Dr. Andrew J. Bonham

Professor of Chemistry & Biochemistry
Dr. Bonham’s Curriculum Vitae

Dr. Bonham is a research biochemist and data scientist with an emphasis on development of biosensors for detection and quantification of bio-markers, and bioinformatic analysis of human epigenetic methylation. At Metropolitan State University of Denver, Dr. Bonham is leading an innovative undergraduate research program focused on engineering new tools and analyses.

Dr. Bonham’s research skills include:
Biochemistry and Molecular Biology: molecular cloning / DNA mutagenesis; protein interface characterization, structure prediction, and engineering; DNA/RNA structure prediction and design; CRISPR/Cas9 human genome-editing design; protein expression, modification, and labeling; enzyme kinetics and thermodynamics; SPR and TIRF binding affinity measurement; radiation training (H3 and P32).
Polymers and nanomaterials: Cross-linking chemistry; hydrogel synthesis and characterization; DNA microarray fabrication; FPLC and HPLC purification; gold nanoparticle and nanorod development; GC-MS analysis.
Spectroscopy and microscopy: fluorescent confocal microscopy; Raman optical spectroscopy; TEM and SEM microscopy; fluorescent anisotropy; AFM microscopy.
Analytical Electrochemistry: square wave voltammetry; surface roughening; signal processing.
Bioinformatics: Python coding for GUI and software development; next-generation sequencing (NGS) data analysis; data science and predictive machine learning; development of Python training materials.

Victoria Colling

Lab Member 2022-
Published
Project: Gold nanoparticle decorated gel polymers for cardiac organoid development

Heart disease is one of the leading causes of death in the United States. The lack of effective treatment options and the shortage of available heart donors has led to extensive research investigating new methods to support the structure and function of myocardium tissue. Specific areas of key interest include improvements in transplantation of tissue, human tissue culturing, and the production of extracellular environments in vivo. One of the greatest challenges is improving methods to better mimic the properties of the natural cell environment, such as binding sites, stiffness, reactivity, and hydration. In this research, a conductive polymer matrix will be developed and characterized, which will serve as a scaffold to support the culturation of cardiac spheroids to be used in academics, research, and in medicine. Gold nanoparticles will be synthesized at high purity and with defined surface functionalization, then integrated into gel polymers to provide high conductivity and further support cell retention, spreading, development of cardiomyocytes, and effective gap junctions. Cardiac spheroids will be developed and analyzed using atomic force microscopy (AFM), then introduced into the scaffold. The introduction of these scaffolds with conductive gold nanoparticles into the process of tissue culturing should better enable effective cardiac spheroid maturation. This work will thus advance cardiac tissue engineering and provide methods of determining treatment effectiveness, contributing to improvement in methods for repairing damaged heart muscle and restoring cardiac function.

Keaton Silver

Lab Member 2022-
Published
Project: Electrochemical DNA Biosensors for Detection of Carrion’s Disease

Carrion’s disease is a neglected tropical infection caused by the bacterium Bartonella bacilliformis. Native to South America and transmitted into human vectors via certain phlebotomine species, infection by B. bacilliformis includes both an acute phase of symptoms, such as fever, hemolytic anemia, and myalgia, in addition to a chronic phase, which triggers the proliferation of endothelial cells, often resulting in blindness, and/or skin lesions in the form of Peruvian warts. Indeed, the acute phase of Carrion’s disease can be fatal if undetected and left untreated, making early detection of infection by B. bacilliformis in humans an essential effort. However, most current methods employed in the detection of Carrion’s disease display low sensitivity and require lengthy, expensive workups in a well-outfitted lab setting. Electrochemical DNA-based (E-DNA) biosensors have proven to be rapid, portable, and effective in their ability to detect the presence of small molecule targets through binding to DNA aptamers specific to their target of interest. Therefore, to address the critical challenge of detection, we have selected an aptamer specific to Pap31, a protein found on the extracellular matrix of B. bacilliformis. This aptamer is being adapted to a biosensor format via guided truncation to a minimally active aptamer, then incorporation into a DNA structure that will change conformation upon binding Pap31. This conformation change is turned into an electrochemical voltammetric readout due to the incorporation of methylene blue, a redox-active tag. This will allow the transduction of Pap31 binding into an electrical current signal, and we are verifying the sensitivity and specificity of this biosensor approach. The successful development of an E-DNA biosensor that is fast, effective, and portable for the detection of Carrion’s disease would offer new possibilities for treatment and health outcomes in many South American communities.