Science
 loRESULTS
  SCIENCE lies at the heart of the mission of the U.S. Environmental Protection Agency (EPA). The Agency must rely on cutting edge research, accurate
  measurements and effective technology to implement its programs to protect the environment and human health. Without sound science and credible data,
  EPA con not wisely set environmental and health standards, clean up contaminated sites, measure ambient air and water quality conditions, or identify the new
  technologies or practices that will reduce releases to the environment. These fact sheets share with you some of our EPA New England's laboratory capabilities
  and exemplify some of the very best science we do to meet our agency mission.
                                  GOAL:
                                  EPA's New England Regional Laboratory, in collaboration with EPA's Office of Research  and Development
                                  and Office of Water, is developing innovative cost-effective analytical capabilities to enhance existing microbial
                                  assessment of water resources by the application of a biochemical technology for rapid, same-day detection and
                                  quantification of naturally occurring microbes and microbial pollution.
KEY  CONTACTS:
JACK  PAAR
Biologist
(617) 918-8604
paar.jack@epa.gov

KATRINA  KIPP
Chief, Ecosystem Assessment
(b!7) 918-8309
kipp.katrina@epa.gov

MICHAEL  KENYON
Director, EPA  New England
Regional Laboratory
(617) 918-8317
kenyon.michael@epa.gov
GENERAL  INFO:


EPA NEW ENGLAND
REGIONAL LABORATORY
11 Technology Dr.
North Chelmsford, MA 01863
(617)  918-8300
www.epa.gov/ne/lab

TOLL-FREE
CUSTOMER  SERVICE
1-800-EPA-7341
                                  PROGRESS:
                                  PCR (Polymerase Chain Reaction) is a biochemical genetic
                                  technique that mimics the natural cellular process of nucleic acid
                                  duplication in living cells (either DNA: deoxyhbonudeic add, or
                                  RNA: ribonudeic aad). DNA and RNA are made up of genes
                                  comprised of unique sequences of nudeotide bases which can
                                  be detected by PCR analysis, thus identifying a specific strain of
                                  bacteria or a spedfic animal, like birds, cows, or humans.

                                  The  regional  laboratory's  quantitative  Real-Time  Poly-
                                  merase Chain  Reaction (qPCR) technology capability is an
                                  innovative and developing scientific tool that has significant
                                  potential for assisting EPA scientists in determining regula-
                                  tory responsibility for fecal coliform pollution in the region's
                                  water resources. EPA New  England is collaborating with
                                  EPA's Office of Research and Development and  Office of
                                  Water to evaluate the best protocols and  test  methods
                                  for utilizing qPCR in support of EPA's mission.  To date,
                                  EPA New England has established three different real-time
                                  qPCR assays capable of analyzing fecal indicators in marine
                                  and fresh water samples and is focusing on microbial source
                                  tracking of fecal contaminants in marine waters off urban
                                  beaches in metropolitan Boston, Massachusetts.

                                  Almost one quarter of the 2.840 water-bodies  in  New
                                  England listed as "impaired" are so dassified because they do
                                  not meet water quality criteria  for bacteria.  Traditional mi-
                                  crobial test methods limit state, federal and tribal regulators'
                                  ability to implement appropriate control measures and/or to
                                  assess human health risks. Traditional microbial methods have
                                  significant holding-time constraints as well as delayed results due
to a 24 hour minimum time for analysis completion. These
methods also cannot distinguish specific differences between
the sources of microbial pollution. The advantage of qPCR is
that in most cases, analysis can be completed in four hours or
less, and scientists do not have the same 6 hour holding-time
limitation required by culturebased test methods. In addition,
qPCR can identify host-specific pollution indicators, or those
bacteria that are only associated with specific species.

The laboratory is also developing  PCR techniques to de-
tect and quantify naturally occurring beneficial bacteria that
digest chemical pollutants and change them into harmless
gases. These methods will support screening assessments
of groundwater microbial communities capable of bioreme-
diation, or the natural degradation of industrial solvents to
non-hazardous break-down products. This will be a valuable
tool to  support the cleanup of hazardous waste sites.

BENEFITS:
Scientists at the EPA's New England Regional Labora-
tory  are continuing in the development and validation of
routine and  repeatable analytical  qPCR methods. These
methods will allow EPA scientists to  rapidly determine
whether or  not samples contain  DNA from known tar-
gets, whether those targets are fecal pollution indicators,
like E. coli, or bacteria capable of metabolizing hazardous
waste,  like the anaerobe Dehalococcoides ethenogenes.
By helping  identify sources of microbial contamination,
qPCR will allow regulators to identify more effective mea-
sures to mitigate pollution.
                                  SEPA
                                                  United States
                                                  Environmental Protection
                                                  Agency
                                EPA-901-F-09-020
                                       April 2009
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