The adsorption breakthrough behavior of nine perfluoroalkyl substances (PFAS) in groundwaters by four bituminous coal-based granular activated carbons (F400, Carbsorb 40, HPC and CMR400) was studied ...using rapid small-scale column tests (RSSCTs). The half breakthrough bed volume (BV50), an indicator of apparent adsorption capacity, correlated with the hydrophobicity of PFAS at a given pH (i.e., Log Dow) for F400, indicating that hydrophobic interaction is important for apparent adsorption capacity of PFAS in groundwater with low dissolved organic concentrations (DOC < 1 mg C/L) and low specific UV absorbances at 254 nm (SUVA254 < 2 L mg−1m−1). Higher empty bed contact time (EBCT) caused steeper PFAS breakthrough curves with respect to throughput, but did not affect apparent adsorption capacity. Three different sizes of F400 (0.13, 0.17, and 0.20 mm) exhibited similar breakthrough profiles of PFAS, indicating that the intraparticle diffusivity was independent of adsorbent diameter in the given conditions. Among the tested carbons, the positively charged adsorbents (F400, HPC, and CMR400) showed higher apparent adsorption capacities for hydrophilic (Log Dow at pH 7 < 0) and marginally hydrophobic PFAS (Log Dow at pH 7 between 0 and 1) than the negatively charged adsorbent (Carbsorb 40). In addition, activated carbons with higher micropore surface areas exhibited higher apparent adsorption capacities of hydrophilic and marginally hydrophobic PFAS among the positively-charged activated carbons, whereas the mesoporous carbon (HPC) exhibited an increasingly larger adsorption capacity for more hydrophobic PFAS compared to the microporous carbon (F400) at a later breakthrough possibly due to less pore blockage.
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•Apparent adsorption capacity of PFAS was proportional to their hydrophobicity.•Overshoot concentrations were observed for hydrophilic short-chain PFBA and PFPeA.•Similar breakthrough profiles were observed among the tested adsorbent sizes.•Micropore surface area was important to determine apparent adsorption capacity.•Mesopores played increasingly important roles for hydrophobic PFAS adsorption.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Tide gauge and satellite data reveal an interannual oscillation of the ocean’s thermoclines east of the Philippines and Taiwan, forced by a corresponding oscillation in the wind stress curl. This ...so-called Philippines–Taiwan Oscillation (PTO) is shown to control the interannual variability of the circulation of the subtropical and tropical western North Pacific. The PTO shares some characteristics of known Pacific indices, for example, Niño-3.4. However, unlike PTO, these other indices explain only portions of the western North Pacific circulation. The reason is because of the nonlinear nature of the forcing in which mesoscale (ocean) eddies play a crucial role. In years of positive PTO, the thermocline east of the Philippines rises while east of Taiwan it deepens. This results in a northward shift of the North Equatorial Current (NEC), increased vertical shear of the Subtropical Countercurrent (STCC)/NEC system, increased eddy activity dominated by warm eddies in the STCC, increased Kuroshio transport off the northeastern coast of Taiwan into the East China Sea, increased westward inflow through Luzon Strait into the South China Sea, and cyclonic circulation and low sea surface height anomalies in the South China Sea. The reverse applies in years of negative PTO.
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BFBNIB, DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Noncoding RNAs (ncRNAs) function with associated proteins to effect complex structural and regulatory outcomes. To reveal the composition and dynamics of specific noncoding RNA-protein complexes ...(RNPs) in vivo, we developed comprehensive identification of RNA binding proteins by mass spectrometry (ChIRP-MS). ChIRP-MS analysis of four ncRNAs captures key protein interactors, including a U1-specific link to the 3′ RNA processing machinery. Xist, an essential lncRNA for X chromosome inactivation (XCI), interacts with 81 proteins from chromatin modification, nuclear matrix, and RNA remodeling pathways. The Xist RNA-protein particle assembles in two steps coupled with the transition from pluripotency to differentiation. Specific interactors include HnrnpK, which participates in Xist-mediated gene silencing and histone modifications but not Xist localization, and Drosophila Split ends homolog Spen, which interacts via the A-repeat domain of Xist and is required for gene silencing. Thus, Xist lncRNA engages with proteins in a modular and developmentally controlled manner to coordinate chromatin spreading and silencing.
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•ChIRP-MS identifies endogenous protein partners associated with specific RNAs•Xist lncRNA binds 81 proteins in two waves during X chromosome inactivation•HnrnpK is required for Xist-mediated chromatin modifications and Polycomb targeting•Spen binds to Xist A-repeat and is required for gene silencing
Development of a general method for identifying RNA-protein interactions in vivo reveals 81 endogenous proteins that associate with Xist RNA in two waves to control mammalian dosage compensation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Heat-shock protein 5 (HSPA5) is a marker for poor prognosis in breast cancer patients and has an important role in cancer progression, including promoting drug resistance and metastasis. In this ...study, we identify that the specific lysine residue 447 (K447) of HSPA5 could be modified with polyubiquitin for subsequent degradation through the ubiquitin proteasomal system, leading to the suppression of cell migration and invasion of breast cancer. We further found that GP78, an E3 ubiquitin ligase, interacted with the C-terminal region of HSPA5 and mediated HSPA5 ubiquitination and degradation. Knock down of GP78 significantly increased the expression of HSPA5 and enhanced migration/invasive ability of breast cancer cells. Knock down of histone deacetylase-6 (HDAC6) increased the acetylation of HSPA5 at lysine residues 353 (K353) and reduced GP78-mediated ubiquitination of HSPA5 at K447 and then increased cell migration/invasion. In addition, we demonstrate that E3 ubiquitin ligase GP78 preferentially binds to deacetylated HSPA5. Notably, the expression levels of GP78 inversely correlated with HSPA5 levels in breast cancer patients. Patients with low GP78 expression significantly correlated with invasiveness of breast cancer, advanced tumor stages and poor clinical outcome. Taken together, our results provide new mechanistic insights into the understanding that deacetylation of HSPA5 by HDAC6 facilitates GP78-mediated HSPA5 ubiquitination and suggest that post-translational regulation of HSPA5 protein is critical for HSPA5-mediated metastatic properties of breast cancer.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
We introduce APEX-seq, a method for RNA sequencing based on direct proximity labeling of RNA using the peroxidase enzyme APEX2. APEX-seq in nine distinct subcellular locales produced a ...nanometer-resolution spatial map of the human transcriptome as a resource, revealing extensive patterns of localization for diverse RNA classes and transcript isoforms. We uncover a radial organization of the nuclear transcriptome, which is gated at the inner surface of the nuclear pore for cytoplasmic export of processed transcripts. We identify two distinct pathways of messenger RNA localization to mitochondria, each associated with specific sets of transcripts for building complementary macromolecular machines within the organelle. APEX-seq should be widely applicable to many systems, enabling comprehensive investigations of the spatial transcriptome.
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•A transcriptome-wide subcellular RNA atlas was generated by proximity labeling•Isoform-level subcellular localization patterns for over 3,200 genes identified•RNA-transcript location correlates with genome architecture and protein localization•Two modes of mRNA localization to the outer mitochondrial membrane uncovered
A newly developed technique reveals the subcellular transcriptomes at many landmarks in the nucleus and cytosol and connects mRNA localization to genome architecture, protein location, and local-translation mechanisms.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Dynamic gene expression during cellular differentiation is tightly coordinated by transcriptional and post-transcriptional mechanisms. An emerging theme is the central role of long noncoding RNAs ...(lncRNAs) in the regulation of this specificity. Recent advances demonstrate that lncRNAs are expressed in a lineage-specific manner and control the development of several cell types in the hematopoietic system. Moreover, specific lncRNAs are induced to modulate innate and adaptive immune responses. lncRNAs can function via RNA-DNA, RNA-RNA, and RNA-protein target interactions. As a result, they affect several stages of gene regulation, including chromatin modification, mRNA biogenesis, and protein signaling. We discuss recent advances, future prospects, and challenges in understanding the roles of lncRNAs in immunity and immune-mediated diseases.
Long noncoding RNAs (lncRNAs) have recently emerged as lineage-specific regulators of gene expression in many biological systems. Satpathy and Chang provide an overview of lncRNA functions in the development and activation of the immune system.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The goal of this study was to examine and predict antiviral peptides. Although antiviral peptides hold great potential in antiviral drug discovery, little is done in antiviral peptide prediction. In ...this study, we demonstrate that a physicochemical model using random forests outperform in distinguishing antiviral peptides. On the experimental benchmark, our physicochemical model aided with aggregation and secondary structural features reaches 90% accuracy and 0.79 Matthew's correlation coefficient, which exceeds the previous models. The results suggest that aggregation could be an important feature for identifying antiviral peptides. In addition, our analysis reveals the characteristics of the antiviral peptides such as the importance of lysine and the abundance of α-helical secondary structures.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In recent decades, wintertime sea surface temperatures off the eastern coast of China have steadily increased. The warming is accompanied by on‐coast wind convergence across East China Sea and by ...stronger northeasterly wind which is spatially inhomogeneous being greatest in the Taiwan Strait. Strong winds favor more frequent cross‐shelf currents and vigorous spreading of heat from the Kuroshio, which warms the coastal sea in a positive feedback loop. The process also weakens the East Asian winter monsoon over eastern China, contributing to its decoupling from the recent rebound of the Siberian High.
Key Points
Recent warming off coastal China is accompanied by stronger northeasterly wind
Stronger winter monsoon spreads heat from Kuroshio producing air‐sea response
The increased wind is detached from the recent rebound of the Siberian High
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Highlights • lncRNAs exert important cellular functions with diverse regulatory mechanisms. • Different targeting strategies yield different insights about the lncRNA locus. • Genetic ablation of ...lncRNAs reveals their important functions in vivo.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract ...biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/ ) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
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