The Microbiome and a Bacterial Infection of Oxytricha trifallax

The microbiome of O. trifallax has been a completely unexplored field of ciliate research. While other bacterial-ciliate relationships have been shown to have great effects on the lifecycles of these other ciliates, both harmful and necessary, no prior studies have yet been performed in O. trifallax. In order to rectify this, studies consisting of both high-throughput sequencing of the bacterial 16s rDNA locus and fluorescence in situ hybridization (FISH) against bacterial 16s rRNA within O. trifallax have been performed, and a great deal of variation has been found. Furthermore, a population of sick O. trifallax cells has been investigated, and this phenotype was determined to have been caused by a bacterial infection where one of the members is of the genus Ralstonia. Various experiments have also been performed in order to recreate this phenotype, and while this was not achieved, these studies have shown that O. trifallax is robust to the presence of some variant bacteria and to the absence of bacteria in general, while susceptible to the presence of others. This evidence suggests both a robustness and a susceptibility of O. trifallax to bacteria depending on which bacteria are present and at what levels they are present

Ptolemy in Philosophical Context: A Study of the Relationships Between Physics, Mathematics, and Theology

This study situates Ptolemy’s philosophy within the second-century milieu of Middle Platonism and the nascent Aristotelian commentary tradition. It focuses on Ptolemy’s adaptation and application of Aristotle’s tripartite division of theoretical philosophy into the physical, mathematical, and theological. In Almagest 1.1, Ptolemy defines these three sciences, describes their relations and objects of study, and addresses their epistemic success. According to Ptolemy, physics and theology are conjectural, and mathematics alone yields knowledge. This claim is unprecedented in the history of ancient Greek philosophy. Ptolemy substantiates this claim by constructing and employing a scientific method consistent with it. In Almagest 1.1, after defining the theoretical sciences, Ptolemy adds that, while theology and physics are conjectural, mathematics can make a good guess at the nature of theological objects and contribute significantly to the study of physics. He puts this claim into practice in the remainder of his corpus by applying mathematics to theology and physics in order to produce results in these fields. After the introductory chapter, I present Ptolemy’s philosophy and practice of the three theoretical sciences. In Chapter 2, I examine how and why Ptolemy defines the sciences in Almagest 1.1. In Chapter 3, I further analyze how Ptolemy defines mathematical objects, how he describes the relationships between the tools and branches of mathematics, and whether he demonstrates in the Harmonics and Almagest that he believed mathematics yields sure and incontrovertible knowledge, as he claims in Almagest 1.1. In Chapter 4, I present Ptolemy’s natural philosophy. While in Chapter 2 I discuss his element theory, in Chapter 4 I focus on his physics of composite bodies: astrology, psychology, and cosmology as conveyed in the Tetrabiblos, On the Kritêrion, Harmonics, and Planetary Hypotheses. I do not devote a chapter to theology, as Ptolemy refers to this science only once in his corpus. Therefore, I limit my analysis of his definition and practice of theology to Chapter 2. In the concluding chapter, I discuss Ptolemy’s ethical motivation for studying mathematics. What emerges from this dissertation is a portrait of Ptolemy’s philosophy of science and the scientific method he employs consistently in his texts.Ph

Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function.

The small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain can interact with the ZTL homologs, LKP2 and FKF1, and the LOV domain of ZTL itself. This suggests a hypothesis that the Kelch repeat domain of ZTL may mediate inter- and intra-molecular interactions of the three LOV/F-box/Kelch proteins and provides added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain

Keeping time in the dark: Potato diel and circadian rhythmic gene expression reveals tissue‐specific circadian clocks

Abstract The circadian clock is an internal molecular oscillator and coordinates numerous physiological processes through regulation of molecular pathways. Tissue‐specific clocks connected by mobile signals have previously been found to run at different speeds in Arabidopsis thaliana tissues. However, tissue variation in circadian clocks in crop species is unknown. In this study, leaf and tuber global gene expression in cultivated potato under cycling and constant environmental conditions was profiled. In addition, we used a circadian‐regulated luciferase reporter construct to study tuber gene expression rhythms. Diel and circadian expression patterns were present among 17.9% and 5.6% of the expressed genes in the tuber. Over 500 genes displayed differential tissue specific diel phases. Intriguingly, few core circadian clock genes had circadian expression patterns, while all such genes were circadian rhythmic in cultivated tomato leaves. Furthermore, robust diel and circadian transcriptional rhythms were observed among detached tubers. Our results suggest alternative regulatory mechanisms and/or clock composition is present in potato, as well as the presence of tissue‐specific independent circadian clocks. We have provided the first evidence of a functional circadian clock in below‐ground storage organs, holding important implications for other storage root and tuberous crops