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M.S. Clark et al.
species, a means has to be found to work on a particular species even if the material is intractable as there is a defined requirement for work in that area. So having
outlined the techniques, the question is how to use them?
In this chapter specific examples will be used to demonstrate how such techniques
are being used to address these important ecological issues in the marine environment, concentrating on lower vertebrates (fish) and invertebrates. These encompass
both population analyses and gene expression (functional) studies to understand
how populations have adapted to and interact with, their environment.
Ultimately, the challenge for the marine biologist is to utilize the tools produced
for the study of model organisms, where significant amounts of sequence data exist
(i.e. resource rich) and to develop these for non-model species, essentially from a
zero base-line. It is not an easy task.
Abbreviations
AFLP
Amplified fragment length polymorphism
BAC
Bacterial artificial chromosome
cDNA
copy/complementary DNA
COI
Cytochrome C oxidase
dbEST
database for ESTs: http://www.ncbi.nlm.nih.gov/dbEST/
DNA
Deoxyribonucleic acid
ER
Endoplasmic reticulum
EST
Expressed sequence tag
GH
Growth hormone
GHRH
Growth hormone releasing hormone
GMPD
Glycosylase mediated polymorphism detection
HSP
Heat shock protein
IPCC
Intergovernmental panel on climate change
MPA
Marine protected area
MPSS
Massively parallel sequencing signature
PR
Prolactin
Q-PCR
Quantitative or Real Time PCR
QTL
Quantitative trait locus/loci
RNA
Ribonucleic acid
SNP
Single nucleotide polymorphism
SSR
Simple sequence repeat
SYBR Green Fluorescent green dye
UTR
Untranslated region
3.1 Tools
This first section will concentrate on the tools available, some of which can be used
in either DNA and/or RNA studies and these are described below. The tools are
M.S. Clark et al.
species, a means has to be found to work on a particular species even if the material is intractable as there is a defined requirement for work in that area. So having
outlined the techniques, the question is how to use them?
In this chapter specific examples will be used to demonstrate how such techniques
are being used to address these important ecological issues in the marine environment, concentrating on lower vertebrates (fish) and invertebrates. These encompass
both population analyses and gene expression (functional) studies to understand
how populations have adapted to and interact with, their environment.
Ultimately, the challenge for the marine biologist is to utilize the tools produced
for the study of model organisms, where significant amounts of sequence data exist
(i.e. resource rich) and to develop these for non-model species, essentially from a
zero base-line. It is not an easy task.
Abbreviations
AFLP
Amplified fragment length polymorphism
BAC
Bacterial artificial chromosome
cDNA
copy/complementary DNA
COI
Cytochrome C oxidase
dbEST
database for ESTs: http://www.ncbi.nlm.nih.gov/dbEST/
DNA
Deoxyribonucleic acid
ER
Endoplasmic reticulum
EST
Expressed sequence tag
GH
Growth hormone
GHRH
Growth hormone releasing hormone
GMPD
Glycosylase mediated polymorphism detection
HSP
Heat shock protein
IPCC
Intergovernmental panel on climate change
MPA
Marine protected area
MPSS
Massively parallel sequencing signature
PR
Prolactin
Q-PCR
Quantitative or Real Time PCR
QTL
Quantitative trait locus/loci
RNA
Ribonucleic acid
SNP
Single nucleotide polymorphism
SSR
Simple sequence repeat
SYBR Green Fluorescent green dye
UTR
Untranslated region
3.1 Tools
This first section will concentrate on the tools available, some of which can be used
in either DNA and/or RNA studies and these are described below. The tools are