Physical Sciences and Mathematics Commons^™

Silent, Fluorescent Labeling Of Native Neuronal Receptors, D Vytla, R E. Combs-Bachmann, A M. Hussey, I Hafez, James Chambers

James Chambers

We have developed a minimally-perturbing strategy that enables labeling and subcellular visualization of endogenous dendritic receptors on live, wild-type neurons. Specifically, calcium-permeable non-NMDA glutamate receptors expressed in hippocampal neurons can be targeted with this novel synthetic tri-functional molecule. This ligand-directed probe was targeted towards AMPA receptors and bears an electrophilic group for covalent bond formation with an amino acid side chain on the extracellular side of the ion channel. This molecule was designed in such a way that the use-dependent, polyamine-based ligand accumulates the chemically-reactive group at the extracellular side of these polyamine-sensitive receptors, thereby allowing covalent bond formation between …

Effect Of Side Chains On Organic Donor (D) And Acceptor (A) Complexes And Photophysical Properties Of D-A Dyads, Amarnath Bheemaraju

Open Access Dissertations

This dissertation aims to understand the effect of incompatible side chains on the complexes of pi-conjugated electron-rich donors and electron-deficient acceptors in solution. The role of incompatible side chains were studied in simple mixtures of organic donor and acceptor molecules that form donor-acceptor complexes. The incompatible branched and linear alkane side chains on the acceptor and donor respectively prevented complex formation between naphthalene diimide acceptor and naphthalene ether donor. However, the incompatible hydrocarbon-fluorocarbon and polar-non polar side chain pairs did not affect complex formation between the donor and acceptor. In quaterthiophene-naphthalene diimide dyads, the incompatibility of the side chain on …

Selective Inhibition And Mechanistic Studies Of The Human O2 Sensor, Prolyl Hydroxylase Domain 2 (Phd2), Shannon Coates Flagg

Open Access Dissertations

Prolyl Hydroxylase Domain 2 (PHD2) has been identified as a key oxygen sensor in humans along with Factor Inhibiting Hypoxia Inducible Factor (FIH). As such PHD2 and FIH play critical roles in myriad pathways of medical relevance by hydroxylation of their target substrate hypoxia inducible factor (HIF), a transcription factor responsible for the regulation of over 100+ genes. With such critical roles in human physiology the ability to selectively regulate these two enzymes could potentially lead the way for novel therapeutic treatments of a vast array of disease states from cancer to myocardial infarction. We report on three classes of …

Controlled Oxygen Activation In Human Oxygen Sensor Fih, Evren Saban

Open Access Dissertations

One of the primary oxygen sensors in human cells, which controls gene expression by hydroxylating the hypoxia inducible transcription factor (HIFα) is the factor inhibiting HIF (FIH). As FIH is an alpha-ketoglutarate dependent non-heme iron dioxygenase, oxygen activation is thought to precede substrate hydroxylation. The coupling between oxygen activation and substrate hydroxylation was hypothesized to be very tight, in order for FIH to fulfill its function as a regulatory enzyme. Coupling was investigated by looking for reactive oxygen species production during turnover. Alkylsulfatase (AtsK), a metabolic bacterial enzyme with a related mechanism and similar turnover frequency, was used for comparison, …

Design And Synthesis Of A New Class Of Self-Cross-Linked Polymer Nanogels, Siriporn Jiwpanich

Open Access Dissertations

The design and engineering of nanoscopic drug delivery vehicles that stably encapsulate lipophilic drug molecules, transport their loaded cargo to specific target sites, and release their payload in a controlled manner are of great interest in therapeutic applications, especially for cancer chemotherapy. This dissertation focuses on chemically cross-linked, water-soluble polymer nanoparticles, termed nanogels, which constitute a promising scaffold and offer the potential to circumvent encapsulation stability issues. A facile synthetic method for a new class of self-cross-linked polymer nanogels, synthesized by an intra/intermolecular disulfide cross-linking reaction in aqueous media, is described here. This simple emulsion-free method affords noncovalent lipophilic guest …

Mutational Analysis Of Geopilin Function In Geobacter Sulfurreducens, Lubna V. Richter

Open Access Dissertations

Geobacter sulfurreducens possesses type IV pili that are considered to be conductive nanowires and a crucial structural element in biofilm formation, enabling electron transfer to insoluble metal oxides in anaerobic sediments and to graphite anodes in microbial fuel cells. The molecular mechanism by which electrons are transferred through the nanowires to the electron acceptor is not fully understood. Prior to the work described in this thesis, the gene (pilA) encoding the structural pilus subunit had been identified, but little was known about the functional translation start codon, the length of the mature secreted protein, or what renders the pili conductive. …

Molecular Designs For Organic Semiconductors: Design, Synthesis And Charge Transport Properties, Tejaswini Sharad Kale

Open Access Dissertations

Understanding structure-property relationship of molecules is imperative for designing efficient materials for organic semiconductors. Organic semiconductors are based on π-conjugated molecules, either small molecules or macromolecules such as dendrimers or polymers. Charge transport through organic materials is one of the most important processes that drive organic electronic devices. We have investigated the charge transport properties in various molecular designs based on dendrons, dendron-rod-coil molecular triads, and conjugated oligomers. The charge transport properties were studied using bottom contact field effect transistors, in which the material was deposited by spin coating.

In case of dendrons, their generation and density of charge transporting …

Colloidal Microcapsules: Surface Engineering Of Nanoparticles For Interfacial Assembly, Debabrata Patra

Open Access Dissertations

Colloidal Microcapsules (MCs), i.e. capsules stabilized by nano-/microparticle shells are highly modular inherently multi-scale constructs with applications in many areas of material and biological sciences e.g. drug delivery, encapsulation and microreactors. These MCs are fabricated by stabilizing emulsions via self-assembly of colloidal micro/nanoparticles at liquid-liquid interface. In these systems, colloidal particles serve as modular building blocks, allowing incorporation of the particle properties into the functional capabilities of the MCs. As an example, nanoparticles (NPs) can serve as appropriate antennae to induce response by external triggers (e.g. magnetic fields or laser) for controlled release of encapsulated materials. Additionally, the dynamic nature …

Caspase-7 Loop Conformations As A Means Of Allosteric Control, Witold Andrej Witkowski

Open Access Dissertations

The caspase family of proteins is critical to biological understanding, because they serve as the final arbiters of life and death, being the initiators and executioners of cell death. Specifically, caspase-7 plays a key role in apoptosis, however its full complement of targets within the cell has not yet been elucidated, nor has its function been targeted by drug design efforts. These factors stem from the lack of fundamental understanding of the structural dynamics of the protein, including the mobile loops that constitute the active site binding groove of caspase-7, and their ability to modulate the function of the protein. …

A Positive Feedback Synapse From Retinal Horizontal Cells To Cone Photoreceptors, Skylar L. Jackman, Norbert Babai, James Chambers, Wallace B. Thoreson, Richard H. Kramer

James Chambers

Cone photoreceptors and horizontal cells (HCs) have a reciprocal synapse that underlies lateral inhibition and establishes the antagonistic center-surround organization of the visual system. Cones transmit to HCs through an excitatory synapse and HCs feed back to cones through an inhibitory synapse. Here we report that HCs also transmit to cone terminals a positive feedback signal that elevates intracellular Ca2+ and accelerates neurotransmitter release. Positive and negative feedback are both initiated by AMPA receptors on HCs, but positive feedback appears to be mediated by a change in HC Ca2+, whereas negative feedback is mediated by a change in HC membrane …

Engineering Nanoparticles Surface For Biosensing: "Chemical Noses" To Detect And Identify Proteins, Bacteria And Cancerous Cells, Oscar Ramon Miranda-Sanchez

Open Access Dissertations

Rapid and sensitive detection of biomolecules is an important issue in nanomedicine. Many disorders are manifested by changes in protein levels of serum and other biofluids. Rapid and effective differentiation between normal and cancerous cells is an important challenge for the diagnosis and treatment of tumor. Likewise, rapid and effective identification of pathogens is a key target in both biomedical and environmental monitoring. Most biological recognition processes occur via specific interactions. Gold nanoparticles (AuNPs) feature sizes commensurate with biomacromolecules, coupled with useful physical and optical properties. A key issue in the use of nanomaterials is controlling the interfacial interactions of …

Institute Overview, Morton Sternheim

STEM Digital

Digital cameras and computers are widely available for students and teachers. However, they are mainly used for documentation: creating PPT presentations, handouts, posters, etc. STEM DIGITAL shows how digital image analysis can be applied to environmental (and other) research in STEM courses. Application to studies of air quality, water quality, arsenic contamination, climate change, diffusion, etc.

Digital Camera Basics, Stephen Schneider

STEM Digital

No abstract provided.

Measuring Lengths And Areas With Adi. Student Guide, Morton Sternheim

STEM Digital

No abstract provided.

Measuring G With Movie Tracker, Stephen Schneider

STEM Digital

No abstract provided.

Detecting And Mixing Colors, Rob Snyder

STEM Digital

How can Analyzing Digital Images software reveal the differences between primary colors of light and primary colors of paints or pigments?

Measuring The Acceleration Of Falling Objects, John Pickle

STEM Digital

Earth's gravity pulls all objects toward its center, and near the Earth's surface. Objects in free fall accelerate at 9.8 m/s² vertically downward, provided air resistance is negligible. This value of acceleration is often referred to as "g". There are many ways to measure this rate of acceleration, and most require a timing device. Typically, stopwatches are the least expensive technology, so these are commonly available in high school science classrooms. With the recent addition of movie cameras on cell phones and digital cameras, another timing tool is available at moderate cost (free if the school policy …

Leaf Leaching Experiment, David Reckhow

STEM Digital

Water treatment engineers and public health officials need to pay careful attention to the presence of dissolved organic matter in water supplies selected for human consumption (i.e., raw drinking waters).

Measuring Albedo With Adi - An Intensity Application, Morton Sternheim

STEM Digital

Why are Polar Regions more affected by global warming than other parts of the globe? One reason (there are others) is that as sea ice melts and more open water appears, more energy is absorbed, and warming accelerates. This is a form of positive feedback and it makes the polar climate change faster than the climate in temperate areas. Increasing vegetation on land also has a similar positive feedback effect. This effect is a change in the albedo – the fraction of the incident sunlight that is reflected back to space.

Stem Digital And Adi In The Classroom, Jennifer Welborn

STEM Digital

Applications of ADI by students at Amherst Regional Middle School

Co2 Diffusion Through Gelatin Experiment, Jennifer Welborn

STEM Digital

An example of measuring lengths.

Natural Organic Matter In Water, David Reckhow

STEM Digital

Formation in Watersheds and Removal in Water Treatment

Using Adi To Quantify A Color Change In Crayfish, Jennifer Welborn

STEM Digital

Do Crayfish Change Color If Their Environment Changes? A Guided Inquiry Lab for 7th grade Life Science

Background: There is anecdotal evidence from bass fisherman that crayfish are able to change color depending on their surroundings. A (cursory) literature review of this phenomenon showed that no formal research has been done in this area. Students had an additional informal lesson about research funding (or lack thereof) because of this finding.

Students designed and conducted a controlled experiment to see the effect of changing environment color on crayfish color.

ADI was used to quantify a color change.

Human Variation In Skin Color And Race As A Social Construct, Jennifer Welborn

STEM Digital

This lesson is part of evolution unit which follows heredity and genetics

The lesson is interdisciplinary in nature in that I discuss the concept of race as a social construct and the idea that there are “black, white, red, yellow” skinned people is something that people developed. It is not based on biology. Race groupings are human-made groups.

Students first learn about mixing light and how to determine black and white from an ADI analysis. They learn that red and green = yellow, etc.

They then photograph each other’s forearms and analyze the images using ADI.

We then discuss skin …

Air Quality: Carbon Dioxide, Deborah Carlisle, Stephen Schneider

STEM Digital

Measuring CO2 with BTB and ADI.

Measuring Angles With Adi, Stephen Schneider

STEM Digital

No abstract provided.

Analyzing Digital Images (Adi) Resources, Rob Snyder

STEM Digital

Basic introduction to installing and using ADI

Arsenic Project Topics, Julian Tyson

STEM Digital

How do analytical chemists make light work in tracking potentially harmful chemicals?

Water Treatment Experiments, David Reckhow

STEM Digital

•The water industry spends a lot of money and effort on removal of natural organic matter (NOM) from drinking waters •Problems with NOM (the more NOM the bigger problem) –NOM interferes with the ability of water treatment systems to remove substances that cause disease •Pathogenic organisms •Toxic chemicals –NOM reacts with chlorine‐based disinfectants forming carcinogenic organic byproducts

Experimental Design For Ozone Projects, Deborah Carlisle, Stephen Schneider

STEM Digital

No abstract provided.