A twist in the tail : SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication

The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2′-hydroxyl acylation analysed by primer extension. Marked differences were found in the long-range interactions of SL9266 when the two widely used genotype 2a JFH-1 (HCVcc) and genotype 1b Con1b sub-genomic replicon systems were compared. In both genomes, there was evidence for interaction of the sub-terminal bulge loop of SL9266 and sequences around nucleotide 9110, though the replication phenotype of genomes bearing mutations that disrupted this interaction was fundamentally different. In contrast, a ‘kissing loop’ interaction between the terminal loop of SL9266 and sequences in the 3′-untranslated X-tail was only detectable in JFH-1-based genomes. In the latter, where both long-range interactions are present, they were independent, implying that SL9266 forms the core of an extended pseudoknot. The presence of the ‘kissing loop’ interaction inhibited the formation of SL9571 in the 3′-X-tail, an RNA structure implicated in genome replication. We propose that, SL9266 may contribute a switch function that modulates the mutually incompatible translation and replication events that must occur for replication of the positive-strand RNA genome of HCV

Sustaining Electron Transfer Pathways Extends Biohybrid Photoelectrode Stability to Years

The exploitation of natural photosynthetic enzymes in semi-artificial devices constitutes an attractive and potentially sustainable route for the conversion of solar energy into electricity and solar fuels. However, the stability of photosynthetic proteins after incorporation in a biohybrid architecture typically limits the operational lifetime of biophotoelectrodes to a few hours. Here, we demonstrate ways to greatly enhance the stability of a mesoporous electrode coated with the RC-LH1 photoprotein from Rhodobacter sphaeroides. By preserving electron transfer pathways, we extended operation under continuous high-light to 33 days, and operation after storage to over two years. Coupled with large photocurrents that reached peak values of 4.6 mA cm−2, the optimized biophotoelectrode produced a cumulative output of 86 C cm−2, the largest reported performance to date. Our results demonstrate that the factor limiting stability is the architecture surrounding the photoprotein, and that biohybrid sensors and photovoltaic devices with operational lifetimes of years are feasible

Absolute frequency measurement of the magnesium intercombination transition 1S0→3P1^1S_0 \to ^3P_1

We report on a frequency measurement of the $(3s^2)^1S_0\to(3s3p)^3P_1$ clock transition of $^{24}$Mg on a thermal atomic beam. The intercombination transition has been referenced to a portable primary Cs frequency standard with the help of a femtosecond fiber laser frequency comb. The achieved uncertainty is $2.5\times10^{-12}$ which corresponds to an increase in accuracy of six orders of magnitude compared to previous results. The measured frequency value permits the calculation of several other optical transitions from $^1S_0$ to the $^3P_J$-level system for $^{24}$Mg, $^{25}$Mg and $^{26}$Mg. We describe in detail the components of our optical frequency standard like the stabilized spectroscopy laser, the atomic beam apparatus used for Ramsey-Bord\'e interferometry and the frequency comb generator and discuss the uncertainty contributions to our measurement including the first and second order Doppler effect. An upper limit of $3\times10^{-13}$ in one second for the short term instability of our optical frequency standard was determined by comparison with a GPS disciplined quartz oscillator.Comment: 8 pages, 8 figure

β\beta-BaB2_2O4_4 deep UV monolithic walk-off compensating tandem

The generation of watt-level cw narrow-linewidth sources at specific deep UV wavelengths corresponding to atomic cooling transitions usually employs external cavity-enhanced second-harmonic generation (SHG) of moderate-power visible lasers in birefringent materials. In this work, we investigate a novel approach to cw deep-UV generation by employing the low-loss BBO in a monolithic walkoff-compensating structure [Zondy {\it{et al}}, J. Opt. Soc. Am. B {\bf{20}} (2003) 1675] to simultaneously enhance the effective nonlinear coefficient while minimizing the UV beam ellipticity under tight focusing. As a preliminary step to cavity-enhanced operation, and in order to apprehend the design difficulties stemming from the extremely low acceptance angle of BBO, we investigate and analyze the single-pass performance of a $L_c=8$mm monolithic walk-off compensating structure made of 2 optically-contacted BBO plates cut for type-I critically phase-matched SHG of a cw $\lambda=570.4$nm dye laser. As compared with a bulk crystal of identical length, a sharp UV efficiency enhancement factor of 1.65 has been evidenced with the tandem structure, but at $\sim-1$nm from the targeted fundamental wavelength, highlighting the sensitivity of this technique when applied to a highly birefringent material such as BBO. Solutions to angle cut residual errors are identified so as to match accurately more complex periodic-tandem structure performance to any target UV wavelength, opening the prospect for high-power, good beam quality deep UV cw laser sources for atom cooling and trapping.Comment: 21 pages, 8 figures, to appear in Opt. Commu

Metabolic changes in summer active and anuric hibernating free-ranging brown bears (ursus arctos)

The brown bear (Ursus arctos) hibernates for 5 to 6 months each winter and during this time ingests no food or water and remains anuric and inactive. Despite these extreme conditions, bears do not develop azotemia and preserve their muscle and bone strength. To date most renal studies have been limited to small numbers of bears, often in captive environments. Sixteen free-ranging bears were darted and had blood drawn both during hibernation in winter and summer. Samples were collected for measurement of creatinine and urea, markers of inflammation, the calcium-phosphate axis, and nutritional parameters including amino acids. In winter the bear serum creatinine increased 2.5 fold despite a 2-fold decrease in urea, indicating a remarkable ability to recycle urea nitrogen during hibernation. During hibernation serum calcium remained constant despite a decrease in serum phosphate and a rise in FGF23 levels. Despite prolonged inactivity and reduced renal function, inflammation does not ensue and bears seem to have enhanced antioxidant defense mechanisms during hibernation. Nutrition parameters showed high fat stores, preserved amino acids and mild hyperglycemia during hibernation. While total, essential, non-essential and branched chain amino acids concentrations do not change during hibernation anorexia, changes in individual amino acids ornithine, citrulline and arginine indicate an active, although reduced urea cycle and nitrogen recycling to proteins. Serum uric acid and serum fructose levels were elevated in summer and changes between seasons were positively correlated. Further studies to understand how bears can prevent the development of uremia despite minimal renal function during hibernation could provide new therapeutic avenues for the treatment of human kidney disease

Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit

Photosynthetic reaction centres show promise for biomolecular electronics as nanoscale solar-powered batteries and molecular diodes that are amenable to atomic-level re-engineering. In this work the mechanism of electron conduction across the highly tractable Rhodobacter sphaeroides reaction centre is characterized by conductive atomic force micro-scopy. We find, using engineered proteins of known structure, that only one of the two cofactor wires connecting the positive and negative termini of this reaction centre is capable of conducting unidirectional current under a suitably oriented bias, irrespective of the magnitude of the bias or the applied force at the tunnelling junction. This behaviour, strong functional asymmetry in a largely symmetrical protein–cofactor matrix, recapitulates the strong functional asymmetry characteristic of natural photochemical charge separation, but it is surprising given that the stimulus for electron flow is simply an externally applied bias. Reasons for the electrical resistance displayed by the so-called B-wire of cofactors are explored

Ramsey interferometry with an atom laser

We present results on a free-space atom interferometer operating on the first order magnetically insensitive |F=1,mF=0> -> |F=2,mF=0> transition of Bose-condensed 87Rb atoms. A pulsed atom laser is output-coupled from a Bose-Einstein condensate and propagates through a sequence of two internal state beam splitters, realized via coherent Raman transitions between the two interfering states. We observe Ramsey fringes with a visibility close to 100% and determine the current and the potentially achievable interferometric phase sensitivity. This system is well suited to testing recent proposals for generating and detecting squeezed atomic states.Comment: published version, 8 pages, 3 figure

Long-distance remote comparison of ultrastable optical frequencies with 1e-15 instability in fractions of a second

We demonstrate a fully optical, long-distance remote comparison of independent ultrastable optical frequencies reaching a short term stability that is superior to any reported remote comparison of optical frequencies. We use two ultrastable lasers, which are separated by a geographical distance of more than 50 km, and compare them via a 73 km long phase-stabilized fiber in a commercial telecommunication network. The remote characterization spans more than one optical octave and reaches a fractional frequency instability between the independent ultrastable laser systems of 3e-15 in 0.1 s. The achieved performance at 100 ms represents an improvement by one order of magnitude to any previously reported remote comparison of optical frequencies and enables future remote dissemination of the stability of 100 mHz linewidth lasers within seconds.Comment: 7 pages, 4 figure

The cyclic GMP modulators YC-1 and zaprinast reduce vessel remodeling through anti-proliferative and pro-apoptotic effects

Guanosine-specific cyclic nucleotide signaling is suggested to serve protective actions in the vasculature; however, the influence of selective pharmacologic modulation of cyclic guanosine monophosphate (GMP)-synthesizing soluble guanylate cyclase (sGC) or cyclic GMP-degrading phosphodiesterase (PDE) on vessel remodeling has not been thoroughly examined. In this study, rat carotid artery balloon injury was performed and the growth-modulating effects of the sGC stimulator YC-1 or the cGMP-dependent PDE-V inhibitor zaprinast were examined. YC-1 or zaprinast elevated vessel cyclic GMP content, reduced medial wall and neointimal cell proliferation, stimulated medial and neointimal cellular apoptosis, and markedly attenuated neointimal remodeling in comparable fashion. Interestingly, sGC inhibition by ODQ failed to noticeably alter neointimal growth, and concomitant zaprinast with YC-1 did not modify any parameter compared to individual treatments. These results provide novel in vivo evidence that YC-1 and zaprinast inhibit injury-induced vascular remodeling through anti-mitogenic and pro-apoptotic actions and may offer promising therapeutic approaches against vasoproliferative disorders. Originally published J Cardiovasc Pharmacol Ther, Vol. 14, No. 2, June 200

Integrated fiber-mirror ion trap for strong ion-cavity coupling

We present and characterize fiber mirrors and a miniaturized ion-trap design developed to integrate a fiber-based Fabry-Perot cavity (FFPC) with a linear Paul trap for use in cavity-QED experiments with trapped ions. Our fiber-mirror fabrication process not only enables the construction of FFPCs with small mode volumes, but also allows us to minimize the influence of the dielectric fiber mirrors on the trapped-ion pseudopotential. We discuss the effect of clipping losses for long FFPCs and the effect of angular and lateral displacements on the coupling efficiencies between cavity and fiber. Optical profilometry allows us to determine the radii of curvature and ellipticities of the fiber mirrors. From finesse measurements, we infer a single-atom cooperativity of up to 12 for FFPCs longer than 200 μm in length; comparison to cavities constructed with reference substrate mirrors produced in the same coating run indicates that our FFPCs have similar scattering losses. We characterize the birefringence of our fiber mirrors, finding that careful fiber-mirror selection enables us to construct FFPCs with degenerate polarization modes. As FFPCs are novel devices, we describe procedures developed for handling, aligning, and cleaning them. We discuss experiments to anneal fiber mirrors and explore the influence of the atmosphere under which annealing occurs on coating losses, finding that annealing under vacuum increases the losses for our reference substrate mirrors. X-ray photoelectron spectroscopy measurements indicate that these losses may be attributable to oxygen depletion in the mirror coating. Special design considerations enable us to introduce a FFPC into a trapped ion setup. Our unique linear Paul trap design provides clearance for such a cavity and is miniaturized to shield trapped ions from the dielectric fiber mirrors. We numerically calculate the trap potential in the absence of fibers. In the experiment additional electrodes can be used to compensate distortions of the potential due to the fibers. Home-built fiber feedthroughs connect the FFPC to external optics, and an integrated nanopositioning system affords the possibility of retracting or realigning the cavity without breaking vacuum