Biochemistry Commons^™

Paper-Based Diagnostic Devices, Spencer A. Schultz, Isabelle C. Noxon, Tyler A. Sisley, Andres W. Martinez

Chemistry and Biochemistry

This chapter will provide an overview of existing diagnostic devices made primarily out of paper and then focus on paper-based microfluidic devices, the next generation of paper-based diagnostic devices that promises to extend the use of paper as a material for fabricating diagnostic devices well into the future.

Chapter Contents:

• 2.1 Introduction
• 2.2 Current paper-based diagnostic devices
• 2.2.1 Dipstick devices
• 2.2.2 Lateral-flow devices
• 2.2.2.1 Vertical-flow devices
• 2.2.3 Paper-based arrays
• 2.3 Paper-based microfluidic devices
• 2.3.1 Fabrication of paper-based microfluidic devices
• 2.3.2 Applications of paper-based microfluidic devices
• 2.4 Conclusions
• References

Pseudoalteromonas Piratica Sp. Nov., A Budding, Prosthecate Bacterium From Diseased Montipora Capitata, And Emended Description Of The Genus Pseudoalteromonas, Silvia Beurmann, Blake Ushijima, Christina M. Svoboda, Patrick Videau, Ashley M. Smith, Stuart P. Donachie, Greta S. Aeby, Sean M. Callahan

Research & Publications

A Gram-stain-negative, motile, rod-shaped bacterium designated OCN003T was cultivated from mucus taken from a diseased colony of the coral Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i. Colonies of OCN003T were pale yellow, 1–3 mm in diameter, convex, smooth and entire. The strain was heterotrophic, strictly aerobic and strictly halophilic. Cells of OCN003T produced buds on peritrichous prosthecae. Growth occurred within the pH range of 5.5 to 10, and the temperature range of 14 to 39 °C. Major fatty acids were 16 : 1!7c, 16 : 0, 18 : 1!7c, 17 : 1!8c, 12 : 0 3-OH and 17 : 0. …

Neuronal Gq Structures In Neurodegeneration, Damian S. Mcaninch

Electronic Theses and Dissertations

This study investigates protein nucleic acid interactions between various proteins and G quadruplex (GQ) forming messenger RNAs (mRNAs) in human neurological disorders. GQ structures are formed in DNA/RNA, when four guanine residues form planar tetrads stabilized by Hoogsteen base pairing, that stack forming a GQ structure stabilized by potassium ions. These GQ structures are targeted by the arginine-glycine-glycine (RGG) repeat domain containing RNA-binding domain.

Three RGG domain containing RNA-binding proteins, all of which have been implicated in neurological disorders, and their interactions with GQ forming mRNAs, were investigated in this study: fused in sarcoma (FUS), fragile X mental retardation protein …

Airborne Measurements Of Western U.S. Wildfire Emissions: Comparison With Prescribed Burning And Air Quality Implications, Xiaoxi Liu, L. Gregory Huey, Robert J. Yokelson, Vanessa Selimovic, Isobel J. Simpson, Markus Müller, Jose L. Jimenez, Pedro Campuzano-Jost, Andreas J. Beyersdorf, Donald R. Blake, Zachary Butterfield, Yonghoon Choi, John D. Crounse, Douglas A. Day, Glenn S. Diskin, Manvendra K. Dubey, Edward Fortner, Thomas F. Hanisco, Weiwei Hu, Laura E. King, Lawrence Kleinman, Simone Meinardi, Tomas Mikoviny, Timothy B. Onasch, Brett B. Palm, Jeff Peischl, Ilana B. Pollack, Thomas B. Ryerson, Glen W. Sachse, Arthur J. Sedlacek, John E. Shilling, Stephen Springston, Jason M. St. Clair

Chemistry and Biochemistry Faculty Publications

Wildfires emit significant amounts of pollutants that degrade air quality. Plumes from three wildfires in the western U.S. were measured from aircraft during the Studies of Emissions and Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Biomass Burning Observation Project (BBOP), both in summer 2013. This study reports an extensive set of emission factors (EFs) for over 80 gases and 5 components of submicron particulate matter (PM1) from these temperate wildfires. These include rarely, or never before, measured oxygenated volatile organic compounds and multifunctional organic nitrates. The observed EFs are compared with previous measurements of temperate …

A Dual-Chamber Method For Quantifying The Effects Of Atmospheric Perturbations On Secondary Organic Aerosol Formation From Biomass Burning Emissions, Daniel S. Tkacik, Ellis S. Robinson, Adam Ahern, Rawad Saleh, Chelsea Stockwell, Patrick Veres, Isobel J. Simpson, Simone Meinardi, Donald R. Blake, Robert J. Yokelson, Albert A. Presto, Ryan C. Sullivan, Neil M. Donahue, Allen L. Robinson

Chemistry and Biochemistry Faculty Publications

Biomass burning (BB) is a major source of atmospheric pollutants. Field and laboratory studies indicate that secondary organic aerosol (SOA) formation from BB emissions is highly variable. We investigated sources of this variability using a novel dual-smog-chamber method that directly compares the SOA formation from the same BB emissions under two different atmospheric conditions. During each experiment, we filled two identical Teflon smog chambers simultaneously with BB emissions from the same fire. We then perturbed the smoke with UV lights, UV lights plus nitrous acid (HONO), or dark ozone in one or both chambers. These perturbations caused SOA formation in …

In Situ Measurements Of Water Uptake By Black Carbon-Containing Aerosol In Wildfire Plumes, Anne E. Perring, Joshua P. Schwarz, Milos Z. Markovic, David W. Fahey, Jose L. Jimenez, Pedro Campuzano-Jost, Brett D. Palm, Armin Wisthaler, Tomas Mikoviny, Glenn Diskin, Glen Sachse, Luke Ziemba, Bruce Anderson, Taylor Shingler, Ewan Crosbie, Armin Sorooshian, Robert Yokelson, Ru Shan Gao

Chemistry and Biochemistry Faculty Publications

Water uptake by black carbon (BC)-containing aerosol was quantified in North American wildfire plumes of varying age (1 to ~40 h old) sampled during the SEAC4RS mission (2013). A Humidified Dual SP2 (HD-SP2) is used to optically size BC-containing particles under dry and humid conditions from which we extract the hygroscopicity parameter, κ, of materials internally mixed with BC. Instrumental variability and the uncertainty of the technique are briefly discussed. An ensemble average κ of 0.04 is found for the set of plumes sampled, consistent with previous estimates of bulk aerosol hygroscopicity from biomass burning sources. The temporal evolution of …

Development Of Tools For Phosphosite-Specific Kinase Identification And Discovery Of Phosphatase Substrates, Pavithra Maheshani Dedigama Arachchige

Wayne State University Dissertations

Phosphorylation is a ubiquitous post translational modification implicated in many diseases, such as cancer. The phosphorylation status of cellular proteins is regulated by the activity of kinases and phosphatases. The biological significance of many phosphorylation events remain unknown because the methods to determine which kinase or phosphatase is responsible for phosphorylation are limited. Previously, we established kinase-catalyzed labeling where kinases accept γ-modified ATP analogs, such as ATP-arylazide and ATP-biotin, to label phosphoproteins. To study substrates of kinases and phosphatases, here we developed two new methods using kinase-catalyzed labeling. As one application, we developed K-CLASP (Kinase-catalyzed CrossLinking And Streptavdin Purification) to …

Design, Synthesis And Biological Evaluation Of Histone Deacetylase (Hdac) Inhibitors: Saha (Vorinostat) Analogs And Biaryl Indolyl Benzamide Inhibitors Display Isoform Selectivity, Ahmed Negmeldin

Wayne State University Dissertations

HDAC proteins have emerged as interesting targets for anti-cancer drugs due to their involvement in cancers, as well as several other diseases. Several HDAC inhibitors have been approved by the FDA as anti-cancer drugs, including SAHA (suberoylanilide hydroxamic acid, Vorinostat). Unfortunately, SAHA inhibits most HDAC isoforms, which limit its use as a pharmacological tool and may lead to side effects in the clinic. In this work we were interested in developing isoform selective HDAC inhibitors, which may decrease or eliminate the side effects associated with non-selective inhibitors treatment. In addition, isoform selective HDAC inhibitors can be used as biological tools …

Development Of Chemical Tools To Investigate Protein S-Glutathionylation In Response To Metabolic Alteration, Kusal Theekshana Gayan Samarasinghe

Wayne State University Dissertations

Oxidative stress is a common characteristic of age-related diseases such as vascular diseases, diabetes and cancer. Many diseases are known to be regulated by glutathionylation. Glutathionylation is referred to as the formation of disulfide bond between a protein cysteine and a glutathione. To understand the molecular mechanisms behind the disease initiation and progression, identification of such glutathionylated proteins is important. Even though existing methods have been widely used, several limitations of these methods hinder the identification of such proteins in disease conditions. Therefore, we developed a versatile chemical method that generates clickable glutathione inside the cells. In this method, we …

Ligand Binding Studies Of A Peptide Targeting Helix 69 Of 23s Rrna In Bacterial Ribosomes, Hyosuk Seo

Wayne State University Dissertations

In the development of finding a peptide targeting H69 of 23S rRNA in bacterial ribosomes, phage display was employed at pH 5.5, a buffer condition previously reported of H69 preferring a closed conformation. After sequencing, several peptides were chosen through sequence alignment, followed by preparation using solid-phase peptide synthesis. The peptides were characterized using MALDI-TOF and purified with HPLC. A truncated peptide TARHIY was selected from FID assay. Through binding studies using ESI-MS, SPR, BLItz, and NMR, the binding properties of the peptide to H69 were determined, such as binding affinity, stoichiometry, and interaction site. The peptide exhibited moderate binding …

The Development Of Chemical Methods To Discover Kinase Substrates And Map Cell Signaling With Gamma-Modified Atp Analog-Dependent Kinase-Catalyzed Phosphorylation, Dissanayaka Mudiyanselage Maheeka Madhubashini Embogama

Wayne State University Dissertations

Kinase-catalyzed phosphorylation plays an important role in cell physiology by regulating a myriad of cellular functions. Thus aberrant kinase activity is implicated in various diseases. Methods are needed to discover kinase substrates and map signaling pathways to explore biology and to help drug discovery. A few techniques are currently available to discover kinase substrate and map cell signaling. However, to augment kinase substrate discovery approaches, it is essential to develop alternative techniques. Pflum has recently discovered cosubstrate promiscuity of protein kinases with gamma-modified ATP analogs. Here, kinase-catalyzed biotinylation with ATP-biotin was used to develop novel tools to discover kinase substrates …

Nanoparticle Targeting To The Central Nervous System, Emily Baker

Williams Honors College, Honors Research Projects

Drug delivery to the central nervous system is complicated by the blood-brain barrier, a vascular structure that prevents free diffusion of molecules into brain tissue. In this study, we examined the in vitro properties of a nanoparticle-based drug delivery system. We used several nanoparticle formulations, both LTP based and PLGA based, to test the cellular uptake and toxicity in microglial cells. Using immunofluorescence imaging, we show that LTP nanoparticles are taken up by microglia. We confirmed that our nanoparticle formulations are non-toxic by two cell viability assays. These results suggest that nanoparticle formulations may be a biocompatible method of delivering …

Dream Of A Conducive Learning Environment: One Dreem For All Medical Students!, Rehana Rehman, Kulsoom Ghias, Syeda Sadia Fatima, Mehwish Hussain, Faiza Alam

Department of Biological & Biomedical Sciences

Objective: To compare students' response assessed by Dundee Ready Educational Environment Measure on the basis of the year of study, gender and pre-medical educational background.Methods: This cross-sectional study was carried out at the Aga Khan University Medical College, Karachi, Pakistan, from June 2014 to March 2015, and comprised medical students. The average scores of Dundee Ready Educational Environment Measure scales and subscales were compared between gender and educational background. Responses were also compared on the basis of year of study.Results: Of the 416 participants, 184 (44%) were males and 232 (56%) were females. There were 100 (24%) students in the …

A New Model For Phd Elective Course, H R. Ahmad, Satwat Hashmi, M H. Mahmood

Department of Biological & Biomedical Sciences

No abstract provided.

Investigating Medicinally Important Portein-Protein And Protein-Ligand Interactions : A Computational Approach, Cooper Ashley Taylor

Honors Theses

Molecular dynamics (MD) simulations and computational chemistry allow for an atomistic understanding of protein-protein and protein-ligand binding motifs. Through the use of MD, medicinally relevant complexes can be examined in detail unattainable by experimental methods. Within this work, systems pertinent to both Alzheimer’s Disease and HIV-1 are probed and thoroughly sampled to help elucidate potential therapeutic pathways. We used molecular dynamics and free energy estimations to gauge the affinity for the binary and ternary complexes of KLC1, APP and JIP1, three proteins all believed to be involved in the propagation of Alzheimer’s Disease. Two areas of thought exist suggesting that …

Myeloperoxidase-Mediated Protein Lysine Oxidation Generates 2- Aminoadipic Acid And Lysine Nitrile In Vivo, Hongqiao Lin, Bruce S. Levison, Jennifer A. Buffa, Ying Huang, Xiaoming Fu, Zeneng Wang, Valentin Gogonea, Joseph A. Didonato, Stanley L. Hazen

Chemistry Faculty Publications

Recent studies reveal 2-aminoadipic acid (2-AAA) is both elevated in subjects at risk for diabetes and mechanistically linked to glucose homeostasis. Prior studies also suggest enrichment of protein-bound 2-AAA as an oxidative post-translational modification of lysyl residues in tissues associated with degenerative diseases of aging. While in vitro studies suggest redox active transition metals or myeloperoxidase (MPO) generated hypochlorous acid (HOCl) may produce protein-bound 2-AAA, the mechanism(s) responsible for generation of 2- AAA during inflammatory diseases are unknown. In initial studies we observed that traditional acid- or basecatalyzed protein hydrolysis methods previously employed to measure tissue 2-AAA can artificially generate …

Alpha-Synuclein: Insight Into The Hallmark Of Parkinson's Disease As A Target For Quantitative Molecular Diagnostics And Therapeutics, Baggio A. Evangelista

Honors Undergraduate Theses

Parkinson’s disease (PD) is the second-most common neurodegenerative disease after Alzheimer’s disease. With 500,000 individuals currently living with Parkinson’s and nearly 60,000 new cases diagnosed each year, this disease causes significant financial burden on the healthcare system - amassing to annual expenditures totaling 200 billion dollars; predicted to increase through 2050. The disease phenotype is characterized by a combination of a resting tremor, bradykinesia, muscular rigidity, and depression due to dopaminergic neuronal death in the midbrain. The cause of the neurotoxicity has been largely discussed, with strong evidence suggesting that the protein, alpha-Synuclein, is a key factor. Under native conditions, …

Real-Time Investigation Of Bulky Lesion Bypass By Y-Family Dna Polymerase, Dpo4, Using Single Molecule Fret, Pramodha Liyanage

Wayne State University Dissertations

DNA is constantly exposed to various DNA damaging agents that are generated by various internal and external sources. Some of this damage may not be able to be repaired by cellular machineries causing DNA replication to be blocked. Once the replication fork is blocked by a DNA adduct, damage tolerance DNA polymerases, mainly Y-family, are able to restore the DNA replication by synthesizing past the DNA adduct. Benzo[a]pyrene (B[a]P) is one of the most studied environmental carcinogens. It is known to make covalent DNA adducts after metabolic activation and the bulkiness of the B[a]P adducts impose a strong barrier to …

Characterization Of Quorum-Quenching Lactonases And Plp-Dependent Aminotransferases: Structure, Mechanism And Alternative Turnover, Romila Nina Mascarenhas

Dissertations

Cell-to-cell communication by bacteria is essential for the regulation of gene expression important in colonization, biofilm formation, virulence and other processes. This communication is called "quorum-sensing" and is mediated by small molecules called autoinducers. One major class of autoinducers used by gram-negative bacteria is N-acyl homoserine lactones (AHL's). Enzymes capable of disrupting this communication are called "quorum-quenching" catalysts and have proven to be invaluable biochemical tools for understanding quorum-sensing pathways. Quorum-quenching enzymes hold promise for application in anti-biofouling, agriculture, aquaculture, bioremediation and other synthetic biology settings. However, the mechanisms that these enzymes use to recognize and process their substrates are …

Novel Role Of The Nociceptin System As A Regulator Of Glutamate Transporter Expression In Developing Astrocytes, Logan Meyer

Theses and Dissertations

Our previous results showed that oligodendrocyte development is regulated by both nociceptin and its G-protein coupled receptor, the nociceptin/orphanin FQ receptor (NOPR). The present in vitro and in vivo findings show that nociceptin plays a crucial conserved role in both human and rodent brain astrocytes, regulating the levels of the glutamate/aspartate transporter GLAST/EAAT1. This nociceptin-mediated response takes place during a critical developmental window that coincides with astrocyte maturation and synapse formation. GLAST/EAAT1 upregulation by nociceptin is mediated by NOPR and the downstream participation of a complex signaling cascade that involves the interaction of several kinase systems, including PI-3K/AKT, mTOR and …