Notes: These authors used the Maxwell® 16 Tissue DNA Purification Kit to extract DNA from 200µl samples of raw meat homogenate from beef, pork, poultry and lamb samples. They also used the Wizard® Genomic DNA Isolation System to extract DNA from cooked meat samples. The extracted DNA was used in real-time, quantitative PCR assays to identify species-specific DNA spiked at 1% in mixed DNA samples. (4353)

Notes: The authors of this paper describe the development of a high-throughput assay to screen for antibody inhibitors of 5´-ectonucleotidase activity (converts AMP to adeonsine plus free phosphate). They used the CellTiter-Glo® Cell Viability Assay to screen for activity. The CellTiter-Glo® luciferase reaction is inhibited by AMP; activity of 5´-ectonucleotidase eliminates AMP, thereby relieving the reaction from inhibition, producing light. The authors demonstrate release of the luciferase reaction from inhibition as a result of 5´-ectonucleotidase activity, and that they were able to show inhibition of 5´-ectonucleotidase activity by anti-5´-ectonucleotidase antibodies. (4261)

Notes: The authors of this study investigated the energetic effects of direct fed microbials on 1-day-old broiler chicks. They looked at body weight, feed consumption, whole-body energy expenditure, organ mass, tissue respiration rates and peripheral blood mononuclear cell (PBMC) ATP levels to explore effects on energy metabolism in control-diet chicks versus chicks receiving direct fed microbials. An ATP assay was used because previous attempts to monitor O₂ use by PMBCs were inconclusive. PBMC ATP levels were measured using the CellTiter-Glo™ Luminescent Cell Viability Assay in 96-well plates using 10 × 10⁵ cells/well. The authors also looked for differences in ATP depletion in control and experimental chick populations by using an ATP synthase inhibitor and a proton ionophore. In this study, the authors concluded that the PMBC isolated from the direct microbial fed animals consumed more ATP/cell than the controls. (4202)

Notes: These authors describe the engineering of an enzyme and substrate to create a novel highly efficient bioluminescence system. The paper introduces NanoLuc™ Luciferase, a small luciferase subunit (19kDa) from the deep-sea shrimp Oplophorus gracilirostris, which provides ∼2.5 millionfold improved luminescence activity in mammalian cells by merging optimization of protein structure with development of a novel imidazopyrazinone substrate (furimazine). The glow-type luminescence (signal half-life >2 hours) produced by the new luciferase has a specific activity ∼150-fold greater than either firefly or Renilla luciferases similarly configured for glow-type assays. In mammalian cells, NanoLuc™ Luciferase shows no evidence of post-translational modifications or subcellular partitioning. The enzyme exhibits high physical stability, retaining activity with incubation up to 55°C or in culture medium for >15 hours at 37°C.
The authors discuss utility of NanoLuc™ Luciferase as a genetic reporter configured for high sensitivity or for response dynamics through addition of a degradation sequence to reduce intracellular accumulation. Data shows the effect of adding a signal sequence to allow export of NanoLuc™ Luciferase to the culture medium, allowing measurement of enzyme activity without cell lysis. (4295)

Notes: To better understand what roles FAM123A may play in signaling, cell behavior and human disease, HT1080 sarcoma cells were plated on MatTek dishes coated with 5mg/ml fibronectin before transfection with Venus (a yellow fluorescent protein)-tagged FAM123A or Venus-WTX, another member of the FAM123 gene family, using FuGENE® HD Transfection Reagent. The cells were imaged the next day for low-resolution analysis. For a higher magnification, dynamic analysis, HT1080 cells were plated onto Delta T dishes coated with 5mg/ml fibronectin and transfected with EGFP-FAM123A and FuGENE® HD Transfection Reagent. The next day, cell images were captured every 10 seconds. Examining the effect of silencing FAM123A, a reporter assay used the pGL4.34[luc2P/SRFRE/Hygro] Vector cotransfected with a CMV-Renilla coreporter and other effector plasmids or siRNA, and luciferase levels assessed using the Dual-Glo® Luciferase Assay System. (4246)

Notes: The authors transiently transfected 2 × 10⁴ HEK293 cells per well of a 96-well plate using the FuGene® HD Transfection Reagent, 0.1µg of DNA and a reagent:DNA ratio of 3:1. (4430)

Notes: Caspase-Glo® 3/7 and Caspase-Glo® 8 Assays were used to assess activation of apoptosis pathways in MC3T3-E1 cells (clonal mouse), U-2 OS human osteoscarcoma cell line and CCL-51 cells (mouse mammary gland tumor cells). Although ibandronate reduced cell proliferation in all cell lines, its effect on activation of caspases was different in neoplastic versus non-neoplastic cells. Caspase-8 and caspase-3/7 activities were reduced in MC3T3-E1 cells after 72 hours treatment with ibandronate. In two tumor cell lines assayed, opposite results were seen: caspase-8 and caspase-3/7 activities increased in U-2 OS cells and in CCL-51 cells. Luminescence was detected using a GloMax® 96 Microplate Luminometer. (Figure 1 in the paper)

To analyze FAS promoter methylation levels, fragments of the targeted promoter regions were generated by digestion of genomic DNA using CpG methylation insensitive restriction enzymes MboII and PstI from cells cultured in the presence of ibandronate for varying lengths of time. The authors demonstrated that FAS promoter methylation is altered in tumor cells in the presence of ibandronate. (4253)

Notes: These authors investigated the effects of various anesthetics on bioluminescence imaging with firefly luciferase. They observed decreases in luminescence with volatile anaethetics, and found increased luciferase expression with injectable anaethetics in intact cells, but not in cell lysates in vitro. They concluded that the decreases in luciferase activity observed with volatile anaesthesia were due to hemodynamic effects, and not due to a direct inhibitory effect on luciferase enzyme itself. The apparent enhancement of luciferase activity with certain injectable anaesthetics appeared to be due to cytotoxic effects that resulted in increased permeablity to luciferase, as the same enhancement was not observed in cell lysates. D-Luciferin was used for in vivo imaging experiments. The pGL4.10 vector (encoding firefly luciferase), Luciferase Assay Reagent, and the GloMax® 96 Microplate Luminometer were used for in vitro assays using cell lysates. (4190)

Notes: The E3 ubiquitin ligase murine double minute 2 (MDM2) regulates transcriptional activity and expression levels of the p53 tumor suppressor protein. In this article, the authors show that the cell fate determinant NUMB interacts with MDM2, disrupting the interaction of MDM2 and p53 and preventing the ubiquitination of p53. To study protein-protein interactions between NUMB and MDM2, the authors used the pFN2A (GST) Flexi® Vector to express full-length and partial NUMB sequences as GST fusion proteins for protein pull-down experiments. To examine their hypothesis that the interaction between NUMB and MDM2 increases p53 levels and thus apoptosis in cells, they treated ZR75 human breast carcinoma cells and A375 human melanoma cells with NUMB-derived peptides and small molecule ligands that block the interaction between NUMB and MDM2. These treatments resulted in increased levels of p53 protein, Annexin V staining as well as caspase-3/7 activity, as determined using the Caspase-Glo® 3/7 Assay System. (4351)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Anabaena sp. (4299)

Notes: This study identified that miR-21 is significantly overexpressed in human cervical squamous cancer tissues and cell lines, and showed that the level of miR-21 correlates with tumor differentiation, and regulates proliferation, apoptosis, and migration of HPV16-positive cells. The authors used gene expression profiling and luciferase reporter assay to identify candidate target genes for miR-21. Wildtype and mutant 3′-UTR sequences from the target gene CCL20 containing putative binding sites for miR-21 were subcloned into the psiCHECK-2 Vector and used to transfect HEK293 cells. The Dual-Luciferase® Reporter Assay System and GloMax® Multi Luminometer were used to measure luciferase activity from both constructs. (4192)

Notes: This study describes the clinical observations and laboratory investigations performed on 170 of the 2,000 suspected West Niles Virus (WNV) cases. These cases were admitted to Aravind Eye Hospital, Madurai, Tamil Nadu with ocular complications. Conventional reverse transcription PCR (RT-PCR) and real-time RT-PCR assays were used to detect WNV infection. In addition, reverse transcription loop-mediated isothermal gene amplification (RT-LAMP) was performed to determine the feasibility of using this method as an alternative cost-effective tool to the real-time RT-PCR.

After proving negative for DENV- and CHIKV, samples were tested for the presence of WNV-specific RNA by RT-PCR, real-time RT-PCR and RT-LAMP assays. RNA was extracted from the patient serum, plasma and infected culture supernatant. The RNA was then eluted in 50µl of nuclease-free water and used as template in the AccessQuick™ RT-PCR System, with primer pairs targeting the env gene.

Amplification was performed in a 50µl total reaction volume with the AccessQuick™ RT-PCR System, using 50pmol of each forward and reverse primer and 2µl of extracted viral RNA. (4331)

Notes: To better understand the role MOV10 protein, a putative RNA helicase and component of the RNA–induced silencing complex (RISC), in reducing retrotransposon activity, 293T human embryonic kidney cells expressing MOV10 and one of three retrotransposons (LINE1 (L1), Alu or SVA) were lysed in a buffer that included RNasin® Ribonuclease Inhibitor, and FLAG-tagged L1 complexes immunoprecipitated and analyzed by mass spectrometry. Several retrotransposon assays were conducted using FuGENE® HD Transfection Reagent for transfected constructs into 293T, HeLa and HeLa-HA cells. (4255)

Notes: 5-aminolevulinic acid (5-ALA)-induced protoprophyrin IX (PpIX) fluorescence is often used for diagnostics and therapy in malignant glioma surgery; however changes in the ability of malignant glioma cells to accumulate PpIX can result in erroneous interpretation of the fluorescent signal and affect the safety of fluorescence-guided surgery. Such changes can result from several factors, including drug interactions. The authors of this paper investigated the effects of antiepiletic drugs (AED) commonly given to glioma patients on the ability of glioma cells to accumulate PpIX. They looked at cell health and metabolism in glioma cells treated with these drugs, including glutathione metabolism. The GSH/GSSG-Glo™ Assay was used to generate a ratio of reduced (GSH) and oxidized (GSSG) glutathione in glioma cell lines (U-87 MG and U373 MG). Cells were seeded at 5 × 10³ cells/well in 96-well plates and treated with either 47µg/ml phenytoin, 104µg/ml levetiracetam or DMSO-only for three days, and the assay was performed as described in the technical manual. Neither test compound effected the GSH/GSSG ratio.  (4211)

Notes: The authors of this paper studied the targeting mode of the Parkinson disease-associated kinase Pink1. They constructed a number of truncation and deletion mutants in the pGEM®-4Z Vector, and verified the identity of these clones using next-generation sequencing. The authors then expressed radiolabeled versions of the various Pink1 constructs using the TNT® Coupled Rabbit Reticulocyte Lysate System. These labeled proteins were used in mitochondrial localization studies.   (4563)

Notes: Genomic DNA was extracted from shoot fragments using an organic extraction procedure and purified using the Wizard® SV Gel and PCR Clean-Up System prior to template preparation by nested PCR. Products from the second PCR were separated by electrophoresis and purified using the Wizard® SV Gel and PCR Clean-Up System prior to pyrosequencing. (4548)

Notes: In this study the Wizard® Genomic DNA Purification Kit was used to isolate DNA from Acinetobacter baumannii. (4274)

Notes: In this study, the authors evaluated whether application of the phytochemical shikonin to the skin of mice was able to augment the effect of a DNA-based anti-tumor vaccine by inducing the cytokine RANTES. As part of the study, the AccessQuick™ System was used in RT-PCR analysis to determine expression of RANTES mRNA in treated and control skin samples. (4288)

Notes: These authors investigated the role of matrix metalloproteinase (MMP-9) in a reversible model of cancer that is initiated by infection with intracellular Theileria parasites. They found that gene induction by parasite infection was associated with trimethylation of histone H3K4 (H3K4me3) at the MMP-9 promoter. The H3K4 methyltransferase SMYD3 was the only histone methyltransferase upregulated upon infection. They therefore investigated the role of SMYD3 overexpression on MMP-9 expression and cell migration, identifying SMYD3 as an important new regulator of MMP-9 transcription. During the study they used the GloMax® Multi Luminometer to measure luminescence and absorbance in reporter and cell viability assays. They also used the Dual-Luciferase® Reporter Assay to measure SMYD3 activity in cells transfected with a SMYD3 reporter, and the pGL4-hRluc/TK plasmid for normalization of the experimental reporter activity. GoTaq® DNA polymerase was used in semi-quantitative RT-PCR. (4189)

Notes: The authors examined the effect of Varicella-zoster virus (VZV) on the NF-κB pathway and found inhibition of the pathway in VZV-infected dendritic cells. To determine which open reading frame (ORF) in the virus was responsible, seven hemagglutatin-tagged ORFs were cloned and transfected into 30% confluent 293FT human embryonic kidney cells (seeded 24 hours before) using FuGENE® HD Transfection Reagent with a 2:6 DNA:reagent ratio. After 48 hours, the cells were harvested for use in flow cytometry or Western blot analysis. An NF-κB reporter assay used 293FT cells seeded in six-well plates at 30% confluency and transfected 2µg of NF-kB GFP reporter vector and 1µg of VAV ORF expression constructs with FuGENE® HD Transfection Reagent. After 24 hours, 20nM of TNF-α was added and the cells incubated another 24 hours before harvest and analysis by flow cytometry. (4245)

Notes: In this paper, FuGENE® HD reagent was used to transiently transfect 293FT human embryonic kidney cells. Transfection conditions were as follows: Cells were grown to 30% confluency in 6-well plates prior to transfection with 3µg DNA at a 3:1 FuGENE® reagent:DNA ratio. (4415)

Notes: The authors used GoTaq® DNA Polymerase to amplify cDNA generated from total RNA (RT-PCR) extracted from murine erythroid leukemia (MEL) cells and mouse erythroid burst-forming units (BFU-Es). These cells were used to study the molecular mechanism of 5-aza-2'-deoxycytidine (5-aza-CdR)-induced erythroid differentiation, a process involved in azanucleotides for treating myelodysplastic syndromes (MDS) that reduces the risk of transformation to acute myeloid leukemia (AML). Treatment of these cells with 5-aza-CdR, a hypomethylation reagent, upregulated genes responsible for heme production and iron uptake. The pGL3 basic vector and promoter were used to create plasmid constructs of different E-box regulatory sequences with a luciferase reporter. The plasmids were cotransfected with c-Myc, Max or both transcription factors into human hepatocytes (HepG2). The Dual-Luciferase® Reporter Assay System was used to identify that the –6kb E-box of the transferrin receptor 1 (TfR1) promoter was a strong enhancer for inducing TfR1 expression when c-Myc and Max formed functional complexes that bound to it. Bisulfite sequencing was performed to study methylation patterns after 5-aza-2’-CdR treatment using the pGEM-T® Easy Vector system to ligate the isolated DNA fragments for TfR1 and Fech (ferrochetalase), which were transformed into E coli. for final sequencing. (4176)

Notes: The authors used a biochemical assay using Xenopus egg extracts to monitor degradation levels of two Wnt pathway components, Axin and ß-catenin, and identify modulators of the Wnt pathway. ß-catenin and Axin were expressed in vitro as firefly and Renilla luciferase fusion proteins, respectively, using the TNT^® SP6 High-Yield Protein Expression System and shown to behave in Xenopus extracts in a similar way to wildtype proteins, which were expressed as radiolabled proteins in rabbit reticulocyte lysate. Degradation of labeled proteins was monitored by SDS polyacrylamide gel electrophoresis and autoradiography, and degradation of luciferase fusion proteins was examined using the Dual-Glo^® Luciferase Assay. Using the Xenopus extract-based assay, the authors screened chemical libraries to identify two modulators of the Wnt pathway, then confirmed this inhibition in HEK 293 cells by demonstrating a decrease in ß-catenin expression with increasing concentrations of the inhibitors. This decrease in ß-catenin-Fluc levels was measured using the Steady-Glo™ Luciferase Assay, and luciferase activity was normalized to cell viability, as determined using the CellTiter-Glo^® Assay. (4181)

Notes: The ability to detect trace protease activity is important for assessing protein purification methods during process development and for confirming the absence of protease in final purified proteins. The authors describe a general protease assay using five peptide-conjugated luciferase substrates and compare it to fluorophore-conjugated general protease assays. (4156)

Notes: This paper describes the evaluation of the HDAC-Glo™ I/II and SIRT-Glo™ Assays. For all enzymes assayed (HDAC-I, HDAC-3, HDAC-6 and SIRT-1), the K_m values obtained using the luminogenic assays were comparable to those reported in the literature. Furthermore, the assays tolerated well the concentrations of DMSO used to deliver known HDAC inhibitors. The authors used the assays to generate dose-response curves and IC₅₀ values for standard inhibitors of several HDAC isoforms. They indicate that all data sets were of high quality and that the IC₅₀ values obtained were comparable to those reported in the literature. The authors screened four HDAC isoforms (HDAC-1, HDAC-3, HDAC-6 and SIRT-1) in duplicate against 640 FDA-approved drugs, and they screened HDAC-6 and SIRT-1 against the Hypha Discovery MycoDiverse natural products library. For both screens, “hits” were classified as compounds that showed >50% inhibition at their screening concentration. For the 640-drug screen, the confirmation of hits was >80%, and the false-positive hit rate was <20%. The Z´-factor values were 0.65 for the HDAC-6 screen and >0.85 for the SIRT-1 in the Hypha Discovery MycoDiverse natural products library screen. A Z´ factor of 0.5 or greater is indicative of an assay with low data variability but good dynamic range. The authors conclude that the HDAC-Glo™ I/II and SIRT-Glo™ Assays met the criteria of sensitivity, signal stability, low background, DMSO tolerance, data variability and dynamic range, and scalability required for a suitable drug-screening assay. (4137)