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BACKGROUND: Exposure to diesel exhaust particles (DEP) has been linked to a variety of adverse health effects, including increased morbidity and mortality from cardiovascular diseases, chronic obstructive pulmonary disease (COPD), metabolic syndrome, and lung cancer. The epigenetic changes caused by air pollution have been associated with increased health risks. However, the exact molecular mechanisms underlying the lncRNA-mediated pathogenesis induced by DEP exposure have not been revealed. METHODS: Through RNA-sequencing and integrative analysis of both mRNA and lncRNA profiles, this study investigated the role of lncRNAs in altered gene expression in healthy and diseased human primary epithelial cells (NHBE and DHBE-COPD) exposed to DEP at a dose of 30 μg/cm2. RESULTS: We identified 503 and 563 differentially expressed (DE) mRNAs and a total of 10 and 14 DE lncRNAs in NHBE and DHBE-COPD cells exposed to DEP, respectively. In both NHBE and DHBE-COPD cells, enriched cancer-related pathways were identified at mRNA level, and 3 common lncRNAs OLMALINC, AC069234.2, and LINC00665 were found to be associated with cancer initiation and progression. In addition, we identified two cis-acting (TMEM51-AS1 and TTN-AS1) and several trans-acting lncRNAs (e.g. LINC01278, SNHG29, AC006064.4, TMEM51-AS1) only differentially expressed in COPD cells, which could potentially play a role in carcinogenesis and determine their susceptibility to DEP exposure. CONCLUSIONS: Overall, our work highlights the potential importance of lncRNAs in regulating DEP-induced gene expression changes associated with carcinogenesis, and individuals suffering from COPD are likely to be more vulnerable to these environmental triggers.

Epitaxial NiO and CrN thin films were deposited on a single-crystal A l 2 O 3 (1 1 ¯ 02) (r-plane sapphire) using magnetron sputtering. The two materials were intentionally deposited into two different deposition chamber designs and under different conditions (temperature, pressure, gases, and energy of sputtered particles). Despite the differences in the deposition condition and material system, both materials had the same feature with uncommon tilted epitaxial growth. Through an in-depth x-ray diffraction analysis of the NaCl (B1)-structured materials on r-plane sapphire, the full twin domain epitaxial relations were determined and can be described as (110) NaCl (B 1) ∥ (4 4 ¯ 03) A l 2 O 3 and [ 1 1 ¯ 2 ] NaCl (B 1) ∥ [ 1 ¯ 1 ¯ 20 ] A l 2 O 3 . This relationship differs from the previously observed orientation of (100) NaCl (B 1) ∥ (1 1 ¯ 02) A l 2 O 3 and [ 100 ] NaCl (B 1) ∥ [ 10 1 ¯ 0 ] A l 2 O 3 . These results are of general relevance for the growth of the extended NaCl (B1)-structured cubic material family onto a r-plane sapphire substrate where similar epitaxial growth can be expected. [ABSTRACT FROM AUTHOR]

Epitaxial NiO and CrN thin films were deposited on a single-crystal A l 2 O 3 (1 1 ¯ 02) (r-plane sapphire) using magnetron sputtering. The two materials were intentionally deposited into two different deposition chamber designs and under different conditions (temperature, pressure, gases, and energy of sputtered particles). Despite the differences in the deposition condition and material system, both materials had the same feature with uncommon tilted epitaxial growth. Through an in-depth x-ray diffraction analysis of the NaCl (B1)-structured materials on r-plane sapphire, the full twin domain epitaxial relations were determined and can be described as (110) NaCl (B 1) ∥ (4 4 ¯ 03) A l 2 O 3 and [ 1 1 ¯ 2 ] NaCl (B 1) ∥ [ 1 ¯ 1 ¯ 20 ] A l 2 O 3 . This relationship differs from the previously observed orientation of (100) NaCl (B 1) ∥ (1 1 ¯ 02) A l 2 O 3 and [ 100 ] NaCl (B 1) ∥ [ 10 1 ¯ 0 ] A l 2 O 3 . These results are of general relevance for the growth of the extended NaCl (B1)-structured cubic material family onto a r-plane sapphire substrate where similar epitaxial growth can be expected. [ABSTRACT FROM AUTHOR]

RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.

The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.

AbstractThe starting point for much of multivariate analysis (MVA) is an n × p data matrix whose n rows represent observations and whose p columns represent variables. Some multivariate datasets, however, may be best conceptualized not as n discrete p-variate observations, but as p curves or functions defined on a common time interval. Here we introduce a framework for extending techniques of multivariate analysis to such settings. The proposed continuous-time multivariate analysis (CTMVA) framework rests on the assumption that the curves can be represented as linear combinations of basis functions such as B-splines, as in the Ramsay-Silverman representation of functional data; but whereas functional data analysis extends MVA to the case of observations that are curves rather than vectors—heuristically, n × p data with p infinite—we are instead concerned with what happens when n is infinite. We present continuous-time extensions of the classical MVA methods of covariance and correlation estimation, principal component analysis, Fisher’s linear discriminant analysis, and k-means clustering. We show that CTMVA can improve on the performance of classical MVA, in particular for correlation estimation and clustering, and can be applied in some settings where classical MVA cannot, including variables observed at disparate time points. CTMVA is illustrated with a novel perspective on a well-known Canadian weather dataset, and with applications to datasets involving international development, brain signals, and air quality. The proposed methods are implemented in the publicly available R package ctmva. Supplementary materials for this article are available online. [ABSTRACT FROM AUTHOR]

Many protein factors are required for mRNA biogenesis and nuclear export, which are central to the eukaryotic gene expression program. It is unclear, however, whether all factors have been identified. Here we report on a screen of >1000 essential gene mutants in Saccharomyces cerevisiae for defects in mRNA processing and export, identifying 26 mutants with defects in this process. Single-molecule FISH data showed that the majority of these mutants accumulated mRNA within specific regions of the nucleus, which included 1) mRNAs within the nucleolus when nucleocytoplasmic transport, rRNA biogenesis, or RNA processing and surveillance was disrupted, 2) the buildup of mRNAs near transcription sites in 3'-end processing and chromosome segregation mutants, and 3) transcripts being enriched near nuclear pore complexes when components of the mRNA export machinery were mutated. These data show that alterations to various nuclear processes lead to the retention of mRNAs at discrete locations within the nucleus.

The limited electrical conductivity of manganese dioxide (MnO2) hinders its broad use as an electrode in all-solid-state supercapacitor devices (ASDs). To overcome this, trivalent gadolinium (Gd) and erbium (Er) ions are incorporated into MnO2, effectively addressing the issue. This involves synthesizing α-MnO2 nanorods infused with Gd and Er by using a modified chemical process. Through the creation of crystal defects, augmentation of electrical conductivity, and increased porosity, the electrochemical performance is significantly enhanced. Cyclic voltammetry and galvanostatic charge–discharge measurements within the range of −0.2 to +0.6 V unveil improved capacitance values of 798 and 647 F g−1 at 1 A g−1 current density for Gd- and Er-doped α-MnO2 respectively, maintaining 92.4% and 89.7% charge retention after 5000 cycles. Analysis reveals that both samples are primarily dominated by electric double-layer capacitance (EDLC). Furthermore, surface capacitance outweighs diffusion-controlled processes in the electrochemical storage mechanism. The Gd-doped α-MnO2 coated device depicts a peak energy density of 78.5 Wh kg–1 at 106.01 W kg–1 power density for 0.5 A g−1 and maximum power density of 498.1 W kg–1 at 9.13 Wh kg–1 energy density for 3 A g−1. Even a handcrafted 1 cm × 1 cm device achieves 2.252 V potential, effectively illuminating commercial LEDs. [ABSTRACT FROM AUTHOR]