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

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BIOINFORMATICS

Accelrys Discovery Studio GeneAtlas 2.1

This patch to the current DS GeneAtlas 2.0 provides additional Linux server support (RedHat 7.2, 8.0 and AS 2.1) and incorporates several bug fixes. DS GeneAtlas is an automated protein annotation pipeline for analyzing protein sequences and identifying their biochemical function.

Accelrys

800.756.4674

http://www.accelrys.com /dstudio/ds_modeling/ds_ geneatlas.html

BIOLOGICAL ASSAYS

Bruker Daltonics BioThreat Profiler

Designed for identifying biological warfare agents using MALDI-TOF mass spectrometry, the BioThreat Profiler is applicable to bacteria, spores, fungi, and toxins, that is, even those biological threats that do not contain any DNA or RNA. The system uses a novel biomarker database for identifying micro-organisms and other biowarfare agents.

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

Bruker Daltonics Novel Biological Agent Detection Arrays

Designed for use with Bruker Daltonics’ APSIS bio-threat identification system, the new biological agent detection arrays are packaged as a combined detection cartridge for the simultaneous detection of anthrax, smallpox, and strains thereof. With the ability to identify several species and strains on one array simultaneously, the system and reagents considerably reduce response time. The APSIS system uses fluorescence detection of specific hybridization of amplified DNA or RNA fragments on microarrays, and can process up to eight arrays in parallel, with each array designed for the simultaneous identification for multiple agents.

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

Midwest Scientific PCV Mini-tube for Cell Counting

Along with Techno Plastic Products, Midwest Scientific has released a new PCV mini-tube for determining packed cell volume. The mini-tube, using 1ml of sample, can quantify packed cell volume (PCV) in a matter of minutes, allowing the user to calculate cell density.

Midwest Scientific

800.227.9997

www.midsci.com

LIMS

GenoLogics ProteusLIMS Version 1.0

ProteusLIMS is designed to manage the large volumes of data generated in the field of proteomics research. The system manages data from all parts of the research process, as well as the research process itself, and has been designed and built from the ground up to be compatible with any computing platform and scientific instrumentation platform.

GenoLogics

866.GLS.LIMS

www.genologics.com

MICROARRAY ANALYSIS

Applied Biosystems Mouse Genome Survey Microarray

Designed for use with the recently introduced Expression Array System, the Mouse Genome Survey microarray contains probes representing a complete, annotated, and fully curated set of approximately 32,000 mouse genes from the public and Celera databases. The system employs the same chemiluminescence technology and well-defined, 60mer probe lengths as the Applied Biosystems Human Genome Survey Microarray. In addition, the annotation file supplied with the mouse microarray provides pre-computed human-mouse ortholog pairs for each gene when available.

Applied Biosystems

800.327.3002

http://info.appliedbiosystems .com/eas

QIAGEN Version 3.0 Array-Ready Oligo Set for the Rat Genome

The new Rat AROS Version 3.0 contains 26,962 70mer probes, representing 22,012 genes and 27,044 gene transcripts. The Ensembl Rat 19.3b.2 database, based on the Rat Genome Sequencing Project, is the data source for the Rat AROS Version 3.0. The Rat AROS provides a library of ready-to-print oligos with the flexibility to spot oligos and detect signals using various printing and hybridization techniques. Each probe is melting-temperature normalized and includes a 5’ amino linker to facilitate substrate attachment.

QIAGEN

800.426.8157

http://oligos.qiagen.com

QIAGEN Array-Ready Oligo Set for the Xenopus tropicalis Genome

With sequence and cluster data from a consortium of scientists at the Wellcome Trust/Cancer Research UK Gurdon Institute in Cambridge, this new oligo set contains 10,898 70mer probes representing Xenopus transcripts.

QIAGEN

800.426.8157

www.qiagen.com/goto/oligosets.

Schott Nexterion Slide E Epoxy Microarray Slide

The Nexterion Slide E provides an active coating chemistry for the immobilization of oligonucleotides. The active layer is made up of reactive epoxy groups that form an immediate and irreversible covalent bond with all the probe’s nucleophilic groups, without requiring UV cross-linking or reduction. An amino modification of the oligonucleotide is only necessary when spotting short oligonucleotides.

Schott

914.831.2200

www.us.schott.com

PCR

SuperArray Bioscience RT-PCR Gene Expression Assay Kit

Designed for DNA microarray data verification, the new SuperArray Bioscience RT Real-Time gene expression assay kit is intended for genome-wide disease characterization, pathway elucidation, functional studies, and for independent verification of DNA microarray data. Each kit includes gene-specific PCR primers designed with proprietary, experimentally verified design algorithms. The PCR primers are optimized for real-time PCR and SYBR Green detection.

SuperArray Bioscience

888.503.3187

www.superarray.com/QRTsearch.php

PROTEOMICS

Agilent Protein In-Gel Tryptic Digestion Kit

The new protein in-gel tryptic digestion kit contains a complete set of reagents to perform ~150 digestions on colloidal Coomassie or fluorescent dye-stained protein bands. It includes modified trypsin, destaining buffers, digestion buffers, reduction reagents, and alkylation reagents, and a simple seven-step protocol for accurate and reproducible digestions.

Agilent Technologies

800.227.9770

www.agilent.com/chem /proteomics

Agilent One-Step Reaction Lys Tag 4H Reagent Kit

The new one-step reaction Lys tag reagent kit can increaase AP-MALDI mass spectrometry sensitivity by a factor of 5 percent to 20 percent, and allows more efficient de novo sequencing of lesser-known proteins. The kit has enough reagent for at least 200 reactions.

Agilent Technologies

800.227.9770

www.agilent.com/chem /proteomics

Bruker Daltonics Proteineer-LC for LC-MALDI-MS/MS

A new LC-ESI-MALDI system for LC-based expression proteomics workflows, the Proteineer-LC uses ESI ion trap mass spectrometry, with a new optimized sample splitting and MALDI fraction collection device, called Proteineer-FC, to enable a seamless LC-MALDI-MS/MS proteomics workflow with our TOF/TOF systems at high sensitivity using the Anchorchip sample plate technology.

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

Bruker Daltonics Top-Down Proteineer Capability for the Apex QE Q-q-FT/MS System

By enabling top-down proteomics on the Apex QE Q-q-FT/MS system, the new capability can identify, determine the primary structure, and localize post-translation modifications directly at the protein level without the need for enzymatic digests. It combines the analytical power of FT/MS equipped with a hybrid ESI-Q-q interface to perform “top-down” analysis of intact proteins in the FTMS analyzer cell, thus avoiding digestion and additional separation steps.

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

Bruker Daltonics UltrOTOF-Q ESI-Q-q-TOF Mass Spectrometer

The new UltrOTOF-Q is an orthogonal time-of-flight (OTOF) mass spectrometer offering two orders of magnitude improvement in sensitivity. The new system also features significantly improved MS/MS sensitivity and sequence coverage for proteomics experiments. The patented co-linear TOF design of the UltrOTOF-Q enables superior mass resolution of greater than 20k in normal mode, and resolution of greater than 40k in MultiPass mode

Bruker Daltonics

978.663.3660

www.daltonics.bruker.com

FFE Weber Prometheus Free Flow Electrophoresis System

The new instrument system from FFE Weber is designed for matrix-free fractionation of proteins and metabolites. The system has three main modes: isoelectric focusing, for focusing separation of species in an inhomogeneous medium (pH-gradient) according to their isoelectric points; zone electrophoresis, for non-focusing separation of species in a homogeneous medium according to their net charge density; and isotachophoresis, for separation of species according to their mobility. The system is available as a standard, enhanced, and automated enhanced version.

FFE Weber

+49.89.57954913

www.ffeweber.de

GeneBio Phenyx Mass Spectrometry Data Analysis Software

Designed for identifying and characterizing proteins and peptides from PMF and tandem-MS mass spectrometry data, the Phenyx software platform provides a family of scoring functions that can be tailored to the function of specific MS instruments, and to specific instrument running conditions, spectra processing parameters, and sample preps and protocols. Phenyx includes dynamic data and results evaluation, inherent database access to support complex workflows and solid architecture available in multiple environments.

GeneBio

+41.22.702.99.00

www.genebio.com/phenyx

Schleicher & Schuell Serum Biomarker Chip

The S&S serum biomarker chip contains 120 different antibodies spotted on S&S FAST slides. The chip contains antibodies specific to serum biomarkers related to human cancers of every major organ. Each sample must be labeled with two different tags, pooled and probed against the antibody microarray in a competitive binding fashion. The processed microarray is scanned at two different wavelengths on a two-color fluorescent scanner.

Schleicher & Schuell

603.352.3810

www.schleicher-schuell.com

Tm Bioscience Tag-It
P450-2C9 and P450-2C19 Mutation Detection Kits

The new kits for P450-2C9 and P450-2C19 genes identify the presence or absence of important mutations in liver enzymes that are common in patients with atypical drug metabolism, which can lead to adverse drug reactions. The Tag-It P450-2C9 kit provides simultaneous detection of 5 different mutations of Cytochrome P450 in a multiplex format, and the Tag-It P450-2C19 kit provides simultaneous detection of 7 mutations in a multiplex format.

Tm Bioscience

416.593.4323

www.tmbioscience.com

RNAi

Agilent RNA Integrity Number Beta Software

Designed for use with the Agilent 2100 bioanalyzer & RNA LabChip kits, the RNA Integrity Number (RIN) software is a tool for helping scientists estimate the integrity of total RNA samples. The RIN extension automatically assigns an integrity number to a eukaryote total RNA sample analyzed on the Agilent 2100 bioanalyzer using the eukaryote total RNA Nano assay. Using this tool, sample integrity is no longer determined by the ratio of the ribosomal bands, but by the entire electrophoretic trace of the RNA sample, including the presence or absence of degradation products.

Agilent Technologies

800.227.9770

www.agilent.com/chem/RIN

Ambion siRNA Electroporation Buffer

The siPORT siRNA Electroporation Buffer is designed for delivery of primary and difficult-to-transfect cells with siRNAs. The buffer offers excellent viability and superior knockdown efficiency with a single reagent, and can be used with multiple types of electroporators to ensure highly efficient siRNA delivery into cells while maintaining high cell viability.

Ambion

800.888.8804

www.ambion.com

Ambion Human, Class-focused siRNA Libraries

The Silencer Nuclear Hormone Receptor siRNA Library and the Silence Caspase and Caspase Related siRNA Library contain siRNAs designed for maximum potency and specificity to expedite functional genomics studies.

Ambion

800.888.8804

www.ambion.com

SAMPLE PREP

MatriCal SonicMan Sonication System

Designed for high-throughput dissolution of compounds, the SonicMan provides a platform to resuspend compounds stored as solutes dissolved in dimethylsulfoxide and stored from 4°C to ¯80°C in 96, 384, and 1536 microplates. Applications include: resuspending compounds initially or after freeze/thaw; shearing genomic data into small fragments for PCR amplification; extract target proteins, RNA/DNA, and enzymes using cell lysis and membrane disruption without using harsh chemicals, including detergents.

MatriCal

509.343.6225

www.matrical.com

QIAGEN BioRobot M48 Workstation

The BioRobot M48 workstation, with MagAttract purification technology, provides fully automated purification of DNA, RNA, or viral nucleic acids from a range of clinically relevant samples, including blood and tissues. The system can process 6 to 48 samples per run with software protocols, an integral UV light allows convenient decontamination of the workstation interior between runs, and disposable filter-tips prevent carryover.

QIAGEN

800.426.8157

www.qiagen.com

QIAGEN MagAttract Virus Mini M48 Kit

The MagAttract Virus Mini M48 kit provides a fully automated procedure for simultaneous purification of viral DNA and RNA from 400 µl serum and plasma for detection in downstream assays. The kit can be used with a broad range of DNA and RNA viruses for life science applications. The kit is for use with QIAGEN’s BioRobot M48 workstation, and provides parallel purification of 48 samples and requires only 15 to 20 minutes setup time.

QIAGEN

800.426.8157

www.qiagen.com

QIAGEN BioSprint Sample Preparation System

Using magnetic-particle technology, the new BioSprint workstations automate the simultaneous preparation of up to 15 or 96 samples. The first kit available, the BioSprint DNA Blood Kit, enables purification of genomic DNA from cells, tissue, and blood. Two workstations with different throughputs are available: the BioSprint 15 and the BioSprint 96 for processing 1¯15 and 1¯96 samples per run, respectively.

QIAGEN

800.426.8157

www.qiagen.com

Quantum Dot Qdot 655 Antibody Conjugation Kit

Designed for conjugating antibodies to Qdot 655 nanocrystals, the Qdot 655 Antibody Conjugation kit contains all necessary reagents and components for two conjugation reactions, each using 300 µg of IgG class antibody, as well as a detailed protocol. The quantum dot-antibody conjugates generated with this kit can be used in applications such as immunohistochemistry, tissue staining, ELISA, western blotting, flow cytometry and other, user-designed experiments.

Quantum Dot

510.887.8775

www.qdots.com

Whatman PlantSaver DNA Storage and Extraction System

The PlantSaver is a four-square version of the Whatman FTA card with a laminated flap that strengthens the card and makes it more robust and suitable for field collection and easy transport of plant samples. DNA samples can be stored at room temperature on FTA for as long as 14 years and a simple DNA purification procedure can be conducted in less than 30 minutes. In addition, DNA collected and purified on the FTA Card can be successfully used in market-assisted selection and genotype analysis.

Whatman

800.441.6555

www.whatman.com

The Scan

Could Mix It Up

The US Food and Drug Administration is considering a plan that would allow for the mixing-and-matching of SARS-CoV-2 vaccines and boosters, the New York Times says.

Closest to the Dog

New Scientist reports that extinct Japanese wolf appears to be the closest known wild relative of dogs.

Offer to Come Back

The Knoxville News Sentinel reports that the University of Tennessee is offering Anming Hu, a professor who was acquitted of charges that he hid ties to China, his position back.

PNAS Papers on Myeloid Differentiation MicroRNAs, Urinary Exosomes, Maize Domestication

In PNAS this week: role of microRNAs in myeloid differentiation, exosomes in urine, and more.