Notes: The authors examined strains of Salmonella enterica serovar Typhi isolated from typhoid cases originating in or around Indonesia or from travelers returning from Indonesia to examine if serovar Typhi from this area has a greater level of genetic diversity compared to other countries. Genomic DNA was isolated using the Wizard® Genomic DNA Purification Kit, diluted to 4 ng/µl and used in locus-specific PCR genotyping. (3980)

Notes: To determine the usefulness of multilocus sequence typing (MLST) in differentiating Candida species during epidemiological studies, the authors investigated the population structure of C. dubliniensis by amplifying the same 10 MLST loci found to be useful in differentiating isolates of C. albicans, a closely related species. PCRs were performed using 1.25 units of GoTaq^® Flexi DNA Polymerase and 1ng of DNA template in a 50µl reaction. (3880)

Notes: The authors used a microfabricated capillary electrophoresis instrument to rapidly assess the genetic relationship between same-sex twins and their parents and siblings. STR typing was performed to determine if the twins were monozyotic or dizygotic and to confirm familial relationships. The authors used the PowerPlex^® 16 System to examine 15 STR loci in this study. (4045)

Notes: This paper describes analysis of DNA samples at a mock crime scene using automated DNA purification followed by STR analysis on a portable microchip system. The mock crime scene was created using "victim" and "suspect" blood stains prepared by spotting 3µl of liquid blood onto paper towels and a cloth shirt. The samples were allowed to dry overnight before placement at the crime scene. Samples were processed at the scene using the Maxwell^® 16 Instrument and DNA IQ™ Casework Sample Kit for DNA extraction, and a microchip analyzer to perform amplification and STR analysis. The 9-plex autosomal STR typing system used in the microchip system included primer sequences from the PowerPlex^® 16 System (D3S1358, THO1, D21S11, D5S818, D13S317, D7S820, vWA and D8S1179) and amelogenin for sex identification. DNA purification from suspect samples was completed in 2 hours, and subsequent STR analysis and generation of a "suspect" DNA profile took a further 3 hours. The entire process from sample collection to generation of a CODIS "hit" took 6 hours. (3922)

Notes: The authors developed seven new human embryonic stem cell (hESC) lines, five with normal karyotypes and two with abnormal karyotypes. They examined their biological characteristics, STR loci, HLA typing, differentiation capability, imprinted genes, DNA methylation and X chromosome inactivation status to determine if hESC lines with abnormal karyotypes are useful experimental tools. STR genotyping was performed using the PowerPlex® 16 System and the ABI PRISM® 3100 Genetic Analyzer. (4040)

Notes: To study the role of connexin42 (cx43) in testis development, the authors generated a conditional cx43 knockout mouse, which lacked the cx43 gene in Sertoli cells. To confirm that the cx43 gene was deleted in these mice, PCR was performed using primers specific to cx43, 1X Colorless GoTaq^® Flexi Reaction Buffer, 2mM MgCl₂, dNTPs and 0.15µl of GoTaq^® DNA Polymerase. Tissue-specific deletion of cx43 was confirmed by amplifying RNA isolated from mouse testis, heart and tail was also confirmed using the same PCR components. (3713)

Notes: The authors analyzed 1,308 samples for concordance between the Identifiler^® kit, AmpFlSTR^® Minifiler™ kit and PowerPlex^® 16 System. DNA was isolated from liquid blood using the manual DNA IQ™ System protocol, and STR amplifications were performed as per the manufacturer's recommendations except that reaction volumes were decreased by half. Amplified products were analyzed using an Applied Biosystems 3130xl and POP™-4 or POP™-6 polymer. Twenty seven disconcordant phenotypes were identified between the Minifiler™ and Identifiler^® kits, 14 between Minifiler™ and PowerPlex^® 16 kits, and 4 between PowerPlex^® 16 and Identifiler^® kits. (3770)

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)