Development of a reporter gene assay to identify control elements required for dosage compensation in Drosophila Melanogaster : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University

Dosage compensation (equalisation of X-linked gene products) occurs in Drosophila melanogaster by a two-fold transcriptional increase of X-linked gene expression in the male. This involves the binding of four proteins, MSL-1, MSL-2, MSL-3 and MLE (collectively known as the MSLs), to hundreds of sites along the length of the male X. The MSLs are thought to recruit MOF, a histone acetyl transferase, which facilitates the increase in transcriptional activity of X-linked genes. The DNA sequences required to target the MSL complex to the X chromosome (known as dosage compensation regulatory elements, or DCREs) remain elusive, despite numerous attempts over the last ten years to identify them. DCREs are thought to be present at multiple sites along the length of the X chromosome, as antibodies to the MSLs bind to hundreds of sites along the X, and autosomal genes transduced to the X usually become dosage compensated. The first objective of this study was to develop a reporter gene assay to screen for DCREs that would minimise problems previously encountered. A construct consisting of the constitutive armadillo promoter fused to the lacZ reporter gene (called arm-lacZ) was flanked by insulator elements which block the repressive effects of the autosomal chromatin environment. Fragments of X-linked DNA were inserted upstream of the armadillo promoter with the premise that males carrying one copy of an autosomal insertion of this construct would express twice the level of ß-galactosidase as females. Transgenic flies carrying autosomal insertions of X-linked fragments plus arm-lacZ were generated and one dose males and females were assayed for ß-galactosidase activity using a spectrophotometric assay. In all cases, males and females expressed the same level of lacZ. This suggests that no DCREs that could confer dosage compensation onto arm-lacZ were present in the X-linked fragments. arm-lacZ is capable of being dosage compensated as males and females carrying one copy of an X-linked insertion of arm-lacZ produce a 2:1 male to female ratio. This implies that DCREs of the 'strength' required to dosage compensate arm-lacZ are rarer than previously thought. A second method of dosage compensation that is independent of the MSLs is thought to occur in Drosophila. The X-linked gene runt is dosage compensated in the absence of the MSLs. It is possible that runt is sex specifically regulated by the female specific Sex lethal protein (Sxl). Sxl down-regulates msl-2 in females by binding to (U)8 or A(U)7 sequences in the msl-2 5' and 3' untranslated regions (UTRs) of the mRNA. runt mRNA contains three Sxl binding sites in its 3' UTR, as do 20 other X-linked genes. The second objective of this project was to determine if Sxl could down regulate a gene in females, purely by the addition of three Sxl binding sites to the 3'UTR. Sxl binding sites were inserted into the 3'UTR of arm-lacZ in the form of a 40 bp synthetic linker containing three of the sites, and also as a 170 bp fragment from the runt 3' UTR. ß-galactosidase assays of flies carrying the Sxl binding sites from runt showed that males expressed an average of 1.31 to 1.46 times the level of lacZ than females. This shows that Sxl can down-regulate a gene if there are Sxl binding sites in its 3' UTR, however, to achieve two-fold regulation, additional factors may be required, or topologically, the sites may not have been in the right position in the 3' UTR for optimal activity of Sxl. Flies carrying the synthetic linker expressed the same level of ß-galactosidase in both sexes which suggests that either additional elements within the 3' UTR are required, or that the spacing between the sites is critical for the action of Sxl

Entanglement Generation of Clifford Quantum Cellular Automata

Clifford quantum cellular automata (CQCAs) are a special kind of quantum cellular automata (QCAs) that incorporate Clifford group operations for the time evolution. Despite being classically simulable, they can be used as basic building blocks for universal quantum computation. This is due to the connection to translation-invariant stabilizer states and their entanglement properties. We will give a self-contained introduction to CQCAs and investigate the generation of entanglement under CQCA action. Furthermore, we will discuss finite configurations and applications of CQCAs.Comment: to appear in the "DPG spring meeting 2009" special issue of Applied Physics

A multiprover interactive proof system for the local Hamiltonian problem

We give a quantum interactive proof system for the local Hamiltonian problem on n qubits in which (i) the verifier has a single round of interaction with five entangled provers, (ii) the verifier sends a classical message on O(log n) bits to each prover, who reply with a constant number of qubits, and (iii) completeness and soundness are separated by an inverse polynomial in n. As the same class of proof systems, without entanglement between the provers, is included in QCMA, our result provides the first indication that quantum multiprover interactive proof systems with entangled provers may be strictly more powerful than unentangled-prover interactive proof systems. A distinguishing feature of our protocol is that the completeness property requires honest provers to share a large entangled state, obtained as the encoding of the ground state of the local Hamiltonian via an error-correcting code. Our result can be interpreted as a first step towards a multiprover variant of the quantum PCP conjecture.Comment: 18 page

Permutation-invariant codes encoding more than one qubit

A permutation-invariant code on m qubits is a subspace of the symmetric subspace of the m qubits. We derive permutation-invariant codes that can encode an increasing amount of quantum information while suppressing leading order spontaneous decay errors. To prove the result, we use elementary number theory with prior theory on permutation invariant codes and quantum error correction.Comment: 4 pages, minor change

Hepatitis C Education and Screening in a Rural Northern Vermont MAT Clinic

Increases in hepatitis C infection rates have mirrored increases in opioid use disorder. This project attempted to determine screening rates of HCV in a medication assisted treatment clinic for opioid use disorder. Additionally it attempted to provide education to patients that had not been screened for HCV.https://scholarworks.uvm.edu/fmclerk/1605/thumbnail.jp

Developing a control system for ARES 2

A great deal of analysis and testing is conducted at the NASA Langley Research Center to support the development of safe and reliable helicopter rotor systems. This work is performed by the Rotorcraft Aeroelasticity Group located in the Transonic Dynamics Tunnel (TDT) facility. Over the past two decades a wide variety of tests have been successfully conducted in the TDT and their results have contributed significantly to the understanding of aeromechanical phenomena in rotor systems. This has led to improved tools for analysis and design, and ultimately to the development, of improved rotor systems. The TDT facility is ideally suited for these tests due to its unique ability to use a heavy gas as a working medium. This allows the model to be scaled such that the results obtained may be readily extrapolated to full scale. Until recently, the rotor system to be tested has been mounted on a fixed balance which is attached to the longeron which is attached to the stand through a single pitching degree of freedom. The testbed used is known as the Aeroelastic Rotor Experimental System (ARES 1). In order to extend the experimental capabilities to investigate the full rotor/body dynamic coupling present in a rotorcraft, a very ambitious project has been undertaken to design and construct a six degree of freedom system that can be controlled so as to emulate the inertial characteristics of a prescribed model fuselage. The electronic and mechanical hardware for this system has already been designed and constructed. This system is known ar ARES II. The rotor and its drive system are mounted on the balance which is attached to the longeron via six hydraulic actuators. This six degree of freedom parallel linkage is referred to in the literature as a Stuart Platform. By properly adjusting the length of the hydraulic actuators it is possible to position and orient the balance relative to the longeron. The longeron is attached to the stand via a pitch degree of freedom to allow testing over various forward flight regimes. One major task remaining to complete this testbed is the design and synthesis of a control system. To do this properly requires an understanding of the kinematics and dynamics of the system and robust control design. A brief description of the development of a control design is given

Universal blind quantum computation

We present a protocol which allows a client to have a server carry out a quantum computation for her such that the client's inputs, outputs and computation remain perfectly private, and where she does not require any quantum computational power or memory. The client only needs to be able to prepare single qubits randomly chosen from a finite set and send them to the server, who has the balance of the required quantum computational resources. Our protocol is interactive: after the initial preparation of quantum states, the client and server use two-way classical communication which enables the client to drive the computation, giving single-qubit measurement instructions to the server, depending on previous measurement outcomes. Our protocol works for inputs and outputs that are either classical or quantum. We give an authentication protocol that allows the client to detect an interfering server; our scheme can also be made fault-tolerant. We also generalize our result to the setting of a purely classical client who communicates classically with two non-communicating entangled servers, in order to perform a blind quantum computation. By incorporating the authentication protocol, we show that any problem in BQP has an entangled two-prover interactive proof with a purely classical verifier. Our protocol is the first universal scheme which detects a cheating server, as well as the first protocol which does not require any quantum computation whatsoever on the client's side. The novelty of our approach is in using the unique features of measurement-based quantum computing which allows us to clearly distinguish between the quantum and classical aspects of a quantum computation.Comment: 20 pages, 7 figures. This version contains detailed proofs of authentication and fault tolerance. It also contains protocols for quantum inputs and outputs and appendices not available in the published versio