Category Archives: Genome

Steminar # 2 9-17-14 Permutations Genome Sorting
Steminar # 2 9-17-14 at Daytona State College. Permutations Genome Sorting presented by Miklos Bona, Dept. of Mathematics, University of Florida.

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An Evening with the Genome Center: Justin Siegel
An Evening with the Genome Center (http://genomecenter.ucdavis.edu) occurs twice each year, and is intended to engage our community about the impacts that the rapid advances in genomics is...

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An Evening with the Genome Center: Justin Siegel - Video

Gragee ft 4th Genome - No Release
CD only track taken from Bass Agenda Vol 2: The War On Error 100 limited edition CDs Remaining copies available from ...

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Gragee ft 4th Genome - No Release - Video

NMSU professor among scientists worldwide testing miniaturized genome sequencer
It fits in the palm of your hand but might someday match the performance of genetic testing instruments hundreds of times its size. Brook Milligan, New Mexico State University biology professor,...

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NMSU professor among scientists worldwide testing miniaturized genome sequencer - Video

Imagine attempting to trace your genetic history using only information from your mother's side. That's what scientists studying the evolution of the red fox had been doing for decades. Now, University of California, Davis, researchers have for the first time investigated ancestry across the red fox genome, including the Y chromosome, or paternal line. The data, compiled for over 1,000 individuals from all over the world, expose some surprises about the origins, journey and evolution of the red fox, the world's most widely distributed land carnivore.

"The genome and the information it contains about our ancestry and evolution is huge," said lead author Mark Statham, an assistant project scientist with the UC Davis Veterinary Genetics Laboratory. "If you're only looking at what your mother's mother's mother did, you're only getting a small portion of the story."

The study, published in the latest issue of the journal Molecular Ecology, represents the most globally comprehensive work yet on the red fox.

Conventional thinking based on maternal genetics suggested that red foxes of Eurasia and North America composed a single interconnected population across the Bering land bridge between Asia and Alaska. In contrast, this new research shows that the red foxes of North America and Eurasia have been almost entirely reproductively isolated from one another for roughly 400,000 years. During this time, the North American red fox evolved into a new species distinct from its Old World ancestors.

The previous view was distorted by the maternal picture because a single female line transferred from Asia to Alaska about 50,000 years ago.

The new genetic research further suggests that the first red foxes originated in the Middle East before beginning their journey of colonization across Eurasia to Siberia, across the Bering Strait and into North America, where they eventually founded the North American population.

"That small group that got across the Bering Strait went on to colonize a whole continent and are on their own evolutionary path," Statham said.

During the red foxes' journey over millennia, ice sheet formation and fluctuating temperatures and sea levels offered periods of isolation and reconnection, impacting their global distribution. Statham said understanding the evolutionary history of the red fox can provide insight into how other species may have responded to climate change and those same environmental shifts.

The research effort, headed by Statham and Ben Sacks, associate adjunct professor and director of the UC Davis Mammalian Ecology and Conservation Unit, involved a network of collaborators and contributors from around the world and relied heavily on specimens in natural history museums.

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Around the world in 400,000 years: Journey of the red fox

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8-Oct-2014

Contact: Edyta Zielinska edyta.zielinska@jefferson.edu 215-955-5291 Thomas Jefferson University @JeffersonUniv

(PHILADELPHIA) Transfer RNAs (tRNAs) are ancient workhorse molecules and part of the cellular process that creates the proteins, critical building blocks of life that keep a cell running smoothly. A new discovery suggests that the number of human genomic loci that might be coding for tRNAs is nearly double what is currently known. Most of the newly identified loci resemble the sequences of mitochondrial tRNAs suggesting unexpected new links between the human nuclear and mitochondrial genomes, links that are not currently understood.

Transfer RNAs (tRNAs) represent an integral component of the translation of a messenger RNA (mRNA) into an amino acid sequence. TRNAs are non-coding RNA molecules and can be found in all three kingdoms of life i.e., in archaea, bacteria and eukaryotes.

At the DNA level, a triplet of consecutive nucleotides known as the "codon" is used to encode an amino acid. Frequently, a given amino acid can be encoded by more than one codon: in fact, there are 61 distinct codons encoding the 20 standard human amino acids. During translation, each of the codons contained in the coding region of the mRNA at hand is recognized by its matching tRNA and the corresponding amino acid added to the nascent amino acid sequence. It has been known for many years that each of these 61 tRNAs has multiple copies spread throughout the genome that is found in the human nucleus. The presence of multiple genomic loci from which the same molecule can be made is a fairly standard trick of genomic organization: processing these loci in parallel can ensure that adequate amounts of each tRNA can be generated quickly enough to meet the high demand that the amino acid translation process imposes on the cell. In addition to the 61 tRNAs that are found in the human nuclear genome, 22 more tRNAs are encoded in the genome of the cellular organelle known as the mitochondrion: the mitochondrion, originally a bacterium itself, uses these 22 tRNAs to make proteins out of the just-over-a-dozen mRNAs that are encoded in its genome.

Recent research efforts have shown that tRNAs can have other roles, which go beyond their involvement in protein synthesis. For example, tRNAs can affect the physiology of a cell, they can modulate the abundance of important molecules, etc. These and other unexpected findings have revived interest in looking at tRNAs, this time under a different prism. But, how many tRNAs are actually encoded by the human genome and could be potentially involved in amino acid translation and other processes?

A team led by Isidore Rigoutsos, Director of the Computational Medicine Center at Thomas Jefferson University (TJU), set out to tackle this question and they have reported their findings in a study that was just published in the journal Frontiers in Genetics. "What we found, frankly, surprised us," said Rigoutsos.

The team searched the 3 billion base pairs of the human genome for DNA sequences that resembled the 530 known nuclear and mitochondrial tRNAs. Even though they used very stringent criteria in their searches, they found 454 "lookalike" loci, i.e., sequences that look like tRNA, but haven't yet been experimentally confirmed as such. The researchers found nearly as many as the known ones with which they started: 81% of these tRNA-lookalikes had not been reported previously. Rather unexpectedly, the team found that most of these new loci resembled some of the 22 mitochondrial tRNAs.

Interestingly, the discovered tRNA lookalikes are not spread uniformly across the 24 chromosomes. Instead, they have penetrated preferentially some chromosomes and have avoided others. For example, chromosomes 1, 2, 7, 8 and 9 claim the lion's share of the discovered tRNA-lookalikes. On the other hand, chromosome 18 contains no lookalikes. Also, some of the codons are particularly over-represented among the lookalikes whereas other codons are absent.

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Conspicuous tRNA lookalikes riddle the human genome

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STBNarea Orange Genome rus - Video

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Newswise An obscure swatch of human DNA once thought to be nothing more than biological trash may actually offer a treasure trove of insight into complex genetic-related diseases such as cancer and diabetes, thanks to a novel sequencing technique developed by biologists at Texas A&M University.

The game-changing discovery was part of a study led by Texas A&M biology doctoral candidate John C. Aldrich and Dr. Keith A. Maggert, an associate professor in the Department of Biology, to measure variation in heterochromatin. This mysterious, tightly packed section of the vast, non-coding section of the human genome, widely dismissed by geneticists as "junk," previously was thought by scientists to have no discernable function at all.

In the course of his otherwise routine analysis of DNA in fruit flies, Aldrich was able to monitor dynamics of the heterochromatic sequence by modifying a technique called quantitative polymerase chain reaction (QPCR), a process used to amplify specific DNA sequences from a relatively small amount of starting material. He then added a fluorescent dye, allowing him to monitor the fruit-fly DNA changes and to observe any variations.

Aldrich's findings, published today in the online edition of the journal PLOS ONE, showed that differences in the heterochromatin exist, confirming that the junk DNA is not stagnant as researchers originally had believed and that mutations which could affect other parts of the genome are capable of occurring.

"We know that there is hidden variation there, like disease proclivities or things that are evolutionarily important, but we never knew how to study it," Maggert said. "We couldn't even do the simplest things because we didn't know if there was a little DNA or a lot of it.

"This work opens up the other non-coding half of the genome."

Maggert explains that chromosomes are located in the nuclei of all human cells, and the DNA material in these chromosomes is made up of coding and non-coding regions. The coding regions, known as genes, contain the information necessary for a cell to make proteins, but far less is known about the non-coding regions, beyond the fact that they are not directly related to making proteins.

"Believe it or not, people still get into arguments over the definition of a gene," Maggert said. "In my opinion, there are about 30,000 protein-coding genes. The rest of the DNA -- greater than 90 percent -- either controls those genes and therefore is technically part of them, or is within this mush that we study and, thanks to John, can now measure. The heterochromatin that we study definitely has effects, but it's not possible to think of it as discrete genes. So, we prefer to think of it as 30,000 protein-coding genes plus this one big, complex one that can orchestrate the other 30,000."

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Biologists Unlock Non-Coding Half Of Human Genome With Novel Sequencing Technique

October 7, 2014

Provided by Janne Hansen, Aarhus University

The cattle genome has now been mapped to a hitherto unknown degree of detail. This constitutes a quantum leap for research into the history and genetics of cattle.

By creating a global database an international consortium of scientists has increased the detailed knowledge of the variation in the cattle genome by several orders of magnitude. The first generation of the new data resource, which will be open access, forms an essential tool for scientists working with cattle genetics and livestock history. The results are published in an article in the prestigious scientific journal Nature Genetics.

Its momentous, says one of the scientists behind the international effort, associate professor Bernt Guldbrandtsen from the Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University. Scientists from Aarhus University the only Danish university to participate have been part of the consortium from the start and have contributed 15 percent of the data.

Ancestral bulls

The data used in the huge database are derived from key ancestor bulls. These bulls have produced millions of descendants and have enormous influence on the genetic composition and characteristics of modern cattle breeds. For example, Holstein bulls in the database have fathered at least 6.3 million daughters worldwide.

The data consist of sequenced genomes for a number of bulls and are based on new sequencing techniques. The article in Nature Genetics describes data from 232 bulls and two cows of the breeds Angus, Holstein, Jersey and Fleckvieh. Since these animals are key ancestors, they carry most of the genetic variations present in the three races.

Currently, the database contains genomes of more than 1,200 animals of different cattle breeds, but as more scientists from other countries gradually join the project, there is a continual inflow of data. Key ancestor bulls have daughters all around the world, so it is a considerable strength of the project that such data are connected into one database.

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Cattle Code Cracked In Detail

Videos of Sasquatch Released By The Genome Project
These videos are property of Adrian Erickson, never before seen prior to this news broadcast.

By: The Bigfoot Project

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Videos of Sasquatch Released By The Genome Project - Video