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.

The People Have Spoken

The US National Cancer Institute asked and the community answered. The verdict: cloud-based public repositories of co-located cancer data and computing resources would be a welcome development — but there are a few things that should be taking into consideration.

In a post on its blog, the NCI's informatics arm reports that it received 68 responses to a solicitation letter from the NCI Head Harold Varmus asking for input on the development of the so-called cancer knowledge clouds.

In their answers, summarized here, the researchers ask that the resource addresses analysis difficulties related to inconsistent file formats and metadata standards; be easy to use; and include an analysis and high performance computing training component. There are also questions about the cost of sustaining the cloud as well as establishing as means of data access that complies with regulatory requirements while not being too restrictive.

This Week in Genome Biology

In the early, online version of Genome Biology, an international team describes findings from an effort to sequence the genome of a commonly grown, green-podded cacao cultivar called Theobroma cacao Matina 1-6. The US Department of Agriculture-Agriculture Research Service's David Kuhn and colleagues from Mars, Indiana University, Hudson Alpha Institute for Biotechnology, IBM, and elsewhere put together a genome assembly representing around 346 million of the estimated 445 million bases in the Matina 1-6 cultivar's genome. Through comparisons with an already sequenced cultivar, gene expression profiling, and other analyses, the team tracked down genes with apparent ties to cacao traits of interest, including pod color.

A Broad Institute-led team reports on computational schemes for detecting and understanding bias in DNA sequence reads. The researchers assessed human and microbial sequence data generated with Illumina, Ion Torrent, Pacific Biosciences, and Complete Genomics platforms, using their methods to look at the nature and source of sequence biases across technologies, sequence sources, and library types. "The assays presented in this paper provide a comprehensive view of sequencing bias, which can be used to drive laboratory improvements and to monitor production processes," the Broad's David Jaffe and colleagues wrote. "Development guided by these assays should result in improve genome assemblies and better coverage of biologically important loci."

Selection pressure protects long non-coding RNAs, or lncRNAs, from mutation in the fruit fly genome, but the same level of selection against mutations doesn't carry over to human lncRNAs, according to a study by two University of Oxford researchers. The pair scrutinized SNP patterns in intergenic lncRNA sequences from 163 Drosophila melanogaster strains and 174 humans. Whereas intergenic lncRNAs in fruit flies tend to harbor a higher-than-usual proportion of rare variants, they found, selection against such changes was less stringent in the human genome, where selection on lncRNAs between genes appeared neutral. Based on such patterns, study authors postulated that "while the sequences of lncRNAs will be well conserved across insect species, such loci in mammals will accumulate greater proportions of deleterious changes through genetic drift."

Court OKs Swabbing Suspects

In a decision that is expected to be praised by police and pummeled by some civil rights groups, the US Supreme Court yesterday upheld the power of government, at every level, to collect and keep DNA samples from people who are arrested for serious crimes, ScotusBlog reports.

Anyone who watches network detective shows knows that DNA evidence and matching offers tremendous value to police, particularly in cold cases. Cops want to be able to expand the pool of genetic 'fingerprints' as much as possible, enabling deep searches to link a suspect who was picked up for one act to others in the past.

But the plaintiffs in the case of Maryland v. King argued that taking DNA samples from someone who is merely suspected of a crime and then trying to match them genetically to other, past crimes without a warrant violates the 'unreasonable search and seizure' aspect of the Fourth Amendment.

The decision was a surprising 5-4 split that saw unlikely alliances, as Justice Antonin Scalia joined the liberal wing of the bench in voting against the ruling and Justice Stephen Breyer swung with conservatives in the majority who agreed that the practice is constitutional.

In his dissenting minority opinion, Scalia said that the Fourth Amendment forbids searching people for evidence of a crime when there is no reason to believe they are guilty of that crime or in possession of incriminating evidence.

"That prohibition is categorical and without exception; it lies at the very heart of the Fourth Amendment," Scalia said in summary from the bench.

The majority opinion held that such searches are not unreasonable and they are not much different from fingerprints, mugshot searches, or police lineups.

There are good reasons for the disagreement, because the constitution likely encouraged disagreement over such important issues, Akhil Reed Amar, a Yale law professor, and Neal Katyal, former acting US solicitor general and Georgetown professor, write in an op-ed in today's New York Times.

The side-switching of the justices and the closeness of the vote suggests that this was a difficult question before the Court, one that Justice Samuel Alito called "perhaps the most important criminal procedure case that this Court has heard in decades."

Still, Amar and Katyal say the majority got this one right. The Fourth Amendment leaves a fair amount of leeway in deciding what is and is not "unreasonable," they add.

"Contrary to Justice Scalia's view, the framers [of the Constitution] did not answer the DNA question in 1791. Rather, the framers posed the question for us, their posterity," Amar and Katyal note.

Sequestration Specs at NIH

There will be fewer grants and fewer patients and all areas of science will be affected by sequestration, according to a new factsheet posted by NIH yesterday.

Compared with 2012, this year NIH will be able to fund around 700 fewer competitive research grants and will be able to admit roughly 750 fewer new patients into the NIH Clinical Center, due to the roughly 5 percent funding cut that was enacted because Congress and the White House could not reach a long-term deficit-reduction agreement.

Existing noncompeting research project grants will be cut by around 4.7 percent, on average, NIH estimates, but in general the duration of these grants will not be shortened.

The institutes will have some flexibility to deal with the funding cut this year "in a fashion that allows them to meet their scientific and strategic goals," NIH says, and these capabilities may vary depending on the institute or center.

The sequestration cuts in a broad stroke, and it does not stipulate any particular scientific areas that will be cut, so it is likely that most of the scientific disciplines will be reduced by around 5 percent, the agency says.

The impact of the sequestration on NIH's intramural research in Bethesda and its off-campus labs will be "substantial," NIH says, particularly because the cut was applied retroactively to the beginning of fiscal year 2013, meaning the agency has to absorb a full year of cuts in less than half a year.

That said, NIH does not expect to furlough or cut employees at its NIH campus or in its off-campus facilities, and instead plans to delay hiring and reduce administrative services contracts, the agency says.