Environmental Biotechnology 2015
Practice exam questions:
1) What do the following mean?
A. CSIA
B. qPCR
C. RT-qPCR
D. Fingerprinting
E. Microarrays
F. SIP
G. EAPs
H. FISH
2) Briefly explain how each of the techniques mentioned in question 1 work.
3) Give the name for the following methods.
A. Chemical analysis that detects the presence of enzymes through a reaction of the
enzyme with chemical surrogates
B. Techniques that provide direct evidence of biodegradation by detection of incorporation
of stable isotopes from isotopically enriched contaminant into microbial cell structures
or generation of terminal products containing stable isotopes from the added
compounds.
C. Provides direct evidence of microbial presence through hybridization to target genes, or
provides indirect evidence of microbial activity by detecting expression of
biodegradation associated genes.
D. Group of methods that provide indirect evidence of microbial community diversity,
structure and overall biomass based on analysis of microbial DNA or cell structures such
as phospholipids.
E. Quickly determines the presence or absence of a large number of targeted DNA
fragments in an environmental sample.
F. Detects expression of biodegradation associated genes by amplifying the mRNA
sequences.
G. Analytical method that quantifies the relative abundance of stable isotopes (such as
13C/12C) in contaminants.
H. Chemical process that generates copies of specific DNA sequences in a quantifiable and
repeatable manner. Used to calculate the number of copies of a specific DNA sequence
that are present in a sample.
4) Name some techniques which can be used to tell us about the following:
A. Provides basic information on community diversity and changes in structure over time.
B. Track individual organisms over time and space within a community, in combination
with other EMDs.
C. Get direct evidence of biological degradation of contaminants.
D. Identify degrading microorganisms; this information can be applied to future analyses.
E. Get direct evidence of enzyme activity and thus indirect evidence of biodegradation of
contaminants.
F. Get direct measurement of presence and indirect measurement of activity of organisms
of interest.
G. Get visual information of the spatial distribution of organisms and cultures.
H. Determine total biomass.
I. Get direct evidence of biological or chemical degradation of contaminants.
J. Generate attenuation rates and mechanisms.
K. Provides information to identify multiple sources of pollutants.
L. Confirms presence and determines abundance of target microbes and genes.
M. Estimate total microbial numbers.
N. Monitor population growth and distribution of microbes involved in bioremediation.
O. Get indirect evidence of biodegradation gene expression and thus biodegradation
activity.
P. Track microbial groups within a community over time and during bioremediation.
Q. Get basic information on community diversity and changes in structure over time.
5) Which EMD (CSIA, qPCR, RTqPCR, Fingerprinting, Microarrays, SIP, EAP, FISH ) would you
use to help answer the following question (there may be more than one EMD for any
question)
A. Are contaminant-degrading microorganisms present?
B. Are contaminant-degrading microorganisms active?
C. Are the microorganisms capable of complete degradation?
D. Is biodegradation occurring?
E. Is the contaminant attenuating abiotically?
F. Are multiple sources contributing to the contamination?
G. If there is a potential for multiple sources, can the sources be distinguished?
H. Are numbers of contaminant- degrading microorganisms and/or genes changing?
I. Is the remediation strategy affecting the numbers or types of contaminant-degrading
microorganisms?
J. Is there a biological basis for intermediates accumulating?
K. Are intermediates being degraded?
L. Is there evidence of abiotic transformation?
M. Is biodegradation occurring?
N. What is the rate of biodegradation?
O. Does the microbial community composition support the remediation strategy?
P. Do contaminant-degrading microorganisms continue to be sufficiently abundant?
Q. Are contaminant-degrading microorganisms remaining active?
R. Is there a biological basis for intermediates accumulating?
S. Are intermediates being degraded?
T. Is there evidence of abiotic transformation?
U. Is biodegradation occurring?
V. What is the rate of biodegradation?
W. Is contaminant degradation likely to continue?
X. Are intermediates being degraded?
Y. Is biodegradation occurring?
Z. What is the rate of biodegradation?
AA. Does the microbial community composition suggest that sufficient contaminant
degradation has occurred?