Sense-making with Inscriptions in Quantum Mechanics

This document provides supporting materials for a paper submitted for review to the Physics Education Research Conference proceedings in July 2016, "Sense-making with Inscriptions in Quantum Mechanics."

Alternate Conformations Regulate Ribosomal Recoding in a Positive-sense RNA Virus

Positive-sense RNA viruses are important animal, plant, insect and bacteria pathogens and constitute the largest group of RNA viruses. Due to the relatively small size of their genomes, these viruses have evolved a variety of non-canonical translation mechanisms to optimize coding capacity expanding their proteome diversity. One such strategy is codon redefinition or recoding. First described in viruses, recoding is a programmed translation event in which codon alterations are context dependent. Recoding takes place in a subset of messenger RNA (mRNAs) with some products reflecting new, and some reflecting standard, meanings. The ratio between the two is both critical and highly regulated. While a variety of recoding mechanisms have been documented, (ribosome shunting, stop-carry on, termination-reinitiation, and translational bypassing), the two most extensively employed by RNA viruses are Programmed Ribosomal Frameshifting (PRF) and Programmed Ribosomal Readthrough (PRT). While both PRT and PRF subvert normal decoding for expression of C-terminal extension products, the former involves an alteration of reading frame, and the latter requires decoding of a non-sense codon. Both processes occur at a low but defined frequency, and both require Recoding Stimulatory Elements (RSE) for regulation and optimum functionality. These stimulatory signals can be embedded in the RNA in the form of sequence or secondary structure, or trans-acting factors outside the mRNA such as proteins or micro RNAs (miRNA). Despite 40+ years of study, the precise mechanisms by which viral RSE mediate ribosome recoding for the synthesis of their proteins, or how the ratio of these products is maintained, is poorly defined. This study reveals that in addition to a long distance RNA:RNA interaction, three alternate conformations and a phylogenetically conserved pseudoknot regulate PRT in the carmovirus Turnip crinkle virus (TCV).

FREQUENCY DOMAIN CHARACTERIZATION OF OPTIC FLOW AND VISION-BASED OCELLAR SENSING FOR ROTATIONAL MOTION

The structure of an animal’s eye is determined by the tasks it must perform. While vertebrates rely on their two eyes for all visual functions, insects have evolved a wide range of specialized visual organs to support behaviors such as prey capture, predator evasion, mate pursuit, flight stabilization, and navigation. Compound eyes and ocelli constitute the vision forming and sensing mechanisms of some flying insects. They provide signals useful for flight stabilization and navigation. In contrast to the well-studied compound eye, the ocelli, seen as the second visual system, sense fast luminance changes and allows for fast visual processing. Using a luminance-based sensor that mimics the insect ocelli and a camera-based motion detection system, a frequency-domain characterization of an ocellar sensor and optic flow (due to rotational motion) are analyzed. Inspired by the insect neurons that make use of signals from both vision sensing mechanisms, advantages, disadvantages and complementary properties of ocellar and optic flow estimates are discussed.