Soil and manure from pig farms where antibiotics are commonly used are prone to harboring antibiotic resistance genes, according to a study in the early, online edition of the Proceedings of the National Academy of Sciences. Researchers from China and the US assessed manure, manure compost, and manure compost-treated soil samples from three large Chinese swine farms, using quantitative PCR arrays to test for 244 antibiotic resistance genes. The search uncovered signs of 149 different antibiotic resistance genes, the group reports, with sequences from a subset of these genes being especially enriched at the commercial swine farm site samples compared to control manure and soil samples Based on the patterns they saw, Michigan State University microbial ecology researcher James Tiedje, the study's senior author, and colleagues concluded that "diverse, abundant, and potentially mobile [antibiotic resistance genes] in farm samples suggest that unmonitored use of antibiotics and metals is causing the emergence and release of [antibiotic resistance genes] to the environment."

In another PNAS study, the University of Oxford's Zoltán Molnár and colleagues from the UK explore gene expression during brain development in mice, focusing on part of the cerebral cortex called the subplate zone. Using array- and RNA sequencing-based data from brain samples collected during mouse embryonic development and in post-natal and adult mice, the researchers gained clues about subplate function by finding genes with distinct expression profiles in that brain area during at least one of the developmental stages considered. Moreover, the group also saw enhanced mouse subplate expression for several of the same genes implicated in past studies of autism and schizophrenia, prompting them to argue for "the importance of the study of transient features of the developing brain to better understand neurodevelopmental disorders."

A team from the UK and the US performed genome-wide copy number analyses on multiple samples from within individual tumors taken from 11 individuals with glioblastoma. Based on alterations across different parts of each tumor, the investigators put together tumor-specific phylogenies and tracked genetic glitches signifying cancer progression in each patient. "Our results reveal the genome-wide architecture of intra-tumor variability in [glioblastoma] across multiple spatial scales and patient-specific patterns of cancer evolution, with consequences for treatment design," the study's authors wrote in a paper slated to appear online this week in PNAS.

On Wired's Threat Level blog, David Kravets describes an upcoming US Supreme Court case that is expected to address whether authorities can take DNA samples from anybody arrested for a serious crime.

According to Kravets, "at least 27 states and the federal government have regulations requiring suspects to give a DNA sample upon some type of arrest, regardless of conviction."

"The upcoming hearing, slated for Feb. 26, has drawn a huge following from civil rights groups, crime victims, federal and state prosecutors and police associations — each arguing their party lines," he writes.

The Supreme Court will be charged with upholding or rejecting a previous decision by the Maryland Court of Appeals in a case involving a man, Alonzo King, who was arrested in 2009 on assault charges, and then convicted for a rape committed years earlier based on a DNA match.

The Maryland court overturned King's conviction, concluding that arrestees do have a Fourth Amendment-guaranteed "weighty and reasonable expectation of privacy against warrantless, suspicionless searches," which is not outweighed by the state's need to accurately identify a suspect via DNA.

According to Kravets, the Supreme Court is probably going to reverse the lower court's conclusion, having suggested as much when it stayed the Maryland decision last July.

Science, Ewan Birney writes in The Observer, can be much more emotional than journal papers can lead people to believe. He recalls a heated argument with a colleague over a set of experiments. "We must have been a sight: two geeks wildly gesticulating and laughing, happy to be friends after a virtual plate-throwing fight," Birney writes, adding "this is not what you write up in your scientific paper."

Other emotions — happiness as well as frustration — come out, too, Birney writes. "Pivotal moments in science can cause an outright physical reaction – a wave of giddiness when you realise you've backed the right idea," he says, but then there also is "the sinking feeling when you just can't make an idea fit."

BGI, Bloomberg Businessweek's Lauren Hilgers writes, has established itself as the largest commercial genomic sequencing company in the world, powered by an army of young, college-educated workers — the average age of BGI's 3,000 workers is 26, she notes.

Not only is BGI expanding in China — when it was associated with the Chinese Academy of Sciences, it was limited to having 90 scientists — it is in the midst of acquiring California-based Complete Genomics, which, Hilgers says, will help BGI improve its data storage capabilities. "Even as BGI improves its technology, its biggest strength remains all those cheap, highly educated analysts," Hilgers adds.

Some workers live in BGI dorms and the company has a number of clubs as well as an annual basketball tournament; Jun Wang, the executive director of BGI likens it to a college campus, Hilgers says. Though, it's a college campus tackling a number of genomic projects.

"When I ask Wang how BGI determines which plants and animals to sequence as part of its '1,000 Plants and Animals' project, he answers, 'We start with anything tasty,'" Hilgers writes.

In Science this week, investigators from Oak Ridge National Laboratory report on the genetic basis for mercury methylation, the process of converting mercury into the neurotoxin methylmercury, by bacteria. The team examined the genomes of two sulfur-reducing bacteria — Desulfovibrio desulfuricans ND132 and Geobacter sulfurreducens PCA — and found that two genes, if deleted alone or together, abolishes the organisms' ability to process mercury. Because these genes are present in other lineages of bacteria and archaea, the ability to produce methylmercury may be more widespread than previously believed.

Also in Science, a multi-institute team of French researchers publish the crystal structure of papillomavirus proteins, offering a potential new target for fighting the infection, which is known to cause a variety of cancers including cervical cancer. Papillomaviruses rely on a protein called E6 to bind to and deactivate certain host proteins. The scientists determined the structure of both human and bovine E6 proteins bound to their host proteins and described two zinc domains and a linker helix that form a hydrophobic binding site. Mutational inactivation of this site disrupts the oncogenic activities of the E6 proteins, suggesting a new area for therapeutic intervention.

Amy Bishop, the University of Alabama in Huntsville biologist who pleaded guilty in the fall to the shooting deaths of three of her colleagues and the attempted murder of three others, had a tragic past, writes Patrick Radden Keefe at The New Yorker. He delves into not only the Alabama shootings — which, at first, appeared to be tied to Bishop's failed bid for tenure — but also the death of her brother Seth Bishop about 25 years earlier in Massachusetts.

Though Amy's shooting of Seth had been ruled accidental at the time, she has since been indicted in that case, though Keefe notes that the case is unlikely to go to trial. Keefe examines that case as there are a number of theories about what may have occurred or about how the case was handled by police or even by the town. In particular, he wonders whether if that case had been handled differently, if it could have made a difference down the line in Alabama.

"In the months that I spent talking with people in Braintree, I came to believe that there had indeed been a coverup, but that it had been an act not of conspiracy but of compassion," he writes, later adding that "it may have seemed that the most charitable way to address the confounding tragedy at Hollis Avenue was simply to move on — a parochial gesture of mercy and denial that had an incalculable cost, decades later, in Alabama."