The Physical Chemistry Underlying the Assembly and Midpoint Potential Control in a Series of Designed Protein-Maquettes

In nature, oxidoreductase proteins are responsible for many enzymatic processes critical to life. These proteins often rely on the presence of non-proteinaceous cofactors to take part in the enzymatic function.  The most common, central to my thesis, is heme B.  Depending on the protein environment, this cofactor can take part in functions as diverse as electron transfer (cytochromes), oxygen transport (hemoglobins), oxygen reduction (oxidases), carbon-hydroxylation (oxygenases), and superoxide production (NADH oxidase). In natural oxidoreductases, determination of the course and rates of heme-protein association, what barriers are encountered, what affinity is achieved, and what are the oxidation-reduction potentials, is critical for understanding the rules of assembly and function of the different activities performed. In the growing field of research attempting to make man-made oxidoreductases, the same understanding is required for progress to be made toward construction of novel enzymes. However, this understanding is still out of reach in natural oxidoreductases because of the immense complexity of natural proteins, while for man-made designs progress has only recently reached a point where an in-depth systematic study can be contemplated. My thesis states: Simple non-natural proteins (maquettes) designed from first principles to ligate heme, can be used to uncover the factors derived from the oligomeric and structural state of related maquette and also derived from porphyrin variants of heme B, that govern rates of  incorporation and ligation of heme B into a maquette. Maquettes are ideal platforms to demonstrate what aspects of a protein govern heme redox potentials, a key parameter underlying the diversity of hemoprotein functions.  The findings from my work provide the first views of heme and maquette assembly: spontaneous, rapid and with high affinity association. They also provide a foundation for understanding what controls redox potentials of the heme and perspective on this control. The work offers insight into similar processes in natural oxidoreductases, but the concepts and principles uncovered in this thesis will be vital in the development of novel functions applied in man-made applications in vitro and in vivo

The Australian Space Eye: studying the history of galaxy formation with a CubeSat

The Australian Space Eye is a proposed astronomical telescope based on a 6U CubeSat platform. The Space Eye will exploit the low level of systematic errors achievable with a small space based telescope to enable high accuracy measurements of the optical extragalactic background light and low surface brightness emission around nearby galaxies. This project is also a demonstrator for several technologies with general applicability to astronomical observations from nanosatellites. Space Eye is based around a 90 mm aperture clear aperture all refractive telescope for broadband wide field imaging in the i and z bands.Comment: 19 pages, 14 figures, submitted for publication as Proc. SPIE 9904, 9904-56 (SPIE Astronomical Telescopes & Instrumentation 2016

Scalable single-photon detection on a photonic chip

We developed a scalable method for integrating sub-70-ps-timing-jitter superconducting nanowire single-photon detectors with photonic integrated circuits. We assembled a photonic chip with four integrated detectors and performed the first on-chip g[superscript (2)](τ)-measurements of an entangled-photon source

On-Chip Detection of Entangled Photons by Scalable Integration of Single-Photon Detectors

Photonic integrated circuits (PICs) have emerged as a scalable platform for complex quantum technologies using photonic and atomic systems. A central goal has been to integrate photon-resolving detectors to reduce optical losses, latency, and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps timing jitter, nanosecond-scale reset time, and sensitivity from the visible to the mid-infrared spectrum. However, while single SNSPDs have been incorporated into individual waveguides, the system efficiency of multiple SNSPDs in one photonic circuit has been limited below 0.2% due to low device yield. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of PICs. Ten low-jitter detectors were integrated on one PIC with 100% device yield. With an average system efficiency beyond 10% for multiple SNSPDs on one PIC, we demonstrate high-fidelity on-chip photon correlation measurements of non-classical light.Comment: 27 pages, manuscript including supporting informatio

PATH-38. ROSETTE-FORMING GLIONEURONAL TUMOR IS DEFINED BY FGFR1 ACTIVATING ALTERATIONS WITH FREQUENT ACCOMPANYING PI3K AND MAPK PATHWAY MUTATIONS

Abstract BACKGROUND Rosette-forming glioneuronal tumor (RGNT) is an uncommon CNS tumor originally described in the fourth ventricle characterized by a low-grade glial neoplasm admixed with a rosette-forming neurocytic component. METHODS We reviewed clinicopathologic features of 42 patients with RGNT. Targeted next-generation sequencing was performed, and genome-wide methylation profiling is underway. RESULTS The 20 male and 22 female patients had a mean age of 25 years (range 3–47) at time of diagnosis. Tumors were located within or adjacent to the lateral ventricle (n=16), fourth ventricle (15), third ventricle (9), and spinal cord (2). All 31 tumors assessed to date contained FGFR1 activating alterations, either in-frame gene fusion, kinase domain tandem duplication, or hotspot missense mutation in the kinase domain (p.N546 or p.K656). While 7 of these 31 tumors harbored FGFR1 alterations as the solitary pathogenic event, 24 contained additional pathogenic alterations within PI3-kinase or MAP kinase pathway genes: 5 with additional PIK3CA and NF1 mutations, 4 with PIK3CA mutation, 3 with PIK3R1 mutation (one of which also contained focal RAF1 amplification), 5 with PTPN11 mutation (one with additional PIK3R1 mutation), and 2 with NF1 deletion. The other 5 cases demonstrated anaplastic features including hypercellularity and increased mitotic activity. Among these anaplastic cases, 3 harbored inactivating ATRX mutations and two harbored CDKN2A homozygous deletion, in addition to the FGFR1 alterations plus other PI3-kinase and MAP kinase gene mutations seen in those RGNT without anaplasia. CONCLUSION Independent of ventricular location, RGNT is defined by FGFR1 activating mutations or rearrangements, which are frequently accompanied by mutations involving PIK3CA, PIK3R1, PTPN11, NF1, and KRAS. Whereas pilocytic astrocytoma and ganglioglioma are characterized by solitary activating MAP kinase pathway alterations (e.g. BRAF fusion or mutation), RGNT are genetically more complex with dual PI3K-Akt-mTOR and Ras-Raf-MAPK pathway activation. Rare anaplastic examples may show additional ATRX and/or CDKN2A inactivation

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

The chemistry and kinematics of two molecular clouds near Sagittarius A

We have analysed the chemical and kinematic properties of the 20 and 50 km s−1 molecular clouds in the Central Molecular Zone of the Milky Way Galaxy, as well as those of the molecular ridge bridging these two clouds. Our work has utilized 37 molecular transitions in the 0.65, 3 and 7-mm wavebands, from the Mopra and NANTEN2 telescopes. The 0.65-mm NANTEN2 data highlights a dense condensation of emission within the western part of the 20 km s−1 cloud, visible in only four other transitions, which are 3-mm H13CN (1–0), H13CO+ (1–0), HNC (1–0) and N2H+ (1–0), suggesting that the condensation is moderately optically thick and cold. We find that while the relative chemical abundances between both clouds are alike in many transitions, suggesting little variation in the chemistry between both clouds; the 20 km s−1, cold cloud is brighter than the 50 km s−1 cloud in shock and high density tracers. The spatial distribution of enhanced emission is widespread in the 20 km s−1 cloud, as shown via line ratio maps. The position velocity diagrams across both clouds indicate that the gas is well mixed. We show that the molecular ridge is most likely part of the 20 km s−1 cloud and that both of them may possibly extend to include the 50 km s−1 cloud, as part of one larger cloud. Furthermore, we expect that the 20 km s−1 cloud is being tidally sheared as a result of the gravitational potential from Sgr A*

Effect of a Brief Video Intervention on Incident Infection among Patients Attending Sexually Transmitted Disease Clinics

In a controlled trial at three urban STD clinics, Lee Warner and colleagues find that showing an educational video in waiting rooms reduced new infections by approximately 10%

Low-jitter single-photon detector arrays integrated with silicon and aluminum nitride photonic chips

We present progress on a scalable scheme for integration of single-photon detectors with silicon and aluminum nitride photonic circuits. We assemble arrays of low-jitter waveguide-integrated single-photon detectors and show up to 24% system detection efficiency