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Full-Text Articles in Physical Sciences and Mathematics
An Investigation Of Antenna, Ligand Side-Chain, And Metal Ion Effects On The Optical And Mri Properties Of Bimodal Lanthanide (Iii) Complexes, Marisa Poveda
Master's Theses
Magnetic Resonance Imaging (MRI) is a leading anatomical imaging modality for disease diagnosis. With the aid of Gd3+ based contrast agents, high resolution images of biological structures can be obtained. However, there is an increased need for contrast agents that are responsive to specific analytes and chemical environments. Paramagnetic Chemical Exchange Saturation Transfer (PARACEST) agents that utilize a paramagnetic lanthanide ion chelated with a ligand have shown great promise in this area. Lanthanide ions also possess luminescence properties that do not suffer from common limitations of conventional optical imaging agents such as autofluorescence and photobleaching. The projects described in …
Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal
Electrostatic Denaturation Of Dna-Cisplatin Adducts, Eddie Madrigal
Master's Theses
In this thesis, electrochemical approaches are used to determine the properties of deoxyribonucleic acid (DNA) by electrostatic denaturation. The electrochemical routine involves an application of a destabilization potential, an equilibration potential, and a square wave voltammogram (SWV) to monitor the extent of melting. Our method uses a monolayer consisting of thiol modified DNA and mercaptohexanol on a gold electrode. These electrodes are then incubated in a complementary sequence tagged with methylene blue. By using our electrostatic denaturation technique, different parameters are explored, such as surface densities, surface coverages, and ionic strengths. As proof of concept, these techniques were applied toward …
Optimizing The Synthesis Of A Theranostic Rhodamine, Alessandra Maisielou Rivera, Jonathan Alexander, Nathaniel Garrison
Optimizing The Synthesis Of A Theranostic Rhodamine, Alessandra Maisielou Rivera, Jonathan Alexander, Nathaniel Garrison
Creative Activity and Research Day - CARD
Current designs for small molecule theranostics, which serve both a diagnostic and therapeutic role, often involve dyes linked to therapeutic agents through a cleavable, traceless linker. In order to facilitate the separation of the dye from the therapeutic in response to a biological or chemical stimulus, linkers must incorporate elements of molecular logic, increasing their complexity and the overall bulk of the small molecule theranostic. By combining the self-immolative molecular logic of the linker into the structure of the dye itself, we hope to create a series of smaller, more atom-economical theranostics. Rhodamine dyes, which naturally possess aromatic rings with …
Synchrotron Photoionization Study Of The O(3p) + Alpha-Angelica Lactone (Aal) At 550 And 700k, Golbon Rezaei
Synchrotron Photoionization Study Of The O(3p) + Alpha-Angelica Lactone (Aal) At 550 And 700k, Golbon Rezaei
Creative Activity and Research Day - CARD
The purpose of this research is to study the oxidation of alpha-angelica lactone (AAL) initiated by O(3P) using the synchrotron radiation from the Advanced Light Source (ALS) at the Lawrence Berkeley National Laboratory. The reaction species are investigated by multiplexed photoionization mass spectrometry. Mass-to-charge ratios, time traces, and photoionization spectra are collected for each primary product to help in their identification. Their adiabatic ionization energies are also obtained. The observed primary products at 550 K are ketene (m/z 42), acetaldehyde (m/z 44), methyl ketene (m/z 56), methyl vinyl ketone (m/z 70), methylglyoxal (m/z 72), dimethyl glyoxal (m/z 86), and 5-methyl-2,4 …
Effect Of Quinoline Amide Substituents On The Luminescence And Magnetic Resonance Imaging (Mri) Properties Of Bimodal Europium (Iii) Complexes, Brooke Aloe, Marisa Poveda
Effect Of Quinoline Amide Substituents On The Luminescence And Magnetic Resonance Imaging (Mri) Properties Of Bimodal Europium (Iii) Complexes, Brooke Aloe, Marisa Poveda
Creative Activity and Research Day - CARD
Surgical intervention is often necessary in the management of cancer; however, sufficient tumor resection is reliant on adequate discrimination between malignant and healthy tissues. A dual-modality imaging agent with Magnetic Resonance Imaging (MRI) and Optical Imaging capabilities has the potential to improve tumor visualization before and during surgery. Administration of the agent would provide preoperative MR images that localize the bulk of the tumor and intraoperative fluorescence imaging would elucidate tumor margins. Macrocyclic lanthanide complexes possess long-lived luminescent lifetimes, making them ideal candidates for this class of imaging probe; however, the use of high energy lasers to directly excite these …
Determining The Impact Of Double-Layer Formation On Electrostatic Dna Melting, Gayatri Raghu
Determining The Impact Of Double-Layer Formation On Electrostatic Dna Melting, Gayatri Raghu
Creative Activity and Research Day - CARD
Electrostatic melting is an electrochemical tool that can be used to analyze the stability of the DNA double helix, allowing for the detection of various mutations in double stranded DNA (dsDNA).1 Here we explore the effect of electrochemical double layer formation on the electrostatic melting of dsDNA in an effort to better understand the mechanism of the aforementioned category of melting. Previous studies from our lab have shown that electrostatic melting curves can be used to distinguish between duplexes that are fully complementary and duplexes that contain a single mismatch.2 Electrostatic melting is assumed to result from the electrostatic repulsion …
Temperature-Dependence Of Electrostatic Dna Melting, Jeffrey Taylor
Temperature-Dependence Of Electrostatic Dna Melting, Jeffrey Taylor
Creative Activity and Research Day - CARD
Electrostatic melting is a recently developed electrochemical tool that can be used to interrogate DNA stability, allowing for discrimination of double-stranded DNA (dsDNA) by base-pair sequence or the presence of mismatches, deletions, and other mutations (1). This type of analysis has potential applications in point-of-care diagnostics. Here we explore the dependence of temperature and potential on the kinetics of electrostatic melting in an effort to better understand the mechanism. Previous studies, by another group, have shown that the potential at which electrostatic melting occurs decreases with temperature in the range 10 – 18 °C, i.e. the melting becomes easier at …
Development Of Hyperpolarizable Macrocyclic 13c-Probes For The Quantification Of Metals In Vivo, Holly Clancy
Development Of Hyperpolarizable Macrocyclic 13c-Probes For The Quantification Of Metals In Vivo, Holly Clancy
Creative Activity and Research Day - CARD
Numerous studies have shown correlations between various diseases, such as cancer and Alzheimer’s disease, and a change in the concentration of metals in tissues. Current blood analysis-based methods of metal quantification do not always provide a sense of metal concentration in tissue samples. With this work, we aim to develop a non-surgical method to quantify metal concentrations in human tissue. Hexadentate ligands such as ethylenediaminetetraacetic acid (EDTA) tagged with a 13C label at the carbonyl position have shown specific shifting of the carbonyl peak upon complexation with various metals via magnetic resonance spectroscopy (MRS). Additionally, these compounds have shown increased …
Synthesis Of Sultams From Vinyl Aziridines And 1,4-Diazabicyclo[2.2.2]Octane Bis(Sulfur Dioxide), John Gandara
Synthesis Of Sultams From Vinyl Aziridines And 1,4-Diazabicyclo[2.2.2]Octane Bis(Sulfur Dioxide), John Gandara
Creative Activity and Research Day - CARD
Sultams are an important functional group found in medicinal compounds with anticancer and enzyme inhibition activity. Traditional methods for sultam synthesis often require harsh conditions and have limited substrate scope. This research focuses on developing a novel methodology for the production of sultams using DABSO (1,4-diazabicyclo[2.2.2]octane bis(sulfur dioxide)) and vinylic aziridines. Our synthetic strategy starts with a Corey-Chaykovsky epoxidation of cinnamaldehyde, followed by an epoxide-opening using sodium azide. The final vinylic aziridine is synthesized by mesylation and Staudinger reduction of the resulting azido alcohol. Reaction of this vinyl aziridine with DABSO may provide a new strategy for synthesizing sultams. Following …
Determining The Mechanical Properties Of The E. Coli Methionine Transporter, Kha Andy Tran
Determining The Mechanical Properties Of The E. Coli Methionine Transporter, Kha Andy Tran
Creative Activity and Research Day - CARD
Adenosine Triphosphate Binding Cassette (ABC) transporters constitute a superfamily of active transporters embedded in the cellular membrane. They consist of two highly conserved nucleotide-binding subunits which bind and hydrolyze ATP, and two diverse transmembrane subunits which provide a pathway for the substrate to pass through the membrane. ABC transporters serve a broad range of vital functions. Various conditions like cystic fibrosis and Stargardt disease are caused by defunct ABC transporters, and certain medical complications like antibiotic drug resistance are linked to promiscuous ABC transporters. Despite the importance of these transporters in crucial biological processes, the mechanisms of many transporters are …
Extraction Of Thyme Leaves And Analysis Of Antibacterial Properties: An Adaptation For Usf Analytical Chemistry Lab Course, Kevin Do, Matthew Barnett
Extraction Of Thyme Leaves And Analysis Of Antibacterial Properties: An Adaptation For Usf Analytical Chemistry Lab Course, Kevin Do, Matthew Barnett
Creative Activity and Research Day - CARD
We streamlined and adapted the thyme leaf extraction and analysis experiment developed by Purcell et al. at the University of California, Berkeley for the analytical chemistry lab course at the University of San Francisco. This experiment used the extraction and analysis of thyme leaves to familiarize students with an integrated laboratory approach, which is becoming increasingly popular in undergraduate chemistry education. The first goal of our research was to adapt the parameters of the experiment to the science writing heuristic (SWH), which moves away from verification-based activities and towards problem-based learning. A lab manual formatted for the SWH gives students …
Synthesis Of Self-Immolative Rhodamine Based Theranostic Agent, Jonathan Alexander, Alessandra Rivera, Nathaniel Garrison
Synthesis Of Self-Immolative Rhodamine Based Theranostic Agent, Jonathan Alexander, Alessandra Rivera, Nathaniel Garrison
Creative Activity and Research Day - CARD
Theranostic agents, a class of molecules that simultaneously serve both a diagnostic and therapeutic function, enable in vivo imaging for early diagnosis and targeted drug delivery within a single entity. Due to recent advances in the synthesis and photophysical properties of the rhodamine scaffold, rhodamine dyes present a promising new direction for theranostic research. Toward the goal of exploring rhodamine dyes as self-immolative prodrugs for theranostic applications, we have synthesized a rhodamine precursor via a telescoped radical bromination/hydrolysis. Upon completion of the full rhodamine synthesis, we will explore and optimize the kinetics of its “turn-on” fluorescence and drug release in …
Exploring The Effect Of Tris Buffer Concentration On Electrochemical Biosensors, Lucas Galante
Exploring The Effect Of Tris Buffer Concentration On Electrochemical Biosensors, Lucas Galante
Creative Activity and Research Day - CARD
Electrochemical biosensors show promise in the medical field for detection of genetic mutations and could translate well into point-of-care devices. Mutations of DNA can be sensitively and accurately detected through a series of electrochemical melts in which the less stable mutated DNA melts faster than the unmutated DNA. In previous work in our laboratory, we measured the extent of this melting by using square wave voltammetry and comparing peak heights. In this work we explored the effects of varied Tris buffer concentrations (5 mM, 10 mM, 20 mM, 30 mM, 40mM, 50 mM, and 100 mM) on cyclic and square …
Towards The Development Of Redox-Responsive Eu(Iii) Complexes For Cancer Imaging, Matthew Derfus
Towards The Development Of Redox-Responsive Eu(Iii) Complexes For Cancer Imaging, Matthew Derfus
Creative Activity and Research Day - CARD
Cancer cells display redox dysregulation and lowered cytosolic pH as a means to maintain their over-proliferation. The development of an approach to probe tissue redox state could potentially allow discrimination between healthy and cancerous tissues. Magnetic Resonance Imaging (MRI) is a non-invasive technique used in the diagnosis of a variety of pathologies. The high spatial resolution and its use of non-ionizing radiation make MRI an attractive technique for cancer screening and detection. The quality of an MR image can be further enhanced with the aid of contrast agents, the majority of which are Gd(III) complexes. Gd(III) complexes provide positive contrast …
Side-Chain Effects On The Mri And Optical Properties Of Bimodal Imaging Agents, Marisa Poveda
Side-Chain Effects On The Mri And Optical Properties Of Bimodal Imaging Agents, Marisa Poveda
Creative Activity and Research Day - CARD
In the management of cancer distinguishing tumor margins is an ongoing issue that can lead to insufficient removal of cancerous cells or excision of healthy tissue. To overcome this, bimodal imaging agents can be used for preoperative MR imaging to localize the bulk of a tumor, while intraoperative fluorescence imaging illuminates tumor margins for more accurate removal of diseased tissue. Lanthanide ions such as Tb(III) and Eu(III) display luminescent capabilities with long-lived luminescence lifetimes, and when chelated with a chromophore containing ligand, these compounds have the potential to act as both MR and optical imaging probes. The goal of this …
A Ficellomycin Inspired Platform: Modulating Cytotoxicity By Tuning The Instability Of Substituted Azabicyclo[3.1.0]Hexanes, Nathaniel Garrison
A Ficellomycin Inspired Platform: Modulating Cytotoxicity By Tuning The Instability Of Substituted Azabicyclo[3.1.0]Hexanes, Nathaniel Garrison
Creative Activity and Research Day - CARD
DNA-damaging natural products, despite their promising activity, are often too toxic for clinical use as anti-cancer chemotherapies. Novel strategies to effectively modulate their cytotoxicity could expand the arsenal of usable drugs. Ficellomycin, a cytotoxic, DNA-alkylating antibiotic with a rare and unstable azabicyclo[3.1.0]hexane core, undergoes an intramolecular cyclization to render itself inert outside of a narrow pH range. Exploration of ficellomycin’s natural capacity for self-regulation may present a novel strategy for modulation of cytotoxicity more generally. Toward this end, we have synthesized a protected ficellomycin precursor in four steps and 6% overall yield. Key steps in the sequence include Sharpless asymmetric …
Investigating The Mechanism Of The E.Coli Atp-Binding Cassette Transporter Metni, Matthew Foronda
Investigating The Mechanism Of The E.Coli Atp-Binding Cassette Transporter Metni, Matthew Foronda
Creative Activity and Research Day - CARD
Intracellular chemical homeostasis is vital for cell survival. A key component for the maintenance of this homeostasis is ABC (ATP-binding cassette) transporters. These highly-conserved transporters utilize the energy from ATP binding and hydrolysis to move a wide array of substrates against their chemical gradient. Mutations can lead to a variety of diseases including cystic fibrosis and drug-resistant tumors. In order to solve these issues, these transporters must be well-studied. This project focuses on the mechanism of the methionine importer MetNI in E. coli, a reliable model for many transporters. Using fluorescence anisotropy, the apo-form of the substrate-binding protein (SBP) was …
Oxidation Of Alpha-Pinene Initiated By O(3p) And Analyze Via Synchrotron Radiation, Ryan Rodriguez
Oxidation Of Alpha-Pinene Initiated By O(3p) And Analyze Via Synchrotron Radiation, Ryan Rodriguez
Creative Activity and Research Day - CARD
Alpha-pinene oxidation is initiated via photolytically generated atomic oxygen O(3P). Reactions were analyzed at 550 K under 4 torr and 750 K at 5 torr. Reaction products are analyzed using multiplexed photoionization mass spectrometry. Vacuum ultraviolet synchrotron radiation is generated at the Advanced Light Source at the Lawrence Berkeley National Laboratory. Kinetic time traces are used to identify primary products, which are then characterized by comparing the experimental photoionization spectra to literature and/or simulated spectra. Calculations using the CBS-QB3 composite method suggest oxygen addition is the favorable pathway vs hydrogen abstraction, agreeing with experimental data. Branching fractions have determined for …
Probing The Oxidation Chemistry Of Dimethoxymethane, A Model Ome Fuel, Rory Mcclish
Probing The Oxidation Chemistry Of Dimethoxymethane, A Model Ome Fuel, Rory Mcclish
Creative Activity and Research Day - CARD
The threat posed by anthropogenic global warming, along with attached mitigation policies, drives the search for alternative fuels or additives; this search requires understanding the combustion chemistry of possible biofuel candidates. The low-temperature oxidation of a potential diesel fuel substitute, dimethoxymethane (DMM, m/z 76), is herein investigated at 500K, 600K, and 700K using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at the Advanced Light Source within the Lawrence Berkeley National Laboratory. The experimental data is resolved in 3 dimensions: time, mass, and photon energy; this allows for identification, characterization, and quantification of primary products. Energetics calculations are carried out …