The ability of next-generation sequencing (NGS) technologies to detect low frequency HIV-1 drug resistance mutations (DRMs) not detected by dideoxynucleotide Sanger sequencing has potential advantages for improved patient outcomes. We compared the performance of an diagnostic (IVD) NGS assay, the Sentosa SQ HIV genotyping assay for HIV-1 genotypic resistance testing, with Sanger sequencing on 138 protease/reverse transcriptase (RT) and 39 integrase sequences. The NGS assay used a 5% threshold for reporting low-frequency variants. The level of complete plus partial nucleotide sequence concordance between Sanger sequencing and NGS was 99.9%. Among the 138 protease/RT sequences, a mean of 6.4 DRMs was identified by both Sanger and NGS, a mean of 0.5 DRM was detected by NGS alone, and a mean of 0.1 DRM was detected by Sanger sequencing alone. Among the 39 integrase sequences, a mean of 1.6 DRMs was detected by both Sanger sequencing and NGS and a mean of 0.15 DRM was detected by NGS alone. Compared with Sanger sequencing, NGS estimated higher levels of resistance to one or more antiretroviral drugs for 18.2% of protease/RT sequences and 5.1% of integrase sequences. There was little evidence for technical artifacts in the NGS sequences, but the G-to-A hypermutation was detected in three samples. In conclusion, the IVD NGS assay evaluated in this study was highly concordant with Sanger sequencing. At the 5% threshold for reporting minority variants, NGS appeared to attain a modestly increased sensitivity for detecting low-frequency DRMs without compromising sequence accuracy.

The Tarfaya-Agadir Basin in offshore Morocco is a frontier exploration area with no deepwater industry well penetrations and limited well control in the updip shelfal equivalent. Recent detailed 3D seismic mapping and study by Shell has identified the presence of two large mass transport complexes (MTCs) in the Tertiary interval, in addition to a number of smaller and younger MTCs. The large MTCs, named Tejas A and Tejas B, exhibit distinct seismic characteristics that may be significant to understanding the evolution of the basin during the Tertiary. The basal Tejas A is characterized by numerous kilometerscale, coherent transported blocks. The size and quantity of transported blocks observed in Tejas A is unique in Morocco and the Atlantic Margin. The MTC in the younger Tejas B is a thick chaotic unit with distinctive downdip erosional lobes. This deposit is overlain by high amplitude, parallel seismic facies. The chaotic seismic facies is often sharp-edged, with well-defined pressure ridges. Only a few small transported blocks and erosional remnants have been observed in Tejas B. Failure deposits account for a significant percentage of the Tertiary stratigraphic interval in the 3D survey area.

Background: LKB1 is a key signaling kinase that regulates cellular growth. Results: The reactive aldehyde 4-hydroxynonenal (HNE) forms adducts on LKB1 that directly inhibit kinase activity. Conclusion: Oxidative modification at Lys-97 by HNE is sufficient for inhibition of LKB1. Significance: This work describes how a key growth suppressor protein is inactivated during states of oxidant stress.

Reactive oxygen species (ROS) are elevated in the heart in response to hemodynamic and metabolic stress, and promote hypertrophic signaling. ROS also mediate the formation of lipid peroxidation-derived aldehydes that may promote myocardial hypertrophy. One lipid peroxidation byproduct, 4-Hydroxy-trans-2-nonenal (HNE), is a reactive aldehyde that covalently modifies proteins thereby altering their function. HNE adducts directly inhibit the activity of LKB1, a serine/threonine kinase involved in regulating cellular growth in part through its interaction with the AMP-activated protein kinase (AMPK), but whether this drives myocardial growth is unclear. We tested the hypothesis that HNE promotes myocardial protein synthesis, and if this effect is associated with impaired LKB1-AMPK signaling. In adult rat ventricular cardiomyocytes exposure to HNE (10 μM for 1 hour) caused HNE-LKB1 adduct formation and inhibited LKB1 activity. HNE inhibited the downstream kinase AMPK, increased hypertrophic mTOR-P70S6K-RPS6 signaling, and stimulated protein synthesis by 27.1 ±3.5%. HNE also stimulated Erk1/2 signaling, which contributed to RPS6 activation but was not required for HNE-stimulated protein synthesis. HNE-stimulated RPS6 phosphorylation was completely blocked using the mTOR inhibitor rapamycin. To evaluate if LKB1 inhibition by itself could promote the hypertrophic signaling changes observed with HNE, LKB1 was depleted in ARVMs using siRNA. LKB1 knockdown did not replicate the effect of HNE on hypertrophic signaling or affect HNE-stimulated RPS6 phosphorylation. Thus, in adult cardiac myocytes HNE stimulates protein synthesis by activation of mTORC1-P70S6K-RPS6 signaling most likely mediated by direct inhibition of AMPK. Because HNE in the myocardium is commonly increased by stimuli that cause pathologic hypertrophy, these findings suggest that therapies that prevent activation of mTORC1-P70S6K-RPS6 signaling may be of therapeutic value.

Background:We describe a novel system control (SC) implemented in an automated AmpliSeq™-based next-generation sequencing (NGS)