Biochemistry, Biophysics, and Structural Biology Commons^™

Investigation Of Electrolytic Flocculation For Microalga Scenedesmus Sp Using Aluminum And Graphite Electrodes, Shihong Liu, Husam A. Abu Hajar, Guy Riefler, Ben J. Stuart

Civil & Environmental Engineering Faculty Publications

Electrolytic flocculation using non-sacrificial electrodes with flocculants added was studied on harvesting Scenedesmus sp. In order to optimize the operating conditions of the electrolytic flocculation process and to quantify the amount of flocculants added, aluminum electrodes were first used in the process. It was found that under optimal conditions, the microalgae removal efficiency using aluminum electrodes could reach 98.5%, while 34.2 mg L^-1 of aluminum ions were released during the process. Different metal electrodes were also studied, but high microalgae removal efficiency was witnessed only using aluminum electrodes, indicating the influence of the aluminum ion in flocculation. When non-sacrificial …

Synthesis And Biological Evaluation Of Phaeosphaeride A Derivatives As Antitumor Agents, Victoria Abzianidze, Petr Beltyukov, Sofya Zakharenkova, Natalia Moiseeva, Jennifer Mejia, Alvin Holder, Yuri Trishin, Alexander Berestetskiy, Victor Kuznetsov

Chemistry & Biochemistry Faculty Publications

New derivatives of phaeosphaeride A (PPA) were synthesized and characterized. Anti-tumor activity studies were carried out on the HCT-116, PC3, MCF-7, A549, К562, NCI-Н929, Jurkat, THP-1, RPMI8228 tumor cell lines, and on the HEF cell line. All of the compounds synthesized were found to have better efficacy than PPA towards the tumor cell lines mentioned. Compound 6 was potent against six cancer cell lines, HCT-116, PC-3, K562, NCI-H929, Jurkat, and RPMI8226, showing a 47, 13.5, 16, 4, 1.5, and 7-fold increase in anticancer activity comparative to those of etoposide, respectively. Compound 1 possessed selectivity toward the NCI-H929 cell line (IC …

Advances In Amino Acid Analysis For Marine Related Matrices And Its Application To Coastal Shelf Settings In The Canadian Arctic, Rachel M. Mcmahon

OES Theses and Dissertations

Amino acids comprise up to 50% of organic matter in cellular material and are a major fraction of oceanic organic carbon. Amino acids are also considered highly labile during organic matter recycling, making them useful proxies for organic carbon cycling. Nevertheless, analysis of individual amino acids has been burdened by lengthy derivatization and complex analysis since the 1950s. In this thesis, I describe the modification of advanced analytical techniques, developed in the biomedical field, for analysis of marine matrices which allow the determination of at least 40 amino acids without the need for lengthy sample preparation and derivatization, twice the …

Characterizing The Activity Of Antimicrobial Peptides Against The Pathogenic Bacterium Clostridium Difficile In An Anaerobic Environment, Adenrele Mojeed Oludiran

Chemistry & Biochemistry Theses & Dissertations

Clostridium difficile is an anaerobic Gram-positive pathogen with high treatment costs and mortality and very high antibiotic tolerance. Antimicrobial host-defense peptides (HDPs) produced naturally by animal immune systems are promising candidates to develop novel therapies for bacterial infection because they cause oxidative stress that damages multiple targets in bacterial cells, so it is difficult for bacteria to evolve resistance to these attacks.

Piscidins, fish-derived HDPs that can also form complexes with copper (Cu) to enhance their activities, are very active against multiple bacterial species in an aerobic environment. We examined their activity against C. difficile and other species in an …

Characterization And Analysis Of Ultrathin Cigs Films And Solar Cells Deposited By 3-Stage Process, Grace Rajan, Krishna Aryal, Shankar Karki, Puruswottam Aryal, Robert W. Collins, Sylvain Marsillac

Electrical & Computer Engineering Faculty Publications

In view of the large-scale utilization of Cu(In,Ga)Se₂ (CIGS) solar cells for photovoltaic application, it is of interest not only to enhance the conversion efficiency but also to reduce the thickness of the CIGS absorber layer in order to reduce the cost and improve the solar cell manufacturing throughput. In situ and real-time spectroscopic ellipsometry (RTSE) has been used conjointly with ex situ characterizations to understand the properties of ultrathin CIGS films. This enables monitoring the growth process, analyzing the optical properties of the CIGS films during deposition, and extracting composition, film thickness, grain size, and surface roughness which …

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin …

Prediction Of Lncrna-Disease Associations Based On Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA–disease associations, especially for novel lncRNAs, remains challenging.

Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA– disease associations based on inductive matrix completion. We compute Gaussian interaction profile kernel of lncRNAs from known lncRNA–disease interactions and functional similarity of diseases based on disease–gene and gene–gene onotology …

Inactivation Of Myeloma Cancer Cells By Helium And Argon Plasma Jets: The Effect Comparison And The Key Reactive Species, Zeyu Chen, Qingjie Cui, Chen Chen, Dehui Xu, Dingxin Liu, H. L. Chen, Michael G. Kong

Bioelectrics Publications

In plasma cancer therapy, the inactivation of cancer cells under plasma treatment is closely related to the reactive oxygen and nitrogen species (RONS) induced by plasmas. Quantitative study on the plasma-induced RONS that related to cancer cells apoptosis is critical for advancing the research of plasma cancer therapy. In this paper, the effects of several reactive species on the inactivation of LP-1 myeloma cancer cells are comparatively studied with variable working gas composition, surrounding gas composition, and discharge power. The results show that helium plasma jet has a higher cell inactivation efficiency than argon plasma jet under the same discharge …

An Investigation Of Atomic Structures Derived From X-Ray Crystallography And Cryo-Electron Microscopy Using Distal Blocks Of Side-Chains, Lin Chen, Jing He, Salim Sazzed, Rayshawn Walker

Computer Science Faculty Publications

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2-4 Å resolutions. The results show that the normalized probability density function of block …

The Biogeochemical Cycling Of Iron, Copper, Nickel, Cadmium, Manganese, Cobalt, Lead, And Scandium In A California Current Experimental Study, Travis Mellett, Matthew T. Brown, P. Dreux Chappell, Carolyn Duckham, Jessica N. Fitzsimmons, Claire P. Till, Robert M. Sherrell, Maria T. Maldonado, Kristen N. Buck

OES Faculty Publications

A 3-day shipboard incubation experiment was conducted in the California Current System in July 2014 to investigate the cycling of iron (Fe), copper (Cu), nickel (Ni), cadmium (Cd), manganese (Mn), cobalt (Co), lead (Pb), and scandium (Sc) under a range of light and particle conditions. Filtered (< 0.2 μm) and unfiltered treatments were incubated under the following light conditions: Dark, light (“UV”), and light without the ultraviolet (UV) wavelengths (“noUV”). The experiment was sampled for carbon and Fe uptake rates, dissolved trace metal concentrations (Fe, Cu, Ni, Cd, Mn, Co, Pb, Sc), Fe and Cu speciation, size-fractionated concentrations of Cd and Fe, and diatom community composition from DNA sequencing. Exposure to UV light increased phytoplankton Fe uptake in the first 24 h of the incubation relative to the noUV treatment, suggesting that a fraction of the ambient ligand-bound Fe was photoreactive. Fe-binding organic ligand production was observed in the unfiltered light treatments in association with increasing chlorophyll a, and evidence for Cu-binding ligand production in these treatments was also observed. Biological uptake of Cd and Co was observed along with scavenging of dissolved Pb. Manganese appeared to be rapidly oxidized by Mn-oxidizing bacteria with concomitant drawdown of dissolved Ni. Scandium displayed similar trends to Fe, reinforcing the limited observations …

Dynamic Control Of Particle Separation In Deterministic Lateral Displacement Separator With Viscoelastic Fluids, Yuke Li, Hongna Zhang, Yongyao Li, Xiaobin Li, Jian Wu, Shizhi Qian, Fengchen Li

Mechanical & Aerospace Engineering Faculty Publications

We proposed an innovative method to achieve dynamic control of particle separation by employing viscoelastic fluids in deterministic lateral displacement (DLD) arrays. The effects of shear-thinning and elasticity of working fluids on the critical separation size in DLD arrays are investigated. It is observed that each effect can lead to the variation of the critical separation size by approximately 40%. Since the elasticity strength of the fluid is related to the shear rate, the dynamic control can for the first time be easily realized through tuning the flow rate in microchannels.

Structure Of The Picornavirus Replication Platform: A Potential Drug Target For Inhibiting Virus Replication, Meghan Suzanne Warden

Chemistry & Biochemistry Theses & Dissertations

Picornaviruses are small, positive-stranded RNA viruses, divided into twelve different genera. Members of the Picornaviridae family cause a wide range of human and animal diseases including the common cold, poliomyelitis, foot and mouth disease, and dilated cardiomyopathy. The picornavirus genome is replicated via a highly conserved mechanism involving a presumed cloverleaf structure located at the 5’ noncoding region of the virus genome. The 5’ cloverleaf consists of three stem loops (B, C, and D) and one stem (A), which interact with a variety of virus and host cell proteins during replication. In this dissertation, human rhinovirus serotype 14 (HRV-14) SLB …