Viruses and Bioinformatics from Virology.uvic.ca
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Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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Biostars - Bioinformatics Explained

Biostars - Bioinformatics Explained | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Tutorials and Q+A Forum for bioinformatic tools. 17 000 + users!

Kathleen McLeod's insight:

Could be an interesting resource!

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The Scale of the Universe - An Interactive Visual Understanding of How Small Viruses and Microorganisms Really Are

Zoom from the edge of the universe to the quantum foam of spacetime and learn about everything in between.
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Humans have alu, cows have BovB. Why is a quarter of the cow genome similar to that of snakes?

Humans have alu, cows have BovB. Why is a quarter of the cow genome similar to that of snakes? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome has bits and pieces of DNA sprinkled around that have copied themselves throughout the genome and jumped around seemingly randomly, creating vast tracts of repetitive sequences, so called "alu" sequences - a name derived from a restriction site "Alu I" right in the middle of the repetitive part. The same is true for the cow genome, where one particular piece of DNA, known as BovB, has run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made of BovB sequences or their descendants.

 

BovB isn’t restricted to cows. If you look for it in other animals, as Ali Morton Walsh from the University of Adelaide did, you’ll find it in elephants, horses, and platypuses. It lurks among the DNA of skinks and geckos, pythons and seasnakes. It’s there in purple sea urchin, the silkworm and the zebrafish.

 

The obvious interpretation is that BovB was present in the ancestor of all of these animals, and stayed in their genomes as they diversified. If that’s the case, then closely related species should have more similar versions of BovB. The cow version should be very similar to that in sheep, slightly less similar to those in elephants and platypuses, and much less similar to those in snakes and lizards.

 

But not so. If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel universe where cows are more closely related to snakes than to elephants, and where one gecko is more closely related to horses than to other lizards.

 

This is because BovB isn’t neatly passed down from parent to offspring, as most pieces of animal DNA are. This jumping gene not only hops around genomes, but between them. 

 

This type of “horizontal gene transfer” (HGT) is an everyday event for bacteria, which can quickly pick up important abilities from each other by swapping DNA. Such trades are supposedly much rarer among more complex living things, but every passing year brings new examples of HGT among animals. For example, in 2008, Cedric Feschotte (now at the University of Utah) discovered a group of sequences that have jumped between several mammals, an anole lizard, and a frog. He called them Space Invaders.

 

The Space Invaders belong to a group of jumping genes called DNA transposons. They jump around by cutting themselves out of their surrounding DNA, and pasting themselves in somewhere new. They’re also relatively rare—they make up just 2 to 3 percent of our genome. BovB belongs to a different class of jumping genes called retrotransposons. They move through a copy-and-paste system rather than a cut-and-paste one, so that every jump produces in a new copy of the gene. For that reason, they spread like wildfire.


Via Dr. Stefan Gruenwald
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Tracing the genetic pathway from the first Eukaryotes to Homo sapiens

Tracing the genetic pathway from the first Eukaryotes to Homo sapiens | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

www.dhushara.com/book/unraveltree/unravel.htm

 

The Tree of Life, in biological terms, has come to be identified with the evolutionary tree of biological diversity. It is this tree which represents the climax fruitfulness of the biosphere and the genetic foundation of our existence, embracing not just higher Eukaryotes, plants, animals and fungi, but Protista, Eubacteria, and Archaea, the realm, including the extreme heat and salt-loving organisms, which appears to lie almost at the root of life itself.


Via Dr. Stefan Gruenwald
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Does DNA have Extraterrestrial Origins?

Does DNA have Extraterrestrial Origins? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

A team of scientists has discovered that adenine an guanine and other DNA building blocks can form in outer space and have been deposited on Earth's surface by meteorites


Via mei, Sakis Koukouvis
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Modern wine owes a significant part of its genetic heritage to 30-million-year-old plant viruses

Modern wine owes a significant part of its genetic heritage to 30-million-year-old plant viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Next time you pour a glass of wine, raise a toast to the 30-milion-year-old viruses that have contributed to the genetic make-up of modern grapes.

 

A team of UQ-led plant scientists has discovered that the Pinot Noir grape variety owes a significant part of its genetic heritage to ancient plant viruses.

 

In a study published in Nature Communications, Dr Andrew Geering and colleagues have mapped the presence of 30-million-year-old viruses in Pinot Noir DNA. Viruses are usually a curse to farmers because of the damage they cause to crops, but this study also suggests they play a vital evolutionary role.

 

Dr Geering, a plant pathologist at the UQ's Queensland Alliance for Agriculture and Food Innovation, said most flowering plant species, even the most primitive ones, contain sequence signatures of viruses in their genetic material.

 

"Animals can move to avoid threats but because plants are anchored to the ground they are obliged to adapt to environmental pressures, such as those brought about by drought or grazing, using novel strategies.

 

"Plants cope with such threats by acquiring new biochemical pathways or growth habits."

 

"Pulling new genetic material from the environment, such as from viruses that infect the plant, means evolution can be sped up considerably."

 

Much like humans, plants are regularly exposed to harmful chemicals or radiation, which can cause damaging and heritable mutations to their genes which, if left unrepaired, could be lethal to their descendants.

 

"Fortunately, there are special mechanisms to repair these mutations. It's during this repair procedure that foreign DNA such as that originating from viruses can be inserted into the plant's own genetic code, much like using putty to fill a crack in the wall."

 

"When this happens, the viral DNA can become 'domesticated' if it provides a selective advantage to the plant."


Via Dr. Stefan Gruenwald, Ed Rybicki
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Diane Johnson's curator insight, November 12, 2014 10:40 AM

So interesting. Nice application for genetics studies.

Ed Rybicki's curator insight, February 5, 2015 7:40 AM

Two of my favourite things - wine and viruses - appear to owe each other something. I'll drink to that!

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Noroviruses: The Perfect Human Pathogens?

Noroviruses: The Perfect Human Pathogens? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Noroviruses are perhaps the perfect human pathogens. These viruses possess essentially all of the attributes of an ideal infectious agent: highly contagious, rapidly and prolifically shed, constantly evolving, evoking only limited immunity, and just moderately virulent, allowing most of those infected to fully recover, thereby maintaining a large susceptible pool of hosts. These characteristics have enabled noroviruses to become the leading cause of endemic diarrheal disease across all age groups, the leading cause of foodborne disease, and the cause of half of all gastroenteritis outbreaks worldwide. In the United States alone, noroviruses are responsible for an estimated 21 million cases of acute gastroenteritis annually, including >70,000 hospitalizations and nearly 800 deaths. In developing countries, where the greatest burden of diarrheal disease occurs, noroviruses have been estimated to cause up to 200 000 deaths each year in children


Via Dr. Stefan Gruenwald
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NCPbiology's curator insight, June 27, 2014 6:28 AM

Interesting extra reading.

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Fungus Discovered In The Amazon That Will Eat Plastic

Fungus Discovered In The Amazon That Will Eat Plastic | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
The Amazon is home to more species than almost anywhere else on earth. One of them, carried home recently by a group from Yale University, appears to be quite happy eating plastic in airless landfills.

Via Geotech Environmental Equipment, ABroaderView, Sakis Koukouvis, Dr. Stefan Gruenwald
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The DNA Learning Center from Cold Spring Harbor Laboratories - 200 educational videos

The DNA Learning Center from Cold Spring Harbor Laboratories - 200 educational videos | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

The mission of Cold Spring Harbor Laboratory's DNA Learning Center is to prepare students and families to thrive in the genomic age.


Via Dr. Stefan Gruenwald
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