A Link between Virulence and Homeostatic Responses to Hypoxia during Infection by the Human Fungal Pathogen Cryptococcus neoformans

Fungal pathogens of humans require molecular oxygen for several essential biochemical reactions, yet virtually nothing is known about how they adapt to the relatively hypoxic environment of infected tissues. We isolated mutants defective in growth under hypoxic conditions, but normal for growth in normoxic conditions, in Cryptococcus neoformans, the most common cause of fungal meningitis. Two regulatory pathways were identified: one homologous to the mammalian sterol-response element binding protein (SREBP) cholesterol biosynthesis regulatory pathway, and the other a two-component-like pathway involving a fungal-specific hybrid histidine kinase family member, Tco1. We show that cleavage of the SREBP precursor homolog Sre1—which is predicted to release its DNA-binding domain from the membrane—occurs in response to hypoxia, and that Sre1 is required for hypoxic induction of genes encoding for oxygen-dependent enzymes involved in ergosterol synthesis. Importantly, mutants in either the SREBP pathway or the Tco1 pathway display defects in their ability to proliferate in host tissues and to cause disease in infected mice, linking for the first time to our knowledge hypoxic adaptation and pathogenesis by a eukaryotic aerobe. SREBP pathway mutants were found to be a hundred times more sensitive than wild-type to fluconazole, a widely used antifungal agent that inhibits ergosterol synthesis, suggesting that inhibitors of SREBP processing could substantially enhance the potency of current therapies

Pillared two-dimensional metal-organic frameworks based on a lower-rim acid appended calix[4]arene

Solvothermal reactions of the lower-rim functionalized diacid calix[4]arene 25,27-bis(methoxycarboxylic acid)-26,28-dihydroxy-4-tert-butylcalix[4]arene (LH₂) with Zn(NO₃)₂•6H₂O and the dipyridyl ligands 4,4/-bipyridyl (4,4/-bipy), 1,2-di(4-pyridyl)ethylene (DPE) or 4,4/-azopyridyl (4,4/-azopy) afforded a series of 2-D structures of the formulae {[Zn(4,4/-bipy)(L)]•2¼DEF}n (1), {[Zn₂(L)(DPE)]•DEF}n (2) and {[Zn(OH₂)₂(L)(4,4/-azopy)]•DEF}n (3) (DEF = diethylformamide)

Effect of incoherent scattering on shot noise correlations in the quantum Hall regime

We investigate the effect of incoherent scattering in a Hanbury Brown and Twiss situation with electrons in edge states of a three-terminal conductor submitted to a strong perpendicular magnetic field. The modelization of incoherent scattering is performed by introducing an additional voltage probe through which the current is kept equal to zero which causes voltage fluctuations at this probe. It is shown that inelastic scattering can lead in this framework to positive correlations, whereas correlations remain always negative for quasi-elastic scattering.Comment: 5 pages latex, 5 eps figure

The improvement of Mo/4H-SiC Schottky diodes via a P2O5 surface passivation treatment

Molybdenum (Mo)/4H-silicon carbide (SiC) Schottky barrier diodes have been fabricated with a phosphorus pentoxide (P2O5) surface passivation treatment performed on the SiC surface prior to metallization. Compared to the untreated diodes, the P2O5-treated diodes were found to have a lower Schottky barrier height by 0.11 eV and a lower leakage current by two to three orders of magnitude. Physical characterization of the P2O5-treated Mo/SiC interfaces revealed that there are two primary causes for the improvement in electrical performance. First, transmission electron microscopy imaging showed that nanopits filled with silicon dioxide had formed at the surface after the P2O5 treatment that terminates potential leakage paths. Second, secondary ion mass spectroscopy revealed a high concentration of phosphorus atoms near the interface. While only a fraction of these are active, a small increase in doping at the interface is responsible for the reduction in barrier height. Comparisons were made between the P2O5 pretreatment and oxygen (O2) and nitrous oxide (N2O) pretreatments that do not form the same nanopits and do not reduce leakage current. X-ray photoelectron spectroscopy shows that SiC beneath the deposited P2O5 oxide retains a Si-rich interface unlike the N2O and O2 treatments that consume SiC and trap carbon at the interface. Finally, after annealing, the Mo/SiC interface forms almost no silicide, leaving the enhancement to the subsurface in place, explaining why the P2O5 treatment has had no effect on nickel- or titanium-SiC contacts

Quantum Computation by Communication

We present a new approach to scalable quantum computing--a ``qubus computer''--which realises qubit measurement and quantum gates through interacting qubits with a quantum communication bus mode. The qubits could be ``static'' matter qubits or ``flying'' optical qubits, but the scheme we focus on here is particularly suited to matter qubits. There is no requirement for direct interaction between the qubits. Universal two-qubit quantum gates may be effected by schemes which involve measurement of the bus mode, or by schemes where the bus disentangles automatically and no measurement is needed. In effect, the approach integrates together qubit degrees of freedom for computation with quantum continuous variables for communication and interaction.Comment: final published versio

Probing Entanglement and Non-locality of Electrons in a Double-Dot via Transport and Noise

Addressing the feasibilty of quantum communication with electrons we consider entangled spin states of electrons in a double-dot which is weakly coupled to in--and outgoing leads. We show that the entanglement of two electrons in the double-dot can be detected in mesoscopic transport and noise measurements. In the Coulomb blockade and cotunneling regime the singlet and triplet states lead to phase-coherent current and noise contributions of opposite signs and to Aharonov-Bohm and Berry phase oscillations in response to magnetic fields. These oscillations are a genuine two-particle effect and provide a direct measure of non-locality in entangled states. We show that the ratio of zero-frequency noise to current (Fano factor) is universal and equal to the electron charge.Comment: 4 double-column pages, REVTeX, 1 eps figure embedded with epsf, equations adde

Differential response to exercise in claudin-low breast cancer

Exposure to exercise following a breast cancer diagnosis is associated with reductions in the risk of recurrence. However, it is not known whether breast cancers within the same molecular-intrinsic subtype respond differently to exercise. Syngeneic mouse models of claudin-low breast cancer (i.e., EO771, 4TO7, and C3(1)SV40Tag-p16-luc) were allocated to a uniform endurance exercise treatment dose (forced treadmill exercise) or sham-exercise (stationary treadmill). Compared to sham-controls, endurance exercise treatment differentially affected tumor growth rate: 1- slowed (EO771), 2- accelerated (C3(1)SV40Tag-p16-luc), or 3- was not affected (4TO7). Differential sensitivity of the three tumor lines to exercise was paralleled by effects on intratumoral Ki-67, Hif1-α, and metabolic programming. Inhibition of Hif1-α synthesis by the cardiac glycoside, digoxin, completely abrogated exercise-accelerated tumor growth in C3(1)SV40Tag-p16-luc. These results suggest that intratumoral Hif1-α expression is an important determinant of claudin-low breast cancer adaptation to exercise treatment

CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

<p>Abstract</p> <p>Background</p> <p>Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the recently emerging many-core architectures and their associated programming models.</p> <p>Findings</p> <p>This paper describes the latest release of the CUDASW++ software, CUDASW++ 2.0, which makes new contributions to Smith-Waterman protein database searches using compute unified device architecture (CUDA). A parallel Smith-Waterman algorithm is proposed to further optimize the performance of CUDASW++ 1.0 based on the single instruction, multiple thread (SIMT) abstraction. For the first time, we have investigated a partitioned vectorized Smith-Waterman algorithm using CUDA based on the virtualized single instruction, multiple data (SIMD) abstraction. The optimized SIMT and the partitioned vectorized algorithms were benchmarked, and remarkably, have similar performance characteristics. CUDASW++ 2.0 achieves performance improvement over CUDASW++ 1.0 as much as 1.74 (1.72) times using the optimized SIMT algorithm and up to 1.77 (1.66) times using the partitioned vectorized algorithm, with a performance of up to 17 (30) billion cells update per second (GCUPS) on a single-GPU GeForce GTX 280 (dual-GPU GeForce GTX 295) graphics card.</p> <p>Conclusions</p> <p>CUDASW++ 2.0 is publicly available open-source software, written in CUDA and C++ programming languages. It obtains significant performance improvement over CUDASW++ 1.0 using either the optimized SIMT algorithm or the partitioned vectorized algorithm for Smith-Waterman protein database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs.</p

Structure and function of the Rad9-binding region of the DNA-damage checkpoint adaptor TopBP1

TopBP1 is a scaffold protein that coordinates activation of the DNA-damage-checkpoint response by coupling binding of the 9-1-1 checkpoint clamp at sites of ssDNA, to activation of the ATR-ATRIP checkpoint kinase complex. We have now determined the crystal structure of the N-terminal region of human TopBP1, revealing an unexpected triple-BRCT domain structure. The arrangement of the BRCT domains differs significantly from previously described tandem BRCT domain structures, and presents two distinct sites for binding phosphopeptides in the second and third BRCT domains. We show that the site in the second but not third BRCT domain in the N-terminus of TopBP1, provides specific interaction with a phosphorylated motif at pSer387 in Rad9, which can be generated by CK2