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Thursday, October 8, 2020

A Living Legacy of Microbiology Celebrates 100 Years

As the world faces an unprecedented pandemic caused by a novel coronavirus, the scientific spotlight has shone brightly on infectious disease research. And although interest in Public Health England’s (PHE) Culture Collections is often focused on its historical cultures, its relevance in our modern world has never seemed sharper.  The National Collection of Pathogenic Viruses (NCPV) has been helping scientists from around the world address the current history-making infectious disease event. It is also anticipating future outbreaks, and building collections of pathogenic viruses to aid research into potential threats to human health. “The question of which virus will be next…

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Wednesday, September 16, 2020

Easy and Affordable: Full-Length 16S HiFi Sequencing with PacBio Service Providers

Analysis of 16S ribosomal RNA has been used for phylogenetics and identifying prokaryotes for decades. But just as scientists have had to refine the Linnaean taxonomy system based on genomic discoveries, improvements in sequencing technology are changing 16S analysis best practices. Several dominant microbial genera in Sakinaw Lake could only be resolved via Full Length 16S or were missed by V4 sequencing (gray boxes). Singer, E. et al. (2016) Researchers at the Joint Genome Institute, for instance, conducted a detailed benchmarking study and found that traditional methods of 16S analysis — which look at just a piece of the gene…

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Tuesday, September 15, 2020

Now Available: Ultra-Low DNA Input Workflow for SMRT Sequencing

The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely!  The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…

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Wednesday, August 19, 2020

A TAL Tale: PacBio Sequencing Helps Unravel Mechanisms of Plant Infection

How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment.  For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing.  Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…

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Monday, April 13, 2020

How Long-read Sequencing Can Help Researchers Address Pressing Questions in COVID-19 Pandemic

Herculean efforts are being made by scientists around the world to respond quickly to the COVID-19 crisis in a race to understand the virus causing the pandemic and develop diagnostics, vaccines, and therapeutics. But many research questions remain. How can long-read SMRT Sequencing technology help fill the gaps? PacBio microbiology expert Meredith Ashby highlighted several opportunities to support coronavirus research in a recent webinar as part of a day-long virtual conference hosted by LabRoots.    Sequencing the viral genome Understanding the basic biology of the virus is essential, and the more detailed our investigation, the better.  Highly accurate, long-read sequencing…

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Wednesday, February 12, 2020

NARMS Scientists Track Antibiotic Resistance in Foodborne Bacteria Using SMRT Sequencing

Launched in 1996, NARMS is a U. S. public health surveillance system that tracks antimicrobial susceptibility of select foodborne enteric bacteria. We hear a lot about the growing crisis of antibiotic resistance in human health, but it turns out this is just the most visible place it appears as it moves through our complex modern environment. For example, when intensive farming is used to feed large urban populations, antibiotic resistance can first emerge on farms and gain access to human communities through the food system.   One of the key groups on the front lines of monitoring antibiotic resistance from farm…

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Friday, December 27, 2019

SMRT Sequencing Highlights – Top Publications of 2019

With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs.   “It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will…

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Wednesday, December 11, 2019

Long-Read Sequencing Could Improve the Sensitivity and Precision of 16S Studies Says Jackson Lab Study

It’s time to revisit the way scientists are using 16S rRNA gene sequencing to study microorganisms, according to a team of Jackson Laboratory researchers.  Popular targets for taxonomy and phylogeny studies because of their highly conserved nature, amplified sequences of the 16S ribosomal RNA genes can be compared with reference databases to determine the identity of the microorganisms that comprise a metagenomic sample. Sequences with a > 95% match are generally considered to represent the same genus, for example, while > 97% matches are considered the same species. However, these matches are often made by sequencing only part of the nine-region, ~1500 bp…

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Wednesday, November 20, 2019

SMRT Sequencing to Help Reveal Secrets of the Soil in Understudied South-East Asian Rainforests

The tropical rainforests of Danum Valley, Borneo, is full of dipterocarp trees, which have a particular symbiotic relationship with fungi that is rare in rainforests elsewhere in the world. Photo by Joe Taylor The most important creatures in a tropical rainforest aren’t necessarily the ones you can see. They work their magic underground, recycling organic matter and processing and transporting vital nutrients for their leafy neighbors above ground.  Microbiologist Joe Taylor wants to learn all about what they are and what they do. And now a grant from PacBio and Maryland Genomics will enable him to reveal some of the…

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Monday, October 7, 2019

Keeping a Close Eye on MRSA: Lessons Learned from PacBio Sequencing Surveillance 

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…

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Wednesday, October 2, 2019

When Complete Isn’t Complete: C. Elegans Genome Gets a Makeover

Cover artwork by Daisy S. Lim It was the first multicellular eukaryotic genome sequenced to apparent completion, but it turns out the Caenorhabditis elegans reference that’s been used as a resource for the past 20 years does not exactly correspond with any N2 strain that exists today.  Assembled using sequence data from N2 and CB1392 populations of uncertain lineage grown in at least two different laboratories during the 1980s and 1990s, accuracy of the C. elegans reference genome is limited both by genetic variants and by the limitations of the technology of the time (clone-based Sanger technology). It is believed…

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Wednesday, August 21, 2019

New Initiative to Generate 5,000 High-Quality Microbial Genomes for Chinese Database

An ambitious project to sequence 5,000 microbial genomes was jointly initiated by a consortium of 10 institutions across China, including Nankai University, China CDC, Academy of Military Medical Science, Third Institute of Oceanography-Ministry of Natural Resources, South China Sea Institute of Oceanology-CAS, China National Center for Food Safety Risk Assessment, Shandong University, Tianjin University of Science & Technology, East China University of Science and Technology, and Tianjin Biochip Corporation (TBC).  TBC, a PacBio service provider in China, has led the sequencing phase of the project, which is expected to be completed by the end of 2019. We recently sat down with…

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Thursday, May 30, 2019

Unraveling Malaria Mysteries with Long-Read Sequencing

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…

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Tuesday, May 7, 2019

Sequencing of Historical Cholera Sample Surprises Sanger Scientists

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…

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Wednesday, April 24, 2019

Now Available: Sequel II System Delivers ~8 Times as Much Data as Previous System

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…

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