Pacific Northwest National Laboratory

About: Pacific Northwest National Laboratory is a facility organization based out in Richland, Washington, United States. It is known for research contribution in the topics: Catalysis & Aerosol. The organization has 11581 authors who have published 27934 publications receiving 1120489 citations. The organization is also known as: PNL & PNNL.

Widespread adenine N6-methylation of active genes in fungi

Abstract: N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages. Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expression-associated epigenomic mark in eukaryotes.

Visual Analytics

Abstract: The information revolution is upon us, and it is guaran-teed to change our lives and the way we conduct our daily business. The fact that we have to deal with not just the size but also the variety and complexity of this in-formation makes it a real challenge to survive the revolu-tion. Enter Visual Analytics, a contemporary and proven approach to combine the art of human intuition and the science of mathematical deduction to directly perceive patterns and derive knowledge and insight from them.

Constraints on sub-GeV dark matter-electron scattering from the DarkSide-50 experiment

Abstract: We present new constraints on sub-GeV dark-matter particles scattering off electrons based on 6780.0 kg d of data collected with the DarkSide-50 dual-phase argon time projection chamber. This analysis uses electroluminescence signals due to ionized electrons extracted from the liquid argon target. The detector has a very high trigger probability for these signals, allowing for an analysis threshold of three extracted electrons, or approximately 0.05 keVee. We calculate the expected recoil spectra for dark matter-electron scattering in argon and, under the assumption of momentum-independent scattering, improve upon existing limits from XENON10 for dark-matter particles with masses between 30 and 100 MeV/c^{2}.

High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis

Abstract: Orthogonal high-resolution separations are critical for attaining improved analytical dynamic range and protein coverage in proteomic measurements. High-pH reversed-phase liquid chromatography (RPLC), followed by fraction concatenation, affords better peptide analysis than conventional strong cation-exchange chromatography applied for 2D proteomic analysis. For example, concatenated high-pH RPLC increased identification of peptides (by 1.8-fold) and proteins (by 1.6-fold) in shotgun proteomics analyses of a digested human protein sample. Additional advantages of high-pH RPLC with fraction concatenation include improved protein sequence coverage, simplified sample processing and reduced sample losses, making this an attractive alternative to strong cation-exchange chromatography in conjunction with second-dimension low-pH RPLC for 2D proteomics analyses.