Extremal transmission at the Dirac point of a photonic band structure

We calculate the effect of a Dirac point (a conical singularity in the band structure) on the transmission of monochromatic radiation through a photonic crystal. The transmission as a function of frequency has an extremum at the Dirac point, depending on the transparencies of the interfaces with free space. The extremal transmission $T_{0}=\Gamma_{0} W/L$ is inversely proportional to the longitudinal dimension $L$ of the crystal (for $L$ larger than the lattice constant and smaller than the transverse dimension $W$). The interface transparencies affect the proportionality constant $\Gamma_{0}$, and they determine whether the extremum is a minimum or a maximum, but they do not affect the ``pseudo-diffusive'' 1/L dependence of $T_{0}$.Comment: 6 pages, 4 figures. Fig. 1 revised, Fig. 4 adde

Integer quantum Hall effect on a six valley hydrogen-passivated silicon (111) surface

We report magneto-transport studies of a two-dimensional electron system formed in an inversion layer at the interface between a hydrogen-passivated Si(111) surface and vacuum. Measurements in the integer quantum Hall regime demonstrate the expected sixfold valley degeneracy for these surfaces is broken, resulting in an unequal occupation of the six valleys and anisotropy in the resistance. We hypothesize the misorientation of Si surface breaks the valley states into three unequally spaced pairs, but the observation of odd filling factors, is difficult to reconcile with non-interacting electron theory.Comment: 4 pages, 4 figures, to appear in Physical Review Letter

Coulomb Blockade Doppelgangers in Quantum Hall States

In this paper, we ask the question: How well can Coulomb blockade experiments correctly identify and distinguish between different topological orders in quantum Hall states? We definitively find the answer to be: Quite poorly. In particular, we write the general expression for the spacing of resonance peaks in a simple form that explicitly displays its dependence on the conformal scaling dimensions of the systems' edge modes. This form makes transparent the general argument that the Coulomb blockade peak spacings do not provide a strongly indicative signature of the topological order of the system, since it is only weakly related to the braiding statistics. We bolster this general argument with examples for all the most physically relevant non-Abelian candidate states, demonstrating that they have Coulomb blockade doppelgangers -- candidate states at the same filling fraction with identical Coulomb blockade signatures, but dramatically different topological orders and braiding statistics.Comment: 12 pages, 1 figure; portions of this paper were formerly included in Appendix C of arXiv:0903.3108; v2: examples added, minor corrections made; v3: discussions of non-uniform filling and of hierarchical counterparts of multi-component states added, minor corrections mad

Energy metabolism in human pluripotent stem cells and their differentiated counterparts

Background: Human pluripotent stem cells have the ability to generate all cell types present in the adult organism, therefore harboring great potential for the in vitro study of differentiation and for the development of cell-based therapies. Nonetheless their use may prove challenging as incomplete differentiation of these cells might lead to tumoregenicity. Interestingly, many cancer types have been reported to display metabolic modifications with features that might be similar to stem cells. Understanding the metabolic properties of human pluripotent stem cells when compared to their differentiated counterparts can thus be of crucial importance. Furthermore recent data has stressed distinct features of different human pluripotent cells lines, namely when comparing embryo-derived human embryonic stem cells (hESCs) and induced pluripotent stem cells (IPSCs) reprogrammed from somatic cells. Methodology/Principal Findings: We compared the energy metabolism of hESCs, IPSCs, and their somatic counterparts. Focusing on mitochondria, we tracked organelle localization and morphology. Furthermore we performed gene expression analysis of several pathways related to the glucose metabolism, including glycolysis, the pentose phosphate pathway and the tricarboxylic acid (TCA) cycle. In addition we determined oxygen consumption rates (OCR) using a metabolic extracellular flux analyzer, as well as total intracellular ATP levels by high performance liquid chromatography (HPLC). Finally we explored the expression of key proteins involved in the regulation of glucose metabolism. Conclusions/Findings: Our results demonstrate that, although the metabolic signature of IPSCs is not identical to that of hESCs, nonetheless they cluster with hESCs rather than with their somatic counterparts. ATP levels, lactate production and OCR revealed that human pluripotent cells rely mostly on glycolysis to meet their energy demands. Furthermore, our work points to some of the strategies which human pluripotent stem cells may use to maintain high glycolytic rates, such as high levels of hexokinase II and inactive pyruvate dehydrogenase (PDH). © 2011 Varum et al

Efficient processing of TFO-directed psoralen DNA interstrand crosslinks by the UvrABC nuclease

Photoreactive psoralens can form interstrand crosslinks (ICLs) in double-stranded DNA. In eubacteria, the endonuclease UvrABC plays a key role in processing psoralen ICLs. Psoralen-modified triplex-forming oligonucleotides (TFOs) can be used to direct ICLs to specific genomic sites. Previous studies of pyrimidine-rich methoxypsoralen–modified TFOs indicated that the TFO inhibits cleavage by UvrABC. Because different chemistries may alter the processing of TFO-directed ICLs, we investigated the effect of another type of triplex formed by purine-rich TFOs on the processing of 4′-(hydroxymethyl)-4,5′,8-trimethylpsoralen (HMT) ICLs by the UvrABC nuclease. Using an HMT-modified TFO to direct ICLs to a specific site, we found that UvrABC made incisions on the purine-rich strand of the duplex ∼3 bases from the 3′-side and ∼9 bases from the 5′-side of the ICL, within the TFO-binding region. In contrast to previous reports, the UvrABC nuclease cleaved the TFO-directed psoralen ICL with a greater efficiency than that of the psoralen ICL alone. Furthermore, the TFO was dissociated from its duplex binding site by UvrA and UvrB. As mutagenesis by TFO-directed ICLs requires nucleotide excision repair, the efficient processing of these lesions supports the use of triplex technology to direct DNA damage for genome modification

Charge transport through weakly open one dimensional quantum wires

We consider resonant transmission through a finite-length quantum wire connected to leads via finite transparency junctions. The coherent electron transport is strongly modified by the Coulomb interaction. The low-temperature current-voltage ($IV$) curves show step-like dependence on the bias voltage determined by the distance between the quantum levels inside the conductor, the pattern being dependent on the ratio between the charging energy and level spacing. If the system is tuned close to the resonance condition by the gate voltage, the low-voltage $IV$ curve is Ohmic. At large Coulomb energy and low temperatures, the conductance is temperature-independent for any relationship between temperature, level spacing, and coupling between the wire and the leads

Overexpression of mitochondrial sirtuins alters glycolysis and mitochondrial function in HEK293 cells

SIRT3, SIRT4, and SIRT5 are mitochondrial deacylases that impact multiple facets of energy metabolism and mitochondrial function. SIRT3 activates several mitochondrial enzymes, SIRT4 represses its targets, and SIRT5 has been shown to both activate and repress mitochondrial enzymes. To gain insight into the relative effects of the mitochondrial sirtuins in governing mitochondrial energy metabolism, SIRT3, SIRT4, and SIRT5 overexpressing HEK293 cells were directly compared. When grown under standard cell culture conditions (25 mM glucose) all three sirtuins induced increases in mitochondrial respiration, glycolysis, and glucose oxidation, but with no change in growth rate or in steady-state ATP concentration. Increased proton leak, as evidenced by oxygen consumption in the presence of oligomycin, appeared to explain much of the increase in basal oxygen utilization. Growth in 5 mM glucose normalized the elevations in basal oxygen consumption, proton leak, and glycolysis in all sirtuin over-expressing cells. While the above effects were common to all three mitochondrial sirtuins, some differences between the SIRT3, SIRT4, and SIRT5 expressing cells were noted. Only SIRT3 overexpression affected fatty acid metabolism, and only SIRT4 overexpression altered superoxide levels and mitochondrial membrane potential. We conclude that all three mitochondrial sirtuins can promote increased mitochondrial respiration and cellular metabolism. SIRT3, SIRT4, and SIRT5 appear to respond to excess glucose by inducing a coordinated increase of glycolysis and respiration, with the excess energy dissipated via proton leak. © 2014 Barbi de Moura et al

Functional characterization of 8-oxoguanine DNA glycosylase of Trypanosoma cruzi

The oxidative lesion 8-oxoguanine (8-oxoG) is removed during base excision repair by the 8-oxoguanine DNA glycosylase 1 (Ogg1). This lesion can erroneously pair with adenine, and the excision of this damaged base by Ogg1 enables the insertion of a guanine and prevents DNA mutation. In this report, we identified and characterized Ogg1 from the protozoan parasite Trypanosoma cruzi (TcOgg1), the causative agent of Chagas disease. Like most living organisms, T. cruzi is susceptible to oxidative stress, hence DNA repair is essential for its survival and improvement of infection. We verified that the TcOGG1 gene encodes an 8-oxoG DNA glycosylase by complementing an Ogg1-defective Saccharomyces cerevisiae strain. Heterologous expression of TcOGG1 reestablished the mutation frequency of the yeast mutant ogg1-/- (CD138) to wild type levels. We also demonstrate that the overexpression of TcOGG1 increases T. cruzi sensitivity to hydrogen peroxide (H2O2). Analysis of DNA lesions using quantitative PCR suggests that the increased susceptibility to H2O2 of TcOGG1-overexpressor could be a consequence of uncoupled BER in abasic sites and/or strand breaks generated after TcOgg1 removes 8-oxoG, which are not rapidly repaired by the subsequent BER enzymes. This hypothesis is supported by the observation that TcOGG1-overexpressors have reduced levels of 8-oxoG both in the nucleus and in the parasite mitochondrion. The localization of TcOgg1 was examined in parasite transfected with a TcOgg1-GFP fusion, which confirmed that this enzyme is in both organelles. Taken together, our data indicate that T. cruzi has a functional Ogg1 ortholog that participates in nuclear and mitochondrial BER. © 2012 Furtado et al