BioInformatics Reviewed
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Contacts:
Email your links to Dr. Karron: karron@casi.net
Class Site Administrator is Peter Cline: peterc@nytimes.com
This page is maintained by Osman Kabir: Osman_Kabir@yahoo.com
UPDATED: December 29, 2001
Link
Ladder:
Name |
Published Links |
Christopher Conway |
8 |
|
Changyou
Yu |
8 |
|
Christoforos
Christoforou |
6 |
|
Mohammed
Kuddus |
6 |
Tawhidul Chowdhury |
5 |
|
Zheng
Li |
5 |
|
Xiadong (Sheldon)
ÝZou |
5 |
|
Xiao
Lin |
3 |
|
Lu
Tang |
3 |
|
Qi
Chen |
2 |
Peter Cline |
2 |
|
Yang
Li |
2 |
|
Gang
Pang |
2 |
|
Kit-yu
Cheng |
1 |
Ma Da |
1 |
Osman Kabir |
1 |
|
Ercan
Kocabasoglu |
1 |
|
Rajiv
Kumar |
1 |
|
Ying
Li |
1 |
Note: As new links are submitted the ladder will be updated. The ladder just displays the top two contributors.
Link: http://www.spectrum.ieee.org/WEBONLY/publicfeature/oct01/bio.htm l
Reviewed by: Peter Cline
Surveying the Current State of affairs in the detection of Biological
Agents Christopher Aston has surveyed the current state of affairs in
Biological warfare. He examines the pros and cons of a number of approaches to
biological agent detection. He also briefly touches on diplomatic measures
for staving off biological attacks and the problems inherent therein.
The bulk of the article focuses on the state of the art in biological
detection methods. The methods reviewed are detecting DNA of disease
pathogens, the use of antibodies to detect the presence of pathogens,
tissue- based sensor, and mass spectrometry.ð All of these methods have
there advantages and disadvantages but it seems overall that tissue- based
electrical impedance and mass spectrometry prove mot effective.
&n! bsp;
Tissue-based electrical impedance uses the fact that many toxins will
trigger measurable and differentiated responses in living cells.
Researchers at Stanford University have successfully constructed a
Handheld sensor that uses this principal. Mammalian cells are cultured in a
laboratory and put in a cartridge that contains a microelectrode array.ð
The introduction of a biotoxin causes ion channels on the cells' membranes
To open or close, causing detectable mill volt changes in the membrane.
Researchers can choose certain immune system cells that produce fluorescent
proteins upon contact with the biological agent to create a visual cue
in the presence of biotoxins. Prototype systems were able to produce this
visual cue within 15 seconds of coming in contact with the biotoxin.
Drawbacks to this approach include trying to keep the! fragile cell
Samples alive in the field.
Mass Spectrometry eliminates this drawback by foregoing living
Bioreagents altogether. It works by heating a liquid sample until it vaporizes and
then Ïbombarding" it with "electron beam to give a charge to the fragments".
Positively charged particles are sorted by mass and charge in a mass
spectrometer, and the ratios of these two measures is used to calculate
molecular weights. A second mass spectrometer breaks these down
further into component amino acids. Each fragment will have a unique amino
acid ratio which can be used to identify it. The system is said to be able
to detect as few as 100 bacteria in a sample. The drawback here is
reducing the device footprint to a size that is useable in the field.
&n! bsp;
In conclusion, Aston admits that these technologies are in their
infancy, but will ultimately be important components in the changing
battlefields of tomorrow's wars. Naturally one may hope that such systems will find a
place monitoring civilian airspaces as well.
Link : http://gaia.fc.peachnet.edu/bio1010/chapter6.htm
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Reviewed by: Mohammed A. Kuddus
This site describes energy and enzymes, which are related with any
physiological tests that are commonly used in biomedical sciences, and
to know how to select and apply the appropriate tests by means of a
computer-based statistical package. The enzyme database can be useful
to anybody working with enzymes and that it can be help in the development
of computer programs involved with the manipulation of metabolic pathways.
The application, movement, and transformation of energy ultimately underlie
All physical and chemical processes. Thermodynamics deals with energy
Relations in general,! but bioenergetics is concerned only with energy in living
systems. The first and second laws of thermodynamics define the
principle of energy conservation in the universe and the direction of a process in
which energy is exchanged between a system and its surroundings.
Energy-requiring and energy-releasing reactions of metabolism are
coupled in living systems, which increases efficiency and allows greater
orderliness. Useful free energy is stored as chemical energy in living cells, most
commonly as ATP. The ADP-ATP cycle links reactions, acting as common
intermediates in sequences in which energy from breakdown reactions
becomes available for biosynthesis reactions. Energy transfers in metabolism
may proceed by phosphoryl group transfer via the ADP-ATP system, by
electron transfer via redox couples! in oxidation-reduction reaction, and by
other means. Redox couples are the oxidized and reduced forms of a compound,
such as the NAD+/NADH couple, and they act as common intermediates in
coupled energy-requiring and energy-releasing reactions involving electron
transfer.
Reaction rates in living systems are modulated by unique protein
catalysts called enzymes, which function primarily by lowering the barrier of
activation energy of a reaction and thereby increase the otherwise
sluggish organic chemical rates. Enzymes are highly efficient catalysts, since
they are highly specific for certain substrate molecules. Specificity of an
enzymeÌs affinity for its substrate depends on the region of the enzyme
called the active site, where enzyme and substrate fit together like a
lock and key. Two ! systems of self-regulation of enzyme actively are feedback
inhibition and co-operativity.
Regulation of the kind of enzyme and the amount of enzyme synthesized
In cells is controlled by the genes. The kind of enzyme made depends on
genetic information encoded in DNA, while the amount of enzyme made is
regulated at the levels of transcription and translation of the informational DNA.
The substrate, or inducer, combines with the repressor product of regulator
gene action and releases the repressor from its association with DNA. Upon
removal of the repressor, transcription proceeds, and enzyme synthesis
can occur in subsequent translation of the messenger RNA copies of DNA
information.
http://genomeathome.stanford.edu/
Reviewed by: Zheng Li
This is the web page of genome@home, a protein
sequence-structure simulation project with a goal of
understanding genomes.
Genes are the functional units of a genome. Each gene
encodes the information for how to make a specific
protein. How a gene specifies the amino acid sequence
in a protein is known. But it is still unclear how and
why many different protein sequences, each encoded by
a different gene, can form the same three-dimensional
protein structure.
Scientists have been workin! g for decades to unravel
the protein "sequence structure relationship. Now
that the human genome and many others are being
sequenced, there is a unique opportunity to compare
natural genomes and their proteins to sets of
laboratory-designed proteins to understand and answer
questions, such as, why does nature choose specific
genes? Can we design better proteins? Why do some
genetic mutations that change the protein sequences
cause diseases and others do not?
Genome@home project uses a computer algorithm, based
on the physical and biochemical rules by which genes
and proteins behave, to design new proteins hence new
genes that have not been found in nature. By comparing
these "virtual genomes" to those found in nature, a
much better understanding of how! natural genomes have
evolved and how natural genes and proteins work can be
obtained. The study is also of practical significance.
All the new protein sequences obtained from the
simulation runs are added into virtual genome protein
design database which could has potential important
applications, such as engineering new proteins for
medical therapy, designing new pharmaceuticals,
assigning functions to the dozens of new genes being
sequenced every day, understanding protein evolution
etc.
Genome@home is a very exciting basic science project
with its study results of potential practical
application significance.
http://www.di.com/AppNotes/ForceVol/FVMain.html
Reviewed by: Osman Kabir
ÝÝÝÝÝÝÝ Applications of Volume Imaging
The web space belongs to Digital Instruments and Veeco
Metrology group. Digital Instruments was co founded by
Dr. Virgil Elings and Dr. John (Gus) Gurley in 1987.
The article explains the physics and application of a
technique called, "Force Volume Imaging." It is based
on the phenomenon that any small particle that
approaches a surface experiences as a reaction a force
before and after that particle makes contact.
Measurements are carried out using an Atomic Force
Microscope (AFM).The data is essentially stored as an
array of force curves over an entire area since most
are not homogeneous surfaces. Measurements of these
forces reveals electrostatic, chemical and magnetic
properties ! of these surfaces. This technique also
allows one to record a topographic image with minimal
damage to the surface. It is believed that this
technique will become the standard for studying
nanoscale forces and interactions.
The article is well organized and does a fair job in
explaining the physicsð behind the procedure and its
application albeit it does use technical lingo, hence
some background knowledge will be required.
http://doegenomestolife.org/
Reviewed by: Zheng Li
This is the web page of U.S. Department of Energy
Genome to Life (GTL) program.
GTL is a program proposed by Department of Energy to
achieve the far- reaching of all the biological goals:
a fundamental, comprehensive, and systematic
understanding of life. In order to achieve this
ambitious goal, the DOE offices of Biological and
Environmental Research and Advanced Scientific
Computing Research have formed a strategic alliance to
meet this grand challenge.
The GTL is a ten-year program.! The plan is to use DNA
sequences from microbes and higher organisms,
including humans, as starting points for
systematically tackling questions about the essential
processes of living systems. Eventually, the program
will move beyond the DNA sequences. It will use
advanced technologies and computational tools and
resources to identify and understand the underlying
mechanisms that enable organisms to develop, survive,
carry out their normal functions, and reproduce under
various environmental conditions.
Microbial Cell Project (MCP), a GLT-related program,
has also been proposed by DOE. MCP takes a
whole-genome approach to understand the function and
regulation of all genes for a single living system and
the pathways in which the protein products interact.
With both GTL and the MCP programs involved in the
collection, integration, and dissemination of diverse
data and the development of appropriate tools, the
researches will eventually contribute to the shifting
of biology from current level of a basically
qualitative science to a more quantitative science.
DOE hopes that the ultimate applications of the
results obtained from these programs will help to
fulfill its broad missions in energy, environmental
remediation, and protection of human health.
Although this web page is for the introduction of
DOE's program, Genome to Life, I enjoyed browsing it
and its related links very much. It has helped me to
better unde! rstand what computational biology and
computer science can do in advancing our knowledge and
understanding of life.
http://www.the- scientist.com/yr2001/oct/prof_011015.html
Reviewed by: Kit-yu Cheng
ÝÝÝÝÝÝÝ Training for the Bioinformatics Boon
Because of the explosion in genomic and proteomics
research, those who have expertise in bioinformatics
are really in high demand.ð Researchers spend more and
more time using computer as their tools.ð A $10
million program has been created to help institutions
and scientists build their bioinformatics.ð Millions
have poured in computer-assisted research as well.
Many universities start to offer short courses to help
scientists who want to deepen their expertise.
Three years ago, the concept of creating a central
online warehouse of genetic maps and data stored on
supercomputers and made freely available on the World
Wide Web was broug! ht forward by Eric Lander, a
genetics scientist and Vincent Cerf, the pioneer of
Worldwide Web.ð In the past three years, the
replication of data on the Web has exceeded anyone's
ability to centralize and streamline it.ð Institutions
are looking for computer specialists who can build
links between databases and find new ways to compare
data.ð To help with these issues, a special interest
group of the American Society for Information Science
and Technology is under development.ð Scientists with
expertise in both biology and computation are sought
after.ð Universities such as University of Pittsburgh
and Duke University are offering classes to people who
are interested in seeking a career in bioinformatics.
It appears universities are very responsive to what
the world is in need of.
http://www.the- scientist.com/yr2001/nov/research2_011126.html
Reviewed by: Ma Da
ÝÝÝÝÝÝÝ Saving Lives Past the Emergency Room
This article introduces some recent studies on inflammatory molecules
attempting to reduce trauma deaths by using knowledge and techniques of
human genome research.
The body's system failure, also known as the multi-organ dysfunction
Syndrome is the main reason that causes trauma patients death in the emergency
room. For scientists, the reason for organ failure is unknown, but the order of
the failure always follows in the same way. The blood supply goes through
the lung and blood-borne bacteria from infection or any inflammatory substances
the body releases against infection also pass through here. Inflammatory
reaction in the lung makes gas exchange very di! fficult, and then a series failure will
follow. Therefore, to understand the inflammation is the key of all. A study on
this puzzle based human genome research was launched through a cooperation
of a large number of institutions and scientists from last October.
Many attempts for solving the problem have been made in the past but
The progress was very limited. One reason is that the research only focused
on each individual inflammatory molecule, but the body's complex interplay was
ignored by the single-factor approach. Today, the human genome project can help
researchers study and compare the complex interactions among genes.
There are promoters and switches in the genome that turn the genes on and off.
Those promoters are often over 1,000 base pairs long. There are a large
number of DNA-binding pr! oteins that read signals, which bind or detach from the
promoter. Therefore we have a lot of switches that interact each other. The
patterns for distinguishing good or bad response can be developed through the
Genomics way.
Though progresses have been made in this study, technology and
Techniques such as complex mathematical models and computers are still needed for
complex systems research. In a positive view, this may be a good news for those
computer majors sitting in Bioinformatics classroom.
Link: http://www.ai.mit.edu/projects/medical- vision/surgery/surgical_navigation.html
Reviewed by: Qi Chen
ÝÝÝÝÝÝÝ Image Guided Surgery
This web page belongs to the Computer Vision Group of the MIT
Artificial Intelligence Lab. It describes a project on Image Guided Surgery that
is collaboration between this group and Brigham and Women's Surgical
planning Laboratory. Parts of the project are developing tools, which will
enable surgeons to visualize internal structures through an automated overlay
of 3D reconstructions of internal anatomy on top of live video views of a
patient.
These tools developed by this group have been successfully used in
neurosurgery.ð The first step of applying of these tools in surgery is
construction of 3D Models of a patient's brain.ð Using automated
techniques and semi- automated techniques, the segmentation of the anatomical
structures that appear in an internal scan such as MR and CT is performed.ð A! fter
segmentation, these MR or CT images can be directly used for surface
registration or for 3D visualization.ð Then, this group uses surface
rendering techniques to display the segmented MRI structures.ð This
rendering process removes hidden portions of the surface, and allows
glimpses into internal structures.ð In the following step, the
coordinates of points on the patient's skin are obtained in order to register the
patient to the segmented MR skin.ð The following automatic registration
process performs a two-step optimization to correlate the MRI
coordinate frame to the operating room frame.ð Using the image tools, the MRI skin
can be removed, which will allow the surgeon have x-ray vision to see where
the internal structures are located.ð These tools also allow the tracking