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New Lab & IT Products for Integrated Biology: Apr 1, 2006



Genedata Expressionist Pro 3.0


Genedata Expressionist Pro 3.0 is a versatile computational solution for ‘omics data integration, processing, and analysis. The software system now adds support for proteomics- and metabolomics-based biomarker studies and exploits a client-server architecture for rapid processing of mass spectrometry data. The new release features a server-based multi-level memory caching system that enables rapid, simultaneous processing of hundreds of MS chromatograms. Expressionist’s automated processing of raw chromatogram data provides a means to perform sensitive, high-throughput biomolecular profiling. The software facilitates integration of MS results with protein sequence search engine results and with genomic and transcriptomic information. These features combine to form an end-to-end MS solution for integrating proteomic and metabolomic data with other biomolecular results.


Lasergene 7

DNAStar has released a major upgrade to the Lasergene sequence analysis software package. Lasergene 7 expands the product’s already broad functionality by introducing automated virtual cloning, enhanced SNP discovery, primer walking, and bootstrapping within this major upgrade. These new capabilities will enhance researchers’ effectiveness and efficiency in the lab and will result in significant user cost savings.


Pathway Studio 4.0

PathwayStudio 4.0 pathway analysis software contains new, powerful tools for microarray data analysis and pathway dynamics simulation, as well as over 1,000 reconstructed pathways. New features and functionality include a pathway simulation module to explore the dynamic behavior of pathways, new tools for building relevance networks from the gene expression data, and Ariadne’s MedScan Reader biomedical literature browser. MedScan Reader enables the viewing and automated extraction of scientific facts from biomedical literature, including Medline abstracts, journal articles, and other source references. PathwayStudio 4.0 comes with ResNet Core, a database of 50,000 validated facts and 1,000+ reconstructed pathways, which can be extended to over 800,000 facts available in the ResNet 4.0 database.

Ariadne Genomics

Phenyx 2.0

Phenyx 2.0 is the latest version of an innovative software platform for proteomics MS data analysis. A number of key features have been added and enhanced since version 1.9, including manual validation functionality, allowing users to manually accept or reject peptide assignments and save and export the modification; new filtering possibilities on the compounds overview to facilitate results interpretation; updated design of the Phenyx desktop and the multiple results views; visualization of submission parameters of multiple jobs from the desktop menu; new representation of peptide sequences; allowing tolerances for both fixed and variable modifications to further improve fine-tuning of submission parameters; and a number of new functionalities are made available in the management console.

Geneva Bioinformatics

ProteinLynx Global Server 2.2.5

Waters announces a new version of its ProteinLynx Global Server software, including enhancements to Waters Protein Expression System. Waters ProteinLynx Global Server 2.2.5 software features new tools that will allow researchers to identify and quantify proteins and biomarkers more efficiently. PLGS 2.2.5 has improved algorithms for efficient protein quantification and identification across large patient/sample sets or time-course studies. A new quantification module allows quantitative data to be generated at the protein or peptide level using any of the commercially available or user-defined labeling technologies such as SILAC, AQUA, ICAT, iTRAQ, etc. The ability to perform both label-free and isotopic labeling approaches now means that PLGS provides unparalleled flexibility to analyze proteomics samples of varying type and complexity.



Protein Kinase SpliceArray

The new Protein Kinase SpliceArray by ExonHit Therapeutics monitors known and potential splice events derived from 568 genes in the human protein kinase gene family, including over 5,550 events. The microarrays are designed to monitor the expression of alternatively spliced transcripts and variants through a patent-protected combination of six exon and junction probes.


TaqMan Low Density Arrays

New Gene Signature Panels are available as part of Applied Biosystems’ TaqMan Low Density Array product line for real-time PCR applications. The new arrays include the Human G Protein-Coupled Receptors Panel, Human Protein Kinase Panel, Mouse Immune Panel, and Human Endogenous Controls Panel. The TaqMan Low Density Arrays are 384-well microfluidic cards designed for analyzing gene expression patterns in many samples across a defined set of gene targets. The arrays use gold standard TaqMan chemistry for quantitative gene expression and combine the accuracy, sensitivity, and high reproducibility of real-time PCR with the convenience of pre-configured panels for target screening and disease association research. The arrays also streamline reaction setup, reduce reagent consumption, and require no liquid-handling robotics.

Applied Biosystems

TopSpot E microarrayer

The TopSpot E microarrayer utilizes non-contact printing technology designed for spotting low and medium density microarrays on a wide range of substrates without damaging the surface. This flexible, stand-alone solution to microarray printing for DNA, oligonucleotides, proteins, and antibodies delivers droplets in the range of 1 nl per dispense. The typical spot size is about 200 microns. The TopSpot E can print several thousands of features per sample without reagent refill. The system has a throughput of up to 60 slides per hour with up to 96 analytes. The TopSpot E comes fully equipped and ready to use. It includes a 24-channel print head, control software, print head cleaning station and accessories. All print heads are reusable and easy to clean.



Agilent 1200 LC

With new rapid-resolution configuration, Agilent’s 1200 liquid chromatography system is the world’s fastest, most comprehensive LC system. With more than 60 instrument modules, it can be configured for all major LC applications, including a new rapid-resolution format as well as prep-scale, standard, narrow, capillary, nanoflow, and Agilent’s revolutionary chip-based liquid chromatography. Now HPLC-Chips are available to apply this technology for both small and large molecule work, with chromatographic separation or just for infusion of samples. Nanospray HPLC-Chip/MS technology can provide customers with more than a 1,000-fold improvement in sensitivity over conventional LC/MS. The new 1200 Series Rapid Resolution System provides up to 20 times faster analysis and 60 percent higher resolution than conventional LC, making it twice as fast and three times as precise as the competition’s best systems. The system can also still run any traditional LC method, making it the most flexible LC on the market.

Agilent Technologies

Ettan nanoLC

GE Healthcare introduces the Ettan nanoLC, a fully bio-inert, robust, nanoscale peptide separation system that delivers highly reproducible performance and is ideal for 1D-liquid chromatography proteomics applications upstream from electrospray ionization mass spectrometry or MALDI MS/MS applications.

GE Healthcare

IgY-R7 Rodent and Single-Component Chemistries

Beckman Coulter announces the IgY-R7 Rodent and Single-Component Chemistries as the newest addition to its family of ProteomeLab Partitioning Systems, for the isolation and analysis of protein-based biomarkers. The new IgY-R7 Rodent Chemistry selectively partitions seven highly abundant proteins — up to 70 percent of the protein mass — from rat or mouse serum or plasma. The new single-component kits specifically capture a choice of seven key, highly abundant plasma proteins, enabling a more targeted approach for specific protein partitioning.

Beckman Coulter


Xencor’s ImmunoFilter technology is the combination of a database and software that researchers can use to predict the immune response, or immunogenicity, of therapeutic proteins and monoclonal antibodies early in the drug discovery process. The advantage with Xencor’s ImmunoFilter product is that it is able to examine a protein sequence for ‘hot spots’ that might cause an immune response by using an experimentally determined database of peptide sequences that favor immune response initiation and software that integrates the database with the queried protein sequence. This combination provides a score on the protein’s ability to cause an immune response, enabling researchers to better predict the effectiveness of a drug in development.


LTQ Orbitrap

Thermo Electron unveiled several new additions to its suite of proteomic solutions. These include Thermo’s novel LTQ Orbitrap hybrid mass spectrometer, new techniques for peptide fragmentation, and software for data interpretation, all of which dramatically enhance and expand the potential for protein identification and quantification. The LTQ Orbitrap is the first commercial mass analyzer based on an entirely new detection principle to be introduced to the market in over 20 years. This hybrid instrument greatly improves protein characterization, accelerates protein database searches, and reduces false identification rates.

Thermo Electron


Burdick & Jackson BMI

The Burdick & Jackson BMI activator is used to synthesize DNA and RNA oligonucleotides for therapeutic and medical diagnostic applications. BMI activator’s unique formulation improves on solubility and performance, providing customers faster coupling time and increased yield compared to traditional Tetrazole activator solutions.



The Cellipon293 is a novel in vitro cationic lipid transfection reagent specifically developed for the delivery of DNA/RNA into HEK-293 cells as well as broad mammalian cells. With high transfection efficiency, low cytotoxicity, and simple protocols, Cellipon29 enables researchers to get satisfactory results easy and fast. The product is cost-effective, providing an option for low-budget laboratories and high-volume users.


DuraScribe T7 Transcription Kit

The DuraScribe T7 Transcription Kit from Epicentre Biotechnologies produces DuraScript RNA transcripts that are completely resistant to RNase A. The kit includes DuraScribe T7 RNA Polymerase, a mutant T7 RNA Polymerase that recognizes the same transcription promoters as standard T7 RNA Polymerase, and efficiently incorporates 2’-Fluorine-dCTP and 2’-Fluorine-dUTP as well as ATP and GTP into full-length DuraScript transcripts. DuraScript RNA is ideal for RNA aptamer generation and ribonuclease protection assays.

Epicentre Biotechnologies

High-Speed Reagent Dispenser

Hamilton introduces a high-speed reagent dispenser for the Microlab Star pipetting workstation. The new module is designed to perform the high-volume dispense steps required by many of today’s assays and XNA purification methods without the cross-contamination risk associated with fixed tip needles or the cost of disposable needles. The high-speed reagent dispenser is faster than both the 96 probe heads and independent pipetting channels that are currently available on most robotic liquid handling platforms. Taking up very little deck space, it can dispense up to four different reagents to a column of plates located on the left or right side of the dispenser.

Hamilton Company

MacroCap SP

The MacroCap SP is a large-pore cation exchange medium for downstream processing that gives high purity and yield of large biomolecules, such as polyethylene glycol-modified proteins. Designed for the purification of large biopharmaceuticals (MW > 150,000), MacroCap SP is a large pore ion exchange medium that allows separation of mono- from oligo- and non-PEGylated proteins with high selectivity and yield under high load conditions. Further enhancing its cost effectiveness, MacroCap offers good clean-in-place stability for ease of use and long media life.

GE Healthcare

MethylDetector Bisulfite Modification Kit

Active Motif’s new MethylDetector Bisulfite Modification Kit simplifies DNA methylation analysis by providing optimized reagents for performing DNA conversion, plus timesaving DNA purification columns and positive control PCR primers. Because the control primers anneal only to converted DNA, they can be used to assess the success of conversion before spending time and money on sequencing or other costly analysis methods.

Active Motif

To tell GT about new recently released products, e-mail [email protected]


The Scan

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.

Sequencing Study Leads to Vaccine Target in Bacteria Behind Neonatal Meningitis

Researchers eBioMedicine track down potential vaccine targets with transposon sequencing on mutant bacteria causing neonatal meningitis in mouse models of the disease.

Multiple Myeloma Progression Influenced by Immune Microenvironment Expression

Researchers in NPJ Genomic Medicine compare RNA sequencing profiles of 102,207 individual cells in bone marrow samples from 18 individuals with rapid or non-progressing multiple myeloma.

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.