Genetic engineering and characterization of LysR-type transcriptional regulators

Thesis (Ph.D.) University of Alaska Fairbanks, 2000This thesis describes research aimed at understanding the structure and function of LysR-type transcriptional regulators. I studied two LysR-type proteins. One from the archaeon Methanococcus jannaschii, MJ-LysR. The other is from Burkholderia cepacia, DgdR. The MJ-LysR is the first putative LysR-type transcriptional regulator found in archaea. It is surprising that a prokaryotic transcriptional regulator is present in archaea, whose basal transcription machinery and RNA polymerase are more closely related to those of eukaryotes. To elucidate the structure and function of M-LysR protein, the gene was subcloned and expressed in E. coli. The gene product was isolated and purified by heat treatment and size exclusion chromatography. An in vitro binding assay showed that the purified protein bound to the intergenic region between the lysR gene and its upstream gene specifically and selectively. The results also showed that the protein maintained its binding activity even at 94C̊. The DNA footprinting data demonstrated a 30 bp protected region. Thus, this protein probably regulates expression of its own structural gene and perhaps the adjacent upstream gene. DgdR protein from Burkholderia cepacia had been previously characterized. The previous study showed that 2-methylalanine, the inducer for the DgdR regulated dgdA gene expression, but not D or L-alanine induced the conformational changes on DNA-protein complex. To further confirm this result, eleven amino acids with structures similar to 2-methylalainine were tested for their ability on affecting the binding of the DgdR protein to its operator site. Among these amino acids tested, only 2-methylalanine, 1-aminocyclopentane-1-carboxylic acid, S-2-aminobutanoic acid, RS-isovaline, and 2-trifluoromethyl-2-aminobutanoic acid generated the measurable band shifting. D- or L-norvaline, 2,2-diethyl glycine, and 2-trifluoromethylalanine did not cause any measurable change. It was concluded that both alkyl side chain size and hydrophobicity are important for the inducer recognition and binding in this protein. To solve the problem in DgdR protein purification caused by low solubility of this protein, a dgdR fusion gene to malE gene was constructed. This fusion gene provides a useful tool to further study and crystallize the DgdR protein

SGDiff: A Style Guided Diffusion Model for Fashion Synthesis

This paper reports on the development of \textbf{a novel style guided diffusion model (SGDiff)} which overcomes certain weaknesses inherent in existing models for image synthesis. The proposed SGDiff combines image modality with a pretrained text-to-image diffusion model to facilitate creative fashion image synthesis. It addresses the limitations of text-to-image diffusion models by incorporating supplementary style guidance, substantially reducing training costs, and overcoming the difficulties of controlling synthesized styles with text-only inputs. This paper also introduces a new dataset -- SG-Fashion, specifically designed for fashion image synthesis applications, offering high-resolution images and an extensive range of garment categories. By means of comprehensive ablation study, we examine the application of classifier-free guidance to a variety of conditions and validate the effectiveness of the proposed model for generating fashion images of the desired categories, product attributes, and styles. The contributions of this paper include a novel classifier-free guidance method for multi-modal feature fusion, a comprehensive dataset for fashion image synthesis application, a thorough investigation on conditioned text-to-image synthesis, and valuable insights for future research in the text-to-image synthesis domain. The code and dataset are available at: \url{https://github.com/taited/SGDiff}.Comment: Accepted by ACM MM'2

Heavy Metals Migration in Soil in Tailing Dam Region of Shuikoushan, Hunan Province, China

AbstractThe nonferrous mining industry in China has been exploiting rich domestic mineral resources in order to sustain rapidly economic and social development. The paper chooses the tailing dam region as the research object in the Shuikoushan, and researches the distribution of Pb, Zn, Cu, Cd, As, Cr, which reveals heavy metal migration regularities in layers from new and old tailing dam region. In addition, this article focuses on making the research of Potential Ecological Risk Index appraisal to the heavy metal contamination level. The results showed that the concentrations of heavy metals in old tailing dam region were much higher than those of in the new tailing dam region. As well, the concentrations of most heavy metal reduced progressively with the soil depth increasing for the new tailing dam region, while the change tendency was inversely for the old one. Potential ecological risk index showed that the potential ecological risks were at low and low to moderate level in tailing dam region

Hepatoprotective mechanism of Silybum marianum on nonalcoholic fatty liver disease based on network pharmacology and experimental verification

The study aimed to identify the key active components in Silybum marianum (S. marianum) and determine how they protect against nonalcoholic fatty liver disease (NAFLD). TCMSP, DisGeNET, UniProt databases, and Venny 2.1 software were used to identify 11 primary active components, 92 candidate gene targets, and 30 core hepatoprotective gene targets in this investigation, respectively. The PPI network was built using a string database and Cytoscape 3.7.2. The KEGG pathway and GO biological process enrichment, biological annotation, as well as the identified hepatoprotective core gene targets were analyzed using the Metascape database. The effect of silymarin on NAFLD was determined using H&E on pathological alterations in liver tissues. The levels of liver function were assessed using biochemical tests. Western blot experiments were used to observe the proteins that were expressed in the associated signaling pathways on the hepatoprotective effect, which the previous network pharmacology predicted. According to the KEGG enrichment study, there are 35 hepatoprotective signaling pathways. GO enrichment analysis revealed that 61 biological processes related to the hepatoprotective effect of S. marianum were identified, which mainly involved in response to regulation of biological process and immune system process. Silymarin was the major ingredient derived from S. marianum, which exhibited the hepatoprotective effect by reducing the levels of ALT, AST, TC, TG, HDL-C, LDL-C, decreasing protein expressions of IL-6, MAPK1, Caspase 3, p53, VEGFA, increasing protein expression of AKT1. The present study provided new sights and a possible explanation for the molecular mechanisms of S. marianum against NAFLD

Adaptive Initialization Method Based on Spatial Local Information for k

k-means algorithm is a widely used clustering algorithm in data mining and machine learning community. However, the initial guess of cluster centers affects the clustering result seriously, which means that improper initialization cannot lead to a desirous clustering result. How to choose suitable initial centers is an important research issue for k-means algorithm. In this paper, we propose an adaptive initialization framework based on spatial local information (AIF-SLI), which takes advantage of local density of data distribution. As it is difficult to estimate density correctly, we develop two approximate estimations: density by t-nearest neighborhoods (t-NN) and density by ϵ-neighborhoods (ϵ-Ball), leading to two implements of the proposed framework. Our empirical study on more than 20 datasets shows promising performance of the proposed framework and denotes that it has several advantages: (1) can find the reasonable candidates of initial centers effectively; (2) it can reduce the iterations of k-means’ methods significantly; (3) it is robust to outliers; and (4) it is easy to implement

The vital role of hole-carriers for superconductivity in pressurized black phosphorus

The influence of carrier type on superconductivity has been an important issue for understanding both conventional and unconventional superconductors [1-7]. For elements that superconduct, it is known that hole-carriers govern the superconductivity for transition and main group metals [8-10]. The role of hole-carriers in elements that are not normally conducting but can be converted to superconductors, however, remains unclear due to the lack of experimental data. Here we report the first in-situ high pressure Hall effect measurements on single crystal black phosphorus, measured up to ~ 50 GPa, and find a correlation between the Hall coefficient and the superconducting transition temperature (TC). Our results reveal that hole-carriers play a vital role in developing superconductivity and enhancing TC. Importantly, we also find a Lifshitz transition in the high-pressure cubic phase at ~17.2GPa, which uncovers the origin of a puzzling valley in the superconducting TC-pressure phase diagram. These results offer insight into the role of hole-carriers in developing superconductivity in simple semiconducting solids under pressure.Comment: 9 pages anf 3 figure

Hybrid multi-strategy chaos somersault foraging chimp optimization algorithm research

To address the problems of slow convergence speed and low accuracy of the chimp optimization algorithm (ChOA), and to prevent falling into the local optimum, a chaos somersault foraging ChOA (CSFChOA) is proposed. First, the cat chaotic sequence is introduced to generate the initial solutions, and then opposition-based learning is used to select better solutions to form the initial population, which can ensure the diversity of the algorithm at the beginning and improve the convergence speed and optimum searching accuracy. Considering that the algorithm is likely to fall into local optimum in the final stage, by taking the optimal solution as the pivot, chimps with better adaptation at the mirror image position replace chimps from the original population using the somersault foraging strategy, which can increase the population diversity and expand the search scope. The optimization search tests were performed on 23 standard test functions and CEC2019 test functions, and the Wilcoxon rank sum test was used for statistical analysis. The CSFChOA was compared with the ChOA and other improved intelligent optimization algorithms. The experimental results show that the CSFChOA outperforms most of the other algorithms in terms of mean and standard deviation, which indicates that the CSFChOA performs well in terms of the convergence accuracy, convergence speed and robustness of global optimization in both low-dimensional and high-dimensional experiments. Finally, through the test and analysis comparison of two complex engineering design problems, the CSFChOA was shown to outperform other algorithms in terms of optimal cost. For the design of the speed reducer, the performance of the CSFChOA is 100% better than other algorithms in terms of optimal cost; and, for the design of a three-bar truss, the performance of the CSFChOA is 6.77% better than other algorithms in terms of optimal cost, which verifies the feasibility, applicability and superiority of the CSFChOA in practical engineering problems

Pressure-induced melting of magnetic order and emergence of new quantum state in alpha-RuCl3

Here we report the observation of pressure-induced melting of antiferromagnetic (AFM) order and emergence of a new quantum state in the honeycomb-lattice halide alpha-RuCl3, a candidate compound in the proximity of quantum spin liquid state. Our high-pressure heat capacity measurements demonstrate that the AFM order smoothly melts away at a critical pressure (Pc) of 0.7 GPa. Intriguingly, the AFM transition temperature displays an increase upon applying pressure below the Pc, in stark contrast to usual phase diagrams, for example in pressurized parent compounds of unconventional superconductors. Furthermore, in the high-pressure phase an unusual steady of magnetoresistance is observed. These observations suggest that the high-pressure phase is in an exotic gapped quantum state which is robust against pressure up to ~140 GPa.Comment: 20 pages, 4 figure