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Brain Endothelial Cells Orchestrate an Anti-Encephalitic State in the Central Nervous System in Response to Peripheral Viral Infection
No full textVertebrates have a unique organ called the brain, which along with the spinal cord forms the central nervous system (CNS). This organ takes in sensory data from the environment for analysis and coordinates appropriate responses, enabling individuals to quickly react to highly complex problems and tasks. However, the CNS is extremely delicate. Neurons, the functional units of the CNS, are non-renewing post-mitotic cells and therefore extremely susceptible to damage. The brain has several layers of protective tissue to prevent both physical and biological trauma for this reason. Yet, in the evolutionary arms race, some pathogens have developed methods to gain access to this privileged Tissue. Orthoflaviviridae are a family of RNA viruses carried by arthropods. While these viruses are typically maintained in enzootic cycles, they occasionally spill over into human hosts. Many flaviviruses, including West Nile virus (WNV), can bypass the blood brain barrier (BBB) and wreak havoc in the CNS. Neurovirulent WNV infection elicits hyperinflammation in the CNS, leading to deleterious clinical outcomes including weakness, memory loss, paralysis, and death. Fortunately, only 1% of individuals infected with WNV progress to the encephalitic stage, although the reasons for this discrepancy remain unclear. Previous research has identified interferons (IFNs), small antiviral cytokines, as critical to control WNV infection. However, most work examines the role of IFN in the periphery or in the CNS only post-neuroinvasion. We still do not fully understand how the CNS responds to viral infection prior to neuroinvasion. This research addresses this gap in three chapters. First, we employ a disease-relevant murine model of WNV infection to demonstrate that the CNS responds immunologically to infection well before neuroinvasion by mounting an antiviral response. We expand the study to examine how the brain responds to diverse pathogenic stimuli of both viral and bacterial origin and find the CNS tailors a unique response depending on the offending insult. Viral motifs like poly(I:C) elicit antiviral genes whereas bacterial components like lipopolysaccharide accurate antibacterial pathways. Lastly, we show that the brain does not respond unless a physiological barrier is breached by contrasting the lack of CNS immune activation observed following airway inflammation. Next, we explore the physiological relevance of these CNS responses and find that footpad administered poly(I:C), but not other toll like receptor (TLR) agonists, protects animals against lethal intracranial WNV challenge. We demonstrate that poly(I:C) must be given prior to neuroinvasion, suggesting the elicited ISGs play a prophylactic role. Comparing brain tissue from animals pretreated with poly(I:C) or vehicle controls we show that poly(I:C) reduces the levels of viral replication and associated host immune responses in the CNS which likely accounts for the reduced disease burden. Lastly, we uncover the mechanism of footpad poly(I:C)-mediated encephalitic protection. Through cytokine profiling we identified several signaling molecules expressed following poly(I:C), but not other TLR agonists. Antibody neutralization experiments revealed that peripheral IFN signaling was critical to confer poly(I:C)-mediated protection into the CNS. Surprisingly, we find that despite utilizing the same receptor, intravenous IFNα, but not IFNβ, can reconstitute encephalitic protection. Further, we find that brain microvascular endothelial cells (BMECs) act as a relay for the IFN message between the periphery and the CNS. AAV-mediated ablation of IFN signaling on BMECs completely ameliorated poly(I:C) induced protection. Our findings raise several interesting implications. First, the brain has a far more active role in early infection than originally appreciated, mounting an antiviral response days before neuroinvasion. We show that sufficient peripheral IFN activity can confer a protective benefit against direct encephalitic challenge, mechanically linking with other studies which have found increased encephalitic incidence in humans with IFN signaling defects. Lastly, we identify a new role for BMECs in flaviviral pathogenesis beyond merely forming a physical barrier between the brain and the circulation. This study may inform new therapeutic treatments, of which there are currently none for flaviviral encephalitis, which target initial peripheral inflammation to limit later neurological damage
How Clonal Ants Clone: The Reproductive Biology of the Clonal Raider Ant, Ooceraca Biroi
No full textBiological evolution occurs as alleles change in frequency over time. How allele frequencies change is affected by the mechanics of reproduction, including the number of copies of each chromosome an organism has (ploidy), whether the organism reproduces sexually or asexually, and how gametes are produced. Disentangling the rules of reproduction is therefore vital to understanding how evolution operates, and thorough study promises novel insights into fundamental cellular phenomena. In this thesis, I describe progress in understanding the reproductive biology of the clonal raider ant, Ooceraea biroi. This species has lost the queen caste, and all individuals are, morphologically, worker females that reproduce asexually. Males are produced occasionally, but are considered effectively vestigial because ant workers do not mate. Due to the ease of keeping these ants in the lab and setting up genetically identical age-matched cohorts, O. biroi is increasingly used for behavioral, molecular, and neurobiological studies of ant biology. However, fundamental questions remain about this species\u27 reproductive biology. I first examine how O. biroi\u27s genome avoids some of the deterioration associated with asexual reproduction. Because O. biroi reproduces via the fusion of two haploid pronuclei following a complete female meiosis, loss of heterozygosity is expected to occur regularly if crossover recombination occurs. Using a combination of whole genome sequencing, cytology, and binomial modeling, I show that crossovers occur regularly in O. biroi meiosis, but heterozygosity loss is avoided due to non-Mendelian inheritance of chromosomes that have recombined with each other. Most violations of Mendel\u27s laws result from selfish genetic elements biasing their own transmission at the expense of the rest of the genome (i.e., meiotic drive), but this represents a rare example of unselfish meiotic drive, a phenomenon that can easily go undetected in traditional genetic studies, and which therefore might be more common than is currently appreciated throughout eukaryotes. Second, I describe my discovery of O. biroi\u27s mode of sex determination. Like all ants, bees, and wasps, O. biroi is haplodiploid, meaning that males are haploid (have one copy of each chromosome) while females are diploid (have two copies of each chromosome). The sex determination mechanisms used by haplodiploids remain poorly understood. Sex chromosomes can not evolve in haplodiploid taxa, but one sex determination mechanism known from bees, ants, and some wasps is complementary sex determination, in which heterozygosity at a sex locus is required to trigger female development. Using whole genome sequencing, I mapped such a locus in O. biroi and determined that it is heterozygous in all females. Following theoretical predictions, many alleles at this locus are maintained at intermediate frequency. This locus is homologous to sex determination loci mapped in two other ant species, suggesting that this sex determination mechanism may have evolved over 100 million years ago. This putative sex determination locus lies in a non-coding genomic region, implying that heterozygosity in gene-regulatory elements may be required for female development in ants. Third, I explore the evolutionary history of asexual reproduction in the genus Ooceraea. Almost nothing is known of the reproductive biology of Ooceraea species other than O. biroi. I collected colonies and assembled the genome of a congeneric yet distant relative, Ooceraea australis. By comparing the whole genomes of multiple individuals from each colony, I found compelling evidence that, like O. biroi, O. australis reproduces asexually via a mechanism that usually (but not always) avoids loss of heterozygosity. This result hints at a rich evolutionary history of asexual reproduction within the genus Ooceraea. Fourth, I formally demonstrated that sexual reproduction occurs rarely in wild populations of O. biroi by characterizing the genome of an asexually reproducing colony that was produced via sexual reproduction between two other clonal lines of O. biroi. Rare sexual reproduction in O. biroi implies that this species\u27 long-term persistence may be facilitated by enjoying the benefits of both sexual and asexual reproduction. Together, these results elucidate the reproductive biology of O. biroi and demonstrate the power of mechanistic studies of non-traditional model organisms to illuminate unappreciated biological processes
Deriving Structural Insights About Mesoscale Chromatin Folding Using Coarse-Grained Oligonucleosome Modeling
No full textHere, I investigate chromatin organization on the scale of a few nucleosomes (~1kb). I developed an experimentally-validated coarse-grained polymer model and applied it 1) to show how chromatin fiber parameters, such as nucleosome spacing and breathing, impact chromatin organization on this scale–the mesoscale 2) to interpret mesoscale sequencing assay data and 3) to demonstrate that spatially-correlated cleavage, not protein protection, primarily drives the shape of the distribution of DNA fragment lengths resulting from ionizing-radiation damage. Pair-wise DNA-DNA contact data from DNA sequencing-based assays have the potential to provide locus-specific information about the relationships between chromatin structure and function. Radiation-induced correlated cleavage of chromatin (RICC-seq) is one such assay that reports on characteristic DNA self-contact lengths by sequencing the single-stranded DNA fragments released from cells exposed to large-dose ionizing radiation. Structural inference is necessary to interpret RICC-seq data in terms of chromatin structures. Here, we develop a mesoscale chromatin modeling framework (meso-wlc) to enable the interpretation of RICC-seq data in terms of oligonucleosome structure ensembles. We find that our model reproduces previously observed patterns of fiber compaction as a function of linker DNA length. Using an exponential model of spatially correlated cleavage by ionizing radiation, we predict RICC-seq fragment length distributions from simulated chromatin structure ensembles to determine the correspondence between chromatin structure parameters and the observed RICC-seq signal. Our results show that RICC-seq signal is sensitive to nucleosome repeat length, the extent of nucleosome breathing and the relative strength of inter-nucleosome interactions. Using a 1D convolutional neural net trained on predicted RICC-seq signal, we show that nucleosome repeat lengths consistent with orthogonal assays can be extracted from experimental RICC-seq data. Our framework thus provides a suite of analysis tools that add an important layer of quantitative structural interpretability to RICC-seq experiments. I use meso-wlc structure ensembles and another mesoscale chromatin model to investigate the effects of linker histone on mesoscale chromatin compaction. These models provide insights into nucleosome spacing and DNA wrapping changes in linker histone-depleted cells. Lastly, I examine whether the RICC-seq fragment length distribution signal is primarily driven by spatially-correlated cleavage or by protein-conferred protection of DNA from radiation. Simulations indicate that the shape of the RICC-seq fragment length distributions is primarily attributable to spatially-correlated cleavage. Overall, I use coarse-grained mesoscale chromatin simulations to learn more about chromatin organization on the mesoscale
The Spatiotemporal Dynamics of Nomadic Behavior in the Clonal Raider Ant, Ooceraea Biroi
No full textNest relocation is integral to the lives of many social insects. Army ants have taken this behavior to the extreme, with many species relocating an entire colony of over 100,000 ants plus brood almost daily. Despite its prevalence, the question of how army ant colonies emigrate has been debated for many decades, and still awaits a definitive answer because conducting well-controlled field experiments with their massive and aggressive colonies is challenging. In ants, the Dorylinae subfamily has given rise to most known army ants. Therefore, performing experiments in non-army ant dorylines that can be maintained in a laboratory setting presents an attractive and viable solution. The clonal raider ant, Ooceraea biroi, is a non-army ant doryline that exhibits army ant-like characteristics. Though nearly impossible to study in the field due to their subterranean lifestyle, their queenless, asexually reproducing colonies render them an ideal model to investigate doryline biology in the lab. Taking advantage of the benefits of O. biroi as a model, I developed an assay in which I could study the dynamics of their never-before-seen nest relocation habits with unprecedented experimental control. In this thesis I present two projects which aimed to 1) discern how nomadism fits into O. biroi\u27s life history, and 2) uncover the sociobehavioral mechanisms that facilitate their emigrations. O. biroi exhibits a phasic colony lifecycle consisting of two stereotyped phases that occur in alternation: the reproductive phase, where the adults remain inside the nest while their eggs and pupae develop, and the brood care phase, where old ants leave the nest to forage and the young ants tend to the larvae at home. In the first experiment, colonies were videorecorded over 1.5 reproductive cycles and had free access to four distinct nest sites. I found that colonies relocated their nest frequently and under phasic control, emigrating only during the brood care phase, when larvae were present in the third and fourth instars. This phasic nomadism exactly parallels what is known from phasic army ants. In my second experiment, I used individually tagged ants and automated behavioral tracking to follow colonies as they emigrated between two nest sites. I found that emigrations could be divided into three qualitative phases: the scouting phase, the relocation phase, and the settling phase. Division of labor was found to be mediated by age and by personal information. Age-related differences in movement patterns underscored the spatiotemporal dynamics of relocating colonies: old ants predominately explored the foraging arena during the scouting phase, and young ants relocated into the target site more quickly than old ants during the relocation phase. Personal information dominated task allocation: recruitment of nestmates was performed by ants that had recently visited the target site. Both age groups participated equally in the task of brood transport. This body of work is foundational to the investigation of doryline and army ant emigration in the lab and has implications for the evolution of army ant-like behavior. It also establishes a novel behavioral system for research in collective behavior and distributed decision-making. Altogether, I expand our knowledge of the clonal raider ant\u27s behavioral repertoire and further its claim as a promising model organism for future research and scientific advancement
Investigation into the Neurogenetics of Vocal Learning in Tursiops Truncatus, the Bottlenose Dolphin
No full textVocal learning, a necessary substrate for speech, is a rare trait found in only five mammalian and three avian lineages. Each of these vocal learning groups is distantly related to one another, and each has a close non-learning relative, indicating that the trait evolved independently in each lineage rather than being present in a common ancestor. Studies in songbirds and humans have demonstrated that functionally analogous forebrain regions within this circuit exhibit specialized gene expression profiles, distinguishing them from the surrounding circuits. Although cetaceans are among the most advanced mammalian vocal learners, the underlying brain circuitry of this behavior remains unknown. By studying the neurogenetics of vocal learning in intelligent mammals, we can gain a deeper understanding of the evolution of spoken language. As a first step in investigating the neurogenetic underpinnings of cetacean vocal learning, we generated a haplotype-phased chromosome-scale reference genome assembly for the bottlenose dolphin (Tursiops truncatus). Bottlenose dolphins are well-documented learners that share significant phenotypic overlap with human language development. Using a trio binning approach developed by the Vertebrate Genome Project (VGP), in which samples from an individual and both parents are sequenced, we generated a fully phased diploid assembly in which both haplotypes were assembled in their entirety. The use of multiple long-read technologies allowed for the generation of a highly intact and accurate genome, which significantly surpassed the quality of previously published assemblies for this species. This genome is now the National Center for Biotechnology Information (NCBI) reference assembly. Building on the success of this work, we co-founded the Cetacean Genome Project (CGP) with the National Oceanic and Atmospheric Administration (NOAA), an initiative aimed at generating comparably high-quality reference genomes for all cetaceans. To make gene expression characterization experiments feasible in dolphins, we first needed to overcome the challenge of collecting and preserving high-quality brain samples from necropsies of stranded dolphins. To this end, we developed a novel brain extraction protocol in which the brain was removed fully intact and preserved in the field, with the left hemisphere placed in chilled formalin and the right hemisphere flash-frozen on dry ice. We utilized this protocol in collaboration with the NOAA stranding response network to opportunistically collect specimens from necropsy procedures. In this study, we demonstrated the feasibility of this methodology for collecting high-quality samples. We expanded this methodology to collect samples from other cetacean species, establishing the North American Cetacean Brain Bank. With this collection of high-quality frozen samples, we investigated whether the dolphin motor cortex exhibits a region with specialized gene expression, similar to that shared between the human laryngeal motor cortex (LMC) and functionally analogous vocal learning nuclei in songbirds (HVC and RA). To screen for the putative “vocal learning” specialized subregion of the identified dolphin motor cortex, we conducted double-label Fluorescent in Situ Hybridization (FISH) experiments for SLIT1, a downregulated marker for these regions, and parvalbumin (PVALB), an upregulated marker. Standard FISH protocols are typically designed for small laboratory specimens. We have developed a large tissue protocol that enables the imaging of whole hemispheres of human and dolphin brains. The brains were sectioned, tape-transferred, and embedded in nitrocellulose. Utilizing this technique, we identified a region of the bottlenose dolphin motor cortex that exhibits the PVALB upregulation and SLIT1 downregulation signatures observed in the LMC and HVC/RA of humans and songbirds. Using the FISH images as a reference point, we dissected samples from the specialized region identified in the dolphin motor cortex and performed single-nuclei RNA sequencing (snRNA-sequencing) of these regions. Initial cell typing revealed that an overwhelming proportion of these cells were glial cells. Although further work is required to fully characterize the transcriptomic identity of this cetacean brain, this body of work provides initial support for the existence of an LMC-analogous region in bottlenose dolphins
Mechanisms and Evolution of Mitoribosomal Small Subunit Biogenesis
No full textThe ribosome is the macromolecular machine responsible for all protein synthesis in the cell and is one of the ancient molecular machines involved in the transfer of genetic information to functional molecules. The ribosome is made up of two conserved ribonucleoprotein complexes: the large subunit, responsible for peptide bond synthesis, and the small subunit, responsible for interrogating the match between mRNA codon and tRNA anti-codon. The assembly of the ribosome is a complex process which is tightly controlled to generate functional subunits which exhibit high translational accuracy and processivity. During ribosome biogenesis, ribosomal proteins and a multitude of additional assembly factors, of which there are over 200 in yeast, orchestrate rRNA processing, folding, and modification. While the vast majority of proteins are made by cytoplasmic ribosomes in eukaryotes, a select few proteins are made by specialized ribosomes in the mitochondria. The existence of these mitoribosomes points to the evolutionary origin of these organelles as proteobacteria which formed a symbiotic relationship with a host archaeal cell. The mitoribosome is responsible for translation of mitochondrially encoded respiratory chain subunits, and therefore assembly of these ribosomes is a key part of cellular energy production. The mitoribosome retains highly conserved regions of bacterial and cytoplasmic ribosomes, but displays many structural and functional differences, most notably significant rRNA deletions and the expansion of the r-protein complement. Little is known about the assembly of the mitoribosome. While some assembly factors involved in the process have been identified, exactly how they work, how biogenesis is controlled, and how the assembly system evolutionarily relates to bacterial and eukaryotic systems, is unknown. To address this, we have used cryo-electron microscopy to determine six high resolution structures of human mitoribosomal small subunits undergoing native assembly (Chapter 2). In structurally characterizing this assembly pathway, we can now understand the role of assembly factors in controlling stepwise folding and modification of key functional centers in the mitochondrial rRNA such as the decoding center. In parallel, we solved structures of three similar mitoribosomal small subunit assembly intermediates from the yeast S. cerevisiae. By comparing these assembly pathways, we can connect ribosome structure with assembly mechanisms to highlight how mature structure and biogenesis are evolutionarily coupled (Chapter 3). Similarities in the human pathway to bacterial small subunit biogenesis spurred us to turn to E. coli to determine whether the conserved assembly factors across these two systems play analogous roles in assembly. In purifying and solving structures of endogenous intermediates from E. coli, we observed surprising aspects of the pathway which have been previously overlooked, including the involvement of a DNA-bending protein (Chapter 4). Together, this work provides the first insights into mitoribosomal small subunit biogenesis, revealing the structure and function of assembly factors, the role of novel players in ribosome assembly pathways, and key principles of small subunit assembly across life
Nurture is Nature: The Molecular Basis of Caregiver Genotype Effects on Larval Growth and Caste Development in the Clonal Raider Ant
No full textThe distinction between nature (genetics) and nurture (environment) is blurry, in part because the environment includes the genes of social partners. This is especially evident for parents and their offspring, where genes expressed in one partner profoundly influence the physiology and behavior of the other. Such indirect genetic effects (IGEs) are mediated through social interactions. Although parental care has evolved in many disparate lineages, in most systems it is challenging to delineate the effects of genetics and environment on the phenotypes of caregivers and offspring. This is because most animals with parental care reproduce sexually, meaning each genotype is represented by a single individual. Moreover, it is often impossible to control the environment that an individual experiences, which is crucial because a single genotype can generate different phenotypes in response to environmental variation (i.e., gene-by-environment interactions). Given these challenges, despite IGEs being ubiquitous, characterizations of how they occur at the molecular level are scarce and incomplete. Most studies have yielded correlations between genes and phenotypic outcomes in social partners, but do not establish causal relationships. Thus, our understanding of the molecular mechanisms underlying IGEs, including those between caregivers and their young, is limited. As a result, it is unknown whether common molecular factors or general rules underlie IGEs across traits and species. The clonal raider ant, Ooceraea biroi, provides a powerful model in which the effects of genetics and environment on social traits can be disentangled. These ants reproduce parthenogenetically and can be maintained in the laboratory under standardized conditions. Colonies can be assembled with different combinations of caregiver and larval genotypes, enabling measurement of IGEs. Therefore, I investigated the effects of caregiver IGEs on larval growth and development by cross-fostering different clonal genotypes of O. biroi. I found that brood phenotypes, including body size, caste morphology, developmental timing, and survival, are shaped by the genotype of their caregivers. I also found that some IGEs are dependent on caregiver age and number, demonstrating that environment modifies how genes in social partners influence phenotype (i.e., IGE-by-environment interactions). In ants, caste identity is strongly correlated with body size, but whether environmental factors can regulate caste traits independently of size, and thus decouple the two, remains controversial. Thus, I tested whether different environmental factors, including caregiver genotype, temperature, and food availability, can modify the allometric relationship between caste trait expression and body size. I found no evidence that the relationship between caste trait expression and body size varied across conditions, indicating limited or no plasticity in the scaling relationship itself. This suggests that body size and other caste traits are developmentally coupled in ants via systemic molecular factors. In contrast, I found that both body size and the scaling relationship varies between genotypes, implying that genetic variation in body size and/or the allometric relationship can influence caste morphology in ants. This also establishes that studying environmental effects, including IGEs, on caste development is fundamentally tied to examining how environment affects body size. My experiments established that caregiver genotype unconditionally influences the final body size of brood. To investigate the molecular basis of this IGE, I conducted RNA-sequencing on larval and adult tissues from a cross-fostering experiment, identifying a modest set of larval genes whose expression is influenced by caregiver genotype. These included neuropeptide genes known to regulate ecdysone synthesis in the prothoracic gland of other insects, including corazonin, prothoracicotropic hormone, pheromone biosynthesis activating neuropeptide, and shadow, which encodes an enzyme in the ecdysone biosynthesis pathway. Using RNA-FISH, I confirmed that cells of the prothoracic gland in larvae express receptors for these neuropeptides. Functional assays then showed that treating larvae with ecdysone or corazonin reduces final body size without affecting developmental duration. These findings support a conserved role for basal ecdysone in regulating larval growth, reveal its importance in caste determination in ants, and show that its levels are modulated by caregiver IGEs. I also discovered that multiple chemosensory protein (CSP) and odorant-binding protein (OBP) genes, canonically associated with olfaction, are differentially expressed in larvae due to caregiver genotype, and their expression in larvae was localized to cells in the fat body that coexpress Desaturase 1 (Desat1 converts saturated fatty acids into unsaturated fatty acids). Also, gene set enrichment analysis shows that processes related to fatty acid catabolism were impacted by caregiver IGEs. This indirectly implicates CSPs and OBPs as relevant to this process, as they are known to bind and carry fatty acids. In support of this, it was found that expression of Obp5 and Csp14 in the larval fat body was activated by starvation. Furthermore, ecdysone and corazonin treatment of larvae had opposing effects on Csp and Obp expression, with ecdysone downregulating these genes. These findings raise the possibility that ecdysone inhibits larval growth by suppressing Csp/Obp expression and lipid catabolism in the fat body. Considering findings in other insects, I hypothesize that the regulation of Csp/Obp expression by ecdysone signaling may be a general phenomenon that applies across tissues and insects. Overall, this work significantly advances our understanding of the molecular basis by which caregiver IGEs influence larval growth, yet many questions remain open
ADP-Heptose and Nucleotide Enhancers Drive Fusobacteria-Induced Inflammation
No full textColonization by Fusobacteria is associated with diverse inflammatory diseases and cancers, but the underlying molecular mechanisms that drive these associations remain elusive. Here I report studies showing that among commensal bacteria, Fusobacteria are uniquely potent activators of nuclear factor kappa B (NF-κB) signaling, a pathway implicated in inflammatory diseases and cancers. I found that Fusobacterium nucleatum secretes pathogen-associated molecular pattern ADP-heptose and ribonucleotides that together, but not individually, strongly induced NF-κB signaling as well as the expression of inflammation and cancer associated genes. This finding suggests a regulatory role for extracellular nucleotides in ADP-heptose detection, and also provides a potentially key mechanism for Fusobacteria\u27s diverse disease associations. In addition, the results of these studies suggest that inhibiting the accumulation of either metabolite could prove therapeutically useful
René Dubos: An Annotated Bibliography
No full textRené Dubos (1901–1982), a prominent 20th century scientist, humanist, and philosopher, was a prolific author. Affiliated for more than 50 years with The Rockefeller Institute for Medical Research/The Rockefeller University, his studies ranged from antibiotics and the role of bacteria in human diseases to formulating broad ecological and environmental questions affecting human health and disease. His seminal writings explore a lifelong belief that a living organism—whether microbe, human being, society, or the Earth itself—could be understood only through its relationships with everything else.
This comprehensive bibliography of more than a thousand works by René Dubos includes brief annotations for each work. The primary works are arranged by books, research articles, essays, short pieces, and unpublished manuscripts. Secondary works about Dubos are arranged by articles, audio-visual recordings, book reviews, and obituaries. A researcher can use this bibliography to explore Dubos’ evolving philosophy, his earnest convictions and prescient warnings, along with his fresh optimist perspectives that remain relevant and continue to grow in importance.https://digitalcommons.rockefeller.edu/rene-dubos-annotated-bibliography/1000/thumbnail.jp
Understanding of Intrinsic Sources of DNA Damage that Drive Human Disease: A Foray into the Study of DNA Interstrand Crosslinks and Genome-Embedded Ribonucleotides
No full textSources of damage to deoxyribonucleic acid (DNA) can be categorized broadly into exogenous and endogenous. Exogenous sources range from environmental (e.g., air pollution, tobacco and alcohol, ultraviolet (UV) radiation due to sun exposure), to pharmaceutical sources (e.g., chemotherapeutics such as cisplatin). The other main category of DNA damage is endogenous, which can range from metabolites such as reactive oxygen species (ROS) produced in the cells as byproducts of metabolic pathways, to incorrect bases incorporated into the genome. In this thesis, I will focus on two types of endogenous DNA damage: 1) interstrand crosslinks (ICLs) formed by DNA damaging aldehydes and 2) genome-embedded ribonucleotides. The clinical pathologies arising in the setting of the improper removal or repair of ICLs or genome-embedded ribonucleotides are diverse. A failure to remove ICLs in humans is the cause of Fanconi anemia (FA), a disease characterized by early bone marrow failure, congenital abnormalities, and an early onset of cancers such as leukemia and head and neck squamous cell carcinomas (HNSCC). On the other hand, failure to appropriately remove genome-embedded ribonucleotides leads to Aicardi-Goutières Syndrome (AGS), a rare autosomal recessive neurological disorder, which clinically mimics a congenital viral infection. Part I of this thesis focuses on the study of the endogenous sources of ICLs in human oral keratinocytes, the precursor cell of HNSCC. Part II of this thesis concentrates on the study of the enzyme RNase H2 and its actions in ensuring genomic stability by removing genome-embedded ribonucleotides