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 studied the defective prophage KplE1 in E. coli K12 to map the binding sites of proteins required for recombination. Prior to in vivo excision assays in two E. coli K12 strains, the presence of three DNA sequences required for recombination was confirmed by PCR using GoTaq^® DNA Polymerase. In vitro excision assays were also performed using linear and supercoiled DNA substrates that were purified using the Wizard^® PCR Clean-Up System. Finally the phage-encoded integraseS (IntS) mRNA was quantitated by real-time RT-PCR. The RNA template was purified from E. coli K12 using the PureYield™ RNA Midiprep System. (3722)

Notes: This study looked at how OX40, a member of the TNFR superfamily, affected the differentiation of CD8 T cells with an OX40 agonist. Recombinant lentiviruses were generated by cotransfection of a vector plasmid, virus-packaging plasmid, envelope plasmid and the helper pAdVAntage™ Vector into HEK 293 cells. The supernatant was collected and used to infect tumor cells which were injected into mice. (3753)

Notes: The authors studied hsp70 mRNA degradation in Drosophila Schneider cells. mRNA deadenylation and decay were monitored by Northern blot. Two of the Northern blot probes used to visualize the mRNA decay products were synthesized by transcription of linearized plasmids using T7 RNA Polymerase and [α-³²P] UTP. A population of deadenylated mRNA was created by hybridizing mRNA with oligo(dT) and treating with RNase H. CCR4•NOT was identified as the main deadenylase involved in mRNA decay, and the PAN2:PAN3 deadenylase was a minor contributor. RNA interference was used to knock down expression of PAN2 and CAF1, a subunit of CCR4•NOT, to assess the effect on mRNA decay. Reduced expression levels of PAN2 and CAF1 were confirmed by semi-quantitative RT-PCR and Western blotting, respectively. RT-PCR was performed using 1.5µg total RNA and 150 units of MMLV Reverse Transcriptase in a 25µl reaction. One microliter of the RT reaction was used as a template in an 80µl PCR using 0.5 units of GoTaq^® DNA Polymerase, 1.5mM MgCl₂ and 1X Green GoTaq^® Flexi Reaction Buffer. (3707)

Notes: The authors of this paper describe the validation of a bioluminescent assay using the CellTiter-Glo^® Reagent to identify novel compounds that inhibit the cytopathic effect of SARS CoV. In this study, three cell viability assay reagents were evaluated: MTS, neutral red, and CellTiter-Glo^® Reagent. The CellTiter-Glo^®-based assay was chosen because it did not require washing or medium removal; it involved minimal pipetting steps and had a short incubation time, which reduced time in the BSL3 containment facility. The assay was used to screen 100,000 compounds and identified several compounds that inhibited CPE while having a minimal effect on cell viability. (3736)

Notes: To examine the effects of hormones on Gas6, a plasma vitamin K-dependent protein that may play a role in cardiovascular disease, the authors developed an ELISA test for Gas6, which they tested on blood from male and female volunteers. A recombinant Gas6 control was developed by reverse transcribing the full-length human Gas6 mRNA from human umbilical vein endothelial cells, amplifying the cDNA using nested PCR and after restriction digestion, ligating the insert into the EcoRI and XbaI sites of the pCI-neo Mammalian Expression Vector. The full-length construct was confirmed by sequencing and then tested in the Gas6 ELISA. (3688)

Notes: The authors examined transcriptional regulation of the vitamin D receptor (VDR) by p53 and p63, a member of the p53 family, under stressed and unstressed conditions. Reporter constructs with the full-length and minimal VDR promoters controlling expression of firefly luciferase were cotransfected with p53 or p63 expression constructs, and transcriptional activation of the VDR promoter was monitored using the Dual-Luciferase^® Reporter 100 Assay System. Results were normalized to Renilla luciferase activity. Interaction between p73, another member of the p53 family, and the VDR promoter was examined using chromatin immunoprecipitation. The imunnopreciptated chromatin was reverse crosslinked, DNA was eluted and VDR and p21 sequences were detected by PCR using GoTaq^® Green Master Mix. (3715)

Notes: To study how chemotherapy affects hair follicles (HF), the researchers microdissected and cultured human anagen VI scalp follicles and treated the cells with 4-Hydroperoxycyclophosphamide (4-HC) at similar concentrations to those received during therapy. After incubation for 24 hours with 30µmol/L of 4-HC, the HFs were homogenized and genomic DNA was purified using the Wizard^® SV Genomic DNA Purification System. To determine if the treatment induced the mitochondrial common DNA deletion, the isolated DNA was subjected to real-time PCR. Further examination of gene expression was performed by isolating total RNA from two HF samples, reverse transcribing 3µg of the RNA using 15U of AMV Reverse Transcriptase and 0.025 µg/µl random primers, and amplifying seven human genes in a TaqMan^® Assay. (3746)

Notes: The authors characterized mutations in the acetyl-coenzyme A carboxylase (ACCase) gene that confer resistance to the herbicide clethodim in the grass weed Lolium rigidum. The ACCase gene was amplified from clethidem-resistant and susceptible plants, then sequenced to identify previously unknown mutations. Amplifications of ACCase were performed using 300ng of genomic DNA and GoTaq^® Green Master Mix. The Wizard^® SV Gel and PCR Clean-Up System was used to purify PCR products directly or from agarose gels. (3721)

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: The authors explored the possibility of a domain-based level of gene expression regulation for chromosomes by integrating the green fluorescent protein (GFP) reporter in 90 different locations in cultured human cells. This integration was accomplished by infecting human embryonic kidney cells (HEK293) with a lentiviral construct carrying the GFP gene under the control of the ubiquitously expressed human phosphoglycerate kinase (PGK), sorting GFP-positive cells by FACS and selecting clones for expansion. Genomic DNA was isolated from the various clones using the Wizard^® SV Genomic DNA Purification System and analyzed by PCR or restriction digested for Southern blotting. (3743)

Notes: Telomeres shorten by 50–100 bases with each cell division, making the telomere a "mitotic counter" that can limit cellular lifespan. Telomerase is a two-component protein consisting of a reverse transcriptase (hTERT) bound to its own RNA template that can act to maintain telomere length in dividing cells. Telomerase is highly active in dividing cells such as germ cells, stem cells and many cancers. This paper investigated the role of methylation of the hTERT promoter and the transcription factor CTCF in regulation of telomerase activity. LacZ reporter plasmids driven by the hTERT minimal promoter were transiently transfected into HeLa cells, and reporter assays were performed on lysate generated using Passive Lysis Buffer. The hTERT minimal promoter did not show activity if all of the CpG sites were methylated. The promoter and first exon of hTERT were amplified using PCR Master Mix from sodium bisulfite-treated genomic DNA isolated from telomerase-positive cell lines and tissues. The resulting fragments were cloned using the pGEM^®-T Vector System II. For the methylation cassette assay, methylated and unmethylated fragments were cloned into a methylated or unmethylated vector using the LigaFast™ Rapid DNA Ligation System. The authors conclude that methylation plays a dual role in regulating hTERT expression. CTCF will bind to the first exon of hTERT when the hTERT CpG island is not methylated, resulting in downregulation of hTERT expression. Although CTCF cannot bind the hTERT promoter when the DNA is completely methylated, the methylation itself completely represses transcription. In situations where there is partial methylation of the promoter, such as in tumor cells, CTCF cannot bind to the promoter, but the partial methylation is not enough to repress transcription, and hTERT is expressed. (3641)

Notes: The authors examined the deacylation activity of acyloxyacyl hydrolase (AOAH) against a protein:lipooligosaccharides (LOS) complex. A soluble, truncated form of endotoxin-binding protein CD14 (sCD14) was expressed with a hexapolyhistidine tag from a baculovirus vector in High Five insect cells and used to form [³H]LOS:protein complexes. These complexes were incubated with AOAH for 4 hours, then purified using the HisLink™ Protein Purification Resin. The degree of deacylation of the LOS was determined using liquid scintillation spectroscopy. No imidazole was used in the binding buffer or rinses. The buffer did contain 0.1% bovine serum albumin. (3698)

Notes: This paper explored the process by which the Eph receptor EphA2 regulates repulsive response in prostatic carcinoma cells via the ephrinA1 ligand. Focal adhesion kinase (FAK) non-related kinase (FRNK; a target in the ephrinA1 ligand cascade) was subcloned into the pTargeT™ Mammalian Expression Vector. This mutant FAK was transfected into PC-3 cells and subjected to a GST-pulldown assay to examine RhoA activation. In addition, PC-3 cells transfected with several targets in the EphA2/ephrinA1 activation cascade including FRNK were subjected to an in vitro three-dimensional migration assay. (3690)

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: While the absence of the Vitamin D receptor (VDR) has profound effects in skin cells, mutation of 25-hydroxyvitamin D 1α-hydroxylase (24OHase), the enzyme required for 1,25-dihydroxyvitamin D₃ (1,25(OH)₂D₃) hormone biosynthesis, has little effect on the skin. To determine how VDR may transactivate independent of the 1,25(OH)₂D₃ ligand, the human 24-hydroxylase promoter was amplified from MCF-7 genomic DNA, digested with XhoI and HindIII and inserted into the pGL3-Basic Vector. Mutations in the proximal and distal vitamin D response elements in the human 24-hydroxylase promoter were introduced using the GeneEditor™ Site-Directed Mutagenesis System. HaCaT cells, primary human fibroblasts or primary human keratinocytes were seeded at a density of 3.2 × 10⁴ cells/well in 12-well plates and transiently transfected with reporter constructs. After 18 hours, the cells were exposed to 1,25(OH)₂D₃, 9-cis-retinoic acid, ethanol vehicle, or no additive and harvested 24 hours later. The luciferase activity of the cell lysates was measured using the Dual-Luciferase^® Reporter Assay System. Five micrograms of RNA purified from mouse keratinocyte and fibroblast cultures was reverse transcribed and amplified for the 24OHase transcripts using the PCR Master Mix. The products were analyzed on ethidium bromide-stained 2% agarose gels. (3695)

Notes: The authors used reporter assays and coimmunoprecipitation experiments to compare the zebrafish (Danio rerio) Toll-IL-1R-containing adaptor molecule 1 (TICAM1) activation of NF-κB and zebrafish type I IFN to mammalian TICAM1 activation. 293H and ZFL (zebrafish liver) cells were cotransfected with 400 ng of TICAM1 construct (mouse, zebrafish or a deletion construct), 400 ng of a reporter construct (e.g., a zebrafish IFN promoter cloned into the pGL3-Basic Vector) and 10 ng of pRL-CMV Vector, an internal control to normalize data. After 24 hours for 293H cells and 48 hours for ZFL cells, the transfected cells were lysed, and luciferase activity was measured using the Dual-Luciferase^® Reporter Assay System. For coimmunoprecipitation experiments, 293H cells were cotransfected with a total of 8µg of plasmids (3µg of zebrafish or mouse TICAM1 construct, 3µg of interacting protein construct, 1µg of the pAdVAntage™ Vector, and 1µg of antiapoptotic protein p35 construct). Forty-eight hours posttransfection, the cells were lysed, the protein bound to affinity resins and analyzed by Western blot. (3755)

Notes: To examine gross changes in DNA content, genomic DNA was isolated from chicken retinospheroid cultures treated with diazinon, an organophosphate pesticide. DNA purified with the Wizard^® SV Genomic DNA Purification System was used to determine changes in total DNA content after pesticide exposure. (3586)

Notes: The authors characterized expression of extracellular proteins by white-rot fungus, Phanerochaete chrysosporium, grown on wood. Temporal expression of these proteins was monitored by relative quantitative RT-PCR. Two micrograms of total RNA was reversed transcribed using 1µg of Random Primers at 37°C for 1 hour. PCRs with one set of PCR primers were performed using 0.5 units of GoTaq^® DNA Polymerase, 1X reaction buffer, 250µM each dNTP, 0.5µM each primer and 1µl of cDNA. PCRs with two sets of PCR primers were performed using 2.5 units of GoTaq^® DNA Polymerase, 1.6X reaction buffer, 500µM each dNTP, 0.5µM each primer and 1µl of cDNA. (3708)

Notes: The authors transfected the myleoid leukemic cell line K562 with the cytosolic sialidase Neu2. Expression of Neu2 resulted in a significant decrease in mRNA levels for the anti-apoptotic factors Bcl-XL and Bcl-2 as determined by real-time PCR. Reverse transcription was carried out with 1µg of total RNA using the ImProm-II™ Reverse Transcription System and random hexamers. cDNA representing 10ng of total RNA was used in a real-time PCR to quantitate Bcl-XL and Bcl-2 mRNA levels. (3725)

Notes: In this study, the HIV Tat gene was expressed in tomato plants. Mice were given 10mg of tomato fruit extract from either transgenic or wild-type plants orally, intraperitoneally and intramuscularly. A strong anti-Tat immune response was obtained in mice immunized with the transgenic fruit, regardless of the administration route. Mice that received oral vaccination developed early evidence of mucosal immunity. Sera from the immunized mice inhibited Tat-dependent transactivation of the HIV long terminal repeat promoter in a luciferase reporter assay. (3706)

Notes: The authors were looking for a method for ligand fishing experiments with plant receptor-like kinases (RLKs). The strategy chosen, functional immobilization on microbeads, used phytosulfokine (PSK) and its carrot cell receptor (DcPSKR1) as the test ligand-receptor pair. DcPSKR1 was cloned into the pHT2 HaloTag^® Vector, adding the HaloTag^® gene to the C terminus of DcPSKR1 or replacing the DcPSKR1 kinase domain. These constructs were transfected into BY-2 cells and expression confirmed by immunoblotting the membrane fraction and staining with DcPSKR1 and Anti-HaloTag antibodies. To confirm activity of the individual proteins, membrane fractions of BY-2 cells expressing the DcPSKR1-HaloTag^® fusion proteins were tested for PSK binding activity to then HaloTag^® binding activity confirmed using the HaloTag^® TMR Ligand. The DcPSKR1-ΔKD-Halo protein was immobilized on HaloLink™ Resin and the K_d measured. The binding of PSK to the immobilized DcPSKR1-ΔKD-Halo protein was visualized by using fluorescently labeled Alexa488-PSK. Columns of HaloLink™ Resin with bound DcPSKR1-ΔKD-Halo protein were used to bind PSK ligands at physiological concentration, elute the ligands with a high-salt buffer and analyzed on LC-MS. (3946)

Notes: Endosomal sorting complexes required for transport (ESCRTs) are necessary for sorting membrane proteins into the intralumenal vesicles of the multivesicular body for eventual degradation by the lysosome/vacuole. Mutations in at least one subunit of the ESCRTs are associated with frontotemporal dementia and ALS. In this study, the authors demonstrate that ESCRTs are required for autophagy and prevention of protein aggregation. They address the question of whether loss of ESCRTs might interfere with proteasome activity. Using the Proteasome-Glo™ Chymotrypsin-Like Cell-Based Assay, they show that proteasome activity is minimally affected in ESCRT-depleted cells. (3847)

Notes: For protein expression profiling of cancer cells treated with 17-allylamino-17-demethoxygeldanamycin (17AAG), a compound with known antitumor activity, lysates were prepared from A2780 cells, a human ovarian adenocarcinoma cell line, and subjected to two-dimensional protein analysis. The spots that varied in intensity in 17AAG-treated cells when compared to control cells were excised and the protein gel slice was reduced, alkylated and in-gel digested using Sequencing Grade Modified Trypsin. (3601)

Notes: The authors sought to identify the mediators of transmission of HIV across the mucosal barrier in humans. They noted that transmission occurs even the genital tract epithelium is seemingly not damaged. In this study they showed that gp340 expressed on primary female genital epithelial cells binds HIV-1 and enhances transmission of otherwise subinfectious amounts of HIV to infect cells, also allowing transmission to occur over longer time periods. Their study methods included plating a variety of cell types, incubating these cells with HIV, and lysing the cells with Luciferase Cell Culture Lysis Reagent, then measuring HIV-1 p24 content by ELISA. (3701)