Adina's Faculty Introduction - ISU ABE
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The presentation resulting from my chair asking me to introduce myself to faculty in ISU ABE.
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Adina's Faculty Introduction - ISU ABE
- 1. Adina Howe, ABE Faculty Retreat, January 8, 2015
- 2. Measurements of health and productivity Biological sequencing, chemical characterization, yield / growth / weight, climate data, structured & unstructured Unifying heterogeneous datasets Moving beyond the Big Data craze:
- 3. Background Purdue University, BSME, Mechanical Engineering Purdue University, MS, Environmental Engineering (Sustainability) University of Iowa, PhD, Environmental Engineering (Microbiology/Bioremediatio n) Michigan State University NSF Postdoc Math and Biology Fellow (cross- training) Computational Biologist Microbiology / Microbial Ecology
- 4. GERMS Lab (Genomics & Environmental Research in Microbial Systems) Jin Choi, PhD, University of Tennessee, ChemE Ryan Williams, PhD, Iowa State, Ecology Evolution Dan Shea, MS, Northeastern, Bioinforma Website: germslab.org
- 5. GERMS Mission We are changing the environment that we live in. To preserve our environmental integrity, we must understand and manage the impacts of global change. Scientific research must inform our decisions and policy. Therefore, we use innovative scientific methods to evaluate and understand our complex
- 6. Towards this Mission: Microbes as lens into understanding global change in the natural world MICROBES IN ECOSYSTEMS NATURE AIR WATER SOIL MICROBIOMES HUMANS/ANIMAL ENGINEERED BIOREACTORS WASTEWATER
- 7. GERMS Vision (5 year goals) To provide scalable, quantitative tools to monitor microbial responses in complex environments To identify the microbial drivers responding to global change in complex environments (e.g., soils, waters, gut) To predict and model the impacts of microbial responses on ecosystem health and servicesTo monitor, evaluate, and manage our microbial partners and their services.
- 8. WATER project: Improved methods to evaluating water quality
- 9. Scalable, quantitative tools to monitor microbial responses in complex environments Data Type Example Cost per sample / Frequency of sampling Precision / Water quality information Challenges Water properties chemical analysis of water quality narrow range of information about services in ecosystem Traditional integrity indicators presence of coliform bacteria detection methods lack specificitity and are often imprecise Phytoplankton community characterization cyanotoxin detection through fractionation of ammonia detection of toxicity may not reveal source Microbial community characterization (16S rRNA) abundance of genes present and assoiated with all cyanobacteria characterization of microbial community structure may not reveal gene function; data volume large for public understanding Proposed MAVeRiC genes (DNA) abundance of genes present associated with specific source of pollution identifying relevant genes of interest to water quality; DNA reveals genes present but not necessarily actively expressed Proposed MAVeRiC genes (RNA) abundance of genes expressed and present associated with specific source pollution identifying relevant genes of interest to water quality
- 10. Scalable, quantitative tools to monitor microbial responses in complex environments Estimating risks from pathogens Biotic integrity of a healthy water system Sources of non point pollution Role of waters in stabilizing climate change Microbial genetic biomarkers can capture…
- 11. MicroArray Value and Risk Chip (MAVeRIC) $24 for 216 bioindicators/sample, estimates gene abundance of biological signals, quantitative PCR Pollution Pathogens Nutrients Toxicity Biodiversity Pollution biomarkers: Non point pollution source markers Pathogen biomarkers: Specific bacteria or virus genes Nutrient cycling biomarkers: Carbon, nitrogen, phosphorus metabolic genes Toxicity biomarkers Biodiversity biomarkers A B C D Monitoring, Evaluating, Predicting
- 12. Scaling: Iowa Lake Waters (John Downing and Chris Filstrup) Integrate measurements of bioindicators with water quality measurements in 132 lakes sampled for a routine EPA-reported, lake water quality assessment program. Interdisciplinary collaboration allowing for evaluation and prediction
- 13. SOIL Project: Microbial drivers of carbon cycling
- 14. Carbon cycling in agricultural soils (in response to global change) Collaboration with Kirsten Hofmockel, ANL, PNNL
- 15. THE DIRT ON SOIL Biodiversity in the dark, Wall et al., Nature Geoscience, 2010 Jeremy Burgress MAGNIFICENT BIODIVERSITY
- 16. THE DIRT ON SOIL SPATIAL HETEROGENEITY http://www.fao.org/ www.cnr.uidaho.edu
- 17. THE DIRT ON SOIL DYNAMIC
- 18. THE DIRT ON SOIL INTERACTIONS: BIOTIC, ABIOTIC, ABOVE, BELOW, S Philippot, 2013, Nature Reviews Microbiology
- 19. Strategy of breaking down complexity: Identifying drivers of carbon degradation Labeled Carbon (Cellulose) Monitoring & Evaluating Soil microbial communities Communities assimilating carbon Cutting edge fluorescent cell sorting
- 20. GUT Project: Identifying the microbes that make us chubby and sick
- 21. How do our microbial partners in our bodies affect our stability and resilience to change? Collaboration with ANL and University of Chicago (Eugene Chang and Daina Rin We have the same genes, but why are you a rounder?
- 22. A fascination with viruses Despite its ferocity in humans, Ebola is a life-form of mysterious simplicity. ..If it were the size of a piece of spaghetti, then a human hair would be about twelve feet in diameter and would resemble the trunk of a giant redwood tree. (Michael Specter, New Yorker) 80% unknown
- 23. Concluding thoughts All my projects depend heavily on collaborations Unifying heterogeneous datasets – improved resolutions, investigating diverse questions Biological data: Rapid, high resolution, cheap Effective integrations are POISED FOR IMPACT. Looking forward to the adventure together!
Editor's Notes
- Thank everyone for being so welcoming! And especially Lisa, Michelle, Steve, Susana, Sylvia for all their help and dealing with my pestering. Today, I’ll be giving a brief overview of some of the research that I’m excited to be tackling in the next 5 years. It’s a real honor to be in this department and I’m confident that I’m going to have a lot of fun here.
- To begin with, its hard for me to be labeled as the Big Data faculty hire. If anything, I think what my goals are here is not the size of the data I use, but the way I use very different kinds of data to answer interesting & impactful questions. The types of data I work with vary broadly, but mainly, my experience lies in leveraging advances in biological sequencing and its accessibility now to describe natural systems.
- I’ll start with a brief background. I’ve got, what I think, is a fairly atypical background – Starting with working with efficient combustion technologies in Mechanical Engineering to moving towards sustainable design in the built environment for my Master’s. I ended up taking a microbiology class that really awakened something in me and ended up studying how bacteria can eat pollutants in groundwater and sediments at the University of Iowa and continued working with the services microbes provide in the environment during my postdoc. At the time, there was a real need for microbiologists to learn to work with new sequencing technologies and the “big data” that was coming out of it, and so I spent a long postdoc re-training in this field and ended up being recruited at Argonne National Lab for a stint. I really wanted to do more research and train students, so I applied here, and here I am.
- So I’m excited to say that I will get to work with students who will help me with many diverse projects. I’ve started what I’ve called the GERMS lab. I like this name a lot because historically, germs has been a word to describe naughty bacteria but today we talk a lot about good germs in our bodies and I want to promote positivity in association with well-behaved and even necessary bacteria surrounidng us. I’ll be joined next week by Jin and Ryan, postdocs. So if you see these two clowns in the hall, make sure you say hi and ask them if they’ve heard what a rough boss I am. In May, Dan will be joining us as a PhD student. The three of these guys make a neat team, a microbiologist, a statistician, and a programmer all interested in the questions I’ll be presenting today.
- Together, as a lab, I hope that we can hold true to this mission statement.
- More specifically, towards this mission, my research involves understanding microbial communities in the natural environment in the face of global change. Great field. Microbes are everywhere, and impact nearly every environment in our lives – even inside our bodies.
- I’m going to give you a brief overview of 3 projects in 3 environments that are working towards this vision.
- The valuation of waters in of the United States, under the Clean Water Act (CWA), has been approached very narrowly. Historically and currently, we are fairly limited to what we measure towards understanding water quality. Simple measurements of these indi- cators can answer public health questions such as ‘should I drink this water?’ or ‘should I swim at this beach?’. How- ever, these measurements are not useful when there is evidence of chronic contamination, and fecal pollution sources need to be identified to address the problem. I’ll argue that today that these values that have been impossible to evaluate due to a lack appropriate technology, estimating risks of illness from toxins or pathogens; biotic integrity of a healthy water system; the sources of non-point pollution; or the role of waters in stabilizing global problems such as climate change.
- The valuation of waters in of the United States, under the Clean Water Act (CWA), has been approached very narrowly. Historically and currently, we are fairly limited to what we measure towards understanding water quality. Simple measurements of these indi- cators can answer public health questions such as ‘should I drink this water?’ or ‘should I swim at this beach?’. How- ever, these measurements are not useful when there is evidence of chronic contamination, and fecal pollution sources need to be identified to address the problem. I’ll argue that today that these values that have been impossible to evaluate due to a lack appropriate technology, estimating risks of illness from toxins or pathogens; biotic integrity of a healthy water system; the sources of non-point pollution; or the role of waters in stabilizing global problems such as climate change.
- As agriculture increases on our planet, we are very concerned about how land management will impact our environment, esp in the face of a warming planet. Microbes in this soil are critical drivers of carbon cycling and decomposition in these systems and we’re very interested in their response to global change. The challenge is that these microbes are living in a very, arguably, the most complex environment on our planet and it is very hard to tease out who is the most critical drivers here.
- Why do we need such vol. of data? Most of us now recognize that microbial communities generally exhibit a high level of diversity, much highter than previously assume by what was revealed by classical microscopy and basic culturing techniques. In soil, even in one gram of soil, there is estimated to be more microbial species than there are stars in the galaxy. We have far to go for any comprehensive characterization of any single soil community. A key question then Is why is soil diversity so high?
- One reason may be that the soil structure provides unique niche that provide a high diversity of food resources. Its varied structure provides stable, protective, and even ancient environments for microorganims.
- Soil investigations are further complicated by the primarily dormant state of the large majority of the soil microbial population. The turnover rate of soil microbes is predicted to be over 30 fold and even up to 300 fold slower than that of microbes in the oceans. And these microbes live in relatively unpredicatlbe patterns of pertubations – for example rainfall or leaf litter introduction. They also undergo defined temporal perturbations – diurnal energy input.
- This complexity in the soil has formed a dynamic microbial ecosystem which interacts with nutrients, plants, and the soil structure itself at multiple scales. I would argue that we as a field are still trying to find tractable methods of accessing these interactions and understanding the drivers of “healthy” or “productive” soils.
- Despite its ferocity in humans, Ebola is a life-form of mysterious simplicity. A particle of Ebola is made of only six structural proteins, locked together to become an object that resembles a strand of cooked spaghetti. An Ebola particle is only around eighty nanometres wide and a thousand nanometres long. If it were the size of a piece of spaghetti, then a human hair would be about twelve feet in diameter and would resemble the trunk of a giant redwood tree.