improve lives in the clinic”, he adds.
The paper “Mutations in the β-tubulin Gene TUBB5 Cause Microcephaly with Structural Brain Abnormalities” is published on December 13, 2012, in the online Journal Cell Reports.
Fragile X Protein Linked to Nearly 100 Genes Involved in Autism
Doctors have known for many years that patients with fragile X syndrome, the most common form of inherited intellectual disability, are often also diagnosed with autism. But little has been known about how the two diagnoses are related.
Now a collaborative research effort at Duke University Medical Center and Rockefeller University has pinpointed the precise genetic footprint that links the two. The findings, published online in the journal Nature on Dec. 12, 2012, point the way toward new genetic testing that could more precisely diagnose and categorize the spectrum of autism-related disorders.
Fragile X syndrome is the most well understood single-gene cause of autism. It results from defects on a small part of the genetic code for a protein that researchers have dubbed the fragile X mental retardation protein, or FMRP.
Normally, FMRP plays an important role controlling production of other proteins in the brain and other organs. It does this by looking for specific genetic patterns located on the messages encoding proteins. When it locates these genetic flags, it attaches to them and, along with other signals, controls where and when protein is made.
In fragile X syndrome, this process breaks down because a defect in the gene causes the body to produce too little, or in some cases, none of the FMRP protein. As a result, additional proteins it would normally regulate are made in the wrong place and at the wrong time. Until now, little was known about how this process worked in people with the autism.
Using a combination of laboratory experiments and advanced bioinformatics, the research team, led by Thomas Tuschl, PhD, a Howard Hughes Medical Institute investigator at Rockefeller University, and Uwe Ohler, PhD, an associate professor in Biostatistics and Bioinformatics at the Duke Institute for Genome Sciences & Policy, identified both the genetic flags that FMRP is looking for and the genes it targets.
(Image courtesy of www.sueblimely.com)
Genetic Researchers Grow A Fish That Has Legs
The fossil record has a lot of strange stories to tell about the evolution of life on Earth, and one of the strangest is how life moved from sea to land. Though clues from the record give the rough outlines of the story—limbs grew from fins in a series of stages in which fins grew longer and narrower—scientists are still filling in the details, trying to determine what genetic changes might have allowed the limbs to grow.
One of the best ways to learn those details is to reproduce the changes that occurred some 400 million years ago—to virtually back in time and alter the development of the land-goer’s living ancestors and see what happens.
Which is what biologist Renata Freitas and colleagues were up to when they added some extra Hoxd13—a gene known to play a role in distinguishing body parts during embryological development— to the tip of a zebrafish embryo’s fin, and watched as the developing fin kept growing.
Their lab findings led the researchers to hypothesize that the secret to limb development may have been a new element in some lobe-finned fish’s DNA. When present, this DNA element would have helped turn on the Hoxd13 gene on the fish embryo’s fins, leading them to lengthen and grow into limbs.
Would you make your DNA and health data public if it may help cure disease?
The 39-year-old Toronto professional is the brave or, perhaps, foolhardy Canadian volunteer who will be first to go public this week in a project that will reveal the coded secrets hidden in her genome, the six billion chemical units of her DNA.
They may include not only her susceptibility to diseases such as cancer but the levels of her propensities to alcoholism, depression or obesity, or even personality traits such as risk-taking. She will also provide the personal context required to make sense of the biological data – her age, height, weight; medical records; details about how she lives, works and plays; and even her photo if she’s game.
This information – everything but her name and address – will be placed on an online database that will be open and available to anyone in the world. Even in this digital age of perpetual show and tell, exposing oneself so completely amounts to a molecular full monty: Even without a name attached, any participant might be identifiable.
Ms. Davies is making a leap of faith that at least 100,000 of her fellow citizens are also being asked to take – even though Canadian law has no strict guidelines on how this confidential knowledge might be used or misused by any insurance company, employer, police force or identity thief.
Britain launches genome database for patients’ DNA
Up to 100,000 Britons suffering from cancer and rare diseases are to have their genetic codes fully sequenced and mapped as part of government plans to build a DNA database to boost drug discovery and development.
Prime Minister David Cameron said on Monday he wanted Britain to “push the boundaries” of scientific research by being the first country to introduce genetic sequencing into a mainstream health service.
His government has set aside 100 million pounds ($160 million) for the project in the taxpayer-funded National Health Service (NHS) over the next three to five years.
"Britain has often led the world in scientific breakthroughs and medical innovations, from the first CT scan and test-tube baby through to decoding DNA," he said in a statement.
"It is crucial that we continue to push the boundaries and this new plan will mean we are the first country in the world to use DNA codes in the mainstream of the health service."
The government said building a database of DNA profiles will give doctors more advanced understanding of a patient’s genetic make-up, their illness and their treatment needs. This should help those who are sick get access to the right drugs and more personalized care more quickly.
The database should also help scientists develop new drugs and other treatments which experts predict “could significantly reduce the number of premature deaths from cancer within a generation”, Cameron’s office said in a statement,
"By unlocking the power of DNA data, the NHS will lead the global race for better tests, better drugs and above all better care," Cameron said.
"If we get this right, we could transform how we diagnose and treat our most complex diseases not only here but across the world, while enabling our best scientists to discover the next wonder drug or breakthrough technology."