Notes: These authors compared the performance of four DNA purification methods for recovery of bacterial and archaeal DNA from fecal material. One of the methods tested was the Wizard® Genomic DNA Purification Kit, which uses a solution-based, enzymatic method for extraction. The Wizard® Genomic method was rated highly on extraction speed, and gave the highest DNA yields. A second method involving mechanical disruption (repeated bead beating) was rated more highly on extraction efficiency from archaea and some bacterial species. The criteria for performance comparison are described fully in the paper. (4219)

Notes: The authors developed a loop-mediated isothermal amplification (LAMP) assay to distinguish between virulent and nonvirulent strains of Vibrio vulnificus by targeting the virulence-correlated gene (vcg). The authors performed PCR using vcg-specific primers and GoTaq^® Hot Start Polymerase in parallel to confirm the LAMP results. (4163)

Notes: These authors used extensive computational analysis of isolates from the 2009 H1N1 outbreak to identify conserved H1N1 sequence signatures that could potentially be used in diagnostic assays to track the spread of specific strains during viral outbreaks. They identified target sequences in the hemagglutinin and neuraminidase genes that were highly conserved among 2009 H1N1 isolates. They then designed primers to amplify those sequences and used them in Taqman® and SYBR® Green-based qPCR assays to create a discriminatory 2009 H1N1 detection assay. They used the AccessQuick™ System in conventional RT-PCR to first establish whether their chosen primers were specific for the 2009 H1N1 isolates. In that assay they amplified representative H1N1 strains spanning from 1930 to the 2009 H1N1, and showed that only the 2009 isolates generated product. (4284)

Notes: The authors sought to determine the function of ceramide and ceramide synthase (CerS6) in mitochondria during post-natal brain development. They derived oligodendrocytes (OLs) from cultured, dissociated rat neonatal cortices. To determine if CerS6 plays in cell death, OLs were treated with glutamate to induce excitotoxicity, and cell death was assessed using the CytoTox-ONE™ Homogeneous Membrane Integrity Assay. To determine if the glutamate-induced excitotoxicity is dependent on ceramide or CerS6, OLs were treated with glumate in the presence or absence of the CerS6 inhibitor, fumonisin B1. To assess the mechanism of cell death resulting from ceramide-dependent glutamate toxicity in OLs, caspase activation during glutamate treatment was measured using the Apo-ONE^® Homogeneous Caspase-3/7 Assay. (4171)

Notes: Serum-starved ARPE cells were treated with the oxidant, t-butylhydroperoxide (tBH), in increasing concentrations for 30 minutes, 1, 2 and 24 hours, and caspase-3/7 activity was measured using the Apo-ONE^® Homogeneous Caspase 3/7 Assay to determine the mechanism of cell death. A dose-dependent increase in caspase-3/7 activity was observed. (4172)

Notes: The authors of this paper were investigating the role of mycobacterial membrane proteins in pathogenesis of Mycobacterium avium subsp. paratuberculosis, causative agent of Bovine Johne’s disease. Membrane enriched protein fractions, either mucosa-derived membranes (MDM) or culture-derived (CDM) of M. avium paratuberculosis from three cows with clinical disease were examined. Initial 2D DIGE and MALDI-TOF-MS analysis was unsatisfactory, so the researchers subjected the membrane preparations to tube-gel trypsin digestion supplemented with the ProteaseMax™ Surfactant, Trypsin Enhancer. They analyzed the proteins using nanoflow-liquid-chromatography-coupled tandem MS. A total of 130 proteins were detected in both MDM and CDM, with 48 predicted membrane proteins; four were not detected in the CDM, implying differential expression in the host. (4214)

Notes: This study analysed the roles of Dcp2 and Nudt16 in nonsense-mediated mRNA decay miRNA-mediated silencing. The authors used various luciferase reporter constructs to evaluate the significance of Dcp2 and Nudt16 in miRNA- and siRNA-mediated gene silencing in wildtype and knockout MEF cells. Various Renilla luciferase constructs containing or lacking miRNA target sites were cotransfected along with a control plasmid encoding firefly luciferase (for normalization purposes). Renilla and firefly luciferase luminescence were measured using the Dual-Luciferase^® Reporter Assay and the GloMax^®-Multi Luminometer. (4204)

Notes: This paper explored potential compounds as agonists of dopamine D2 receptor (D2R) with a bias toward β-arrestin signaling. Based on the aripiprazole scaffold, compounds were synthesized and tested in a D2-mediated Gi-coupled isoproterenol-stimulated cAMP production assay using HEK293T cells expressing D2R transfected with pGloSensor™-22F cAMP Plasmid. Assessing β-arrestin recruitment to agonist-stimulated receptors was determined using HTLA cells stably expressing β-arrestin-TEV protease and a tetracycline transactivator-driven luciferase exposed to agonist or D2 test ligand with or without reference agonist. After 18 hours, medium was removed from the cells, 1X Bright-Glo™ Reagent added and luminescence measured. (4518)

Notes: This study investigated the genetic basis of carbapenem resistance in the multidrug resistant Acinetobacter baumannii isolate, Ab244. Transposable elements are known to play an important role in multidrug resistance in A. baumannii. The authors used a multiplex PCR approach to detect the presence of known resistance genes and insertion elements, followed by RT-PCR to study expression of the genes identified. For RT-PCR, cDNA was synthesized from 100 ng of RNA using the AccessQuick™ RT-PCR System. Results of the study indicated that the bla_OXA-132 gene was inactivated in A. Baumannii AB244 by insertion of ISAba16, and that carbapenem resistance in that isolate was due to an alternate resistance mechanism caused by overexpression of the bla_OXA-58 gene. (4344)

Notes: The authors created a stably transfected HEK293 cell line expressing a luminogenic cAMP-binding protein using GloSensor™ technology to quantify cAMP levels in live cells. The HEK293 cells express a beta₂-adrenergic receptor (β₂AR ), a G_s-coupled receptor, that when activated with an agonist, stimulates the production of cAMP. The cell line was used to demonstrate that the phosphorylation pattern (“barcode”) of the β₂AR created by various G protein-coupled receptor kinases (GPKs) affects the binding and function of beta-arrestin and subsequent internalization of β₂AR. GloSensor™ transfection and transcription were confirmed by stimulation of endogenous β₂AR with isoproterenol. Endogenous β₂ARs in HEK293 cells were prestimulated with either vehicle DMSO or isoproterenol, then washed and rechallenged with serially diluted isoproterenol. In cells transfected with control siRNA, pretreatment with isoproterenol induced a 50% loss of the maximal cAMP signal when rechallenged. Cells transfected with siRNA targeting GRK2, GRK6, or both GRK2 and GRK6 showed impairment of this desensitization. This GRK knockdown effect decreased the change observed in the maximal cAMP response (E_max) after isoproterenol pretreatment. (4138)

Notes: Wizard® Genomic DNA Purification Kit was used to extract DNA from Aspergillus sojae for GS FLX titanium fragment sequencing. (4542)

Notes: 2 ×10⁶ hESCs were transfected 4 days following subculture with 2μg of BsaI linearized pBS-PGK-neo-lox at a 1:3 DNA to reagent ratio using FuGENE® HD Transfection Reagent. (4426)

Notes: These authors showed that expression of the serine protease inhibitor elafin is regulated by epigenetically controlled expression of the transcription factor Foxa2. Treatment of melanoma cells with a DNA methyltransferase inhibitor induced elafin expression, resulting in reduced proliferation and increased apoptosis. Luciferase reporter assays were used to show that Foxa2 binding was required for activation of elafin expression, and that Foxa2 binding was activated by treatment with the methyltransferase inhibitor. These assays used a pGL3-Basic Vector construct in which expression of firefly luciferase was driven by the upstream region bearing the Foxa2 binding site. The pRL-TK Vector, expressing Renilla luciferase, was used as a normalization control. The AccessQuick™ System was used for RT-PCR analysis to show that Foxa2 mRNA was barely detectable in melanoma cells.  (4345)

Notes: These authors investigated whether ETX toxin production in C. perfringens type D is regulated by the Agr-like quorum sensing system, the VirS/VirR system, or both. They demonstrated that an agr mutant lacked ETX expression, and showed that lack of VirR had no effect on ETX production. The AccessQuick™ System was used in RT-PCR analysis of RNA isolated from mutant, wildtype and reconstituted (complemented) strains to confirm absence of agr transcripts in mutant strains. RT-PCR was also used to confirm the presence of etx transcripts in wild type strains, and their absence in the agr mutant. Previous studies had shown that toxin production is upregulated upon contact with enterocyte-like Caco-2 cells. This study showed that the agr operon is required for such upregulation. (4289)

Notes: The authors examined the localized expression of Lgr5, a putative cancer marker, in sporadic colorectal adenomas and carcinomas by immunohistochemistry. They also determined the level of microsatellite instability (MSI) in paired normal and tumor tissues using the MSI Analysis System, Version 1.1. Their results showed that the majority of LGR5-positive tumors had low levels of MSI. (4109)

Notes: RNA purified from polysome gradient fractions was treated with RQ1 RNase-Free DNase then inactivated by adding 2mM EGTA and heating the reaction to 65°C for 10 minutes. RQ1 RNase-Free DNase was also used to treat total RNA extracted from 3T3–3e5 cells. In both cases, the treated purified RNA was used for cDNA synthesis. (4186)

Notes: The authors examined the strains of Dengue virus serotype 1 (DENV-1) found in the State of Rio de Janeiro since it was introduced in 1986. Viral RNA was extracted from patient serum samples or cell culture and 5µl of RNA reverse transcribed and amplified using the AccessQuick™ RT-PCR System with primers for the 2,325bp C/prM/M/E region of DENV-1. The products were sequenced and aligned to examine how the virus had evolved over time. (4342)

Notes: These authors investigated the differences in gut microbial flora between obese and normal-weight subjects. They used the Wizard® Genomic DNA Purification Kit to extract DNA from diluted fecal extracts. The extracted DNA was analyzed by PCR to identify Bacteroidetes and Firmicutes. Differences in distribution of these phyla was between the subject groups were identified. (4220)

Notes: The authors of this paper investigated the molecular mechanisms through which fumaric acid esters affect the progression and pathology of multiple sclerosis. The authors looked at the activation of the Nrf2 transcriptional pathway which plays a role in defense against oxidative stress. A stable reporter cell line expressing eight copies of the gluthione-S-transferase 2 antioxidative response elements cloned upstream of the luciferase complementary DNA in a pGL4.26 vector. Reporter cells were stimulated with dimethylfumarate for 24 hours and luciferase activity measured using the Luciferase Assay System. A strong dose-dependent induction of antioxidative response elements was observed. Next, the authors looked at the effects of fumaric acid esters on the inhibitor of Nrf2, Keap 1. C-terminal, V5-tagged Keap1 protein was transfected into 293 cells. Forty-eight hours post transfection, cells were treated with dimethyl fumarate. Samples were lysed, Keap1-V5 was immunoprecipitated and gel purified. The protein was digested with trypsin in the presence of ProteaseMAX™ Surfactant, Trypsin Enhancer. Peptide pools were analyzed using liquid chromatography-tandem mass spectrometry. The authors were able to show that the Keap1 protein was modified in response to treatment. (4215)

Notes: The authors investigated the suppression of E. coli O157:H7 in sand-based livestock bedding and hypothesized that suppression of E. coli O157:H7 growth was mediated by an environmentally stable population of pathogen-suppressing bacteria. These bacteria were identified by terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S rRNA gene sequences isolated from used bedding followed by cloning and sequencing of the most abundant terminal restriction fragments. Amplifications were performed using the GoTaq^® Flexi DNA Polymerase, then PCR products were cloned into the pGEM^®-T Easy Vector. The PureYield™ Plasmid Miniprep System was used to purify plasmids for sequencing. (4165)

Notes: The authors wanted to generate zebrafish that were genetically homogeneous by inbreeding siblings. To monitor the genotype of the strains being bred, genomic DNA was isolated from either fin clips of living fish or one quarter of an ethanol-fixed fish using the Maxwell^® 16 System. The purified gDNA was then used to determine simple sequence length polymorphisms (SSLP) for marker alleles. (4149)

Notes: This study compared the effects of zymosan and LPS on human monocyte-derived dendritic cells (DCs). The  authors found that zymosan-activated DCs had a unique cytokine expression profile. In zymosan-activated DCs, high levels of GM-CSF and IL-27, rather than IL-12 p70, were involved in Th1 cell activation. As part of the study, RT-PCR was used to investigate the molecular basis of this failure to induce production of active IL-12 p70. Expression levels of the biologically inactive subunits of IL-12 p70 (p40 and p35) was assessed using the AccessQuick™ RT-PCR System. The results showed that zymosan induced expression of p40, but not p35 mRNA, indicating that lack of induction of p35 was the reason for failure to induce active IL-12 p70. (4348)

Notes: The authors used the CellTiter®-Glo Assay to assess the effect of HER2-Affitoxin on cell viability of gastric carcinoma NCI-N87 cells, which overexpress HER2. The HER2-Affitoxin is a fusion protein of a HER2-specific Affibody and modified Pseudomonas aeruginosa exotoxin A (PE 38). This fusion protein was designed to offer an alternative method for treating tumors that do not respond to trastuzumab or have acquired resistance to current therapies. The CellTiter-Glo® Assay was used to calculate HER2-Affitoxin IC₅₀ values of cells in culture. They describe the mechanism of action as follows: HER2-Affitoxin binds to HER2 protein on the cell surface, is internalized, where it blocks protein synthesis in the cytosol via ADP ribosylation of eEF-2. (4131)

Notes: Yuangheng He and colleagues asked how the weak alkaline compound chloroquine (CQ) enhances the anti-inflammatory effects of synthetic glucocorticoids like dexamethasone, which are used to treat a host of inflammatory and autoimmune diseases. In the process they explored the intersection of lysosomal degradation pathways and glucocorticoid receptor signaling. They used Dual-Glo® Luciferase Assay System to look at glucocorticoid receptor-mediated (GR) activation and repression of reporters in AD293 cells under a variety of conditions (presence or absence of CQ; stripped serum, loss of lysosome synthesis, inhibition of V-ATPase, etc). They also used HaloTag® protein fusions to observe the fate of GR populations in the presence or absence of CQ and in the presence or absence of compounds that impair proteasome function. Live-cell imaging of GR-HaloTag® protein fusions revealed a dynamic association of the GR with lysosomes. The authors showed that glucocorticoid signaling is regulated by lysosomes. (4203)

Notes: The authors identified three genetic loci involved in chemokine-mediated antimicrobial effects against Bacillus anthracis using a transposon mutant library in which a transposon is randomly inserted into the B. anthracis genome, then treating the mutant cells with chemokine to select for resistant cells. To identify the transposon insertion site, and thus the resistance-conferring loci, the authors amplified regions flanking the transposon by PCR using the GoTaq^® Green Master Mix. (4167)