Category Archives: Genome

Undergraduate students at Massey University are being given the opportunity to contribute to an international genome sequencing project - one that could eventually remedy the problem of antibiotic resistance.

Massey students will be the first international collaborators on this prestigious project, which is run by the Science Education Alliance (SEA) out of the Howard Hughes Medical Institute (HHMI) in Maryland, USA.

The Phage Hunters Advancing Genomics and Evolutionary Science (PHAGES) program focuses on finding new bacteriophages - a form of virus that target and destroy only specific strains of bacteria. Because of their specificity, they have the potential to be used as an alternative to antibiotics as they do not affect the bodys own supply of helpful bacteria.

Students will be isolating, naming and sequencing a newly discovered bacteriophage to reveal its genetic makeup, all while also learning the skills needed to work in the field of microbiology. Along with more standard assignments, the class will also participate in blogging about their experiences in the Phage Hunt NZ Blog which will allow them to practice their science communication skills.

At the end of the paper the top student will have the opportunity to travel to the United States to present the classes findings at the PHAGES symposium alongside other students from around the United States.

Dr Heather Hendrickson, a senior lecturer in molecular biosciences, is leading the program and says this is an invaluable experience for students, which sets them up to make some exciting discoveries in the future.

"Discovery and study of new bacteriophages in this program will give students an opportunity to learn about how bacteriophages, like the ones they are discovering, can contribute to medicine and health in the future. In a world where DNA sequencing is getting cheaper, the program also provides students with practical skills they can use."

"This is an exciting beginning and we are thrilled to be welcomed into this dynamic program."

The HHMI SEA PHAGES program is being incorporated into the Bachelors of Natural Science at Massey at Albany. Students from other programs are more than welcome to join the paper. The Phage Hunt will be taught as a Bachelor of Natural Sciences special topic course this year as paper 246.301. Students interested in enrolling for the paper should contact Heather Hendrickson directly.

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NZ students join prestigious international genome project

Forbidden Grimoire Vs Genome Project Forbidden Ritual

By: Crystallin Music

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Forbidden Grimoire Vs Genome Project Forbidden Ritual - Video

By Laurel Maloy, contributing writer, Food Online

The FDAs Technology Transfer program is responsible for ensuring that the scientific and technological discoveries made by government scientists are made available to private enterprise. According to the FDAs Alice Welch, Ph.D., FDA scientists and researchers have been at the forefront of about 20 patentable inventions, annually, over the last few years. Technology Transfer also enables the FDA to collaborate with organizations and researchers, both outside and inside the governments purview, in order to advance its regulatory mission. Partnerships are built in order to advance innovations that will ultimately protect the health of people and animals.

The Genome Trakr collaboration is one such example of forward-thinking, advanced science at work to trace foodborne pathogens and ensure the safest possible food supply. The Genome Trakr data base will make it possible to trace a foodborne pathogen back to its source more quickly and with more accuracy than the methods currently in place. Welch predicts this pathogen detection network will transform food safety.

Whole Genome Sequencing (WGS) has been hovering at the edge of food safety for a while. Excitement has built within the scientific community as the potential for practical, worldwide application has been realized. A year ago, European research suggested that DNA Barcoding might be the future of food traceability. There was actually no question as to its ability to do so; the questions regarding it were more along the lines of what the costs would be and if it would be a truly cost-effective solution.

Traceability, in an ever-expanding food supply chain, has become the red herring of food safety. There have been myriad examples of how traceability could have and will improve response time to foodborne illness outbreaks. This topic, out of necessity, has become a primary focus. It has been stressed by the Food Safety Modernization Act (FSMA) and has been the behind-the-scene buzzword every time a foodborne illness outbreak occurs.

Consumers are demanding to know where and when their food comes from this thirst for knowledge has sparked a huge debate over Country of Origin (COOL) labeling. Traceability has been the topic of hundreds of news articles regarding food safety and has resulted in surprising collaborations. Universities, health agencies, and the government have been waging a war against foodborne illnesses with numerous battles having been won. The war is still far from over, but the good guys are making significant headway.

Genome Trakr is being developed through the FDAs Center for Food Safety and Applied Nutrition (CFSAN), the Office of Regulatory Affairs (ORA) and a host of other federal and state public health laboratories. Its goal is to isolate individual pathogens collected from environmental and food samples, and then compare them to pathogens collected from ill patients. This database will not only more quickly and accurately provide an assessment for the size and location of a foodborne outbreak the process can potentially identify the single ingredient in a particular recipe that is causing the illnesses. This makes it possible to move more expediently to remove the contaminated food from commerce, meaning fewer illnesses, hospitalizations, and deaths.

Welch talks about the older testing methods and their limitations. She explains that the evolution of pathogens occurs so quickly that older methods cannot identify the unique genetic signatures required for effective traceability. As the Genome Trakr database grows, it will be possible to say if a particular Salmonella strain is from the East or West Coast, or from Germany, for instance. As pathogen samples are collected, the entire genome sequence is uploaded to the database maintained at the National Center for Biotechnology Information (NCBI). Since its inception in February of 2012, genome sequences have been added for more than 11,000 individual isolates, with impressive results. In early 2014, Genome Trakr was used to match food and environmental samples with human biological samples, confirming the source of a Listeria outbreak. It is easy to imagine that the Jensen Farms Listeria outbreak that killed 29 in 2011 could have been halted even faster than it was. In one of the fastest investigations ever, it only took 10 days from the first case to trace back to Jensen Farms, considered, at the time, to be a record.

Last fall, the FDAs WGS project, in collaboration with CFSAN, NCBI, and the Association of Public Health Laboratories (APHL), won the 2014 Health and Human Services (HHS) Innovates award competition. The Centers for Disease Control and Prevention (CDC) has produced a video called, Whole Genome Sequencing: The Future of Food Safety, which details real-time surveillance of Listeriosis utilizing WGS. This is an exciting time for food safety. This technology and its potential to save lives is one of the greatest innovations the food-processing and manufacturing industry has ever seen.

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Genome Trakr Is A Food Safety And Traceability Game Changer

As butterflies go, the Eastern tiger swallowtail is pretty scary. Their caterpillars look more like stubby snakes, complete with a fake green head, faux black and yellow eyes, and an orange, forked, fleshy "tongue." That tongue-like structure (officially called an osmeterium) can evert, expand, and move, releasing a stinky substance in the process.

Scientists know a lot about these popular butterflies -- which are honored as the state insect in five states despite the appearance and odor associated with their young -- but they hadn't managed to sequence their genome. Now, researchers writing in the Cell Press journal Cell Reports on February 12th have sequenced the complete genome of one wild-caught individual, and they say that it has already told them more than they had anticipated about the butterflies and some of their most intriguing features.

The report also shows that it's now possible to buy the genome of essentially any wild insect for a very reasonable price. That ability opens the door for sequencing many more genomes at an even faster pace, which is necessary if scientists are going to get better at learning to predict or perhaps even change an animal's characteristics based on their DNA alone.

"With our protocols, the cost per new genome falls below $4,000, making insect sequencing projects feasible for college and, in the foreseeable future, high school students," said Nick Grishin of the University of Texas Southwestern Medical Center. "Go out, catch a bug, sequence the genome, learn something new. Isn't it wonderful?"

Now back to those swallowtails: Grishin said their primary goal was really to devise a way to sequence genomes with high levels of genetic variation at a reasonable cost, but they were in for some surprises. The genome data uncovered mutations in proteins that are responsible for the circadian rhythm, which might explain why Eastern tiger swallowtails break free of their chrysalises right away instead of sleeping through the winter as their cousins the Canadian tiger swallowtails must do.

They also found something that appears to explain where the caterpillars got that stinky substance they use to scare off predators. The analysis shows that a gene encoding enzymes that synthesize stinky terpenes got multiplied in the swallowtail genome. The butterflies have many diverse proteins in the family instead of just one or two.

Cool as the Eastern tiger swallowtails may be, the new findings are just the beginning of many more butterfly genomes yet to come. "We think the power of comparative genomics can be fully exploited only when there are thousands of genomes available," Grishin said. Stay tuned.

Cell Reports, Cong et al.: "Tiger Swallowtail genome reveals mechanisms for speciation and caterpillar defense"

Story Source:

The above story is based on materials provided by Cell Press. Note: Materials may be edited for content and length.

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How the Eastern tiger swallowtail got 'scary'

Personal Genome Pioneers interviewed by Robert Krulwich and Carl Zimmer - Part 6 of 12
In 2010, we brought together, on one stage, nearly everyone in the world whose full genome had been sequenced. We knew that, with the pace of genome sequenci...

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Personal Genome Pioneers interviewed by Robert Krulwich and Carl Zimmer - Part 6 of 12 - Video

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Chinese scientists have completed the genome sequencing of Vanilla Shenzhenica, providing insight that will further fuel research into vanilla and the development of related industries.

The genome sequencing project, which the scientists said has produced the world's first orchid genetic map, was a collaboration between Fujian Agriculture and Forestry University and the National Orchid Conservation Center of China, which is based in Shenzhen, in July 2014.

A genome is the full complement of an organism's DNA; complex molecules that direct the formation and function of all living organisms. The size of an organism's genome is measured by the number of bases it contains -- base pairs being the building blocks of DNA.

"The research has helped us to understand the evolutionary history of the orchid, and it's of great importance to the conservation and breeding of the species," said Lan Siren, head of Fujian Agriculture and Forestry University at a press conference on Feb. 7.

Liu Zhongjian, chief scientist with the National Orchid Conservation Center of China said that the genome sequencing would make it possible to alter orchid properties through transgenic technology, indicating a possibility that a synthetic version of vanilla may be produced in the future.

Vanilla is the world's second expensive spice after saffron. It is widely used in food, cosmetics, tobacco and pharmaceutical products.

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China completes vanilla genome sequencing

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Shadow Clans - R.A.G.E. (Rapid Ageing Genome)
http://igg.me/at/shadowclans (Please support Shadow Clans) Shadow Clans Independent Film Project Shot on location in Manila, Philippines This reel is part of a larger body of work that will...

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Shadow Clans - R.A.G.E. (Rapid Ageing Genome) - Video

Large ground finch (Geospiza magnirostris) on Daphne Major island, Galpagos B. R. Grant

For more than four decades, the husband and wife team of Peter and Rosemary Grant travelled to the isolated Galapagos archipelago to watch evolution unfold in front of them.

They were studying some of the 15 species of Darwin's finches, so named because the famed naturalist observed them during the 1830s on his trip aboard the H.M.S. Beagle. Over the years, they noticed the beak size changed among species in response to its food supply - one species developed a smaller beak to take advantage of different seeds - which demonstrated evolution was happening much quicker than Darwin could ever have imagined.

Now, they have tapped the power of sequencing technology to understand the genetic underpinning of these changes. For the first time, scientists have sequenced the genomes of all the famous finches that inspired Charles Darwin's theory of natural selection.

In a study reported Thursday in Nature, the Grants, along with Leif Andersson of Uppsala University and several other authors, detailed the results from sequencing the genome of 120 birds from all of Darwin's finches.

For the DNA, the Grants provided drops of blood samples collected since 1987. They were especially interested in range of beak sizes, which had caught Darwin's eye because they were so much more diverse than the birds he had seen in Europe.

Comparing two species with blunt beaks and two with pointed beaks, they identified 15 regions of the genome as being very different. Six of these contained genes that previously have been associated with craniofacial and/or beak development.

Most significant, they found that genetic variation in the ALX1 gene is associated with variation in beak shape not only between species of Darwin's finches but also among individuals of the medium ground finch.

"This is a very exciting discovery for us since we have previously shown that beak shape in the medium ground finch has undergone a rapid evolution in response to environmental changes," Princeton University's Rosemary Grant said. "Now we know that hybridization (interbreeding between species) mixes the different variants of an important gene, ALX1."

The scientists also were able to show hybridization between a warbler finch and the common ancestor of tree and ground finches goes back more than 500,000 years and 800,000 years.

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Scientists sequence the genome of Darwin's finches