Geometric Quantum Computation

We describe in detail a general strategy for implementing a conditional geometric phase between two spins. Combined with single-spin operations, this simple operation is a universal gate for quantum computation, in that any unitary transformation can be implemented with arbitrary precision using only single-spin operations and conditional phase shifts. Thus quantum geometrical phases can form the basis of any quantum computation. Moreover, as the induced conditional phase depends only on the geometry of the paths executed by the spins it is resilient to certain types of errors and offers the potential of a naturally fault-tolerant way of performing quantum computation.Comment: 15 pages, LaTeX, uses cite, eepic, epsfig, graphicx and amsfonts. Accepted by J. Mod. Op

Generalization of geometric phase to completely positive maps

We generalize the notion of relative phase to completely positive maps with known unitary representation, based on interferometry. Parallel transport conditions that define the geometric phase for such maps are introduced. The interference effect is embodied in a set of interference patterns defined by flipping the environment state in one of the two paths. We show for the qubit that this structure gives rise to interesting additional information about the geometry of the evolution defined by the CP map.Comment: Minor revision. 2 authors added. 4 pages, 2 figures, RevTex

Structure and Function of the TIR Domain from the Grape NLR Protein RPV1

The N-terminal Toll/interleukin-1 receptor/resistance protein (TIR) domain has been shown to be both necessary and sufficient for defense signaling in the model plants flax and Arabidopsis. In examples from these organisms, TIR domain self-association is required for signaling function, albeit through distinct interfaces. Here, we investigate these properties in the TIR domain containing resistance protein RPV1 from the wild grapevine Muscadinia rotundifolia. The RPV1 TIR domain, without additional flanking sequence present, is autoactive when transiently expressed in tobacco, demonstrating that the TIR domain alone is capable of cell-death signaling. We determined the crystal structure of the RPV1 TIR domain at 2.3 Å resolution. In the crystals, the RPV1 TIR domain forms a dimer, mediated predominantly through residues in the αA and αE helices ("AE" interface). This interface is shared with the interface discovered in the dimeric complex of the TIR domains from the Arabidopsis RPS4/RRS1 resistance protein pair. We show that surface-exposed residues in the AE interface that mediate the dimer interaction in the crystals are highly conserved among plant TIR domain-containing proteins. While we were unable to demonstrate self-association of the RPV1 TIR domain in solution or using yeast 2-hybrid, mutations of surface-exposed residues in the AE interface prevent the cell-death autoactive phenotype. In addition, mutation of residues known to be important in the cell-death signaling function of the flax L6 TIR domain were also shown to be required for RPV1 TIR domain mediated cell-death. Our data demonstrate that multiple TIR domain surfaces control the cell-death function of the RPV1 TIR domain and we suggest that the conserved AE interface may have a general function in TIR-NLR signaling.This research was supported by the Australian Research Council (ARC) Discovery Projects DP120100685 and DP160102244. BK is a NHMRC Research Fellow (1003325 and 1110971). SW is funded by ARC DECRA (DE160100893)

Crystallization and X-ray diffraction analysis of the N-terminal domain of the Toll-like receptor signalling adaptor protein TRIF/TICAM-1

As part of the mammalian innate immune response, Toll-like receptors 3 and 4 can signal via the adaptor protein TRIF/TICAM-1 to elicit the production of type-I interferons and cytokines. Recent studies have suggested an auto-inhibitory role for the N-terminal domain (NTD) of TRIF. This domain has no significant sequence similarity to proteins of known structure. In this paper, the crystallization and X-ray diffraction analysis of TRIF-NTD and its selenomethionine-labelled mutant TRIF-NTDA66M/L113M are reported. Thin plate-like crystals of native TRIF-NTD obtained using polyethylene glycol 3350 as precipitant diffracted X-rays to 1.9 Å resolution. To facilitate phase determination, two additional methionines were incorporated into the protein at positions chosen based on the occurrence of methionines in TRIF homologues in different species. Crystals of the selenomethionine-labelled protein were obtained under conditions similar to the wild-type protein; these crystals diffracted X-rays to 2.5 Å resolution. The TRIF-NTD and TRIF-NTDA66M/L113M crystals have the symmetry of space groups P2 12121 and P1, and most likely contain two and four molecules in the asymmetric unit, respectively. These results provide a sound foundation for the future structure determination of this novel domain

Purification, crystallization and preliminary X-ray analysis of adenylosuccinate synthetase from the fungal pathogen Cryptococcus neoformans

With increasingly large immunocompromised populations around the world, opportunistic fungal pathogens such as Cryptococcus neoformans are a growing cause of morbidity and mortality. To combat the paucity of antifungal compounds, new drug targets must be investigated. Adenylosuccinate synthetase is a crucial enzyme in the ATP de novo biosynthetic pathway, catalyzing the formation of adenylosuccinate from inosine monophosphate and aspartate. Although the enzyme is ubiquitous and well characterized in other kingdoms, no crystallographic studies on the fungal protein have been performed. Presented here are the expression, purification, crystallization and initial crystallographic analyses of cryptococcal adenylosuccinate synthetase. The crystals had the symmetry of space group P2(1)2(1)2(1) and diffracted to 2.2 angstrom resolution

ガーネット、サマータウン、グローバル・イシューズ案内 : 英語教材のフィクション対ノンフィクション

For the sake of the Japanese learners of English who love reading, this paper introduces three different series of readers: Garnet Oracle Readers, Summertown Readers, and National Geographic's Global Issues. Garnet Oracle and Summertown are both so-called graded readers. The former are for highschool and university students who study English as a foreign or second language while the latter are written for business people who have to learn English as a lingua franca. Both are,however, original fictional stories, some of which are quite enjoyable and really worth reading. Peter Viney, Garnet's main author, can write a variety of genres: for example, Space Romance is a romantic sci-fi story in an impressive setting; A Tidy Ghost is a witty ghost story whose terror dramatically changes into sheer humor at the ending; but,above all,his Underground is highly recommended because of the unforgettable character Tommy, a mute elderly man who lives in the London underground, saving the protagonist in big trouble. Summertown's counterpart must be James Schofield. Although his amateurish suspense stories tend to be rather boring, his humorous stories such as Room Service and Double Trouble are readable with a lot of laughter. National Geographic's Global Issues may seem to be no comparison with these interesting stories since they are serious nonfiction pamphlets edited for American high school students. Despite the foreign language, Japanese students can also appreciate the discussed, grave environmental problems of our planet Earth where the population explosion has been causing disastrous situations. In a sense, fact is truly stranger than fiction. So, which is more interesting, fiction or nonfiction? I hope you read the three series and decide for yourself

Crystal structure of the Melampsora lini effector AvrP reveals insights into a possible nuclear function and recognition by the flax disease resistance protein P

The effector protein AvrP is secreted by the flax rust fungal pathogen (Melampsora lini) and recognized specifically by the flax (Linum usitatissimum) P disease resistance protein, leading to effector‐triggered immunity. To investigate the biological function of this effector and the mechanisms of specific recognition by the P resistance protein, we determined the crystal structure of AvrP. The structure reveals an elongated zinc‐finger‐like structure with a novel interleaved zinc‐binding topology. The residues responsible for zinc binding are conserved in AvrP effector variants and mutations of these motifs result in a loss of P‐mediated recognition. The first zinc‐coordinating region of the structure displays a positively charged surface and shows some limited similarities to nucleic acid‐binding and chromatin‐associated proteins. We show that the majority of the AvrP protein accumulates in the plant nucleus when transiently expressed in Nicotiana benthamiana cells, suggesting a nuclear pathogenic function. Polymorphic residues in AvrP and its allelic variants map to the protein surface and could be associated with differences in recognition specificity. Several point mutations of residues on the non‐conserved surface patch result in a loss of recognition by P, suggesting that these residues are required for recognition.This research was supported by Australian Research Council (ARC) Discovery Projects DP120100685, DP130104098 and DP160102244. XZ was a recipient of an ANZ Trustees PhD Scholarship for Medical Research in Queensland. BK is a National Health and Medical Research Council (NHMRC) Principal Research Fellow (1003325 and 1110971). MB was a recipient of an ARC Discovery Early Career Research Award (DE130101292)

A high-fat diet catalyzes progression to hyperglycemia in mice with selective impairment of insulin action in Glut4-expressing tissues

Insulin resistance impairs postprandial glucose uptake through glucose transporter type 4 (GLUT4) and is the primary defect preceding type 2 diabetes. We previously generated an insulin-resistant mouse model with human GLUT4 promoter-driven insulin receptor knockout (GIRKO) in the muscle, adipose, and neuronal subpopulations. However, the rate of diabetes in GIRKO mice remained low prior to 6 months of age on normal chow diet (NCD), suggesting that additional factors/mechanisms are responsible for adverse metabolic effects driving the ultimate progression of overt diabetes. In this study, we characterized the metabolic phenotypes of the adult GIRKO mice acutely switched to high-fat diet (HFD) feeding in order to identify additional metabolic challenges required for disease progression. Distinct from other diet-induced obesity (DIO) and genetic models (e.g., db/db mice), GIRKO mice remained leaner on HFD feeding, but developed other cardinal features of insulin resistance syndrome. GIRKO mice rapidly developed hyperglycemia despite compensatory increases in β-cell mass and hyperinsulinemia. Furthermore, GIRKO mice also had impaired oral glucose tolerance and a limited glucose-lowering benefit from exendin-4, suggesting that the blunted incretin effect contributed to hyperglycemia. Secondly, GIRKO mice manifested severe dyslipidemia while on HFD due to elevated hepatic lipid secretion, serum triglyceride concentration, and lipid droplet accumulation in hepatocytes. Thirdly, GIRKO mice on HFD had increased inflammatory cues in the gut, which were associated with the HFD-induced microbiome alterations and increased serum lipopolysaccharide (LPS). In conclusion, our studies identified important gene/diet interactions contributing to diabetes progression, which might be leveraged to develop more efficacious therapies