written by: Ted Striegel (MS student, Hawthorne lab) and Graham Stewart (MS student, Palmer lab)
Dr. Joe Russell is a senior scientist at MRIGlobal, a nonprofit contract research institute that conducts research on a wide array of topics (including chemical and biological surveillance, biosafety and security). The institute receives much of its funding from contracts with the U.S. Department of Energy and Department of Defense. Dr. Russell had a circuitous academic path to MRIGlobal, including time spent studying astrophysics and analysing marine sediment samples. His talk centered on a new technology developed by the institute - the Mercury Lab.
Dr. Joe Russell is a senior scientist at MRIGlobal, a nonprofit contract research institute that conducts research on a wide array of topics (including chemical and biological surveillance, biosafety and security). The institute receives much of its funding from contracts with the U.S. Department of Energy and Department of Defense. Dr. Russell had a circuitous academic path to MRIGlobal, including time spent studying astrophysics and analysing marine sediment samples. His talk centered on a new technology developed by the institute - the Mercury Lab.
The idea for Mercury Lab was born from the need to quickly and effectively manage harmful and fast-spreading diseases. Outbreaks of disease present a large challenge to scientists attempting to diagnose the pathogen responsible. When there is a disease outbreak in a remote location, such as ebola in a Guinean village, there may not be nearby facilities capable of processing samples and identifying the pathogen in time to treat those affected and prevent further cases. Dr. Russell and MRIGlobal felt compelled to respond to this need using their expertise. Their solution, still under development, is the Mercury Lab (Figure 1). This is a mobile diagnostic center, consisting of everything you would need to process and identify pathogenic samples, self-contained in a rolling suitcase. In essence, this technology will allow researchers to bring the lab to the field and get results quickly.
The development of the Mercury Lab was not a smooth process, and met with several failures early on that shed light on necessary improvements to the design. The first “prototype” of the lab was merely reagents, pipettes, a mobile DNA sequencer (Oxford Nanopore’s MinION), and portable iPhone-based thermocycler (Biomeme’s two3) - essential tools for molecular biological analysis - in a backpack. No lab bench-like surface was included. This first idea, tested by Dr. Russell on an expedition to southern Florida in search of arboviruses (e.g. mosquito-vectored viruses), showed the necessity of logistical items as simple as a stable, well laid-out working surface, reliable portable power, and modest protection from the elements such as wind. He was able to collect and complete extractions using samples of Culex cedecei mosquitoes on site. The lack of logistical support described above precluded the use of the sequencer to carry out analyses in the field, and the identification of Everglades virus in one of the samples did not come until this analysis was carried out in the lab later on. Despite the lack of on-site analysis, the success of on-site extraction still showed the immense value of the concept.
Further functional additions and improvements to field-capability mark the latest versions of the Mercury Lab. The next iteration of the lab featured a flip-out table surface and basic equipment - sequencer, thermocycler, and miniature computer for data analysis. This version made apparent the need for input from an engineering team. The computer, encased in insulating styrofoam for protection, quickly overheated and crashed in a field test, sending Dr. Russell back to the drawing board.
To create the current version of the Mercury Lab, MRIGlobal contracted with an engineering firm to bring some much-needed expertise into the product design. This version features 4℃ and -20℃ cold storage, fold out workbench, bioinformatics computational capacity, and can run off a 6V motorcycle or 12V car battery. The last feature is extremely important, since a limitation on the utility of any such mobile laboratory is power supply. Vehicle batteries are very common throughout the world and can be procured in nearly any remote location where the Mercury Lab would be deployed.
In tandem with the development of the Mercury Lab, the scientists at MRIGlobal have created several tools to aid researchers in the field of biosurveillance. For example, to improve early pathogen identification the team developed PanGIA (Pan-Genomics for Infectious Agents), which provides an interactive interface through which users can quickly explore bioinformatic data and find taxonomies based on adjustable parameters. Another such tool is the Vorpal algorithm – developed by Dr. Russell’s colleague, Phil Davis – which helps scientists find genomic motifs that are predictive of certain phenotypes-of-interest (such as causing hemorrhagic fever in arboviruses). This tool generates a library of conserved kmers (small nucleotide sequences of a specified length k) using sequences from known organisms that display the trait, then checks for presence of similar kmers in batches of sequences from environmental samples. If some matching kmers are present, this indicates that organisms having the same harmful trait are present in the sample. In this way, Vorpal can identify the presence of pathogenic microbes even if the microbe taxa are as yet unknown to the scientific community.
Although much is planned in the immediate future for Dr. Russell, one highlight is a proposed field test of the Mercury Lab on St. Catherine’s Island in Georgia. This is a private island off the Georgia coast, historically used for zoological research. Much of the island is undisturbed, presenting a unique opportunity to test technologies in a setting similar to a remote field site. In particular, St. Catherine’s presents a unique opportunity for studying arboviral molecular biology in primate-hosted sylvatic cycles, as it houses a self-sustaining population of ringed-tailed lemurs, brought to the island decades ago to create an essential living laboratory for multidisciplinary research. By bringing the likes of Mercury, PanGIA, and Vorpal to St. Catherine’s, Dr. Russell can test these technologies in true field scenarios, and collect data that will allow him and his colleagues to make further improvements. It will surely not be long until the Mercury Lab is commonplace in field research and fulfilling its potential to help many people across the globe.
Ted Striegel (@TedStriegel) is an MSc student in Dave Hawthorne’s lab, and studies insect trapping methodology and native bee subcommunity diversity.
Graham Stewart (@wet_naturology) is an MSc student in Margaret Palmer’s lab, and studies carbon cycling in restored and natural freshwater wetlands.
The development of the Mercury Lab was not a smooth process, and met with several failures early on that shed light on necessary improvements to the design. The first “prototype” of the lab was merely reagents, pipettes, a mobile DNA sequencer (Oxford Nanopore’s MinION), and portable iPhone-based thermocycler (Biomeme’s two3) - essential tools for molecular biological analysis - in a backpack. No lab bench-like surface was included. This first idea, tested by Dr. Russell on an expedition to southern Florida in search of arboviruses (e.g. mosquito-vectored viruses), showed the necessity of logistical items as simple as a stable, well laid-out working surface, reliable portable power, and modest protection from the elements such as wind. He was able to collect and complete extractions using samples of Culex cedecei mosquitoes on site. The lack of logistical support described above precluded the use of the sequencer to carry out analyses in the field, and the identification of Everglades virus in one of the samples did not come until this analysis was carried out in the lab later on. Despite the lack of on-site analysis, the success of on-site extraction still showed the immense value of the concept.
Further functional additions and improvements to field-capability mark the latest versions of the Mercury Lab. The next iteration of the lab featured a flip-out table surface and basic equipment - sequencer, thermocycler, and miniature computer for data analysis. This version made apparent the need for input from an engineering team. The computer, encased in insulating styrofoam for protection, quickly overheated and crashed in a field test, sending Dr. Russell back to the drawing board.
To create the current version of the Mercury Lab, MRIGlobal contracted with an engineering firm to bring some much-needed expertise into the product design. This version features 4℃ and -20℃ cold storage, fold out workbench, bioinformatics computational capacity, and can run off a 6V motorcycle or 12V car battery. The last feature is extremely important, since a limitation on the utility of any such mobile laboratory is power supply. Vehicle batteries are very common throughout the world and can be procured in nearly any remote location where the Mercury Lab would be deployed.
In tandem with the development of the Mercury Lab, the scientists at MRIGlobal have created several tools to aid researchers in the field of biosurveillance. For example, to improve early pathogen identification the team developed PanGIA (Pan-Genomics for Infectious Agents), which provides an interactive interface through which users can quickly explore bioinformatic data and find taxonomies based on adjustable parameters. Another such tool is the Vorpal algorithm – developed by Dr. Russell’s colleague, Phil Davis – which helps scientists find genomic motifs that are predictive of certain phenotypes-of-interest (such as causing hemorrhagic fever in arboviruses). This tool generates a library of conserved kmers (small nucleotide sequences of a specified length k) using sequences from known organisms that display the trait, then checks for presence of similar kmers in batches of sequences from environmental samples. If some matching kmers are present, this indicates that organisms having the same harmful trait are present in the sample. In this way, Vorpal can identify the presence of pathogenic microbes even if the microbe taxa are as yet unknown to the scientific community.
Although much is planned in the immediate future for Dr. Russell, one highlight is a proposed field test of the Mercury Lab on St. Catherine’s Island in Georgia. This is a private island off the Georgia coast, historically used for zoological research. Much of the island is undisturbed, presenting a unique opportunity to test technologies in a setting similar to a remote field site. In particular, St. Catherine’s presents a unique opportunity for studying arboviral molecular biology in primate-hosted sylvatic cycles, as it houses a self-sustaining population of ringed-tailed lemurs, brought to the island decades ago to create an essential living laboratory for multidisciplinary research. By bringing the likes of Mercury, PanGIA, and Vorpal to St. Catherine’s, Dr. Russell can test these technologies in true field scenarios, and collect data that will allow him and his colleagues to make further improvements. It will surely not be long until the Mercury Lab is commonplace in field research and fulfilling its potential to help many people across the globe.
Ted Striegel (@TedStriegel) is an MSc student in Dave Hawthorne’s lab, and studies insect trapping methodology and native bee subcommunity diversity.
Graham Stewart (@wet_naturology) is an MSc student in Margaret Palmer’s lab, and studies carbon cycling in restored and natural freshwater wetlands.
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