Transcription factors (TFs) are biologically important proteins that interact with transcription machinery and bind DNA regulatory sequences to regulate gene expression by modulating the synthesis of the messenger RNA. The regulatory sequences comprise of short conserved regions of a specific length called motifs . TFs have very diverse roles in different cells and play a very significant role in development. TFs have been associated with carcinogenesis in various tissue types, as well as developmental and hormone response disorders. They may be responsible for the regulation of oncogenes and can be oncogenic. Consequently, understanding TF binding and knowing the motifs to which they bind is worthy of attention and research focus. Various projects have made the study of TF binding their main focus; nevertheless, much about TF binding remains confounding. Chromatin immunoprecipitation in conjunction with deep sequencing (ChIP-seq) techniques are a popular method used to investigate DNA-TF interactions in vivo. This procedure is followed by motif discovery and motif enrichment analysis using relevant tools. Protein Binding Microarrays (PBMs) are an in vitro method for investigating DNA-TF interactions. We use a motif enrichment analysis tools (CentriMo and AME) and an empirical quality assessment tool (Area under the ROC curve) to investigate which method yields motifs that are a true representation of in vivo binding. Motif enrichment analysis: On average, ChIP-seq derived motifs from the JASPAR Core database outperformed PBM derived ones from the UniPROBE mouse database. However, the performance of motifs derived using these two methods is not much different from each other when using CentriMo and AME. The E-values from Motif enrichment analysis were not too different from each other or 0. CentriMo showed that in 35 cases JASPAR Core ChIP-seq derived motifs outperformed UniPROBE mouse PBM derived motifs, while it was only in 11 cases that PBM derived motifs outperformed ChIP-seq derived motifs. AME showed that in 18 cases JASPAR Core ChIP-seq derived motifs did better, while only it was only in 3 cases that UniPROBE motifs outperformed ChIP-seq derived motifs. We could not distinguish the performance in 25 cases. Empirical quality assessment: Area under the ROC curve values computations followed by a two-sided t-test showed that there is no significant difference in the average performances of the motifs from the two databases (with 95% confidence, mean of differences=0.0088125 p-value= 0.4874, DF=47) .

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The analysis of protein residues recovered from archaeological artifacts provides a unique opportunity to reveal new information about past societies. However, many scientists are currently unwilling to accept protein-based results due to problems in method development and a basic lack of agreement regarding the ability of proteins to bind to, and preserve within, artifacts such as pottery. In this paper, I address these challenges by conducting a two-phase experiment. First, I quantitatively evaluate the tendency of proteins to sorb to ceramic matrices by using total organic carbon analysis and spectrophotometric assays to analyze samples of experimentally cooked ceramic. I then test a series of solvent and physical parameters in order to develop an optimized method for extracting and preparing protein residues for identification via mass spectrometry. Results demonstrate that protein strongly sorbs to ceramic and is not easily removed, despite repeated washing, unless an appropriate extraction strategy is used. This has implications for the future of paleodietary, conservation ecology and forensic research in that it suggests the potential for recovery of aged or even ancient proteins from ceramic matrices.

High-voltage activated calcium channels underlie many critical functions in excitable cells and their dysfunction has been implicated in a myriad of cardiovascular and neurological diseases. These channels are multimeric protein complexes composed of α1, β, and α2δ subunits; currently, all calcium channel blockers target either the pore-forming α1 or extracellular-facing α2δ auxiliary subunit. These pharmacological agents have been invaluable in delineating the individual function of each subunit within excitable cells that express multiple calcium channels. Yet, no current tool allows similar pharmacological dissection of individual cytosolic β subunits, preventing our understanding of how distinct β subunits affect the function of calcium channel complexes. Further, small-molecule calcium channel blockers are highly-valued therapeutics for certain conditions, yet their propensity for off-target effects precludes their use in other diseases. In certain applications, genetically-encoded calcium channel blockers may enable channel inhibition with greater tissue-precision and versatility than is achievable with small molecules. Previous work that found the family of RGK proteins powerfully inhibits high-voltage activated calcium channels in part via an association with the β subunit. However, the myriad functions of RGK proteins limit the utility of this approach. In this work, we circumvent this issue by isolating single-domain antibodies (nanobodies) that target the auxiliary CaVβ subunit. We then paired these nanobodies with the powerful enzymatic activity of the HECT domain E3 ubiquitin ligase Nedd4L, to selectively target the calcium channel for ubiquitination. We found this strategy effectively eliminated functional calcium channels from the surface of HEK293 cells, myocytes, and DRG neurons. This modular design permitted us to characterize a pan-β inhibitor (CaV-aβlator) in chapter 2 while refining the approach with a β1-selective channel inhibitor in chapter 3. In chapter 4 I demonstrate that it is possible to hijack the endogenous ubiquitin machinery of the cell by creating Divas: divalent nanobodies that are capable of recruiting endogenous Nedd4L to regulate the calcium channel. Finally, we demonstrate the potential for these genetically-encoded calcium inhibitors to be employed as therapeutic agents by targeting CaV-aβlator to sensory neurons in order to reduce the onset of neuropathic pain. Altogether, this work lays the foundation for nanobody-based genetically-encoded calcium channel inhibitors that have the potential to achieve superior precision in regards to molecular and tissue specificity.

Despite the variety of successful reports of the preservation, recovery, and identification of archaeological proteins in general, there are few positive reports regarding mass spectrometry-based identification of ceramic-bound proteins. In large part, this shortage is due to the lack of consideration for the unique taphonomic histories of such residues and, in general, methods development. Further, because negative results are rarely published, there is no baseline to which results can be compared. This paper attempts to address these challenges via a multi-pronged approach that uses mass spectrometry and complementary approaches to evaluate ceramic-bound protein preservation in both controlled, actualistic experiments, and in archaeological artifacts. By comparing the results obtained from protein-spiked, experimentally-aged ceramic to those obtained from both faunal and ceramic archaeological materials, an enhanced perspective on protein preservation and subsequent recovery and identification is revealed. This perspective, focusing on taphonomy, reveals why negative results may be the norm for ceramic artifacts when non-targeted methods are employed, and provides insight into how further method development may improve the likelihood of obtaining positive results.

Neutrophils and macrophages accumulate at sites of inflammation and cause chronic inflammation leading to various diseases. Therefore, to better understand chronic disease pathways it is important to investigate the properties of macrophage accumulation in inflamed tissues. The I-domain of the macrophage receptor integrin aDb2 plays a vital role in macrophage retention by binding to CEP (carboxyethyl pyrrole), a ligand available at inflammatory sites. This thesis mainly focuses on evaluating the binding site within integrin aDb2 that binds carboxyethyl pyrrole (CEP)-modified proteins. So, a recombinant plasmid construct containing the integrin I-domain was developed. Seven non-conserved amino acids were mutated by PCR-site-directed mutagenesis to create a mutant construct. After expressing in E. coli, the binding affinities of wild-type and mutant I-domains to CEP were analyzed using biolayer interferometry. It was found that a patch of seven positively charged amino acids contributes to the strong binding of the I domain to CEP.

No description available.

No description available.

Affinity molecules can serve as precision tools for selective recognition and measurement of specific biomolecules in the fields of therapeutic drug monitoring and quality control in recombinant protein production. In therapeutic drug monitoring, affinity molecules can enable the accurate quantification of drug concentrations within physiological fluids, enhancing both the safety and efficacy of clinical treatments. In the realm of recombinant protein production, these molecules can allow precise isolation and measurement of desired recombinant proteins from complex mixtures by selectively targeting specific protein tags or domains, ensuring the consistency and purity of protein products. Currently, antibodies are most commonly used affinity reagents in these fields but are limited by production complexity, batch variability, high cost, and low stability. Aptamers, known as ‘chemical antibodies’ but composed of nucleotides, are considered potential next-generation affinity reagents. Aptamers are obtained via a synthetic process, termed SELEX, of iterative affinity selection and polymerase chain reaction (PCR) amplification of target-binding members from a randomized oligonucleotide library. This process is traditionally labor and resource-intensive and time-consuming. In this thesis, microfluidic technology is employed to enable time-efficient and cost-effective generation of aptamers for monoclonal antibodies and recombinant proteins toward applications in therapeutic drug monitoring and quality control of recombinant protein production. This thesis starts with a comparative study of three SELEX strategies for aptamer isolation, including those using conventional agarose bead-based partitioning, microfluidic affinity selection (called “chip-selection SELEX”), and fully integrated microfluidic affinity selection and PCR amplification (termed “full-chip SELEX”). The comparison results indicate that chip-selection SELEX offers the lowest cost and highest efficiency in aptamer isolation. We then use chip-selection SELEX to streamline the process of isolating anti-idiotype aptamers targeting human monoclonal antibodies against spike protein of SARS-CoV-2 virus. The process is completed within only 5 rounds of SELEX within two days, which represented a significant improvement when compared to conventional methods whose completion generally requires more than 10 SELEX rounds in up to a month. These anti-idiotype aptamers are combined with a graphene-based affinity nanosensor to enable rapid antibody concentration measurements to inform therapeutic decisions in a timely manner. In addition, a microfluidic dual-aptamer sandwich assay with highly efficient isolation of aptamers is developed to enable rapid and cost-effective detection of tag-fused recombinant proteins. This approach addresses both the limitations of current dual-aptamer assays and commonly encountered difficulties in the lack of aptamers available for such assays, by first using chip-selection SELEX to generate aptamers and then employing these aptamers to implement a microfluidic dual-aptamer assay for quality control during recombinant protein production. Despite the high efficiency in aptamer isolation using chip-selection SELEX, the full-chip SELEX platform is still desired for minimal manual operation and reagent consumption. The current full-chip SELEX platform has low isolation efficiency and could not offer information of affinity selection process. Herein, by introducing asymmetric PCR into the full-chip SELEX process, we improve the efficiency in aptamer isolation and can successfully monitor the selection progress. This real-time monitoring capability allows us to identify the optimal point to terminate the SELEX process, preventing the potential loss of aptamer candidates and reducing the overall consumption of time and reagents. In addition, introducing solution phase-based asymmetric PCR addresses a notable technical challenge of on-chip PCR bead replenishment, toward complete automation of the full-chip SELEX platform. Furthermore, a holder equipped with connection pins is designed to enable the reversible connection between gold electrodes and electrical wires. This design promotes the reusability of gold electrode-deposited glass substrates, resulting in a substantial reduction in chip fabrication costs. In addition to the SELEX protocol development effort, we also present efficient and cost-effective microfluidic approaches for post-SELEX aptamer characterization, including aptamer identification and kinetic aptamer-target binding measurements. To mitigate the expensive and time-consuming nature of aptamer identification from SELEX-generated target-binding sequence pools, we present an approach that is based on a cost-effective and efficient procedure to generate modified single-stranded DNA copies of the aptamer candidates and then assess the affinity of the resulting modified ssDNA strands to target molecules. The approach is applied to identify aptamers from 12 candidates with consistent results, but at a cost three times lower than that of established methods. We also present a microfluidic fluorescence assay, which exploits a synergistic combination of microfluidic technology and fluorescence microscopy, to realize cost-effective and multiplexed measurement of kinetics of aptamer-target analyte binding without requiring special-purpose equipment.

Turnover of synaptic vesicle (SV) proteins is vital for the maintenance of healthy and functional synapses. I recently showed that SV protein turnover is driven by neuronal activity in an endosomal sorting complex required for transport (ESCRT)-dependent manner. The ESCRT pathway comprises a series of protein complexes (ESCRT-0, I, II, III) that capture cargo and catalyze its sorting into multivesicular bodies (MVBs) for delivery to lysosomes. ESCRT-mediated protein degradation faces spatiotemporal challenges in neurons, as ESCRT components must undergo long-distance anterograde transport from soma to synapses in order to capture and sort cargo into MVBs. Moreover, MVBs and MVB-associated ESCRT-III proteins undergo retrograde transport back to the soma, where degradative lysosomes primarily reside. How ESCRT machinery is transported to and from synapses in morphologically complex neurons remains poorly understood. Here, I use live imaging approaches to characterize the axonal transport of ESCRT-0 protein Hrs and ESCRT-III protein CHMP2b, representing the initial and final components of the ESCRT pathway. In addition, I investigate the consequences of frontotemporal dementia (FTD)-causative mutant CHMP2b‸(intron5) on CHMP2b axonal transport and synaptic localization. I find that Hrs is transported on a subset of Rab5⁺ early endosomes, and that neuronal activity stimulates the motility and synaptic delivery of these Hrs⁺ vesicles. Furthermore, I identify kinesin motor protein KIF13A as essential for the activity-dependent anterograde transport of Hrs to presynaptic boutons and the degradation of SV membrane proteins. While CHMP2b also undergoes activity-dependent transport to presynaptic sites, this transport is typically retrograde and associated with Rab7, suggesting that a large fraction of CHMP2b⁺ vesicles represent late endosomes undergoing transport from presynaptic terminals to the soma. In contrast, vesicles carrying the CHMP2b‸(intron5) mutant exhibit aberrant oscillatory behavior reminiscent of a tug-of-war between motor proteins that disrupts their transport to presynaptic sites and contributes to defects in their maturation and activity-dependent transport. I demonstrate that these phenotypes are due in part to deficient binding of CHMP2b‸(intron5) to kinesin binding protein (KBP), which I identify as a key regulator of CHMP2b axonal transport. Together, these data demonstrate a novel activity- and KIF13A-dependent mechanism for mobilizing axonal transport of ESCRT-0 machinery to initiate the degradation of SV membrane proteins, and shed light on the mechanisms of CHMP2b/MVB transport and the etiology of CHMP2b‸(intron5)-induced FTD.