Articles by Aileen Constans

SELDI-TOF still struggles to prove its worth as a clinical diagnostic tool

Soon after the surprising announcement that the human genome had far fewer genes than most had expected, researchers began to realize that there were still a great many unexplored transcriptional start sites. Tom Gingeras' team at Affymetrix, along with Kevin Struhl of Harvard University and colleagues, confirmed some of these findings in a 2004 Hot Paper by mapping the binding sites for three DNA transcription factors: Sp1, cMyc, and p53. Using a combination of high-density olig

Credit: COURTESY OF PAUL KENYON" /> Credit: COURTESY OF PAUL KENYONMothering, good or bad, sticks with an individual according to a Hot Paper by McGill University researchers Michael Meaney, Ian Weaver, and Moshe Szyf. In 2004, the authors showed that in rat pups, high levels of licking, grooming, and arched-back nursing (LG-ABN) lowered the methylation state of the NGF1-A binding site of the glucocortoid exon 17 promoter, thereby increasing activation of the glucocortoid receptor gene

How first-generation pooch genomes presaged things to come

Credit: © 2003 Nature Publishing Group" /> Credit: © 2003 Nature Publishing Group Sentinel lymph node biopsy, in which lymph nodes that receive direct drainage from a primary tumor site are excised to determine the extent of metastasis, is routinely used to accurately stage melanomas and breast cancers. The technique is time-consuming, difficult to learn, and involves the injection of a potentially hazardous radioactive tracer and a blue detection dye with temporary side effects.

Credit: Courtesy of Imperial College London" /> Credit: Courtesy of Imperial College London The photosynthetic enzyme Photosystem II (PSII) generates all of Earth?s atmospheric oxygen through a thermodynamically unfavorable reaction, splitting water into hydrogen and oxygen using solar energy. ?It?s been the Holy Grail of photosynthesis research ? to obtain structural information about the catalytic center where this very remarkable reaction occurs,? says biochemist James Barber o

Here are five tips to getting the most out of your next gene-association study

For most researchers DNA microarrays are synonymous with high-throughput gene expression analysis. But they also are invaluable genotyping tools. Now that the International HapMap Project (see article, p.68) is complete companies are putting ?these tools into researchers hands, including the HumanHap300 BeadChip from San Diego-based Illumina, whose construction is illustrated here.Unlike other microarray platforms, in which specific oligonucleotide probes are either synthesized

Credit: Christian Darkin/Photo Researchers Inc." /> Credit: Christian Darkin/Photo Researchers Inc. Breeders have long known that assisted reproductive technologies lead to a higher incidence of so-called large-offspring syndrome in cattle and sheep. In 2003, Andrew Feinberg of Johns Hopkins and Michael DeBaun of Washington University, St. Louis provided the first evidence that the same phenomenon can occur in humans.1 Using an epidemiol

Anxious to get going with RNAi? These tips will make your next knockdown a knockout

Invented a half-century ago by Nobel laureate Wolfgang Paul, the quadrupole mass filter has become an integral part of some of the most sophisticated mass spectrometers. Consisting of four parallel metal rods on which a fixed direct-current voltage and alternating radio-frequency voltage are applied, quadrupole mass filters allow users to selectively filter all ions except for those of a specified mass to charge ratio (m/z), depen

RNAi: Five Tips to Better Silencing - Table 1: siRNA Construction KitsCompanyKitsiRNAs per kit (or yield in mg RNA/ml)Price (USD)Ambionwww.ambion.comMEGAscript RNAi Kit20$285Silencer siRNAConstruction Kit15$535Epicentrewww.epicentre.comMessageMuterShRNAi Production Kit10$225Genlantiswww.genlantis.comDicer siRNA Generation

RNAi: Five Tips to Better Silencing - Table 2: RNAi-Specific Viral KitsCompanyKitSize (reactions)Price (USD)Ambionwww.ambion.compSilencer Adeno 1.0-CMV System5$520pSilencer 5.1 Retro System20$250Invitrogenwww.ambion.comBLOCK-iT AdenoviralRNAi Expression System20$941BLOCK-iT InducibleLentviral RNAi System20$1594

RNAi: Five Tips to Better Silencing - Table 3: siRNA Transfection ReagentsCompany Maximum transfections/mlPrice/ml (USD)Ambionwww.ambion.comsiPORT neoFXtransfection reagent1,250$185siPORT aminetransfection reagent660$345siPORT lipidtransfection reagent1,250$210B-Bridge Internationalwww.b-bridge.comQuick Step transfection reagent

RNAi: Five Tips to Better Silencing - Table 4: Selected Online siRNA-Design ToolsDeveloperNameURLRef.AmbionsiRNA Target Finderwww.ambion.com/techlib/misc/siRNA_finder.html1DharmaconsiDESIGNwww.dharmacon.com/sidesign/2GenScriptSiRNA Construct Builderhttps://www.genscript.com/ssl-bin/app/rnai?op=known siR