Energetics and kinetics of Li intercalation in irradiated graphene scaffolds

In the present study we investigate the irradiation-defects hybridized graphene scaffold as one potential building material for the anode of Li-ion batteries. Designating the Wigner V22 defect as a representative, we illustrate the interplay of Li atoms with the irradiation-defects in graphene scaffolds. We examine the adsorption energetics and diffusion kinetics of Li in the vicinity of a Wigner V22 defect using density functional theory calculations. The equilibrium Li adsorption sites at the defect are identified and shown to be energetically preferable to the adsorption sites on pristine (bilayer) graphene. Meanwhile the minimum energy paths and corresponding energy barriers for Li migration at the defect are determined and computed. We find that while the defect is shown to exhibit certain trapping effects on Li motions on the graphene surface, it appears to facilitate the interlayer Li diffusion and enhance the charge capacity within its vicinity because of the reduced interlayer spacing and characteristic symmetry associated with the defect. Our results provide critical assessment for the application of irradiated graphene scaffolds in Li-ion batteries.Comment: 23 pages, 5 figure

Metabolic Impacts of Using Nitrogen and Copper-Regulated Promoters to Regulate Gene Expression in Neurospora crassa.

The filamentous fungus Neurospora crassa is a long-studied eukaryotic microbial system amenable to heterologous expression of native and foreign proteins. However, relatively few highly tunable promoters have been developed for this species. In this study, we compare the tcu-1 and nit-6 promoters for controlled expression of a GFP reporter gene in N. crassa. Although the copper-regulated tcu-1 has been previously characterized, this is the first investigation exploring nitrogen-controlled nit-6 for expression of heterologous genes in N. crassa. We determined that fragments corresponding to 1.5-kb fragments upstream of the tcu-1 and nit-6 open reading frames are needed for optimal repression and expression of GFP mRNA and protein. nit-6 was repressed using concentrations of glutamine from 2 to 20 mM and induced in medium containing 0.5-20 mM nitrate as the nitrogen source. Highest levels of expression were achieved within 3 hr of induction for each promoter and GFP mRNA could not be detected within 1 hr after transfer to repressing conditions using the nit-6 promoter. We also performed metabolic profiling experiments using proton NMR to identify changes in metabolite levels under inducing and repressing conditions for each promoter. The results demonstrate that conditions used to regulate tcu-1 do not significantly change the primary metabolome and that the differences between inducing and repressing conditions for nit-6 can be accounted for by growth under nitrate or glutamine as a nitrogen source. Our findings demonstrate that nit-6 is a tunable promoter that joins tcu-1 as a choice for regulation of gene expression in N. crassa

Direct Quantitative Analysis of Biomarkers using Mass Spectrometry

Point-of-care (POC) diagnostics describes a step in the medical treatment process where drugs can be monitored in a patient’s body on-site and in a timely fashion. Mass spectrometry (MS) can provide a quick, efficient, and highly accurate method of analysis of patient biofluids and tissues. Developing methods to bring this diagnostic mechanism to hospitals and clinics has the potential to improve patient care through, for example, personalized medicine. Our goal was to develop a way to effectively introduce internal standard (IS), a necessary chemical for the analytical process, to low-volume biofluid samples. Additionally, the effective direct quantitation of biomarkers with MS was demonstrated using a rat model of nicotine metabolism and the detection of 3-HPMA in urine. By pre-coating silica glass capillary tubes with a fixed volume with IS, biological samples, such as blood, can be obtained in the tube through capillary action and mixed with the IS before deposition for analysis. This method was applied to several different drugs and they were analyzed using a triple quadrupole mass spectrometer. It was optimized for the detection of the metabolite cotinine through a study of solvents and elution processes. Additionally, cotinine was quantified in rat’s blood using this method and the acrolein metabolite 3-HPMA was quantified in urine. Additional work is needed to expand this method for the rapid detection of other biomarkers. In the future, this can contribute to the expanded use of MS in clinical care and improved POC diagnostics

Generalising Deep Learning MRI Reconstruction across Different Domains

We look into robustness of deep learning based MRI reconstruction when tested on unseen contrasts and organs. We then propose to generalise the network by training with large publicly-available natural image datasets with synthesised phase information to achieve high cross-domain reconstruction performance which is competitive with domain-specific training. To explain its generalisation mechanism, we have also analysed patch sets for different training datasets.Comment: Accepted for ISBI2019 as a 1-page abstrac

Prediction and analysis of the secreteomic in Corynebacterium glutamicum ATCC 13032

Corynebacterium glutamicum is an outstanding organism used for amino acid production. Its ability to secrete L-glutamate has been known for almost fifty years now. The complete nucleotide sequence of C. glutamicum ATCC 13032 genome was previously determined and allowed the reliable prediction of 3056 protein-coding genes within this genome using computational methods. The 3056 open reading frames (ORFs) of C. glutamicum ATCC 13032 were used for the prediction of secreted proteins by bioinformatics approaches, such as SignalP 3.0 and Proteome Analyst. 167 proteins were predicted to be secreted and contain signal peptides, whose amino residues were relatively conserved. Among them, 10 have RR-motif signal peptide and 46 have SignalPaseII signal peptide. Total of 167 secreted proteins have functional descriptions, many of which were enzymes that are involved in metabolism. This prediction method has given good insights into the whole secreted proteome of C. glutamicum and provided basis to further studies of its secretomic features at a genome level

Strong and Confined Acids Catalyze Asymmetric Intramolecular Hydroarylations of Unactivated Olefins with Indoles

In recent years, several organocatalytic asymmetric hydroarylations of activated, electron-poor olefins with activated, electron-rich arenes have been described. In contrast, only a few approaches that can handle unactivated, electronically neutral olefins have been reported and invariably require transition metal catalysts. Here we show how an efficient and highly enantioselective catalytic asymmetric intramolecular hydroarylation of aliphatic and aromatic olefins with indoles can be realized using strong and confined IDPi Brønsted acid catalysts. This unprecedented transformation is enabled by tertiary carbocation formation and establishes quaternary stereogenic centers in excellent enantioselectivity and with a broad substrate scope that includes an aliphatic iodide, an azide, and an alkyl boronate, which can be further elaborated into bioactive molecules

PRAS: Predicting functional targets of RNA binding proteins based on CLIP-seq peaks.

RNA-protein interaction plays important roles in post-transcriptional regulation. Recent advancements in cross-linking and immunoprecipitation followed by sequencing (CLIP-seq) technologies make it possible to detect the binding peaks of a given RNA binding protein (RBP) at transcriptome scale. However, it is still challenging to predict the functional consequences of RBP binding peaks. In this study, we propose the Protein-RNA Association Strength (PRAS), which integrates the intensities and positions of the binding peaks of RBPs for functional mRNA targets prediction. We illustrate the superiority of PRAS over existing approaches on predicting the functional targets of two related but divergent CELF (CUGBP, ELAV-like factor) RBPs in mouse brain and muscle. We also demonstrate the potential of PRAS for wide adoption by applying it to the enhanced CLIP-seq (eCLIP) datasets of 37 RNA decay related RBPs in two human cell lines. PRAS can be utilized to investigate any RBPs with available CLIP-seq peaks. PRAS is freely available at http://ouyanglab.jax.org/pras/