Monthly Archives: May 2017

To biologists, the beaver is known as Castor canadensis. Its scientific name flaunts unabashed ties to Canada. Its common English name, however, is the North American beaver.

The animal attracted shiploads of Europeans to North America, where they reshaped the landscape in much the same way beavers reshape wetland environments. However, Canada specifically acknowledged the role the large, smelly, flat-tailed rodent played (albeit reluctantly) in shaping European headgear and this countrys development. In 1937, the country made the beaver the go-to imprint on the nickel.

Another milestone in Canadas claim to the beaver occurred this year, when Canadian researchers published the animals genome sequence.

The leader of the research team, University of Toronto molecular genetics professor Stephen Scherer, says he chose the beaver genome because of Canadas 150th anniversary and to mark our territory.

After starting his work, Scherer learned researchers in Oregon were working on the North American Beaver Genome Project. He challenged his Canadian team to be first.

Six months later, they completed the sequence.

Making the victory even more Canadian, the team sequenced the genome using a new, made-in-Canada approach.

Ward is the 10-year-old beaver from the Toronto Zoo that donated tissue samples to the project. The new method allowed the scientists to assemble Wards genome from the ground up without relying on a reference genome.

Researchers first constructed a rough draft of Wards genome with long fragments of his DNA, then fleshed it out with shorter fragments. They then assembled the sum of messenger RNA found in Wards blood and tissue samples to serve as a scaffold for the genome.

Messenger RNA molecules carry precise recipes for beaver proteins from Wards DNA to his cellular protein-building machinery. Finally, the scientists compared their results with related mammal genomes and corrected the sequence manually.

According to the results, the genome of Castor canadensis or the North America beaver comprises 2.7 billion base pairs, which reside in the 40 pairs of chromosomes within the nucleus of each of Wards cells. Thats slightly less than the approximately three billion base pairs found in the human genome. Each chromosome contains hundreds to thousands of genes, which carry the detailed instructions for making beavers beavers or humans humans and offers insights into how the animal evolved in North Americas environments through time.

This is only the latest incident of Canadians scent-marking the beaver as a significant part of our historic, cultural and now scientific territory, but Canada has been part of the genome-sequencing movement since 1998, when it announced the Canadian Biotechnology Strategy, formed Genome Canada, and joined the Human Genome Project. British Columbia is home to one of Genome Canadas technology centres, and Canadian researchers are exploring how genomics can be used to fight disease, maintain health and safeguard forests, crops, and other species from invasive pests and climate change.

For example, scientists from B.C., France, Israel, the U.S. and elsewhere recently finished sequencing the sunflower genome one of the most challenging genomes published to date, says UBC professor Loren Rieseberg, a senior researcher.

As the only major crop domesticated in North America, the sunflower provides much fodder for research. It serves as a model for how new species arise and for understanding solar tracking and plant growth.

Not only have we sequenced the sunflowers genome, but we have also built physical and genetic maps of its structure, which increases the genomes value for research and breeding.

This lays the foundation for work to use the sunflowers stress resistance and ability to grow in different climates and conditions, including drought, to adapt other crops to climate change.

These are two recent genomic advances Canadians helped make happen. Perhaps, at some point in the future, genomics research will become as much a part of the Canadian identity as Castor canadensis is.

keiran_monique@rocketmail.com

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Monique Keiran: Beaver's genome mapped for our 150th - Times Colonist

May 24, 2017 by Sandy Fleming Credit: University of Kent

Through her work, Dr Rebecca O'Connor in the School of Biosciences, found previously undiscovered, fundamental flaws in the pig genome, the results of which have contributed to improved mapping of the pig genome.

In pigs which provide 43 percent of the meat consumed worldwide a chromosome defect can affect fertility.

With each pig producing as many as 14 piglets per litter, a faulty chromosome can reduce this by as much as half, with massive economic costs to the producer.

Dr O'Connor's research, carried out in the Griffin Laboratory, has led to the development of chromosome screening devices for both pigs and cattle and a chromosome screening service to multiple agricultural food providers.

Now with 13 clients in eight different countries, the team are screening hundreds of samples a year, as well as adapting the method to screen for chromosome abnormalities in other species.

The research findings were presented to agricultural industry leaders at the Pig Breeders Round Table Conference, one of the foremost international conferences on livestock genetics, held at the University of Kent in May 2017.

Explore further: From Mediterranean coasts to Tatra Mountains and beyond: Plant chromosome number variation

More information: R. E. O'Connor et al. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly, Animal Genetics (2017). DOI: 10.1111/age.12548

Chromosome number is the most basic feature concerning the genome of a species, and it is known for about one third of higher plant species. In particular, for plants of Italy, Slovakia, and Poland, online chromosome number ...

In many animal species, the chromosomes differ between the sexes. The male has a Y chromosome. In some animals, however, for example birds, it is the other way round. In birds, the females have their own sex chromosome, the ...

In a study to be presented on Feb. 5 in an oral plenary session at 8 a.m. PST, at the Society for Maternal-Fetal Medicine's annual meeting, The Pregnancy Meeting, in San Diego, researchers will report that cell free DNA analysis ...

(PhysOrg.com) -- Researchers from The Australian National University have discovered that the male-specific Y-chromosome is shrinking and its happening at different rates across species.

Hokkaido University researchers have revealed that key sex-determining genes continue to operate in a mammalian species that lacks the Y chromosome, taking us a step further toward understanding sex differentiation.

In the beef industry, if a cow does not get pregnant after breeding, she becomes an economic liability in the herd. Lack of calf production can significantly reduce annual revenue for producers.

There are significant gaps in our knowledge on the evolution of sex, according to a research review on sex chromosomes from Lund University in Sweden. Even after more than a century of study, researchers do not know enough ...

(Phys.org)Eusocial insects are predominantly dependent on chemosensory communication to coordinate social organization and define group membership. As the social complexity of a species increases, individual members require ...

Scientists using a high-resolution global climate model and historical observations of species distributions on the Northeast U.S. Shelf have found that commercially important species will continue to shift their distribution ...

If you open Google and start typing "Chinese cave gecko", the text will auto-populate to "Chinese cave gecko for sale" just US$150, with delivery. This extremely rare species is just one of an increasingly large number ...

Plant scientists at the University of Cambridge have found a plant protein indispensable for communication early in the formation of symbiosis - the mutually beneficial relationship between plants and fungi. Symbiosis significantly ...

Almost 150 years after Charles Darwin first proposed a little-known prediction from his theory of sexual selection, researchers have found that male moths with larger antennae are better at detecting female signals.

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Scientists overcome pig genome flaw - Phys.org - Phys.Org

May 25, 2017 Credit: Susanna M. Hamilton, Broad Communications

The Broad Institute of MIT and Harvard will release version 4 of the industry-leading Genome Analysis Toolkit under an open source software license. The software package, designated GATK4, contains new tools and rebuilt architecture. It is available currently as an alpha preview on the Broad Institute's GATK website, with a beta release expected in mid-June. Broad engineers announced the upgrade, as well as the decision to release the tool as an open source product, at Bio-IT World today.

The new version is built on a new architecture, allowing significant streamlining of individual tools and support for performance-enhancing technologies such as Apache SparkTM. This new framework brings improvements to parallelization, capitalizing on cloud deployment and making the process of analyzing vast amounts of genomic data easier, faster, and more efficient.

"We wanted to remove traditional barriers of scale while offering the same high level of data quality our users expect," said Eric Banks, Senior Director of Data Sciences and Data Engineering at Broad and a creator of the original GATK software package. "Thanks to the rapid adoption of cloud computing, researchers can finally do away with many of the infrastructure-related complications that have hampered progress, especially at smaller institutions and startups."

Today, more than 45,000 academic and commercial users worldwide rely on the GATK, running millions of analyses. The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. In addition to improving the performance of these established tools, GATK4 extends this scope of analysis to include copy number and structural variation, for both germline and somatic research applications.

Fully open source software

GATK4 will be released as a fully open source product, thanks in part to a collaboration between Broad Institute and Intel Corporation to advance high-performance analytics so researchers can study massive amounts of genomic data from diverse sources worldwide.

At the Intel-Broad Center for Genomic Data Engineering, software engineers and researchers have spent the last several months building, optimizing, and widely sharing new tools and infrastructure to help scientists integrate and process genomic data. GATK4 has benefited from this collaboration, which has helped engineers optimize best practices in hardware and software for genome analytics to make it possible to combine and use research data sets that reside on private, public, and hybrid clouds.

"Releasing GATK4 as open source was the obvious next step for our team," said Geraldine Van der Auwera, Associate Director of Outreach and Communications within the Data Science and Data Engineering group at the Broad Institute. "We believe it's the most effective way to support the community, and we hope it continues to grow, innovate, and help researchers make insights that are essential for future human health breakthroughs." "It is critical for progress in biomedicine that the software we use for analysing the genomes of millions of people is robust and well understood," said Ewan Birney, Director of EMBL-EBI and Chair of the Global Alliance for Genomics and Health (GA4GH). "Releasing GATK software with an open source license directly supports open innovation, data re-use and data re-analysis in the global biomedical community."

"The GATK tools are crucial for both germline and cancer analyses," said Robert L. Grossman of the University of Chicago Department of Medicine and an expert in biomedical informatics. "Releasing GATK4 as an open source software package will increase adoption, and benefit the community."

"Open sourcing the GATK is a big deal for open genomics, and for open science in general," said Jeremy Freeman, manager of computational biology at the Chan Zuckerberg Initiative (CZI). "Not only does it make this critical tool available to as broad as possible an audience for use, reuse, inspection, and contributionit provides a powerful example to the community for how an existing project can embrace open source."

"Open source code is a foundation of efficient biomedical research," said Brad Chapman, a research scientist at the Harvard T.H. Chan School of Public Health. "It enables reproducibility, reuse and remixing by removing barriers for sharing and distributing analyses. The Broad Institute's GATK team leads in the development of scalable, sensitive and specific variant calling algorithms, and open sourcing GATK4 will allow frameworks like Blue Collar Bioinformatics to make these methods broadly available to the scientific research community."

"Cloudera has always been a supporter and believer in the power of open source code," said Tom White, data scientist at Cloudera and a member of the Apache Hadoop PMC. "We've been excited to contribute to the GATK codebase, to make it run smoothly on Apache Spark and Cloudera. This next phase of the GATK, powered by Spark and open source software, will expand access and improve collaboration among genomic data scientists."

"The open sourcing of GATK4 is a great step for genomics, allowing for scalability and performance gains to be openly available to the research, biotech and pharmaceutical communities," said Jason Waxman, corporate vice president and general manager of Data Center Solutions at Intel. "GATK4, when run on Intel's new reference architecture, can achieve a 5X speed-up compared to earlier versions of the software."

"We at Google are excited to see this new release," said Ilia Tulchinsky, Google Cloud Healthcare Engineering Lead. "We've been collaborating with the Broad Institute for the past three years to enhance genomic processing on Google Cloud Platform. As a strong supporter for open source technology, we believe that making GATK available this way will facilitate its use by genomic scientists everywhere. As fellow collaborators with Intel, we particularly look forward to enabling researchers to run GATK4 on Google Cloud using the upcoming Intel Xeon processor Scalable family."

"The GATK is one of the most widely utilized software packages in the life sciences, and our team has worked very productively with Broad to accelerate it for use on Azure," said Geralyn Miller, Director, AI & Research, Microsoft. "This new model will greatly facilitate this effort going forward, and we are excited to continue and expand our efforts around GATK on Azure."

"With the open source launch of GATK4, there is an opportunity to create a global community that can collaborate together and advance the state of art in bioinformatics," said Hong Tang, chief architect at Alibaba Cloud, the cloud computing arm of Alibaba Group. "We look forward to closely working with Broad Institute in bringing the cloud-based GATK service to genomics customers in China, as well as in ongoing GATK research and development."

In addition to offering GATK4 as an open source toolkit, Broad Institute will continue to offer user support, training, and outreach on its popular user support forum. GATK4, like many of the Broad Institute's genome analysis tools, will be available through the Broad Institute's cloud based analysis platform, FireCloud.

Explore further: Google joins effort to boost genomics research

Google announced Wednesday it was teaming up with university scientists to use its computing platform to accelerate efforts in genomics research.

In a sign of the growing importance of the Internet "cloud," software group Cloudera said Monday it raised a whopping $900 million to expand its big data corporate services.

Microsoft has joined the Linux Foundation, the latest sign that the software giant is embracing open-source technologies it formerly treated with hostility.

Cloud computing is a more efficient and cheaper alternative for researchers wanting to access and analyse large amounts of human genomic data, a local study has found.

Apple today announced that its Swift programming language is now open source. As an open source language, the broad community of talented developersfrom app developers to educational institutions to enterprisescan contribute ...

Judging from technology-watching sites, Intel has something to worry about and it involves a rather well known place on the technology map called Redmond, Washington. Look for the sign that says Microsoft. There.

There are significant gaps in our knowledge on the evolution of sex, according to a research review on sex chromosomes from Lund University in Sweden. Even after more than a century of study, researchers do not know enough ...

(Phys.org)Eusocial insects are predominantly dependent on chemosensory communication to coordinate social organization and define group membership. As the social complexity of a species increases, individual members require ...

Scientists using a high-resolution global climate model and historical observations of species distributions on the Northeast U.S. Shelf have found that commercially important species will continue to shift their distribution ...

If you open Google and start typing "Chinese cave gecko", the text will auto-populate to "Chinese cave gecko for sale" just US$150, with delivery. This extremely rare species is just one of an increasingly large number ...

Plant scientists at the University of Cambridge have found a plant protein indispensable for communication early in the formation of symbiosis - the mutually beneficial relationship between plants and fungi. Symbiosis significantly ...

Almost 150 years after Charles Darwin first proposed a little-known prediction from his theory of sexual selection, researchers have found that male moths with larger antennae are better at detecting female signals.

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Genome Analysis Toolkit 4 (GATK4) released as open source ... - Phys.Org

May 24, 2017 Spinach plant, Castelltallat, Catalonia. Credit: Victor M. Vicente Selvas / public domain

"I'm strong to the finich, 'cause I eats me spinach!" said Popeye the Sailor Man.

While you may not gulp spinach by the can-fuls, if you love spanakopita or your go-to appetizer is spinach artichoke dip, then you'll be excited to know that new research out of Boyce Thompson Institute (BTI) will make it even easier to improve this nutritious and delicious, leafy green.

Today in Nature Communications, researchers from BTI and the Shanghai Normal University report a new draft genome of Spinacia oleracea, better known as spinach. Additionally, the authors have sequenced the transcriptomes (all the RNA) of 120 cultivated and wild spinach plants, which has allowed them to identify which genetic changes have occurred due to domestication.

"The spinach genome sequence and transcriptome variants developed in this study provide a wealth of valuable information that can be used to breed spinach with better disease-resistance, higher yield and better quality," asserted Zhangjun Fei, the project's lead researcher from BTI.

Better breeding for stronger spinach

Spinach, which is native to central Asia, is now cultivated worldwide, with a reported annual production of 24.3 million tons in 2014. Since it was first domesticated, gardeners and breeders have improved many agronomically important traits, such as leaf quality and nutrition, and over time these improvements have re-shaped the spinach genome. In turn, breeders today can use genomic information to speed up improvements, which is especially important for combatting significant diseases, like downy mildew.

Known as the 'late blight' of spinach, the downy mildew disease has devastated crops throughout California, and has recently popped up in Upstate New York. Armed with a better understanding of the spinach genome, the researchers have identified several genes that may confer resistance to the downy mildew pathogen. Once identified in a resistant variety of spinach, such genes could be quickly transferred to other, possibly more nutritious varieties, boosting their immune systems to fight this disease while still maintaining marketable traits.

Insights into spinach domestication

Of particular interest to the researchers is the discovery that the genomes of cultivated spinach varieties are not too different from their wild progenitors. When a plant is domesticated, its genome will evolve over centuries of selection. In many cases, it gets forced through a bottleneck of genetic changes necessary for cultivation, creating a very different plant from that which was first brought out of the wild. A great example is the comparison of maize (corn) to its ancestor, teosinte.

"By analyzing transcriptome variants of a large collection of cultivated and wild spinach accessions, we found that unlike other vegetable crops such as tomato and cucumber, spinach has a weak domestication bottleneck," explained first author, Chen Jiao.

This was great news because it means there is still much room for spinach improvement, but it also made it tougher to pinpoint genomic markers that could speed up the breeding process. Nonetheless, the team identified many regions in the genome directly attributable to the domestication process, that could be possibly linked to valuable traits, such as bolting, leaf number, and stem length

When asked for her favorite spinach recipe, first author Chen Jiao replied, "I usually make spinach salad for my family twice a week. It is very nutritious and easy to make. I just throw a handful of baby spinach, some croutons and fried bacon, and boiled eggs in a bowl and then drizzle all with bottled dressing."

So the next time you eat a luscious, green spinach salad, thank a scientist for keeping you healthy and strong!

Explore further: Dole recalls some spinach after salmonella found in sample

More information: Nature Communications (2017). DOI: 10.1038/NCOMMS15275

Dole Fresh Vegetables says it's recalling some of its bagged spinach distributed in 13 states as a precaution after a random sample tested positive for salmonella.

California officials say the E. coli bacterium recently discovered in U.S.-produced bags of spinach is found in nearly all Salinas Valley waterways.

Salinity and nutrient-depleted soil are two major constraints in crop production, especially for vegetable crops. In the January 2016 issue of the Journal of the American Society for Horticultural Science, researchers Chenping ...

California health officials said the strain of E. coli bacteria that has killed three people and sickened 201 others has been found near a spinach farm.

A natural compound hidden away in spinach has been shown to reduce food cravings between meals and could help prevent obesity, a Swedish scientist said on Monday.

Far from being a food spoiler, the fluorescent lighting in supermarkets actually can boost the nutritional value of fresh spinach, scientists are reporting. The finding could lead to improved ways of preserving and enhancing ...

There are significant gaps in our knowledge on the evolution of sex, according to a research review on sex chromosomes from Lund University in Sweden. Even after more than a century of study, researchers do not know enough ...

(Phys.org)Eusocial insects are predominantly dependent on chemosensory communication to coordinate social organization and define group membership. As the social complexity of a species increases, individual members require ...

Scientists using a high-resolution global climate model and historical observations of species distributions on the Northeast U.S. Shelf have found that commercially important species will continue to shift their distribution ...

If you open Google and start typing "Chinese cave gecko", the text will auto-populate to "Chinese cave gecko for sale" just US$150, with delivery. This extremely rare species is just one of an increasingly large number ...

Plant scientists at the University of Cambridge have found a plant protein indispensable for communication early in the formation of symbiosis - the mutually beneficial relationship between plants and fungi. Symbiosis significantly ...

Almost 150 years after Charles Darwin first proposed a little-known prediction from his theory of sexual selection, researchers have found that male moths with larger antennae are better at detecting female signals.

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Newly-published spinach genome will make more than Popeye ... - Phys.Org