Category Archives: Genome

US scientists have delayed cancer cell growth by using genome editing to remove a protein.

Removing an enzyme known as Tudor-SN delayed the replication of cellsfrom human kidney and cervical cancers in the lab.

'We know that Tudor-SN is more abundant in cancer cells than healthy cells, and our study suggests that targeting this protein could inhibit fast-growing cancer cells,' said Dr Reyad Elbarbary of the University of Rochester, New York, and lead author.

Normal cells divide and replicate through the process known as the cell cycle. If the cycle is disrupted, cells can become cancerousand replicate uncontrollably, forming tumours.

One regulatory component of the cell cycle is micro RNA (miRNA) - small noncoding RNA molecules which adjust gene expression. The Rochester team showed that removing Tudor-SN through genome editing increased the amount of miRNA present. The miRNA reduced the expression of genes critical to the progression of the cell cycle from the 'preparatory' phase to the replication phase.

Although the research is at a very early stage, the team hope their findings could lead to a new treatment option for cancer. They next plan to investigate how Tudor-SN works with other molecules in the cell cycle, in order to develop drugs to target it.

'Because cancer cells have a faulty cell cycle, pursuing factors involved in the cell cycle is a promising avenue for cancer treatment,' said Professor Lynne Maquat of the University of Rochester, and senior author.

Dr Thomas Cox of the Garvan Institute of Medical Research,Australia, who was not involved in the study, told Cosmos magazine that targeting miRNAis difficult and technically challenging. 'This study is saying: "Well, if we cant target microRNAs directly, can we target something regulating them?"'

The study was published in Science.

Read more here:
Genome editing used to slow cancer growth - BioNews

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.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Read more:
Scientists overcome pig genome flaw - Phys.org - Phys.Org

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

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

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.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

More here:
Newly-published spinach genome will make more than Popeye ... - 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.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Read the original post:
Genome Analysis Toolkit 4 (GATK4) released as open source ... - Phys.Org

Sign Up for

Our free email newsletters

Researchers are pushing forward on a project to one day create a synthetic genome of humans and other organisms, a development that could result in new ways to treat disease and even affect our fundamental understanding of human biology, yet also presents challenging ethical questions. At a recent scientific meeting, questions remained about how much should be shared with the public.

More than 200 prominent geneticists, biologists, technologists, and enthusiasts recently gathered in downtown Manhattan for a meeting of GP-write, a project with the goal to "understand the blueprint for life provided by the Human Genome Project."

The researchers plan to develop the scientific and technological tools necessary to synthesize genetic code inexpensively and efficiently. While the ease with which scientists can read DNA has sped up dramatically in the past 15 years, their ability to write it is much further behind. They can synthesize small bits of DNA, and even have created small viral and bacterial genomes from scratch, but eventually the goal is to tackle genomes of more complex microbes, plants, and even humans. Accomplishing this could give scientists cell lines for research and the production of biologic drugs, safer and innovative therapies to treat disease, microbes that could help nourish our bodies where food is scarce, or even complex data storage.

This was the second meeting of GP-write. Last year's meeting, held in Boston in May, drew controversy, mostly due to its opacity. Concerns about the ethics driving an advance as dramatic as a synthetic human genetic code, something that has the capacity to "completely redefine the core of what now joins all of humanity together as a species," as one researcher wrote, demand constant dialogue beyond the scientific community. But instead of inviting that conversation, the meeting appeared closed and secretive it was capped at 130 scientists with no members of the media present.

The meeting organizers say their hands were tied by scientific publishing rules an article outlining their work was going to be published in the journal Science, which does not allow researchers to discuss results publicly before publication (the article was published the following month). Media coverage of the meeting itself, however, contained a lot of hype and few facts, since the organizers couldn't talk to the press. However, GP-write's organizers did listen to public feedback generated from those articles, Nancy Kelley, the coordinator of GP-write, told Vocativ, and broadened the focus of the project beyond synthesizing human DNA.

Though they do plan to synthesize human DNA eventually, they realized that "the human part needed to be put off until the ethical implications were fully explored," Kelley said.

For this year's meeting, Kelley said, the project organizers wanted a more open meeting, and 22 reporters representing well-known magazines, newspapers, and web sites were on the list of attendees (I had recently reported on GP-write for CNBC). Some of the initial sessions were live streamed to hundreds of viewers, Kelley said. The overall vibe was congenial and collaborative.

But there was a caveat. The night before the meeting, members the media received an email that included a media policy. Because some of the presentations contain unpublished data, we were asked, as "a professional courtesy," to "refrain from sharing screen shots of the slide presentations and any scientific data shared at the meeting unless you have permission from the presenter" or "publishing any content without permission from the scientist in question." A bolded note to the same effect was inside the packet of materials handed to all attendees. The speakers were supposed to note on their slides whether the data was unpublished, Kelley said, but sometimes they forgot. Some people still took photos of slides, but the Twitter dialogue was relatively sparse.

For most researchers, the policy didn't seem strange. Several scientists and ethicists told Vocativ it's common to limit what can be shared at scientific meetings to promote openness within the scientific community because it allows researchers to discuss their unpublished work without violating journals' policies and without fear of others beating them to it.

The policy is in line with "standard norms of academic discourse at scientific conferences," Barbara Evans, the director of the University of Houston Law Center and one of the speakers who mentioned the importance of transparency in GP-write, told Vocativ via email. "It's a little counterintuitive, but true, that reasonable restrictions on communication can serve to promote transparency, if the restrictions encourage people to feel comfortable about sharing their original thoughts and ideas."

To others, however, the policy was less natural. There were many attendees who were not actively participating in research and might not have ever come to a scientific meeting, so they weren't used to the rule, especially because there was such little unpublished data presented. And, given the number of speakers who mentioned the importance of public interface and participation, the policy could even seem contradictory to some journalists.

"But despite opening their doors, [GP-write organizers] still have a ways to go to embrace transparency. The day before the meeting, a PR exec gave reporters new ground rules: No publishing content without permission from the scientist involved," reads Stat News' email newsletter sent before the meeting started.

One attendee named Bryan Bishop, whose interest in biology is strictly a hobby, took transcripts of the first of the talks and posted links to them on Twitter. He told Vocativ he was tapped on the shoulder by one of the meeting organizers and asked to stop. The following exchange happened on Twitter:

Bishop said he didn't know about the media policy and told Vocativ via email: "I think that everyone means well at GP-write. I don't feel offended they are still figuring how GP-write works and what's in their DNA I wasn't expecting a blanket 'don't post any content at all' especially after hearing the Center say kind words about the virtues of transparency and inclusiveness."

If anyone is restricting the transparency of the meeting, it's the scientific journals, said Eliza Strickland, a senior associate editor at engineering magazine IEEE Spectrum. "I fault these journals for wielding their power in an old-fashioned and outdated way that interferes with the free flow of scientific information, but I don't fault scientists or conference organizers for complying with their rules."

Journal policy or not, transparency has to be at the heart of GP-write, and last year's firestorm showed what can happen if it appears compromised. Jeffrey Bessen, a chemistry graduate student at Harvard who is on GP-write's public outreach committee, felt the media policy is justified, but says that he understands the "optics" of appearing as transparent as possible. "I think there's trust to be regained. That policy to me doesn't read like it's not transparent, but to someone else it might."

The project organizers know this and say they are committed to it. Various sessions at the two-day meeting were dedicated to ethical concerns and public outreach; a committee met to discuss how the organizers can best have an open conversation about their work. The dialogue will be ongoing, especially if the scientists get closer to synthesizing a human genome.

"We're going to continue to be as open as we possibly can," Kelley said.

This article originally appeared at Vocativ.com: Scientists working to build a human genome struggle with transparency.

See the original post:
If scientists build a synthetic human genome, does the public have a right to know? - The Week Magazine

More than a dozen companies have sprouted up in recent years to sell thousands of genetic health tests, ranging from Google-backed 23andMe to Roche.

But the consumers who order the tests often face months-long waits to get an appointment with a genetics expert who can explain the results. That's because there are fewer than 5,000 genetic counselors in the United States, which falls far short of the demand. Given the lack of training programs, genetic experts predict that the supply won't reach an equilibrium until 2024.

So a group of health veterans is forming a new technology startup called Genome Medical to train genetic experts, and provide $149 video consultations to both doctors and patients.

The company was founded by Lisa Alderson and Randy Scott, former executives from Invitae, a company that is aiming to become the "Amazon for genetics," and Harvard Medical School geneticist Robert Green.

In an exclusive interview with CNBC, Alderson said the company has raised more than $12 million from Canaan Partners, Illumina Ventures, and others.

Recent studies have found that genetic testing costs patients and their insurers between $300 million and $600 million each year in the U.S. alone. The market for precision medicine, which involves a boost in human genetic testing, is expected to reach $87.79 billion by 2023.

Alderson said genetic-testing companies are increasingly willing to pay for access to experts, who can help patients understand their results. The initial areas of focus for the company include reproductive health, cancer and preventative medicine.

Illumina, maker of DNA sequencing machines, is partnering up with Genome Medical for its program, known as Understand Your Genome, which offers whole genome sequencing to professionals for $2,900.

Illumina's vice president of applied genomics Dawn Barry said that Genome Medical's experts will help consumers determine if they need the test at all and what to expect. Barry described the technology as a "critical connection."

Federal regulators have expressed concern about companies that offer genetic information to consumers, without expert oversight. The U.S. Food and Drug Administration made that clear in November of 2013 when it ordered direct-to-consumer testing company 23andMe to stop selling its tests, although the FDA more recently approved 23andMe tests for some specific functions. (23andMe is not a partner of Genome Medical.)

"There will be a tremendous increase and interest in utilizing genetic testing," added Genome Medical's Green. "But everyone agrees that the current medical workforce isn't prepared for that."

More:
Start-up Genome Medical is training experts to help you figure out what your genetic tests mean - CNBC

Researcher at the Sidra Medical Center in Qatar.

IBM has announced a new healthcare-focused collaboration with Qatar's Sidra Medical and Research Center.

Sidra is a biomedical research hospital and educational institution that's spearheading the Qatar Genome Program (QGP), one of the world's largest national genome medical research projects.

Sidra will now use IBM technology as the compute and storage infrastructure for the research center. Specifically, IBM's flash storage systems and software-defined infrastructure will be used to manage and store clinical genome sequencing data as well as provide Sidra's technology infrastructure capabilities that underpin the project.

"Analyzing hundreds of samples in parallel on a regular basis requires a robust HPC system to handle the load properly," said Dr. Mohamed-Ramzi Temanni, manager of the Bioinformatics Technical Group at Sidra. "The Sidra and IBM work effort is unique -- it was a joint collaboration between our bioinformatics experts who led the complex analysis component and built the pipelines while IBM customized the system to ensure best performance and ease of use."

In a similar collaboration, IBM announced that it's working with the University of Michigan's non-profit tranSMART Foundation to optimize its translational research platform, which is used by scientists to share pre-competitive translational research data.

IBM said the Foundation is using Power8 servers at the university for research and development and to host its web-based training for the tranSMART platform. These servers also serve as a public showcase of the foundation's open-source, open-data, and open-science approach to translational research.

The rest is here:
IBM's compute, storage tech powers Qatar Genome Program | ZDNet - ZDNet

May 23, 2017 (Left) Shell of the deep-sea mussel Bathymodiolus platifrons and (right) shallow-water mussel Modiolus philippinarum. Credit: Hong Kong Baptist University

A joint research led by Hong Kong Baptist University (HKBU) and the Hong Kong University of Science and Technology (HKUST) has assembled the 1.64 gigabytes genome of a deep-sea mussel, which is roughly equivalent to 50% of the size of human genome. This is the first decoded genome among all deep-sea macrobenthic animals, revealing a complete set of DNA. The discovery gives wider insights into future research on the mechanisms of symbiosis in other marine organisms such as giant tubeworms and giant clams.

The research team, led by HKUST's Chair Professor of Division of Life Science Professor Pei-Yuan Qian and HKBU's Associate Professor of Biology Dr Jian-Wen Qiu, has published the research findings in prestigious international academic journal Nature Ecology & Evolution in early April.

The team used a specimen collected in 2013 during Dr Qiu's participation in China's manned submersible Jiaolong's expedition of the South China Sea for the research. Deep-sea organisms including mussels thrive in the extreme environments of hydrothermal vents and cold seeps which are characterised by high hydrostatic pressure, lack of photosynthesis-derived food, variable temperatures and high concentrations of toxic substances. Despite their ability to survive under stressful conditions, a lack of genomic resources has hindered the understanding of their molecular mechanisms of adaptation.

The study sequenced the genome of the deep-sea mussel Bathymodiolus platifrons as well as its shallow-water relative Modiolus philippinarum collected from a local softshore in Tingkok for comparison of genomic features. Through phylogenetic analysis, the research team discovered that modern deep-sea mussels are the descendants of shallow-water mussels, and their ancestors migrated to the deep sea approximately 110 million years ago, providing evidence to support a hypothesis that their ancestors survived through an extinction event during the global anoxia period associated with the Palaeocene-Eocene Thermal Maximum which occurred around 57 million years ago.

Genome comparison revealed that the great expansion of several gene families in the deep-sea mussel may be related to its adaptation to the deep sea. For instance, the expansion of the "heat shock protein 70 family", a family of proteins that are produced by a cell in response to exposure to stressful conditions, may help the mussel stabilise protein structures. The expansion of the "ABC transporters family", the unit of the transport system, may enhance the mussel's ability to move toxic chemicals outside its gill epithelial cells.

The expansion of gene families related to immune recognition, endocytosis and caspase-mediated apoptosis indicates the mussel's adaptation to the presence of chemoautotrophic endosymbionts in its gills. An additional proteomic analysis of the deep-sea mussel gill reveals nutritional and energetic dependency of the mussel on its methanotrophic symbionts.

Professor Qian said, "The study has provided genomic resources for understanding how the deep-sea mussel has adapted to the abiotic stresses and lack of photosynthesis-derived food in the deep-sea chemosynthetic environment. The general mechanisms of symbiosis revealed in the study are of relevance to other symbiotic organisms such as deep-sea tubeworms and giant clams."

Dr Qiu said, "The genomic resources will facilitate various studies, including genetic connectivity among deep-sea populations, which is relevant to the establishment of deep-sea marine reserves."

Explore further: Symbiosis bacteria produce a variety of toxins that appear to save mussels from being eaten

More information: Jin Sun et al, Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes, Nature Ecology & Evolution (2017). DOI: 10.1038/s41559-017-0121

Journal reference: Nature Ecology & Evolution

Provided by: Hong Kong Bapstist University

Imagine you have a tenant living in your house. They're keeping your fridge topped up. But in addition to this, they're producing all kinds of toxic substances. More harm than good? Not necessarily; it all depends what you're ...

The search for new energy sources to power mankind's increasing needs is currently a topic of immense interest. Hydrogen-powered fuel cells are considered one of the most promising clean energy alternatives. While intensive ...

Dr Pim Bongaerts, a Research Fellow at The University of Queensland's Global Change Institute (GCI) and ARC Centre of Excellence for Coral Reef Studies, and lead author of the study, said deep reefs share coral species with ...

The gradual rise in oceanic acidity is weakening the shells of shellfish, corals and sea urchins, making them vulnerable to predation and damage from oceanic movements.

Seafloor communities within New Zealand's Exclusive Economic Zone (EEZ) need better protection against deep-sea mining, according to a Victoria University of Wellington researcher working with NIWA scientists to investigate ...

A diving expedition off the north coast of Scotland is set to discover the secrets of mussels as big as size 9 shoes.

Organisms in nature adapt and evolve in complex environments. For example, when subjected to changes in nutrients, antibiotics, and predation, microbes in the wild face the challenge of adapting multiple traits at the same ...

Biological engineers at Utah State University have successfully decoded and reprogrammed the biosynthetic machinery that produces a variety of natural compounds found in fungi.

The blue whale, which uses baleen to filter its prey from ocean water and can reach lengths of over 100 feet, is the largest vertebrate animal that has ever lived. On the list of the planet's most massive living creatures, ...

The spectacular variety of colours and patterns that butterflies use to ward off potential predators may result from highly localised environmental conditions known as "microhabitats", researchers have found.

Female vampire bats form strong social bonds with their mothers and daughters as they groom and share regurgitated meals of blood. They also form friendships with less closely related bats. Gerry Carter, post-doctoral fellow ...

Snakes, although as social as birds and mammals, have long been thought to be solitary hunters and eaters. A new study from the University of Tennessee, Knoxville, shows that some snakes coordinate their hunts to increase ...

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Read the original:
Research decoding the first deep-sea mussel genome published - Phys.Org

Biofuels International Magazine

Sequencing of Green Alga Genome Provides Blueprint to Advance Clean Energy, Bioproducts ScienceBlog.com (blog) Plant biologists have sequenced the genome of a particularly promising species of green alga, providing a blueprint for new discoveries in producing sustainable biofuels, antioxidants, and other valuable bioproducts. The researchers targeted ... Big progress for algae biofuels? Green alga genome sequencedBiofuels International Magazine Algae can do pretty much anythingInnovators Magazine all 4 news articles »

Go here to see the original:
Sequencing of Green Alga Genome Provides Blueprint to Advance Clean Energy, Bioproducts - ScienceBlog.com (blog)