It’s a murder mystery of massive proportion, albeit on a miniature scale: Male-killing among several species of insects, caused by selfish symbiotic bacteria. Swiss researchers believe they have finally solved a question that has stumped scientists for decades, with potential implications for pest and infection control. [caption id="attachment_31327" align="alignright" width="270"] Researchers have identified the toxin responsible for selective killing of male fruit flies (left) using PacBio sequencing.[/caption] In a recent Nature publication, Toshiyuki Harumoto and Bruno Lemaitre of the Global Health Institute at the École Polytechnique Fédérale de Lausanne (EPFL) in Lausanne, Switzerland, have reported their findings regarding a toxin…
[caption id="attachment_28544" align="alignright" width="300"] SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson.[/caption] When was the last time you sent your DNA off to a day at the spa? Olga Pettersson of the SciLifeLab at Uppsala University lets her molecules relax for up to a week at room temperature to enable them to untangle, achieve better chemical purity, and better sequencing output. It was one of many practical pointers shared by presenters at the popular three-day gathering of PacBio users in Leiden, Netherlands last month. SMRT Leiden featured the scientific discoveries and analytical achievements of more than 30…
[caption id="attachment_26599" align="alignright" width="300"] Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose.[/caption] The genomes of 3,000 strains of bacteria, including some of the deadliest in the world, are now available to researchers as part of an ambitious project by the UK’s National Collection of Type Cultures (NCTC), in partnership with the Wellcome Sanger Institute and PacBio. Plague, cholera, streptomyces, and 250 strains of E. coli, are among the reference genomes created, as well as all ‘type strains’ of the bacteria in the collection -- the first strains that describe…
A new review in Nucleic Acids Research offers a sweeping look at human sequencing applications for SMRT Sequencing, finding that “[t]he myth that SMRT sequencing is too error prone … is being expunged and replaced by evidence that it offers advantages over short-read sequencers.” The authors conclude with a prediction about the ultimate potential for SMRT Sequencing and other “third-generation” platforms: “Just as second-generation platforms stepped beyond Sanger sequencing and enabled a revolution in genomics medicine, third-generation single molecule sequencing platforms will likely be the next genetic diagnostic revolution.” “Single molecule real-time (SMRT) sequencing comes of age: applications and utilities…
In an unprecedented crowd-sourced effort stoked by social media, 72 scientists collaborated via 25 conference calls and 3,323 emails to produce a new high-quality Aedes aegypti mosquito genome. Assembled using PacBio long-read sequencing, the resource could provide the DNA map researchers need to combat the pest and the infectious diseases it spreads, including Zika, dengue, chikungunya, and yellow fever. Eager to share the results with the scientific community, lead author Leslie B. Vosshall, first author Benjamin Matthews, both of Rockefeller University, and colleagues at several other institutions, published a pre-print of their paper, “Improved Aedes aegypti mosquito reference genome assembly…
[caption id="attachment_21181" align="alignright" width="287"] Courtesy of NIAID[/caption] In a recent paper, scientists in Germany call for a genomic database of Klebsiella pneumoniae strains to accelerate strain identification as well as drug-resistance status. To that end, they used SMRT Sequencing to generate high-quality assemblies for 16 isolates collected in German hospitals. “Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing” comes from lead authors Andreas Zautner and Boyke Bunk, senior authors Jorg Overmann and Wolfgang Bohne, and collaborators at University Medical Center and other institutes in Germany. The urgency to characterize K. pneumoniae strains comes from…
A new publication reports the discovery and analysis of a nightmare bacterium that’s genetically resistant to all commercially available classes of antibiotics. The paper, “Stepwise evolution of pandrug-resistance in Klebsiella pneumonia,” came out this month in Scientific Reports from Nature. Lead authors Hosam Zowawi and Brian Forde, along with senior author David Paterson and several collaborators, studied an isolate recovered from the urine of an 87-year-old patient who was hospitalized in the United Arab Emirates last year. They used SMRT Sequencing to characterize the strain and its genetic mechanisms for drug resistance. That strain, MS6671, “was found to be non-susceptible to…