Open Access. Powered by Scholars. Published by Universities.®
Physical Sciences and Mathematics Commons™
Open Access. Powered by Scholars. Published by Universities.®
- Discipline
-
- Chemistry (11)
- Life Sciences (7)
- Analytical Chemistry (3)
- Social and Behavioral Sciences (3)
- Amino Acids, Peptides, and Proteins (2)
-
- Biochemistry (2)
- Biochemistry, Biophysics, and Structural Biology (2)
- Chemicals and Drugs (2)
- Environmental Chemistry (2)
- Environmental Sciences (2)
- Medicine and Health Sciences (2)
- Pharmacology, Toxicology and Environmental Health (2)
- Toxicology (2)
- Analytical, Diagnostic and Therapeutic Techniques and Equipment (1)
- Bioinformatics (1)
- Civil and Environmental Engineering (1)
- Earth Sciences (1)
- Engineering (1)
- Environmental Engineering (1)
- Environmental Health (1)
- Environmental Health and Protection (1)
- Environmental Indicators and Impact Assessment (1)
- Environmental Microbiology and Microbial Ecology (1)
- Environmental Monitoring (1)
- Geology (1)
- Hydrology (1)
- Inorganic Chemistry (1)
- Medicinal-Pharmaceutical Chemistry (1)
- Microbiology (1)
- Institution
- Publication Year
- Publication
- Publication Type
- File Type
Articles 1 - 16 of 16
Full-Text Articles in Physical Sciences and Mathematics
Application Of A 14c-Assay To Assess Methanotrophic Biodegradation Of Tce In Low Ph Groundwater, Evan Groome
Application Of A 14c-Assay To Assess Methanotrophic Biodegradation Of Tce In Low Ph Groundwater, Evan Groome
All Theses
Current biological strategies for remediating trichloroethylene (TCE) in low pH aquifers (i.e., pH14C-TCE assay was developed to determine pseudo first-order rate constants for the degradation of TCE in microcosms containing soil and groundwater from the Boeing Michigan Aeronautical Research Center (BOMARC) superfund site, where the pH ranges from 4.1 to 4.9. The 14C-TCE assay was also adapted to calculate soil-normalized rate constants for data from this site, as well as data that Szwast21 collected from the Beltsville Agricultural Research Center (BARC). In addition to natural attenuation, biostimulation through amendments of methane and nutrients were also assessed. This treatment …
Purification And Activity Analysis Of A Highly Active Recombinant Catalase From Psychrophilic Bacterium Psychrobacter Cryohaloentis, Andrew Stewart
Purification And Activity Analysis Of A Highly Active Recombinant Catalase From Psychrophilic Bacterium Psychrobacter Cryohaloentis, Andrew Stewart
Honors Program Theses
To date, the genus Psychrobacter includes 37 recognized bacterial species isolated from different sources ranging from Siberian permafrost (P. cryohalolentis) to seal feces (P. lutiphocae). Due to its diverse ecological niches, several species belonging to the genus have different enzymatic activities with potential applications in bioremediation and the food industry. In this study, a bioprospecting approach was used to perform a in depth analysis of a Psychrobacter-like bacterial strain isolated from goose feces (designated as Psychrobacter unknown). The phylogenetic analysis of 16S rRNA gene and homologous sequence studies suggest that the strain may represent a novel species of the Psychrobacter …
Aptamer-Based Assay For Detection Of Ochratoxin A, Amanda Nicole Bartley
Aptamer-Based Assay For Detection Of Ochratoxin A, Amanda Nicole Bartley
FIU Electronic Theses and Dissertations
Ochratoxin A (OTA) is a potent mycotoxin found in a wide range of agricultural products that has been linked to mitochondrial damage and renal disease. The standard methods for OTA analysis currently rely on the use of high-performance liquid chromatography (HPLC) coupled to fluorescence detection or mass spectrometry. Toward a highthroughput analysis of OTA, a single-stranded DNA aptamer, modified with a fluorophore, coupled to a complementary sequence, modified with a FRET-based quencher that dissociates in the presence of the target toxin, is proposed. In order to integrate “target trapping,” aptamer immobilization methods were explored to mediate interference issues. Assays were …
The Enzymatic Activity And Inhibition Of Dape Encoded N-Succinyl-L,L-Diaminopimelic Acid Dessucinylase, Tahirah Heath
The Enzymatic Activity And Inhibition Of Dape Encoded N-Succinyl-L,L-Diaminopimelic Acid Dessucinylase, Tahirah Heath
Dissertations
The bacterial enzyme DapE is a hydrolase in the late stage of the mDAP/lysine biosynthetic pathway that catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (L,L-SDAP) to succinic acid and L,L-diaminopimelate (DAP). The product DAP is ultimately converted to m-DAP and then to lysine which is used in the construction of proteins, whereas for humans, lysine is an essential amino acid obtained through diet. DapE has been shown to be conserved across many strains of bacteria. The m-DAP produced through the succinylase pathway is used by both gram negative and gram-positive bacteria in the construction of the essential peptidoglycan cell wall. Because …
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar Ali, Eric Olson, Adam Urbach
Adam R Urbach
This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity …
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar A. Ali, Eric M. Olson, Adam R. Urbach
Effects Of Sequence Context On The Binding Of Tryptophan-Containing Peptides By The Cucurbit[8]Uril-Methyl Viologen Complex, Omar A. Ali, Eric M. Olson, Adam R. Urbach
Chemistry Faculty Research
This paper describes a novel assay for measuring the relative extent of peptide binding in a large parallel format and the use of this assay to explore the effects of sequence context on the binding of tryptophan (Trp)-containing peptides by the synthetic receptor comprising the noncovalent complex between cucurbit[8]uril and methyl viologen (i.e. Q8√MV). The extent of quenching of Trp fluorescence upon binding to Q8√MV was used to measure the relative extent of binding and thus the relative affinities of 104 Trp-containing peptides, in parallel, using a fluorescence plate reader. This study resulted in the remarkable observation that the identity …
The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver
The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver
Heath Ecroyd
Thioflavin T (ThT) dye fluorescence is used regularly to quantify the formation and inhibition of amyloid fibrils in the presence of anti-amyloidogenic compounds such as polyphenols. However, in this study, it was shown, using three polyphenolics (curcumin, quercetin and resveratrol), that ThT fluorescence should be used with caution in the presence of such exogenous compounds. The strong absorptive and fluorescent properties of quercetin and curcumin were found to significantly bias the ThT fluorescence readings in both in situ real-time ThT assays and single time-point dilution ThT-type assays. The presence of curcumin at concentrations as low as 0.01 and 1 uM …
Detection Of Protein By Microdrop Analysis, Yogeshkumar Radadiya
Detection Of Protein By Microdrop Analysis, Yogeshkumar Radadiya
All Capstone Projects
Analysis of protein depends particularly on protein concentration. Protein concentration measurement is the most important part in the research work to conduct protein-related studies. Although there are many methods available for this purpose, each method has certain limitations. The aim of the experiment is to develop either new or modified analytical method for the analysis and detection of protein using newly introduced micro-plate reader equipped with Take-3 microplate with the help of Gen-5 software. An ideal assay should be simple and easy to carry out. Another aspect to be taken into consideration are low inference, stability of measured components and …
Determination Of Protein Using Microdrop Assay, Hardik Khared
Determination Of Protein Using Microdrop Assay, Hardik Khared
All Capstone Projects
After purification of protein, it is important to know the concentration of protein in our samples. Concentration or amount of protein in the sample is determined by different assay as BCA (bicinchoninic acid) Assay, Bradford Assay, and Lowery Assay. There are different methods available to perform these assays, which have some limitations, restrictions, advantages and disadvantages. These methods require large amounts of costly reagents, proteins and most importantly, valuable time. To overcome these problems a new method is developed called Microdrop Protein Analysis. This new method required a very small amount of reagents and protein mixtures (2-5 µʅ volume) and …
Development Of Luminescent Sensing Systems With Clinical Applications, Daniel F. Scott
Development Of Luminescent Sensing Systems With Clinical Applications, Daniel F. Scott
University of Kentucky Doctoral Dissertations
As the move towards the miniaturization of many diagnostic and detection systems continues, the need for increasingly versatile yet sensitive labels for use in these systems also grows. Luminescent reporters provide us with a solution to many of the issues at hand through their unique and favorable characteristics. Bioluminescent proteins offer detection at extremely low concentrations and no interference from physiological fluids leading to excellent detection limits, while the vast number of fluorescent proteins and molecules available allows the opportunity to select a tailored reporter for a specific task. Both provide relatively simply instrumentation requirements and have exhibited great promise …
Multichannel Spectrophotometry For Analysis Of Organophosphate Paraoxon In Beverages, Miroslav Pohanka, Jana Zdarova Karasova, Kamil Kuca, Jiri Pikula
Multichannel Spectrophotometry For Analysis Of Organophosphate Paraoxon In Beverages, Miroslav Pohanka, Jana Zdarova Karasova, Kamil Kuca, Jiri Pikula
Turkish Journal of Chemistry
Multichannel spectrophotometry was performed to assay for paraoxon in spiked beverages. A 96-well microplate was used for this purpose. The measuring protocol was based on inhibition of the enzyme acetylcholinesterase by paraoxon that resulted in decreased or no reaction of the enzyme product thiocholine with Ellman's reagent (5,5'-dithiobis [2-nitrobenzoic acid]). The above assay was practically tested using spiked drinking water, mineral water, and coffee. Analytical parameters such as the limit of detection, time, and sample size consumption were adequate. The limit of detection for beverages ranged from 32 to 48 ppb corresponding to 0.32-0.48 ng of paraoxon in absolute values. …
The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver
The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver
Faculty of Science - Papers (Archive)
Thioflavin T (ThT) dye fluorescence is used regularly to quantify the formation and inhibition of amyloid fibrils in the presence of anti-amyloidogenic compounds such as polyphenols. However, in this study, it was shown, using three polyphenolics (curcumin, quercetin and resveratrol), that ThT fluorescence should be used with caution in the presence of such exogenous compounds. The strong absorptive and fluorescent properties of quercetin and curcumin were found to significantly bias the ThT fluorescence readings in both in situ real-time ThT assays and single time-point dilution ThT-type assays. The presence of curcumin at concentrations as low as 0.01 and 1 uM …
A Fluorescence Quenching Assay To Discriminate Between Specific And Non-Specific Inhibitors Of Dengue Virus Protease, C Bodenreider, D Beer, T Keller, S Sonntag, D Wen, Li Yap, Y H Yau, S G Shocat, D Huang, T Zhou, A Caflisch, X C Su, Kiyoshi Ozawa, G Otting, S G. Vasudevan, J Lescar, S P. Lim
A Fluorescence Quenching Assay To Discriminate Between Specific And Non-Specific Inhibitors Of Dengue Virus Protease, C Bodenreider, D Beer, T Keller, S Sonntag, D Wen, Li Yap, Y H Yau, S G Shocat, D Huang, T Zhou, A Caflisch, X C Su, Kiyoshi Ozawa, G Otting, S G. Vasudevan, J Lescar, S P. Lim
Faculty of Science - Papers (Archive)
In drug discovery, the occurrence of false positives is a major hurdle in the search for lead compounds that can be developed into drugs. A small-molecular-weight compound that inhibits dengue virus protease at low micromolar levels was identified in a screening campaign. Binding to the enzyme was confirmed by isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR). However, a structure-activity relationship study that ensued did not yield more potent leads. To further characterize the parental compound and its analogues, we developed a high-speed, low-cost, quantitative fluorescence quenching assay. We observed that specific analogues quenched dengue protease fluorescence and showed …
Designing Surface Chemistries For In Situ Afm Investigations Of Biomolecular Reactions With Proteins At The Nanoscale, Johnpeter Ndiangui Ngunjiri
Designing Surface Chemistries For In Situ Afm Investigations Of Biomolecular Reactions With Proteins At The Nanoscale, Johnpeter Ndiangui Ngunjiri
LSU Doctoral Dissertations
In situ atomic force microscopy (AFM) characterizations and lithography can be applied to investigate the orientation, reactivity and stability of protein molecules adsorbed on nanostructures of self-assembled monolayers at near-physiological conditions. Automated nanografting was used to fabricate regular arrays of nanopatterns of ù-functionalized n-alkanethiols with designated terminal chemistries. After writing nanopatterns, protein binding occurs selectively on carboxylate-terminated nanopatterns via covalent bonds that are formed using N-ethyl-N'(dimethylaminoporpyl)-carbodiimide and N-hydroxysuccinimide activation. The amine groups of lysine residues of proteins bond covalently to nanopatterns of carboxylate-terminated alkanethiol self-assembled monolayers, to form a robust surface attachment for sustained contact-mode AFM imaging during biochemical reactions. …
Eliminating Absorbing Interference Using The H-Point Standard Addition Method: Case Of Griess Assay In The Presence Of Interferent Heme Enzymes Such As Nos, Perera N. Indika, Mekki Bayachou
Eliminating Absorbing Interference Using The H-Point Standard Addition Method: Case Of Griess Assay In The Presence Of Interferent Heme Enzymes Such As Nos, Perera N. Indika, Mekki Bayachou
Chemistry Faculty Publications
Standard calibration methods used to determine trace analytes usually yield significant deviations from the actual analyte value in the presence of interferents in the assay media. These deviations become of particular concern when the concentration of the analyte is low, and when the results are used to draw mechanistic or kinetic conclusions, for instance in enzyme structure-function studies. In these circumstances, the H-point standard addition method (HPSAM) provides superior precision and accuracy. This method is developed here for the case of the spectrophotometric Griess assay used to determine nitrite in various enzymology investigations, such as nitrite determination in studies of …
Development And Standardization Of A Short-Term Assay For Evaluating Polluted Estuarine And Coastal Environments: The Medaka Embryo-Larval Assay, Michael Frederick Helmstetter
Development And Standardization Of A Short-Term Assay For Evaluating Polluted Estuarine And Coastal Environments: The Medaka Embryo-Larval Assay, Michael Frederick Helmstetter
OES Theses and Dissertations
The eggs of the Japanese medaka (Oryzias latipes) were employed in a number of studies to develop a routine, standardized assay which can assess the acute and sublethal impacts of individual toxicants and complex mixtures. The eggs of this Cyprinodont minnow were topically treated with each toxicant or mixture dissolved in membrane permeable dimethylsulfoxide (DMSO) solvent. Nine chemicals were initially evaluated with two, pentachlorophenol (PCP) and tributyltin chloride (TBTCl), subsequently selected for extensive evaluations of salinity tolerance and the accuracy of the topical exposure method for representing a typical immersion exposure. The amount of material actually penetrating the eggs was …