cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Temperature Screening Of Trisaccharide (GlcNAc?1, 3Gal?1, 4Glc) Synthesis In Recombinant Escherichia Coli By Fermentation
Creators: name: Zhang, Chi
Publisher: name: Georgia State University
Year: 2018

description: This study reported an improved method of trisaccharide (GlcNAc?1, 3Gal?1, 4Glc) synthesis by fermentation of recombinant Escherichia Coli. The first part was designed for an induction temperature study. We want to compare the level of enzyme activity at different temperature and select the best condition to repeat the induction temperature in a fermenter to improve the production yield. First, the trisaccharide was synthesized at different induction temperature by direct fermentation (4L flask) of E. coli JM109 (DE3) harboring the LgtA-pET22b plasmid. The bacterial growth and trisaccharide production were compared. Second, the best condition for bacterial growth and induction of recombinant enzyme expression was repeated in a fermenter to improve its production yield. After simple two-step purification, final products were obtained with purity above 90% and all products were characterized by MALDI-TOF and HPLC.
Determining xE2-xE3 Pair of RNF38 by Phage Display for Orthogonal Ubiquitin Transfer
Creators: name: Rios, Nicolas
Publisher: name: Georgia State University
Year: 2018

description: Ubiquitin (UB) cascades in vivo are complex to study with cross-reactivity of E1-E2 pairs, E2-E3 pairs, and E3-substrate pairs. RNF38, RING finger protein 38, is a RING-type E3 ligase in the UB transfer cascade in the cell, and the role of RNF38 in cell regulation is unknown, but one study identifies p53 ubiquitination. Previously, the orthogonal UB transfer (OUT) cascade with xUB~xE1 and xE1~xE2 pairs is used to determine xE2-xE3 pair. The current project focuses on generating RNF38 Ring domain libraries with the randomization of four key residues in the E2-binding site then selecting out specific xE2-xRNF38 RING pairs allowing exclusive transfer of xUB to substrate proteins of RNF38. RNF38 RING library is displayed on the surface of M13 phage for the selection of RING mutants binding with xE2. After identifying functional xE2-xRNF38 pairs, xRNF38 is used to assemble the OUT cascade to identify potential substrates by proteomics.
Elucidating Ubiquitin Chain Formation Catalyzed by E2 Enzymes through use of a Di-Ubiquitin Probe
Creators: name: Carpenter, Tomaya
Publisher: name: Georgia State University
Year: 2018

description: Ubiquitin plays a major role in many cellular processes including protein degradation. Ubiquitin attaches to a lysine group of a substrate molecule through its carboxyl terminal end, resulting in monoubiquitination and the subsequent post-translational modification of the protein. Substrate modifications are far more complex due to seven ubiquitin lysine residues which serve as acceptors for the conjugation with other ubiquitin molecules. The focus of this thesis is centered on the elucidation of ubiquitin chain formation through catalysis of E2 cascade enzymes. Here, we incorporate (NŒ-L-Thiaprolyl-L-lysine) site specifically at the K11 position of ubiquitin. The incorporated protein is deprotected forming an acceptor ubiquitin molecule, which we utilize for ligation with a donor molecule to construct a di-ubiquitin probe and conjugate with a specific E2 enzyme. Future studies are aimed at retrieving a three-dimensional structure for this DiUb-E2 conjugate to understand the mechanisms of multiple proteins involved in ubiquitin chain synthesis.
Atomic Resolution X-Ray Crystal Structure of HIV-1 Protease in Complex with Atazanavir
Creators: name: Baumert, Andrew
Publisher: name: Georgia State University
Year: 2018

description: Human immunodeficiency virus (HIV) is a pandemic that has infected nearly 1% of the world population. Despite numerous FDA approved antiviral drugs, HIV drug resistance remains a large challenge. HIV protease is an enzyme that is required by the virus to cleave Gag and Gag-Pol polyproteins into functional and structural proteins necessary for viral maturation. Currently, nine clinical inhibitors target HIV protease, but multiple clinical viral strains have developed resistance to these drugs. Therefore, it is necessary to continue developing new drugs to tackle the problem of HIV drug resistance, and X-ray crystallography is one tool that is used to study how drug candidates bind to HIV-1 protease. In order to study the interactions between inhibitor atazanavir and HIV-1 protease, the crystal structure of the complex has been solved at atomic resolution (1.09 ). This structure will improve the design of new inhibitors for resistant protease.
Characterizing the Heme Uptake Proteins HtaB and ChtB in Corynebacterium diphtheriae
Creators: name: Ferrell, Brandon
Publisher: name: Georgia State University
Year: 2018

description: Corynebacterium diphtheriae is a Gram-positive, pathogenic bacterium. Pathogenic bacteria require iron as a key nutrient for survival. C. diphtheriae utilizes a direct heme uptake system in which the heme binds to a receptor protein that transfers the heme along the pathway to an ABC transporter, which facilitates the transfer of heme into the bacterial cell. This heme uptake pathway is encoded by the hmu and cht gene loci, which includes the genes for the surface-anchored proteins HtaB and ChtB. HtaB is proposed to have a function in transporting the heme obtained by HtaA to HmuT. ChtB is proposed to have a similar function to that of HtaB. Bioinformatics analysis shows that both HtaB and ChtB contain conserved tyrosine and histidine residues that are consistent with that of HtaA domains. A combination of UV-visible, circular dichroism, resonance Raman, and fluorescence spectroscopy have been used to characterize these proteins further.
Synthesis and Analysis of Pyridine Derivatives as Small Molecule Antagonists of CXCR4
Creators: name: Virani, Saniya
Publisher: name: Georgia State University
Year: 2018

description: Chemokines, largest family of cytokines, regulate cell trafficking through interaction of GPCR. Chemokines are classified into categories depending on the pattern of cysteine residue. Chemokine receptor type 4 (CXCR4) is a cell surface receptor important when cells migrate during inflammation and has been linked to various disease pathways such as cancer metastasis, inflammation disease, HIV-1 proliferation, and auto-immune disorders. CXCR4 along with its cognate ligand CXCL12 have been projected to regulate metastases sites in invasion of breast cancer cells. Several pyridine analogues have been synthesized as potential CXCR4 antagonists via reductive amination. These compounds are analyzed through proton and carbon NMR, high- resolution mass spectrometry, and melting point. After synthesis, the analogues undergo several assays at Emory University in Shim lab. The assays include Binding affinity assay, Matrigel invasion assay, and Carrageenan paw edema test.
Improvement Of Vesicular Stomatitis Virus In Order To Enhance Its Oncolytic Effects
Creators: name: Enadi, Zahra
Publisher: name: Georgia State University
Year: 2018

description: Cancer is one of the most deadly diseases around the world. Oncolytic virus (OV) therapy is an anti-cancer approach based on using viruses to selectively target and kill cancerous cells and also their ability to stimulate antitumor immune responses. Vesicular stomatitis virus (VSV) has been investigated as a great platform for an oncolytic agent. Many modifications have been made to VSV to improve its oncolytic effects. One of such modifications by our lab is inserting Smac gene in the genome of VSV to generate armed VSV-S and VSV-?55S. The hypothesis is based on the fact that VSV infection triggers apoptosis through the intrinsic mitochondrial pathway, so overexpression of Smac via infection by armed VSV will reinforce apoptosis and increase the rate of cell killing. We conducted several experiments to examine effects of the inserted gene in viral replication and the enhancement in killing cancer cells compared to wild type VSV.
The Energetics and Reversibility of Oxyanions Adsorption/Desorption on Pure and Aluminium-Substituted Ferrihydrite
Creators: name: Namayandeh, Alireza
Publisher: name: Georgia State University
Year: 2018

description: This work examines the adsorption, desorption, and reversibility of five oxyanions (chloride, nitrate, sulfate, phosphate and arsenate) with ferrihydrite (Fh) using mostly thermodynamics data acquired from flow microcalorimetry.  In addition, the role of aluminum incorporation on the physical and chemical properties of Fh is investigated. The adsorption of phosphate, sulfate, arsenate, chloride, and nitrate by Fh was examined at pH 5.6, and the enthalpy of interaction (DH) was found to follow a positive Hofmeister series such as ( =  < < < .  The DH values and reversibility of adsorption mirrored their modes of surface complexation. The adsorption/desorption and reversibility of sulfate on three Fh samples precipitated with  0, 12 and 24 mol % Al were examined at both pH 5.6 and 3.0. Results show an increase in the heat of exchange, irreversibility, and a fraction  of inner-sphere complexes with increasing Al concentration and decreasing pH values.
A Novel Method for Synthesis of 2'-SeMeANA-dT
Creators: name: Zheng, Lingrui
Publisher: name: Georgia State University
Year: 2018

description: Nucleic acids are fundamental building blocks of living systems? genetic information, and are also responsible for regulating organisms? protein synthesis, catalysis, etc. To better understand nucleic acids? functions and working mechanisms, it is essential to obtain their structures. So far, the most common and powerful method to reveal the structures of macromolecules is X-ray crystallography. However, for nucleic acids structure determination, two problems are to be solved using such technology ? crystallization and phasing. Selenium modification of nucleic acids has been proven to help address the two problems from native ones, without drastically affect their conformations. Also, previous studies suggest selenium modification enhances specific base pairing, especially against U-G wobble pair. With such feature, modified nucleic acids may be utilized by sequence-based diagnostics and therapies.
In this thesis, synthesis of 2?-arabino SeMe modified thymine is discussed. Such modification is believed to be compatible with B-form DNA structure determination.
Synthesis and Photophysical Properties of Phenoxazine Analogs Designed as Potential Antimalarials
Creators: name: Kananda, Carl
Publisher: name: Georgia State University
Year: 2018

description: The phenoxazine core has been explored in the development of chromophoric systems that have seen use as fluorescent probes and therapeutic agents in combating illnesses of many forms. This thesis reports the synthesis and evaluation of some novel phenoxazine and benzo[a]phenoxazine analogs. Phenoxazinium are charged lipophilic molecules and the recent resurgence of ?-Delocalized Lipophilic Cations (DLC) hypothesis in the combat against protozoan illnesses has prompted focus on the synthetic exploration of the derivatization of their architectures in medicinal chemistry. The principle aim of these modifications were to synthesize a focused library of systematically modified analogs catering to the enhancement of related ?drug like? properties found throughout the literature of their development as antimalarials.
Determination of Mouth-level Exposure to Catechol in Mainstream Cigarette Smoke
Creators: name: Ngac, Phuong
Publisher: name: Georgia State University
Year: 2018

description: Smokers' mouth-level exposure to catechol, a potent co-carcinogen generated in the combustion of cigarette tobacco and transferred in the resulting mainstream cigarette smoke (MSS), was estimated via post-smoking, cigarette filter analysis of solanesol, an endogenous component of tobacco. The objectives of this study were to: (1) develop a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method to quantify catechol deliveries in MSS; (2) assess solanesol?s potential as a marker to estimate MSS catechol exposure by comparing the filter efficiencies of solanesol and catechol; and (3) establish calibration models from the correlation of measured solanesol cigarette filter levels with measured mainstream smoke catechol levels using commercial cigarettes. The results from a cigarette filtration study showed that the filter efficiencies of solanesol were proportional to that of catechol regardless the physical parameters of the filter. The relation between mainstream smoke delivery of catechol and filter solanesol was investigated, and a linear regression model was established for three popular United States cigarette brands. These established linear regression models could potentially be used to estimate the mouth-level intake of catechol in cigarette smoke.
Formative Olmec
Creators: name: Moreiras Reynaga, Diana
Publisher: name: Database of Religious History (DRH)
Year: 2022

description: The Olmec civilization thrived in what is now the present-day Gulf Coast of Mexico. They developed religious and artistic traditions that extended far and wide into ancient Mesoamerica during the Formative/pre-Classic period. The Olmec developed regal-ritual centers with main plazas, pyramids, and public spaces near naturally sacred places (e.g., springs, water sources, caves) so that the general population could congregate for ceremonial religious rituals. The Olmec practiced shamanism and had an organized priesthood. The Olmec elite, shamans, and priests were at the top of the social hierarchy and were in charge of maintaining their religious and cultural traditions. There have been six Olmec supernatural beings or deities identified by Mesoamerican scholars, and while their names are not known, they have been numbered I through VI and associated with natural phenomena including: sky, fertility, rain, earth, agriculture and maize. We know a lot about Olmec religion thanks to their impressive and unique artistic traditions, as well as from later Mesoamerican religious traditions that borrowed Olmec concepts, ideology, and iconography and turned these into their own religious traditions, such as the Maya society. Due to this, the Olmec has been described as the "Mother culture" of Mesoamerica and is known as the first organized religion in this particular region of the Americas.
Understanding Integrase-DNA Interactions in Retroviruses Through 3'-processing
Creators: name: Ferris, Zachary
Publisher: name: Georgia State University
Year: 2018

description: Retroviral integrase is one of the key enzymes needed to integrate viral DNA into a host cell?s genome for many retroviruses including HIV. Integrase?s role is three-fold. It prepares the ends of the DNA so that they can successfully bind to the target genomic DNA via 3?-processing, it creates a complex with the viral DNA that is capable of transporting it into the nucleus, and it facilitates the insertion of the viral DNA into the host genome. The goal of this research is to help determine what sequence and structural characteristics of the viral DNA terminus are responsible for successful integrase binding and 3?-processing. Through the use of polyacrylamide gel electrophoresis (PAGE) and 32P end labeling, different substrates are introduced to integrase and the effectiveness of the enzyme in binding to the DNA and carrying out 3?-processing is observed. The importance of terminal structural characteristics as well as individual nucleotides are then determined through a combination of PAGE results, modeling, and NMR-based structural comparisons.
The Utilization of Alternative Synthetic Methods for Further Optimization of Cyanine Dyes and their Potential Use in Imaging and Photodynamic Therapy
Creators: name: Marmarchi, Fahad
Publisher: name: Georgia State University
Year: 2018

description: The work presented in this thesis aims utilizes the versatility of cyanine dyes. Although large libraries have generated for these compounds, their remains an unmet need for alternative synthetic procedures that both optimizes and allows the dyes to be tailored for the desired use. The cyanine dye scaffold contains many points of modification but the central carbon remains a point that requires further research. In addition, among the heterocyclic compound that can be used in the synthesis of cyanine dyes, the quinoline heterocycle offer interesting optical variations to the dyes and can be utilized in the applications that do not require highly fluorescent compounds. The dyes presented showcase a superior synthetic procedure, and incorporate the quinoline heterocycle in novel compounds.
Kinetic Viscosity Effects Reveal a Protein Isomerization in the Reductive Half-Reaction of Nitronate Monooxygenase
Creators: name: Vodovoz, Maria
Publisher: name: Georgia State University
Year: 2019

description: 3-Nitropropionate (3-NPA) is a toxin that is produced by various organisms as a protection mechanism against predators. This toxin naturally occurs as an ester glycoside and can be hydrolyzed by the intestinal flora after ingestion. Once hydrolyzed, the toxin can be fatal by halting the Krebs cycle and the electron transport chain. Nitronate monooxygenase from Neurospora crassa(NcNMO), an FMN-dependent enzyme, catalyzes the oxidation of 3-NPA via a single electron transfer. In this study, we investigated the kinetic mechanism of NcNMO using steady-state and rapid kinetics with 3-NPA as substrate in the presence of various concentrations of viscosigen. The rate of the reductive half-reaction, which is not diffusion-controlled, increased with added viscosigen suggesting that the electron transfer is gated by a slower conformational change.
Synthesis and Properties of Lipoic Acid Stabilized Gold Nanoclusters
Creators: name: Tran, Minh Tri
Publisher: name: Georgia State University
Year: 2019

description: Disulfide lipoic acid was used to synthesize new aqueous soluble gold nanomaterials. The first one is an ultra-small plasmonic nanoparticle displaying a weak plasmonic band at 520 nm. At the transition zone between larger metallic nanoparticles and smaller non-metallic nanoclusters, intriguing electrochemical and optical features were observed. The other cluster is a new molecular-like nanocluster with unique optical features. Distinct UV-visible absorption bands were observed corresponding to discrete energy states/orbitals along with a weak photoluminescence if ultracentrifuge purification is adopted. Dialysis purification yielded a tenfold increase in photoluminescence while the absorption bands diminish. This transition is attributed to the gradual oxidation of some of the sulfur atoms at the core-ligand interface. Annealing with a known amount of excess thiol is shown to expedite and better control the transitions observed through the synthesis and purification along with yielding an enhancement of the electrochemiluminescence by more than ten folds.
Photoelectron Spectra and Formation Mechanisms of Interstellar C3H2O Isomers from Quantum Mechanical Calculations
Creators: name: Johnson, Rebecca
Publisher: name: Georgia State University
Year: 2019

description: Investigating the elusive relationship between our interstellar medium and its assortment of complex organic molecules (COMs) allows us to explore possible precursors to the building blocks of life. A wealth of COMs including aldehydes, ketones, alcohols, and esters have been detected in a giant molecular cloud almost 26,000 light-years away from Earth named Sagittarius B2. This includes exotic COMs that must have been formed from non-equilibrium reactions. Spectroscopic studies by Kaiser and coworkers1 investigated the formation and abundances of C3H2O isomers from carbon monoxide and acetylene in reaction conditions similar to those on interstellar ice grain surfaces found within Sagittarius. Following recent computational and experimental efforts2, the excited state chemistry for the formation of C3H2O compounds is explored in more depth. In this contribution, we will simulate photoelectron spectra and provide molecular-level insight into the formation of these isomers on the basis of ground and excited state quantum mechanical calculations.
Enhanced Electrochemiluminescence and Current Signals from Metal Nanoclusters and Their Surface Assemblies by Prototype Tertiary Amines
Creators: name: Yi, Meijun
Publisher: name: Georgia State University
Year: 2019

description: Interactions between metal nanoclusters and tertiary amine compounds are demonstrated to generate and strengthen the near infrared electrochemiluminescence (ECL) and current signals upon electrode activation. The catalytic effects of aqueous soluble gold nanoclusters (Au NCs) on the oxidation of prototype tertiary amine are firstly established in solution measurements with the materials system of Au22 lipoic acid (Au-LA) nanoclusters and a common pH buffer HEPES. The near IR ECL and current signals are correlated by potential scanning and step methods under systematic varied HEPES and nanocluster concentrations. Strategies to deposit the nanoclusters on electrode surface are developed to improve the signal and enhancement for future applications. The deposition strategies are further applied to prepare surface assemblies of organic soluble bimetallic Au25-xAgx nanoclusters with controlled morphology and coverage. Piperazine derivative drug cetirizine is found to enhance ECL signals from this bimetallic nanocluster-functionalized electrode devices that can be further developed for sensing applications.
Exploring the Dynamics of Glycolytic Regulation Through Two Enzymes: Human Enolase and Liver Pyruvate Kinase
Creators: name: Shouaib, Abdullah
Publisher: name: Georgia State University
Year: 2019

description: Understanding how conformational dynamics play a role in metabolic regulation is an important objective in various biological disciplines. Using Molecular Dynamics (MD) simulations, we attempt to elucidate the dynamics involved in regulating two glycolytic enzymes: human liver pyruvate kinase (hL-PYK) and human enolase. Despite being metabolically coupled, both enzymes are regulated quite differently: hL-PYK can undergo allosteric modulation, while enolase is competitively inhibited. In the hL-PYK study, we discern a mechanism of allostery induced by the allosteric activator fructose-1,6-bisphosphate, and the inhibitor alanine. In the case of enolase, previous studies have attempted to make isoform-specific inhibitors of the enzyme; to further explore this objective, we compare the dynamics of two conserved isozymes, enolase 1 and 2, through MD simulations. As a proof of concept, we find compounds that discriminate between the two homologues by performing ensemble virtual screening on MD derived free enolase structures.
An Innovative Way To Synthesize 2'-SeMeANA-U AND 2'-SeMeANA-C
Creators: name: Hassan, Mohammad Sazid
Publisher: name: Georgia State University
Year: 2020

description: Nucleic acids are complex macromolecules that can store and transfer information for generations; they are an integral part of the central dogma of molecular biology. Structural determination of nucleic acids is crucial to learn about their characteristics and functions. However, there are two problems in determining the structure of a nucleic acid: the phasing problem and the crystallization problem. Selenium modification of nucleic acids is an ideal way to counter both issues. This thesis paper focuses on the synthesis of 2?-SeMe-arabino modification of uridine and cytidine as they both may enhance the crystallization capabilities of B-form DNA. Advances in these studies may lead to the discovery of new drugs and therapeutics designed to target diseases with minimum dosage and highest precision possible.
The Synthesis and Optical Properties of the Squaraine Scaffold and Ph Responsive Cyanine Dyes Containing Pyridine at the Meso-Carbon
Creators: name: Lovett, Wheeler
Publisher: name: Georgia State University
Year: 2020

description: This thesis introduces a brief review of the phenomena of fluorescent dyes, then a discussion on the synthesis and applications of water-soluble squaraine dyes. It then transitions to the discussion of the synthesis and characterization of hydrophilic and hydrophobic squaraine dye derivatives of indolenine as well as the synthesis of a selection of benzothiazole derived pentamethine cyanine dyes with a meso-pyridine substituent. The structural identification of these compounds was performed using various spectroscopic techniques. Experiments confirmed in the later portion of the thesis characterize the optical properties including solvatochromism and pH responsiveness.
Characterization of Heme Binding to PEFR, A Marr Transcriptional Regulator
Creators: name: Andrews, Rosemary
Publisher: name: Georgia State University
Year: 2020

description: PefR is a heme-binding transcriptional regulator found in Streptococcus pyogenes, a ?-hemolytic pathogen that can be fatal. Heme binding results in the release of the protein from DNA and allows for the transcription of a proposed heme efflux system. The overall goals of this work were to devise an effective protocol to purify DNA-free PefR, verify the stoichiometry of heme binding, and identify the axial ligand. Strep-tagged PefR was purified by a variety of protocols, the most effective of which utilized high salt concentrations in the buffers and an ion-exchange column. Based on UV/visible studies of PefR, we suggest that heme binds via Cys109. Homology models place Cys109 in a region that several MarR proteins utilize to bind their ligands, supporting our hypothesis.
Synthesis, Characterization, Optical Properties and DNA Cleavage Study of Symmetrical Pentamethine Cyanine Dyes Containing Quinoline Moieties
Creators: name: Ilina, Kristina
Publisher: name: Georgia State University
Year: 2020

description: This thesis outlines a review of the history, synthetic procedures, optical properties, and applications of quinoline-containing cyanine dyes in the first chapter. The second chapter introduces the synthesis, characterization, and optical properties of new symmetrical pentamethine cyanine dyes and their potential application in photodynamic therapy (PDT). The structure identification of final compounds was done by 1H and 13C nuclear magnetic resonance (NMR) and mass spectrometry. The studies were performed after full characterization and determination of optical and physicochemical properties. Several representative dyes were selected for analysis of their DNA photocleavage activity.
Characterization of Heme Uptake Proteins; HtaB, ChtB, and ChtA from Corynebacterium Diphtheriae Approaches to the Reaction of Dechloromonas Aromatica Chlorite Dismutase with Nitrite
Creators: name: Odhiambo, Catherine
Publisher: name: Georgia State University
Year: 2020

description: Heme is a source of iron for many pathogenic bacteria. Corynebacterium diphtheriae, the first protein in the system is HtaA, ChtA, and/or ChtC; heme is transferred to HtaB or ChtB. Heme is then mobilized into the cytosol by the ABC transporter where iron is released by the heme oxygenase.
Growth and expression temperatures for ChtA were of 37 ?C and induction OD600 between 0.6 and 0.9. Final IPTG concentration of 0.3 mM. ChtA extinction coefficient is 1.4 x 105 M-1 cm-1 at the Soret. ChtA is less stable than HtaA-CR2 to denaturation in guanidinium hydrochloride.
Dechloromonas aromatica chlorite dismutase (DaCld) detoxifies chlorite to chloride and dioxygen. Chlorite sources often have nitrite. The goal is to identify the structure of this adduct.
Temperatures of growth and expression, 30 and 20 ?C, respectively, an induction OD600 of 0.30, and a final IPTG concentration of 0.1 mM resulted in the desired holo DaCld.
Digital Qualifiziert - Joachim Schachtner & Susan Trinitz
Creators: name: (:Unkn) Unknown
Publisher: name: Max-Planck-Gesellschaft zur Förderung der Wissenschaften
Year: 2021

description: Starten wollen wir den Podcast mit einem Blick in die Arbeitsgruppe Digital Qualifiziertes Personal der Allianz der Wissenschaftsorganistionen. Dazu haben wir uns den Vorsitzenden der Arbeitsgruppe und seine Stellvertreterin eingeladen. Sie selbst bringen unterschiedliche Blickwinkel mit: der eine kommt aus der universitären Welt, die andere vertritt eine außeruniversitäre Forschungseinrichtung. Was beide eint, ist Ihre Leidenschaft fürs Digitale. Der eine ist Prof. Dr. Joachim Schachter. Er ist Präsident der Technischen Universität Clausthal, die andere ist Susann Trinitz. Sie verantwortet bei der Helmholtz Gemeinschaft die Helmholtz Information und Datascience Academy. Freuen Sie sich auf ein spannendes Gespräch über Hürden und Chancen der Digitalisierung, den inneren Schweinehund und welche Kompetenzen für die Lehre wichtig sind. Und last but not least natürlich auch, was wir 2020 gelernt haben. Quelle: www.soundcloud.com
Current and New Novel Combination Treatments for Metastatic Triple-Negative Breast Cancer
Creators: name: Pauls, Mehrnoosh
name: Chia, Stephen
name: LeVasseur, Nathalie
Publisher: name: Multidisciplinary Digital Publishing Institute
Year: 2022

description: Triple-negative breast cancer (TNBC) has a worse prognosis and remains the most challenging breast cancer subtype to treat. This is largely related to the heterogeneity of this disease and the lack of reliable oncological targets. In this review, we discuss the current standard-of-care treatment options for metastatic TNBC, including recent advances with the use of immunotherapy, PARP inhibitors and antibody-drug conjugates. This review also explores new agents and novel combinations arising in the field for the treatment of advanced TNBC.
Simulation of Photoelectron Spectra of Small Organic Molecules
Creators: name: Mahbub, Md
Publisher: name: Georgia State University
Year: 2020

description: Photoelectron spectroscopy (PES) is a technique that uses photons in the energy range above a molecules? ionization threshold to probes the electronic structure of that molecule. Interpretation of the PES spectra often requires support from theory and computer modeling. This thesis focuses on the calculation of the total photoionization cross sections, which requires accurate wave functions of the initial and final states of the system. While the initial and final state of the molecular system can be represented using a single orbital, the final state also requires a description of the free electron wave function. At this moment, no black-box method exists that can be applied in a fast and systematic way to obtain accurate photoelectron spectra of polyatomic molecular systems. We will present a series of benchmarks using approximate and easy to implement treatments of the photoelectron wave functions, where we will compare computed and experimental photoionization spectra
Investigating the Role of Hydration and DNA Dynamic Alterations in DNA Recognition by A Heterocyclic Diamidine
Creators: name: Ha, Van
Publisher: name: Georgia State University
Year: 2020

description: Target recognition by DNA-binding ligands, such as drugs, occurs in an aqueous environment, in which water (near unit mole fraction, ~55 M) dominates every solute. A quantitative account of how water molecules are disposed in DNA/ligand binding is indispensable for understanding the driving forces that confer high-affinity and selectivity. We are investigating the DNA sequence selectivity of a model DNA minor groove-binding heterocyclic diamidine, DB1976, which shows therapeutic activity in acute myeloid leukemia, systemic fibroses, and obesity-related liver disorders in vivo. The DNA minor groove is richly populated with water molecules. Studies based on explicit-solvent MD simulation have shown distinct DNA dynamics upon drug-DNA complexes. We have cooperated the role of hydration and conformational dynamics in contributing to drug selectivity. Moving forward, our goal is to evaluate the structure-hydration relationships of designed diamidines to site-specific and nonspecific DNA as part of their biophysical characterization as potential therapeutic agents.
Enhancement of Anti-tumor Efficacy of an Armed Oncolytic Virus: VSV-SKPC
Creators: name: Luker, Breona
Publisher: name: Georgia State University
Year: 2021

description: Immunotherapy for treatment of pancreatic ductal adenocarcinoma (PDAC) continues to be an area of focus in the field of oncology. PDAC remains mostly incurable. The newest pillar of cancer treatments, immunotherapy, provides promises to patients as a viable option. However, the immunosuppressive microenvironment of PDAC tumors is one of the limitations on treatment efficacy. Thus, it was strategized that reactivation of the tumor?s suppressive microenvironment could lead to an increased efficacy of treatment. The use of an armed oncolytic virus (OV) to infect the tumor has shown a potential to alter the tumor microenvironment (TME) more effectively in comparison with its wildtype counterpart. Vesicular stomatitis virus (VSV) was engineered to express Smac, (VSV-S), a protein found in the intrinsic pathway of apoptosis. The ability of Smac to interact with the inhibitor of apoptosis proteins (IAPs) makes VSV-S more effective in killing cancer cells. In addition, it was determined that adapting the virus to the cell line by limited dilution increased VSV-S to selectively target the murine cancer cell, KPC. Using a C57BL/6 mice model, subcutaneous implanted KPC tumors were intratumorally injected with VSV-SKPC. After the infection by VSV-S, tumor size was greatly reduced and the survival rate was greatly increased. In the infected tumors, neutrophils were significantly increased, whereas macrophages were largely reduced, especially immunosuppressive M2-macrophages. The overall TME was also more immunologically active, which is proven by the reduced levels of cytokines and biomarkers including TGF-??, Arginase -1 and IL-10. This study indicates that the treatment of VSV-S was successful in the reactivation of the immunosuppressive TME and inhibition of tumor growth.
Genomic Epidemiology Analysis of SARS-CoV-2 Transmission Dynamics in Belarus
Creators: name: Adeniyi, Ayotomiwa
Publisher: name: Georgia State University
Year: 2021

description: The recent outbreak of the COVID-19 virus has brought about the need for the implementation of Non-Pharmaceutical Interventions (NPIs) by governments and public health departments to fight the spread of the virus. Belarus, a small country in the eastern part of Europe implemented a small amount of NPI protocols to control the spread of the virus.
This thesis focuses on the usage of genomic epidemiological methods to analyze the origin and spread of SARS-CoV-2 in Belarus. Results showed that the number of case introductions and exports to other countries are indeed substantial. It was detected that the Belarussian SARS-CoV-2 genetic diversity originated from at least eighteen separate introductions from different geographical regions.
Calculated Vibrational Properties of Asymmetrically Hydrogen Bonded Benzoquinones and Naphthoquinones
Creators: name: Ilanikashkouli, Mohammadnabi
Publisher: name: Georgia State University
Year: 2021

description: Quinones are ubiquitous in biochemistry, where they typically function as electron carriers in processes such as photosynthesis and respiration. Quinones bound in protein complexes are often studied using Fourier-transform infrared (FTIR) difference spectroscopy (DS). With FTIR DS it is possible to probe even small changes in hydrogen bonding between the quinones and nearby protein residues. However, the interpretation of FTIR DS is complicated by multiple overlapping contributions to the spectra. Here we employ density functional theory (DFT) based vibrational frequency calculations on benzoquinone (BQ) and naphthoquinone (NQ) model systems to help untangle the intrinsic and environmental factors that could shift the quinone?s vibrational mode frequencies and intensities. Specifically, we systematically study the effect that hydrogen bonds and quinone substituents have on the ??=?? mode vibrational frequencies of the neutral and one-electron reduced BQs and NQs.
Can We Build Roller Coasters?
Creators: name: Čondić-Jurkić, Karmen
Publisher: name: Conscience
Year: 2025

description: The Open Molecular Software Foundation (OMSF) is a nonprofit organization dedicated to advancing the development, accessibility, and sustainability of open-source software in the molecular sciences. By fostering collaboration among researchers from academia and industry, OMSF aims to accelerate scientific progress and innovation in the world of molecules. This talk will highlight OMSF's mission to create a sustainable ecosystem for open molecular software, its key initiatives, and how the community can contribute to and benefit from its efforts. It will also cover some of the challenges and learnings we made on the way.
Supplementary document for In vivo fluorescence molecular imaging of vascular endothelial growth factor in rats with early diabetic retinopathy - 5511961.pdf
Creators: name: Zhang, Lu
name: Ding, Yunhe
name: Chen, Xinjian
name: Xiang, Dehui
name: Shi, Fei
name: Chen, Yanyun
name: Yan, Shenshen
name: Zhang, Xinyuan
name: Tian, Jie
name: Sivaprasad, Sobha
Publisher: name: Optica Publishing Group
Year: 2025
Subjects: Uncategorized

description: Supplementary figures in the manuscript.
Synthesis and Optical Properties of Red Shifted Donor Acceptor Fluorophores as Potential Agents for Biomedical Applications
Creators: name: Ersoy Ozmen, Guliz
Publisher: name: Georgia State University
Year: 2021

description: In this study, the synthesis, characterization, optical properties and TD-DFT studies of 21 near infra-red (NIR) fluorophores, and cytotoxicity of selected four compounds are presented. Fluorophores have a chloroacrylic acid acceptor unit and various donor units such as indole, benzothiazole, benzo[e]indole, and quinoline. Further modifications are also done at the linker with t-butyl and phenyl groups. The fluorophores showed strong absorption in the NIR (700-970 nm) region due to their unique intramolecular charge transfer (ICT) between chloroacrylic acid and the donor moieties. The emission wavelength maxima of the fluorophores were between 798-870 nm. Compound 123 with quinoline donor moiety, showed an emission wavelength above 1000 nm. Time dependent density functional theory (TD-DFT) calculations showed that the charge transfer occurs from the donor groups to the acceptor chloroacrylic acid moiety. Fluorophores were also shown to possess a charge separation character.
Unprecedented DNA Photocleavage Mediated by Quinolinium Pentamethine Carbocyanine Dyes in the NIR Wavelength Range
Creators: name: Ahoulou, Effibe
Publisher: name: Georgia State University
Year: 2021

description: Here we report the DNA photocleavage abilities of near-infrared (NIR) quinolinium pentamethine carbocyanine dyes substituted with either bromine, chlorine, or hydrogen at the meso-carbon position. We are interested in developing these cyanine dyes as treatment agents in photodynamic cancer therapy because they can be activated to selectively kill diseased cells with NIR light that deeply penetrates biological tissues. UV-visible, CD, and fluorescence spectra show that the brominated quinolinium cyanine dyes 4 and KI2 are stable in aqueous buffer and bind to DNA in a non-intercalative manner both externally and in the DNA minor groove. Reactions run in the presence and absence of fluorescent probes and chemical additives reveal that irradiation of dye 4 and KI2 with 707?759-nm and 830-905 nm NIR light respectively generates Type I hydroxyl radicals that form direct strand breaks in plasmid DNA in high yield.
Separation of Short and Medium-Chain Fatty Acids Using Capillary Electrophoresis with Indirect Photometric Detection
Creators: name: Pham, Uyen
Publisher: name: Georgia State University
Year: 2021

description: Short and medium-chain fatty acids (SMCFA) are known as essential metabolites found in gut microbiota that function as modulators in the development and progression of many inflammatory conditions as well as in the regulation of cell metabolism. Currently, there are few simple and low-cost analytical methods available for the determination of SMCFA. This work focuses on the identification and measurement of SMCFA in rat feces utilizing capillary electrophoresis with indirect photometric detection (CE-IPD). In chapter 2, several parameters are optimized for maximum resolution, efficiency, and signal-to-noise ratio of FAs. The developed CE-IPD method is next validated in chapter 3 to quantify the FAs in healthy rat feces. Application to a pilot study on the influences of developmental stages (adult vs. adolescent) and various drug treatments on fecal SMCFA concentration in rats demonstrates the proposed CE-IPD method is an efficient tool for investigations on biological functions of SMCFA in clinical laboratories.
Enzyme Kinetics and Structural Studies of Drug Resistant HIV Protease
Creators: name: Verhoff, Sarah
Publisher: name: Georgia State University
Year: 2022

description: In 2020, 37.7 million individuals were living with HIV. If an individual infected with HIV does not undergo proper treatment, then the patient may obtain the disease acquired immunodeficiency syndrome. Although there are a myriad of HIV treatments and FDA-approved clinical inhibitors, drug resistance is the main obstacle to successful treatment plans. HIV protease is an essential protein that cleaves Gag and Gag-Pol polyproteins to yield infectious HIV. Due to HIV's rapid mutation, it is vital to develop more effective treatments and drugs for drug-resistant strains. X-ray crystallography and enzyme kinetics experiments are used to understand the binding of inhibitors to HIV proteases and aid the development of novel clinical inhibitors for resistant mutants of the protease. The binding of peptide analogs was studied for highly drug-resistant mutant PRS17 with a V48G mutation to wildtype residue. The revertant mutation showed small changes in inhibition or protease structure relative to PRS17.
Engineering an Orthogonal Ubiquitin Transfer (OUT) Cascade for Cbl-b, an E3 Ubiquitin Ligase Regulating Innate Immunity against Cancer Cells and Inhibition of the ubiquitin-proteasome system by peptidomimetic foldamer mimicking E2 N-terminal-helix
Creators: name: Jeong, In
Publisher: name: Georgia State University
Year: 2022

description: Cbl-b is a representative member of Ring E3 that regulates cytotoxicity of the natural killer (NK) cells. Cbl-b also ubiquitinates TAM family of RTKs including Tyro3, Axl and Mer on the surface of NK cells to unleash their killing instinct against cancer cells. I focused on using phage display to engineer the Ring domain of Cbl-b so it can function as an xE3 to exclusively transfer an engineered UB (xUB) through an engineered xE1-xE2 cascade to its substrate proteins. The development of an orthogonal UB transfer (OUT) cascade of Cbl-b will enable us to profile its direct ubiquitination targets. Additionally, I used in-vitro ubiquitination to get the inhibition of sulfono-?-AA peptide, a new class of peptidomimetic foldamer, to mimic the …-1 helix of E2 and thereby inhibiting E1/E2 protein-protein interaction so as to disrupt the ubiquitination signaling cascade.
Profiling Substrates of HECT and U-box E3 Ligases via Orthogonal Ubiquitin Transfer Cascade and Mimicking the Activity of HECT E3 Ligase with a ƒ-AA Peptide
Creators: name: Jeong, Geon
Publisher: name: Georgia State University
Year: 2022

description: E6-associated protein (E6AP) is a member of HECT domain family of E3 ubiquitin (UB) ligase that is responsible for many biological processes. E6AP may be paired with the papillomavirus oncoprotein E6 when E6 is present in the host to recruit substrates for degradation. This may hinder the host?s antiviral response and lead to cancer development. A damaged HECT domain of E6AP has been reported in patients with Angelman Syndrome. When Legionella pneumophila enters the human body, 330 bacterial effector proteins are arranged to employ the Dot/Icm type IV secretion system, T4SS. Bacterial effector proteins: GobX, LubX, and RavN are reported to mimic the U-box E3 ligase to hijack and thrive for proliferation. Our lab has developed an orthogonal ubiquitin transfer (OUT) cascade to monitor the movement of engineered UB through the engineered E1-E2-E3 cascade. In this study, OUT cascade was utilized to profile substrates that may lead to new discoveries.
Developing a patient decision aid for atypical nevi excision
Creators: name: Roland-Mcgowan, Jaclyn
name: Freeman, Caleb
name: Yu, Wesley
Publisher: name: Oregon Health and Science University
Year: 2024
Subjects: subject: Dysplastic Nevus Syndrome
subject: Decision Support Techniques
subject: Physician-Patient Relations
subject: patient decision aids

description: Shared decision-making integrates patient values with clinical evidence and is paramount in patient-doctor collaboration. Dermatology is especially appropriate for such collaborative approaches, as the severity of a condition may be determined by the patient’s experience of symptoms, making patient input particularly important. Patient Decision Aids (PDAs) offer a promising avenue aiming to empower patients with current evidence for informed choices aligning with their values. Our PDA holds promise for broader applications, including integration into clinical trials.
Boden eine Sprache geben - 10 Thesen für die Kommunikation von Bodenthemen
Creators: name: Beblek, Anita
name: Diehl, Katharina
name: Kühlberg, Sabine
Publisher: name: My University
Year: 2018
Subjects: subject: Boden
subject: Kommunikation
subject: Bodenschutz
subject: boden
subject: Boden | Fläche

description: Die unzureichende Wahrnehmung des Bodens in der Politik und der Gesellschaft liegt nicht nur in der Komplexität des Themas begründet, sondern auch in der Art und Weise, wie es aufbereitet und kommuniziert wird. In einem Forschungsprojekt wurden die betreffenden Lücken und Defizite identifiziert und Empfehlungen für die praktische Arbeit abgeleitet. Die vorliegenden 10 Thesen für die Kommunikation von Bodenthemen sind ein Hilfestellung für diejenigen, die aktiv im Bodenschutz tätig sind und denen eine zielgruppengerechte und erfolgreiche Kommunikation von Bodenthemen eine Herzensangelegenheit ist. Fragen, wie der richtige Umgang mit Social Media werden genauso beleuchtet, wie das ansprechende Formulieren von Texten oder die Auswahl geeigneter Fotomotive.
Validation of a Patient-Reported Outcome Measure for Moist Desquamation among Breast Radiotherapy Patients
Creators: name: Duzenli, Cheryl
name: Chan, Elisa K.
name: Koulis, Theodora
name: Grahame, Sheri
name: Singer, Joel
name: Morris, David
name: Spence, Josslynn
name: Lee, Terry C. K.
name: Burns, Levi
name: Olson, Robert
Publisher: name: Multidisciplinary Digital Publishing Institute
Year: 2023

description: There has been an increasing interest in patient-reported outcome (PRO) measures in both the clinical and research settings to improve the quality of life among patients and to identify when clinical intervention may be needed. The primary purpose of this prospective study was to validate an acute breast skin toxicity PRO measure across a broad sample of patient body types undergoing radiation therapy. Between August 2018 and September 2019, 134 women undergoing adjuvant breast radiotherapy (RT) consented to completing serial PRO measures both during and post-RT treatment and to having their skin assessed by trained trial radiation therapists. There was high patient compliance, with 124 patients (92.5%) returning to the clinic post-RT for at least one staff skin assessment. Rates of moist desquamation (MD) in the infra-mammary fold (IMF) by PRO were compared with skin assessments completed by trial radiation therapists. There was high sensitivity (86.5%) and good specificity (79.4%) between PRO and staff-reported presence of MD in the IMF, and there was a moderate correlation between the peak severity of the MD reported by PRO and assessed by staff (rho = 0.61, p < 0.001). This prospective study validates a new PRO measure to monitor the presence of MD in the IMF among women receiving breast RT.