Clipmarks | Silkweaver's 'genetics' clips

DNA could reveal your surname

Fri, 10 Oct 2008 23:11:56 GMT

clipped by: Silkweaver
clipper's remarks: Cool and... frightening

Scientists at the world-leading Department of Genetics at the University of Leicester – where the revolutionary technique of genetic fingerprinting was invented by Professor Sir Alec Jeffreys- are developing techniques which may one day allow police to work out someone's surname from the DNA alone.

Doctoral research by Turi King has shown that men with the same British surname are highly likely to be genetically linked. The results of her research have implications in the fields of forensics, genealogy, epidemiology and the history of surnames.

Dr King said: "In Britain, surnames are passed down from father to son. A piece of our DNA, the Y chromosome, is the one part of our genetic material that confers maleness and is passed, like surnames, from father to son. Therefore, a link could exist between a man's surname and the type of Y chromosome he carries. A simple link between name and Y chromosome could in principle connect all men sharing a surname into one large family tree.

Tags: dna, genealogy, forensics

Molecular Biology - A video

Tue, 30 Sep 2008 17:53:21 GMT

clipped by: Silkweaver

Clip Source: mrbarlow.wordpress.com

Molecular biology is really hard to understand.

For example, in each cell of our body there are 3 billion letters of genetic code in our DNA. This code controls everything our cells do. Particularly, the code contains instructions for making proteins that have different functions around the body.

[Video]

I think visualising this really complex stuff can help you understand it. Fortunately, so does Drew Berry from the Walter and Eliza Hall Institute of Medical Research (WEHI). He runs WEHI TV and creates heaps of molecular animations. Here is an extended clip explaining an awful lot of stuff:

Tags: biology, genetics, science, molecular biology

23andMe slashes price on personal genetics test

Tue, 09 Sep 2008 23:55:01 GMT

clipped by: Silkweaver
clipper's remarks: Along with providing genetic information to individuals, 23andMe is also compiling databases of customers' genetic information to make available to researchers seeking new insights into those links.

The price cut will ideally mean an influx of new information that will speed discoveries in the lab, said Linda Avey, who co-founded the Mountain View-based company last November.

Clip Source: www.physorg.com

A Google-backed startup that analyzes customers' genetic makeup to predict health risks and provide ancestry information has slashed the price on its personal DNA test, the company announced Tuesday.

The decision by 23andMe Inc. to cut the price of its test from $999 to $399 could herald a price war in the small but buzz-heavy marketplace for direct-to-consumer genetic testing. The company's main competitors charge anywhere from just under $1,000 to $2,500 for similar services.

According to 23andMe, next-generation DNA analysis chips have made the process of scanning a person's genes significantly cheaper.

By cutting the price of its service, the company hopes to increase demand and hasten the day when a full genetic screening becomes routine medical practice, said 23andMe co-founder Anne Wojcicki.

"We really believe strongly that at some point everyone who's born will be genotyped. You'll have your information and you'll use that to help guide some of your health care decisions."

Tags: genome, dna analysis

“Junk DNA” May Have Triggered Key Evolutionary Changes in Human Thumb and Foot

Mon, 08 Sep 2008 01:36:34 GMT

clipped by: Silkweaver
clipper's remarks: A rapidly evolving sequence from the human genome drives gene activity in the developing thumb, wrist and ankle of mouse embryos, suggesting the sequence may have contributed to key evolutionary changes in the human limbs that allowed us to walk upright and use tools.

An indication of their biological importance, many of these non-coding sequences have remained similar, or “conserved,” even across distantly related vertebrate species such as chickens and humans. Recent functional studies suggest some of these “conserved non-coding sequences” control the genes that direct human development.

Clip Source: opa.yale.edu

Out of the 3 billion genetic letters that spell out the human genome, Yale scientists have found a handful that may have contributed to the evolutionary changes in human limbs that enabled us to manipulate tools and walk upright.

Results from a comparative analysis of the human, chimpanzee, rhesus macaque and other genomes reported in the journal Science suggest our evolution may have been driven not only by sequence changes in genes, but by changes in areas of the genome once thought of as “junk DNA.”

Those changes activated genes in primordial thumb and big toe in a developing mouse embryo, the researchers found.

“Our study identifies a potential genetic contributor to fundamental morphological differences between humans and apes

In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic “switches” to turn genes on or off.

Tags: genetics, junk dna, ontogenesis

Cancer Redefined

Sat, 06 Sep 2008 00:37:54 GMT

clipped by: Silkweaver
clipper's remarks: The studies have also revealed to scientists looking to treat these diseases just how difficult their challenge really is. "For the first time, these are giving you the complete picture of these two cancer types," Velculescu says. "This is important, because if we ever want to cure cancer, we have to know what's wrong with it. And unfortunately, what appears to be wrong with most cancers is more complicated than we may have anticipated."

Clip Source: www.technologyreview.com

In three new studies that could redefine how cancer is viewed, researched, and treated, scientists have created a detailed map of the genetic mutations that underlie two of the deadliest forms of the disease: pancreatic cancer and glioblastoma

Scientists have known for decades that cancer develops in response to genetic changes that cause cells to grow and divide uncontrollably. But uncovering each of these changes, and understanding how they lead to disease, is a Herculean task--one that involves sequencing and analyzing upward of 100 different kind of tumors, with hundreds of different patient samples of each.

And while some believe that systematically cataloging the mutations could provide unprecedented insight into fighting or even preventing cancers, others believe that the high cost of such research might not be worth the rewards. These papers provide the first glimpse at what the rewards could be.

Tags: cancer, genetics

Exploding chromosomes fuel research about evolution of genetic storage

Sat, 23 Aug 2008 13:01:12 GMT

clipped by: Silkweaver
clipper's remarks: Dinoflagellates are stuffed at the core with tightly compacted chromosomes, yet these organisms contain neither histones nor nucleosomes. "What takes care of neutralizing DNA, to allow chromosomes to condense?" Levi-Setti asked. "Most biology books do not tell you."

Other scientists had already identified positively charged atoms called cations as neutralizing factors. They found that dinoflagellate chromosomes explode upon the removal of calcium and magnesium cations.

Levi-Setti has produced the first images of the distribution of these cations in dinoflagellate chromosomes. These images verify that cations, mainly of calcium and magnesium, neutralize DNA's enormous negative charge, and further suggest a critical role in folding the protein as well.

The finding raises questions about the evolution of chromosomes, Rizzo said. "Did dinoflagellates once have histones and then lost them? Or did dinoflagellates never have histones and just 'figured out' a different way to fold lar

Clip Source: www.labspaces.net

Human cells somehow squeeze two meters of double-stranded DNA into the space of a typical chromosome, a package 10,000 times smaller than the volume of genetic material it contains.

"It is like compacting your entire wardrobe into a shoebox," said Riccardo Levi-Setti, Professor Emeritus in Physics at the University of Chicago.

Now research into single-celled, aquatic algae called dinoflagellates is showing that these and related organisms may have evolved more than one way to achieve this feat of genetic packing.

Even so, the evolution of chromosomes in dinoflagellates, humans and other mammals seem to share a common biochemical basis

Packing the whole length of DNA into tiny chromosomes is problematic because DNA carries a negative charge that, unless neutralized, prevents any attempt at folding and coiling due to electrostatic repulsion.

In humans and mammals, proteins called histones partially neutralize the DNA's negative charge.

Tags: genetics, chromosomes, evolution

THE ORIGIN OF BIOLOGICAL INFORMATION

Sun, 10 Aug 2008 22:13:40 GMT

clipped by: Silkweaver
clipper's remarks: Yet Muller and Newman insist that population genetics, and thus evolutionary biology, has not identified a specifically causal explanation for the origin of true morphological novelty during the history of life. Central to their concern is what they see as the inadequacy of the variation of genetic traits as a source of new form and structure. They note, following Darwin himself, that the sources of new form and structure must precede the action of natural selection (2003:3)–that selection must act on what already exists. Yet, in their view, the “genocentricity” and “incrementalism” of the neo-Darwinian mechanism has meant that an adequate source of new form and structure has yet to be identified by theoretical biologists. Instead, Muller and Newman see the need to identify epigenetic sources of morphological innovation during the evolution of life. In the meantime, however, they insist neo-Darwinism lacks any “theory of the generative”

Clip Source: www.answertheskeptic.com

In a recent volume of the Vienna Series in a Theoretical Biology (2003), Gerd B. Muller and Stuart Newman argue that what they call the “origination of organismal form” remains an unsolved problem.

In making this claim, Muller and Newman (2003:3-10) distinguish two distinct issues, namely

(1) the causes of form generation in the individual organism during embryological development and

(2) the causes responsible for the production of novel organismal forms in the first place during the history of life.

To distinguish the latter case (phylogeny) from the former (ontogeny), Muller and Newman use the term “origination” to designate the causal processes by which biological form first arose during the evolution of life.

They further argue that we know more about the causes of ontogenesis, due to advances in molecular biology, molecular genetics and developmental biology, than we do about the causes of phylogenesis–the ultimate origination of new biological forms during the remote past.

Tags: theoretical biology, evolution, phylogeny, ontogeny

Brain Imaging Helps Explain Behavior

Sat, 09 Aug 2008 01:23:22 GMT

clipped by: Silkweaver
clipper's remarks: The fMRI study showed that, during the viewing of angry faces, the activity of a structure called the insula, involved in the response to unpleasant situations, depended on which version of the CREB1 gene a participant inherited.

“We were surprised to see that variation in the CREB1 gene would account for more than 20 percent of the difference in how healthy participants weighed different options and expressed specific preferences,”

Clip Source: psychcentral.com

An innovative research study uses imaging techniques to identify a connection between brain reward systems and a gene variant

The findings have implications for how genes may influence healthy or dysfunctional behavior involving choices in many different areas

This work helps connect our psychological understanding of why we like some things and not others with the genetic mechanisms that define our range of behaviors

The current report connects molecular genetics with earlier studies of choice and preference and with investigations of the brain’s reward circuitry

The researchers focused on a gene called CREB1 that has been implicated in animal studies of the brain’s reward/aversion function

found that depressed men with a particular variation near the gene coding for CREB report greater difficulty suppressing anger

associated the same variation with a threefold greater risk of suicidal thinking in major depressive disorder patients soon after beginning antidepressant therapy

Tags: neuroscience, behavior, genetics

'Transsexuality gene' makes women feel like men

Sat, 02 Aug 2008 18:46:38 GMT

clipped by: Silkweaver
clipper's remarks: Complex behaviors are never the result of a single factor, or a single gene.

Clip Source: www.newscientist.com

A gene variant has been identified that appears to be associated with female-to-male transsexuality – the feeling some women have that they belong to the opposite sex.

While such complex behaviour is likely the result of multiple genes, environmental and cultural factors, the researchers say the discovery suggests that transsexuality does have a genetic component.

The variation is in the gene for an enzyme called cytochrome P17, which is involved in the metabolism of sex hormones.

Its presence leads to higher than average tissue concentrations of male and female sex hormones, which may in turn influence early brain development.

However, Janett Scott, former president of the Beaumont Society, a UK support group for transgender people, is concerned that positing a biological basis for transsexuality may encourage people to try and cure it

Tags: gender study, transexuality, genetics

The Future of Babies

Sat, 02 Aug 2008 18:34:47 GMT

clipped by: Silkweaver
clipper's remarks: Since embryos will be grown in labs, mutations to embryos could be corrected and improvements could be engineered. Yet there will be no "designer babies " because no single gene is that predictive of a "perfect" child.

Clip Source: www.popsci.com

Clip Source: www.livescience.com

Artificial wombs and experiments on human embryos grown in the lab will be commonplace and no big deal ethically in 30 years, several scientists predict.

They envision a scenario just like test-tube babies, which shocked us 30 years ago but now are fairly routine and acceptable to most people.

That is one of many predictions about the future of assisted reproduction and other baby-related medical advances in a special news report, "Making Babies: The Next 30 Years," in the July 16 issue of the journal Nature.

Newborns and 100-year-olds alike could have children. Infertility will be eradicated.

Labs will be able to generate sperm and eggs for anybody.

Human embryos will be made from sperm and egg cells derived from pluripotent stem cells (the kind that can develop into any of the body's cell types).

Fetuses will freely float in artificial placentas or uteruses of fluid, with umbilical cords attached to machines.

The old-fashioned way is cheaper and more fun and that won't change in 30 years

Tags: fertility, babies, artificial womb, genetics

Were Ancient Viruses a Key to Human Evolution?

Fri, 01 Aug 2008 23:30:05 GMT

clipped by: Silkweaver
clipper's remarks: Heidmann believes that without endogenous retroviruses mammals might never have developed a placenta, which protects the fetus and gives it time to mature, which eventually led to live birth, one of the hallmarks of human evolutionary success over birds, reptiles, and fish. Eggs cannot eliminate waste or draw the maternal nutrients required to develop the large brains that have made mammals so versatile. “These viruses made those changes possible. It is quite possible that, without them, human beings would still be laying eggs.”

Clip Source: www.dailygalaxy.com

Endogenous retroviruses, however, once they infect the DNA of a species they become part of that species: they reside within each of us, carrying a record that goes back millions of years.

These viral fragments are fossils that reside within each of us, carrying a record that goes back millions of years.

Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.

That is until Thierry Heidmann who runs the laboratory at the Institut Gustave Roussy, on the southern edge of Paris, brought one to life.

Heidmann named the virus Phoenix, after the mythical bird that rises from the ashes, because he is convinced that this virus and others like it have much to tell about the origins and the evolution of humanity.

endogenous retroviruses are two things at once: genes and viruses. And those viruses helped make us who we are today just as surely as other genes did.

I am not certain that we would have survived as a species without them.

Tags: genetics, virology, evolution

10 Big Questions for Maverick Geneticist J. Craig Venter on America's Energy Future

Fri, 01 Aug 2008 02:23:12 GMT

clipped by: Silkweaver
clipper's remarks: I think the real challenge won't necessarily come from biology, because biology is infinitely scalable, but from engineering. [If we can overcome that,] we have the potential to stop using oil and coal hopefully within the next 10 to 20 years, and even start reducing the CO2 concentrations in the atmosphere.

Read further on site.

Clip Source: www.popularmechanics.com

Independent geneticist J. Craig Venter raced an international consortium of scientists to map the human genome in the 1990s. Now he's putting the same cutting-edge science to work on today's energy crisis, engineering a whole new generation of biofuels.

So how did you get from mapping the human genome to creating biofuels?

We considered the biggest issues facing society that we thought we could impact. What's happening to the environment and getting weaned off oil and coal are the biggest issues out there.

Is it similar to the genome project? More daunting?

Nobody thought that such a massive project as sequencing the human genome could be undertaken by a single team, like we did. But that challenge is minor compared to trying to replace the 30 billion barrels of oil that we use globally each year, and the 3 billion tons of coal. The scale of that is beyond my imagination.

Tags: energy, genetics, biotechnology

Possible 'Sleep Gene' Identified

Wed, 30 Jul 2008 11:15:37 GMT

clipped by: Silkweaver
clipper's remarks: When closed, the channel shuts down and the fly sleeps. The insomniac fruit flies had less of the Sleepless-produced protein.

The lack of sleep didn't come without consequences. The Sleepless fruit flies lived about half as long as fruit flies that did not carry the mutation. They also experience impaired coordination and restlessness in their few hours of sleep.

Clip Source: www.sciencedaily.com

While scientists and physicians know what happens if you don't get six to eight hours of shut-eye a night, investigators have long been puzzled about what controls the actual need for sleep.

Researchers at the University of Pennsylvania School of Medicine might have an answer, at least in fruit flies. In a recent study of fruit flies, they identified a gene that controls sleep.

The idea that so much time is spent in sleep is intriguing. Also, sleep deprivation has serious health consequences and impairs cognitive function.

Fruit flies typically sleep 12 hours a day

Sehgal and her team studied 3,500 fruit flies and found mutants that survived on little to no sleep

The sleepless flies had a mutation of a gene that Sehgal and her team have named Sleepless.

They believe the Sleepless gene encodes a protein that affects whether potassium ion channels in the brain stay open or closed. When the channels are open, the brain is connected and working – the fly is awake.

Tags: genetics, sleep, brain

How the Personal Genome Project Could Unlock the Mysteries of Life

Sun, 27 Jul 2008 22:40:16 GMT

clipped by: Silkweaver
clipper's remarks: ...You would very quickly begin to see meaningful and powerful correlations between particular genetic sequences and particular physical characteristics, from height and hair color to disease risk and personality.

Church has done more than imagine such an undertaking; he has launched it: The Personal Genome Project, an effort to make those correlations on an unprecedented scale, began last year with 10 volunteers and will soon expand to 100,000 participants. It will generate a massive database of genomes, phenomes, and even some omes in between.

Clip Source: www.wired.com

George Church is dyslexic, narcoleptic, and a vegan. He is married with one daughter, weighs about 210 pounds, and has worn a pioneer-style bushy beard for decades. He has elevated levels of creatine kinase in his blood, the consequence of a heart attack. He enjoys waterskiing, photography, rock climbing, and singing in his church choir.

If this all seems like too much information, well, blame Church himself. As the director of the Lipper Center for Computational Genetics at Harvard Medical School, he has a thing about openness, and this information (and plenty more, down to his signature) is posted online

He's hoping to demonstrate that all this personal information — even though we consider it private and somehow sacred — is actually fairly meaningless, little more than trivia.

As Church sees it, the only real utility to his personal information is as data that reflects his phenotype

Imagine that we could collect complete sets of data — genotype and phenotype — for a whole population.

Tags: genome, personal genome project

Prevailing theory of aging challenged in Stanford worm study

Sat, 26 Jul 2008 23:07:35 GMT

clipped by: Silkweaver
clipper's remarks: To see whether these signal molecules were part of a wear-and-tear aging mechanism, the researchers exposed worms to stresses thought to cause aging, such as heat (a known stressor for nematode worms), free-radical oxidation, radiation and disease. But none of the stressors affected the genes that make the worms get old.

So it looked as though worm aging wasn’t a storm of chemical damage. Instead, Kim said, key regulatory pathways optimized for youth have drifted off track in older animals. Natural selection can’t fix problems that arise late in the animals’ life spans, so the genetic pathways for aging become entrenched by mistake. Kim’s team refers to this slide as “developmental drift.”

Clip Source: www.thinkgene.com

Age may not be rust after all. Specific genetic instructions drive aging in worms, report researchers at the Stanford University School of Medicine.

Their discovery contradicts the prevailing theory that aging is a buildup of tissue damage akin to rust, and implies science might eventually halt or even reverse the ravages of age.

The question of what causes aging has spawned competing schools of thought.

One side says inborn genetic programs make organisms grow old.

This theory has had trouble gaining traction

The alternate theory holds that aging is an inevitable consequence of accumulated wear and tear

But the Stanford team’s findings told a different story. “Our data just didn’t fit the current model of damage accumulation, and so we had to consider the alternative model of developmental drift

They found hundreds of age-regulated genes switched on and off by a single transcription factor called elt-3, which becomes more abundant with age.

Tags: aging, molecular biology, genetics