Chromosome Painting, Gene Mapping of Tasmanian Devil Facial Tumor Disease
Deakin, Bender et al., PLoS Genetics
A team led by investigators at the Australian National University reports its use of "chromosome painting and gene mapping to deconstruct the DFTD [Tasmanian devil facial tumor disease] karyotype and determine the chromosome and gene rearrangements involved in carcinogenesis." Through its analysis, the team produced detailed maps of both the devil and tumor karyotypes, which the researchers say will aid future genomic investigations into the transmissible cancer.
At The Crux blog, Mike Taylor — a dinosaur paleobiologist at the University of Bristol in the UK — says that academic publishing is "in a horrible mess," and that authors and publishers have increasingly antagonistic relationships. The Cost of Knowledge boycott — the refusal of more than 6,000 researchers to write, edit, or review articles for Elsevier because of the publisher's support for the Research Works Act — illustrates this new tense relationship, Taylor says.
While issues like RWA were the "immediate triggers" of the anger, they aren't the real cause. "Now there are no technical barriers to access, the only way publishers can charge for it is by making barriers: paywalls. So we have a huge and tragic disconnect: what publishers want — barriers — is the exact opposite of what authors want — universal access. It’s authors vs. publishers," he adds.
New Scientist's Michael Brooks recently spoke with Princess Sumaya bint El Hassan of Jordan — who is also president of that country's Royal Scientific Society — about how science is perceived and how it should be used to "serve all the world's people." In the Arab world, the princess says, there isn't a clear understanding that science can improve lives. That may be because research priorities are geared towards the needs of a few, and not global issues. "When you think of the money spent on obesity-related research in comparison with the money spent on researching energy, water, environment and food, I'm not sure we have prioritized our research properly," she says. "The link between science and society is very important — you can't just be researching for research's sake. If there isn't an impact on people, what is the point?" The princess also tells Brooks that Jordan is developing a mentoring program for young scientists to start "nurturing a new generation of scientists in emerging nations."
This Week in Nucleic Acids Research
Researchers at Spain's Universitat Pompeu Fabra show in a paper published online in advance in Nucleic Acids Research this week that a subset of genes dependent upon the transcription factor Pap1 "only require nuclear Pap1 for activation, whereas another subset of genes … do need oxidized Pap1 to form a heterodimer with the constitutively nuclear transcription factor Prr1." The Pompeu Fabra team adds that "the ability of Pap1 to bind and activate drug tolerance promoters is independent on Prr1, whereas its affinity for the antioxidant promoters is significantly enhanced upon association with Prr1," which suggests to the team that "the activation of both antioxidant and drug resistance genes in response to oxidative stress share a common inducer, H2O2, but alternative effectors."
In another paper published online in advance in Nucleic Acids Research, a team led by investigators at New Zealand's University of Otago compares the performance of three existing pipelines for aligning bisulphite converted sequencing reads, providing "provides guidance to advance sequence-based methylation data analysis for molecular biologists."
Finally, Anthony Bugaut and Shankar Balasubramanian at University of Cambridge discuss the roles of 5'-untranslated region RNA G-quadruplexes in translation regulation and targeting in a Nucleic Acids Research paper this week. In their review, Bugaut and Balasubramanian consider "progresses in the study of 5'-UTR RNA G-quadruplex-mediated translational control."
Roy Britten, who discovered that mammalian genomes includes a number of repetitive sequences, has died, reports the Los Angeles Times. He was 92. Britten, along with his colleague David Kohne at the Carnegie Institution, used a renaturation approach to show that mammalian DNA contains repetitive sequences."It soon became clear that actual genes, which serve as the blueprint for proteins, enzymes, and other cellular components, accounted for only a few percent of the genome," the LA Times says. Britten later moved to Caltech. His work "provided the most accurate images of what DNA is like until sequencing came along decades later," adds Caltech's Eric Davidson.
Plant cell biologist Anne Osterrieder from Oxford Brookes University in the UK says that when it comes to successfully engaging the public and communicating their ideas, researchers have to get creative. Writing in the Guardian, Osterrieder says that despite the fact that most people agree that it's important to engage children in science and communicate effectively with the public, "motivation and active involvement varies hugely and too often it is down to a few passionate individuals to drive engagement projects forward." While official outreach activities at universities tend to focus on school talks and workshops, there are a variety of other ways researchers can reach out, she adds — writing in school magazines, keeping blogs, and even producing fun science videos in collaboration with musicians and artists are all good places to start. Participating in social media is another good way to reach the public. Osterrieder says she now has "confidence and determination in using a variety of engagement channels to take science to a wider audience. I hope that others feel similarly encouraged in using innovative outreach techniques to help inspire the next generation of scientists."
Working with ancient DNA isn't easy, but Russian researchers have reported that they've generated living plants from the fruit of an arctic flower that has been dead for 32,000 years, reports The New York Times' Nicholas Wade. The campion-like fruit was stored by a squirrel in its burrow in Siberia, and lay buried under the frost until scientists dug it up a few years ago. "This would be the oldest plant by far that has ever been grown from ancient tissue. The present record is held by a date palm grown from a seed some 2,000 years old that was recovered from the ancient fortress of Masada in Israel," Wade adds.
The field of ancient DNA has gained credibility as new technologies have allowed researchers to do things like reconstitute the Neandertal genome, Wade says. "The Russian researchers tried to germinate the campion seeds [they found in the burrow], but failed. They then took cells from the placenta, the organ in the fruit that produces the seeds. They thawed out the cells and grew them in culture dishes into whole plants," he adds. "If the ancient campions are the ancestors of the living plants, this family relationship should be evident in their DNA. ... If the claim is true, then scientists should be able to study evolution in real time by comparing the ancient and living campions. Possibly other ancient species can be resurrected from the permafrost, including plants that have long been extinct."
Martin Fenner from Germany's Hannover Medical School Cancer Center tells the Raleigh, NC-based News & Observer about his efforts to make science more social. The main issue, Fenner says, is that scientists have few incentives for that kind of work. "Researchers are valued by their publications and grants, and other contributions to science — producing research data, communicating science, teaching, et cetera — usually fall under the table," he says. Fenner is working on two initiatives, Open Researcher and Contributor ID, or ORCID, and Altmetrics, both of which aim to change that. ORCID assigns researchers a number to make identifying their research contributions easier, while Altmetrics measures the impact of blog posts, tweets, and more. "A more networked science makes a lot of sense for science as a whole, but at least initially, offers little extra value to the individual researcher," Fenner says. "This makes change difficult."
Renato Dulbecco, the genome sequencing proponent who shared the 1975 Nobel Prize in medicine "for his role in drawing a link between genetic mutations and cancer," has died, reports The New York Times. He was 97. A founding fellow of the Salk Institute for Biological Studies in La Jolla, Calif., Dulbecco's prize-winning work "showed that certain viruses could insert their own genes into infected cells and trigger uncontrolled cell growth, a hallmark of cancer," the Times says, adding that this discovery "provided the first solid evidence that cancer was caused by genetic mutations." In 1986, Dulbecco "proposed cataloging all human genes to gain deeper insights into cancer," the Times reports, thus "providing the intellectual impetus for the Human Genome Project."
In a paper published online in advance in PNAS this week, an international team led by investigators at the Broad Institute reports on its "discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma by whole-exome sequencing." Using this technique, the team sequenced 55 primary tumor samples from DLBCL patients and their matched normal tissue, finding recurrent mutations in genes known to be functionally relevant in the disease and somatic mutations in genes for which a functional role in DLBCL was not previously suspected, including MEF2B, MLL2, BTG1, GNA13, ACTB, P2RY8, PCLO, and TNFRSF14.
Researchers at Yale University and at the University of Illinois at Chicago report on the structural basis for the recognition of completely divergent anticodon loops of natural isoacceptor tRNAs by a single aminoacyl-tRNA synthetases in Saccharomyces cerevisiae. The team says such recognition "facilitates the reassignment of the genetic code in yeast mitochondria."
Elsewhere in the PNAS Early Edition, researchers at the University of California, San Diego, and their colleagues report on an "association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans." The UCSD-led team identifies SNPs that it says contribute "to the proportional area of human visual cortex."
Henry Louis Gates, Jr., on His Genome
From both his genome sequence and a paper record trail, Harvard University’s Henry Louis Gates, Jr., was able to delve into his ancestry, reports BusinessWeek. "It turns out that I'm descended on my mother's side from a white woman who was impregnated by a black slave, and on my father's side from an Irishman who conceived with a black woman named Jane Gates," he says, later adding: "I was searching for African roots, and they led to an African kingdom called the United Kingdom." Gates adds that he found nothing that worried him about his health.
'Announcement We've Been Waiting For'
"My Twitter feed just exploded," Matthew Herper says. "No one is talking about much else right now," the Broad Institute's Chad Nusbaum tells Forbes. "This is the megaton sequencing announcement we've been waiting for," Nick Loman writes at Pathogens: Genes and Genomes.
We are, of course, referring to Oxford Nanopore's announcement of two new DNA strand-sequencing systems at the Advances in Genome Biology and Technology meeting held on Marco Island, Fla., last week. (Our sister publication In Sequence has more on the GridIon and MinIon.)
In addition to sending shockwaves across the blogs and on Twitter — "ILMN [Illumina] cheers storing genomes on a USB stick while Oxford Nanopore was showing sequencing genomes with a USB stick," @rob_carlson writes, while @GenomeBiology says "Oxford Nanopore had everyone talking at lunch. Is the MinIon going to be the next-next-gen? Wow," and @Copenhagenomics calls the new technology "a potential game changer" — Nanopore's announcements shook up the stock market, presumably causing the declines observed in some sequencing companies' share values Friday afternoon. (GenomeWeb Daily News breaks those declines down.)
"Too many amazing @nanopore tweets to retweet them all," Loman says. Daily Scan couldn't agree more.
In PLoS Genetics this week, a team led by investigators at the Australian National University reports its use of "chromosome painting and gene mapping to deconstruct the DFTD [Tasmanian devil facial tumor disease] karyotype and determine the chromosome and gene rearrangements involved in carcinogenesis." Through its analysis, the team produced detailed maps of both the devil and tumor karyotypes, which the researchers say will aid future genomic investigations into the transmissible cancer.
Elsewhere in the journal, researchers at the University of Southern California present "evidence from the heritable cancer syndrome multiple endocrine neoplasia type 2B" that positive selection for new disease mutations has occurred in the human germline. The USC team also says its study may be "useful for studying other disease mutations with similar characteristics and could uncover additional germline selection pathways or identify true mutation hot spots."
Over in PLoS Computational Biology, a separate team led by researchers at USC discusses the "use of gene ontology annotations to assess functional similarity among orthologs and paralogs." The researchers show there is a global ascertainment bias in experiment-based gene ontology annotations for human and mouse genes, and say that "GO annotations are often incomplete, potentially in a biased manner, and subject to an “open world assumption” (absence of an annotation does not imply absence of a function), and that conclusions drawn from a novel, large-scale GO analysis should whenever possible be supported by careful, in-depth examination of examples, to help ensure the conclusions have a justifiable biological basis."
So-called "mega-corrections" are starting to creep into the scientific record, say Ivan Oransky and Adam Marcus in Lab Times. Consider a correction published in Nature in September that took three paragraphs to explain what was wrong with one figure, they write. Or a correction published in the Journal of Cell Sciences in December that explained major errors in three different figures and corrected the list of authors as well as the funding source. "We're all for correcting the scientific record, no matter what that takes," Oransky and Marcus write. "We've argued … that scientists should embrace post-publication peer review, of which this would be a sort." However, they question whether mega-corrections are the best way to go about ensuring the accuracy of the scientific record.
The guidelines of the Committee on Publication Ethics, the authors add, suggest that journals issue a correction rather than a retraction if a small part of an otherwise reliable paper is in error. "So, it ends up depending on what you consider 'a small portion,'" Oransky and Marcus say. "Americans have paid the price for portion size creep, with more and more people becoming obese and diabetic. Journals would do well to avoid the scientific version of that fate."