BioInformatics Reviewed Links

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Link: http://www-cxro.lbl.gov/microscopy/
 
Reviewed by: Changyou Yu
 
ÝÝÝÝÝÝÝ Soft X-ray Microscopy Applying to Biology
 
This web site belongs to The Center for X-Ray Optics (CXRO) at the 
Lawrence Berkeley National Laboratory (LBNL), it describes a new high resolution 
soft x-ray microscope (XM-1) built by the Center that can be used in a 
variety of biological applications including mapping the morphological variation 
of genetically altered sperm cells.
 
 
XM-1 provides transmission images from samples up to ten microns thick 
and has a spatial resolution of 43 nm, as measured with a knife edge 
object, using the 10% to 90% intensities. It uses bending magnet radiation from 
the Advanced Light Source, a third generation s!
ynchrotron facility at the
Berkeley National Laboratory. A condenser zone plate is used to 
Illuminate the sample and acts as a linear monochromator. The radiation 
transmitted through the sample is then enlarged by an objective zone lens plate on 
an x-ray CCD camera. Sample positions and focus in the x-ray microscope 
sample stage are mutually indexed to the stage of a visible light microscope, 
which is used to investigate, locate, and align interesting parts of the 
sample.
 
Especially new with XM-1 are the full incorporation of state-of-the-art
visible light microscopes and its ease of operation guaranteed by 
precision mechanics and computer control.
 
 
X-ray microscopy primaril!
y uses a natural contrast mechanism for 
biological specimen in water. In the extensive study conducted by Dr. Greg 
Denbeaux's research group at this center, XM-1 was successfully used to map the 
life cycle of malaria parasites (Plasmodium falciparum) in intact human red 
blood cells. Abnormalities in the parasites development with protease 
inhibitor treatments and membrane protein deficiencies have been investigated and 
were linked to parasite mortality. New structures in green alga 
(Chlamydomonas), uniquely visible with soft x-rays, have been confirmed and analyzed in
unfixed samples.





http://www.pharmabiotech.ch/reports/proteomics/
 
Reviewed by: Xiaodong (Sheldon) ZouÝ 
 
ÝÝÝÝÝÝÝÝÝÝÝÝ Proteomic Technology
 
ÝÝÝÝÝ This link describes and evaluates the proteomic
technologies that will play an important role in drug
discovery, molecular diagnostics and practice of
medicine in the post-genomic era - the first decade of
the 21st century. Most commonly used technologies are
2-D gel electrophoresis for protein separation and
analysis of proteins by mass spectrometry.
Microanalytical protein characterization with
m!
ultidimentional liquid chromatography/mass
spectrometry improves the throughput and reliability
of peptide mapping. Matrix-Assisted Laser Desorption
Mass Spectrometry (MALDI-MS) has become a widely used
method for determination of biomolecules including
peptides, proteins. Functional proteomics technologies
include yeast two-hybrid system for studying protein-
protein interactions. Establishing a proteomics
platform in the industrial setting initially requires
implementation of a series of robotic systems to allow
a high-throughput approach for analysis and
identification of differences observed on 2-D
electrophoresis gels. Protein chips are also proving
to be useful. Proteomic technologies are now being
integrated into the drug discovery process as
complimentary to genomic approaches. Toxicoproteomics,
i.e. the evaluat!
ion of protein expression for
understanding of toxic events, is an important
application of proteomics in preclincial drug safety.
Use of bioinformatics is essential for analyzing the
massive amount of data generated from both genomics
and proteomics.
ÝÝÝ Proteomics is providing a better understanding of
pathomechanisms of human diseases. Analysis of
different levels of gene expression in healthy and
diseased tissues by proteomic approaches is as
important as the detection of mutations and
polymorphisms at the genomic level and may be of more
value in designing a rational therapy. Protein
distribution / characterization in body tissues and
fluids, in health as well as in disease, is the basis
of the use of proteomic technologies for molecular
diagnostics. Proteomics will play an im!
portant role in
medicine of the future which will be personalized and
will combine diagnostics with therapeutics.
The number of companies involved in proteomics has
increased remarkably during the past few years. More
than 215 companies have been identified to be involved
in proteomics and 165 of these are profiled in the
report. The markets for proteomic technologies are
difficult to estimate as they are not distinct but
overlap with those of genomics, gene expression, high
throughput screening, drug discovery and molecular
diagnostics.
ÝÝÝÝÝ Collectively, the current value of markets for
proteomic technologies is about $2 billion and is
expected to increase to $6 billion by the year 2005
and $10 billion by the year 2010. 2-D gel
electrophoresis is the largest single segment worth!

about $600 million. The largest expansion will be in
bioinformatics and protein biochip technologies.





Link: http://www.hospitalmanagement.net/index.html
 
Reviewed by: Xiaodong (Sheldon) ZouÝ 
 
ÝÝÝÝÝÝÝÝÝÝÝ Robotic-assisted surgery
 
ÝÝ This web site detailedly introduces the history,
current application, development and future of
Robotic-assisted surgery. Robots provide a steady and
predicable interface with the patient that may be
scaled down in size, allowing for smaller incisions
and shorter lengths of stay. Proponents of robotics
suggest that, in time, these technologies will
leverage the advantages of the human mind (the
surgic!
al and anatomical knowledge of the physician),
and technologically correct the deficiencies of the
human hand by miniaturizing its function in the form
of robots that are more capable of making small,
precise movements. The result will be less invasive
surgery, less trauma to tissues, quicker recovery
times and more cost-effective surgical interventions.
 
ÝÝ One of the pioneering efforts in the development of
robotic-assisted surgery has been a joint
collaboration in the United States between the
National Aeronautics and Space Administration (NASA),
the Jet Propulsion Laboratory and private interest,
MicroDexterity Systems. As part of the Jet Propulsion
Laboratory's Telerobotics Program, these interests
formed the Robot Assisted MicroSurge!
ry (RAMS) project
in the early 1990s. The purpose of this programme was
to build the technology and workstations necessary to
improve robotic dexterity, enabling microsurgical
procedures to advance to the point that they could be
applied to procedures of the eyes, ear, nose, throat,
face, hand, and brain.
ÝÝÝ RAMS is designed to permit telemanipulation of the
robotic devices, and has a share' function in which
surgeons can interactively operate the robot with
other surgeons participating in the intervention.
Other advances of RAMS include features that may
improve patients' clinical outcomes who are treated by
less experienced surgeons. This is accomplished by
RAMS features that improve surgeons positioning and
movements that are susceptible to myoclonic tremor.
This unsteadin!
ess of the human hand prevents some
surgeons from accurately practising fine-motor
manoeuvers during an operation.
ÝÝÝ By 1994, the RAMS project had successfully
developed a robotic arm measuring 2.5cm in diameter
and 25cm in length that was capable of six degrees of
motion. The following year a system of kinematics and
high-level control was added that included an
electronic safety system. This technology was
successfully tested at the Cleveland Clinic Foundation
in the late 1990s during a simulated eye microsurgery.
Subsequent work produced a dual-arm telerobotic
microsurgery workstation that was capable of
microsurgical suturing.
ÝÝ The first coronary artery bypass surgery was
performed in Germany in 1998 using a system called
Intuitiv!
e. During the procedure, rather than
splitting the sternum and opening the chest cavity as
is usually done during bypass surgery, the surgeons
made only small incisions less than one centimeter
wide. Through these incisions were placed Intuitive's
three robotic arms, one holding a camera and the other
two holding surgical instruments. During the operation
the surgeon had a full image of the heart's anatomy on
a television monitor and was able to successfully
complete the bypass.
ÝÝ This protocol of robotic heart surgery
characterized by small incisions and the use of
cameras and robotic arms is now being applied to more
areas of cardiovascular surgery. It is now becoming
more common for heart valve replacements to be
performed with robotic-assistance and the early
results are !
noteworthy. Because the procedures are
less invasive, patients are less likely to have
bleeding complications and hospitals and health plans
less likely to bear the financial burden of these
complications. Patients report less post-operative
pain and hospital lengths of stay have also been
reduced.
ÝÝ As the population ages, hip replacement surgery is
becoming more common with hundreds of thousands of
replacements performed each year. Robotics is
providing a new tool to surgeons in both surgical
planning and assisting during the actual surgical
procedure.
ÝÝ In the planning phase of hip replacement surgery,
x-ray computed tomography is used to produce an image
of the patient's femur. This allows the physician to
use the three-dimension image o!
f the femur shape to
select the appropriate hip replacement joint from a
catalogue. This spatial information of the patient's
unique femur shape is then provided to the robot so
that the initial robotic drilling is placed precisely
where it is needed.
ÝÝ At the Ames Research Center in Mountain View,
California, NASA scientists are developing a robotic
device that will have the capability to learn the
characteristics of the human brain using neural net
software. The robot, with a small probe, has the
ability to enter the skull and feel the surface of the
brain structure using a pressure sensor. Because brain
tumors have different densities than normal brain
tissue, the robot is designed to assist surgeons in
locating cancerous areas and tumor boundaries. The
learning capability of t!
he probe also allows for it to
distinguish between brain and arterial tissue. Thus,
when it reaches the surface of an artery it will stop
before penetrating the vessel and causing a bleed, a
common complication of brain surgery.Drawing upon
other advantages of robotics, the Ames Research Center
robot is a fraction of the size of the probes normally
used during brain surgery (0.2 inches in diameter).
This reduces the risk of brain injury and surgical
complications that can leave patients debilitated and
drive up medical expenses. This technology also has
the capability of using the probe to detect
differences in temperature, acidity, and presence of
chemicals, making its successful application in other
clinical domains likely.
Ý As the cost of robotics decreases and production and
c!
ompetition increase, the use of robotic-assisted
surgeries will grow. This has the potential to
decrease surgical complication rates and the hospital
costs associated with them. Patients receiving the
less invasive robotic-assisted surgeries are likely to
have less pain and to therefore report higher
satisfaction with their treatment, the hospital
treating them, and their health plan.





Link: http://folding.stanford.edu
 
Reviwed by: Tawhidul ChowdhuryÝ 
 
ÝÝÝÝÝÝÝ Folding@home
 
The web page folding.stanford discusses how Dr. Pandeís group at 
Stanford University of chemistry department has developed a new way to simulate
protein folding on a very large number of home computers. This project 
is dispersed over the internet. The owners of these computers volunteer 
unused computer cycles to work out the vast number of folding permutations in
parallel. A central server coordinates the assignment of work and 
harvesting results.
 
Recent discoveries emphasize the fact that it is very important to
understand the process of protein folding because protein folding and 
errors in folding (mis-folding) are found to be related to a large number of
diseases suc!
h as Alzheimerís disease, Cystic fibrosis, Mad Cow disease. 
Even many cancers are believed to be resulted from protein mis-folding.
 
The key property of proteins is to perform a variety of biochemical
functions. In order to carryout their functions, proteins take on a
particular shape, known as ìfoldî. First, proteins assemble themselves, 
and then they perform their functionalites. This self assembly is called
folding. They can fold as fast as of a millionth of a second.Ý Even 
though the protein folding is very fast on a personís timescale, it is 
remarkably long for computers to simulate. To solve theÝ protein folding problem
Pandeís group divided the work in a multiple process. They have used
distributed computing techniques andÝ supercluster of thousands of 
computer processors to study the protein folding. They are simulating a total 
folding time by using the software called ìFolding@home 2.0î.
 
Anybody who wants to participate in this project need to download the
software ìFolding@home 2.0î. It is a client software comes with a 
screen saver functionality. When this client software is installed, the 
console runs in the background and it has graphical window that allows the user 
to see the protein being simulated. The screen saver runs just like any 
other screen saver except runs the calculation in the background. The 
clientís computer will automatically upload the results to server each time it 
will finish its work unit, and will download a new job sporadically when the
clientís computer wi!
ll connect to the internet.





Link: http://www.techreview.com/web/cameron/cameron060401.asp
 
Reviewed by: Changyou Yu
 
ÝÝÝÝÝÝÝ Living Array Speeds Gene Research
 
 
This article describes emerging technology using microarrays of living 
cells and its impact on drug development and biomedical research. The 
technique is being developed by a research team at the Whitehead Institute for 
Biomedical Research in Cambridge.
 
 
Dr. David Sabatini and his team first printed an array of about 200 DNA
samples, each corresponding to a particular gene, onto a glass slide. 
The slide was then placed in a culture of mammalian cells, which adhered to 
and covered it. The DNA was absorbed by the contacting cells. By dividing, 
the !
group formed distinct cell clusters, each manufacturing the particular
protein encoded in the absorbed DNA. The remaining cells surrounded 
these clusters and acted as controls. As a result, a living array of gene
expression is created, giving researchers a unique test bed in which to
experiment with gene and protein behavior. Next, the team prepared a 
slide with an array of 200 genes, they observed that certain genes killed the
cells, others caused the cells to stick together, and others activated
certain signaling pathways in the cells. This implies that cell 
microarrays could contain up to 10,000 cell clusters each should be possible.
 
 
This technique possesses many advantages over current techniques. By 
using cell microarray, the desired function A!
ND the side effects of the 
target drug can be revealed in a single day instead of months, which breaks a 
major bottleneck of current drug discovery. It also provides a nature 
environment for unstable proteins, especially for membrane protein which can't 
exist apart from the cell membrane. By printing the contents of a DNA library 
onto a series of cell microarrays, a researcher could hold in one hand a set 
of slides on which the entire human genome is being expressed thus ease 
the cell microarrays containing up to 10,000 cell clusters each should be
possible.
 
 
Iinformatics technology, which stores, manipulates, analyzes and 
visualizes information, has been playing an increasing role in biological and 
medial research and applications inc!
luding drug design. Microarray, which has 
the capability for massive parallel analysis, is one example. Though no 
single microarray technology can provide all the answers, as the arsenal of
microarray techniques increases, we're closer to unravel the secrets of 
the genome with one gene at a time.





Link: http://www.stanford.edu/dept/news/pr/01/shenoy1128.html
 
Reviewed by: Zheng Li
 
 
ÝÝÝÝÝÝÝ Bioengineering
 
This article reports the news that Stanford engineer
Krishna Shenoy and a group of researchers at Caltech
have shown in a recent study that electrical signals
from the parietal reach region (PRR), the part of the
brain responsible for planning arm movements, can be
used to control the movement of a cursor on a computer
screen. Using signals from an electrode implanted in
the PRR of a monkey, the researchers were able to
mimic the animal arm movements with the movements of a
cursor called a prosthetic icon. Eventually, the
monkey was able to control the icon by thought alone.
 
Previous studies have shown that the motor neurons
responsible for moving an arm can be used to control
robotic arms, com!
puter cursors or other devices. But
this study is the first to show that the cells
responsible for planning those movements can do the
same. 
 
The advantage of using planning cells is that they
encode a simpler set of parameters than motor cells
do. Whereas motor cells generate complex signals that
control the three-dimensional path of an arm as it
moves toward its target, planning cells encode
primarily two parameters: where and when to move.
Systems based on planning cells may be able to use
fewer brain cells, and thus simpler electronics, than
those based on motor cells. Planning cells are also
less likely than motor cells to change function over
the course of prolonged paralysis. 
 
The study is a signi!
ficant advance in the growing
field of neural prosthetics implanted devices that
eventually may help severely paralyzed patients regain
some of their lost functions. However, the current
system is still a long way from helping people who are
paralyzed. Three major challenges remain: developing a
better understanding of the brain, especially its
ability to adapt to injury and other changes;
designing electrodes that can function in the brain
for extended periods of time; and engineering an
overall system that is reliable, efficient and
compact. 





http://robotics.eecs.berkeley.edu/~mcenk/medical/
 
Reviewed by: Lu Tang 
 
 
ÝÝÝÝÝÝÝ Medical Robotics
 
This website describes a joint project between the
University of California at Berkeley, Endorobotics
Corporation, and the University of California at San
Francisco. The goal of this project is to develop
improved tools for endoscopic manipulation, sensing,
and human interfaces for a teleoperative surgical
workstation. Surgeon can use this tools for Minimally
Invasive Surgery(MIS). MIS is a revolutionary approach
in surgery. The operation is performed with
instruments and viewing equipment inserted into the
body. In this article, it explains this project in
detail from six parts: telesurgical workstation,
virtual reality training simulator, some manipulators,
human interfaces, bilateral teleoperation!
 system
design and tactile sensing/display.
 
The complete telesurgical workstation will incorporate
two robotic manipulators with dextrous manipulation
and tactile sensing capabilities. The goal is to
design a system which is both highly dextrous and
intuitive to use, allowing complex surgical operations
to be performed with minimally invasive techniques.
 
The second application of this project is to develop a
virtual reality simulator for MIS. In the context of
this application, they develop real-time finite
element models for soft tissue behavior. They
incorporate these models in the VR simulations to
generate a realistic environment for training. Then,
researchers develop the visual and haptic displays
!
that can be used as the human interface for high
fidelity feedback. 
 
Manipulators: Endo-platform, designed by Jeff
Wendlandt, allows finer positioning control for
endoscopic tools. The researchers of this group also
design multi-degree-of-freedom end effectors with an
appropriate surgeon-machine interface to build
laparoscopic manipulators that are more versatile and
dextrous. Their laparoscopic manipulator design is
composed of two stages. The first stage is for gross
positioning of the end effector. The second stage is
the 3 DOF millirobot. It has a 2DOF wrist and a
gripper, driven by hydraulic actuators.
 
Human interface is a crucial part of telesurgical
workstation. It is important to provide the surgeon

with an intuitive interface to control the manipulator

and receive feedback, restoring the dexterity and
sensation of open surgery. The human interfaces
include surgical master, the prototype glove-like
device, and visual display.
 
The telesurgical workstation will be a teleoperation
system. In this project, they design model-based
algorithms for bilateral master-slave teleoperation
with force feedback. They use force and torque
measurements from the manipulators as well as position
information in controlling the robot.
 
Tactile sensation is extremely important in open
surgery to allow the surgeon to feel structures
embedded in tissue. Teletaction allows sensing and
display of tactile information to the surgeon.!
 In
teletaction, a tactile sensor array can be used to
sense contact properties remotely. To provide local
shape information, an array of force generators can
create a pressure distribution on a finger tip,
synthesizing an approximation to a true contact. In
this project, the researchers design a variety of
small tactile sensors intended to be mounted on a
laparoscopic manipulator. The prototype 5x5 pneumatic
display designed by Michael Cohn has a maximum force
range of 0.3 N per element, a 3 dB point of 8 Hz, and
3 bits of force resolution. In order to construct an
effective tactile feedback device, they design a
bidigital mock tactile display which can be use to
determine how well people can feel features embedded
inside soft media.





Link: http://www.nytimes.com/2001/12/20/science/20QUAN.html
 
Reviewed by: Mohammed Kuddus
 
ÝÝÝÝÝÝÝ Efforts to Transform Computers Reach Milestone
 
The article relates the latest efforts to push computers beyond what 
they are currently capable of by using quantum mechanics. Bioinformatics 
involves the use of high-powered computers to analyze life sciences data, while
quantum computing explores ways to overcome limitations on component
miniaturization. Bioinformatics supports the design and analysis of
algorithms for sequencing the genome, reconstruction of evolutionary 
trees and genome likeness, protein folding and problems including learning of
meaning and predicting properties of genome data are in focus. On the 
other hand, quantum computation deals with the design and analysis of quantum
algorithms that demonstrably outperform classical methods for the!
 same
problem. Developing the software and technology for this requires a 
thorough knowledge of algorithms, mathematics, probability theory, information
theory, statistical methods and preferably quantum mechanics. Quantum
mechanics has long been the focus of researcher's interest in
small-molecules because this allows large macromolecules to be 
examined. The opportunities to exploit these new technologies in computational 
biology and bioinformatics to provide novel insights into macromolecules are of
tremendous value. The quantum bioinformatics database is a significant
project generating and exploiting
experimental data in complex, high-throughput, multidisciplinary 
research programs and are both major challenges in target and drug-discovery
processes.
 
Dr. Issac L. Chung and Dr. P!
eter Shor are working on quantum computing
techniques for breaking otherwise considered unbreakable codes. Recently,
scientists at the IBM Almaden Research Center in San Jose, Calif. 
Announced that they have performed a simple calculation, factoring the number 15,
with a quantum computer. In the quantum computing experiment scientists 
made their calculations manipulating single atoms, thus, the calculationís 
steps could be carried out simultaneously. Dr. Peter Shor, the scientists at 
A T & T laboratories, who proved the theoretical possibility of quantum 
computing, was impressed with this new development. Dr. Issac L. Chung, who led 
the researchers, from IBM and Stanford University, in this experiment used 
a molecule consisting primarily of fluorine and carbon atoms. These atoms 
can point up or down, indicating 1 or 0, the two symbols of binary 
a!
rithmetic.
 
Furthermore, quantum mechanics permits an atom to point both up and 
down, known as 1 and 0, at the same time. Therefore, two atoms can register 
for quantities (00, 01, 10, 11) at the same time. Three atoms can hold 
eight numbers and four atoms can hold 16. In the IBM experiment, they used 
seven atoms with the capability of registering 128 numbers simultaneously. 
These atoms in a vial of liquid were placed inside a machine called a nucleus
magnetic resonance spectrometer, similar to an MRI. To delicately flip 
the atoms back and forth between 1 and 0, scientists had to bombard the
molecules with a precise sequence of electromagnetic pulses. In 
conclusion, because factoring large numbers requires calculations that require
tremendous amount of time- factoring a 310 digit numbers with 292 computers would take hundreds of millions of years- Cryptographers feel that two long prime numbers multiplied together would yield an unbreakable code. Not so,if quantum computing continues advancing.   



Links:Ý http://www.nytimes.com/2001/12/20/science/20QUAN.htmlÝÝÝÝÝÝÝ http://www.qubit.comÝÝÝÝÝÝÝ http://squint.stanford.edu/ Reviewed by: Changyou Yu Quantum computing is a fundamentally new mode of information processing that can be performed only by harnessing physical phenomena unique to quantum mechanics (especially quantum interference).  Conventional Turing machine (silicon) computers with Relational Databases cannot cross reference in non polynomial (NP) time. Quantum computers are being built using NMR (at Stanford, MIT, etc.)and Grovers Algorithm will solve NP complete database searches, impossible today. This would allowdiseases to be understood at the mole!
cular level using a technique similar to genetic interferometry. Quantum genomic computing (QGC) could also allow humans to live long lives by allowing predictive medicine to preventdisease. A DNA monitor/QGC could resolve a genetic disease in real time. Thus preemptive molecular treatments become possible. This early warning system is based on DNA correlations to existing DNA databases which now grow exponentially, Genbank, Human Genome. If expanded to much larger scale, quantum computers could also possibly take the entire human genome as an input and decode it, which is impossible in the conventional computing.   



Link: http://www.stanfordhospital.com/newsEvents/newsReleases/122001/givenCamera.html  Reviewed by: Gang Pan ÝÝÝÝThis article reports a new device, called the m2A capsule to detectbleeding in the patientís small intestine without invasive surgery.Researchers at Stanford tested this device which was developed byIsreal-based Given Imaging, Ltd. ÝÝ The procedure for testing this device has been summarized as follows: After fasting for an eight hour period, the patient swallows themicro-camera, which is equipped with a!
 sensor, battery pack, and recorder that is attached to a belt worn by the patient. Leland McGraw, the second test-patient stated that there was no discomfort swallowing the capsule. The capsuleís progress through the intestine is monitored via the receiver.Images are captured and recorded by the sensor. After two to four hours, liquid and solid food can be consumed. Eight hours after the procedure, the patient is free to remove the belt pack. The following day, images aredownloaded to a computer workstation and the location of the problem isidentified. The m2A capsule is excreted by the patient. ÝÝ The non-invasive manner in which the capsule works is its key advantage above all other approaches available today. This new device does indeedprovide a unique i!
nexpensive and innovative way to view inside the small intestine.



 Link: http://www.eurekalert.org/pub_releases/2001-11/cshl-ncp112801.php Reviewed by: Xiao Lin  New computer program detects overlooked gene segments This article describes research in thebioinformatics program at Cold Spring HarborLaboratory.Ý Scientists there have now developed a computer program thatis ÝÝÝÝ good at finding first segments and "on"switches of genes. The program called "First ExonFinder" or "FirstEF"was developed by Michael Zhangand his colleagues. It is tailored toward detectingthese features in the human genome sequence, but itwill also be useful for annotating other mammaliangenomes. Zhang explains that the "FirstEF" is the first programthat can readily and accurately detect a class of genesegments that has previously been extraordinarilydifficult to find and it's like looking for buriedtreasure.The gene segments occur at the very beginningof genes, and are called &qu!
ot;non-coding first exons.Because they do not encode protein segments,non-coding first exons are undetectable byconventional computer programs that rely on proteincoding patterns found in DNA. Instead, FirstEF recognizes five other DNA"signatures" that betray the presence and location offirst exons in genes. The biological basis of some ofthese telltale genetic signatures is unknown.But theyare real, and perhaps someday biology will explain whythey are there. One such signature is the frequencywith which two building blocks of DNA, C and G, occurnext to each other. Despite the fact that they do notencode protein, non-coding !
first exons are essentialcomponents of gene structure and function.Consequently, the ability to detect non-coding firstexons is crucial for scientists wishing to study genesfor a wide variety of biological and biomedicalapplications. Zhang and his colleagues used FirstEF to analyze theentire human genome later on. They identified some68,000 first exons. This result does not necessarilymean that there are 68,000 or so human genes, becausea single gene can use alternative first exons.Moreover, the total number of genes in an organism'sgenome depends on other, subtle definitions of whatconstitutes a gene. Nevertheless, Zhang believes the!
reare 50 to 60,000 human genes and that previousestimates of 30 to 40,000 human genes are too low. Because of finding the promoters of genes is asignificant bottleneck in current DNA research andgene promoters and first exons are related, theFirstEF is a crucial discovery which kills two birdsin one stone. 



  Link: http://www.fwradiology.com/bdcnews2.htm Reviewed by: Mohammed Kuddus Future Developments in Breast Cancer Detection This website describes the developments and concerns regarding breastcancer detection. Breast cancer is the most common cancer in American women and is responsible for one of every three cancer diagnoses in the United States. The best test currently available for detection is mammography. The first article is concerned with two developing breast cancer detectiontechnologies, digital mammography and computer-aide!
d diagnosis, which will make mammography more accurate and improve early stage detection. Digital mammography is a technique that relies on computers to help generatemammogram images instead of using X-ray film, this allows for greatercontrol of the image and doctors can see the breast in a variety of ways and focus on particular areas. Computer-aided diagnosis is a technology in which a mammogram is scanned by a computer that is programmed to identify theshapes of breast lumps or patterns of calcium deposits on the mammogram that are often encountered with breast cancer. This article describes the success of a walking event, Making Stridesagainst Breast Cancer that raises not only money but, also, !
awareness in the fight against breast cancer, in Fort Wayne, Indiana, October 17 beginning and ending in Headwaters Park. The event originated in Massachusetts in 1993 and by 1997 had grown to 20 sites in 13 states involving over 200,000participants and raising over $20 million nationwide. The sponsors for this event are Fort Wayne Radiology and Parkview Memorial Hospital, WANE-TV, and Newschannel 15. All the money raised by Making Strides Against Breast Cancer will be used for breast cancer with 40% going to the National AmericanCancer Societyís research program. This article reports the Vera Bradly Classic golf and tennis event, founded by Patricia Miller and Barbara Baekgaard, attended by 364 peo!
ple who joined to fight breast cancer. The events raised $250,000, which surpassed by$25,000 Vera Bradleyís goal, making the grand total $830,000. This article also reports new weapons such as the new drugs, Taxol,Taxotere, Xeloda, and old drugs such as Tamoxifen, as well as, new insights and new treatments that are being used in the fight against breast cancer. Taxol and Taxotere are powerful new chemotherapy agents that when combined with older agents, Cytoxan and Adriamycin, lowers the death rate in women. Xeloda is a new oral drug that specifically targets cancer cells. Tamoxifen, an old antiestrogen drug, is now being used on women with high risks for breast cancer to prevent them from developi!
ng breast cancer. New insights in to the basic biology of breast cancer reveals HER-2 a molecule present on the surface of breast cancer cells and now scientists are testing the use of monoclonal antibodies to HER-2. A new type of treatment, tumor angiogenesis inhibition, has shown this to be a potent inhibitor of cancer growth and also capable of destroying established cancers. In this article advises women in preparing for mammograms to save time and remove needless anxiety. First it suggests getting in touch with any other facility a patient might have gotten a mammogram, it lists personalinformation she should record to present to the doctor, suggests the patient wear a two piece outfit and not !
use deodorant or necklaces. The last article gives pre-registration information for Fort Wayneís Radiology Team, which will have a walking event on October 17. This website gives hope to a future where woman can have breast cancerdetected early, thus, sparing their lives. This future will be a result of research combined with charity organization 



 Link: http://www.neci.nj.nec.com/homepages/eric/seq.ps Reviewed by: Christopher Conway DNA Sequences Useful for Computation  This paper discusses strategies for choosing a data encoding for use in DNA computing. Taking a naive approach to setting up a computation with DNA, one may assume it is sufficient to encode data in strands of DNA longÝ enough to guarantee uniqueness. Given four nucleotides (A, T, C and G), one might assume a sequence of length k would!
 have the potential of encoding 4^k values using a common-sense base-4 encoding. Unfortunately, the mechanics of DNA computation prevent such an encoding from being useful. In a common DNA computation, a bit of data may be encoded as a sequence X and many bits of data may beÝ arranged linearly in a molecule. If there exists a sufficiently long subsequence of X that is reproduced elsewhere in the molecule, or in another molecule that does not contain X, it is possible for the complement of X to hybridize with that subsequence, frustrating attempts to extract only strands containing X. Furthermore, if there is a long subsequence of X such that the subsequence's c!
omplement also appears, data molecules may begin to hybridize with themselves. The longer the subsequences, the more likely these errors are to occur. Thus, it is desirable to minimize the length of these potentially repeated subsequences, while at the same time maximizing the number of potential encodings. The authors attempt to derive some constraints for choosing encoding schemes such that there are no repeated subsequences (or subsequence complements) longer than a given length k. They suggest an encoding scheme consisting of a set of sequences of length k separated by spacer sequences of k A's (i.e., k copies of the nucleotide adenine). A number of constraints are placed o!
n the choice of valid encoding sequences. The authors conclude that the maximum size set satisfying all of these constraints for k=2m+1 or k=2m, k>=5, is 3 x 4^(k-2) + 5 x 4^(k-4) - 2 x 4^(m-1). This implies there are only 208 potential satisfactory sequences for k=5, 816 for k=6 and 3232 for k=7, far fewer values than would be attainable using a simple base-4 encoding. 



http://www.neci.nj.nec.com/homepages/eric/dpr.ps Reviewed by: Christopher Conway ÝÝÝÝÝÝÝ Dynamic Programming using DNA  The author discusses the merits of using DNA computation to implementdynamic programming algorithms. Instead of using a brute force approach, as Adleman implemented in his solution to the traveling salesman problem, the data density of DNA is used to surmount the memory limitations faced by conventional computers in approaching large dynamic programmingproblems, such as graph connectivity. The graph connectivity problem is stated thusly: given a graph, G = (V,E), and vertices S and T, determine if there is a path from S to T in G. Ifevery vertex has at most m neighbors and if you can create a biochemical mechanism to compute the functions f_1, ... , f_m, where f_i(V) returnsthe ith neighbor of V, then the problem can be solved using the following procedure:  (1) Start with a solution D containing strands representing thevertex S.  (2) Use PCR to create m copies of D, separated into m vats, D_1,..., D_m. (3) Compute the function f_i in D_i, for i in 1..m.  (4) Pour the resultant solutions back into a single vat. (5) Test for the targetvertex T. If T it is not present in the !
solution, repeat beginning at step 2.The procedure implements a breadth-first search on G. After the firstiteration, the solution contains all of the neighbors of S. After thesecond, it contains all of the vertices of path length 2 from S. Butwhereas a conventional computer can solve the graph connectivity problem using BFS in O(|E|), a DNA computer can solve the problem in O(d), where d = max{ distance(u,v) : u,v in V }. This is because a conventional computer must visit each edge of the graph in series, while the DNA computer visits every edge in each layer of the graph in parallel. The procedure is limited to graphs where |V| < 10^17 and to graphs thatare balanced in the number of edges leadin!
g to each vertex. If a graphcontains some vertices with many more edges leading into them than others, some reachable vertices may become "lost" in the solution, as the strands they generate will be dominated by the more connected vertices.