Artificial Photosynthesis of C1–C3 Hydrocarbons from Water and CO_2 on Titanate Nanotubes Decorated with Nanoparticle Elemental Copper and CdS Quantum Dots

The conversion of CO_2 and water into value-added fuels with visible light is difficult to achieve in inorganic photocatalytic systems. However, we synthesized a ternary catalyst, CdS/(Cu-TNTs), which is assembled on a core of sodium trititanate nanotubes (TNTs; Na_xH_(2–x)Ti_3O_7) decorated with elemental copper deposits followed by an overcoat of CdS quantum dot deposits. This ternary photocatalyst is capable of catalyzing the conversion of CO_2 and water into C1–C3 hydrocarbons (e.g., CH_4, C_2H_6, C_3H_8, C_2H_4, C_3H_6) upon irradiation with visible light above 420 nm. With this composite photocatalyst, sacrificial electron donors are not required for the photoreduction of CO_2. We have shown that water is the principal photoexcited-state electron donor, while CO_2 bound to the composite surface serves as the corresponding electron acceptor. If the photochemical reaction is carried out under an atmosphere of 99.9% ^(13)CO_2, then the product hydrocarbons are built upon a ^(13)C backbone. However, free molecular H_2 is not observed over 5 h of visible light irradiation even though proton reduction in aqueous solution is thermodynamically favored over CO_2 reduction. In terms of photocatalytic efficiency, the stoichiometric fraction of Na^+ in TNTs appears to be an important factor that influences the formation of the observed hydrocarbons. The coordination of CO_2 to surface exchange sites on the ternary catalyst leads to the formation of surface-bound CO_2 and related carbonate species. It appears that the bidentate binding of O═C═O to certain reactive surface sites reduces the energy barrier for conduction band electron transfer to CO_2. The methyl radical (CH_3•), an observed intermediate in the reaction, was positively identified using an ESR spin trapping probe molecule. The copper deposits on the surface of TNTs appear to play a major role in the transient trapping of methyl radical, which in turn self-reacts to produce ethane

Photocatalytic H_2 production on trititanate nanotubes coupled with CdS and platinum nanoparticles under visible light: revisiting H_2 production and material durability

The photocatalytic production of molecular hydrogen (H_2) on ternary composites of Pt, CdS, and sodium trititanate nanotubes (Na_xH_(2−x)Ti_3O_7, TNTs) is examined in an aqueous 2-propanol (IPA) solution (typically 5 vol%) at a circum-neutral pH under visible light (λ > 420 nm). The H2 production rates are dependent on the Pt-loading level, and the optimum production rate in the Pt/CdS/TNTs is approximately six times higher than that in Pt/CdS/TiO_2. A D2O solution containing 5 vol% IPA leads only to the production of D_2 molecules, whereas increasing the IPA amount to 30 vol% leads to the production of DH molecules. This indicates that the Pt/CdS/TNTs composites enable H_2 production via true water splitting under our typical experimental conditions. X-ray photoelectron spectroscopy (XPS) analyses of the as-synthesized Pt/CdS/TNTs and those used for 6 and 12 h show that metallic Pt on the CdS/TNTs is less susceptible to oxidation than Pt on CdS/TiO_2. In addition, photocorrosion of CdS (i.e., sulfate formation) is significantly inhibited during the photocatalytic H_2 production reactions in the Pt/CdS/TNTs because of the efficient charge transfer via the TNTs framework. The Pt/CdS/TNTs samples are thermally more stable than Pt/CdS/TiO_2 and CdS/TNTs, effectively inhibiting the formation of CdO during the thermal synthesis. Detailed surface characterizations of the as-synthesized ternary composites are performed using X-ray diffraction, transmission electron microscopy, energy dispersive spectroscopy, and XPS

Incorporating Distant Sequence Features and Radial Basis Function Networks to Identify Ubiquitin Conjugation Sites

Ubiquitin (Ub) is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3) enzymes. Three major enzymes participate in ubiquitin conjugation. They are – E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF) network to identify protein ubiquitin conjugation (ubiquitylation) sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub) sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (−20∼+20) revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information), which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence features of Ub sites can improve predictive performance. Additionally, the independent test demonstrates that the proposed method can outperform other ubiquitylation prediction tools

Elevated expression of TDP-43 in the forebrain of mice is sufficient to cause neurological and pathological phenotypes mimicking FTLD-U

TDP-43 is a multifunctional DNA/RNA-binding factor that has been implicated in the regulation of neuronal plasticity. TDP-43 has also been identified as the major constituent of the neuronal cytoplasmic inclusions (NCIs) that are characteristic of a range of neurodegenerative diseases, including the frontotemporal lobar degeneration with ubiquitin+ inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS). We have generated a FTLD-U mouse model (CaMKII-TDP-43 Tg) in which TDP-43 is transgenically overexpressed in the forebrain resulting in phenotypic characteristics mimicking those of FTLD-U. In particular, the transgenic (Tg) mice exhibit impaired learning/memory, progressive motor dysfunction, and hippocampal atrophy. The cognitive and motor impairments are accompanied by reduced levels of the neuronal regulators phospho–extracellular signal-regulated kinase and phosphorylated cAMP response element-binding protein and increased levels of gliosis in the brains of the Tg mice. Moreover, cells with TDP-43+, ubiquitin+ NCIs and TDP-43–deleted nuclei appear in the Tg mouse brains in an age-dependent manner. Our data provide direct evidence that increased levels of TDP-43 protein in the forebrain is sufficient to lead to the formation of TDP-43+, ubiquitin+ NCIs and neurodegeneration. This FTLD-U mouse model should be valuable for the mechanistic analysis of the role of TDP-43 in the pathogenesis of FTLD-U and for the design of effective therapeutic approaches of the disease

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population.

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (P interaction  = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications