Instrumental development of novel detection methods for liquid chromatography and capillary electrophoresis

The versatility and exceptional efficiencies afforded by modern liquid chromatography (LC) have made it indispensable for separations and quantitative analysis in virtually every discipline within the physical and biological sciences. Despite rapid advances in column technology, the development and applications of LC have been slowed by the absence of truly universal and highly sensitive detectors. On the other hand, the recent explosive growth of capillary electrophoresis (CE) applications has created challenges in developing highly efficient detectors. This dissertation presents the development and improvements of instrumental techniques for detection in LC and CE. The first chapter reviews the current status of the various detection methods for LC and CE;Section I presents the first universal detector based on magneto-optical rotation (MOR) for high performance liquid chromatography (HPLC). The experimental results confirm the linear dependance of the MOR signal on the analyte concentration. The feasibility of this method is demonstrated in the detection of polynuclear aromatic hydrocarbons, where the limit of detection is in the sub-microgram range;For the first time, a novel axial-beam on-column absorption detector for open tubular capillary liquid chromatography is described in Section II. The axial coupling of source light with the capillary columns and the use of optical waveguide capillary columns made it possible to utilize the full length of the sample bands inside the capillary columns as the path length for absorbance measurements. For a typical 10 [mu]m i.d. capillary column, the axial-beam detection provides an increase of up to 1000 times in path length and a 192-fold associated improvement on the limit of detection;The project described in the third section is the optimization of detectability in the laser-based polarimetric detector for HPLC. A mathematical simulation is performed in order to optimize the detectability of the detector. The designing parameters of the detector are systematically chosen for optimum performance. The experimental verification of the optimized parameters provides the performance approaching the shot-noise limit;Finally, Section IV demonstrated the feasibility of axial-beam absorption detection for capillary electrophoresis using a conventional light source. The cross-beam and axial-beam detection schemes can be easily switched. The high stability of light intensity, variable wavelength and UV ability make this detector attractive. The improved limit of detection in the axial-beam arrangement should make CE with absorption detection feasible to a wider range of applications

Chaos signatures of current phase transition in a toroidal trap

In this work we demonstrate how the directed motion of atomic Bose-Einstein condensates in a toroidal trap can be controlled by applying a zero-mean oscillatory driving field. We show that due to the self-trapping effect in momentum space, the oscillatory amplitude of the current can be significantly suppressed and a nearly constant directed current can be obtained preserving the initial current values, by decreasing the driving amplitude, even when the atomic interactions are relatively small. We also reveal numerically the mean-field chaos can serve as an indicator of a quantum phase transition between the vanishing current regime and nonvanishing current regime. Our results are corroborated by an effective three-mode model, which provides an excellent account of the ratchet dynamics of the system.Comment: 7 pages, 9 figure

Analytical results for the superflow of spin-orbit-coupled Bose-Einstein condensates in optical lattices

In this paper, we show that for sufficiently strong atomic interactions, there exist analytical solutions of current-carrying nonlinear Bloch states at the Brillouin zone edge to the model of spin-orbit-coupled Bose-Einstein condensates (BECs) with symmetric spin interaction loaded into optical lattices. These simple but generic exact solutions provide an analytical demonstration of some intriguing properties which have neither an analog in the regular BEC lattice systems nor in the uniform spin-orbit-coupled BEC systems. It is an analytical example for understanding the superfluid and other related properties of the spin-orbit-coupled BEC lattice systems.Comment: 9 pages, 6 figure

Interface-engineered ferroelectricity of epitaxial Hf\u3csub\u3e0.5\u3c/sub\u3eZr\u3csub\u3e0.5\u3c/sub\u3eO\u3csub\u3e2\u3c/sub\u3e thin films

Ferroelectric hafnia-based thin films have attracted intense attention due to their compatibility with complementary metal-oxide-semiconductor technology. However, the ferroelectric orthorhombic phase is thermodynamically metastable. Various efforts have been made to stabilize the ferroelectric orthorhombic phase of hafnia-based films such as controlling the growth kinetics and mechanical confinement. Here, we demonstrate a key interface engineering strategy to stabilize and enhance the ferroelectric orthorhombic phase of the Hf0.5Zr0.5O2 thin film by deliberately controlling the termination of the bottom La0.67Sr0.33MnO3 layer. We find that the Hf0.5Zr0.5O2 films on the MnO2-terminated La0.67Sr0.33MnO3 have more ferroelectric orthorhombic phase than those on the LaSrO-terminated La0.67Sr0.33MnO3, while with no wake-up effect. Even though the Hf0.5Zr0.5O2 thickness is as thin as 1.5nm, the clear ferroelectric orthorhombic (111) orientation is observed on the MnO2 termination. Our transmission electron microscopy characterization and theoretical modelling reveal that reconstruction at the Hf0.5Zr0.5O2/ La0.67Sr0.33MnO3 interface and hole doping of the Hf0.5Zr0.5O2 layer resulting from theMnO2 interface termination are responsible for the stabilization of the metastable ferroelectric phase of Hf0.5Zr0.5O2. We anticipate that these results will inspire further studies of interface-engineered hafnia-based systems

MAPK8 and CAPN1 as potential biomarkers of intervertebral disc degeneration overlapping immune infiltration, autophagy, and ceRNA

BackgroundIntervertebral disc degeneration (IDD) is one of the most common health problems in the elderly and a major causative factor in low back pain (LBP). An increasing number of studies have shown that IDD is closely associated with autophagy and immune dysregulation. Therefore, the aim of this study was to identify autophagy-related biomarkers and gene regulatory networks in IDD and potential therapeutic targets.MethodsWe obtained the gene expression profiles of IDD by downloading the datasets GSE176205 and GSE167931 from the Gene Expression Omnibus (GEO) public database. Subsequently, differentially expressed genes (DEGs) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene ontology (GO), and gene set enrichment analysis (GSEA) were performed to explore the biological functions of DEGs. Differentially expressed autophagy-related genes (DE-ARGs) were then crossed with the autophagy gene database. The hub genes were screened using the DE-ARGs protein–protein interaction (PPI) network. The correlation between the hub genes and immune infiltration and the construction of the gene regulatory network of the hub genes were confirmed. Finally, quantitative PCR (qPCR) was used to validate the correlation of hub genes in a rat IDD model.ResultsWe obtained 636 DEGs enriched in the autophagy pathway. Our analysis revealed 30 DE-ARGs, of which six hub genes (MAPK8, CTSB, PRKCD, SNCA, CAPN1, and EGFR) were identified using the MCODE plugin. Immune cell infiltration analysis revealed that there was an increased proportion of CD8+ T cells and M0 macrophages in IDD, whereas CD4+ memory T cells, neutrophils, resting dendritic cells, follicular helper T cells, and monocytes were much less abundant. Subsequently, the competitive endogenous RNA (ceRNA) network was constructed using 15 long non-coding RNAs (lncRNAs) and 21 microRNAs (miRNAs). In quantitative PCR (qPCR) validation, two hub genes, MAPK8 and CAPN1, were shown to be consistent with the bioinformatic analysis results.ConclusionOur study identified MAPK8 and CAPN1 as key biomarkers of IDD. These key hub genes may be potential therapeutic targets for IDD

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Abstract Background Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. Results To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. Discussion Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. Conclusions Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.https://deepblue.lib.umich.edu/bitstream/2027.42/142394/1/12864_2018_Article_4533.pd

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Abstract Background Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy. Results To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells. Discussion Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway. Conclusions Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment

LRP16 Integrates into NF-κB Transcriptional Complex and Is Required for Its Functional Activation

BACKGROUND: Nuclear factor κB (NF-κB)-mediated pathways have been widely implicated in cell survival, development and tumor progression. Although the molecular events of determining NF-κB translocation from cytoplasm to nucleus have been extensively documented, the regulatory mechanisms of NF-κB activity inside the nucleus are still poorly understood. Being a special member of macro domain proteins, LRP16 was previously identified as a coactivator of both estrogen receptor and androgen receptor, and as an interactor of NF-κB coactivator UXT. Here, we investigated the regulatory role of LRP16 on NF-κB activation. METHODOLOGY: GST pull-down and coimmunoprecipitation (CoIP) assays assessed protein-protein interactions. The functional activity of NF-κB was assessed by luciferase assays, changes in expression of its target genes, and its DNA binding ability. Annexin V staining and flow cytometry analysis were used to evaluate cell apoptosis. Immunohistochemical staining of LRP16 and enzyme-linked immunosorbent assay-based evaluation of active NF-κB were performed on primary human gastric carcinoma samples. RESULTS: We demonstrate that LRP16 integrates into NF-κB transcriptional complex through associating with its p65 component. RNA interference knockdown of the endogenous LRP16 in cells leads to impaired NF-κB activity and significantly attenuated NF-κB-dependent gene expression. Mechanistic analysis revealed that knockdown of LRP16 did not affect tumor necrosis factor α (TNF-α)-induced nuclear translocation of NF-κB, but blunted the formation or stabilization of functional NF-κB/p300/CREB-binding protein transcription complex in the nucleus. In addition, knockdown of LRP16 also sensitizes cells to apoptosis induced by TNF-α. Finally, a positive link between LRP16 expression intensity in nuclei of tumor cells and NF-κB activity was preliminarily established in human gastric carcinoma specimens. CONCLUSIONS: Our findings not only indicate that LRP16 is a crucial regulator for NF-κB activation inside the nucleus, but also suggest that LRP16 may be an important contributor to the aberrant activation of NF-κB in tumors