Fruit genomic specialist Dr. Sean Myles tells us why genomics is the future of apple breeding.
Month: November 2019
Digging into Mic
Corrosion-causing bacteria account for approximately 20 percent of corrosion failures in oil and gas pipelines, and billions of dollars of damage each year. Yet, relatively little is known about how this phenomenon, known as Microbiologically Influenced Corrosion (MIC), occurs.
In 2016, a $7.8 million collaborative research project involving four universities in Alberta and Atlantic Canada was launched with the aim of filling in some of our knowledge gaps about MIC. Managing Microbial Corrosion in Canadian Offshore and Onshore Oil Production (“geno-Mic” for short) uses genomics to better predict how, where and why MIC occurs and how to mitigate it. Ultimately, a better understanding of MIC could improve infrastructure integrity, reduce the potential of oil spills, and improve worker safety – potentially reducing operating costs and saving Canada’s oil and gas industry $300-500 million over 10 to 20 years.
The project is funded by the federal government under Genome Canada’s Large-Scale Applied Research Project Competition (LSARP) with additional support from multiple university and industry partners, and is co-managed by Genome Alberta and Genome Atlantic.
Dr. Lisa Gieg, University of Calgary, is a co-lead on the project. Dr. Gieg was in Halifax recently for a project meeting and to present at ISMOS-7, an international scientific conference on microbiology and molecular biology in the oil and gas industry. We caught up with her for an update on the project three years in and to find out how project scientists are filling some of those knowledge gaps.
An interview with Dr. Lisa Gieg
Genome Atlantic: Why do we know so relatively little about MIC – and how is this project trying to change that?
A:MIC is one of the several ways by which corrosion of materials can occur – and one of the challenges with understanding and diagnosing MIC is that it is not an isolated mechanism. That is, while microorganisms play a key role in the corrosion, their metabolism is affected by the chemical environment surrounding them (e.g., kinds of carbon, such as fatty acids or hydrocarbon; or electron acceptors, like oxygen, nitrate, or sulfate, pH) and the surrounding physical conditions, such as temperature and pressure. MIC is very complicated because many factors can affect whether microorganisms will thrive and metabolize in such a way that leads to corrosion. Thus, it’s difficult to pinpoint that corrosion is solely due to the action of microorganisms. Put another way, microorganisms are everywhere, but whether their activity leads to corrosion can be difficult to sort out because of other corrosion that may occur due to the chemical and physical environment.
Based on studies with pure cultures of microorganisms such as sulfate-reducing microorganisms (SRM), a lot is already known about specific mechanisms of MIC, but less is known about other types of microorganisms, and how communities of microorganisms can work together in a way that leads to corrosion. Also, MIC has often been studied in ‘isolation’ – e.g., by microbiologists, or chemists, or engineers. Rarely have all these disciplines come together to tackle the MIC problem.
The geno-MIC project is unique in that it has researchers in many different disciplines such as these working together towards a better understanding of MIC. We are approaching an understanding of MIC from a holistic point of view. We are using genomics to identify key microorganisms present in different environments for which we know the physical conditions (or operating conditions – temperature, pressure, fluid flow rates, etc.), and the chemical conditions (pH, chemical composition, etc.), and determining corrosion rates under these different conditions. In this way, we start to look for trends as to which kinds of microorganisms are most actively contributing to corrosion under different oil and gas operating conditions (e.g., in different kinds of pipelines, processing facilities, produced waters, etc.). When we identify the key microorganisms and the conditions most conducive to promoting MIC, we will know which organisms to target to better monitor and mitigate MIC.
Does MIC manifest itself differently in onshore and offshore pipelines?
A: Microbial corrosion can occur in both environments, but differences in the mechanisms of MIC are due to the chemical environment surrounding the microbial communities. Offshore, because seawater is used in many of the operations, sulfate is present in relatively high concentrations (20-30 mM) which readily stimulates sulfate-reducing microorganisms (SRM). This microbial metabolic process yields hydrogen sulfide which reacts with iron in carbon steel infrastructure to form FeS (iron sulfide) which is highly corrosive.
Onshore, sulfate may be present in some systems, but not always, so other microorganisms are likely playing more important roles. For example, we recently studied a sample collected from a leaking pipeline, and while all indications strongly pointed to MIC as the major mechanism of corrosion, neither sulfate nor SRM were present in substantial amounts – many other kinds of microorganisms were more abundant and were most likely the key players in the corrosion scenario. We are still in the process of identifying exactly how these other kinds of microorganisms are behaving in order to corrode metal. In almost all cases of MIC, microorganisms attached to pipe surfaces are the most detrimental, but we still have a lot to discover in terms of the many ways and the kinds of microorganisms that may be contributing to metal corrosion.
Three years in, what are some of the main things you’ve found out? And what are the next steps?
A: The major objective of our project is to gain a better understanding of MIC under different conditions in order to better detect and manage this important yet poorly understood mechanism of corrosion. Our project has 4 major activities (1) Knowledge – where we aim to identify the different kinds of microbes and activities associated with MIC and are building a MIC database in order to do this; (2) Devices & Assays – where we aim to develop tools for MIC monitoring/detection; (3) Models – where we aim to better predict MIC; and (4) Translation – where we aim to better understand the gaps between academic research and industry uptake, to incorporate research findings into industry standards, and to help industry consider MIC as part of corrosion management strategies.
To date, the project has developed several predictive and risk-based models and we are in the process of validating these with field data from our industry partners. For the translation piece, our team has been hosting stakeholder workshops and conference forums/workshops on the topic of MIC and are actively involved in either creating new standards (on the topic of using molecular microbiological methods for MIC) or updating industry standards related to MIC (e.g., through NACE International, and DNV-GL).
For the Knowledge and Devices/Assays activities, we have been analyzing many field samples from different kinds of oil and gas operations (offshore and onshore, collected from infrastructure operated under different physical conditions such as temperature/pressure) by characterizing microbial communities, chemistry, and corrosion rates. This data is being entered into a new database also being developed by the project that we will ultimately use to discern trends in the data – again – for the purpose of identifying which microbial players are most corrosive under different conditions so that we can better detect (through devices and assays), monitor for, and mitigate MIC.
When will the project wrap up?
A: We officially wrap up in October 2020 but are applying for a no-cost extension so hope to continue the project until October 2021. We will be looking for opportunities to continue some aspects of the project beyond that date, either through another LSARP, GAPP (Genome Canada’s Large-Scale Applied Research Project and Genomic Applications Partnership Program), or another funding avenue.
How will the project results be integrated into industry practices or operations?
A: Our project team is actively involved in meeting with our industry partners on an ongoing basis. We host workshops and forums on MIC a few times a year, bringing together academic researchers and industry stakeholders (oil and gas operators, service companies, chemical suppliers, consultants) so that we can learn from each other and have an ongoing dialog about the challenges and the tools that can be used/developed to determine whether MIC will be a problem in a given system.
We are also involved in preparing industry standards related to the topic of MIC that a lot of industry stakeholders look to for guidance on dealing with corrosion detection and management. For example, several team members (academic and industry partners) are in the process of developing a new NACE International standard on Molecular Microbiological Methods – essentially outlining the best practices towards using genomics for identifying microorganisms in oil and gas samples. Finally, predictive or risk-based models developed in the geno-MIC project are being reviewed by our industry partners who are also providing field data for their validation. Thus, our geno-MIC team is doing research in close conjunction with industry, which will help immensely with the uptake/use of our research findings by them.
Why Bioleaching is primed for prime time
Using rock’s naturally occurring bacteria to extract metal from ore isn’t nearly as experimental or futuristic as some people might think. Neri Botha, an extractive metallurgist with the Research Productivity Council (RPC) in Fredericton, N.B., says the technique, known as bioleaching, is primed to be ready for prime time in the mining industry.
“The technology is ready,” she says, “but the commercialization is lagging behind. What is needed is the right opportunity where the obstacles necessitate the process, making it worth taking on any perceived risk, due to the process being relatively novel. Government support for the environmentally friendlier process could also help,” she adds.
Bioleaching has been around at least since 1000 BC when the Romans and Phoenicians utilized the process to recover copper from streams passing through ore bodies. It was first used commercially in a South African gold mine in 1986. As a South African-trained professional engineer, Botha has kept a close watch on developments in this area since her days at the University of Pretoria, where a course in hydrometallurgy first sparked her interest in this novel process.
Bioleaching works, Botha explains, “by utilizing certain microorganisms to accelerate the rate of dissolution of sulfide minerals using their enzymes. These microorganisms, known as mesophiles or moderate thermophiles, could be isolated from mine water, or from ores, or from sulphur-bearing hot springs etc.”
Genomics plays a critical role in helping sort out the identities of the microorganisms, and Botha has been researching genomics applications for the mining industry for many years, with ongoing support from Genome Atlantic.
She explains that in the mining industry, bioleaching’s economic and environmental advantages – particularly in gold mining, but also in nickel, cobalt and copper mining – are spurring intense interest.
The reason for this is the depletion of conventional high-grade reserves. The situation, she says, has created a need to treat lower grade ores as well as re-treat old tailing sites to extract residual metals. Bioleaching makes those propositions not only doable but economically feasible. For tailing sites, bioleaching presents opportunities to unlock their value as well as to remediate them with the added bonus of producing no atmospheric pollution. The technique also boasts low capital and operating costs.
RPC, New Brunswick’s provincial research institution where Botha has worked since 2012, is considered an important centre of bioleaching expertise in the world’s scientific community. That expertise has developed in conjunction with the institution’s mandate to engage in industry-driven applied research. RPC has been involved in various types and phases of bioleaching projects in over 30 countries since 1989.
Currently, RPC is assisting on a primary copper bioleaching project now under development with an Ontario based engineering firm. In addition, the institution is working on a chalcopyrite bioleaching project in Zambia and on a cobalt research project in the United Kingdom (CoG3). Other research projects in progress, Botha says, concern “the gold extraction process for Newfoundland ores and we are also involved with Rare Earth Element Research.”
The U.K. project, CoG3, is particularly prestigious. The focus is on safeguarding the supply of cobalt, a metal critical to advanced technology, for such things as batteries and superalloys. The project, led by the National History Museum in the U.K., involves a research consortium of six universities, three research institutes and eight industrial partners. RPC is part of the technical advisory committee.
Bioleaching is a “proven technology,” says Botha, “especially in the gold industry and for secondary copper minerals as well as other metals.” When it comes to gold, she says bioleaching is “uniquely situated to assist in the extraction of problematic ores containing locked gold.” The metal can be locked for physical or chemical reasons or it can be trapped in the ore’s sulphide lattice. Bioleaching could potentially unlock it.
“Certain minerals still present challenges though, such as chalcopyrite,” she pointed out. Chalcopyrite is the brassy yellow mineral in which copper is commonly found. It tends to form passivating or unreactive layers of oxides on its surface,” she said, “These layers limit the recovery of copper at temperatures and redox conditions suitable for microbial culturing.” She adds, “significant research has thus gone into this and the world’s first primary copper bioleaching plant is currently being built, incorporating RCP findings.”
Once this new plant is running, she foresees bioleaching becoming standard for copper extraction within a few years. As secondary copper minerals and high-grade ores continue to deplete, she says, the bulk of the world’s unexploited copper reserves are becoming increasingly less economic to mine by conventional means.
In many cases, bioleaching, with some help from genomics, presents an irresistible solution, which Botha expects will make it a mainstream mining technology very soon.
Testimonial: RPC’s Eric Cook
RPC’s Eric Cook talks about Genome Atlantic’s unique role in funding and enabling applied R&D that benefits Atlantic Canada.
New Brunswick’s RPC – harnessing the power of genomics
The Research and Productivity Council of New Brunswick (RPC) tells us how genomics is helping them with their cutting-edge work.
featuring: Eric Cook, CEO-RPC, Dr. Diane Botelho, CSO-RPC, Neri Botha, Extractive Metallurgist – RPC
The future of personalized health & human performance
In today’s data revolution, genomics is emerging as a potential game changer for medicine and human performance, fuelled, in part, by pioneering work in precision personalized data underway on Canada’s east and west coasts. This exciting development was examined in a recent panel discussion hosted and emceed by Genome Atlantic on “The Future of Personalized Health & Human Performance” during BioPort Atlantic 2019.
Dr. Steve Armstrong, Genome Atlantic’s President and CEO and the panel’s emcee, teed up the discussion by posing the following questions:
“If you were diagnosed with cancer today, wouldn’t you want a treatment plan that is custom designed for you, your genetic blueprint and your specific cancer? If your son or daughter had an unexplained illness and you were bouncing from specialist to specialist for years on end, wouldn’t you want to bring this diagnostic odyssey to an end? Or if you were the owner of the Pittsburgh Penguins, home of our local hero Sydney Crosby, wouldn’t you want to ensure that Sid and the team were performing at their best? In all three examples, what kind of data would you need to make that happen?”
To answer these questions, the panel tapped three well known trailblazers who use data every day in their quest to improve human health and well-being: Dr. Janessa Laskin, a BC Cancer medical oncologist and the clinical leader of the Personalized Oncogenomics (POG) initiative in Vancouver; Dr. Christopher McMaster, Scientific Director of the CIHR Institute of Genetics and Director of the Scientific and Clinical Hub for Orphan Drug Development (formerly IGNITE), both based at Dalhousie University in Halifax; and Dr. Travis McDonough, founder and CEO of Kinduct, a Halifax-based athlete management and monitoring company with professional sports team clients from around the world.
POG is the world’s only cancer research project that uses whole genome sequencing, including transcriptomic (RNA) data to search for personalized treatments for patients with metastatic cancer, a malady Dr. Laskin characterizes as “a disease of the genome.” Dr. Chris McMaster and his group have uncovered a potential therapy for congenital sideroblastic anemia, a condition in which the bone marrow fails to produce enough healthy red blood cells, and are developing treatments for inherited Parkinson’s disease and for familial exudative vitreoretinopathy, a hereditary disorder that can cause vision loss. Meanwhile, Kinduct collects, sifts and aggregates a vast array of data, including genomic information, on individual athletes to come up with comprehensive regimes to improve athletic performance.
Dr. Janessa Laskin
Dr. Laskin said one of the challenges of using genomics to find and then target the drivers of an individual’s cancer is the realization that “we have been extremely siloed in the way we think about cancer and how we think about drugs. But now we have technology that tells us that a particular drug might be very useful in multiple different kinds of cancers and genome technology is helping us figure that out.”
What we are learning, she said, is that drugs not normally used for cancer or for a particular type of cancer can be strong therapeutic possibilities to attack drivers of a particular cancer based on its genomic analysis. Drugs normally used for hypertension, for instance, have been selected for use in some POG cancer treatments, as well as drugs conventionally deployed in different types of cancer. For example, based on an individual’s genomic data, a drug approved for lung cancer might be appropriate for a particular case of pancreatic cancer.
These findings have potential disruptive consequences, she said: “We have to think about how regulatory authorities are approving drugs and funding drugs, so they aren’t just siloed in particular applications in one particular tumour type.”
Dr. Christopher McMaster
The growing role for genomics in human health and other fields is largely due to the plummeting cost of creating the data, said Dr. McMaster. “The human genome was sequenced in 2003,” he said, adding, “It took a decade and it cost over $1 billion. In 2019 we can sequence the human genome in a few weeks for about a thousand dollars.” No technology, he said, has accelerated at such a pace.
Dr. McMaster’s research lab uses genomic data to uncover therapies for orphan diseases, most of which are currently untreatable. For orphan diseases which used to take five-seven years and up to $30,000 of tests to detect with certainty, Dr. McMaster said advances in genomics mean “we can now diagnose these cases by sequencing the [patients’] genomes in a matter of weeks. It’s speeding up a diagnosis without increasing costs to the health care system.”
Sometimes called “rare diseases,” orphan diseases are not rare at all when viewed as a category. More than 7,000 diseases fall into this grouping. In Canada, it has been estimated, one in 40 children are born with an orphan disease and because it is often life-limiting, 35 per cent of them fail to reach their fifth birthday.
“The nice thing about inherited diseases is, it’s a single gene in which a mutation is causing a disease,” said Dr. McMaster, so there is “an immediate cause to an effect.” With the help of Genome Canada, Genome Atlantic and other partners, he is now involved in a “scientific-clinical hub to come up with treatments.”
For most inherited disease there is no current treatment. “So, this hub is looking to lead Canada in terms of bringing medicines into the clinic and into the market for treating cases with inherited diseases,” he said. Helping advance this ambition, the Food and Drug Administration in the U.S. offers Rare Pediatric Disease Priority Review Vouchers which help companies move qualifying drugs to the front of the review line in the approval process. The express provision brings cost savings to drug developers, ranging from $100 million to $250,000.
Dr. Travis McDonough
The software company, Kinduct, grew out of Mr. McDonough’s experience in the healthcare industry where 3-D medical examinations and rehabilitation programming generate a slew of compartmentalized data. Elite sports do the same thing with even more varied types of data – all sorts of player monitoring and player tracking, for instance. Kinduct figured out how to put it all together and draw helpful conclusions to optimize performance and wellness in professional sport.
“Essentially we create better athletes,” said Dr. McDonough. The goals, he said, are to create “vigorous, stronger, faster athletes,” mitigate costs associated with soft tissue injuries, identify “the next great athlete out there,” and capitalize on the new markets starting to appear for monetization.
Kinduct aggregates reams of data, including DNA, and with the help of AI engines, the company contextualizes and analyzes it. Detected trends can then lead to recommendations or interventions for the athlete – from nutrition to training programs and playing strategies. Kinduct is now considered a world leader in Athlete Management Systems and many professional sports teams, including in the NHL, have jumped aboard. Kinduct, he said, is now also starting to work with player associations.
“It’s been a crazy journey for us,” Dr. McDonough admitted. While focused on elite professional sport, he said, opportunities to move into related areas with Kinduct’s methodology of data collection and analysis seem boundless – from sports medicine to horses in equestrian sports.
“We hope that the people who attended were inspired”
“The panelists are recognized leaders in clinical care, orphan disease research and human performance and each brought to the table information on the incredible advancements they’re pioneering,” said Dr. Steve Armstrong. “We heard about a revolutionary new approach to cancer therapy, the progress being made in treating rare diseases in children at the IWK, and how a Halifax-based company is helping professional sports teams get the most of their athletes. These seemingly disparate topics are linked together by the ability to custom-tailor treatments and optimize performance thanks to personalized data.”
“We hope that the people who attended were inspired and that they left feeling optimistic about a future made brighter by the transformative power of personalized data and genomics.”