Pace Lab projects fall in to two large categories: RNase P and Search. P people study RNaseP, a catalytic RNA that functions in the conversion of pre-tRNA to functional tRNA, and its associated proteins through biochemical and biophysical methods. Search researchers use molecular methods such as cloning and sequencing to study microorganisms in environmental and medical situations.
Search" researchers use molecular methods such as cloning and sequencing to detect microorganisms in various environments. The circle to the left illustrates our basic "molecular method" for detecting organisms in a sample. These are the techniques used by both medical and environmental "search".
A significant part of what we do in environmental search is expansion of the three domain tree of life. Since many microbes are difficult to culture, many have only recently been discovered through sequencing of conserved genes such as that for the small subunit of the ribosomal RNA.
Drinking Water Microbiology -- This project aims to develop an understanding of the microbiology of drinking water and drinking water sources. As a new focus area of the project, samples will be collected from municipal drinking water taps and source water along major rivers. Graduate student Kim Ross, postdocs Kevin McCabe and Eric Holinger are the primary personnel. Our water supply work funded by the Sloan Foundation. Current project include sampling municipal water systems on the Colorado Front Range, the Los Angeles area, and along the Missouri/Mississippi river basin.
Indoor Environments -- This project, funded by the Sloan Foundation, examines the microbial communities in human environments incuding hospitals, homes, public buildings, and water systems. As a result of finding Mycobacterium spp. in many indoor and drinking water ecosystems, we are interested in finding a gene that successfully differentiates between different species/strains of Mycobacteria. Postdoc Kevin McCabe, graduate student Kim Ross and technician Kristen Peterson work on this project.
Microbially-induced Concrete Corrosion -- Concrete corrosion is a major financial drain for wastewater utilities. In this project, we aim to characterize what types of communities are present in different environments and to devise a metals-based inhibition material. Graduate student Ali Ling works on this project in collaboration with members of Dr. Mark Hernadez's laboratory in Environmental Engineering.
CAFOs -- Concentrated animal feeding operations bring together large numbers of people and animals in an enclosed environment. This project, funded by NIOSH, examines the microbial constituents of air in CAFOs to determine a) what microbes are present and b) whether we can detect specific microorganisms of concern. Work was previously completed by graduate student Mari Rodriguez and postdoc Piret Koll.
Guerrero Negro -- The Guerrero Negro hypersaline microbial mat of Baja California, Mexico has been a research site for the Pace Lab for years. The Bacterial, Archaeal, and Eukaryotic microbial diversity are the subjects of several studies previously conducted by Dr. John Spear, Dr. Ruth Ley, and undergraduates Alicia Berger and Leah Feazel, as well as ongoing investigation by Drs. Charles Robertson and Kirk Harris.
Yellowstone Microbial Mats -- This study is interested in dicovering what organisms form the multicolored microbial mats surrounding Yellowstone's hot springs. This study has been conducted by Kim Ross and Leah Feazel with the help of undergraduates Nikki Held, Mallory Chan, and graduate rotation students.
Baumgartner LK, Dupraz C, Buckley DH, Spear JR, Pace NR, and Visscher PT. (2009) Microbial species richness and metabolic activities in hypersaline microbial mats: Insight into biosignature formation through lithification. Astrobiology 9:861-874.
Baumgartner, LK, Spear, JR, Buckley, DH, Pace, NR, Reid, RP, Dupraz, C, and Visscher, PT (2009) Microbial diversity in modern marine stromatolites, Highborne Cay, Bahamas. Environ Microbiol. Published online July 6.
Kunin, V, Raes, J, Harris, JK, Spear, JR, Walker, JJ, Ivanova, N, von Mering, C, Bebout, BM, Pace, NR, Bork, P, and Hugenholtz, P (2008) Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat. Mol Syst Biol 4:198.
Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, Maresca JA, Bryant DA, Sogin ML, Pace NR. (2006) Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol. 72(5):3685-95.
D, Walker JJ, Mojzsis SJ, Pace NR. (2005) Composition
and structure of microbial communities from stromatolites
of Hamelin Pool in Shark Bay, Western Australia. Appl
Environ Microbiol. 71(8):4822-32.
BM, Anbar AD, Des Marais D, Morrison D, Pace NR. (2005)
Don't dismiss astrobiology. Science. 308(5721):495-7.
This research area includes studies of RNase P RNA, its catalytic function and associated proteins, as well as other functional RNAs such as miRNAs.
Analysis of Bacterial RNase P Structure--The fine structure of bacterial Ribonuclease P is still being resolved by comparing structures from different bacteria. Kinetics, mutational analyses, covariation, and X-RAY crystallography,are techniques commonly utilized by the P researchers: Alexei, Lika, Donnie, Katrina and Sina.
Eukaryal RNase P--Steve Marquez studies the RNase P molecule of eucaryotic organisms. In eucaryotes there are many more affiliated proteins needed for the catalytic function of RNase P
Dalby AB, Frank DN, St Amand AL, Bendele AM, Pace NR. (2006) Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal microbiota. Appl Environ Microbiol. 72(10):6707-15.
Kazantsev AV, Krivenko AA, Harrington DJ, Carter RJ, Holbrook SR, Adams PD, Pace NR. (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci U S A. 100(13):7497-502
Krivenko AA, Kazantsev AV, Adamidi C, Harrington DJ, Pace NR. (2002) Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr. 58(Pt 7):1234-6.
Johne's Disease Acid fast and FISH Images
Cystic Fibrosis -- Kirk Harris uses sequencing to analyze bacterial community composition in lung sputum and bronchial lavages of CF patients. This is useful because frequently the exacerbation-causing organisms are not brought into culture in the hospital lab. Potentially, this work could be used to drive treatment of CF patients based on the bacterial pathogens identified through sequencing.
Johnes's Disease -- An ongoing study of the microbial community composition in the intestines of Crohn's Disease cattle. This is a gastro-intestinal disease that may be caused by bacteria and is becoming more prevalent. Previous studies in the lab have studied inflammatory bowel disease (IBD) and chrone's disease in humans.
MRSA -- Methicillin-resistant Staphylococcus aureus (MRSA) represents an increasing risk especially in hospital nosocomial infections.
Atopic Dermatitis -- increasingly common skin condition in children, causes inflammation, lesions, and itchiness. Often associated with microbial infection.
Prostatitis -- inflamation of the prostate affects 50% of all men at some point in their life. Prostatitis maybe bacterial or non-bacterial by hospital culture results.
Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR.(2007) Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis.Proc Natl Acad Sci 104(51):20529-33.
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci. 104(34):13780-5
St Amand AL, Frank DN, De Groote MA, Basaraba RJ, Orme IM, Pace NR. (2005) Use of specific rRNA oligonucleotide probes for microscopic detection of Mycobacterium tuberculosis in culture and tissue specimens. J Clin Microbiol. 2005 Oct;43(10):5369-71.
Gardner EM, Burman WJ, DeGroote MA, Hildred G, Pace NR. (2005) Conventional and molecular epidemiology of macrolide resistance among new Mycobacterium avium complex isolates recovered from HIV-infected patients. Clin Infect Dis. 41(7):1041-4.
St Amand AL, Frank DN, De Groote MA, Pace NR.(2005)
Use of specific rRNA oligonucleotide probes for microscopic
detection of Mycobacterium avium complex organisms in
tissue. J Clin Microbiol. 43(4):1505-14
Angenent LT, Kelley ST, St Amand A, Pace NR, Hernandez MT. (2005) Molecular identification of potential pathogens in water and air of a hospital therapy pool. Proc Natl Acad Sci U S A. 102(13):4860-5.Frank DN, Spiegelman GB, Davis W, Wagner E, Lyons E, Pace NR. (2003) Culture-independent molecular analysis of microbial constituents of the healthy human outer ear. J Clin Microbiol. 41(1):295-303.
The Pace lab is located in the department of Molecular, Cellular, and Developmental Biology (MCDB) in the Gold Biosciences Building on the CU flagship campus in Boulder, CO. CU-Boulder is home to 11 Nobel Laureates, 9 MacArthur Fellows (including Dr. Pace!), 33 members of the National Academies, and nearly 30,000 students.
Our lab is located in the foothills of the Rocky Mountains, in Boulder, Colorado. Boulder is a great city for academics with the University of Colorado, NCAR, NOAA, NIST, and a strong biotechnology industry. It is also a great place to live because of the fabulous weather, outdoor activities galore, a lively music scene and nightlife, and good dining.