genome-project

Your genome, every human’s genome, consists of a unique DNA sequence of A’s, T’s, C’s and G’s that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively.

From the TED-Ed Lesson How to sequence the human genome - Mark J. Kiel

Animation by Marc Christoforidis

Genealogy to genomics: The national obsession of Iceland

Dawn Field, author of Biocode, explains how Iceland produced the first ever ‘national genome’:

“The island of Iceland is famous for its beauty, geothermal activity, whale watching and the Aurora Borealis, among other wonders of nature. Along with the beloved blue lagoon, it is now famous for having produced the first ‘national genome’. Researchers have been working towards this goal since 1996 when Dr. Stefansson founded a company called Decode to study the genetics of his country. Iceland has a population of around 325k people living in an area of 103,000 km², making it not only one of the most breathtaking places on earth but also the most sparsely populated country in Europe. Peopled by less than 20,000 people from neighbouring regions of Scandinavia, Ireland, and Scotland only 1,100 years ago its isolated population also boasts impressive historical genealogical records complemented by extraordinary modern health records.

In a set of groundbreaking research papers published in the world’s top journal Nature, Decode researchers report findings from completion of genomes of 2,636 Icelanders. More importantly, these core genomes were used to ‘impute’ the genomes of another 100,000 closely related individuals producing a genomic map of  almost 1/3 of the county’s population. Among the many findings are new insights into rare mutations and the largest survey to date of ‘lost genes’. Almost 8 % of Icelandic genomes lack a working version of at least one gene and a total of 1,171 ‘knockout’ genes could be identified. Other ‘national genome’ projects are now underway – from the Dutch genome project to the Korean genome project.”

Image: Iceland, waterfall in winter, by Diana Robinson. CC-BY-ND-2.0 via Flickr.

Every dollar we invested to map the human genome returned $140 to our economy — every dollar. Today our scientists are mapping the human brain to unlock the answers to Alzheimer’s. They’re developing drugs to regenerate damaged organs, devising new materials to make batteries 10 times more powerful. Now is not the time to gut these job-creating investments in science and innovation.

First comprehensive atlas of human gene activity released

A large international consortium of researchers has produced the first comprehensive, detailed map of the way genes work across the major cells and tissues of the human body. The findings describe the complex networks that govern gene activity, and the new information could play a crucial role in identifying the genes involved with disease.

“Now, for the first time, we are able to pinpoint the regions of the genome that can be active in a disease and in normal activity, whether it’s in a brain cell, the skin, in blood stem cells or in hair follicles,” said Winston Hide, associate professor of bioinformatics and computational biology at Harvard School of Public Health (HSPH) and one of the core authors of the main paper in Nature. “This is a major advance that will greatly increase our ability to understand the causes of disease across the body.”

The research is outlined in a series of papers published March 27, 2014, two in the journal Nature and 16 in other scholarly journals. The work is the result of years of concerted effort among 250 experts from more than 20 countries as part of FANTOM 5 (Functional Annotation of the Mammalian Genome). The FANTOM project, led by the Japanese institution RIKEN, is aimed at building a complete library of human genes.

Researchers studied human and mouse cells using a new technology called Cap Analysis of Gene Expression (CAGE), developed at RIKEN, to discover how 95% of all human genes are switched on and off. These “switches”—called “promoters” and “enhancers”—are the regions of DNA that manage gene activity. The researchers mapped the activity of 180,000 promoters and 44,000 enhancers across a wide range of human cell types and tissues and, in most cases, found they were linked with specific cell types.

“We now have the ability to narrow down the genes involved in particular diseases based on the tissue cell or organ in which they work,” said Hide. “This new atlas points us to the exact locations to look for the key genetic variants that might map to a disease.”

Science Cult: What Is the Human Genome Project?

The Human Genome Project is kind of a really big deal.

An estimated 3 billion dollars and fifteen years of research (per project renual) are dedicated to the Human Genome Project - a scientific venture to identify each and every sequence of human DNA so that scientists can both determine the purpose of each gene, and possibly eradicate individual unwanted genes!

Yes! Isn’t that crazy? What the Human Genome Project means is that one day in the not too distant future, parents might be able to pick and choose the genes that they would like for their unborn child. And though it might sound like we’re pretty far away from that, remember that prenatal genetic testing - a process that allows expecting mothers to see mutation and genetic disorder before the child is born - is the present. 

But the Human Genome Project isn’t one hundred percent cold science. A lot of ethical questions are raised when we’re talking about possibly genetically engineering perfect people. Historians, legal scholars, and health-care professionals among others are also on board the HGP in order to keep raising and discussing questions about what this kind of advancement might mean for our future. 

When people are free to pick and choose what their offpsring might look, act, and excel at, what would that mean for natural selection? Racial diversity? Human values?

DNA: Celebrate the unknowns | Philip Ball

On the 60th anniversary of the double helix, we should admit that we don’t fully understand how evolution works at the molecular level, suggests Philip Ball.

This week’s diamond jubilee of the discovery of DNA’s molecular structure rightly celebrates how Francis Crick, James Watson and their collaborators launched the ‘genomic age’ by revealing how hereditary information is encoded in the double helix. Yet the conventional narrative — in which their 1953 Nature paper led inexorably to the Human Genome Project and the dawn of personalized medicine — is as misleading as the popular narrative of gene function itself, in which the DNA sequence is translated into proteins and ultimately into an organism’s observable characteristics, or phenotype.

Sixty years on, the very definition of 'gene’ is hotly debated. We do not know what most of our DNA does, nor how, or to what extent it governs traits. In other words, we do not fully understand how evolution works at the molecular level.

That sounds to me like an extraordinarily exciting state of affairs, comparable perhaps to the disruptive discovery in cosmology in 1998 that the expansion of the Universe is accelerating rather than decelerating, as astronomers had believed since the late 1920s. Yet, while specialists debate what the latest findings mean, the rhetoric of popular discussions of DNA, genomics and evolution remains largely unchanged, and the public continues to be fed assurances that DNA is as solipsistic a blueprint as ever.

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A karyotype showing all 22 pairs of human chromosomes, plus X and Y.

Sequence of events

The Human Genome Project http://www.genome.gov/10001772 (HGP) celebrated its 10th anniversary on Sunday.

Like the Apollo program’s mission to put a man on the moon, the HGP had a singular, spectacular goal: Deciphering the exact order of the 3 billion genetic letters (the nucleotides A, T, G and C) http://en.wikipedia.org/wiki/Nucleotide that encode the “blueprint” for making a human – and perhaps more importantly, what ails him or her.

“All human disease is genetic in origin,” Nobel laureate Paul Berg has observed, and the last decade, thanks to the HGP, has gone quite a way to proving it. In 1990, when the HGP began, mutations in only 53 genes were known to cause disease; the number is now almost 3,000 with more found almost daily.

The HGP opened new and unexpected venues for research and launched untold numbers of studies and investigations, large and small. Tools like genome-wide association studies, which identify the thousands of genomic variations that can affect an individual’s predisposition to disease or its underlying pathology, would not be possible without the success of the HGP. Last year’s ENCODE consortium of more than 440 researchers in 32 international labs published a flurry of studies describing 4 million genomic regions (some previously dismissed as “junk DNA”) that may be regulatory switches that turn genes on and off.

As scientists have pieced together the incredibly complex fabric of our genes (and those of other organisms, from chimpanzees to sea urchins), they have applied that knowledge to real-life (and death) issues. For example, the hugely popular use of statins to lower cholesterol levels and reduce heart disease, for example, began as a pre-HGP investigation into a rare, hereditary condition called familial hypercholesterolemia.

With technological advances, the costs and time involved in genetic science have dropped dramatically. The first human genome cost $1 billion to sequence and took 13 years. These days, it’s less than $5,000 (and closing on the mystical $1,000 price tag) and takes just one or two days for a full sequence.

Medical science is already using personalized genome information as the basis for a variety of treatments, from cancer to hair loss. In the years ahead, your genes will likely instruct and inform your doctors about almost every aspect of your care.

Biology’s Big Problem: There’s Too Much Data to Handle

Twenty years ago, sequencing the human genome was one of the most ambitious science projects ever attempted. Today, compared to the collection of genomes of the microorganisms living in our bodies, the ocean, the soil and elsewhere, each human genome, which easily fits on a DVD, is comparatively simple. Its 3 billion DNA base pairs and about 20,000 genes seem paltry next to the roughly 100 billion bases and millions of genes that make up the microbes found in the human body.

And a host of other variables accompanies that microbial DNA, including the age and health status of the microbial host, when and where the sample was collected, and how it was collected and processed. Take the mouth, populated by hundreds of species of microbes, with as many as tens of thousands of organisms living on each tooth. Beyond the challenges of analyzing all of these, scientists need to figure out how to reliably and reproducibly characterize the environment where they collect the data.

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Homo sapiens chromosome 15 genomic contig, GRCh37.p10 Primary Assembly

I wanted to see what DNA would look like translated directly into RGB pixel values.  My method assigns 2-bit values to each base pair (A, C, G, & T).  Each triplet of base pair values is then translated directly into a 6-bit RGB pixel value.  For example, the sequence ATG is equivalent to a single RGB pixel value: 0, 255, 170.

Source: http://www.ncbi.nlm.nih.gov/nuccore/NT_037852.6?from=1&to=2212114&report=fasta

NCBI Reference Sequence: NT_037852.6
>gi|224514874|ref|NT_037852.6| Homo sapiens chromosome 15 genomic contig, GRCh37.p10 Primary Assembly

Intellectuals in their self-flattering wish-fulfillment say that knowledge is power, but the truth is that knowledge further empowers only those who have or can acquire the power to use it.
—  R.C. Lewontin
vimeo

Flow Genome Project is a trans-disciplinary, international organization committed to mapping the genome of Flow by 2020 and open sourcing it to everyone

We were lucky enough to have award-winning documentary filmmaker Ondi Timoner interview co-founders Steven Kotler and Jamie Wheal as part of her series on innovators and entrepreneurs who are using technology to transform our lives.  Learn about our founding mission, amazing collaborators, and vision for the future.

The Flow State: Flow states, peak experiences, in the zone, runner’s high, being unconscious—the lingo is endless. The experience though lives up to the hype. Time slows down, self vanishes, there’s a complete merger between action and awareness— it almost sounds like nonsense, but fifty years of serious research says otherwise. Flow states are now known to optimize performance, enhance creativity, drive innovation, , accelerate learning, amplify memoryand underpin happiness itself.

The Problem: The people who want to study Flow states aren’t that good at having them; the people who are really good at having Flow states aren’t all that interested in studying them. As a result, researchers are balkanized, their work occasionally marginalized. There are no coordinated scientific efforts, little cross-pollination of ideas and—as a result—no real roadmap towards discovery and application.

The Invitation: If this mission calls to you, and you’d like to join the Project and help us map the genome of Flow, let us know, and welcome to the conversation!

Film Project

I am doing a film project and would like volunteers to be interviewed either by Skype or Google hangout. The interview would consist of a list of questions that everyone will be asked. The questions are all geared to common life experiences. If you are interested in volunteering for this project please respond or reblog. I will approach you by message. All footage will be edited and put on my Youtube Channel. My intentions for this project is to inspire a cognitive shift in how we regard one another as a whole by demonstrating or similarities in life experience. I thank you all for your time and attention. Once I get 12 or more people I will begin this project. 

Speeding up gene discovery

New gene-editing system enables large-scale studies of gene function.

Since the completion of the Human Genome Project, which identified nearly 20,000 protein-coding genes, scientists have been trying to decipher the roles of those genes. A new approach developed at MIT, the Broad Institute, and the Whitehead Institute should speed up the process by allowing researchers to study the entire genome at once.

The new system, known as CRISPR, allows researchers to permanently and selectively delete genes from a cell’s DNA. In two new papers, the researchers showed that they could study all the genes in the genome by deleting a different gene in each of a huge population of cells, then observing which cells proliferated under different conditions.

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Welcome to the Storyverse™ (by smalldemonsvideo)

Small Demons introduces Storyverse, a story genome project. From the protagonists’ favorite restaurant to a favorite character’s favorite drink - Small Demons says that these are the details that connect you to stories. And if you’re paying attention, they can open up a world of their own. Down the rabbit hole we go…

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Diane Andre of Parks Canada helps collect a scat sample from the boreal forest north of Deline, Northwest Territories for genetic analysis.

stevia-badger - Thanks again for another great question!

Q. Have they assembled a caribou genome yet?

A. As far as I am aware, no one has amplified a entire caribou genome yet! However, my research group is very interested in moving in that direction and has consistently written genomic aspirations into every recent grant proposal. As the cost of sequencing goes down, the chances of having the resources for this type of work goes up. I think it would be safe to say we might have a caribou genome in the next 5 years.

Learn more about my PhD research here.