Genome from Southern Africa Sheds Light on Human Origins

What can DNA from the skeleton of a man who lived 2,330 years ago in the southernmost tip of Africa tell us about ourselves as humans? A great deal when his DNA profile is one of the earliest diverged – oldest in genetic terms – found to-date in a region where modern humans are believed to have originated roughly 200,000 years ago.

The man’s mitochondrial DNA was sequenced to provide clues to early modern human prehistory and evolution. Mitochondrial DNA provided the first evidence that we all come from Africa, and helps us map a figurative genetic tree, all branches deriving from a common “Mitochondrial Eve.”

Read more: http://www.laboratoryequipment.com/news/2014/09/genome-southern-africa-sheds-light-human-origins

partofyourbadgirlshenanigans said:

Skimmons, 21 please :))

SEND ME A SHIP AND A NUMBER AND I’LL WRITE A SHORT FIC

21. best friends sibling au

Most people think that Jemma’s best friend is Fitz, which is justifiable the amount of time in which they have hung out and in the fact that they’ve never really been separated but it’s more like Fitz isn’t her only best friend.

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mustardmeercat said:

I really have no clue what happened because my dad has a PhD in zoology was a prof. At Harvard sequenced the genome of the tsetse fly ( which carries sleeping sickness). Started a university in South Africa, and has won many awards for his work yet HE FED MY CUTTLE FISH STEAK.

Starts off paragraph of superfluous details with “i have no clue what happened” ends paragraph with exactly what happened. 😂 fact: your dad committed 1st degree cuttlefishicide

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

700,000-Year-Old Horse Genome Shatters Record for Sequencing of Ancient DNA

My latest story for Wired is up, and I was more excited writing this one than I have been in a long time. Because of advancements in DNA sequencing technology, people decode new genomes every day. Even though the human genome project is still less than 15 years old, people have started to think this isn’t that exciting.

It reminds me of exoplanets … we’ve just gotten a little jaded by what is still an amazing discovery, every time!!

Well, get excited, folks … because a team of scientists from around the world sequenced the oldest genome ever using DNA found in a fossilized horse bone. They shattered the previous record by over 600,000 years and rewrote horse evolution in the process!! We’ll be sequencing million-year-old genomes in no time.

See, DNA degrades over time. That’s why Jurassic Park can never happen (sorry). This horse bone was buried in cold permafrost, and although it was still in pretty rough shape, these DNA wizards were still able to piece it together into an entire genome. That’s like a 21-billion piece jigsaw puzzle!!

Among a laundry list of accomplishments, each of which could have been its own cover story, they sequenced the genome of that little modern horse up there, called a Przewalski’s horse. From origins stretching back 4 million years ago, they are the last truly wild horses left on Earth (the escaped domestics that roam America dont count), and are cute, and worth saving.

Head on over to Wired and check out all the details! There’s so, so much more …

PS - This summer science writing gig in San Francisco is pretty rad, as you can probably tell by my excitement :) I’m busy as hell with “real” journalism stuff like this, but MAN is it cool!

I recently created Music Video Genome. It’s essentially Pandora for music videos (or a personalized MTV). Through the power of VHX’s new API, Last.fm and YouTube, it made it quite simple to accomplish.

This past weekend I participated in a video hackday. You get 24 hours to start and finish a video based project. At the end everyone demos their speed hack.

My project morphed several times over the course of the weekend, but the final result ended up being something I’m really enjoying.

I called it Genome because it’s not that simple to match music videos to real songs. Most music “videos” on YouTube are just a stupid static image. Granted not all songs have music videos, but it would be amazing if I could crowd-source the documentation of music videos to songs. If a song does not have an official music video, fans could make their own and have it bubble up as the official video.

Circle of Life

The genome of Gloeobacter violaceus, drawn as a gorgeous circular plot by visionary biological data artist Martin Krzywinski (from this paper). Within its concentric layers of information are buried genome composition, relation to other species, and overall genetic structure. It’s also very pretty.

Gloeobacter is an ancient photosynthetic bacterium that branched off the rest of the photosynthetic tree (including cyanobacteria and, later, plants) and has its own strange way of eating sunlight. 

Krzywinski’s informative and beautiful data visualizations are featured at Wired Science, check ‘em out: Circle of Life: The Beautiful New Way to Visualize Biological Data

A little-known fact: Invertebrates make up more than 70% of the approximately 1.9 million described species on earth!  

The Global Invertebrate Genomics Alliance researchers are hoping to sequence the whole genomes of many of these weird and wonderful creatures. Read more in their Journal of Heredity article.

Image credit: Vallicula multiformis (platyctenid; Ctenophora), Pherecarida sp. (fireworm; Annelida), Epimeria robusta (amphipod; Crustacea), Phoronopsis californica (horseshoe worm; Phoronida), Flabellum sp. (solitary coral; Cnidaria), Millnesium sp. (water bear; Tardigrada), Glass sponge (Porifera), Collosondeis sp. (sea spider; Pycnogonida). Reproduced with permission from Greg Rouse.

Cancer-resistant blind mole rat gets genome sequence

"Scientists have sequenced the genome of the blind mole rat, a mammal that digs with its teeth, has skin over its eyes and lives for more than 20 years.

Its underground lifestyle means coping with no light, very little oxygen and an awful lot of dirt.

It is also resistant to cancer, like its distant cousin the naked mole rat.

The new work, published in the journal Nature Communications, will help unpick those secrets and the wider adaptation of animals to difficult environments.” 

Learn more from bbcnews.

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.

[Read more]

New Tool Pinpoints Genetic Sources Of Disease

Scientists have shown a connection between the “map” of genes in the genome and the “map” of reversible chemical changes to DNA, the epigenome.  Their finding could help disease trackers find patterns in those overlays that could offer clues to the causes of and possible treatments for complex genetic conditions.

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The word gene was first used in English in 1911, derived from the German word Gen, created in 1905 by Danish scientist Wilhelm Ludvig Johannsen (1857-1927) from the Ancient Greek word γενεα (genea) meaning generation or race (of people). The word genome was first used in 1920 by professor of botany Hans Winkler of the University of Hamburg. He patterned the word on the word chromosome, a combination of the Ancient Greek words χρομος (chromos meaning color) and σομος (somos meaning body). Unfortunately he followed the example set by the recently coined words rhizome and biome, both of which took only part of the root suffix for -somos and rendered it -omos. The genome is defined as the entirety or collection of genetic material needed to form an individual. In addition to the word genome, the word gene now forms a part of many more English words: genetic, etc.

Scientists working at the European Bioinformatics Institute recently used the structure of DNA to store data-DNA after all is nothing more than the storage device for all that genetic material. Using the building blocks of DNA, Ewan Birney and Nick Goldman (read about their story by clicking here) converted Shakespeare’s Sonnet 18 and sent the result to a gene sequencing lab. A few weeks later they received a test tube with the newly created DNA which when they sequenced gave back their encoded Sonnet. The sonnet they chose was particularly appropriate:

Shall I compare thee to a summer’s day?
Thou art more lovely and more temperate:
Rough winds do shake the darling buds of May,
And summer’s lease hath all too short a date:
Sometime too hot the eye of heaven shines,
And often is his gold complexion dimm’d;
And every fair from fair sometime declines,
By chance or nature’s changing course untrimm’d;
But thy eternal summer shall not fade
Nor lose possession of that fair thou owest;
Nor shall Death brag thou wander’st in his shade,
When in eternal lines to time thou growest:
So long as men can breathe or eyes can see,
So long lives this and this gives life to thee.

While Shakespeare had three children, they were not terribly prolific, and the gene pool that issued from Shakespeare ended in 1670 with the death of his last grandchild.

Image of the human chromosome (and therefore genome) courtesy National Human Genome Research Institute, released to the public domain.

Image of William Shakespeare also in the public domain.

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