Monthly Archives: April 2014

Human Genetics Biology Project
Type 1 Diabetes documentary.

By: Brett Rawlings

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Human Genetics Biology Project - Video

Brad Swonetz/Redux/Eyevine

As a teenager in Germany, Steve Horvath, his identical twin Markus and their friend Jrg Zimmermann formed 'the Gilgamesh project', which involved regular meetings where the three discussed mathematics, physics and philosophy. The inspiration for the name, Horvath says, was the ancient Sumerian epic in which a king of Uruk searches for a plant that can restore youth. Fittingly, talk at the meetings often turned to ideas for how science might extend lifespan.

At their final meeting in 1989, the trio made a solemn pact: to dedicate their careers to pursuing science that could prolong healthy human life. Jrg set his eye on computer science and artificial intelligence, Markus on biochemistry and genetics, and Steve says that he planned to use mathematical modelling and gene networks to understand how to extend life. Jrg did end up working in artificial intelligence, as a computer scientist at the University of Bonn in Germany, but Markus fell off the wagon, his brother says, and became a psychiatrist.

Steve, now a human geneticist and biostatistician at the University of California, Los Angeles (UCLA), says that he finally feels poised to make good on the promise. Through a hard-fought project that involved years of solo work, multiple rejections by editors and reviewers and battling through the loss of a child, he has gathered and analysed data on more than 13,000 human tissue samples1. The result is the a cellular biological clock that has impressed researchers with its accuracy, how easy it is to read and the fact that it ticks at the same rate in many parts of the body with some intriguing exceptions that might provide clues to the nature of ageing and its maladies.

Horvath's clock emerges from epigenetics, the study of chemical and structural modifications made to the genome that do not alter the DNA sequence but that are passed along as cells divide and can influence how genes are expressed. As cells age, the pattern of epigenetic alterations shifts, and some of the changes seem to mark time. To determine a person's age, Horvath explores data for hundreds of far-flung positions on DNA from a sample of cells and notes how often those positions are methylated that is, have a methyl group attached.

He has discovered an algorithm, based on the methylation status of a set of these genomic positions, that provides a remarkably accurate age estimate not of the cells, but of the person the cells inhabit. White blood cells, for example, which may be just a few days or weeks old, will carry the signature of the 50-year-old donor they came from, plus or minus a few years. The same is true for DNA extracted from a cheek swab, the brain, the colon and numerous other organs. This sets the method apart from tests that rely on biomarkers of age that work in only one or two tissues, including the gold-standard dating procedure, aspartic acid racemization, which analyses proteins that are locked away for a lifetime in tooth or bone.

I wanted to develop a method that would work in many or most tissues. It was a very risky project, Horvath says. But now the gamble seems to be paying off. By the time his findings were finally published last year1, the clock's median error was 3.6 years, meaning that it could guess the age of half the donors to within 43 months for a broad selection of tissues. That accuracy improves to 2.7 years for saliva alone, 1.9 years for certain types of white blood cell and 1.5 years for the brain cortex. The clock shows stem cells removed from embryos to be extremely young and the brains of centenarians to be about 100.

Such tight correlations suggest there is something seemingly immutable going on in cells, says Elizabeth Blackburn of the University of California, San Francisco, who won a Nobel prize for her research on telomeres caps on the ends of chromosomes that shorten with age. It could be a clue to undiscovered biology, she suggests. And there may be medical implications in cases in which epigenetic estimates do not match a person's birth certificate.

In the months since Horvath's paper appeared, other researchers have replicated and extended the results. The study has stirred up excitement about potential applications, but also debate about the underlying biology at work.

It's something new, says Peter Visscher, chair of quantitative genetics at the University of Queensland in Australia. If he's right that there is something like an inherently epigenetic clock at work in ageing, that is very interesting. It must be important.

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Biomarkers and ageing: The clock-watcher

By ASHLEY CHU

With a five-year, $10 million grant from the National Institute of Child Health and Human Development, a Center for Reproductive Genetics will be established on both Cornells Ithaca and Weill Cornell Medical School campuses.

The CRG is aimed at understanding the genetic basis for processes that give rise to healthy gametes for reproduction, said Prof. Paula Cohen, biomedical sciences, who is director of the CRG. If you dont have healthy eggs and sperm, then this can lead to all sorts of issues such as birth defects, miscarriages, preterm delivery and infertility.

This grant which the University announced it had received on April 1 marks a significant milestone for groups researching reproductive genetics, according to Cohen.

This is the first time that a number of groups are being funded collectively to ask the same questions and, as such, this is likely to bring rapid advances in our knowledge, Cohen said. In science, so often we work in isolated bubbles, but this center grant, which encompasses five different investigators in four different projects, is likely to lead to bigger and quicker advances.

The center aims to address these issues at the basic research level in a joint effort between the two campuses, which Cohen describes as the bench-to-bedside approach.

Given that the CRG is based on both the Ithaca and Weill Cornell campuses, we hope to translate our findings from the lab into the clinic to help infertile couples and to understand how birth defects arise in humans, Cohen said.

The CRGs research focus is to understand how healthy gametes are produced, but more specifically, how the defects that arise during gametogenesis are produced.

This grant will enable cutting-edge research, using the latest technological advances and discoveries, to better understand fundamental processes in mammalian spermatogenesis. Jen Grenier

Given how important healthy eggs and sperm are for sexual reproduction and how conserved the genetic processes are that give rise to these cells, its surprising to find that human gametogenesis the process that gives rise to sperm and eggs is extremely error prone, Cohen said. In fact, between 40 and 60 percent of human eggs contain the wrong complement or number of chromosomes, and this situation can lead to spontaneous miscarriages or birth defects such as Down syndrome and Klinefelter syndrome.

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Center for Reproductive Genetics Established With $10 Million Grant

A new genome analysis method has confirmed that Neanderthals interbred with ancestors of Eurasians, a new study reports.

The findings, published in the April 2014 issue of the journal Genetics, explains how Neanderthals most likely interbred with modern humans after they migrated out of Africa. The new technique ruled out the other popular theory that humans who left Africa evolved from the same ancestral subpopulation where Neanderthals evolved from.

"Our approach can distinguish between two subtly different scenarios that could explain the genetic similarities shared by Neanderthals and modern humans from Europe and Asia," Konrad Lohse, study co-author and population geneticist at the University of Edinburgh in Scotland,said in a statement.

The method differs from others in that it used one genome from Neanderthals, Eurasians, Africans and chimpanzees rather than comparing genomes from many modern humans. The same method will have other uses to, especially in studies of suspected interbreeding where limited samples are available.

We did a bunch of math to compute the likelihood of two different scenarios," Laurent Frantz, study co-author and evolutionary biologist at Wageningen University in the Netherlands,told The Verge. "We were able to do that by dividing the genome in small blocks of equal lengths from which we inferred genealogy."

Scientists developed the method after studying the history of insect populations in Europe and rare pig species in Southeast Asia.

"This work is important because it closes a hole in the argument about whether Neanderthals interbred with humans. And the method can be applied to understanding the evolutionary history of other organisms, including endangered species," Mark Johnston, editor-in-chief of the journal Genetics, said.

Frantz thinks the study may also change the way evolution is perceived.

"There have been a lot of arguments about what happened to these species," he said. "Some think that we outcompeted [other hominins] or that they were killed by humans, but now we can see that it's not that simple."

Neanderthals may have been recruited into certain human populations that they may have been in contact with on a daily basis. This goes against a commonly held perception of evolution where species struggled to survive.

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Neanderthals Interbred With Humans? New Method Closes A Hole In Evolution Argument