High-throughput experimentation (HTE) is a form of accelerated testing which allows for many hundreds or thousands of experiments to be conducted in parallel or in rapid sequence. Recent advances in chemical reaction miniaturization have enabled HTE application toward chemical reaction exploration, and the resultant datasets present exciting opportunities for the incorporation of machine learning (ML) with organic chemistry to expedite reaction optimization and discovery. Disclosed herein is a modular HTE chemistry reaction platform with rapid and inexpensive data acquisition capabilities for training ML algorithms on organic chemistry. Comprising almost entirely off-the-shelf components and algorithms which will be made open-source, this platform facilitates data democratization through distributed generation. Underpinning this workflow is an innovative titration-based analysis method for semi-automated and quantitative conversion data acquisition at a rate of under fifteen seconds per sample. Requisite to this platform’s success are solutions to solid and liquid reagent distribution, reaction incubation, and fast, quantitative reaction analysis which is demonstrated in a proof-of-concept screening of the SNAr reaction toward the synthesis of proteolysis targeting chimera (PROTACs). It is hoped this platform lowers the barrier for entry to HTE for chemists through its modularity, approachability, and low operating costs. / 2024-06-16T00:00:00Z

Carla Abarca Ph.D. Thesis / The selective separation of valuable minerals by froth flotation is a critical unit operation in mineral processing. Froth flotation is based on the ability of chemical reagents, called collectors, to selectively lower the surface energy of valuable mineral particles, facilitating attachment of the modified mineral particles to air bubbles in the flotation cell. The mineral laden bubbles rise to the surface forming a froth phase that can be isolated. Novel cationic polystyrene nanoparticle collectors have been developed recently to be used as effective flotation collectors, aiming to recover challenging nickel sulfide ores that respond poorly to conventional molecular flotation collectors. However, optimizing nanoparticle flotation collectors is a challenge. An effective nanoparticle collector candidate should meet three requirements: (1) it should be colloidally stable in the flotation media; (2) it should be hydrophobic enough to change the mineral surface and induce an air bubble-mineral particle attachment; and (3) specifically and strongly bind to metal-rich minerals. Producing nanoparticles that are simultaneously colloidally stable and sufficiently hydrophobic presents a problematic task. Thus, a delicate balance of nanoparticle properties is required for commercially viable nanoparticle collectors. This thesis presents a promising approach for discovering and characterizing novel nanoparticle collectors by using high throughput screening techniques. Developed was a workflow for fast fabrication and testing of nanoparticle candidates, including: (1) parallel production of large nanoparticle libraries covering a range of surface chemistries, (2) a high throughput colloidal stability assay to determine whether a nanoparticle type is stable in flotation conditions; (3) an automated contact angle assay to reject nanoparticles that are not hydrophobic enough to induce efficient bubble-particle attachment, and; (4) a laboratory flotation test in sodium carbonate (pH~10) with the best nanoparticle candidates. The automated colloidal stability assay was based on the optical characterization of diluted nanoparticle dispersions in multiwell plates, yielding critical coagulation concentrations (CCCs) of sodium carbonate. To pass this screening test, the CCC of candidate nanoparticles must be greater than the effective carbonate concentration in commercial flotation cells. Since the nanoparticle size affects the intrinsic light scattering properties of the nanoparticles, two routes were developed. The colloid stability assay was suitable for nanoparticles ranging between 50 nm and 500 nm, since nanoparticle size. The automated contact angle assay used a miniature 16-well plate format where flat glass slides were exposed to 200 μL nanoparticle dispersions. The cationic nanoparticles formed a saturated adsorbed monolayer on the glass, and after rinsing and drying, the water contact angle was automatically measured. Effective nanoparticle candidates had contact angles greater than 50 degrees, a criterion developed with model experiments. During the development of the automated workflow platform, a series of nanoparticles with methyl-ended PEG-methacrylate monomers were prepared. Although the PEG chains greatly enhanced colloidal stability, the particles were too hydrophilic to be effective collectors. Interestingly, nanoparticles with long PEG chains acted as froth modifiers, giving wetter and more robust foams as well as increased entrainment of materials that did not adhere to bubbles. Conventional laboratory scale latex synthesis methodologies are far too inefficient to generate large library of candidate nanoparticles. Instead, we started with a few parent nanoparticle types and then used Click chemistry to generate a large range of surface chemistries. Specifically copper-mediated azide alkyne cycloaddition reaction was used to functionalize the surface of azide nanoparticles with different chemical groups, ranging from hydrophilic amine-terminated PEG chains, to hydrophobic hexane-terminated materials. The Click library exhibited an extensive range of critical coagulation concentrations and contact angle values. For example, for a given parent azide nanoparticle, the contact angles ranged from 62 to 101 degrees, depending upon the density and type of click reagent. A novel paper chromatographic method was developed for the quantitative determination surface azide. This assay was critical for determining the surface density of functional groups from the click reactions. Overall, high throughput screening techniques were designed and applied to the development of nanoparticle collectors for froth flotation. Automated screening assays of critical coagulation concentration and contact angle proved to be effective in obtaining flotation domain maps, and finding the most promising nanoparticle collectors for froth flotation. I believe the work in this thesis is one of the first reported uses of high throughput methodologies for the development of mineral flotation reagents. / Thesis / Doctor of Philosophy (PhD) / Novel cationic polystyrene nanoparticle collectors have been developed to be used as effective flotation collectors, aiming to recover challenging nickel sulfide ores that respond poorly to conventional molecular flotation collectors. However, optimizing nanoparticle flotation collectors is a challenge. This thesis presents a promising approach for discovering and characterizing novel nanoparticle collectors by using high throughput screening techniques and click chemistry. Development of nanoparticle libraries and automated screening assays of critical coagulation concentration and contact angle proved to be effective in obtaining flotation domain maps, and finding the most promising nanoparticle collectors for froth flotation.

Master of Science / Department of Biochemistry and Molecular Biophysics / Phillip Klebba / Iron acquisition is a component of Gram-negative bacteria pathogenesis, therefore as a form of 'nutritional immunity' host organisms sequester iron. To obtain iron bacteria secrete siderophores that scavenge iron. The E. coli outer membrane protein FepA actively transports the siderophore ferric enterobactin into the periplasm. We observe this uptake reaction by fluorescently labeling FepA in live bacteria, monitoring quenching that occurs upon binding of FeEnt, and then fluorescence recovery during transport. Energy poisons azide, arsenate, and 2,4-dinitrophenol were evaluated to determine sensitivity to known transport inhibitors. We developed and optimized methods to screen for iron transport inhibitors using a cell-based high-throughput screening platform. These inhibitors may have broad spectrum bacteriostatic antibiotic properties.

Were he alive today, would Louis Pasteur still champion culture methods he pioneered over 150 years ago for identifying bacterial pathogens? Or, might he suggest that new molecular techniques may prove a better way forward for quickly detecting the true microbial diversity of wounds? As modern clinicians faced with treating complex patients with diabetic foot infections (DFI), should we still request venerated and familiar culture and sensitivity methods, or is it time to ask for newer molecular tests, such as 16S rRNA gene sequencing? Or, are molecular techniques as yet too experimental, non-specific and expensive for current clinical use? While molecular techniques help us to identify more microorganisms from a DFI, can they tell us ‘who done it?', that is, which are the causative pathogens and which are merely colonizers? Furthermore, can molecular techniques provide clinically relevant, rapid information on the virulence of wound isolates and their antibiotic sensitivities? We herein review current knowledge on the microbiology of DFI, from standard culture methods to the current era of rapid and comprehensive ‘crime scene investigation' (CSI) techniques.

Intracellular delivery of macromolecules is crucial for the success of many research and clinical applications. Several conventional intracellular delivery methods have been used for many years but are still inadequate for several applications because of the issues associated with toxicity, low-throughput, and/or difficulty to target certain cell types. In this study, we developed and evaluated new high-throughput intracellular delivery methods for the efficient delivery of macromolecules while maintaining high cell viability. First, we studied the feasibility of using an array of nanoneedles, with sharp tip diameters in the range of tens of nanometers, to physically make transient holes in cell membranes for intracellular delivery. Puncture loading and centrifuge loading methods were developed and assessed for the effect of various experimental parameters on cell viability and delivery efficiency of fluorescent molecules. In both methods, high-throughput intracellular delivery was feasible by creating transient holes in cell membranes with the sharp tips of the nanoneedles. The second physical intracellular delivery method we studied was a novel microfluidic device that created transient holes in the cell membrane by mechanical deformation and shear stress to the cell. We observed efficient delivery of fluorescent molecules and studied the effect of device design and flow pressure on the delivery efficiency compared to data in the literature. We accounted for cell loss and clogging in the microfluidic devices and determined the true loss of cell viability associated with this method. Lastly, we investigated the possibility of intracellular delivery using nanoparticles on a leukemia cell line. Among number of materials for nanoparticles tested, mesoporous silica/poly-L-lysine nanoparticles were selected for further intracellular delivery study based on cell viability and intracellular delivery capability. We demonstrated the co-delivery of protein and plasmid by encapsulating into and coating onto the surface of the nanoparticles, respectively, which would be advantageous for certain therapeutic strategies. In summary, this work introduced two new intracellular delivery methods involving nanoneedles and novel nanoparticles, and provided an early, independent assessment of microfluidic delivery, showing the strengths and weaknesses of each method. These methods can be further optimized for a number of laboratory and clinical applications with continued research.

Phage display technology has emerged as the dominant approach in antibody engineering. Here I describe my work in developing a high-throughput method of reliably generating intracellular antibodies. In my first data chapter, I present the first known high-throughput pipeline for antibody-phage display libraries of synthetic diversity and I demonstrate how increasing the scale of both target production and library selection still results in the capture of antibodies to over 50% of targets. In my second data chapter, I present the construction and validation of a novel scFv-phage library that will serve as the first step in my proposed intrabody pipeline. Antibodies obtained from this library will be screened for functionality using a novel yeast-two-hybrid approach and have numerous downstream applications. This high-throughput pipeline is amenable to automation and can be scaled up to thousands of domains, resulting in the potential generation of many novel therapeutic reagents.

Phage display technology has emerged as the dominant approach in antibody engineering. Here I describe my work in developing a high-throughput method of reliably generating intracellular antibodies. In my first data chapter, I present the first known high-throughput pipeline for antibody-phage display libraries of synthetic diversity and I demonstrate how increasing the scale of both target production and library selection still results in the capture of antibodies to over 50% of targets. In my second data chapter, I present the construction and validation of a novel scFv-phage library that will serve as the first step in my proposed intrabody pipeline. Antibodies obtained from this library will be screened for functionality using a novel yeast-two-hybrid approach and have numerous downstream applications. This high-throughput pipeline is amenable to automation and can be scaled up to thousands of domains, resulting in the potential generation of many novel therapeutic reagents.

The colony formation assay (CFA) is the gold standard for measuring cytotoxic effects on cells. To increase efficiency, the CFA was converted to a 96-well format using an automated colony counting algorithm. The 96-well CFA was validated using ionizing radiation (IR) on the FaDu and A549 cancer cell lines. Its ability to evaluate combination therapies was investigated using cisplatin and IR. The 96-well CFA was transferred to a robotic platform for evaluation as a high-throughput screen (HTS) readout for the discovery of novel anti-cancer compounds, and radiosensitizers. Screening yielded eight putative anti-cancer hits, and five putative radiosensitizing hits. Secondary screening confirmed 6/8 anti-cancer compounds, and 0/5 radiosensitizing compounds. Thus, the 96-well CFA can be adopted as an alternative assay to the 6-well CFA in the evaluation of cytotoxicity in vitro, providing a possible readout to be utilized in HTS for discovering anti-cancer compounds, but with limited applicability in discovering radiosensitizers.

<div><p>Wheat is among the most important cereal crops in the world today with respect to the area harvested (219 million ha), production (772 million tonnes), and productivity (3.53 tons/ha). However, global wheat production goals for the coming decades are falling short of needed increases. Among the leading factors hindering yields is abiotic stress which is present in nearly 38% of wheat acres globally. Nevertheless, many standard wheat breeding programs focus on yield and yield related traits (i.e. grain yield, plant height, and test weight) in ideal environments rather than evaluating traits that could lead to enhanced abiotic stress tolerance. In this thesis, we explore the use of root and high-throughput phenotyping strategies to aid in further development of abiotic stress tolerant varieties. </p><p>In the first three experiments, root phenotypes were evaluated in two nitrogen (N) treatments. Over a series of seedling, adult, and multiple-growth-stage destructive plant biomass measurements, above-ground and below-ground traits were analyzed in seven geographically diverse wheat accessions. Root and shoot biomass allocation in fourteen-day-old seedlings were analyzed using paper-roll-supported hydroponic culture in two Hoagland solutions containing 0.5 (low) and 4.0 (high) mM of N. Root traits were digitized using a WINRhizo platform. For biomass analysis at maturity, plants were grown in 7.5-liter pots filled with soil mix using the same concentrations of N. Traits were measured as plants reached maturity. In the third N experiment, above- and below-ground traits were measured at four-leaf stage, stem elongation, heading, post-anthesis, and maturity. At maturity, there was a ~15-fold difference between lines with the largest and smallest root dry matter. However, only ~5-fold difference was observed between genotypes for above-ground biomass. In the third experiment, root growth did not significantly change from stem elongation to maturity. </p><p>In the final experiment, two of these lines were selected for further evaluation under well-watered and drought treatments. This experiment was implemented in a completely randomized design in the Controlled Environment Phenotyping Facility (CEPF) at Purdue University. The differential water treatments were imposed at stem elongation and continued until post-anthesis, when all plants were destructively phenotyped. Image-based height and side-projected area were associated with height and shoot dry matter with correlations of r=1 and r=0.98, respectively. Additionally, 81% of the variation in tiller number was explained using convex hull and side-projected area. Image-based phenotypes were used to model crop growth temporally, through which one of the lines was identified as being relatively more drought tolerant. Finally, the use of the Munsell Color System was explored to investigate drought response.</p><p>These experiments illustrate the value of phenotyping and the use of novel phenotyping strategies in wheat breeding to increase adaptation and development of lines with enhanced abiotic tolerance.</p></div><br>

Thesis advisor: Charles S. Hoffman / The biological roles of the most recently discovered mammalian cyclic nucleotide phosphodiesterase (PDE) family, PDE11, are poorly understood, in part due to the lack of selective inhibitors. To address this need for such compounds I completed a ~200,000 compound high throughput screen (HTS) for PDE11 inhibitors using a yeast-based growth assay. Further characterization of lead candidates using both growth-based assays in the fission yeast Schizosaccharomyces pombe and in vitro enzyme assays identified four potent and selective PDE11 inhibitors. I examined the effect of these compounds on human adrenocortical cells, where PDE11 is believed to regulate cortisol levels. One compound, along with two structural analogs, elevates cAMP levels and cortisol production through PDE11 inhibition, thus phenocopying the behavior of adrenocortical tumors associated with Cushing syndrome. These compounds can be used as research tools to study the biological function of PDE11, and can also serve as leads to develop therapeutic compounds for the treatment of adrenal insufficiencies. This study further validates the yeast-based HTS platform as a powerful tool for the discovery of potent, selective and biologically-active PDE inhibitors. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Biology.