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New Lab & IT Products for Integrated Biology: Jun 1, 2004

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BIOINFORMATICS

Accelrys DataServe 2.0

DataServe 2.0 is a new version of the automated public sequence database updating service from Accelrys. DataServe contacts the NCBI GenBank database, retrieves new DNA and protein sequences, then combines and reformats them into cumulative updated databases that can be accessed by the GCG Wisconsin Package.

Accelrys
800.756.4674
www.accelrys.com

Bioinformatics Solutions RAPTOR 2.0 Protein Structure Prediction Software

RAPTOR 2.0 uses linear programming to perform threading-based protein structure prediction. Other features in the software include its ability to add NMR constraint data, an intuitive PyMOL-based graphical interface (PROView) which allows users to simultaneously visualize and manipulate predicted structure and sequence alignment data, an up-to-date PDB library, and intranet Web server capability.

Bioinformatics Solutions
519.885.8288
www.bioinformaticssolutions.com

GenePattern Gene Expression Analysis Software

Scientists at MIT’s Broad Institute have released GenePattern, a flexible software package that allows biomedical researchers to perform custom gene expression analysis experiments, record and replay analyses, and use tools from many different software sources within a single interface. A researcher can use GenePattern through a simple user interface or a powerful scripting language, and a computational biologist can add a software module written in any language. This new microarray analysis package is available to researchers for free download.

Broad Institute
www.broad.mit.edu/cancer/software/genepattern

Synamatix SynaBASE Structural Sequence Database

SynaBASE, a structural sequence database, is a hierarchical network system that identifies complex relationships between biological sequence patterns. Proprietary data structures and algorithms for genome comparison, database searching, and sequence annotation, among others, are used to build and maintain SynaBASE.

Synamatix
+60 3 8996 0984
www.synamatix.com

BIOLOGICAL ASSAYS

BD Biosciences Matrigel Matrix and Rat Tail Collagen I

Designed for in vivo angio-genesis assays and to augment the growth of human tumors in nude mice, the Matrigel high concentration matrix is a solubilized basement membrane preparation extracted from EHS mouse sarcoma, a tumor rich in ECM proteins. Its major component is laminin, followed by collagen IV, heparan sulfate proteoglycans, and entactin. BD rat tail collagen I is used in applications where a sturdy gel provides maximal support to maintain the three dimensional structure.

BD Biosciences Discovery Labware
800.343.2035
www.bdbiosciences.com

Promega Rapid Response Reporter Vectors

Designed for quantitative cellular analysis and functional genomics applications, the Rapid Response reporter vectors allow measurement of smaller and more transient changes in transcription compared to their predecessors. The vectors contain degradation sequences that yield a dramatic improvement in the temporal coupling between transcription and reporter signal. The product is available in firefly or Renilla luciferase configurations and is compatible with a wide range of Promega luminescent detection reagents.

Promega
608.277.2545
www.promega.com

MICROARRAY ANALYSIS

Applied Biosystems Expression Array System

The new microarray analysis platform from ABI, the Expression Array system, is now ready for shipping. The technology relies on 2-inch by 3-inch microarrays only readable with ABI instrumentation, and a dual method for detecting gene expression in biological samples — combining chemiluminescence with fluorescence. Each probe contains a 60-mer oligo, used in the chemiluminescence process imaged by a CCD camera, and a 24-mer oligo, which is lit up fluorescently by light-emitting diodes to locate each of the 35,000 spots on the array.

Applied Biosystems
800.327.3002
www.appliedbiosystems.com

Mirus Label IT µArray Dual Labeling Kit

Designed for use in microarray applications, the Label IT kit contains reagents for labeling nucleic acid samples with fluorescein and biotin, as well as a complete protocol with guidelines on hybridization and secondary detection for microarray applications. The kits provide robust performance, high signal-to-noise ratios, low background, and sensitive detection of low copy number transcripts.

Mirus
888.530.0801
www.genetransfer.com

QIAGEN Array-Read Oligo Set for the Xenopus tropicalis Genome

This new set of oligos from QIAGEN contains 10,898 70mer probes representing Xenopus transcripts, and provides a tool for microarray analysis of Xenopus gene expression. Sequence and cluster data were provided by Dr. Jim Smith of the Wellcome Trust/Cancer Research UK Gurdon Institute of Cancer and Developmental Biology in Cambridge. The Xenopus Array-Ready Oligo Set is provided in a 384-well plate format with 600 pmol of probe per well.

QIAGEN
800.426.8157
www.qiagen.com

SciGene Series 700 Microarray Oven

The new line of ovens and rotators from SciGene are designed for mixing while hybridizing popular array formats. The Model 777 accommodates up to 48 Affymetrix GeneChips or 20 Agilent SureHyb chambers using specially designed rotators. A general-purpose rotator is also available for mixing and heating nearly any style hybridization chamber.

SciGene
800.342.2119
www.scigene.com

VizX

Version 2004.2 continues the company’s commitment to helping scientists ‘understand the biology’ behind their microarray data by incorporating a unique new pathways report, streamlined support for Affymetrix GEO datasets, CLARA clustering analytics, Boxplot visualization graphics and enhanced Gene Ontologies operations. Building upon almost two years of continual quarterly enhancements, the update is available now and is automatically provided to all existing and new GeneSifter users at no additional cost.

VizX Labs
877.932.4363
www.vizxlabs.com

PCR

Applied Biosystems SDS Software v2.2

The Enterprise edition of SDS software v2.2 is a high-throughput application for storage, organization, and analysis of large amounts of gene expression and genotyping data on the Applied Biosystems 7900HT real-time PCR system. Version 2.2 supports 21 CFR part 11, providing security, auditing functions, electronic signatures, and electronic record-keeping.

Applied Biosystems
800.345.5224
www.appliedbiosystems.com

PROTEOMICS

Agilent LC/MSD Trap Security Pack 1.0 Software

The new software for the Agilent ion trap MS family supports compliance with FDA 21 CFR Part 11 criteria and associated Good Laboratory Practice and Good Manufacturing Practice regulations. The program stores all metadata and audit logs, includes secure, time-stamped, user-independent audit trails that track all system events and user actions, and protects electronic records for retrieval throughout the records retention period, including result versioning so that processed results are not overwritten.

Agilent Technologies
800.227.9770
www.agilent.com/chem/proteomics

Agilent Technologies Updated Spectrum Mill MS Proteomics Software

The upgraded version of Agilent’s Spectrum Mill MS proteomics software now includes support for the International Protein Index protein database, the ability to identify additional amino acid modifications such as perdeuteromethylation, support for Agilent''''s new lysine mass tagging reagent, which enhances identification of proteins by matrix-assisted laser desorption/ionization MS.

Agilent Technologies
800.227.9770
www.agilent.com/chem/proteomics

Caliper Life Sciences LabChip 90 Automated Electrophoresis System Protein Assay

As an alternative SDS-PAGE, the new protein assay is designed for sizing and quantifying proteins. The LabChip 90 system is capable of automated sampling from 96-well microtiter plates, increasing sample throughput.

Caliper Life Sciences
877.Lab.Chip
www.caliperLS.com

Decodon Delta2D 3.1.3 2D Gel Analysis Software

The updated version of Decodon’s Delta2D software now supports the use of an internal standard, the requantify tool has been remodeled to add and remove spots more easily, the program now indicates the spot matching quality, and automatically creates labels for all selected spots in the dual view. A t-test was also added to the statistics table and spots can be labeled automatically with their ID.

Decodon
+49 (0)3834 51 52 30
http://www.decodon.com/Support/downloads.html

Thermo Finnigan TSQ Quantum Ultra EMR Triple Quad Mass Spec

The new version of Finnigan’s TSQ Quantum Ultra series of triple quadrupole mass spectrometers, the TSQ Quantum Ultra EMR, offers higher resolution and an extended mass range of up to 3000 Daltons for applications in proteomics. The new instrument allows high-resolution analysis of a whole new class of biopolymers including peptides, polysaccharides, and oligonucleotides.

Thermo Finnigan
800.532.4752
www.thermo.com

RNAi

Ambion MessageAmp II aRNA Amplification Kit

The MessageAmp II aRNA amplification kit incorporates the newly engineered ArrayScript M-MLV RT to maximize yields of full-length cDNA. MessageAmp II selects and amplifies mRNA from as little as 100 ng of input RNA in a single round of amplification for microarray analysis. MessageAmp II includes reagents optimized for each step of the reaction and incorporates Ambion’s patented MEGAscript High Yield Transcription technology.

Ambion
800.888.8804
www.ambion.com

Ocimum Biosolutions iRNAwiz siRNA Design Software

The iRNAwiz software provides tools for organizing sequence data, designing siRNAs, and tracking and analyzing successful templates. In addition, the program allows the user to define his own search templates, set regions of interest based on a wide variety of criteria like ORFs, UTR regions, introns and exons, secondary structures, motifs and domains, and post-design analysis of successful siRNA.

Ocimum Biosolutions
866.227.7512
www.ocimumbio.com

SAMPLE PREP

BD Biosciences PuraMatrix Peptide Hydrogel

PuraMatrix peptide hydrogel is a novel synthetic matrix used to create defined three-dimensional microenvironments for a variety of cell culture experiments. This material consists of standard amino acids and > 99% water. Under physiological conditions, the peptide component self-assembles into a 3D hydrogel that exhibits a nanometer-scale fibrous structure. BD PuraMatrix Peptide Hydrogel is biocompatible, resorbable, injectable, and devoid of animal-derived material and pathogens.

BD Biosciences
800.343.2035
www.bdbiosciences.com

Epicentre BACMAX DNA Purification Kit

Designed for isolating high-quality BAC DNA, the BACMAX scalable protocol is based on a modified alkaline-lysis procedure that typically yields 0.6 to 25 µg of BAC DNA from 1.5 to 100 ml cultures of a single-copy BAC. Selective precipitation steps and the incorporation of Epicentre’s RiboShredder RNase Blend remove contaminants that degrade DNA and interfere with downstream applications.

Epicentre
800.284.8474
www.epicentre.com/bacmax.asp

GenVault Personal Archive DNA Storage System

The Personal Archive utilizes GenVault’s 384-well microplates, called GenPlates, that contain solid-state elements for extracting DNA from blood samples or buccal (cheek) cells upon contact, trapping the DNA in a format that can be stored and shipped at room temperature without special biohazard labeling and treatment. The capacity of the Personal Archive system is 990 GenPlates and includes sample management software that tracks the locations of GenPlates within the storage cabinet.

GenVault
760.268.5200
www.genvault.com

Harvard Apparatus Sample Clean-up SpinColumns

Designed for cleaning up DNA, RNA, protein, peptide, and nucleotide samples, Harvard Apparatus SpinColumns have a broad range of sampling sizes from the ultra-micro SpinColumn at 10 to 25 µl, micro spin column from 25 to 75 µl and the macro from 75 to 150 µl. SpinColumns are in single and 96 well format. The 96 well format has a volume of 25 to 100 µl.

Harvard Apparatus
800.272.2775
www.harvardapparatus.com

Lucigen CopyRight BAC, Fosmid, and Insert Cloning Kits

The new cloning kits from Lucigen offer both unbiased cloning of large DNAs for high fidelity, and "on command" copy amplification for high yields. Transcription terminators in the CopyRight vectors eliminate problems seen when cloning large DNAs containing toxic genes, AT- or GC-rich regions, hairpins, nucleotide repeats, inverted sequences, or strong promoters.

Lucigen
888.575.9695
www.lucigen.com

MatriCal MatriPress Freezer Rack

MatriCal’s newest line of compression stackers, the MatriPress freezer rack, is a portable, spring-loaded storage system that holds lidded standard height or deep well plates and prevents sample evaporation or uptake of water. Unlike conventional heat seals and sticky films that allow only a limited number of plate accesses, the MatriSeal lids are robotics friendly and provide easy plate access without damaging the plates or leaving adhesive residue behind.

MatriCal
509.343.6225
www.matrical.com

QIAGEN Rneasy 96 Universal Tissue Kit

QIAGEN’s new Rneasy 96 universal tissue kits provide manual and automated high-throughput RNA purification from all types of animal tissue, including difficult-to-lyse fibrous and fatty tissues. The procedure produces high yields of total RNA, ready to use in all downstream applications, including real-time RT-PCR and array analysis.

QIAGEN
800.426.8157
www.qiagen.com

USB Ligate-IT Rapid Ligation Kit

Designed for a variety of ligation procedures such as vector cloning, TA cloning or library construction, the new Ligate-IT kit provides quick ligation in 5 minutes for cohesive ends and 10 minutes for blunt ends. The kit includes USB T4 DNA ligase, nuclease-free water, and a specially formulated 5X Reaction Buffer which enhances the activity of T4 DNA Ligase, especially on blunt-end fragments.

USB
216.765.5000
www.usbweb.com

SNPs AND GENOTYPING

Illumina BeadStation 500G SNP Genotyping Platform

Illumina is now shipping its BeadStation 500G SNP genotyping platform, which can analyze samples on either of two bead-based Illumina array platforms: the 16-sample Sentrix BeadChip and the 96-sample Array Matrix. A software upgrade allows the unit to be upgraded to a BeadStation 500GX to enable gene expression profiling. The benchtop system is designed for individual research groups and core labs that have throughput requirements ranging from 6,000 to 300,000 genotypes per day.

Illumina
800.809.4566
www.illumina.com

To tell GT about new recently released products, e-mail John MacNeil, Senior Editor, at [email protected]

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.