Notes: Three protocols using ReliaPrep™ Blood gDNA Miniprep System kit and three protocols based on the classical phenol-chloroform extraction method were compared with respect to the yield and quality of the extracted DNA from 24 male sand flies. To evaluate the integrity and purtiy of the extracted DNA, PCR reactions were performed in a final volume of 25μL, containing 5μL of gDNA, 12.5μL of GoTaq MasterMix. (4981)

Notes: The authors amplified the HLA-A, B, C, DRB1, DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci by PCR. The amplicons were then quantified with the QuantiFluor® dsDNA System prior to library preparation and Illumina (MiSeq) sequencing. (4799)

Notes: Th authors made purified bacterial DNA into amplicon libraries, quantified using the QuantiFluor® dsDNA System and sequenced on an Illumina MiSeq. (4801)

Notes: The authors quantified amplicon libraries using the QuantiFluor® dsDNA System and the GloMax®-Multi Detection System prior to pooling and sequencing on a 454-GS-FLX Titanium System. (4795)

Notes: The authors examined the usefulness of additional Y-STRs in distinguishing between unknown DNA donor and a database sample and for familial searching or estimating the geographical origin of the donor. They generated Y-STR haplotypes for 535 patrilineal-unrelated males from Flanders (Belgium). This geographic region was chosen because the Y-chromosomal variation and distribution are well characterized. By typing an additional 5 Y-STR loci (23 loci compared to 17), the authors were able to better discriminate between men with nearly identical Y-STR haplotypes, with a much lower number of uninformative Y-STR haplotype matches. A 23-locus haplotype was also more valuable for familial DNA searching and estimating the geographical origin of a DNA donor. (4505)

Notes:   (5199)

Notes: Researchers were looking for alternative methods to using transposase vectors carried by lentiviruses to insert genes into cellular DNA without the cytotoxicity that may occur if the transposase gene integrated into the genome. In this paper, the authors worked out a method to generate lentiviral particles that carried the transposase protein for delivery of genes at an equal efficiency as the conventional plasmid-based method. The reporter gene NanoLuc® luciferase was amplified from the pNL1.1[Nluc] Vector and cloned into a gag-pol-integrase-defective packaging construct. Firefly luciferase was cloned into the PB transposon lentiviral vector. Gag-pol constructs expressing the hyperactive piggyback (PB) transposase were also created. Lentiviral particles (LPs) were generated by cotransfection of several plasmids into 293T cells. One day prior to transduction, HeLa cells were seeded at a density of 10⁴ cells/well in a 96-well plate, then NanoLuc® LPs with or without pseudotyping by Vesicular Stomatitis Virus envelope glycoprotein were added. After 48 hours, luminescence was measured using the Nano-Glo® Luciferase Assay System. To analyze how well the firefly luciferase gene was transferred, HaCaT and ARPE-19 cells were seeded at 1,000 cells/well in a 96-well plate one day before transduction with increasing amounts of either wildtype or mutated PBase/firefly luciferase transposon LPs. After ten days, the transduced cells were assessed for luminescence using the ONE-Glo™ Luciferase Assay System. HEK293 cells, primary keratinocytes and normal human dermal fibroblasts were seeded at 5,000 cells/well in 24-well plates the day before transduction and then incubated with either wildtype or mutated PBase/firefly luciferase transposon LPs. After eight days, firefly luminescence was measured. (4448)

Notes: Human Genomic DNA: Male was used to construct a reference mock clinical sample. (4545)

Notes: The authors of this study sought to apply a genotyping-by-sequencing approach to genotype cattle from the US and Africa. They collected blood samples from 47 unrelated animals slaughtered in the US and Nigeria. Genomic DNA was extracted and then quantitated using the QuantiFluor® dsDNA System on a SpectraFluor Plus plate-format fluorometer before being used for next-generation sequencing. (4508)

Notes: In this study, the authors evaluated “genotyping-by-sequencing” for the economically important lodgepole pine and white spruce conifer species. DNA samples extracted from dormant vegetative buds and DNA was quantitated using Quantifluor® ds DNA System on a SpectraFluor Plus plate-format fluorometer. (4507)

Notes: The authors extracted DNA from dormant vegetative buds and quantitated DNA using the QuantiFluor® dsDNA System on a SpectraFluor Plus plate-format fluorometer prior to NGS (4917)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Haemophilus influenzae. (4336)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Babesia spp. (4310)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Flavobacterium psychrophilum. (4334)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Campylobacter coli. (4316)

Notes: This study examined how well primers developed in 1990 and 2004 for type A rotavirus (RVA) were able to genotype (G type) currently circulating RVAs in Asia. The VP7 gene from RVA was amplified using 2µl of dsRNA template with the AccessQuick™ RT-PCR System in a total volume of 50µl. The G type was determined using hemi-nested multiplex PCR using 1µl of the VP7 cDNA and PCR Master Mix in a final volume of 50µl. The final products were sequenced. (4340)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Fusobacterium nucleatum. (4335)

Notes: DNA templates are often amplified by PCR during library generation prior to next-generation sequencing, but amplification can introduce biases and duplications that are not easily corrected. In this paper, the authors developed a simple method to count the number of input template molecules to reduce these PCR-related problems: The ligation of a degenerate base region to all fragments during library creation. To evaluate their approach to correct for biases and duplications, the authors created a library using Human Genomic DNA, amplified the library by inverse PCR using the GoTaq^® Hot Start Polymerase and 1X Colorless GoTaq^® Flexi Buffer, sequenced the resulting DNA fragments and assessed the quality of the next-generation sequencing data. (4160)

Notes: Mineral accumulation was studied in Arabidopsis thaliana comparing loci involved with growing in soil versus hydroponics. An F2 population derived from a cross between Landsberg erecta (Ler; maternal parent) and Eringsboda-1 (Eri-1; paternal parent) was propagated by single seed descent for nine successive generations in soil.
The flower buds of three plants per line were collected, and the DNA extracted using the Wizard® Magnetic 96 DNA Plant System and used for genotyping with 90 amplified fragment length polymorphism PCR (AFLP) and 39 single sequence length polymorphisms (SSLP) markers to build a genetic map of quantitative trait loci (QTL). (4136)

Notes: This study examined the genotype-phenotype correlation of the two major UGT isoforms, UGT1A1 and UGT1A6, involved in resveratrol metabolism. Genomic DNA was isolated from 30mg human liver tissue samples (normal and metastatic) using the Wizard^® SV Genomic DNA Purification System. The purified DNA was eluted with 65°C water and 200–400ng of eluted DNA was used in a PCR-RFLP UGT1A6 genotyping assay. Amplification was carried out using PCR Master Mix in a final volume of 50µl, and the amplimers digested with appropriate restriction enzymes. (4018)

Notes: The authors describe a new form of PCR, co-amplification at lower denaturation temperature PCR (COLD-PCR), to detect low-level somatic mutations. This technique is based on the facts that a) each DNA sequence has a critical denaturation temperature (T_c), which is lower than the melting temperature (T_m) and below which PCR efficiency decreases dramatically and b) Tc depends on DNA sequence. The authors used GoTaq^® Flexi DNA Polymerase and mutation-specific TaqMan^® probes for tumor protein 53 (TP53) and epidermal growth factor receptor (EGFR) to detect low-level somatic mutations in a mixture of wildtype and mutant DNAs. Conventional TaqMan^_® technology can detect mutant alleles at an abundance of 10–20% of that of the wildtype allele; using COLD-PCR the authors were able to increase selectivity 15- to 30-fold, detecting as little as 0.8% mutuant alleles. (4038)

Notes: In 1991, the remains of murdered Emperor Nicholas II, Empress Alexandra and three of their five children were discovered. Until recently, the remains of the two other children were never found. In July of 2007 human bone fragments were discovered at a second grave site in the Ural region of Russia. The authors performed DNA typing to determine if these remains were those of the two missing children. Bone fragments and teeth were subjected to mitochondrial and nuclear DNA typing. DNA was quantitated using the Plexor® HY System. Nuclear DNA analysis was performed, in part, using the PowerPlex® S5 System. A comparison of mitochondrial DNA sequences from remains in the first and second graves and from maternal reference samples confirmed that the remains constituted a family with a "Queen Victoria" mitotype (Empress Alexandra was the granddaughter of Queen Victoria). Y-STR analysis of both sets of remains was performed, and the results confirmed that the Y-STR haplotypes of the two sets of male remains matched, and this haplotype matched that of several descendants from an unbroken paternal lineage of Nicholas I, father of Nicholas II. The mitochondrial and Y-STR haplotypes and autosomal STR profile also matched those obtained from a bloodstained shirt that Nicholas II was wearing during an assassination attempt. (3967)

Notes: These authors used the Maxwell^® 16 System to isolate DNA from frozen whole blood samples infected with Plasmodium falciparum. The isolated DNA was used in a qPCR-based SNP genotyping assay that sought to uniquely identify the parasites based on their SNP marker profile. (3962)

Notes: The authors developed a new human prostate cancer cell line, CWR22Pc, that is both androgen-dependent and able to produce tumors in dihydrotestosterone-supplemented nude mice. To confirm that CWR22Pc cells are derived from primary CWR22 human prostate xenograft tumors, the authors performed genotyping at 8 STR loci and amelogenin using the PowerPlex^® 1.2 System. DNA purification from the cell line and original tumor samples was performed using the Wizard^® Genomic DNA Purification Kit. (4041)

Notes: Somatic cell nuclear transfer technique was used to generate human blastocyst-stage embryos using nuclei from adult male fibroblasts cell lines and enucleated oocytes. Genomic DNA was analyzed using the PowerPlex® 16 system to confirm the genetic identity of the blastocyst cells. (3952)