Pollution-intensive industrial manufacturing processes threaten the health of ecosystems and societies through toxic waste streams and energy intensive processes that lead to greenhouse gas emissions. Biological systems present more sustainable routes to many useful industrial chemicals by using enzymes at low temperatures, but the time and effort required to optimized...
Genetic studies have found variants in the protein-degrading autophagy-lysosomal pathway (ALP) to be among the most common risk factors for developing Parkinson’s disease (PD). Macroautophagy (MA) is the arm of this pathway which delivers cytosolic components to lysosomes for degradation and is essential for neuronal health. The defining pathological protein...
SCN2A encodes the NaV1.2 voltage-gated sodium channel, which is thought to contribute to the development of the central nervous system. Pathogenic variants in SCN2A have been associated with neurodevelopmental disorders (NDD), including developmental and epileptic encephalopathies (DEE), intellectual disability (ID), and autism spectrum disorder (ASD). These disorders represent a significant...
Pediatric high-grade gliomas (pHGGs) are aggressive pediatric CNS tumors and an important subset are characterized by mutations in H3F3A, the gene that encodes Histone H3.3 (H3.3). Substitution of Glycine at position 34 of H3.3 with either Arginine or Valine (H3.3G34R/V), was recently described and characterized in a large cohort...
Autism spectrum disorder (ASD) and intellectual disability (ID) are two of the most highly prevalent neurodevelopmental disorders (NDDs), each affecting roughly 2% of the population. Despite the need for therapies, few exist due to a myriad of challenges, such as the complex underlying genetic etiology and historic inaccessibility of neural...
CD95/Fas ligand (CD95L) is a well characterized activator of extrinsic apoptosis. CD95L protein binds to its cognate receptor, CD95/Fas/APO-1, inducing apoptotic signaling in sensitive cells. However, expression of CD95L is toxic even in the absence of CD95. We previously reported that the CD95L open reading frame (ORF) is enriched for...
CD95/Fas ligand (CD95L) is a well characterized activator of extrinsic apoptosis. CD95L protein binds to its cognate receptor, CD95/Fas/APO-1, inducing apoptotic signaling in sensitive cells. However, expression of CD95L is toxic even in the absence of CD95. We previously reported that the CD95L open reading frame (ORF) is enriched for...
Tumor-initiating cells with reprogramming plasticity are thought to be essential for cancer development and metastatic regeneration in many cancers; however, the molecular mechanisms are not fully understood. We have previously identified that CD44, a breast tumor-initiating cell marker, drives mammosphere self-renewal and multicellular aggregation of circulating tumor cell (CTC) clusters,...
The ability to regenerate lost tissues or organs is widespread in the animal kingdom, but the mechanistic basis underpinning this process is incompletely understood. The planarian flatworm Schmidtea mediterranea has an incredibly robust and flexible capacity for regeneration, able to regenerate an entire organism from arbitrary starting points. This makes...
Genetic variation in genes regulating metabolism may be advantageous in some settings but not others. The non-failing adult heart relies heavily on fatty acids as a fuel substrate and source of ATP. In contrast, the failing heart favors glucose as a fuel source. A bootstrap analysis for genes with deviant...
For some inducible genes, the rate and molecular mechanism of transcriptional activation depend on the prior experiences of the cell. This phenomenon, called epigenetic transcriptional memory, accelerates reactivation, and requires both changes in chromatin structure and recruitment of poised RNA polymerase II (RNAPII) to the promoter. A well-established model for...
Ensuring adequate water quality is essential for human health and for effective allocation of resources in agriculture, energy, and manufacturing. However, the current state-of-the-art for water quality testing requires expensive equipment and technical expertise to analyze samples and takes days to obtain results from off-site labs, making it inaccessible to...
SAMDI-MS, which stands for self-assembled monolayers (SAMs) for matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS), is a powerful tool that has enabled the development of novel high-throughput screening and experimentation methods for decades. SAMDI-MS works by immobilizing analytes to functionalized SAMs prior to MS analysis and is capable of...
Reproduction requires a complex orchestration of processes from the formation of the reproductive system through the successful development of the fetus, and nutrients are necessary to fuel these processes during many aspects of reproduction. Zinc is an essential metal that is fundamental in gamete maturation, gonadogenesis, and fertilization. Disruption in...
Methanotrophs, bacteria that can metabolize methane, remain a promising solution to mitigating the effects of climate change by removing atmospheric methane and converting it to useful chemical precursors. However, a full understanding of the main enzyme they use to oxidize methane, particulate methane monooxygenase (pMMO), is critical for harnessing their...
MYC regulates multiple gene programs, raising questions about the potential selectivity and downstream transcriptional consequences of MYC inhibitors as cancer therapeutics. MYC func-tions to either globally amplify RNA production or selectively regulates genes by repression or ac-tivation. In models of MYC inhibition by small molecules the functionality of MYC is...
DNA double-strand breaks (DSBs) are caused by either endogenous agents or exogenous ionizing radiation and chemicals. Incorrect DSB repair can lead to undesired genome rearrangements. Homologous recombination (HR) and non-homologous end-joining (NHEJ) pathways are two major DNA repair pathways that repair DSBs and maintain genome integrity. When homologous DNA is...
CD99-Like 2 (CD99L2) is a 52 kDa type I glycoprotein expressed on leukocytes and endothelial cells as well as other cell types in mice. It is related to CD99, although it shows only 32% sequence identity. CD99L2 has been shown to play a role in leukocyte extravasation in mice under...
Glioblastoma multiforme (GBM) is the most prevalent primary central nervous system tumor, characterized by resistance to therapeutic intervention, inevitable recurrence, and ultimately patient death. The dismal prognosis is due in part to underlying molecular factors that promote an intratumoral cellular state heterogeneity and protect tumor cells from cell death pathways....
RNA viruses cause a wide range of diseases that range from mild respiratory illness to fatal hemorrhagic fevers. To combat these pathogens, most cells in the human body scan the cell for viruses and activate a potent cell-intrinsic immune response by producing interferon (IFN), a cytokine that amplifies the innate...
The purpose of my thesis research has been to understand the formation of mitotic chromosome structure by using chromosome micromanipulation. Folding mitotic chromosomes from their loose interphase form into their individualized, compacted form is required for easy handling of the chromosomes for cell division. This process is facilitated by several...
Protein homeostasis, or proteostasis, is essential for preserving all cellular functions and involves a balance of protein synthesis, folding, trafficking, and degradation. A collapse in proteostasis is a common feature of many neurodegenerative disorders that are characterized by the accumulation of insoluble protein aggregates in the brain. Parkinson’s disease (PD)...
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive disease, affecting children and adults. Chemotherapy regimens show high response rates but have debilitating effects and carry risk of relapse. Until now, no targeted therapy has been approved. In addition, 40% of patients will relapse and their treatment options are limited because...
Parasitic nematode infections are common in both humans and livestock populations around the globe. In humans, these infections cause illness which can be debilitating. In livestock, parasitic nematode infections result in poor animal health and wellbeing as well as decreases in the yield of these animals. The decrease in yield...
The treatment of AML remains to be a challenge due to the high rates of resistance and relapse experienced by patients after initial therapy. The MAPK-interacting kinases 1 and 2 (MNK1/2) have generated increasing interest as therapeutic targets for AML due to their critical role in malignant hematopoietic transformation via...
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease characterized by motor neuron (MN) degeneration and resulting in progressive paralysis and death. ALS is genetically heterogeneous, disease pathophysiology is not completely understood, and there are no effective drug therapies. To develop broadly applicable therapeutics, we examine disease mechanisms in the...
Mitochondria-lysosome contacts are recently identified sites for mediating crosstalk between both organelles, but their role in normal and diseased human neurons remains unknown. We used super-resolution and live-cell microscopy in human iPSC-derived neurons to demonstrate that mitochondria-lysosome contacts can dynamically form in the soma, axons, and dendrites of human neurons,...
Symbiotic relationships involve a life-long interaction between host and bacteria, and there is much we do not understand about how these interactions are developed and maintained. During the horizontal recruitment of beneficial bacteria by hosts, a complex set of molecular signals and communication ensures specificity. On the bacterial side, these...
Cytokines made by macrophages play a critical role in determining the course of Legionella pneumophila infection. Prior, murine-based modeling indicated that the cytokine response initiated upon recognition of L. pneumophila involves a subset of Toll-like receptors, namely TLR2, TLR5, and TLR9. Using shRNA/siRNA knockdowns and subsequently CRISPR/Cas9 knockouts (KO), I...
In nearly all Eukaryotes, the membrane-enclosed nucleus contains the vast majority of the cellular genome. Within this sub-cellular compartment, the nuclear architecture facilitates genomic chromatin organization. Controlling chromosomal loci’s spatial positioning relative to subnuclear structures and each other can have local and global effects on gene expression. Moreover, chromatin organization...
Regulatory RNAs are found throughout nature controlling critical cellular processes and enabling cells to sense and respond to their environment. In order to provide genetic regulation, these RNAs can selectively bind to target molecules, proteins, and invading pathogens, all while modulating gene expression on both the transcriptional and translational level....
Prions are self-perpetuating, alternative protein conformations associated with neurological diseases and normal cellular functions. Saccharomyces cerevisiae contains many endogenous prions – providing a powerful system to study prionization. Previously, the Li Lab demonstrated that Swi1, a component of the SWI/SNF chromatin-remodeling complex, can form the prion [SWI+]. A small region,...
Transcription of nucleic acids (DNA and RNA) is a hallmark of life, taking the information stored within genomic nucleic acids and converting it into a form that is useful for producing the proteins necessary for cellular and organismal function. In eukaryotes, transcription of DNA into messenger RNA (mRNA) requires the...
When properly regulated, inflammation leads to the recruitment and activation of circulating leukocytes to maintain and restore tissue homeostasis. Although this process is critical for successful wound healing and the elimination of pathogens and infections, misdirected inflammation can exacerbate pathology and cause substantial morbidity and mortality. Inflammation a fundamental process...
The insulin/Insulin-Like Growth Factor (IGF) pathway is essential for linking nutritional status to growth and metabolism. MicroRNAs (miRNAs) are short RNAs that are players in the regulation of this process. The miRNA miR-7 shows highly conserved expression in insulin-producing cells across the animal kingdom. However, its conserved functions in regulation...
The evolutionarily conserved COMPASS family of methyltransferases implements histone H3 lysine 4 (H3K4) methylation, an epigenetic mark associated with transcriptional activation. Given the high mutational prevalence of COMPASS subunits across cancers and neurodevelopmental disorders, understanding COMPASS function would lend important insights into disease pathogenesis to facilitate development of effective therapies....
Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative...
Although centrosomes nucleate and organize microtubules in mitotically-dividing cells, spindles in female reproductive cells (oocytes) form in their absence. In some organisms acentrosomal spindle assembly is mediated by acentriolar microtubule organizing centers (MTOCs) that are thought to functionally replace centrosomes. However, spindle assembly in human oocytes does not require MTOCs;...
Heart failure due to genetic cardiomyopathy is associated with a range of phenotypic expression. The studies in this body of work interrogated the role of noncoding variation in modifying cardiomyopathy phenotypes. We used cap analysis of gene expression in heathy and failed left ventricles to define the regulatory environment of...
This dissertation focuses on the development of quantitative approaches for characterizing endogenous signaling pathways and designing new pathways in mammalian cells. I demonstrate how mathematical descriptions that are formulated to explain gene expression patterns can also serve as a powerful springboard for deeper analyses into the properties and functions of...
Proper partitioning of mitochondria and mtDNA is critical for cellular health. Investigations into mitochondrial inheritance, specifically how mtDNA inheritance is coupled with the inheritance mitochondrial compartment, are still in the early stages. We use budding yeast as a model polarized cell system to study a mitochondrial Myo2-adaptor protein, Mmr1, in...
Bacteria often coordinate virulence factors to fine-tune the host response during infection. These coordinated events can include toxins counteracting or amplifying effects of another toxin or though regulating the stability of virulence factors to remove their function once it is no longer needed. Multifunctional autoprocessing repeats-in toxin (MARTX) toxins are...
Periodic exposure to light and dark as a result of rotation of the Earth have served as a major evolutionary pressure to partition divergent biological processes to different phases of the day. Mammals display periods of activity/inactivity, wake/sleep, and feeding/fasting during distinct portions of the day. In mammals, these activities...
Uterine leiomyomas (fibroids) are a major source of gynaecologic morbidity in reproductive age women and are characterised by the excessive deposition of a disorganised extracellular matrix, resulting in rigid benign tumours. Clinically, leiomyoma patients usually present with pelvic pain, urinary incontinence, as well as heavy cyclic and non-cyclic bleeding. Curative...
Background: Glioblastoma (GBM) tumors are the most malignant brain cancers and are characterized as Grade IV astrocytomas by the World Health Organization. GBM tumors can be classified into three molecular subtypes known as proneural, classical, and mesenchymal. In addition, GBM tumors also have a small population of cells known as...
Animals must establish the correct form during development. Regeneration is a process by which some animals reestablish their form following injury. This process requires both the generation of new missing cells after injury, and information to pattern new cells to reestablish the correct form. Planarian flatworms have an almost unlimited...
The histone methyltransferase DOT1L methylates lysine 79 (K79) on histone H3 and is implicated in active transcription. Here we show that DOT1L is overexpressed in Prostate cancer (PCa) and is associated with poor clinical outcome. Genetic and chemical inhibition of DOT1L selectively impaired viability of androgen receptor (AR)-signaling competent PCa...
Skeletal muscle is one of the most abundant tissues in the body and makes up over 40% of the total body mass. It is important for mobility and posture maintenance as well as plays a central role in whole body metabolism. Skeletal muscle is made up of bundles of muscle...
Prostate cancer (PCa) is the most common non-cutaneous cancer among U.S. men. Lack of effective treatments for advanced disease make it a significant public health concern. However, PCa’s long natural history makes it an excellent target for prevention approaches that reduce overtreatment of indolent disease, treatment related morbidity, and mortality....
NSD2, a histone methyltransferase specific for methylation of histone 3 lysine 36 (H3K36), exhibits a glutamic acid to lysine mutation at residue 1099 (E1099K) in childhood acute lymphocytic leukemia (ALL). Cells harboring this mutation can become the predominant clone in relapsing disease. We studied the effects of this mutant enzyme...