Articles
Microarrays
on the Spot Year in Review
By Steve Casey
With this final column for Microarrays on the Spot, I felt it would be
important to look back over the year and highlight the tremendous scientific and
medical advancements that have been made in microarrays and pharmacogenomics.
Gene Expression Profiling of Esophageal Cancer Using Laser Capture
Microdissected Samples
By Michelle Chen , Kaho Minoura , Siqun Wang , Tetsuo Noda , Tetsuichiro Muto ,
Yoshio Miki
Clinical biopsy samples of esophageal cancer and surrounding normal cells
were excised by laser capture microdissection and analyzed with DNA microarrays
for global gene expression studies. Genes involved in the keratin biosynthetic
pathway were found to be significantly affected in these squamous cell
carcinomas. Our findings provide a plausible mechanism for the alteration of
keratin synthesis observed in over 95% of hereditary squamous cell carcinomas in
esophageal cancer. This study also demonstrates the feasibility of using a
minimum amount of clinical sample to decipher complex disease and disease
processes at the molecular level.
Discovery of Bone Metastasis Genes by Functional Genomics
By Xin Lu , Yibin Kang
Genomic profiling technology has revolutionized the field of metastasis
research. The authors review the successful application of gene expression
profiling in the discovery of bone metastasis genes in breast cancer. In
addition, the authors describe several methods for the functional validation of
metastasis genes and discuss the potential applications of their research in the
diagnosis and treatment of metastatic cancer.
Can Genetic Algorithms Solve the Problems with Predictive Biology?
By Lukas K. Buehler
An unsolved problem in drug design is the capriciousness of complex systems
and the unpredictability of their future behavior. Genetic algorithms are tools
developed to improve rational drug design through simplification. Yet, such a
strategy avoids rather than solves the problems of complexity.
Corporate Capabilities
Nanostream, Inc.
General Company Description, Chief Chromatographic Techniques Supported,
Markets Served
Dharmacon, Inc.
Dharmacon, a business unit within the Fisher Biosciences group, is the
world's leading provider of reliable, high-quality RNA oligonucleotides, small
interfering RNA (siRNA), and related RNA interference (RNAi) products and
technologies. Using our core expertise in chemistry, biology, bioinformatics,
and production, we have developed industry-leading siRNA design and chemical
modification and delivery technologies for maximizing the efficiency of gene
silencing.
Pierce Biotechnology, Inc.
As a business unit of Fisher Biosciences, Pierce is the world leader of the
supply of products for protein research and for the scale-up to manufacturing
levels (when needed) for scientists and organizations working to increase the
quality of life in health-related areas. We also offer Endogen®-brand ELISA
test kits and reagents that are used to measure the presence of cytokines that
are critical to immune system research. Under the SearchLight® Brand, the
company provides sample-testing services and protein-array products for
multiplex screening of biomarkers.
Sigma-Aldrich Corporation
Sigma-Aldrich was incorporated in 1975 and is based in St. Louis, Missouri.
We are a leading life science and high-technology company. Our biochemical and
organic chemical products and kits are used in scientific and genomic research,
biotechnology, pharmaceutical development, diagnosis of disease, and as key
components in pharmaceutical and other high-technology manufacturing. We have
customers in life science companies, universities, and government institutions,
hospitals and in industry. We operate in 35 countries and offer 90,000 chemicals
and 30,000 equipment products.
Ventana Medical Systems Inc.
Ventana Medical Systems Inc., established the Molecular Discovery Systems
(MDS) division to leverage the company's core business of immunohistochemistry
and in situ hybridization slide processing technology in drug discovery and
research laboratories.
Products
50 µl to 5 ml Membrane-Bottom Filter Plates
The new 96-well and 384-well filter plates from Harvard Apparatus, with their
rigid polypropylene construction, high-strength single or dual filter membranes,
and patent-pending sealing process, bring speed and high throughput to sample
filtration on a microliter to milliliter scale.
ATP-Dependent DNAse
The latest ATP-dependent DNAse from EPICENTRE Biotechnologies selectively
digests linear double-stranded DNA but has no activity on nicked, closed
circular dsDNA or supercoiled DNA. The product is designed to aid in the removal
of bacterial genomic DNA from vector preparations, while avoiding contamination
of DNA fragments.
Automated Petri Dish Filling System
The MEDIAJET automated Petri dish filling system incorporates into a single
unit, features such as a new mechanical dish guidance system, monitored by a set
of sensors throughout the filling process, new intuitive, self-explanatory,
operating software, and a unique 'Agar Spread Function' capability that improves
the efficiency of agar use through automated, homogeneous distribution.
Cardiotoxicity Report Service
ToxScreen Report for Cardiotoxicity, a predictive toxicogenomic service to
assist pharmaceutical and biotechnology companies in assessing heart toxicities
is Gene Logics newest addition to their service offering, expanding upon
currently offered models in hepatotoxicity and allowing both of these toxicities
to be addressed with a single short-term study.
Custom Oligonucleotides
Invitrogen Corporation recently introduced tube-based oligos at the 25nmole
starting synthesis scale. This advance will allow researchers to procure more
than twice the quantity of primers for the same price they were previously
paying in their increasingly complex drug discovery and molecular diagnostic
applications including gene expression studies, biomarker analysis and
functional genomics experiments
Dry Powder Disperser
The Ankersmid PD-10 Dry Powder Disperser draws powders into a vacuum chamber
to be dispersed by high shear forces. Agglomerates are broken down without
damaging fragile particles, allowing gravitational sedimentation to produce
uniform deposition of particles on microscope slides. The PD-10 can be used for
dry, fluffy, dense, hazardous or toxic powders.
EA Data Manager software for the 2400 Series II
CHNS/O Analyzer
This SQL-based software interface can be used with a standard PC to perform a
variety of tasks, including: collection and storage of data; performance of
advanced calculations; recalculation of results; ability to run queries and
generate statistics; creation of reports and archiving of data. In addition, the
new Windows-based interface allows users to track instrument history and monitor
components, while adhering to 21 CFR Part 11 compliance for regulated
environments.
His MultiTrap 96-Well Filter Plates
GE Healthcares new His MultiTrap FF and His MultiTrap HP prepacked
96-well filter plates allow great flexibility and consistent well-to-well and
plate-to-plate performance to ensure high reproducibility. This is achieved
through their prepacked form, designed to save time and improve reproducibility,
and a design that permits both manual and automated use.
Human Exon 1.0 ST Array
The GeneChip Human Exon 1.0 ST Array from Affymetrix now offers whole-genome,
exon-level expression profiling on a single array. Designed to interrogate
approximately one million exons, the GeneChip exon arrays offer a new and high
resolution view to examine alternatively expressed exons.
Human Phospho-MAPK Antibody Array Kit
The Human Phospho-Mitogen-activated Protein Kinase (MAPK) Array, now
available in kits from R&D Systems, is a potential tool for simultaneously
detecting the relative phosphorylation of nine MAPKs and nine other serine/threonine
kinases without performing numerous immunoprecipitation and/or Western blots
Increased Cell Line Distribution
Asterand, Inc., a supplier of human tissues and related services, recently
announced the distribution of nine cell lines for cancer research, developed at
the Barbara Ann Karmanos Cancer Institute of Wayne State University. The new
lines include specific types of lymphoma, leukemia, and various other cancers.
Kinase Assay Kits
Unlike FRET or traditional fluorescence quenching assays, where quenching is
equimolar between donor and receptor, Calbiochems TruLight Kinase Assay
Kits use polymer superquenching, which results in more sensitive assays. In
addition, these kits do not require special equipment, radioactive materials, or
secondary (detector) enzymes or antibodies.
Mass Spectrometric Data Management Software
Advanced Chemistry Development, Inc. has just released an upgrade to their ACD/MS Manager software.
ACD/Ion Presence allows users to automatically find and
label LC/MS peaks with a specified mass, and identify and label peaks with a
user-specified difference from a reference mass value. This will greatly aid
researchers in targeting peaks for a parent drug, searching for expected
metabolite transformations, finding expected impurities, or quickly identifying
the targeted compound in high-throughput purity analysis.
Metal-Removal SPE product line
Part of Polymer Laboratories' (PL) StratoSpheres product range, the metal
scavenging series consists of specially functionalized polymeric SPE devices
which remove charged and uncharged metal species, including platinum, palladium,
tin, lead and ruthenium, from a variety of organic solvents and analytical
mixtures. The new products include PL-Urea MP SPE, PL-Thiourea MP SPE and
PL-Guanidine MP SPE, and the recently introduced PL-Thiol MP SPE product.
PCR system
Applied Biosystems recently released 7500 Fast Real-Time PCR System was
designed to significantly reduce real-time PCR run times. Now using 96-well
format PCR reaction plates, the 7500 Fast Real-Time PCR Systems increased
speed will enable scientists to more easily share the system in multi-user
environments. The systems 96-well format can also be integrated into
existing laboratory workflows.
Protein Blotting Handbook
Millipore Corporation recently released the fifth edition of its Protein
Blotting Handbook, which includes techniques for protein blotting including 17
protocols for protein transfer, visualization, and immunodetection. More than 50
pages in length, this reference guide also contains more than 30 blot
photographs, references and a glossary of blotting terminology.
Protein-Coated Microplates
Greiner Bio Ones CELLCOAT 96 and 384 well microplates are now available
with Collagen Type I, Poly-D-Lysine and Poly-L-Lysine coatings. Poly-D-Lysine
and Poly-L-Lysine are synthetic proteins that give the surface of the microplate
a positive charge, allowing cells to spread more evenly and adhere more easily
QPCR Software
The MxPro QPCR Software is the most recent evolution of Staragenes
quantitative PCR (QPCR) data analysis software designed for their Mx3000P and
Mx3005P QPCR Systems.
RNA FFPE Kit
The Absolutely RNA FFPE kit represents the latest generation of RNA
purification kits. These kits utilize paraffin-embedded samples, with an
"easy-to-use", optimized, and non-toxic method of RNA purification
Redox-Capable Electrochemical Detector
ESA Biosciences combines both coulometric and amperometric detection in a
flexible, high-performance electrochemical detector with the new Coulochem III
detector system. Thanks to ESAs patented electrodes, the Coulochem III
detector can now offer redox capability in a single cell.
Two-Step QRT-PCR Master Mix
For accurate two-step QRT-PCR, Stratagene has now introduced both the
Brilliant SYBR Green SideStep and the FullVelocity SYBR Green QRT-PCR Master
Mixes, which allow for QRT-PCR directly from cells without RNA purification and
greatly reduced processing times, respectively.
Suppliers
GE Healthcare
GE Healthcare provides transformational medical technologies that are shaping
a new age of patient care. GE Healthcares expertise in medical imaging and
information technologies, medical diagnostics, patient monitoring and life
support systems, disease research, drug discovery, and biopharmaceutical
manufacturing technologies is helping physicians detect disease earlier and to
tailor personalized treatments for patients. GE Healthcare offers a broad range
of products and services that are improving productivity in healthcare and
enhancing patient care by enabling healthcare providers to better diagnose and
treat cancer, heart disease, neurological diseases, and other conditions.
Headquartered in the United Kingdom, GE Healthcare is a $15 billion unit of
General Electric Company (NYSE: GE). Worldwide, GE Healthcare employs more than
43,000 people committed to serving healthcare professionals and their patients
in more than 100 countries.
Harvard Apparatus, Inc.
Harvard Apparatus was founded in 1901 by Dr. William T. Porter of the Harvard
Medical School. Harvard Apparatus developed a name not only for quality but also
for innovation. Harvard Apparatus invented the mechanical syringe pump in the
1950s and introduced the first microprocessor controlled syringe pumps in the
1980s. Today Harvard Apparatus continues this tradition with the most advanced,
easiest-to-use programmable syringe pumps, the PHD 2000 series. Harvard
Apparatus also developed first volume controlled- and then pressure-controlled
ventilators, pulsatile blood pumps, transducers, amplifiers, recorders,
glassware and many other specialized bioscience research products. Harvard
Apparatus is now part of the Harvard Bioscience family of companies. Harvard
Bioscience (Nasdaq: HBIO) is a global developer, manufacturer and marketer of a
broad range of specialized products, primarily scientific instruments.
INTEGRA Biosciences
Biotechnology has become the key to modern Life Science. Its use in
PharmaceuticalR&D, in Medical Diagnostics and in Food and Beverage QC
Laboratories is widespread and indispensable. INTEGRA Biosciences is committed
to maintain a high level of competence in these fields of applications to
provide laboratory professionals with innovative solutions for their everyday
laboratory work. Since the foundation of the company in 1965, INTEGRA
Biosciences has consistently focused on its core competences in Microbiology and
Cell Biology. Continuous investment in future developments has brought a strong
pipeline of groundbreaking products to laboratories worldwide. In 1999 the
manufacturing company of the well known PIPETBOY and FIREBOY product ranges was
integrated into the INTEGRA Biosciences group. The following acquisition of an
Engineering company in 2002 announced a new era of growth and innovation. This
started with the successful consolidation of all activities R&D,
Manufacturing and S&M - into the newly expanded building in Chur ,
Switzerland. INTEGRA Biosciences new dynamic spirit is reflected in the
responsiveness to customer demands. The close collaboration between marketing
specialists, staff scientists, manufacturing and design engineers results in the
ability to translate customer needs quickly into reliable and easy-to-use
Laboratory tools. With more than 100000 PIPETBOYs - worldwide - in the
hands of laboratory professionals, the name INTEGRA Biosciences and its
reputation for quality and reliability have become synonymous. All other INTEGRA
products including FIREBOY, VACUSAFE, CELLINE, CELLROLL, CELLSPIN, MEDIACLAVE
and TECNOMAT enhance this reputation often they are benchmarks other
products are judged on. Today INTEGRAs Labtools for Microbiology and Cell
Cultivation are widely used all around the world. More then 60
distribution-partners form a world-wide sales network providing responsive and
competent services to customers. These distribution partners are supported by a
highly motivated and experienced team of specialists at the new headquarter in
Chur, Switzerland. INTEGRA Biosciences is an ISO 9001:2000 certified company.
Metropolitan Computing Corporation
Process Analytical Instrumentation, Monitoring & Control
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