Life Sciences Commons^™

Photophysical And Optical Properties Of Semiconducting Polymer Nanoparticles Prepared From Hyaluronic Acid And Polysorbate 80, Adam Langlois, Gage T. Mason, Michael H.L. Nguyen, Mehdi Rezapour, Paul Ludovic Karsenti, Drew Marquardt, Simon Rondeau-Gagné

Chemistry and Biochemistry Publications

Copyright © 2019 American Chemical Society. A nanoprecipitation procedure was utilized to prepare novel diketopyrrolopyrrole-based semiconducting polymer nanoparticles (SPNs) with hyaluronic acid (HA) and polysorbate 80. The nanoprecipitation led to the formation of spherical nanoparticles with average diameters ranging from 100 to 200 nm, and a careful control over the structure of the parent conjugated polymers was performed to probe the influence of π-conjugation on the final photophysical and thermal stability of the resulting SPNs. Upon generation of a series of novel SPNs, the optical and photophysical properties of the new nanomaterials were probed in solution using various techniques including …

Mitochondria Imaging And Targeted Cancer Treatment, Tinghan Zhao

Dissertations

Mitochondria are essential organelles as the site of respiration in eukaryotic cells and are involved in many crucial functions in cell life. Dysfunction of mitochondrial metabolism and irregular morphology have been frequently found in human cancers. The capability of imaging mitochondria as well as regulating their microenvironment is important both scientifically and clinically. Mitochondria penetrating peptides (MPPs), certain peptides that are composed of cationic and hydrophobic amino acids, are good candidates for mitochondria targeting. Herein, a novel MPP, D-argine-phenylalanine-D-argine-phenylalanine-D-argine-phenylalanine-NH₂ (rFrFrF), is conjugated with a rhodamine-based fluorescent chromophore (TAMRA). The TAMRA-rFrFrF probe exhibits advantageous properties for long-term mitochondria tracking of …

Computational Studies And Design Of Pparγ And Glut1 Inhibitors, Suliman Almahmoud

Theses & Dissertations

The peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-dependent transcription factor of the nuclear receptor superfamily that controls the expression of a variety of genes involved in fatty acid metabolism, adipogenesis, and insulin sensitivity. PPARγ is a target for insulin-sensitizing drugs, and it plays a significant function in prostate cancer. PPARγ antagonists have anti-proliferative effects in a broad range of hematopoietic and epithelial cell lines. The ligand binding domain (LBD) of PPARγ is large and has orthosteric and allosteric binding sites. Several PPARγ-ligand co-crystal structures show two bound molecules, one to the orthosteric pocket and a second to the allosteric …

Sideromycin Pathway Elucidation: Insights Into Salmycin Biosynthesis, Transport Paradigms, And Drug Release, Gerry Sann Macaraeg Rivera

Arts & Sciences Electronic Theses and Dissertations

Antibiotic resistance is an increasing threat in today’s society. In order to overcome resistant bacteria, it is necessary to discover new drugs with novel mechanisms of action. This work focuses on the sideromycin pathway, encompassing the biosynthetic production, mechanism of entry and hydrolysis-mediated drug release. Sideromycins are an interesting approach to combat the rise of antibiotic resistance since they provide a different avenue that overcomes problems that arise when entering the cell. The dissertation is separated into distinct sections dealing with the various areas of interest in the sideromycin pathway, particularly for the sideromycin, salmycin, produced by Streptomyces violaceus. The …

Development And Application Of Mass Spectrometry-Based Protein Footprinting In Structural Proteomics, Ming Cheng

Arts & Sciences Electronic Theses and Dissertations

Integral mass spectrometry (MS) has emerged as an important tool for protein structural characterization. It readouts are a broad range of structural information, including stoichiometry, interactions, conformations and conformation change, and dynamics. Protein footprinting is a pivotal component in the intergral MS toolkit.My dissertation centers around the development and application of protein footprinting to characterize protein structure. It is divided into seven chapters.Chapter 1 serves as the introduction for integral mass spectrometry in structural proteomic.In Chapter 2, we extended the fast-photochemical oxidation of proteins (FPOP) platform by adding the trifluoromethyl radical (•CF3) as a new reagent. We discovered that •CF3 …

Oh Chemistry Of Non-Methane Organic Gases (Nmogs) Emitted From Laboratory And Ambient Biomass Burning Smoke: Evaluating The Influence Of Furans And Oxygenated Aromatics On Ozone And Secondary Nmog Formation, Matthew M. Coggon, Christopher Y. Lim, Abigail R. Koss, Kanako Sekimoto, Bin Yuan, Jessica B. Gilman, David H. Hagan, Vanessa Selimovic, Kyle J. Zarzana, Steven S. Brown, James M Roberts, Markus Müller, Robert Yokelson, Armin Wisthaler, Jordan E. Krechmer, Jose L. Jimenez, Christopher Cappa, Jesse H. Kroll, Joost De Gouw, Carsten Warneke

Chemistry and Biochemistry Faculty Publications

Chamber oxidation experiments conducted at the Fire Sciences Laboratory in 2016 are evaluated to identify important chemical processes contributing to the hydroxy radical (OH) chemistry of biomass burning non-methane organic gases (NMOGs). Based on the decay of primary carbon measured by proton transfer reaction time-of-flight mass spectrometry (PTR-ToF-MS), it is confirmed that furans and oxygenated aromatics are among the NMOGs emitted from western United States fuel types with the highest reactivities towards OH. The oxidation processes and formation of secondary NMOG masses measured by PTR-ToF-MS and iodide-clustering time-of-flight chemical ionization mass spectrometry (I-CIMS) is interpreted using a box model employing …

Total Phenolic And Flavonoid Contents Of Anacyclus Pyrethrum Link Plant Extracts And Their Antioxidant Activity, Hanane Elazzouzi, Nadia Zekri, Touriya Zair, Mohamed Alaoui El Belghiti

Karbala International Journal of Modern Science

In this study, Anacyclus pyrethrm Link (roots) is a medicinal plant from the Asteraceae family, endemic to Morocco and is widely used in traditional medicine; was investigated for their total phenolics, flavonoids contents and antioxidant activities. The quantitative estimation of total flavonoids and phenols by the colorimetric method showed that the extracts were prepared by fractionation of the crude hydromethanolic extract (ethyl acetate and n-butanol). The phenol content of various extracts, estimated by the Folin-Ciocalteu method, was between 1,44 and 12,82 mg EAG / g extract of A. pyrethrum. Moreover, it is clear that ethyl acetate was the …

Design Of Reinforced Concrete Deep Beams Using Particle Swarm Optimization Technique, Qais F. Hasan, Dler A. Al-Mamany, Omer K. Fayadh

Karbala International Journal of Modern Science

Researches available in literature interrelating neural networks to civil engineering design problems, especially for beep beams, are very rare. Therefore, an optimization algorithm is developed and verified in this study and coded using MATLAB functions to determine the optimum cost design of reinforced concrete deep beams. ACI 318-14 code method is used benefiting from iterative particle swarm optimization technique due to its efficiency and reliability. Minimizing total cost is used as the objective function in terms of four decision variables. Self-adaptive penalty function technique is used to handle constraints for each of the 300 randomly selected particles, and in each …

Artificial Bee Colony Algorithm For Solving Fuzzy Multi-Objective Bed Allocation Model, Abdulhakeem Luqman Hasan

Karbala International Journal of Modern Science

With the improvement of the medical services frameworks rivalry, hospitals face more and more challenges. In the interim, allotment of resource has a crucial influence on performing competitive benefits in a hospitals. To choose the suitable beds number is one of the most essential tasks in hospital administration. Anyway, in true condition, bed allotment choice is a multiple-side problem with weakness and haphazardness of the information available. It is so sophisticated. Therefore, the research about bed allotment difficulty is comparatively rare under considering multiple departments, nursing hours, and stochastic information about arrival and service of patients. In this paper, we …

Performance Study Of The Membrane Based Layered Double Hydroxides ‘Znal-Gh’ In The Purification Of Groundwater, Jaouad Zerhouni, Omar Qabaqous, Fouzia Rhazi Filali, Mohammed Naciri Bennani, Najib Tijani

Karbala International Journal of Modern Science

The objective of this work is focused on the preparation and characterization of plan microfiltration membrane Zn₃Al-Gh and the study of their efficiency in the treatment of ground water. This membrane was carried by using the support of the clay such as Ghassoul ‘Gh’ prepared by using dry uniaxial compaction method. The layered double hydroxides (LDH) based on Zn₃Al-CO₃with molar ratio (Zn²⁺/Al³⁺=3) was deposited on support by direct co-precipitation method.

The characterizations of the membrane LDH-Gh ‘Zn₃Al-Gh’ and deposited layer Zn₃Al-CO_3, was done by scanning …

Evaluation Of Atmospherically Gases Using Models Flaash And Quac To Hyper-Spectral Imagery, Asmaa Maher

Karbala International Journal of Modern Science

The important step is correction of the effect of atmospheric on hyper-spectral imagery of the VIS “visible”, short wave & NIR “near-infrared” spectral range. In general, the cause for limiting the use of hyperspectral images is the atmospheric effects, so, atmospheric correction is necessary for any accurate processing. In this work, two atmospheric correction techniques have been applied on Hyper-spectral image. From the raw original image and also from the FLAASH and QUAC atmospheric corrected images the spectra of vegetation, water and soil were extracted. The acquisition data for study contained Hyperion bands for year “2015” images over each of …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Characterization Of The Dimerization Domains On The Mannose-6-Phosphate/Insulin-Like Growth Factor Ii Receptor, Tyler Degener

Theses/Capstones/Creative Projects

The mannose-6-phosphate/insulin-like growth factor II (M6P/IGF2) receptor is a transmembrane protein known to sequester growth factors from the extracellular matrix. This behavior suggests a mechanism of tumor suppression. Structurally, the receptor’s extracellular region is segmented into 15 homologous repeats, which are divided further into 5 triplet domains, labelled 1-3, 4-6, 7-9, 10-12, and 13-15. What is notable about the triplets is their propensity to form dimers with triplets on a second M6P/IGF2 receptor. In fact, previous studies indicate that this protein functions optimally when dimerized. Thus, the purpose of this experiment is to characterize these domain interactions. Using a urea …

Comprehensive Investigation Of Bioactive Steroidal Alkaloids In Veratrum Californicum, Matthew West Turner

Boise State University Theses and Dissertations

Veratrum californicum, commonly referred to as corn lily or Californian false hellebore, grows in high mountain meadows and produces bioactive steroidal alkaloids, including cyclopamine. Cyclopamine is a potent inhibitor of the Hedgehog (Hh) signaling pathway. Our lab has optimized methods to extract cyclopamine and related steroidal alkaloids from V. californicum, and implemented in-house Hh signaling bioactivity evaluation of these steroidal alkaloids using a Shh-Light II cell assay. A survey of extraction methods and solvents resulted in the identification of conditions most favorable for alkaloid extraction yield and antagonist activity in the Shh-Light II cell assay. The highest amount …

Probing Of Carbohydrate-Protein Interactions Using Galactonoamidine Inhibitors, Jessica B. Pickens

Graduate Theses and Dissertations

Glycoside hydrolases are ubiquitous and one of the most catalytically proficient enzymes known, and thus understanding their mechanisms are crucial. Most research has focused on the interaction of the glycon of substrates and their inhibitors within the active site of glycoside hydrolases. The inhibitors employed to probe these interactions generally had small aglycons (i.e. a hydrogen atom, amidines, small aliphatic groups, or benzyl groups). Here, the interactions of the aglycon with glycoside hydrolases are examined by probing the active sites with a library of 25 galactonoamidines. The studies described in this dissertation aim to increase the understanding of stabilization of …

The Curious Case Of Nad-Cleaving Nudix Hydrolases, Atreyei Ray

Theses and Dissertations

Nudix proteins are members of a large family of homologous enzymes that hydrolyze nucleoside diphosphates linked to other compounds (x). These enzymes have catalytic activity on a wide range of substrates such as dNTPs (both canonical and their oxidized forms), nucleotide sugars, alcohols, dinucleoside polyphosphates, dinucleotide cofactors, and nucleoside diphosphates linked to RNA. The bacterial genome encodes around 13, while the human genome encodes for 22 such nudix proteins.

The E. coli genome encodes for a mutT mutator gene, the progenitor of the family expressing the MutT pyrophosphohydrolase (NudA) protein (Treffers et al., 1954; Bhatnagar et al., 1988). The enzyme …

Rotational Tuning Of Transmembrane Helix Properties Based On The Precise Placements Of Aromatic And Charged Residues, Matthew J. Mckay

Graduate Theses and Dissertations

Designed model transmembrane peptides and oriented 2H and 15N solid-state nuclear magnetic resonance (NMR) spectroscopy were used to analyze how simple sequence modifications can influence peptide structure, behavior and dynamics as well as for determining the pKa of glutamic acid at the membrane interface. The GW5,19ALP23 (acetyl-GGALW(LA)6LWLAGA-amide) peptide framework adopts a well-defined tilted orientation in lipid bilayers (DLPC, DMPC and DOPC) and undergoes low amounts of dynamic motion. The sequence was initially modified by moving the Trp residues outwards to positions 4 and 20. This new sequence GW4,20ALP23 (acetyl-GGAW(AL)7AWAGA-amide) displays high amounts of signal averaging of NMR observables caused by …

The Antimicrobial Activity And Cellular Targets Of Plant Derived Aldehydes And Degradable Pro-Antimicrobial Networks In Pseudomonas Aeruginosa, Yetunde Adewunmi

Dissertations

Essential oils (EOs) are plant-derived products that have been long exploited for their antimicrobial activities in medicine, agriculture, and food preservation. EOs represent a promising alternative to conventional antibiotics due to the broad-range antimicrobial activity, low toxicity to human commensal bacteria, and the capacity to kill microorganisms without promoting resistance. Despite the progress in the understanding of the biological activity of EOs, many aspects of their mode of action remain inconclusive. The overarching aim of this work was to address these gaps by studying molecular interactions between antimicrobial plant aldehydes and the opportunistic human pathogen Pseudomonas aeruginosa. We initiated …

Asymmetric Synthesis Of The C29-C34 Moiety Of Fragment A Of The Antascomicin B & Thermal Azole Based Claisen Rearrangements, Dharma Theja Nannapaneni

Graduate Theses and Dissertations

The dissertation describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B and Thermal azole based Claisen rearrangements. In chapter 1, we describes asymmetric synthesis towards C29-C34 moiety of fragment A of the Antascomicin B. The non-immunosuppressant Rapamycin, Ascomycin, and Tacrolimus (FK506), strongly binds with FKBP12, the ligand FKBP12 complexes responsible for immunosuppressive activity. Antascomicin B structurally related to Rapamycin, Ascomycin, and Tacrolimus (FK506), binds strongly to FKBP12, yet does not shown immunosuppressive activity. The ligand FKBP12 binding complexes shown to have potent neuroprotective and neurogenerative properties in mouse models of Parkinson’s disease. The linear synthesis of …

Effects Of The Dihydrouracil Lesion On Dna Using 1h/31p 1d And 2d Solution Nmr, Benjamin M. Boyd

MSU Graduate Theses

The effects of the dihydrouracil lesion in DNA were studied using two dimensional NMR spectroscopy. The sequence used was based off of the Drew-Dickerson Dodecamer, with the cytosine in the three position replaced by a dihydrouracil. All of the nonexchangeable proton chemical shifts, with the exception of the H2, H5’, and H5’’, of the lesioned DNA were identified using NOESY spectra and then compared to the chemical shift values of the Drew Dickerson Dodecamer. The largest differences in chemical shifts were observed in the nucleotides neighboring the lesion, both within the strand and on the opposite strand. The imino exchangeable …

Isotopic Characterization Of Nitrogen Oxides (NoX), Nitrous Acid (Hono), And Nitrate (PNo3-) From Laboratory Biomass Burning During Firex, Jiajue Chai, David J. Miller, Eric Scheuer, Jack Dibb, Vanessa Selimovic, Robert Yokelson, Kyle K. Zarzana, Steven Brown, Abigail R. Koss, Carsten Warneke, Meredith Hastings

Chemistry and Biochemistry Faculty Publications

New techniques have recently been developed and applied to capture reactive nitrogen species, including nitrogen oxides (NOx D NOCNO2), nitrous acid (HONO), nitric acid (HNO3), and particulate nitrate (pNO3 ), for accurate measurement of their isotopic composition. Here, we report – for the first time – the isotopic composition of HONO from biomass burning (BB) emissions collected during the Fire Influence on Regional to Global Environments Experiment (FIREX, later evolved into FIREX-AQ) at the Missoula Fire Science Laboratory in the fall of 2016. We used our newly developed annular denuder system (ADS), which was verified to completely capture HONO associated …

Covalently Functionalized Sawdust For The Remediation Of Phosphate From Agricultural Wastewater, Daniel Meister, David Ure, Angela Awada, Jean-Claude Barrette, Joel Gagnon, Bluent Mutus, John F. Trant

Chemistry and Biochemistry Publications

Phosphate remediation from wastewater is rapidly becoming an ever more attractive process due to a combination of both the economic pressure of increasing phosphate scarcity and the environmental damage caused by untreated agricultural runoff. Ideally, remediated phosphate will be recoverable and would be able to be reused as fertilizer. Many different resins have been investigated, but due to the scale of the challenge, any feasible solution will involve the use of very inexpensive waste products as the solid support. Sawdust, functionalized with iron-binding ligands, is such a potential resin. Sawdust alone binds 0.3 g/kg of phosphate which is insufficient. Iron …

Salty Sensors, Fresh Ideas: The Use Of Molecular And Imaging Sensors In Understanding Plankton Dynamics Across Marine And Freshwater Ecosystems, Trisha Lyn Spanbauer, Christian Briseno-Avena, Kathleen Johnson Pitz, Elizabeth A. Suter

Faculty Works: Biology, Chemistry, and Environmental Studies

Understanding plankton dynamics in marine ecosystems has been advanced using in situ molecular and imaging instrumentation. A range of research objectives have been addressed through high‐resolution autonomous sampling, from food web characterization to harmful algal bloom dynamics. When used together, molecular and imaging sensors can cover the full‐size range, genetic identity, and life stages of plankton. Here, we briefly review a selection of in situ instrumentation developed for the collection of molecular and imaging information on plankton communities in marine ecosystems. In addition, we interviewed a selection of instrumentation developers to determine if the transfer of sensor technology from marine …

Aerial And Ground-Based Optical Gas Imaging Survey Of Uinta Basin Oil And Gas Wells, Seth N. Lyman, Trang Tran, Marc L. Mansfield, Arvind P. Ravikumar

Bingham Research Center

We deployed a helicopter with an infrared optical gas imaging camera to detect hydrocarbon emissions from 3,428 oil and gas facilities (including 3,225 producing oil and gas well pads) in Utah’s Uinta Basin during winter and spring 2018. We also surveyed 419 of the same well pads from the ground. Winter conditions led to poor contrast between emission plumes and the ground, leading to a detection limit for the aerial survey that was between two and six times worse than a previous summertime survey. Because the ground survey was able to use the camera’s high-sensitivity mode, the rate of detected …

Sustainable Solutions, Fall/Winter 2020, Issue 41

Sustain Magazine

No abstract provided.

The Total Syntheses Of Jbir-94 And Two Synthetic Analogs And Their Cytotoxicities Against A549 (Ccl-185) Human Small Lung Cancer Cells, Cathy L. Mangum, Mica B. Munford, Alyssa Sam, Sandra K. Young, Jeremy T. Beales, Yagya Prasad Subedi, Chad D. Mangum, Tanner J. Allen, Miranda S. Liddell, Andrew I. Merrell, Diana I. Saavedra, Becky L. Williams, Nicole Evans, Joseph L. Beales, Mike A. Christiansen

Chemistry and Biochemistry Faculty Publications

We here disclose the total syntheses of the natural polyphenol JBIR-94 and two nonnatural analogs, whose structures are of interest for their bioactivity potential as radical scavengers. Although we initially attempted this by dually acylating both of putrecine’s amine nitrogens in a single pot, our endeavors with this method (which has been successfully reported by other groups) proved ineffectual. We accordingly opted for the lengthier approach of acylating each amine individually, which gratuitously prevailed and also aligns with separate literature precedent. Moreover, we here share our analysis of these target compounds’ cytotoxicities and IC₅₀ values against A549 (CCL-185) human …

How Oxygen Availability Affects The Antimicrobial Efficacy Of Host Defense Peptides: Lessons Learned From Studying The Copper-Binding Peptides Piscidins 1 And 3, Adenrele Oludiran, David S. Courson, Malia D. Stuart, Anwar R. Radwan, John C. Putsma, Myriam L. Cotten, Erin B. Purcell

Chemistry & Biochemistry Faculty Publications

The development of new therapeutic options against Clostridioides difficile (C. difficile) infection is a critical public health concern, as the causative bacterium is highly resistant to multiple classes of antibiotics. Antimicrobial host-defense peptides (HDPs) are highly effective at simultaneously modulating the immune system function and directly killing bacteria through membrane disruption and oxidative damage. The copper-binding HDPs piscidin 1 and piscidin 3 have previously shown potent antimicrobial activity against a number of Gram-negative and Gram-positive bacterial species but have never been investigated in an anaerobic environment. Synergy between piscidins and metal ions increases bacterial killing aerobically. Here, we …

Characterization Of Β-2-Microglobulin Pre-Amyloid Oligomers And Their Role In Amyloid Inhibition, Tyler M. Marcinko

Doctoral Dissertations

In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint, bone, and organ function, and eventually causes organ failure. To understand the early stages of the amyloid assembly process, we have employed a series of biophysical tools including chromatography, spectroscopy, and most especially, native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble pre-amyloid oligomeric species. We have also collaborated and integrated computational modeling to help better understand and rationalize the structural basis behind oligomerization. Recently, several small molecules have been identified …

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pK_a on host-guest interactions …

Fate Of The Organophosphate Insecticide, Chlorpyrifos, In Leaves, Soil, And Air Following Application, Supta Das, Kimberly J. Hageman, Madeleine Taylor, Sue Michelsen-Heath, Ian Stewart

Chemistry and Biochemistry Faculty Publications

A field study was conducted to further our understanding about the fate and transport of the organophosphate insecticide, chlorpyrifos, and its degradation product, chlorpyrifos oxon. Leaf, soil and air sampling was conducted for 21 days after chlorpyrifos application to a field of purple tansy (Phacelia tanacetifolia). Air samples were collected using a high-volume air sampler (HVAS) and seven battery-operated medium-volume active air samplers placed around the field and on a 500-m transect extending away from the field. Chlorpyrifos was detected every day of the sampling period in all matrices, with concentrations decreasing rapidly after application. Chlorpyrifos oxon was …