Frequency evaluation of the doubly forbidden 1S0→3P0^1S_0\to ^3P_0 transition in bosonic 174^{174}Yb

We report an uncertainty evaluation of an optical lattice clock based on the $^1S_0\leftrightarrow^3P_0$ transition in the bosonic isotope $^{174}$Yb by use of magnetically induced spectroscopy. The absolute frequency of the $^1S_0\leftrightarrow^3P_0$ transition has been determined through comparisons with optical and microwave standards at NIST. The weighted mean of the evaluations is $\nu$($^{174}$Yb)=518 294 025 309 217.8(0.9) Hz. The uncertainty due to systematic effects has been reduced to less than 0.8 Hz, which represents $1.5\times10^{-15}$ in fractional frequency.Comment: 4 pages, 3 figure -Submitted to PRA Rapid Communication

Distribution of Brevetoxin (PbTx-3) in Mouse Plasma: Association with High-Density Lipoproteins

We investigated the brevetoxin congener PbTx-3 to determine its distribution among carrier proteins, including albumin and blood lipoproteins. Using a radiolabeled brevetoxin tracer (PbTx-3), we found that 39% of the radiolabel remained associated with components in mouse plasma after > 15 kDa cutoff dialysis. Of this portion, only 6.8% was bound to serum albumin. We also examined the binding of brevetoxin to various lipoprotein fractions. Plasma, either spiked with PbTx-3 or from mice treated for 30 min with PbTx-3, was fractionated into different-sized lipoproteins by iodixanol gradient ultracentrifugation. Each fraction was then characterized and quantified by agarose gel electrophoresis and brevetoxin radioimmunoassay, respectively. In both the in vitro and in vivo experiments, the majority of brevetoxin immunoreactivity was restricted to only those gradient fractions that contained high-density lipoproteins (HDLs). Independent confirmation of brevetoxin binding to HDLs was provided by high molecular weight (100 kDa cutoff) dialysis of [(3)H]PbTx-3 from lipoprotein fractions as well as a scintillation proximity assay using [(3)H]PbTx-3 and purified human HDLs. This information on the association of brevetoxins with HDLs provides a new foundation for understanding the process by which the toxin is delivered to and removed from tissues and may permit more effective therapeutic measures to treat intoxication from brevetoxins and the related ciguatoxins

Testing ultrafast mode-locking at microhertz relative optical linewidth

We report new limits on the phase coherence of the ultrafast mode-locking process in an octave-spanning Ti:sapphire comb. We find that the mode-locking mechanism correlates optical phase across a full optical octave with less than 2.5 micro Hz relative linewidth. This result is at least two orders of magnitude below recent predictions for quantum-limited individual comb-mode linewidths, verifying that the mode-locking mechanism strongly correlates quantum noise across the comb spectrum.Comment: Expanded discussion to include correlated noise terms, made minor formatting changes, added a reference, and fixed typographical errors. 10 pages, 5 figure

Estimating the Redshift Distribution of Faint Galaxy Samples

We present an empirical method for estimating the underlying redshift distribution N(z) of galaxy photometric samples from photometric observables. The method does not rely on photometric redshift (photo-z) estimates for individual galaxies, which typically suffer from biases. Instead, it assigns weights to galaxies in a spectroscopic subsample such that the weighted distributions of photometric observables (e.g., multi-band magnitudes) match the corresponding distributions for the photometric sample. The weights are estimated using a nearest-neighbor technique that ensures stability in sparsely populated regions of color-magnitude space. The derived weights are then summed in redshift bins to create the redshift distribution. We apply this weighting technique to data from the Sloan Digital Sky Survey as well as to mock catalogs for the Dark Energy Survey, and compare the results to those from the estimation of photo-z's derived by a neural network algorithm. We find that the weighting method accurately recovers the underlying redshift distribution, typically better than the photo-z reconstruction, provided the spectroscopic subsample spans the range of photometric observables covered by the photometric sample.Comment: 14 pages, 9 figures, submitted to MNRA

Measurement of the strong interaction induced shift and width of the 1s state of kaonic deuterium at J-PARC

The antikaon-nucleon interaction close to threshold provides crucial information on the interplay between spontaneous and explicit chiral symmetry breaking in low-energy QCD. In this context the importance of kaonic deuterium X-ray spectroscopy has been well recognized, but no experimental results have yet been obtained due to the difficulty of the measurement. We propose to measure the shift and width of the kaonic deuterium 1s state with an accuracy of 60 eV and 140 eV respectively at J-PARC. These results together with the kaonic hydrogen data (KpX at KEK, DEAR and SIDDHARTA at DAFNE) will then permit the determination of values of both the isospin I=0 and I=1 antikaon-nucleon scattering lengths and will provide the most stringent constraints on the antikaon-nucleon interaction, promising a breakthrough. Refined Monte Carlo studies were performed, including the investigation of background suppression factors for the described setup. These studies have demonstrated the feasibility of determining the shift and width of the kaonic deuterium atom 1s state with the desired accuracy of 60 eV and 140 eV.Comment: 12 pages, 9 figure

Ferritin is secreted via 2 distinct nonclassical vesicular pathways

Ferritin turnover plays a major role in tissue iron homeostasis, and ferritin malfunction is associated with impaired iron homeostasis and neurodegenerative diseases. In most eukaryotes, ferritin is considered an intracellular protein that stores iron in a nontoxic and bioavailable form. In insects, ferritin is a classically secreted protein and plays a major role in systemic iron distribution. Mammalian ferritin lacks the signal peptide for classical endoplasmic reticulum–Golgi secretion but is found in serum and is secreted via a nonclassical lysosomal secretion pathway. This study applied bioinformatics and biochemical tools, alongside a protein trafficking mouse models, to characterize the mechanisms of ferritin secretion. Ferritin trafficking via the classical secretion pathway was ruled out, and a 2:1 distribution of intracellular ferritin between membrane-bound compartments and the cytosol was observed, suggesting a role for ferritin in the vesicular compartments of the cell. Focusing on nonclassical secretion, we analyzed mouse models of impaired endolysosomal trafficking and found that ferritin secretion was decreased by a BLOC-1 mutation but increased by BLOC-2, BLOC-3, and Rab27A mutations of the cellular trafficking machinery, suggesting multiple export routes. A 13-amino-acid motif unique to ferritins that lack the secretion signal peptide was identified on the BC-loop of both subunits and plays a role in the regulation of ferritin secretion. Finally, we provide evidence that secretion of iron-rich ferritin was mediated via the multivesicular body–exosome pathway. These results enhance our understanding of the mechanism of ferritin secretion, which is an important piece in the puzzle of tissue iron homeostasis

Do Natural Proteins Differ from Random Sequences Polypeptides? Natural vs. Random Proteins Classification Using an Evolutionary Neural Network

Are extant proteins the exquisite result of natural selection or are they random sequences slightly edited by evolution? This question has puzzled biochemists for long time and several groups have addressed this issue comparing natural protein sequences to completely random ones coming to contradicting conclusions. Previous works in literature focused on the analysis of primary structure in an attempt to identify possible signature of evolutionary editing. Conversely, in this work we compare a set of 762 natural proteins with an average length of 70 amino acids and an equal number of completely random ones of comparable length on the basis of their structural features. We use an ad hoc Evolutionary Neural Network Algorithm (ENNA) in order to assess whether and to what extent natural proteins are edited from random polypeptides employing 11 different structure-related variables (i.e. net charge, volume, surface area, coil, alpha helix, beta sheet, percentage of coil, percentage of alpha helix, percentage of beta sheet, percentage of secondary structure and surface hydrophobicity). The ENNA algorithm is capable to correctly distinguish natural proteins from random ones with an accuracy of 94.36%. Furthermore, we study the structural features of 32 random polypeptides misclassified as natural ones to unveil any structural similarity to natural proteins. Results show that random proteins misclassified by the ENNA algorithm exhibit a significant fold similarity to portions or subdomains of extant proteins at atomic resolution. Altogether, our results suggest that natural proteins are significantly edited from random polypeptides and evolutionary editing can be readily detected analyzing structural features. Furthermore, we also show that the ENNA, employing simple structural descriptors, can predict whether a protein chain is natural or random