Organic chemistry is an enabling science, that has given scientist the ability to construct and manipulate small molecules. The relationship that bridges the classic study of chemical reactivity and synthesis at the molecular level with the broader field of the life sciences continues to flourish and has expanded its impact tremendously. The study of complex, bioactive small molecules, their synthesis, and the development of new reactions has laid the foundation for many of these advancements to build upon. The contents of this thesis contribute to this goal and hope to be of use for future generations and the development of the field.
\r\n\r\nThe first chapter describes the total synthesis of the furanobutenolide-derived norcembranoid diterpenoid ineleganolide, a secondary metabolite produced by sinularia soft corals. Displaying cytotoxic bioactivity, the chemical structure has intrigued chemists for several decades. We describe a successful synthesis of the natural product in 14 steps, enabled by several unique cascade reactions.
\r\n\r\nThe second chapter details the total synthesis of Lycojapomine A and B, two members of the lycopodium alkaloids. To achieve a practical and concise synthetic route, we developed a photoreaction for the stepwise dearomatization of a pyrrole heterocycle. Building off the simple and easily accessible starting material, we can synthesize each of the complex target molecule in 13 steps.
\r\n\r\nInspired by the previously utilized photochemistry, the third chapter details a new catalytic method for the generation of alkyl radicals directly from alcohols. We achieved this transformation by photo irradiation of a titanium porphyrin catalyst and showcase its ability to deoxygenate several different alcohols, by generation of the carbon-centered radical.
", "doi": "10.7907/4sc5-0e50", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18700", "collection": "thesis", "collection_id": "18700", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292026-200819986", "primary_object_url": { "basename": "PhD-Thesis-RJ-Chadha-Final.pdf", "content": "final", "filesize": 69956436, "license": "other", "mime_type": "application/pdf", "url": "/18700/1/PhD-Thesis-RJ-Chadha-Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Stimulated Raman Imaging for Spatial Metabolomics: From Metabolite Mapping to Cellular Function", "author": [ { "family_name": "Chadha", "given_name": "Rahuljeet Singh", "orcid": "0000-0002-3805-6144", "clpid": "Chadha-Rahuljeet-Singh" } ], "thesis_advisor": [ { "family_name": "Wei", "given_name": "Lu", "orcid": "0000-0001-9170-2283", "clpid": "Wei-Lu" } ], "thesis_committee": [ { "family_name": "Semlow", "given_name": "Daniel R.", "orcid": "0000-0001-6538-9713", "clpid": "Semlow-D-R" }, { "family_name": "Stoltz", "given_name": "Brian M.", "orcid": "0000-0001-9837-1528", "clpid": "Stoltz-B-M" }, { "family_name": "Karthikeyan", "given_name": "Smruthi", "orcid": "0000-0001-6226-4536", "clpid": "Karthikeyan-Smruthi" }, { "family_name": "Wei", "given_name": "Lu", "orcid": "0000-0001-9170-2283", "clpid": "Wei-Lu" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Metabolism encompasses the full network of chemical reactions sustaining life- the creation, utilization, and storage of biologically active small molecules known as metabolites. Understanding how these molecules are organized in space and real time, at the subcellular level, has long been a fundamental bottleneck in advancing our knowledge of cellular metabolism. In recent years, stimulated Raman scattering (SRS) microscopy has emerged as a powerful approach to visualize metabolism directly in living systems, offering high sensitivity, chemical selectivity, and a non-destructive imaging modality uniquely suited to longitudinal studies. Despite these attributes, metabolic imaging with SRS remains in its early stages relative to the well-established fluorescence-based and mass spectrometry imaging methods that dominate the field.
\r\n\r\nTherefore, this thesis aims to push the boundaries of SRS microscopy toward quantitative, spatially resolved metabolomics to enable direct visualization of metabolic activity in living systems. By applying emerging Raman probes across diverse biological systems, this work reveals metabolic vulnerabilities that deepen insight into disease mechanisms and can inform therapeutic development.
\r\n\r\nIn Chapter 1, we introduce metabolic imaging using SRS microscopy and underscore its unique advantages for longitudinal imaging in living biosystems. We cover both label-free (untargeted) and labeled (targeted) approaches using SRS to probe metabolism in situ. We discuss both the advantages and current limitations of SRS microscopy and propose strategies for integrating it with complementary functional \u201c-omics\u201d techniques to gain deeper insight into cellular metabolism.
\r\n\r\nIn Chapter 2, we explore the use of untargeted SRS microscopy to non-invasively characterize the chemical landscape of engineered living materials (ELMs) in real-time. By correlating spectral data with the mechanical properties of genetically modified biofilms, we find multiscale metabolic heterogeneity within these systems. This approach enables quantitative, real-time monitoring of ELMs that would enable improved design in applications spanning biomedicine, sustainability, and responsive materials.
\r\n\r\nIn Chapter 3, we utilize targeted SRS microscopy to tackle critical questions in cardiovascular health with a focus on understanding the metabolic basis of diabetes. In collaboration with the Chen Lab at City of Hope Medical Center and the TeSlaa lab at UCLA, we observe glycogen accumulation in live endothelial cells under diabetic stress. By imaging glutamine and lactate metabolism using Raman probes for the first time in this system, we reveal how intracellular glycogen pools shape early metabolic adaptations in the endothelium during glucose deprivation- providing new insight into the vascular ramifications of hyperglycemia.
\r\n\r\nIn Chapter 4, we introduce MATRIX-SRS (Metabolic Activity TRacing of the trIcarboXylic acid cycle by Stimulated Raman Scattering microscopy), a platform for spatially resolved, quantitative imaging of TCA cycle activity in live cells. By combining deuterium-labeled metabolic probes with hyperspectral stimulated Raman scattering microscopy, we directly visualize and map TCA-associated metabolism at subcellular resolution. We next integrate density functional theory (DFT) with reaction network modeling to develop a robust in situ quantification pipeline in live cells. Using this approach, we identify a global attenuation of TCA activity during epithelial-to-mesenchymal transition (EMT) and, for the first time, achieve absolute quantification of deuterium-labeled biomass in live cells under native and drug-treated conditions, establishing a general framework for live-cell spatial metabolomics.
\r\n\r\nIn Chapter 5, we present MetaboRamics, highly multiplexed metabolic imaging using stimulated Raman for spatial metabolomics in live cells. Through rational probe design, isotope editing, and robust spectral unmixing, we establish a 16-color metabolic palette spanning key pathways alongside endogenous protein, lipid, and redox signals, with organelle-targeted probes enabling spatial interactomics. We apply this high-content platform to EMT to observe a global metabolic rewiring in mesenchymal cells. We further resolve subcellular adaptations under diverse metabolic stress conditions in live epithelial cells. MetaboRamics enables 16-plex, subcellular metabolomics in living systems and opens new avenues for applications in drug discovery and clinical diagnostics.
\r\n\r\nThrough these studies, I demonstrate the power of stimulated Raman imaging for subcellular, spatiotemporal metabolomics to visualize metabolism in living systems and uncover its roles in both health and disease.
", "doi": "10.7907/n5c3-jw36", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" }, { "id": "thesis:18748", "collection": "thesis", "collection_id": "18748", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-194656412", "primary_object_url": { "basename": "Maria_Altshuller_PhD_Thesis.pdf", "content": "final", "filesize": 266738599, "license": "other", "mime_type": "application/pdf", "url": "/18748/1/Maria_Altshuller_PhD_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Molecular Mechanisms of DNA Interstrand Cross-Link Repair by the Fanconi Anemia Pathway", "author": [ { "family_name": "Altshuller", "given_name": "Maria", "orcid": "0009-0006-8174-7713", "clpid": "Altshuller-Maria" } ], "thesis_advisor": [ { "family_name": "Semlow", "given_name": "Daniel R.", "orcid": "0000-0001-6538-9713", "clpid": "Semlow-Daniel-R" } ], "thesis_committee": [ { "family_name": "Shan", "given_name": "Shu-ou", "orcid": "0000-0002-6526-1733", "clpid": "Shan-Shu-ou" }, { "family_name": "Dunphy", "given_name": "William G.", "orcid": "0000-0001-7598-8939", "clpid": "Dunphy-W-G" }, { "family_name": "Guttman", "given_name": "Mitchell", "orcid": "0000-0003-4748-9352", "clpid": "Guttman-M" }, { "family_name": "Voorhees", "given_name": "Rebecca M.", "orcid": "0000-0003-1640-2293", "clpid": "Voorhees-R-M" }, { "family_name": "Semlow", "given_name": "Daniel R.", "orcid": "0000-0001-6538-9713", "clpid": "Semlow-D-R" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "DNA interstrand cross-links (ICLs), which consist of a covalent link between complementary DNA strands, are among the most cytotoxic lesions that cells encounter, as the ICL blocks strand separation during replication and transcription. The Fanconi anemia (FA) pathway is the primary mechanism through which proliferating cells repair ICLs encountered during DNA replication, and mutations in FA pathway genes cause the inherited bone marrow failure and cancer predisposition syndrome Fanconi anemia. Despite considerable progress in elucidating the molecular mechanism of FA pathway-mediated ICL repair, fundamental questions remain about how specific ICL substrates are processed and how the replication fork dynamics that accompany repair are regulated. This thesis addresses these questions using cell-free extracts prepared from Xenopus laevis eggs, which enable biochemical characterization of ICL repair. We first investigated the repair of ICLs induced by colibactin, a gut microbiome-derived genotoxin implicated in the pathogenesis of colorectal cancer. We demonstrate that the FA pathway is responsible for replication-coupled repair of colibactin-induced ICLs and identify the translesion synthesis polymerases that bypass the unhooked ICL remnant, providing mechanistic insight into how cells process this clinically relevant lesion. We then uncovered a phosphoregulatory axis governing replication fork dynamics during ICL repair, showing that the ataxia-telangiectasia mutated (ATM) kinase promotes nucleolytic resection of reversed fork intermediates through the nucleases EXO1 and DNA2-WRN, and that this resection is constrained by opposing PP2A phosphatase activity. This regulatory mechanism ensures productive fork restoration. Finally, we present preliminary evidence that X-shaped replication intermediates are sufficient to activate FA pathway signaling and ICL unhooking in the absence of ongoing replication, suggesting that these structures may serve as the trigger for FA pathway activation independently of the replisome. Taken together, this work advances our mechanistic understanding of how cells tolerate ICL stress and illuminates regulatory mechanisms that ensure accurate and efficient ICL repair.", "doi": "10.7907/tqmn-gv72", "publication_date": "2026", "thesis_type": "phd", "thesis_year": "2026" } ]