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Asymmetric Synthesis Of Bioactive Scaffolds Via Organocatalysis, Melody Guo

Yale Graduate School of Arts and Sciences Dissertations

Chiral catalysts allow chemists to access enantioenriched materials without the use of proportionate amounts of chiral reagents, while lowering the energy barrier of the original reaction. One way to form bioactive, heteroatom-containing scaffolds asymmetrically is through the use of chiral organocatalysts. This dissertation covers the development of stereoselective reaction methodology to access bioactive scaffolds and mechanistic investigations into intriguing features therein. Chapter 1 describes the development of the asymmetric synthesis of axially chiral quinazolinones. In this project, complementary applications for two different scaffold classes of chiral phosphoric acid (CPA) catalysts are found. We observe that while a C2-symmetric CPA catalyst …

Interpretable And Data-Driven Machine Learning Models For Analyzing High-Dimensional Biological Data, Junchen Yang

Yale Graduate School of Arts and Sciences Dissertations

High-dimensional biological data, including single-cell omics, are prevalent in modern biology for characterizing a wide range of biological processes and phenomena. Although our capacity to generate such data has expanded at an unprecedented pace, significant challenges remain in extracting the informative features and the underlying biological signals. In particular, these datasets not only exhibit high dimensionality but also suffer from issues including inherent noise, low signal-to-noise ratio, and intrinsic heterogeneity. While machine learning models hold great promise for analyzing such data, their complexity and sensitivity to data characteristics often impede biological interpretability. To address these interconnected challenges, this thesis develops …

Studies On The Structural Basis Of Oxygenic Photosynthesis, David Flesher

Yale Graduate School of Arts and Sciences Dissertations

Oxygenic photosynthesis — performed on all seven continents by green plants, algae, and cyanobacteria — supports the global biome through its ability to capture and store light energy. This is achieved through a series of protein complexes collectively known as the photosynthetic apparatus. During my PhD research, I’ve investigated the structural basis for how these protein complexes capture this light energy and transduce it to redox energy. My thesis work, summarized in this dissertation, can be grouped in two broad research themes: (i) structural studies on Nature’s water oxidation reaction, explored in Part I of this dissertation; and (ii) the …

Light Sheet Microscopy For 3d Nanoscale Imaging, Hannahmariam Mekbib

Yale Graduate School of Arts and Sciences Dissertations

Advances in expansion microscopy, a super resolution microscopy technique in which samplesare expanded up to ~8,000 times their original volume, require new microscope modalities to image the large sample sizes. These new techniques should be suitable for imaging large sample volumes, yet need to maintain the high 3D resolution of 250-500 nm of high-end confocal microscopy to provide the maximum level of detail and thereby reveal nanoscale cellular ultrastructure. Axially Swept Light Sheet Microscopy (ASLM) has emerged as a promising technique for generating high-resolution images at high-throughput. However, current designs struggle with the trade-off between limited resolution and field-of-view (FOV) …

Integrated Multiscale Mechano-Biological Study Of Lung And Liver Tissues, Hugh Xiao

Yale Graduate School of Arts and Sciences Dissertations

Tissues and bodily fluids undergo continuous changes as a natural life cycle process. Extracellular matrices (ECMs), which provide structural and biochemical support for the cells, and extracellular fluids (ECFs), which transport nutrients, oxygen, and waste products, exhibit several mechanical properties that can impact cell behaviors. These properties include, for example, fibrillar alignment, density, and stiffness of ECMs, and osmolarity and viscosity of ECFs. These mechano-biological cues can impact cell behaviors and change tissue landscapes. Fibrosis is known for thickened extracellular matrix, which involves many changes in mechanical properties of extracellular environment. There is much to be explored as to how …

The Role Of Alkbh1 In The Epigenetic Regulation Of Extraembryonic Development And Early Embryogenesis, Myles Harris Alderman Iii

Yale Graduate School of Arts and Sciences Dissertations

Successful embryogenesis requires regulated and organized stem cell differentiation from the very first cell fate decision through terminal differentiation of daughter cells within tissues. A key regulatory mechanism of stem cell differentiation and cellular identity is epigenetic regulation, whereby sequence-preserving modifications to individual bases of DNA and histone-modifications work in concert to regulate nucleosome deposition and chromatin accessibility. The past several decades of stem cell and epigenetics research have uncovered a complex regulatory environment during placental development that is not only necessary for the propagation of any mammalian species or individual, but approximates that of malignant disease. Studying the basic …

Functionalized Dna Nanostructures For Membrane Engineering, Qiancheng Xiong

Yale Graduate School of Arts and Sciences Dissertations

DNA nanotechnology is a powerful tool for constructing precisely designed nanostructures with applications in diverse fields, including synthetic biology, nanomedicine, and biomolecular engineering. This dissertation explores the use of DNA nanotechnology in membrane engineering, focusing on developing DNA endoskeleton-supported membranes and large functionalized DNA-toxin nanopores. The first approach encountered challenges while constructing interlocked DNA nanostructures for endoskeleton-supported membranes. The negative results highlighted the need to optimize the interlocked DNA endoskeleton cage design further to ensure its practical application in templating fully exposed, continuous membranes. The second approach incorporated pneumolysins into DNA-origami channels to create large, functionalized DNA-toxin nanopores. These hybrid …

Engineering The Emergent Properties Of Complex Communities, Chang-Yu Chang

Yale Graduate School of Arts and Sciences Dissertations

Microorganisms perform critical functions throughout the biosphere and in biotechnology: from the biogeochemical cycle to the production of sourdough. The overwhelming majority of these functions are usually emergent from the collective outcomes of a large number of microorganisms living in a diverse community. Controlling and manipulating the functions of complex microbial communities is a major aspiration in modern biology. However, we lack a quantitative understanding of how often these functions are emergent, and when it occurs, how we can engineer the emergent properties of microbial communities. In this dissertation, I combine computational approaches with experiments using microbial communities to explore …

Uncovering The Function And Molecular Mechanism Of Mili In Mouse Germline Stem Cells, Yuqi Wang

Yale Graduate School of Arts and Sciences Dissertations

Mouse germline stem cells (GSCs) play critical roles in spermatogenesis by self-renewal and differentiation into daughter spermatogonia. Like other stem cells, the proper functions of mouse GSCs are governed by a delicate regulatory network. PIWI proteins belong to the Argonaute protein family, and they act with piRNAs to control gene expression through transcriptional and post-transcriptional regulation. Extensive research has demonstrated the vital functions of PIWI proteins in germline development, stem cell maintenance, and transposon control. Despite this, the role of PIWI in mammalian GSCs remains largely unknown. MILI is one of three murine PIWI proteins. Recent study has discovered that …

Internal And External State-Dependent Modulation Of Visual Perception And Cortical Processing, Mitchell Paul Morton

Yale Graduate School of Arts and Sciences Dissertations

The ability of humans and other animals to perceive and understand stimuli in the visual world is substantially modulated by internal and external states. Internal states, such as arousal and attention, influence how we can perceive stimuli even when the physical characteristics of that stimulus are constant. Additionally, external configuration of objects in the visual world can influence our perceptual abilities, even when other characteristics remain unchanged. We first studied internal state-dependent modulation of perception by examining what states were associated with accurate perception at threshold, a condition in which the physical properties of a stimulus remain constant, and a …

Monitoring Translation Regulation By Structured Rna Elements, Caroline Focht

Yale Graduate School of Arts and Sciences Dissertations

Translation initiation across domains of life is a tightly regulated process, and functional RNA motifs are critical regulatory features. This dissertation largely focuses on developing a novel technique with which to quantify the effect these RNA elements have on translation initiation and on unraveling the functional requirements of these structures. I have leveraged RelE’s ribosome-dependent endonuclease activity to develop a quantitative assay for translationally regulated mRNAs and validated this method on two bacterial translational riboswitches. I have also demonstrated its applicability to eukaryotic systems by showing that RelE can measure isoform-driven differences in ribosome loading between yeast 5′ leader sequences. …

Understanding Distinct Roles Of Egfr Family Mutations In Different Cancers, Chun Hu

Yale Graduate School of Arts and Sciences Dissertations

The epidermal growth factor receptor (EGFR) is frequently mutated in human cancer and is an important therapeutic target. EGFR inhibitors have been successful in lung cancer, where mutations in the intracellular tyrosine kinase domain activate the receptor, but not in glioblastoma multiform (GBM), where mutations occur exclusively in the extracellular region. In this dissertation, I show that common extracellular GBM mutations prevent EGFR from discriminating between its activating ligands. Different growth factor ligands stabilize distinct EGFR dimer structures that signal with different kinetics to specify or bias outcome. EGF itself induces strong symmetric dimers that signal transiently to promote proliferation. …

Translational Systems Metabolism In Health And Disease, Brooks Phillip Leitner

Yale Graduate School of Arts and Sciences Dissertations

The breakdown, synthesis, and interconversion of macronutrients is essential to sustaining life and driving pathological mechanisms rooted in disease. With attempts to combat the metabolic underpinnings of disease, it has become clear that focus on individual metabolites, proteins, or genes cannot fully explain the complexity of dysregulated metabolism in systemic conditions such as obesity, cancer, and sepsis. With the advent of accessible Omics techniques and hordes of open access data it has become possible to study metabolism as a whole—at the level of gene transcription, translation, and metabolism. A major goal of this PhD thesis was to integrate isotope tracing …

Synthetic Studies Of Colibactin, A Carcinogenic Gut Microbiome Metabolite, Kevin Mark Wernke

Yale Graduate School of Arts and Sciences Dissertations

The human microbiota is now understood to be intimately linked to host physiology. Recent studies indicate that microbiota species which possess a biosynthetic gene cluster – termed clb – contribute to the development and progression of colorectal cancer. Bacteria possessing the clb gene cluster are correlated to colorectal cancer (CRC) in humans, initiate colonic tumor and polyp formation in murine models, and induce DNA interstrand cross-links in cell models. Furthermore, clb+ bacteria induce a unique mutational signature which has been detected in a number of human tumor samples. Early studies by Oswald and co-workers established that the final product of …

The Role Of Mink1 In Congenital Heart Disease: Regulation Of Spemann Organizer Cell Fate And Multiciliated Cell Specification, Vaughn Colleluori

Yale Graduate School of Arts and Sciences Dissertations

Congenital Heart Disease (CHD) is the most common birth defect and leading cause of infant mortality, yet molecular mechanisms explaining CHD remain mostly unknown. Sequencing studies are identifying CHD candidate genes at a brisk rate including MINK1, a serine/threonine kinase. However, a plausible molecular mechanism connecting CHD and MINK1 is unknown. Here, we reveal that mink1 is required for proper heart development due to its role in left-right patterning. Mink1 regulates canonical Wnt signaling to define the cell fates of the Spemann organizer and the Left-Right Organizer, a ciliated structure that breaks bilateral symmetry in the vertebrate embryo. To identify …

The Parkinson’S Gene Vps13c Encodes An Er-Lysosome Lipid Transfer Protein Linking Lysosomal Lipid Homeostasis And Cgas/Sting-Mediated Innate Immunity, William Franklin Hancock-Cerutti

Yale Graduate School of Arts and Sciences Dissertations

Biallelic loss-of-function mutations in VPS13C cause early-onset Parkinson’s Disease (PD), and the VPS13C locus is a GWAS hit for sporadic PD risk. VPS13C is a member of the VPS13 family, which in humans contains three other proteins, VPS13A, VPS13B, and VPS13D, all with ties to neurological diseases. Mutations in VPS13A cause chorea-acanthocytosis a Huntington’s like syndrome with dysmorphic erythrocytes, mutations in VPS13B cause the neurodevelopmental disorder Cohen syndrome, and mutations in VPS13D cause spastic ataxia with varying presentation. The molecular function of these proteins, why their loss cause neurological diseases, and why they are each associated with distinct diseases despite …

Riboswitches As Versatile Scaffolds For Ligand Recognition And As Tools For Drug Discovery, Harini Sadeeshkumar

Yale Graduate School of Arts and Sciences Dissertations

Riboswitches are highly structured, noncoding RNAs that bind specific ligands to regulate gene expression. To date, over fifty riboswitch classes have been validated to control fundamental biological processes and recognize various coenzymes, nucleotides, signaling molecules, ions, and other important ligands. As described in Chapter 1, careful study of these various riboswitches reveals an incredible diversity in their structural and biochemical characteristics as well as their function. Herein is detailed the efforts to validate long-standing orphan riboswitch classes involved in essential cellular functions such as maintaining nucleotide pools, managing ion toxicity, osmoregulation, and ATP production.The ykkC family of riboswitches are a …

Engineering Functional Distal Lung Epithelium, Katherine Leiby

Yale Graduate School of Arts and Sciences Dissertations

The potential for lung tissue engineering to generate lung tissue capable of gas exchange ultimately rests upon the ability to reconstitute a functional barrier between the air and blood spaces in the engineered lung alveolus. The success of this endeavor will rely in large part on the recapitulation of an alveolar epithelium, comprising alveolar epithelial type 1 cells (AEC1s) and type 2 cells (AEC2s), which provides a surface for gas diffusion, actively maintains critical features of blood-gas barrier function, and comprises resident AEC2 stem cells for ongoing maintenance and repair of the distal lung. Yet, since the beginning of this …

Molecular Mechanisms Of Atg-9 Localization And Function In Neurons, Sisi Yang

Yale Graduate School of Arts and Sciences Dissertations

Autophagy is a cellular degradation pathway essential for neuronal health andfunction. Autophagosome biogenesis occurs at synapses, is locally regulated and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In my thesis work, I determine that trafficking of ATG-9, the only transmembraneprotein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP- 3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in …

Studies Towards The Synthesis Of Diaporthein B And Studies Towards The Synthesis Of Darobactin A, Ian Tingyung Hsu

Yale Graduate School of Arts and Sciences Dissertations

In the first chapter of this thesis, I describe the development of two convergent, fragment-based strategies to prepare the oxidized carbon scaffold of diaporthein B (1). Diaporthein B (1), initially isolated from the fungal genus Diaporthe, is an antimycobacterial pimarane diterpene that exhibited a minimum inhibitory concentration (MIC) of 3.1 µg⋅mL–1 against M. tuberculosis, as well as half-maximal inhibitory concentrations of 1.5–3 µM against HCT and LoVo colon cancer cell lines. The first synthetic approach towards diaporthein B (1) furnished the tricyclic carbon skeleton 154 in 9 steps from (R)-carvone through a diastereoselective 1,2-addition between two elaborated cycloalkenones, a novel …

Nutrition And Hookworm Infection: A Causal Analysis Of The Literature, Mengting Su

Public Health Theses

Hookworm infection is one of the neglected tropical diseases, particularly in low and middle-income countries, but we know relatively little about causal evidence related to malnutrition. This is mainly due to the relatively small research community compared to those investigating the impact of hookworm infection on host nutritional status and disease complications. Causal inference is critical in epidemiology and biomedical research because it can be a powerful tool in enlightening prevention efforts and developing etiology models. The application of causal criteria to address complex epidemiological research questions is indeed helpful in proposing more interventions to improve the health and well-being …

Tracking Single Cell Lineages In Saccharomyces Cerevisiae, Guste Urbonaite

Yale Graduate School of Arts and Sciences Dissertations

The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce yeast DropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. I modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the …

Co-Distribution Of Ambient Light At Night And Incidence Of Human Cancers And Covid-19, Yidan Meng

Public Health Theses

Introduction and BackgroundThere are increasing concerns about the effects of artificial lights on human health, including hormone-related disease and immune functions. In January 2020, the outbreak of COVID-19 disrupted everyone’s life, and people who infected have various severity. Thus, we want to analyze whether people exposed to different ambient light at night (LAN) levels make them more susceptible to COVID-19 for our summer research. Besides the effects of LAN on immune functions, we also discussed the association of LAN and multiple cancers in seven states of Northeastern U.S. We used similar statistical and geographic analysis methods and separate them into …

Classic Article: On The Oxidation Of Organic Matter In Marine Sediments By Bacteria, Selman A. Waksman, Margaret Hotchkiss

Journal of Marine Research

The question as to whether the organic matter in the sea bottom is inert or is available as a nutrient for the bottom fauna and bottom-inhabiting bacteria is a problem of special interest in the cycle of life in the sea. A number of marine animals, making up the benthos or the bottom fauna, must depend upon this organic matter for their nutrition while the sea bottom also harbors an extensive bacterial population which require the energy to be derived from various nutrient elements for cell synthesis and respiration...

Medicine@Yale November/December 2017 Volume 13, Issue 4, Yale School Of Medicine Office Of Communications

Medicine@Yale - development newsletter

Medicine@Yale : advancing biomedical science, education and health care was a print and online newsletter which published news about academics, research and philanthropy for alumni, donors, faculty, students and the general public. It was initially published 6 times a year and then changed to a quarterly schedule. The first issue came out June/Jul. 2005. The final issue was published in May/June 2022, vol. 17, issue 1. Published by Yale School of Medicine, Office of Communications.

Racial Disparities In Renal Cell Carcinoma: A Single Payer Healthcare Experience, Abiodun Mafolasire

Yale Medicine Thesis Digital Library

Introduction: Significant racial disparities in survival for renal cell carcinoma (RCC) exist between whites and blacks. Differences in access to care and comorbidities are possible contributors. To investigate if racial disparities persist when controlling for access to care, we analyzed data from a single payer healthcare system.

Methods: As part of a case-control study within the Kaiser Permanente Northern California system, pathologic and clinical records were obtained for RCC cases (2,152 white, 293 black) diagnosed from 1998 to 2008. Patient demographics, comorbidities, tumor characteristics, and treatment status were compared between whites and blacks. Overall survival and disease specific survival (DSS) …

Salivary Cortisol As A Measure Of Stress Reactivity In Adolescents With Psychiatric Disorders, Cortlyn Wilhelmina Brown

Yale Medicine Thesis Digital Library

Objective: The aims of this study were to 1) examine salivary cortisol distributions in a nationally representative sample of U.S. adolescents; and to 2) evaluate whether youth with mood and anxiety disorders are associated with differential salivary cortisol response to an acute mild stressor.

Background: An association between mood disorders and hypothalamic-pituitary-adrenal (HPA) axis dysfunction, as indicated by elevated levels of cortisol, has been well established [1, 2]. Although studies have suggested that these differences emerge early in the development of mood disorders in children and adolescents [3] the samples have generally been very small and primarily derived from clinical …

Identification Of Fetal Genomic Copy Number Deletions Associated With Preeclamptic Mothers In The Caucasian Population, Tze-An Yuan

Public Health Theses

Genetic determinants that are associated with preeclampsia still remain elusive

nowadays, which might have resulted from limited understanding of the underlying

pathogenesis mechanisms and the fetal contributions. By using genome-wide association study approach, we identified 2 candidate copy number deletions of the highest odds ratio ranking on chromosome 1 and 19, from 283 US white babies born by the mothers with preeclampsia. Based on the molecular and biological functions of the genes entailed the deleted regions, which contain CTSK, ARNT, and ACTN4, we proposed that these two candidate genomic deletions might be associated with preeclampsia. In a further attempt to …

Spatial Distribution And Sociodemographic Composition Of High Grade Cervical Lesion Clusters In Connecticut 2008-2013, Aref Senno

Public Health Theses

Introduction: HPV is necessary for the development of invasive cervical cancer. There were 530,000 cases and 275,000 deaths attributable to cervical cancer in 2008. Since the introduction of HPV vaccines in 2006, the incidence of high grade cervical lesions (HGCL)—precancerous lesions which may develop into cervical cancer—has decreased significantly. Some changing sociodemographic trends in disease burden have been previously reported since 2008.

Objectives: The objectives of this analysis were to identify regions of Connecticut with high rates of HGCLs and to describe how trends of disease changed over time in the post-vaccine era.

Methods: This is a descriptive analysis of …

The Effect Of E-Cadherin Loss On Melanoma Formation And Metastasis, Lara Rosenbaum

Yale Medicine Thesis Digital Library

Melanoma is the most lethal form of skin cancer and accounts for the majority of skin cancer related mortality. Early metastases are characteristic of melanoma and are an ominous sign, as current therapeutic interventions have little effect on overall survival. The lack of accurate prognostic indicators and effective therapies emphasize the need for a better understanding of the genetic and phenotypic changes in melanoma formation and progression. One such change is the loss of E-cadherin, which normally plays a role in cell-cell adhesion and is thought to be a central feature of epithelial-mesenchymal transition (EMT). Maintenance of E-cadherin in melanoma …