Laboratory of Molecular Responses

Lab Description

The diversity of life on Earth can’t be seen with the naked eye, the vastness of life as we know it is microbial. These simple yet elegant creatures are responsible for the air we breathe, for providing important vitamins and nutrients to our own bodies, and for cycling nutrients in the environment, a critical ecosystem service for life.

Microorganisms face a barrage of challenges in their microscale environments, both temporally and spatially. We’re interested in understanding how microorganisms respond and adapt to environmental stress (e.g., nutrient starvation and UV exposure) at the molecular level, and how these molecular adaptations influence rates of productivity, transcend evolutionary history, and inform the geochemistry of early Earth.

The Laboratory of Molecular Responses is fully equipped for state of the art molecular biology, genomics, bioinformatics, and culture-based research and has capabilities to facilitate high-throughput work and recombinant DNA research. It also has full instrumentation, supporting equipment and computational resources.

Joe Grzymski, Ph.D. 
Associate Research Professor/Primary Investigator
Email: joeg@dri.edu
Phone: (775) 673 7478

Degrees:
B. A., Bowdoin College, Departments of Biology and Philosophy
Ph.D., Rutgers University, Institute of Marine and Coastal Sciences

Bio: I am a Jersey boy who came to Reno to enjoy the Sierra Nevada mountains and avoid traffic. After graduating from college I received a Fulbright Scholarship and worked for more than a year in Trondheim, Norway at the Biological Station http://www.ntnu.edu/map/heggdalen/trondheim-biological-station/. After living the good life in Norway I returned to the States to do my graduate work in Oscar Schofield’s lab at Rutgers http://rucool.marine.rutgers.edu/. I did postdoctoral work in photochemistry and photobiology in the lab of Prof. David Mauzerall at Rockefeller University. I moved to Reno to do a postdoc in Alison Murray’s lab and fell in love with the West. My lab is focused on understanding how microorganisms respond to their environment. We are specifically interested in the molecular and long-term evolutionary response to stresses such as UV, high and low temperature and low nutrients. My philosophy of running a lab is simple – surround myself with people smarter than me and stay out of their way while providing them the tools to do great work.

Iva Neveux 
Staff Molecular Biologist/Lab Manager
Email: iva.neveux@dri.edu
Phone: (775) 673 7385

Degrees:
M.S., Masaryk University, Molecular Biology and Genetics, Czech Republic
M.S., University of Nevada, Microbiology

Bio: I came to the United States from the Czech Republic to deepen my knowledge of molecular biology. Prior to working at DRI I spent seven years gaining experience in biochemistry, cell biology, histology, microbiology and electrophysiology at Southern Illinois University and the University of Nevada. I am very excited to be involved with state-of-the-art research at Desert Research Institute in Reno. In addition to managing the laboratories, my duties include field sample collection, experimental work with lab grown organisms, molecular extractions, cloning, protein work, etc.  I am enjoying what I do – my job has given me many opportunities to work on a variety of different projects, collaborate with some great scientists, as well as explore a distant and pristine part of the world – the area around the Antarctic peninsula. When I am not pipetting in the lab, I practice and teach yoga, play piano, enjoy backcountry skiing, backpacking and traveling.

Robert Read 
Staff Research Scientist
Email: robert.read@dri.edu
Phone: (775) 673 7425

Degrees:
M.S., University of Nevada, Biochemistry

Bio: I originally came to the Desert Research Institute to complete my undergraduate senior research thesis and haven’t looked back since.  I was born and raised here in Reno, subsequently completing my Bachelors and Masters degree in Biochemistry and Molecular Biology at the University of Nevada. Working at the DRI has proven incredibly exciting due to the cutting-edge research I’m privileged to collaborate on everyday.  My main duties are the management and analysis of a majority of the data received from the molecular work accomplished on our lab grown organisms. When not doing computer data analysis, I also assist with some of the field sampling and experimental lab work on our organisms.  In my free time I enjoy playing golf, traveling, and coaching high school baseball.

Carl Staub
Electrical Engineer

Bio: Carl Staub is an electrical engineer with a long and productive career in instrument development and application. Mr. Staub has 30-years of experience designing innovative technologies and equipment in the fields of optics, spectroscopy, chemical detection, electronics, and solid-state lighting. He has engineered industry-accepted spectrophotometers specific to food quality control that are used by food processors in 39 countries; has created unique interactive protocols to optimize the processing of temperature and process-rate sensitive food compounds; and has designed novel, substrate-based lighting systems for military applications. Mr. Staub is President/CEO of Agtron Incorporated; President/CEO of Lumenautix, LLC; and is serving as the CEO of EMS Genomics, LLC.

Cost minimization is the name of the game. Have you ever wondered why genome architecture can be so drastically different between microorganisms, such as differences in genome size and codon usage (e.g., GC content)? Suprisingly, many of these characteristics can be explained by the theory of cost minimization: A theory that predicts how evolutionary adaptations to nutrient limitation get imprinted in the genomes of microorganisms and how these “hard-coded” genetic features get manifested as a diversity of ecophysiologies and niche differentiation.

Wouldn’t you say that you’re tired of reading papers that simply focus on the genetic potential of ecosystems based on the presence or absence of genes and gene pathways? Instead, how about thinking of contemporary systems in the context of their long term selective pressures that have resulted in evolutionary modifications to microorganisms over millions of years? We demonstrated the utility of this concept in our paper The significance of nitogen cost minimization in proteomes of marine microorganisms (ISME 2012, 6, 71-80), where we demonstrate that nitrogen limitation is a major selective pressure acting on the genomes of open-ocean microorgansims. We found that 1) amino acid sequences from the open-ocean are reduced in N, but increased in average mass compared with coastal-ocean microrganisms, 2) an increase in average mass of amino acids is a function of increased A+T codon usage, and 3) the compounding effect of higher A+T codon usage can lower the total cellular N budget by 2.7-10%…. So what does this mean? It means that over millions of years, nitrogen limitation leaves a significant mark on how open-ocean microbial communities function in the modern ocean and that nitrogen limitation is a stronger selective force than previously thought.

Annual 10m depth nitrate concentration for the worlds ocean.

Much of our research builds on the ideas of this seminal work. See below for our current and past projects

Transcriptomic Adaptations to Nitrogen Limitation

Nitrogen limitation can affect the genome architecture of organisms over geologic time, but what are the contemporary adaptations to these long-term selective pressures? This work investigates the effects of nitrogen limitation on the primary transcriptome of Prochlorococcus  MED4 (in collaboration with The Chisholm Lab, MIT)

Project Lead: Robert Read 

Regulatory Mechanisms of Nitrate Dissimilation 

The fate of oxidized forms of nitrogen (i.e., NO3 and NO2) to reduced forms of nitrogen (i.e., NH4+, N2O, or N2) depends on a variety of factors but is of major importance for nitrogen loss (as N2O or N2) or nitrogen retention (NH4+) in ecosystems. This work investigates the effects of carbon to nitrogen ratio and subtrate concentration on pathway selection during nitrate dissimilation (respiratory ammonification versus denitrification) in a newly discovered soil microorganisms, Intrasporangium calvum, which possess a dual-pathway for nitrogen dissimilation (in collaboration with the Stahl and Winkler Labs, UW; Sullivan Lab, UNR; Blank Lab, USDA-ARS).

Project Lead: Dave Vuono

Molecular Responses of Diatoms to UV Exposure 

Diatoms in the southern ocean experience tremendous environmental stress from UV exposure. This work investigates the effects of UV exposure on the transcriptome of Corethron hystrix to enable gene discovery.

Project Leads: Robert Read and Iva Neveux 

Technology Development 

Multiplexed real-time microbial growth measurments, usually performed in small volumes in 96-well plates, are extremely powerful for understanding microbial growth rates under different environmental conditions. When these data are paired with molecular-based tools, results can be even more powerful, but are restricted to sample volume. Scaling up in volume for molecular analyses in serium vials and balch-tubes for studying anaerobic metabolisms requires laborious and tedious manual measurements. We are developing a real-time microbial growth quantification instrument using open-source, software driven automation, remote visualization, and data aquisition. We are currently beta-testing.

Project Leads: Dave Vuono, Bruce Lipp (AIC) and Carl Staub

Past Projects

Antarctica

https://www.dri.edu/mission-antarctica

 Indian Ocean

http://indigovexpeditions.com/

https://www.dri.edu/dees-news/4748-citizen-science-model-proposed-to-fill-fundamental-ocean-data-gap

http://www.takepart.com/article/2014/09/09/citizen-scientists-can-help-save-oceans-while-sailing-seas

CONTACT

Joe Grzymski, Ph.D.
Lab Director
Joe.Grzymski@dri.edu 

LAB LOCATION

Desert Research Institute
2215 Raggio Parkway
Reno, NV 89512

DIVISION

Earth & Ecosystem Sciences