A disconnect exists between the behavior of transcriptional and genetic regulation in bacterial systems when comparing phenotypic patterns and dynamics of a population to those observed at the single cell level. In this thesis, we developed a number of tools and assays to better understand, overcome, and predict the challenges...
The ability to track labeled cancer cells in vivo would allow researchers to study their distribution, growth and metastatic potential within the intact organism. Magnetic Resonance (MR) imaging is invaluable for tracking cancer cells in vivo as it benefits from high spatial resolution and absence of ionizing radiation. However, many...
The circadian clock is a biological oscillator present in all terrestrial life forms that aligns organismal functions with the daily rising and setting of the sun. In mammals clocks are expressed both in pacemaker cells in the brain that are directly entrained by light as well as in all peripheral...
Fungi have an immense untapped store of natural products, small molecules that can often be repurposed as pharmaceuticals. The genes that encode secondary metabolic machinery are often genomically co-localized into biosynthetic gene clusters. Because of the immense energetic costs that goes into producing the biosynthetic pathway and its products, strict...
In yeast, inducible genes such as INO1, PRM1 and HIS4 reposition from the nucleoplasm to nuclear periphery upon activation. This leads to a physical interaction with nuclear pore complex (NPC), interchromosomal clustering, and stronger transcription. Repositioning to the nuclear periphery is controlled by cis-acting transcription factor (TF) binding sites located...
Regeneration is a complex biological phenomenon. Organisms that regenerate must possess robust mechanisms that direct new tissue production of the appropriate size and pattern to allow for correct and functional integration with preexisting tissue structures. Planarians are flatworms capable of regenerating from nearly any injury, making them a powerful system...
Glioblastoma multiforme (GBM) is the most prevalent primary central nervous system malignancy. Due to the aggressive nature of these tumors and our inability to adequately treat them, only 3-5% of patients survive longer than 3 years post-diagnosis. The standard of care for newly diagnosed GBM is surgical resection followed by...
The development of metal-based probes has provided major benefits to understanding basic biological process and clinical outcomes. Metals offer access to geometries that carbon alone cannot attain, along with valuable magnetic, optical, and binding properties. Metals have proven to be particularly useful in advancing molecular imaging, a field that seeks...
Natural products provide a renewable resource of novel chemical structures with relevance to the pharmaceutical, agricultural and materials industries. Genome sequencing has revealed that these industries currently rely on only a fraction of the number of natural products that exist in nature. Based on the impact that known natural products...
Bacterial gene expression requires numerous steps that are energetically costly and tightly regulated. Following transcription of messenger-RNA, the translation of mRNA into protein is further regulated by a variety of sequence features both within and upstream of coding sequences. Collectively, these features contribute to the control of translation initiation, elongation,...
Topoisomerases are ubiquitous enzymes involved in maintaining the supercoiled state of DNA in the cell. Structural, biophysical, and biochemical studies have provided an overall view of the mechanisms of DNA transformation by these enzymes, but many aspects, particularly their dynamic characteristics, remain poorly understood. Type IA topoisomerases change the topology...
Metabolite biosensors are powerful tools for basic biological research, medical diagnostics, and biotechnological applications. However, a generalizable strategy for developing new metabolite biosensors when an existing sensor cannot be found in nature, is a persistent challenge. Furthermore, while transcription factor biosensors have the broadest range of applications, the pool of...
In eukaryotic organisms, genomic DNA is organized and condensed into repeating arrays of nucleosomes. The histone protein octamer of each nucleosome wraps 147 base pairs of DNA, effectively restricting access by transcription factors and other regulatory proteins to that region. An additional histone, histone H1, binds the DNA outside the...
Nucleosome organization influences gene activity by controlling DNA accessibility to transcription machinery. In this thesis, we have developed a chemical biology approach to determine mammalian nucleosome positions genome-wide. Using this strategy, we uncover surprising new features of nucleosome organization in mouse embryonic stem cells. In contrast to the prevailing model,...
Intrahepatic islet transplantation is a promising therapeutic option for the treatment of Type-1 diabetes that offers the ability to restore endogenous insulin production. Widespread use of islet transplantation is currently limited by poor survival of transplanted islets due to the harsh environment of the liver portal vein, prompting investigation into...
The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex, composed of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. Here, I show...
Methanobactins (Mbns) are a growing family of ribosomally produced, post-translationally modified natural products that exhibit a high affinity for copper. These compounds were initially identified in methanotrophic bacteria, which oxidize methane to methanol as their sole source of carbon. One of the key enzymes in this metabolic pathway, particulate methane...
Certain inducible genes show faster reactivation if they were recently expressed. This epigenetic phenomenon is called transcriptional memory and is inherited for several generations after the first round of induction. During this phase, genes show several conserved molecular features that are essential for faster reactivation: peripheral localization of the gene,...
What follows is a strictly post-genomic dissertation. Over the past five years, I have strived to leave the nucleus behind, and even the endoplasmic reticulum and golgi apparatus. The human genome was sequenced over 15 years before the submission of this document, and the world changed somewhat less than anticipated—besides...
The purpose of the egg is to give rise to offspring in sexually reproducing organisms. Zinc thresholds became connected to egg quality from initial breakthrough discoveries in M. musculus which demonstrated that large-scale zinc fluxes occur during meiotic maturation, and these fluxes are required to maintain female egg viability. Numerous...
The follicle is the functional unit of the mammalian ovary and serves as a tightly controlled microenvironment where granulosa cells nurture the growth and maturation of the oocyte. Early events in follicular development are autonomous of the hypothalamic-pituitary-gonadal axis and are instead controlled by local factors that are used in...
The neural crest is a unique, vertebrate specific stem cell population that gives rise to a diverse set of derivatives in the embryo, including sensory neurons, glial cells, melanocytes, and craniofacial structures such as cartilage, bone, and connective tissue. Unlike other multipotent stem cell populations present at this time, neural...
Chromatin organization involves a hierarchy of length scales ranging from a few tens of nanometers in nucleosomes to hundreds of nanometers for chromosomal territories. This physical nanostructure is regulated by the genetic code, differential methylation and histone modifications that comprise the histone code, as well as non-molecular factors, such as...
Meiosis is a specialized form of cell division where chromosomes are duplicated once and segregated twice, in order to reduce the chromosome number by half to generate haploid gametes. In contrast to mitosis, oocyte meiosis in many species occurs in the absence of centrosomes, the microtubule organizing centers that nucleate...
Caenorhabditis elegans has been a highly productive model organism. However, most of the knowledge gained from the species has come a single strain isolated in Bristol, England in 1951. However, there exists significant potential in the natural variation present in the species to make discoveries. In this dissertation, I describe...