Notes: The authors used the PowerPlex^® 16 System to perform DNA typing of 27 sets of World War II skeletal remains found in two mass graves in Slovenia. Each bone sample was sanded to remove potential contaminants from exterior surfaces, then washed and air-dried. The same procedure was used to process teeth, except that the teeth were not sanded. DNA was isolated from the bone powder using organic extraction, then quantified. DNA was amplified using the PowerPlex^® 16 System as per the manufacturer's recommendations; for samples with small amounts of DNA, the number of cycles was increased to 32 and the elongation time extended to 90 seconds. Fifteen sets of remains yielded full profiles, and 12 sets yielded partial profiles, with the least successful profile including 13 loci. DNA was also extracted and amplified from 69 reference buccal swab samples from potential relatives. (3817)

Notes: These authors compared standard culture conditions, DNA isolation and analysis (e.g, sequencing) with a liquid culture, DNA isolation and a homogeneous fluorescent detection system for identifying mycobacterial species. The standard DNA extraction began with a loopful (3–mm³ sphere) of bacterial colony grown on Ogawa slants that used glass beads to mechanically disrupt the cells. The resulting lysate was extracted using phenol/chloroform, and DNA purified from the aqueous phase using a robotic liquid handler AGE-96 (Biotec) and the MagneSil^® Blood Genomic, Max Yield System. The DNA extractions were used in PCR and sequencing reactions. (3700)

Notes: The authors compared two DNA extraction methods: the International Commission on Missing Persons silica method and the standard phenol:chloroform method to determine the preferred method for extraction of DNA from skeletal remains. The efficacy of DNA extraction was measured by real-time PCR to quantify DNA and to check for the presence of PCR inhibitors, and by amplification with the PowerPlex^® 16 System. DNA was extracted from processed bone powder, and 10µl of the final extract was amplified using the PowerPlex^® 16 System and GeneAmp^® PCR System 9700 according to the manufacturer's recommendations, except that the extension time was doubled from 30 seconds to 60 seconds for the first 10 cycles and from 45 seconds to 90 seconds for the next 22 cycles. Amplified products were detected using the ABI PRISM^® 3100 Genetic Analyzer. The authors concluded that the silica-based method gave better results in autosomal STR typing than the organic extraction method. (3818)

Notes: The authors examined whether genetic differences at the HLA class I locus affect development of Epstein Barr Virus-associated diseases. Peripheral blood mononuclear cells were isolated from asymptomatic EBV-seropositive and seronegative individuals and patients with acute infectious mononucleosis. DNA was isolated, and genotypes at two HLA class I loci and one HLA class III locus, as a control, were determined by PCR. The 10µl PCRs contained 25ng of DNA, 1X GoTaq^® Flexi Reaction Buffer, 2.5mM MgCl₂, 200µM dNTP, 0.5 units of GoTaq^® Flexi DNA Polymerase and 25µM of forward and reverse primer, one of which was labeled with 6-FAM fluorescent dye. The results show that HLA class I polymorphisms might predispose people to develop infectious mononucleosis upon EBV infection. (3712)

Notes: The authors developed a multilocus sequence typing scheme (MLST) to examine sequence variation and discriminate between Aspergillus fumigatus strains. They also examined the distribution of MAT1-1 and MAT1-2 sexual idiomorphs in 100 clinical and environmental isolates. Sexual idiomorphs were determined using PCR and a reverse primer to both idiomorphs and a forward primer specific to either MAT-1 or MAT-2. PCRs consisted of 2mM MgCl₂, 200µM DNTPs and 2.5 units of GoTaq^® DNA Polymerase. (3714)

Notes: These authors generated a set of probes that could be used in fluorescence in situ hybridization (FISH) analyses for karyotyping studies on maize chromosomes. Specific target regions composed of genes or gene clusters and free from repetetive elements were identified for each chromosome. Target regions were amplified by PCR, gel purified using the Wizard^® SV Gel and PCR Clean-Up System, and tested in a FISH assay. Probes showing low background were selected, subcloned into the pGEM^® -T Vector and sequenced to confirm identity. (3627)

Notes: Saliva samples from a total of 142 dogs (36 different pure breeds and several cross breeds) were collected on cotton swabs. Genomic DNA was isolated using the ReadyAmp™ Genomic DNA Purification System. Single amplifications of six canine STR loci were performed using 1–5µl of saliva DNA extract. (3424)

Notes: In this study, genomic DNA was extracted from 99 frozen thymic epithelial tumor samples using the Wizard^® SV Genomic DNA Purification System. Purified DNA was used in TaqMan SNP genotyping assays for 13 epidermal growth factor receptor (EGFR) gene mutations. (3585)

Notes: The expression level of the seven-transmembrane Epstein-Barr virus-induced receptor 2 (EBI2) was measured in peripheral blood mononuclear cells. Total RNA was isolated from T-lymphocytes, B-lymphocytes, monocytes and NK cells, and reverse transcribed using the ImProm-II™ Reverse Transcription System. The resulting cDNA was quantitated using real-time PCR. (3449)

Notes: To examine the flowering time for three new Arabidopsis thaliana recombinant inbred lines (RIL), genomic DNA was isolated from leaves of 92 Arabidopsis accessions and from flower buds of the three RILs using the Wizard^® Magnetic 96 DNA Plant System. The purified DNA was used for single sequence length polymorphisms (SSLPs) genotyping. (3417)

Notes: To study sarcolemmal ATP-sensitive K+ (KATP) channels, transgenic mice were generated that express SUR2A, the proposed regulatory protein of the complex. Genomic DNA was extracted from mouse ears using the Wizard^® SV Genomic DNA Purification System and used for genotyping transgenic animals.
(3584)

Notes: The authors evaluated a 96-channel microfabricated capillary array electrophoresis (µCAE) device for forensic STR typing using the PowerPlex^® 16 System and the AmpFlSTR^® Profiler Plus^® kit. DNA was isolated from one semen (sperm and nonsperm fractions), nine saliva, four blood and two mixed blood stains using either organic extraction or the DNA IQ™ System, then .5–1.0 ng was amplified using the PowerPlex^® 16 System and the AmpFlSTR^® Profiler Plus^® kit according to the manufacturer's instructions. Amplified products were analyzed initially using an ABI PRISM^® 310 or Hitachi FMBIO^® II instrument, then using the µCAE device. All 48 samples, as well as all minor alleles in 3:1 mixture samples, were accurately typed using the µCAE device. (3772)

Notes: The authors developed a new set of miniplex primers for DNA typing of degraded DNA from human skeletal remains. The miniplex primers produced smaller amplicons (50–280 base pairs) than standard STR systems. The DNA-typing results obtained with the miniplex primers were compared to results obtained with the PowerPlex^® 16 System. The authors determined that larger loci failed to amplify when using degraded DNA and that the degradation cut-off length of template fragments occurred predominantly at 200bp and is not kit-dependent. (3808)

Notes: The authors generated Y-STR haplotype frequency data for several ethnic populations in Poland using the PowerPlex^® Y System. DNA was isolated using Chelex^® resin and a proteinase K protocol and amplified, and amplification products were detected using an ABI PRISM^® 310 Genetic Analyzer. (3869)

Notes: The authors conducted a classical twin study to define the genetic contribution to cytokine production and regulation of T cell-specific transcription factors. Twins were classified as monozygotic and dizygotic by typing 15 short tandem repeat loci using the PowerPlex^® 16 System. (3807)

Notes: On November 20, 2002, an explosion in a munitions facility left 7 people dead, 100 injured and 5 missing. The authors used DNA typing to identify 2 tissue samples and 19 bone samples. These samples, as well as reference samples from relatives of the missing persons, were analyzed using the PowerPlex^® 16 System. DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and concentrated, then amplified using 28–30 cycles. For bone samples, the cycle number was increased to 35. The success rate was 90% (19 of 21 samples identified; 2 of 21 samples had a high degree of contamination and could not be identified). (3819)

Notes: To rapidly characterize somatic mutations in the EGF receptor in lung cancer tissues, genomic DNA was extracted from lung biopsies using the Wizard^® SV Genomic DNA Purification System. The extracted DNA was used in a LightCycler SNP genotyping assay to determine the genotype of common loci associated with improved patient response to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. (3588)

Notes: GoTaq^® DNA Polymerase was used in PCR genotyping of Giardia intestinalis. Primers were designed around a 177 bp sequence of the glutamete dehydrogenase gene (gdh). Typing was based on previously reported assemblages of gdh from cats, dogs, cows and monkeys. PCR was performed in a total reaction volume of 25μl using 1.25 units of GoTaq^® DNA Polymerase.
(3364)

Notes: These authors used DNA typing to identify human skeletal remains found in mass graves. DNA was isolated using standard phenol/chloroform extraction, the DNA IQ™ System or other methods. A modified DNA IQ™ System protocol was developed using 2g of pulverized bone. DNA was quantitated using the AluQuant^® Human DNA Quantitation System or Quanti-Blot™ Human DNA quantitation kit. DNA typing was performed using several STR amplification kits, including the PowerPlex^® 16 System. In some cases mitochondrial DNA testing was necessary due to the degree of nuclear DNA degradation. Of the 481 samples, 385 were amplified successfully and 109 sets of remains were identified. (3640)

Notes: These authors used a new DNA purification method that combines cetyltrimethylammonium bromide (CTAB) and isoamyl alcohol/chloroform extraction to isolate DNA from bones soaked in water, burned bones, or bones that had been buried for a long time. Following the CTAB and isoamyl alcohol/chloroform extraction, PCR inhibitors were removed using the DNA IQ™ System or the QIAquick PCR Purification Kit. The authors preferred the DNA IQ™ System because of its speed and ease-of-use. (3642)

Notes: This paper discusses automated DNA purification from a variety of forensic casework samples using the DNA IQ™ System on a Beckman BioMek® 2000 Laboratory Automated Workstation.  DNA was purified from various forensic casework samples including vaginal swabs, blood stains, tissue and samples.  The researchers also tested diluted and contaminated samples and the ability of the DNA IQ™ System on the Beckman BioMek® 2000 to purify DNA from these samples.  The PowerPlex® 1.1 System was used as a representative forensic laboratory typing system to test the contaminant level in all of the DNA IQ™ purified DNA samples.  (3052)

Notes: These authors assessed the risk of transmitting genetic defects to children after intracytoplasmic sperm injection (ICSI) for treatment of male factor infertility. Genomic DNA was isolated from blood of both parents and children using the Wizard® Genomic DNA Purification Kit. Multiplex amplification of 22 sequence tagged sites on the Y chromosome was then performed on 123 samples using the Y Chromosome Deletion Detection System, Version 1.1 and a prototype Multiplex E from Promega. (3117)

Notes: GoTaq^® DNA Polymerase was used in a multiplexed genotyping reaction with three primers to differentiate wild-type, heterozygous, and mutant transgenic mouse alleles simultaneously. The wild-type target was 670bp and the mutant or knockout target was 1,030bp. Various other amplimers (1.4kb, 471bp, & 311bp) were subcloned with the aid of the pGEM^®-T Easy Vector System. (3360)

Notes: The authors evaluated the ability of the PowerPlex^® 16 System to amplify degraded DNA samples and compared the results with those obtained using the AmpFlSTR^® SGM Plus^® kit. They amplified DNA from six whole blood samples that had been stored at 4°C or room temperature for 20 days, DNA isolated from six pairs of archived whole blood samples, and from corresponding plasma samples that had been stored below –20°C for 1–3 years and were assumed to be degraded. Amplifications were assembled and performed using protocols optimized in their laboratory. For the whole blood and plasma samples stored below –20°C, the PowerPlex® 16 System gave eight full profiles and the SGM Plus^® kit gave six full profiles. No differences were observed between the two kits with DNA extracts stored at 4°C or room temperature. As expected, the frequency of allele dropout increased as the amplified fragment length increased. (3876)

Notes: The Wizard^® Genomic DNA Purification System was used to isolate genomic DNA from clinically isolated Haemophilus influenzae samples.  The genomic DNA was then digested with EcoRI and used in Southern blots to identify the presence of various Haemophilus influenzae adhesin genes. (3102)