Synthesis, self-assembly and applications of tribenzopenta-phene derivatives and triphenylene-based conjugated foldamers

Title from PDF of title page, viewed on March 12, 2014Dissertation advisor: Zhonghua PengVitaIncludes bibliographic references (pages 154-171)Thesis (Ph. D.)--Dept. of Chemisty and and Pharmaceutical Sciences. University of Missouri--Kansas City, 2013Polycyclic aromatic hydrocarbons (PAHs) are interesting discotic liquid crystalline materials. Their often planar or near-planar geometry and extended π-delocalization render them appealing π-π stacking building blocks which can be utilized to dictate controlled self-assembly processes. In addition, the potentially high charge mobility along the stacked PAH column may find applications in sensors, field effect transistors and photovoltaic cells. In this dissertation, efficient synthetic approaches to tribenzopentaphene (TBP) derivatives are reported and their optical, electrochemical, self-assembly, and photovoltaic properties are studied. It is shown that TBP derivatives are good electron donors which, when coated on pre-grown perylenediimide (PDI) nanofibers can significantly enhance the photocurrent response of the PDI nanofibrils. The peripheral substituents on the TBP core are found to exhibit significant effect on its self-assembly properties which in turn affects the photocurrent response of the PDI/TBP heterojunction nanofibrils. Heterjunction solar cells using TBP derivatives as the donor and PDI or PCBM as the acceptor have also been fabricated and a power conversation efficiency of 0.12% has been achieved. Conjugated oligomers and polymers which can self-organize into a helical conformation have been extensively studied. Such studies have not only led to much better understanding of the principles behind noncovalent folding, but also brought about a number of exciting applications from selective and specific guest binding, functional group organization, to reactive sieves. The major driving forces responsible for the folding of π-conjugated systems are π-π stacking and solvophobic interactions. The strength of the π-π interaction depends on the size and the electronic nature of the aromatic systems. In general, the larger the size of the planar aromatic system is, the stronger the π-π interaction will be. Interestingly, studies on conjugated foldamers have so far been limited to single-ring aromatic systems, in which the mere existence of π-π interactions is questionable. Polycyclic aromatic systems (PCA), as far as we know, have not been utilized in conjugated foldamers. It is envisioned that, with PCAs in the conjugated polymer backbone, the polymer will not only exhibit much stronger propensity for folding due virtually to their stronger π-π stacking interactions, but also may lead to conjugated systems with very interesting electronic and optical properties. In the second part of this dissertation, we report the synthesis and optical properties of triphenylene-containing conjugated foldamers. Systematic optical property studies show that such polymers indeed fold in a variety of solvents. Depending on the solvents, the polymer may also adopt a random coil conformation or interchain aggregation. Among the three conformations, the folding conformation is found to exhibit the highest fluorescence quantum yield.Abstract -- Illustrations -- Tables -- Acknowledgements -- Synthesis and characterizations of new discotic tribenzopentaphene derivatives -- Photoconductivity and photovolataic applications of tribenzopentaphene derivatives -- Synthesis, self-assembley, and applications of a diphenyl-substituted tribenzopentaphene -- Syntheses and optical properties of triphenylene-containing conjugated foldamers -- Reference

Comparison of secondary signs as shown by unenhanced helical computed tomography in patients with uric acid or calcium ureteral stones

AbstractUnenhanced helical computed tomography (UHCT) has evolved into a well-accepted diagnostic method in patients with suspected ureterolithiasis. UHCT not only shows stones within the lumen of the ureter, it also permits evaluation of the secondary signs associated with ureteral obstruction from stones. However, there we could find no data on how secondary signs might differ in relation to different compositions of ureteral stones. In this study, we compared the degree of secondary signs revealed by UHCT in uric acid stone formers and in patients forming calcium stones. We enrolled 117 patients with ureteral stones who underwent UHCT examination and Fourier transform infra-red analysis of stone samples. Clinical data were collected as follows: age, sex, estimated glomerular filtration rate (eGFR), urine pH, and radiological data on secondary signs apparent on UHCT. The uric acid stone formers had significantly lower urine pH and eGFR in comparison to calcium stone formers, and on UHCT they also had a higher percentage of the secondary signs, including rim sign (78.9% vs. 60.2%), hydroureter (94.7% vs. 89.8%), perirenal stranding (84.2% vs. 59.2%) and kidney density difference (73.7% vs. 50.0%). The radiological difference was statistically significant for perirenal stranding (p=0.041). In conclusion, we found that UHCT scanning reveals secondary signs to be more frequent in patients with uric acid ureteral stones than in patients with calcium stones, a tendency that might result from an acidic urine environment

BN-embedded monolayer graphene with tunable electronic and topological properties

Finding an effective and controllable way to create a sizable energy gap in graphene-based systems has been a challenging topic of intensive research. We propose that the hybrid of boron nitride and graphene (h-BNC) at low BN doping serves as an ideal platform for band-gap engineering and valleytronic applications. We report a systematic first-principles study of the atomic configurations and band gap opening for energetically favorable BN patches embedded in graphene. Based on first-principles calculations, we construct a tight-binding model to simulate general doping configurations in large supercells. Unexpectedly, the calculations find a linear dependence of the band gap on the effective BN concentration at low doping, arising from an induced effective on-site energy difference at the two C sublattices as they are substituted by B and N dopants alternately. The significant and tunable band gap of a few hundred meVs, with preserved topological properties of graphene and feasible sample preparation in the laboratory, presents great opportunities to realize valley physics applications in graphene systems at room temperature

Substrate Specificity and Plasticity of FERM-Containing Protein Tyrosine Phosphatases

SummaryEpidermal growth factor receptor (EGFR) pathway substrate 15 (Eps15) is a newly identified substrate for protein tyrosine phosphatase N3 (PTPN3), which belongs to the FERM-containing PTP subfamily comprising five members including PTPN3, N4, N13, N14, and N21. We solved the crystal structures of the PTPN3-Eps15 phosphopeptide complex and found that His812 of PTPN3 and Pro850 of Eps15 are responsible for the specific interaction between them. We defined the critical role of the additional residue Tyr676 of PTPN3, which is replaced by Ile939 in PTPN14, in recognition of tyrosine phosphorylated Eps15. The WPD loop necessary for catalysis is present in all members but not PTPN21. We identified that Glu instead of Asp in the WPE loop contributes to the catalytic incapability of PTPN21 due to an extended distance beyond protonation targeting a phosphotyrosine substrate. Together with in vivo validations, our results provide novel insights into the substrate specificity and plasticity of FERM-containing PTPs

Antidotal efficacies of the cyanide antidote candidate dimethyl trisulfide alone and in combination with cobinamide derivatives

Formulation optimization and antidotal combination therapy are the two important tools to enhance the antidotal protection of the cyanide (CN) antidote dimethyl trisulfide (DMTS). The focus of this study is to demonstrate how the formulation with polysorbate 80 (Poly80), an excipient used in pharmaceutical technology, and the combinations with other CN antidotes having different mechanisms of action enhance the antidotal efficacy of the unformulated (neat) DMTS. The LD50 for CN was determined by the statistical Dixon up-and-down method on mice. Antidotal efficacy was expressed as antidotal potency ratio (APR). CN was injected subcutaneously one minute prior to the antidotes’ injection intramuscularly. The APR values of 1.17 (dose: 25 mg/kg bodyweight) and 1.45 (dose: 50 mg/kg bodyweight) of the neat DMTS were significantly enhanced by the Poly80 formulation at both investigated doses to 2.03 and 2.33, respectively. The combination partners for the Poly80 formulated DMTS (DMTS-Poly80; 25 and 50 mg/kg bodyweight) were 4-nitrocobinamide (4NCbi) (20 mg/kg bodyweight) and aquohydroxocobinamide (AHCbi; 50, 100, and 250 mg/kg bodyweight). When DMTS-Poly80 (25 and 50 mg/kg bodyweight; APR = 2.03 and 2.33, respectively) was combined with 4NCbi (20 mg/kg bodyweight; APR = 1.35), significant increase in the APR values were noted at both DMTS doses (APR = 2.38 and 3.12, respectively). AHCbi enhanced the APR of DMTS-Poly80 (100 mg/kg bodyweight; APR = 3.29) significantly only at the dose of 250 mg/kg bodyweight (APR = 5.86). These studies provided evidence for the importance of the formulation with Poly80 and the combinations with cobinamide derivatives with different mechanisms of action for DMTS as a CN antidote candidate

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database (http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system

A Genetic Polymorphism (rs17251221) in the Calcium-Sensing Receptor Gene (CASR) Is Associated with Stone Multiplicity in Calcium Nephrolithiasis

Calcium nephrolithiasis is one of the most common causes of renal stones. While the prevalence of this disease has increased steadily over the last 3 decades, its pathogenesis is still unclear. Previous studies have indicated that a genetic polymorphism (rs17251221) in the calcium-sensing receptor gene (CASR) is associated with the total serum calcium levels. In this study, we collected DNA samples from 480 Taiwanese subjects (189 calcium nephrolithiasis patients and 291 controls) for genotyping the CASR gene. Our results indicated no significant association between the CASR polymorphism (rs17251221) and the susceptibility of calcium nephrolithiasis. However, we found a significant association between rs17251221 and stone multiplicity. The risk of stone multiplicity was higher in patients with the GG+GA genotype than in those with the AA genotype (chi-square test:P = 0.008;odds ratio  =  4.79;95% confidence interval, 1.44–15.92;Yates' correction for chi-square test:P = 0.013). In conclusion, our results provide evidence supporting the genetic effects of CASR on the pathogenesis of calcium nephrolithiasis

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 <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

Atrial fibrillation genetic risk differentiates cardioembolic stroke from other stroke subtypes

AbstractObjectiveWe sought to assess whether genetic risk factors for atrial fibrillation can explain cardioembolic stroke risk.MethodsWe evaluated genetic correlations between a prior genetic study of AF and AF in the presence of cardioembolic stroke using genome-wide genotypes from the Stroke Genetics Network (N = 3,190 AF cases, 3,000 cardioembolic stroke cases, and 28,026 referents). We tested whether a previously-validated AF polygenic risk score (PRS) associated with cardioembolic and other stroke subtypes after accounting for AF clinical risk factors.ResultsWe observed strong correlation between previously reported genetic risk for AF, AF in the presence of stroke, and cardioembolic stroke (Pearson’s r=0.77 and 0.76, respectively, across SNPs with p &lt; 4.4 × 10−4 in the prior AF meta-analysis). An AF PRS, adjusted for clinical AF risk factors, was associated with cardioembolic stroke (odds ratio (OR) per standard deviation (sd) = 1.40, p = 1.45×10−48), explaining ∼20% of the heritable component of cardioembolic stroke risk. The AF PRS was also associated with stroke of undetermined cause (OR per sd = 1.07, p = 0.004), but no other primary stroke subtypes (all p &gt; 0.1).ConclusionsGenetic risk for AF is associated with cardioembolic stroke, independent of clinical risk factors. Studies are warranted to determine whether AF genetic risk can serve as a biomarker for strokes caused by AF.</jats:sec