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SAMUEL D. SIBLEY

      Research Associate, Department of Pathobiological Sciences

 

 

 

 

 

 

 

Education and Training

September 2011 – June 2012: Howard Hughes Medical Institute Teaching Fellowship

August 2003 – January 2010: University of Wisconsin, Madison, WI

Ph.D., Environmental Chemistry and Technology; Minor: Hydrogeology

Thesis: Concentration and Molecular Detection of Bovine Adenoviruses for Fecal Source Tracking

August 2001 - July 2003: Georgia Institute of Technology, Atlanta, GA

M.S., Earth and Atmospheric Sciences (geochemistry focus)

Thesis: The Impact of Salt Marsh Hydrogeology on Dissolved Uranium (Abstract; .pdf)

August 1996 -  May 2000: Cornell University, Ithaca, NY.    

B.S. (Magna Cum Laude), Science of Earth Systems

Sam Sibley, PhD

 

Research Associate

Fields of Interest

Supervisor: Dr. Tony Goldberg

Virus discovery, deep sequencing

Scientific Teaching

Applied environmental microbiology

Pathogen detection and discrimination

Groundwater quality, Surface water-groundwater interaction

Environmental fate and transport of contaminants and pathogens, influences of solution chemistry

Dissolved organic matter impacts on natural and engineered systems

 Water re-use/reclamation

 

555 Science Drive

Madison, WI 53711

P: 608.265.4849

ssibley@wisc.edu

Complete vitae (pdf)

 

Research Description

Today, few questions are more imperative (or personally intriguing) than how and why do viral pathogens emerge. Considering steady advance of climate change, globalization and population growth, and the resulting widespread encroachment of human activities into natural biomes, the stage is set for virus emergence in “hot spot” areas around the world. As part of a global network of collaborators investigating virus emergence, I am investigating the diversity and transmission pathways of blood-borne viruses infecting humans and non-human primates in and around Kibale National Park, Uganda. This research involves the optimization and application of next-generation (“deep”) sequencing methods on the Illumina MiSeq platform for the discovery of novel viruses. Our research has already uncovered a number of novel viruses, including simian hemorrhagic fever viruses infecting red colobus monkeys.

Additional research that I have conducted at UW-Madison includes (1) investigating the resistance of pathogenic prion prions to chemical and enzymatic degradation; (2) confirming the presence and determining the source(s) of fecal contamination to groundwater through the concentration and detection of host-specific, DNA viruses (adenoviruses and polyomaviruses); (3) exposing the diversity of livestock adenoviruses through the design and optimization of “broad-spectrum” PCR assays; (4) elucidating chemical interactions involved in the binding of dissolved natural organic matter with antibiotics; and (5) identifying (using Fourier transform infrared photoacoustic spectroscopy) fouling material on ultrafiltration and reverse osmosis membranes.

 

Related Media

NYT, September 11, 2011: “The Real Threat of ‘Contagion.’

“More than three-quarters of all emerging infectious diseases originate when microbes jump from wildlife to humans. Our vulnerability to such diseases has been heightened by the growth in international travel and the globalization of food production. In addition, deforestation and urbanization continue to displace wildlife, increasing the probability that wild creatures will come in contact with domesticated animals and humans.”

The Wisconsin Idea.  To “…influence and improve people’s lives beyond the university classroom.”

October 27, 2010. “Testing Well Water for Microorganisms.” Video and Newsletter produced by the UW-WRI describing my on-going viral source tracking work.

NYT,  September 17, 2009: “Health Ills Abound as Farm Runoff Fouls Wells.”

“MORRISON, Wis. — All it took was an early thaw for the drinking water here to become unsafe…more than 100 wells were polluted by agricultural runoff within a few months, according to local officials. As parasites and bacteria seeped into drinking water, residents suffered from chronic diarrhea, stomach illnesses and severe ear infections.”

NYT, October 16, 2009: “E.P.A. Vows Better Effort on Water.”

“The Environmental Protection Agency said on Thursday that it would overhaul enforcement of the Clean Water Act, as lawmakers sharply criticized the agency’s decade-long lapses in punishing polluters.”

 

 

 

 

Links & Resources

 

UW-Madison

Kibale EcoHealth Project

Goldberg Laboratory

WI State Lab of Hygiene

EC&T

 

ICTV Virus Database

NCBI GenBank

NCBI BLAST

NCBI Primer BLAST

 

VMRI Adenovirus Genomics & Taxonomy Lab (Budapest)

 

VMRI Adenovirus Taxonomy

 

American Type Culture Collection (ATCC)

Felix d'Hérelle Reference Center for Bacterial Viruses

 

Public Health Canada:

Infectious Substance (MSDS)

 

NEBcutter 2.0

 

Webcutter 2.0

 

 

Methods

 

Illumina Sequencing

Sequencing Video

Basic qPCR Optimization (Eppendorf) 

 

Touch-down PCR (Bitesize Bio)

 

Professional Activities

Instructor, 2011 – 2012, Biology 375: Exploring Biology (Univ. Wisconsin)

Reviewer, 2012, Environmental Science and Technology (Elsevier)

Reviewer, 2008, Environmental Pollution (Elsevier)

 

 

 

Selected Publications and Presentations

 

 

Lauck M., S.D. Sibley, D. Hyeroba, T.C. Friedrich, T.L. Goldberg, D.H. O’Connor. Discovery of novel RNA viruses in non-human primates from Kibale National Park, Uganda. Great Plains Emerging Diseases Conference, April 27 – 28, 2012, Iowa City, IA. (Accepted)

Sibley, S.D.; C.J. Hedman, S.C. Long, and J.A. Pedersen. Detection of Adenoviruses and Polyomaviruses in Groundwater for Fecal Source Attribution. 112th American Society of Microbiology General Meeting, June 16-19, 2012, San Francisco, CA. (Accepted)

Sibley, S.D. Enhancing freshmen appreciation for Structure and Function through exploration of respiratory morphology. University of Wisconsin Teaching and Learning Symposium, May 24, 2012, Madison, WI. (Submitted)

Sibley, S.D., T.L. Goldberg, and J.A. Pedersen. Improved Detection of Adenoviruses in Cattle Wastes Using Novel Broad-spectrum Primers. Appl. Environ. Microbiol., 2011,  77:5001-5008. doi: 10.1128/AEM.00625-11.

Sibley, S.D. and J.A. Pedersen. Interaction of the macrolide antibiotic clarithromycin with dissolved humic substances. Environ. Sci. Technol. 2008, 42:422-428. doi: 10.1021/es071467d.

Sibley, S.D. and J.A. Pedersen. Recovery of Sorbed Bacteriophages and Adenovirus from Nano-Aluminum Oxide Fiber Filters. 108th American Society of Microbiology General Meeting, June 1 - 5, 2008, Boston, MA. [poster (PDF)]

Gu, C., K.G. Karthikeyan, S.D. Sibley, and J.A. Pedersen. 2007. Complexation of the antibiotic tetracycline with humic acid. Chemosphere 66:1494-1501. doi:10.1016/j.chemosphere.2006.08.028.

Sibley, S.D., P. Schramm, and J.A. Pedersen. Analysis of Natural Organic Matter Foulants on Reverse Osmosis Membranes. 27th Annual Midwest Environmental Chemistry Workshop, Oct 15-17, 2004, Madison, WI.