Bioinformati
295
Part B | 10.1
10. Bioinformatic Techniques on Marine Genomics
A. Mir Bilal, H. Mir Sajjad, Inho Choi, Yoon-Bo Shim
Marine biotechnology is the industrial, medical or environmental application of biological
resources from the sea. Since the marine environment is the most biologically and chemically
diverse habitat on the planet, marine biotechnology has in recent years delivered a growing
number of major therapeutic products, industrial
and environmental applications, and analytical tools. These range from the use of a snail
toxin to develop a pain control drug to metabolites from a sea squirt to develop anticancer
therapeutic and marine enzymes to remove bacterial biofilms. In addition, well-known and
broadly used analytical techniques are derived
from marine molecules or enzymes, including
green fluorescence protein gene tagging methods and heat resistant polymerases used in the
polymerase chain reaction. Advances in bacterial
identification, metabolic profiling, and physical handling of cells are being revolutionized by
techniques such as mass spectrometric analysis of
bacterial proteins. Advances in instrumentation
and a combination of these physical advances
with progress in proteomics and bioinformatics
are accelerating our ability to harness biology for
commercial gain. Single cell Raman spectroscopy
and microfluidics are two emerging techniques
that we try to touch a bit in this chapter. In this
chapter, we provide a brief survey and update of
the most powerful and rapidly growing analytical techniques as used in marine biotechnology,
together with some promising examples of less
10.1 Background ....................................... 295
10.2 Marine and Bacterial Fluorescence
Shining Light on Biological Questions.. 297
10.3 Recent Advances in Imaging
Techniques for Marine Biotechnology .. 297
10.4 Chemical Analysis
of Volatile Microbial Metabolites ......... 297
10.5 Bioinformatics Resources .................... 298
10.6 Large-Scale Sequence Analysis ............ 299
10.7 Integrating Sequence
and Contextual Data ........................... 300
10.8 Proteomics as Potential Tool for Survey
in Marine Biotechnology..................... 301
10.9 Proteomics and Seafood ..................... 301
10.10 Present Status and Future Trends
of Proteomics in Marine Biotechnology 302
10.11 Pharmacophore Model Hypo1,
Virtual Screening for Identification
of Novel Tubulin Inhibitors
with Potent Anticancer Activity ........... 302
10.11.1 CBM4-2 Carbohydrate Binding
Module from a Thermostable
Rhodothermus marinus
Xylanase ................................ 303
10.12 The Polymerase Chain Reaction:
A Marine Perspective .......................... 303
10.13 Conclusions and New Frontiers ........... 303
References................................................... 304
well-known earlier stage methods which may
make a bigger impact in the future.
10.1 Background
Genomics is the study of the structure, function, and
diversity of genomes; genome is the collective term
for all the genetic information contained in a particular organism. Genomics has brought about a revolution
in all fields of biology. Genomic analysis, from originally limited to one or a small number of genes to
large numbers of genes or even to the complete set that
make up a genome, differentiates the genomic approach
from the classical biological approach. High throughput methodologies adapted for the analysis of multiple
gene sets has led to substantial technical advances and
to the development of new ways of thinking about bi-
295
Part B | 10.1
10. Bioinformatic Techniques on Marine Genomics
A. Mir Bilal, H. Mir Sajjad, Inho Choi, Yoon-Bo Shim
Marine biotechnology is the industrial, medical or environmental application of biological
resources from the sea. Since the marine environment is the most biologically and chemically
diverse habitat on the planet, marine biotechnology has in recent years delivered a growing
number of major therapeutic products, industrial
and environmental applications, and analytical tools. These range from the use of a snail
toxin to develop a pain control drug to metabolites from a sea squirt to develop anticancer
therapeutic and marine enzymes to remove bacterial biofilms. In addition, well-known and
broadly used analytical techniques are derived
from marine molecules or enzymes, including
green fluorescence protein gene tagging methods and heat resistant polymerases used in the
polymerase chain reaction. Advances in bacterial
identification, metabolic profiling, and physical handling of cells are being revolutionized by
techniques such as mass spectrometric analysis of
bacterial proteins. Advances in instrumentation
and a combination of these physical advances
with progress in proteomics and bioinformatics
are accelerating our ability to harness biology for
commercial gain. Single cell Raman spectroscopy
and microfluidics are two emerging techniques
that we try to touch a bit in this chapter. In this
chapter, we provide a brief survey and update of
the most powerful and rapidly growing analytical techniques as used in marine biotechnology,
together with some promising examples of less
10.1 Background ....................................... 295
10.2 Marine and Bacterial Fluorescence
Shining Light on Biological Questions.. 297
10.3 Recent Advances in Imaging
Techniques for Marine Biotechnology .. 297
10.4 Chemical Analysis
of Volatile Microbial Metabolites ......... 297
10.5 Bioinformatics Resources .................... 298
10.6 Large-Scale Sequence Analysis ............ 299
10.7 Integrating Sequence
and Contextual Data ........................... 300
10.8 Proteomics as Potential Tool for Survey
in Marine Biotechnology..................... 301
10.9 Proteomics and Seafood ..................... 301
10.10 Present Status and Future Trends
of Proteomics in Marine Biotechnology 302
10.11 Pharmacophore Model Hypo1,
Virtual Screening for Identification
of Novel Tubulin Inhibitors
with Potent Anticancer Activity ........... 302
10.11.1 CBM4-2 Carbohydrate Binding
Module from a Thermostable
Rhodothermus marinus
Xylanase ................................ 303
10.12 The Polymerase Chain Reaction:
A Marine Perspective .......................... 303
10.13 Conclusions and New Frontiers ........... 303
References................................................... 304
well-known earlier stage methods which may
make a bigger impact in the future.
10.1 Background
Genomics is the study of the structure, function, and
diversity of genomes; genome is the collective term
for all the genetic information contained in a particular organism. Genomics has brought about a revolution
in all fields of biology. Genomic analysis, from originally limited to one or a small number of genes to
large numbers of genes or even to the complete set that
make up a genome, differentiates the genomic approach
from the classical biological approach. High throughput methodologies adapted for the analysis of multiple
gene sets has led to substantial technical advances and
to the development of new ways of thinking about bi-