They spoke about omentum, chemosynthesis, chromothripsis, and… Tasmanian devils? This year’s virtual two-day SMRT Leiden Scientific Symposium and Informatics Developers Meeting was certainly educational. With the pandemic and increased difficulty in being able to connect in person, we wanted to provide a forum for young investigators, post docs, and faculty to come together and share their research experiences during these abnormal times. The result? 27 speakers—the majority of whom were young investigators—sharing data and discoveries, and their advice for early-career scientists. There was a great spectrum of presentations. The first keynote featured fun facts about Dominette (first Bos taurus…
As new strains of the SARS-CoV-2 virus emerge—including variants that appear to make the virus more contagious or potentially more likely to effect the efficacy of the new vaccines—it’s clear that continued genomic surveillance will be essential as we try to rein in the COVID-19 pandemic. Fortunately, scientists have been using all the tools at their disposal, including SMRT Sequencing platforms from PacBio. In a talk presented at a virtual American Society for Microbiology event in December 2020, Labcorp’s Michael Levandoski spoke about using the Sequel II System for mapping COVID-19 outbreaks by location and over time. Watch Levandoski’s full…
As the flurry of research around the SARS-CoV-2 virus continues at an unprecedented pace, scientists are beginning to tackle some of the more complex immunological responses with the help of Single Molecule, Real-Time (SMRT) sequencing. Hundreds of people tuned in live to a special May 7 webinar, “Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing.” Meredith Ashby, Director of Microbial Genomics at PacBio, described some of the resources being generated by both PacBio and our users in order to help labs who are using SMRT Sequencing technology to investigate SARS-CoV-2 and COVID-19. These include two microbial sequencing…
Harm van Bakel When MRSA hits your hospital, what do you do? If you’re located in Europe or other places where infection rates are still relatively low, you can take a seek-and-destroy approach, isolating an affected patient and working out in concentric circles to identify contacts and potential transmissions. If you’re in New York City, however, the strategy is not so simple. Hospital-associated infections with methicillin-resistant Staphylococcus aureus are endemic in the Big Apple, and this has required a fresh approach to treat and prevent the costly bacterial menace. At Mount Sinai Hospital, the strategy now involves SMRT Sequencing. Established…
Plasmodium falciparum Malaria is a complicated killer, and efforts to develop effective vaccines have been hindered by gaps in our understanding of both the parasite that causes the infection, Plasmodium falciparum, and its transmitter, the mosquito. Like many virulent parasites, P. falciparum has evaded close genetic scrutiny due to its complex and changing composition. Its 23 Mb haploid genome is extremely AT rich (~80%) and contains stretches of highly repetitive sequences, especially in telomeric and subtelomeric regions. To make matters more complicated, it expands its genetic diversity during mitosis via homologous recombination, leading to the acquisition of new variants of…
They are the unwelcome comeback kids: Measles, mumps and other old-time diseases that were once nearly extinct are on the rise in suburban communities as well as developing nations. In order to better understand the evolution of these microbial menaces, researchers at the Wellcome Sanger Institute and Public Health England have been sequencing historical samples deposited in the UK’s National Collection of Type Cultures (NCTC). The latest is a strain of cholera-causing bacteria (Vibrio cholerae) extracted in 1916 from the stool of a British soldier who was convalescing in Egypt. Researchers at the Sanger Institute revived the WWI soldier’s bacteria…
We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…
Researchers rely on PacBio long-reads for richness and resolution when probing genomes, and these same attributes are becoming increasingly relevant in clinical settings. One field where the technology shows particular promise is infectious disease control. When a disease outbreak hits a hospital, it is crucial that the pathogen and its transmission path are rapidly and accurately identified. As PacBio researchers demonstrated in CLP magazine, current microbial detection techniques that rely solely on short-read DNA sequences can misidentify pathogens, resulting in incorrect prognosis and misinformed treatment decisions. SMRT Sequencing, on the other hand, can paint a complete picture of entire genomes,…
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. Researchers have identified the toxin responsible for selective killing of male fruit flies (left) using PacBio sequencing. 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 in Spiroplasma poulsonii, one…
SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson. 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 speakers. Inge Kjaerbolling of…
Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose. 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 the species and are…
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…
Courtesy of NIAID 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 the rapid rise of…
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…