Genetics and DNA
Important Advance in Understanding Human Genome
The Encyclopedia of DNA Elements (ENCODE) project, an international collaboration of more than 440 scientists in 32 labs in United States, the United Kingdom, Spain, Singapore and Japan, has announced the results of a five-year study of the regulation and organization of the human genome.
Vitruvian Man by Leonardo da Vinci / the ENCODE project’s logo (Stanford University / leonardodavinci.stanford.edu / ENCODE project)
The results have been published in one main integrative paper and five other papers in the journalNature, 18 papers in Genome Research, six papers in Genome Biology and a series of reviews in theJournal of Biological Chemistry.
“The ENCODE project not only generated an enormous body of data about our genome, but it also analyzed many issues to better understand how the genome functions in different types of cells. These insights from integrative analyses are really stories about how molecular machines interact with each other and work on DNA to produce the proteins and RNAs needed for each cell to function within our bodies,” said Dr Ross Hardison of Pennsylvania State University, a co-author of reviews in the Journal of Biological Chemistry.
“The Journal of Biological Chemistry recognized that the results from the ENCODE project also would catalyze much new research from biochemists and molecular biologists around the world. Hence, the journal commissioned these articles not only to communicate the insights from the papers now being published but also to stimulate more research in the broader community,” he said.
The human genome consists of about 3 billion DNA base pairs, but only a small percentage of DNA actually codes for proteins. The roles and functions of the remaining genetic information were unclear to scientists and even referred to as ‘junk DNA.’ But the results of the ENCODE project is filling this knowledge gap. The findings revealed that more than 80 percent of the human genome is associated with biological function.
The study showed in a comprehensive way that proteins switch genes on and off regularly – and can do so at distances far from the genes they regulate – and it determined sites on chromosomes that interact, the locations where chemical modifications to DNA can influence gene expression, and how the functional forms of RNA can regulate the expression of genetic information.
The results establish the ways in which genetic information is controlled and expressed in specific cell types and distinguish particular regulatory regions that may contribute to diseases.
“The deeper knowledge of gene regulation coming from the ENCODE project will have a positive impact on medical science,” Dr Hardison said. “For example, recent genetic studies have revealed many genomic locations that can affect a person’s susceptibility to common diseases. The ENCODE data show that many of these regions are involved in gene regulation, and the data provide hypotheses for how variations in these regions can affect disease susceptibility.”
Bibliographic information: The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74; doi: 10.1038/nature11247
source: http://www.sci-news.com/genetics/article00569.html, http://www.youtube.com/watch?v=PsV_sEDSE2o
Now archaeologists and geneticists are beginning to tell the same story, thanks to improved estimates of DNA’s mutation rate — the molecular clock that underpins genetic dating1–4. “It’s incredibly vindicating to finally have some reconciliation between genetics and archaeology,” says Jeff Rose, an archaeologist at the University of Birmingham, UK. Archaeologists and geneticists may now be able to tackle nuanced questions about human history with greater confidence in one another’s data. “They do have to agree,” says Aylwyn Scally, an evolutionary genomicist at the Wellcome Trust Sanger Institute in Hinxton, UK. “There was a real story.”
The concept of a DNA clock is simple: the number of DNA letter differences between the sequences of two species indicates how much time has elapsed since their last common ancestor was alive. But for estimates to be correct, geneticists need one crucial piece of information: the pace at which DNA letters change.
- Fathers bequeath more mutations as they age
- Human migrations: Eastern odyssey
- Ancient DNA reveals secrets of human history
Geneticists have previously estimated mutation rates by comparing the human genome with the sequences of other primates. On the basis of species-divergence dates gleaned — ironically — from fossil evidence, they concluded that in human DNA, each letter mutates once every billion years. “It’s a suspiciously round number,” says Linda Vigilant, a molecular anthropologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. The suspicion turned out to be justified.
In the past few years, geneticists have been able to watch the molecular clock in action, by sequencing whole genomes from dozens of families5 and comparing mutations in parents and children. These studies show that the clock ticks at perhaps half the rate of previous estimates, says Scally.
In a review published on 11 September1,Scally and his colleague Richard Durbin used the slower rates to reevaluate the timing of key splits in human evolution. “If the mutation rate is halved, then all the dates you estimate double,” says Scally. “That seems like quite a radical change.” Yet the latest molecular dates mesh much better with key archaeological dates.
Take the 400,000–600,000-year-old Sima de Los Huesos site in Atapuerca, Spain, which yielded bones attributed to Homo heidelbergensis, the direct ancestors of Neanderthals. Genetic studies have suggested that earlier ancestors of Neanderthals split from the branch leading to modern humans much more recently, just 270,000–435,000 years ago. A slowed molecular clock pushes this back to a more comfortable 600,000 years ago (see ‘Better agreement over the human story’).
SOURCE: REF. 1
A slower molecular clock could also force scientists to re-think the timing of later turning points in prehistory, including the migration of modern humans out of Africa. Genetic studies of humans around the world have suggested that the ancestors of Europeans and Asians left Africa about 60,000 years ago. That date caused many to conclude that 100,000-year-old human fossils discovered in Israel represented a dead-end migration rather than the beginning of a global exodus, says Scally. Scally’s calculations put “out of Africa” closer to 120,000 years ago, suggesting that the Israeli sites represent a launching pad for the spread of humans into Asia and Europe.
The latest genetic dates also fit with several sites in the Middle East that contain tools apparently made by modern humans but dating to around 100,000 years ago. At that time, sea levels between Africa and the Arabian Peninsula were lower than they are now, and a wetter climate would have made the peninsula lush and habitable, perhaps beckoning modern humans out of Africa. Rose, who works one such site, in Oman, says that he “has been over the moon” since reading Scally and Durbin’s paper.
The revised molecular clock may also help to settle a debate over whether humans ventured further into Asia more than 60,000 years ago, says Michael Petraglia, an archaeologist at the University of Oxford, UK, who favours an early date.
Although a slowed molecular clock may harmonize the story of human evolution, it does strange things when applied further back in time, says David Reich, an evolutionary geneticist at Harvard Medical School in Boston, Massachusetts. “You can’t have it both ways.”
For instance, the slowest proposed mutation rate puts the common ancestor of humans and orang-utans at 40 million years ago, he says: more than 20 million years before dates derived from abundant fossil evidence. This very slow clock has the common ancestor of monkeys and humans co-existing with the last dinosaurs. “It gets very complicated,” deadpans Reich.
Some researchers, including Scally, have proposed that the mutation rate may have slowed over the past 15 million years, thereby accounting for such discrepancies. Fossil evidence suggests that ancestral apes were smaller than living ones, and small animals tend to reproduce more quickly, speeding the mutation rate.
Little concrete evidence supports this idea, says Reich. He agrees that the molecular clock must be slower than was thought, but says that the question is how slow. “My strong view right now is that the true value of the human mutation rate is an open question.”
(20 September 2012)
- Scally, A. & Durbin, R. Nature Rev. Genet. 13, 745–753 (2012).
- Langergraber, K. E. et al. Proc. Natl Acad. Sci. USAhttp://dx.doi.org/10.1073/pnas.1211740109 (2012).Show context
- Hawks, J. Proc. Natl Acad. Sci. USA http://dx.doi.org/10.1073/pnas.1212718109 (2012).Show context
- Sun, J. X. et al. Nature Genet. http://dx.doi.org/10.1038/ng.2398 (2012).Show context
- Kong, A. et al. Nature 488, 471–475 (2012).
Show context source: http://www.nature.com/news/studies-slow-the-human-dna-clock-1.11431
World’s First Genetically Modified Babies ‘Created’ in US
In a developing story, the Daily Mail is now reporting that the very first (admitted) group of genetically modified babies have been ‘created’ in the United States. The scientists involved reportedly announced the result on the night of June 27th, stating that 30 babies were born using genetic modification techniques. Furthermore, 2 of the babies tested were found to contain genes from a total of 3 different parents. The experiment also lasted over 3 years or more according to the researchers, which may be one of many.
The ‘GM babies’ were born into women who had trouble conceiving their own children. In order to ‘birth’ the babies, extra genes from a female donor were inserted into the women’s eggs before they were fertilized. After conception, scientists fingerprinted 2 of the one-year-old children and confirmed that they inherited DNA from 3 adults — one man and 2 women. What this means is that due to inheriting these extra genes through the genetic modification process, they will now be able to pass them along to their offspring. In other words, these genetically modified babies — if allowed to mate with non-GM humans — could potentially alter the very genetic coding of generations to come.
Genetecists state that this genetic modification method may one day be used to create babies “with extra, desired characteristics such as strength or high intelligence.”
The news comes after it was previously reported by British scientists that scientists were creating human-animal ‘monsters’. Such reports highlight the fact that rampant genetic experimentation is already taking place on many humans around the world, which has led a large number of scientists to call for new rules regarding the outlandish practice. Chinese scientists have already admittedly inserted human stem cells into goat fetuses, and United States researchers have actively researched the concept of engineering a mouse with human brain cells.
Many experts are now speaking out against the announcement, including leading fertility experts and major organizations. John Smeaton, national director of the Society for the Protection of Unborn Children, said:
“It is a further and very worrying step down the wrong road for humanity”
Genes thought to affect IQ might not
Oct. 2, 2012
the Association for Psychological Science
and World Science staff
Most of the genes long thought to be linked to intelligence, simply aren’t, a new study has concluded.
“We are not saying the people who did earlier research in this area were foolish,” said Christopher Chabris, a psychological scientist at Union College in New York who co-led the study. “They were using the best technology and information they had available.”
Nor do Chabris and his colleagues deny that intelligence is hereditary and genetic. But they say it now turns out that this intangible quality is probably too complex to sum up in a few genes. It may be some time before researchers can identify intelligence’s specific genetic roots, say the researchers, whose findings are published online in the research journal Psychological Science.
Chabris and David Laibson, a Harvard economist, led an international team of researchers that analyzed a dozen genes using large data sets that included both intelligence testing and genetic data. In nearly every case, the researchers found that intelligence could not be linked to the specific genes tested.
“We only found one gene that appeared to be associated with intelligence, and it was a very small effect. This does not mean intelligence does not have a genetic component. It means it’s a lot harder to find the particular genes, or the particular genetic variants, that influence the differences in intelligence,” said Chabris.
It had long been believed, on the basis of studies of identical and fraternal twins, that intelligence was a heritable trait. The new research affirms that conclusion. But older studies that picked out specific genes had flaws, Chabris said, primarily because of technological limits that prevented researchers from probing more than a few locations in the human genome to find genes that affected intelligence.
Also, “at the time, it was believed that individual genes would have a much larger effect — they were expecting to find genes that might each account for several IQ points,” Chabris explained. IQ is a widespread measure of intelligence in which average intelligence is scored as 100, while higher or lower intelligence are scored higher or lower. The score is meant to measure a person’s intelligence as compared to the average for their age group, as a percentage.
Chabris said additional research is needed to determine the exact role genes play in intelligence.
“As is the case with other traits, like height, there are probably thousands of genes and their variants that are associated with intelligence,” he said. “And there may be other genetic effects beyond the single gene effects. There could be interactions among genes, or interactions between genes and the environment. Our results show that the way researchers have been looking for genes that may be related to intelligence — the ‘candidate gene’ method — is fairly likely to result in false positives, so other methods should be used.”
DNA molecules can ‘teleport’, Nobel Prize winner claims
Experiment spots spooky quantum imprinting effect
A Nobel Prize winning biologist has ignited controversy after publishing details of an experiment in which a fragment of DNA appeared to ‘teleport’ or imprint itself between test tubes.
According to a team headed by Luc Montagnier, previously known for his work on HIV and AIDS, two test tubes, one of which contained a tiny piece of bacterial DNA, the other pure water, were surrounded by a weak electromagnetic field of 7Hz.
Eighteen hours later, after DNA amplification using a polymerase chain reaction, as if by magic the DNA was detectable in the test tube containing pure water.
Oddly, the original DNA sample had to be diluted many times over for the experiment to work, which might explain why the phenomenon has not been detected before, assuming that this is what has happened.
The phenomenon might be very loosely described as ‘teleportation’ except that the bases project or imprint themselves across space rather than simply moving from one place to another.
To be on the safe side, Montagnier then compared the results with controls in which the time limit was lowered, no electromagnetic field was present or was present but at lower frequencies, and in which both tubes contained pure water. On every one of these, he drew a blank.
The possible quantum effect – the apparent imprinting of the DNA on the water – is not in itself the most contentious element of the experiment, so much as the relatively long timescales over which it appears to manifest itself. Quantum phenomena are assumed to show their faces in imperceptible fractions of a second and not seconds minutes and hours, and usually at very low temperatures approaching absolute zero.
Revealing a process through which biology might display the underlying ‘quantumness’ of nature at room temperature would be startling.
Montagnier’s experiment will have to be repeated by others to have any hope of being taken seriously. So far, some scientists have been publically incredulous.
“It is hard to understand how the information can be stored within water over a timescale longer than picoseconds,” said the Ruhr University in Bochum’s Klaus Gerwert, quoted by New Scientist magazine, which broke the story (requires registration).
What does all of this mean? It could be that the propagation of life is able to make use of the quantum nature of reality to project itself in subtle ways, as has been hinted at in previous experiments. Alternatively, it could be that life itself is a complex projection of these quantum phenomena and utterly depends on them in ways not yet understood because they are incredibly hard to detect.
Speculatively, (and Montagnier doesn’t directly suggest anything so unsubstantiated), it could also be the little-understood quantum properties of the water molecule and not just its more obvious chemical bonding properties that gives it such a central role in the bio-engineering of life-forms. Water might be a good medium in which DNA can copy itself using processes that hint at quantum entanglement and ‘teleportation’ (our term).
Montagnier’s paper goes on to discuss the phenomenon he claims to have uncovered using ‘quantum field theory’ within the context of his personal interest, disease propagation.