Setting Standards

A number of organizations across the world announced last week that they were working to form an alliance to develop standards so researchers would be able to share genomic and clinical data. "The idea is to focus not on the creation of individual data sets but to focus on the standards and shared principles and ethics that would make it possible for many people to build things that would be individually innovative and yet collectively could learn from each other," the Broad Institute's David Altshuler tells ScienceInsider in a Q&A.

Altshuler notes that it is "an ambitious proposal" and that working groups will be set up later this year to begin discussing technical standards, ethics, and more. He says they hope to come up with standards so researchers can share information, but also so that participants can determine how their data is used.

"We're going to try to come together and work together and develop a menu of options and technical standards to implement them so that people can make decisions," he says, adding that "[i]f it turns out there's a set of data that, because of permissions, can only be used for certain purposes, then that's exactly what should happen."

Slow Process

The European Court of Auditors says that the Framework Programme 7 grant-awarding process, the main way that the European Union funds scientists, is overly bureaucratic, ScienceInsider reports. The program is to end this year.

The main problem is that program rules require changes to how universities and research institutes tracked projects — according to the court's report, 59 percent of recipients had to put in a new recording system, modify their system, or have two parallel systems in place. Further, program rules were also inconsistently interpreted.

The report, ScienceInsider adds, could lead to changes to the EU's next funding scheme, Horizon 2020.

The European Commission has already made changes to the Framework Programme 7 rules so they are more similar to current practices, a commission spokesperson tells ScienceInsider, adding that "this will continue in Horizon 2020."

This Week in PLOS

Individuals with chronic periodontitis tend to have distinct microbial communities in deep pockets around their teeth compared to those at healthier sites closer to the surface, according to a PLOS One study by Virginia Commonwealth University researchers. The team used 16S ribosomal RNA gene sequencing to characterize paired shallow and deep oral microbiome samples from 88 individuals with chronic periodontal disease. Along with microbiome shifts between the shallow and deep dental pocket sites in each person — which varied with factors such as smoking status or race — the analysis pointed to possible differences between the collections of bugs contributing to cavities and those linked to periodontal disease.

A PLOS Genetics study looks at genetic variants influencing traits such as height, weight, body fat, or waist and hip measurements that differ between men and women. Members of the international Genetic Investigation of Anthropometric Traits, or GIANT, consortium drew on data for 133,723 individuals for a meta-analysis aimed at finding sexually dimorphic genetic contributors to these and other anthropometric traits. That analysis, followed by a validation study involving more than 137,000 other individuals, led to variants at seven loci showing significant ties to waist-related traits in women but not men.

In PLOS Neglected Tropical Diseases, French researchers take a look at genetic patterns found in Madagascar's black rats — an animal reservoir for the plague-causing pathogen Yersinia pestis. The team used microsatellite markers to gauge genetic structure and diversity in nearly 1,300 animals in four black rat populations sampled in mountainous or flat parts of the island, looking at how these profiles corresponded to the serotype of Y. pestis detected in the rats when the pathogen was present. Genetic structure was highest for rats living in mountainous regions of Madagascar, study authors note, though more research is needed to understand genetics in the plague reservoir animals relates to the pathogen's presence and spread.

Dirt Map

Microbes are everywhere, and researchers taking part in the Earth Microbiome Project aim to find out how microorganisms living in soil help support other life on Earth, Jonathon Keats at Wired reports. Janet Jansson from Lawrence Berkeley National Laboratory and her colleagues are collecting samples from a number of locations to tease out the DNA from such organisms.

"The plan is to build a global 'gene atlas,' then to work out how nutrients and waste products migrate through the ecosystem," Keats adds. "Eventually that understanding might allow us to engineer microbes to be ultraefficient producers of biofuel, or even take control of the carbon cycle."

Researchers are particularly interested in samples from the English Channel, farms in the Midwest US, and the Gulf of Mexico near the Deepwater Horizon oil spill. From those sites, they hope to better understand how "small things shape big ecosystems," Keats says.

New Head for Max Planck Society

Martin Stratmann has been selected to direct the Max Planck Society, the Nature News Blog reports. The Max Planck Society oversees 80 research institutes in Germany and about a dozen centers elsewhere, and it has an annual budget of €2.0 billion (US$2.6 billion) that comes from the German federal and state budgets.

Stratmann, who has led the Interface Chemistry and Surface Engineering department at the Max Planck Institute for Iron Research, will take over his new position in June, 2014. He is to succeed Peter Gruss, a developmental biologist, who has led the society since 2002.

A Certain Fuzziness

While adding more data can clarify relationships between organisms and place them on the tree of life, sometimes more data can make the picture look fuzzier. "[J]ust as the spinal column and limbs created contrasting maps of primate evolution, scientists now know that different genes in the same organism can tell different stories," writes Emily Singer at Wired.

Researchers are now turning to algorithms to sort out such phylogenetic relationships, Singer adds. In a recent Nature paper, researchers from Vanderbilt University used a common concatenation approach to build a phylogenetic tree based on 1,070 genes and 23 yeast species and they further built a series of trees based on the genes individually. They then tried to reconcile their trees. However, "none of the 1,070 gene trees agreed with each other, with the concatenation phylogeny or with the [extended majority-rule consensus] phylogeny," the researchers write.

"I am not so sure we know what the true relationships are," Yale University's Michael Donoghue, who was not part of the study, tells Singer. "If we aren't sure what the truth is, we can't tell if we have the right tree."

This Week in Science

In Science this week, a team of Swiss and German researchers report new details about the regulation of Hox genes, which are clustered together in the genome and control body shape and limb development. In the study, the researchers show that during mouse limb development, Hox genes are transcribed in two waves, the first controlling arm and forearm development and the second responsible for digit formation. To do so, the Hox genes interact with a telomeric domain when mouse limbs are just forming and later swing toward the centromeric chromosomal domain, establishing new contacts to specify digits. Notably, the centromeric domain is shut down at the right time in development even if the telomeric domain is deleted, suggesting that the two regions operate independently.

Also in Science, investigators from the Fred Hutchinson Cancer Research Center present their genetic analysis of the fruit fly that they conducted to help understand how relatively new genes evolve functions critical to life. The team traced the evolutionary steps of the Drosophila gene Umbrea, which is less than 15 million years old yet is essential for chromosome segregation and normal development. They found that a series of steps, including the loss of an ancestral heterochromatin-localizing domain followed by alterations that rewired its protein interaction network, led to the gene's acquisition of species-specific centromere localization activity. The work gives insights into how young genes gain essential functions.

Shifting Programs

A hearing held by the House of Representatives science committee earlier this week examined the Obama administration's plan to reorganize US science education programs, ScienceInsider reports. The reorganization would affect some 226 programs at a dozen agencies, consolidating them and moving them to under the aegis of just three agencies, the Department of Education, the National Science Foundation, and the Smithsonian.

While ScienceInsider notes that the proceedings were bereft of partisan bickering, "that comity resulted in a steady stream of skepticism flowing from both sides of the aisle." In particular, legislators seemed concerned about the fate of programs currently at National Aeronautics and Space Administration, the National Institutes of Health, the Department of Energy, and the National Oceanic and Atmospheric Administration, whose budgets would decrease under the administration's plan.

"Normally, I support efforts to reduce duplicative programs," Representative Randy Hultgren (R-Ill.) said at the hearing. "But this reorganization seems rushed and poorly planned. The president's proposal seems to be taking a number of successful initiatives being done by high-quality groups at the local level and running a majority of them through a federal bureaucracy in Washington."

John Holdren, the president's science adviser, told the panel that the reorganization favored programs for "improving K-12 instruction, reforming undergrad programs around evidence based practices, streamlining the graduate fellowship process, and amplifying engagement activities," according to ScienceInsider.

The Science Lobby

Researchers need to lobby for science, writes Jai Ranganathan, a conservation biologist and co-founder of the SciFund Challenge, at Scientific American's Guest Blog. This is especially the case, he adds, as budgets diminish due to the sequester.

Other sectors affected by budget cuts — and he points to defense as an example — lobby for their cause and for their slice of the federal budget.

"The scientific community must also do the same, by convincing the public that it is worth spending tax dollars on research," Ranganathan says. "Scientists: this isn't someone else's job — this is your job, starting immediately."

He suggests a number of ways that scientists can engage with the public such as giving talks, writing blog posts, or posting science videos to YouTube. "Honestly, it doesn't really matter what method we use, so long as we connect to the public on a frequent basis with our science," he adds.

Global Alliance, Global Standards

More than 70 research organizations from across the world have joined together to develop a common framework to share genetic and clinical data, the New York Times reports. Among the organizations that have signed the letter of intent for this effort are the US National Institutes of Health, the Wellcome Trust, BGI-Shenzhen, and Genome Canada, GenomeWeb Daily News adds.

"The question is whether and how we make it possible to learn from these data as they grow, in a manner that respects the autonomy and privacy choices of each participant," David Altshuler from the Broad Institute tells the Times.

According to the white paper put together by the group, the aim of the effort is to develop a global alliance and technological tools for secure data storage that conform to standard principles.

This Week in Nature

In Nature this week, a multi-institute team led by Chalmers University of Technology researchers report on how an analysis of the fecal gut metagenome can be used to identify patients with type II diabetes. Using shotgun sequencing, the investigators characterized the gut metagenomes of 145 European women with normal, impaired, and diabetic glucose control, and observed "compositional and functional alterations in the metagenomes" of those with type II diabetes. They also developed a mathematical model based on metagenomic profiles that could identify type II diabetics, as well as women with diabetic-like metabolisms, with high accuracy. Importantly, the scientists also applied their model to a Chinese cohort, finding that metagenomic markers for type II diabetes differ, highlighting the need to make metagenomic predictive tools specific for the ethnicity of population studied.

GenomeWeb Daily News has more on this study, here.

Meanwhile, in Nature Genetics, an international group of researchers report on the identification of two susceptibility loci for osteosarcoma. The team conducted a genome-wide association study of 941 individuals with the disease and 3,291 cancer-free adults. They identified two susceptibility regions of the genome, with one harboring a possible candidate gene.

Also in Nature Genetics, a multi-national group of researchers report on the identification of four new susceptibility loci for atopic dermatitis. They used high-density genotyping of 2,425 German individuals with the disease and more than 5,400 controls, followed by replication in around 7,100 cases and 15,480 controls from Germany, Ireland, Japan, and China. The project uncovered the new loci and replicated previous associations, bringing the number of aptopic dermatitis risk loci in European people to 11.

Genomics -- So Hot Right Now

Genomics researchers are 'hotter' than those working in any other field, according to an analysis by Thomson Reuters ScienceWatch that gauges how 'hot' a researcher was during the last year by how many times their recent papers were cited.

Genomics investigators accounted for a sizable section of the hottest boffins in 2012, and the most scorching of these was Richard Wilson at Washington University School of Medicine, who was part of the team behind the Nature report "A Map of Human Genome Variation from Population-scale Sequencing" that detailed findings from the 1,000 Genomes Project. Wilson had 15 total papers from 2010 to 2012 that were cited last year.

Some familiar faces are strewn among the fieriest of the researchers working in genomics during the last year, but some new names crept into the list of the scientists with the most oft-cited papers.

Broad Institute Director and President Eric Lander is still on fire, Thomson found, as he contributed to that Nature paper as well, and he had an additional 12 other highly cited reports, which included genomics research into cancers of the ovaries, blood, and brain, and a report on missing heritability that was among the year's hottest papers. Lander was the hottest on the list during the two previous years.

Decode Genetics President Kari Stefansson made a comeback, jumping to the top of the genomics pyre after missing it last year. He had 13 reports on genomic aspects of Parkinson's disease, schizophrenia, and Alzheimer's cited last year.

Three of Wilson's fellow Washington University in St. Louis investigators joined him on the hot list, including Elaine Mardis, Li Ding, and Robert Fulton. They contributed to the same 1,000 Genomes paper and authored two other reports that landed in the top papers of the year. University of Michigan biostatistician Goncalo Abecasis, another author on the Nature paper, landed on the list for a dozen recent papers on GWAS studies of diabetes, body-mass index, and cardiovascular disease risk.

Jun Wang from BGI also made the list with 14 hot papers.

The University of Birmingham's Gregory Lip popped up in the survey for the first time, due to his reports on various aspects of atrial fibrillation.

Another newcomer, Rob Knight, a Howard Hughes Medical Institute investigator at the University of Colorado, made the hot list for 14 papers that examined the human microbiome.

The Social Network

You can't fault social network ResearchGate for a lack of ambition.

Intended to help researchers better connect to one another, the startup aims to do nothing less than create "a complete total mindset change of all the scientists in the world," says co-founder Ijad Madisch.

As Forbes' Tomio Geron reports this week, it will now have $35 million worth of help to do so.

The company has closed a Series C financing round led by Bill Gates and Tenaya Capital, providing it with funds to pursue its goal of opening up and accelerating scientific research.

The site, which currently counts 2.9 million users, lets scientists post information about their work and skills, allowing them to more easily identify potential collaborators. Madisch also "wants scientists to publish raw data from their research on" the site, Geron writes, noting that this could potentially let them "get feedback in real-time to their research, instead of waiting months or years for research to be published in top journals."

Of course, convincing researchers to eschew the top journals for an open-source social network platform is no easy task, as Madisch admits. Also potentially a challenge for site — making money.

"The company hasn't focused heavily on generating revenue yet," Geron notes.