Shotgun proteomics: Tools for analysis of marine particulate proteins

National Natural Science Foundation of China [40821063, 40376032, 40476053]; Ministry of Science and Technology [2008DF100440]; Program for New Century Excellent Talents in Xiamen UniversityThis study sought a high resolution and high-throughput method to identify and characterize proteins from marine particulate organic matter (POM) using proteomic approaches. The results showed that only a limited number of discrete protein spots were distinguished using two-dimensional electrophoresis (2-DE). Most protein spots were faint and small in 2-DE gels, with a heavy unresolved smeared staining background, indicating 2-DE was not a good high resolution method to separate particulate proteins for identification and characterization. The shotgun proteomic approach combining one-dimensional electrophoresis and capillary liquid chromatography-tandem mass spectrometry as well as the NCBI protein database search was successfully applied to identify and characterize particulate proteins. Using this approach, 737 proteins matching one or more peptides were detected in a POM sample collected from the 41 m water layer in the basin area of the western South China Sea. Of these, 184 were identified as high-confidence proteins matching two or more peptides, including photosynthetic proteins, transporters, molecular chaperones, and porins. In addition to these proteins with known functions, a significant number of novel proteins (accounting for similar to 30% of the proteins identified) were also detected. The identification of a large number of high-confidence proteins in the POM sample demonstrated that the shotgun proteomic approach is reliable and feasible for the study of particulate proteins and will provide a powerful tool to comprehensively investigate the nature and dynamics of POM in the ocean

Scalar Three-point Functions in a CDL Background

Motivated by the FRW-CFT proposal by Freivogel, Sekino, Susskind and Yeh, we compute the three-point function of a scalar field in a Coleman-De Luccia instanton background. We first compute the three-point function of the scalar field making only very mild assumptions about the scalar potential and the instanton background. We obtain the three-point function for points in the FRW patch of the CDL instanton and take two interesting limits; the limit where the three points are near the boundary of the hyperbolic slices of the FRW patch, and the limit where the three points lie on the past lightcone of the FRW patch. We expand the past lightcone three-point function in spherical harmonics. We show that the near boundary limit expansion of the three-point function of a massless scalar field exhibits conformal structure compatible with FRW-CFT when the FRW patch is flat. We also compute the three-point function when the scalar is massive, and explain the obstacles to generalizing the conjectured field-operator correspondence of massless fields to massive fields.Comment: 42 pages + appendices, 10 figures; v2, v3: minor correction

Review of risk factors for human echinococcosis prevalence on the Qinghai-Tibet Plateau, China: a prospective for control options

Objective: Echinococcosis is a major parasitic zoonosis of public health importance in western China. In 2004, the Chinese Ministry of Health estimated that 380,000 people had the disease in the region. The Qinghai-Tibet Plateau is highly co-endemic with both alveolar echinococcosis (AE) and cystic echinococcosis (CE). In the past years, the Chinese government has been increasing the financial support to control the diseases in this region. Therefore, it is very important to identify the significant risk factors of the diseases by reviewing studies done in the region in the past decade to help policymakers design appropriate control strategies. Review: Selection criteria for which literature to review were firstly defined. Medline, CNKI (China National Knowledge Infrastructure), and Google Scholar were systematically searched for literature published between January 2000 and July 2011. Significant risk factors found by single factor and/or multiple factors analysis were listed, counted, and summarized. Literature was examined to check the comparability of the data; age and sex specific prevalence with same data structures were merged and used for further analysis. A variety of assumed social, economical, behavioral, and ecological risk factors were studied on the Plateau. Those most at risk were Tibetan herdsmen, the old and female in particular. By analyzing merged comparable data, it was found that females had a significant higher prevalence, and a positive linearity relationship existed between echinococcosis prevalence and increasing age. In terms of behavioral risk factors, playing with dogs was mostly correlated with CE and/or AE prevalence. In terms of hygiene, employing ground water as the drinking water source was significantly correlated with CE and AE prevalence. For definitive hosts, dog related factors were most frequently identified with prevalence of CE or/and AE; fox was a potential risk factor for AE prevalence only. Overgrazing and deforestation were significant for AE prevalence only. Conclusion: Tibetan herdsmen communities were at the highest risk of echinococcosis prevalence and should be the focus of echinococcosis control. Deworming both owned and stray dogs should be a major measure for controlling echinococcosis; treatment of wild definitive hosts should also be considered for AE endemic areas. Health education activities should be in concert with the local people's education backgrounds and languages in order to be able to improve behaviors. Further researches are needed to clarify the importance of wild hosts for AE/CE prevalence, the extent and range of the impacts of ecologic changes (overgrazing and deforestation) on the AE prevalence, and risk factors in Tibet

Trust transfer between contexts

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.This paper explores whether trust, developed in one context, transfers into another, distinct context and, if so, attempts to quantify the influence this prior trust exerts. Specifically, we investigate the effects of artificially stimulated prior trust as it transfers across disparate contexts and whether this prior trust can compensate for negative objective information. To study such incidents, we leveraged Berg’s investment game to stimulate varying degrees of trust between a human and a set of automated agents. We then observed how trust in these agents transferred to a new game by observing teammate selection in a modified, four-player extension of the well-known board game, Battleship. Following this initial experiment, we included new information regarding agent proficiency in the Battleship game during teammate selection to see how prior trust and new objective information interact. Deploying these experiments on Amazon’s Mechanical Turk platform further allowed us to study these phenomena across a broad range of participants. Our results demonstrate trust does transfer across disparate contexts and this inter-contextual trust transfer exerts a stronger influence over human behavior than objective performance data. That is, humans show a strong tendency to select teammates based on their prior experiences with each teammate, and proficiency information in the new context seems to matter only when the differences in prior trust between potential teammates are small

Deep strong light-matter coupling in plasmonic nanoparticle crystals

In the regime of deep strong light–matter coupling, the coupling strength exceeds the transition energies of the material, fundamentally changing its properties; for example, the ground state of the system contains virtual photons and the internal electromagnetic field gets redistributed by photon self-interaction. So far, no electronic excitation of a material has shown such strong coupling to free-space photons. Here we show that three-dimensional crystals of plasmonic nanoparticles can realize deep strong coupling under ambient conditions, if the particles are ten times larger than the interparticle gaps. The experimental Rabi frequencies (1.9 to 3.3 electronvolts) of face-centred cubic crystals of gold nanoparticles with diameters between 25 and 60 nanometres exceed their plasmon energy by up to 180 per cent. We show that the continuum of photons and plasmons hybridizes into polaritons that violate the rotating-wave approximation. The coupling leads to a breakdown of the Purcell effect—the increase of radiative damping through light–matter coupling—and increases the radiative polariton lifetime. The results indicate that metallic and semiconducting nanoparticles can be used as building blocks for an entire class of materials with extreme light–matter interaction, which will find application in nonlinear optics, the search for cooperative effects and ground states, polariton chemistry and quantum technology

Crystal Structures of the ATPase Domains of Four Human Hsp70 Isoforms: HSPA1L/Hsp70-hom, HSPA2/Hsp70-2, HSPA6/Hsp70B', and HSPA5/BiP/GRP78

The 70-kDa heat shock proteins (Hsp70) are chaperones with central roles in processes that involve polypeptide remodeling events. Hsp70 proteins consist of two major functional domains: an N-terminal nucleotide binding domain (NBD) with ATPase activity, and a C-terminal substrate binding domain (SBD). We present the first crystal structures of four human Hsp70 isoforms, those of the NBDs of HSPA1L, HSPA2, HSPA5 and HSPA6. As previously with Hsp70 family members, all four proteins crystallized in a closed cleft conformation, although a slight cleft opening through rotation of subdomain IIB was observed for the HSPA5-ADP complex. The structures presented here support the view that the NBDs of human Hsp70 function by conserved mechanisms and contribute little to isoform specificity, which instead is brought about by the SBDs and by accessory proteins.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1

Intermediate scalings in holographic RG flows and conductivities

We construct numerically finite density domain-wall solutions which interpolate between two AdS 4 fixed points and exhibit an intermediate regime of hyperscaling violation, with or without Lifshitz scaling. Such RG flows can be realized in gravitational models containing a dilatonic scalar and a massive vector field with appropriate choices of the scalar potential and couplings. The infrared AdS 4 fixed point describes a new ground state for strongly coupled quantum systems realizing such scalings, thus avoiding the well-known extensive zero temperature entropy associated with AdS2×R2. We also examine the zero temperature behavior of the optical conductivity in these backgrounds and identify two scaling regimes before the UV CFT scaling is reached. The scaling of the conductivity is controlled by the emergent IR conformal symmetry at very low frequencies, and by the intermediate scaling regime at higher frequencies

Holographic Hall conductivities from dyonic backgrounds

We develop a general framework for computing the holographic 2-point functions and the corresponding conductivities in asymptotically locally AdS backgrounds with an electric charge density, a constant magentic field, and possibly non-trivial scalar profiles, for a broad class of Einstein-Maxwell-Axion-Dilaton theories, including certain Chern-Simons terms. Holographic renormalization is carried out for any theory in this class and the computation of the renormalized AC conductivities at zero spatial momentum is reduced to solving a single decoupled first order Riccati equation. Moreover, we develop a first order fake supergravity formulalism for dyonic renormalization group flows in four dimensions, allowing us to construct analytically infinite families of such backgrounds by specifying a superpotential at will. These RG flows interpolate between AdS$_4$ in the UV and a hyperscaling violating Lifshitz geometry in the IR with exponents $1<z<3$ and $\theta=z+1$. For $1<z<2$ the spectrum of fluctuations is gapped and discrete. Our hope and intention is that this analysis can serve as a manual for computing the holographic 1- and 2-point functions and the corresponding transport coefficients in any dyonic background, both in the context of AdS/CMT and AdS/QCD

Investigation of Two Fermi-LAT Gamma-Ray Blazars Coincident with High-energy Neutrinos Detected by IceCube

After the identification of the gamma-ray blazar TXS 0506+056 as the first compelling IceCube neutrino source candidate, we perform a systematic analysis of all high-energy neutrino events satisfying the IceCube realtime trigger criteria. We find one additional known gamma-ray source, the blazar GB6 J1040+0617, in spatial coincidence with a neutrino in this sample. The chance probability of this coincidence is 30% after trial correction. For the first time, we present a systematic study of the gamma-ray flux, spectral and optical variability, and multiwavelength behavior of GB6 J1040+0617 and compare it to TXS 0506+056. We find that TXS 0506+056 shows strong flux variability in the Fermi-Large Area Telescope gamma-ray band, being in an active state around the arrival of IceCube-170922A, but in a low state during the archival IceCube neutrino flare in 2014/15. In both cases the spectral shape is statistically compatible (≤2σ) with the average spectrum showing no indication of a significant relative increase of a high-energy component. While the association of GB6 J1040+0617 with the neutrino is consistent with background expectations, the source appears to be a plausible neutrino source candidate based on its energetics and multiwavelength features, namely a bright optical flare and modestly increased gamma-ray activity. Finding one or two neutrinos originating from gamma-ray blazars in the given sample of high-energy neutrinos is consistent with previously derived limits of neutrino emission from gamma-ray blazars, indicating the sources of the majority of cosmic high-energy neutrinos remain unknown