Structural Properties of the Caenorhabditis elegans Neuronal Network

Despite recent interest in reconstructing neuronal networks, complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear. Even for Caenorhabditis elegans, whose neuronal network is relatively small and stereotypical from animal to animal, published wiring diagrams are neither accurate nor complete and self-consistent. Using materials from White et al. and new electron micrographs we assemble whole, self-consistent gap junction and chemical synapse networks of hermaphrodite C. elegans. We propose a method to visualize the wiring diagram, which reflects network signal flow. We calculate statistical and topological properties of the network, such as degree distributions, synaptic multiplicities, and small-world properties, that help in understanding network signal propagation. We identify neurons that may play central roles in information processing and network motifs that could serve as functional modules of the network. We explore propagation of neuronal activity in response to sensory or artificial stimulation using linear systems theory and find several activity patterns that could serve as substrates of previously described behaviors. Finally, we analyze the interaction between the gap junction and the chemical synapse networks. Since several statistical properties of the C. elegans network, such as multiplicity and motif distributions are similar to those found in mammalian neocortex, they likely point to general principles of neuronal networks. The wiring diagram reported here can help in understanding the mechanistic basis of behavior by generating predictions about future experiments involving genetic perturbations, laser ablations, or monitoring propagation of neuronal activity in response to stimulation

Rapid and effective oxidative pretreatment of woody biomass at mild reaction conditions and low oxidant loadings

BACKGROUND: One route for producing cellulosic biofuels is by the fermentation of lignocellulose-derived sugars generated from a pretreatment that can be effectively coupled with an enzymatic hydrolysis of the plant cell wall. While woody biomass exhibits a number of positive agronomic and logistical attributes, these feedstocks are significantly more recalcitrant to chemical pretreatments than herbaceous feedstocks, requiring higher chemical and energy inputs to achieve high sugar yields from enzymatic hydrolysis. We previously discovered that alkaline hydrogen peroxide (AHP) pretreatment catalyzed by copper(II) 2,2΄-bipyridine complexes significantly improves subsequent enzymatic glucose and xylose release from hybrid poplar heartwood and sapwood relative to uncatalyzed AHP pretreatment at modest reaction conditions (room temperature and atmospheric pressure). In the present work, the reaction conditions for this catalyzed AHP pretreatment were investigated in more detail with the aim of better characterizing the relationship between pretreatment conditions and subsequent enzymatic sugar release. RESULTS: We found that for a wide range of pretreatment conditions, the catalyzed pretreatment resulted in significantly higher glucose and xylose enzymatic hydrolysis yields (as high as 80% for both glucose and xylose) relative to uncatalyzed pretreatment (up to 40% for glucose and 50% for xylose). We identified that the extent of improvement in glucan and xylan yield using this catalyzed pretreatment approach was a function of pretreatment conditions that included H(2)O(2) loading on biomass, catalyst concentration, solids concentration, and pretreatment duration. Based on these results, several important improvements in pretreatment and hydrolysis conditions were identified that may have a positive economic impact for a process employing a catalyzed oxidative pretreatment. These improvements include identifying that: (1) substantially lower H(2)O(2) loadings can be used that may result in up to a 50-65% decrease in H(2)O(2) application (from 100 mg H(2)O(2)/g biomass to 35–50 mg/g) with only minor losses in glucose and xylose yield, (2) a 60% decrease in the catalyst concentration from 5.0 mM to 2.0 mM (corresponding to a catalyst loading of 25 μmol/g biomass to 10 μmol/g biomass) can be achieved without a subsequent loss in glucose yield, (3) an order of magnitude improvement in the time required for pretreatment (minutes versus hours or days) can be realized using the catalyzed pretreatment approach, and (4) enzyme dosage can be reduced to less than 30 mg protein/g glucan and potentially further with only minor losses in glucose and xylose yields. In addition, we established that the reaction rate is improved in both catalyzed and uncatalyzed AHP pretreatment by increased solids concentrations. CONCLUSIONS: This work explored the relationship between reaction conditions impacting a catalyzed oxidative pretreatment of woody biomass and identified that significant decreases in the H(2)O(2), catalyst, and enzyme loading on the biomass as well as decreases in the pretreatment time could be realized with only minor losses in the subsequent sugar released enzymatically. Together these changes would have positive implications for the economics of a process based on this pretreatment approach

The Drosophila caspase Ice is important for many apoptotic cell deaths and for spermatid individualization, a nonapoptotic process

Caspase family proteases play important roles in the regulation of apoptotic cell death. Initiator caspases are activated in response to death stimuli, and they transduce and amplify these signals by cleaving and thereby activating effector caspases. In Drosophila, the initiator caspase Nc (previously Dronc) cleaves and activates two short-prodomain caspases, Dcp-1 and Ice (previously Drice), suggesting these as candidate effectors of Nc killing activity. dcp-1-null mutants are healthy and possess few defects in normally occurring cell death. To explore roles for Ice in cell death, we generated and characterized an Ice null mutant. Animals lacking Ice show a number of defects in cell death, including those that occur during embryonic development, as well as during formation of adult eyes, arista and wings. Ice mutants exhibit subtle defects in the destruction of larval tissues, and do not prevent destruction of salivary glands during metamorphosis. Cells from Ice animals are also markedly resistant to several stresses, including X-irradiation and inhibition of protein synthesis. Mutations in Ice also suppress cell death that is induced by expression of Rpr, Wrinkled (previously Hid) and Grim. These observations demonstrate that Ice plays an important non-redundant role as a cell death effector. Finally, we demonstrate that Ice participates in, but is not absolutely required for, the non-apoptotic process of spermatid differentiation

A Spitzer MIPS Study of 2.5-2.0 M\odot Stars in Scorpius-Centaurus

We have obtained Spitzer Space Telescope Multiband Imaging Photometer for Spitzer (MIPS) 24 {\mu}m and 70 {\mu}m observations of 215 nearby, Hipparcos B- and A-type common proper motion single and binary systems in the nearest OB association, Scorpius-Centaurus. Combining our MIPS observations with those of other ScoCen stars in the literature, we estimate 24 {\mu}m B+A-type disk fractions of 17/67 (25+6%), 36/131 (27+4%), and 23/95 (24+5%) for Upper Scorpius (\sim11 Myr), Upper Centaurus Lupus (\sim15 Myr), and Lower Centaurus Crux (\sim17 Myr), respectively, somewhat smaller disk fractions than previously obtained for F- and G-type members. We confirm previous IRAS excess detections and present new discoveries of 51 protoplanetary and debris disk systems, with fractional infrared luminosities ranging from LIR/L\ast = 1e-6 to 1e-2 and grain temperatures ranging from Tgr = 40 - 300 K. In addition, we confirm that the 24 {\mu}m and 70 {\mu}m excesses (or fractional infrared luminosities) around B+A type stars are smaller than those measured toward F+G type stars and hypothesize that the observed disk property dependence on stellar mass may be the result of a higher stellar companion fraction around B- and A-type stars at 10 - 200 AU and/or the presence of Jupiter-mass companions in the disks around F- and G- type stars. Finally, we note that the majority of the ScoCen 24 {\mu}m excess sources also possess 12 {\mu}m excess, indicating that Earth-like planets may be forming via collisions in the terrestrial planet zone at \sim10 - 100 Myr.Comment: 62 pages, 17 figures including 6 colo

Brownian Thermal Noise in Multilayer Coated Mirrors

We analyze the Brownian thermal noise of a multi-layer dielectric coating, used in high-precision optical measurements including interferometric gravitational-wave detectors. We assume the coating material to be isotropic, and therefore study thermal noises arising from shear and bulk losses of the coating materials. We show that coating noise arises not only from layer thickness fluctuations, but also from fluctuations of the interface between the coating and substrate, driven by internal fluctuating stresses of the coating. In addition, the non-zero photoeleastic coefficients of the thin films modifies the influence of the thermal noise on the laser field. The thickness fluctuations of different layers are statistically independent, however, there exists a finite coherence between layers and the substrate-coating interface. Taking into account uncertainties in material parameters, we show that significant uncertainties still exist in estimating coating Brownian noise.Comment: 26 pages, 18 figure

The impact of local sources and long-range transport on aerosol properties over the northeast U.S. region during INTEX-NA

We use data collected aboard the NASA DC-8 aircraft during the summer 2004, Intercontinental Transport and Chemical Evolution Experiment over North America (INTEX-NA) field campaign to examine the origin, composition, physical and optical properties of aerosols within air masses sampled over and downwind of the northeastern U.S. We note that aerosol concentrations within the region exhibited steep vertical gradients and significant variability in both time and space. An examination of air mass chemical signatures and backward trajectories indicates that transport from four, significantly different source regions contributed to the variability: the subtropical Atlantic Ocean (AO); the U.S. west coast and eastern Pacific (WCP); the U.S. east coast and Midwestern states (EC); and northwest Canada and Alaska (CA). AO air masses were typically confined to below 2 km altitude, exhibited low pollutant contents, contained enhanced levels of sea salt, and were typically observed when the Bermuda High strengthened. The most common air mass present in the upper troposphere, WCP air often contained weak dust and aged pollution enhances from convective input occurring over the central part of the continent. CA air exhibited enhancements in anthropogenic pollution tracers below 2 km and contained some black-carbon rich haze layers between 3 and 5 km that could be traced to forest fires burning in western Canada and Alaska. EC air was prevalent at lower elevations throughout the study area and exhibited enhanced scattering along with elevated levels of sulfate aerosols and combustion tracers. There is an overall balance between the observed cations and anions for all cases, except EC air mass below 4 km

Coulomb interactions at quantum Hall critical points of systems in a periodic potential

We study the consequences of long-range Coulomb interactions at the critical points between integer/fractional quantum Hall states and an insulator. We use low energy theories for such transitions in anyon gases in the presence of an external periodic potential. We find that Coulomb interactions are marginally irrelevant for the integer quantum Hall case. For the fractional case, depending upon the anyon statistics parameter, we find behavior similar to the integer case, or flow to a novel line of fixed points with exponents $z=1$, $\nu > 1$ stable against weak disorder in the position of the critical point, or run-away flow to strong coupling.Comment: 12 pages, REVTEX, 1 figur

Observational evidence for the convective transport of dust over the central United States

Bulk aerosol composition and aerosol size distributions measured aboard the DC-8 aircraft during the Deep Convective Clouds and Chemistry Experiment mission in May/June 2012 were used to investigate the transport of mineral dust through nine storms encountered over Colorado and Oklahoma. Measurements made at low altitudes (\u3c5 km mean sea level (MSL)) in the storm inflow region were compared to those made in cirrus anvils (altitude \u3e 9 km MSL). Storm mean outflow Ca2+ mass concentrations and total coarse (1 µm \u3c diameter \u3c 5 µm) aerosol volume (Vc) were comparable to mean inflow values as demonstrated by average outflow/inflow ratios greater than 0.5. A positive relationship between Ca2+, Vc, ice water content, and large (diameter \u3e 50 µm) ice particle number concentrations was not evident; thus, the influence of ice shatter on these measurements was assumed small. Mean inflow aerosol number concentrations calculated over a diameter range (0.5 µm \u3c diameter \u3c 5.0 µm) relevant for proxy ice nuclei (NPIN) were ~15–300 times higher than ice particle concentrations for all storms. Ratios of predicted interstitial NPIN (calculated as the difference between inflow NPIN and ice particle concentrations) and inflow NPIN were consistent with those calculated for Ca2+ and Vc and indicated that on average less than 10% of the ingested NPIN were activated as ice nuclei during anvil formation. Deep convection may therefore represent an efficient transport mechanism for dust to the upper troposphere where these particles can function as ice nuclei cirrus forming in situ

Error analysis of free probability approximations to the density of states of disordered systems

Theoretical studies of localization, anomalous diffusion and ergodicity breaking require solving the electronic structure of disordered systems. We use free probability to approximate the ensemble- averaged density of states without exact diagonalization. We present an error analysis that quantifies the accuracy using a generalized moment expansion, allowing us to distinguish between different approximations. We identify an approximation that is accurate to the eighth moment across all noise strengths, and contrast this with the perturbation theory and isotropic entanglement theory.Comment: 5 pages, 3 figures, submitted to Phys. Rev. Let

Large-scale Graphitic Thin Films Synthesized on Ni and Transferred to Insulators: Structural and Electronic Properties

We present a comprehensive study of the structural and electronic properties of ultrathin films containing graphene layers synthesized by chemical vapor deposition (CVD) based surface segregation on polycrystalline Ni foils then transferred onto insulating SiO2/Si substrates. Films of size up to several mm's have been synthesized. Structural characterizations by atomic force microscopy (AFM), scanning tunneling microscopy (STM), cross-sectional transmission electron microscopy (XTEM) and Raman spectroscopy confirm that such large scale graphitic thin films (GTF) contain both thick graphite regions and thin regions of few layer graphene. The films also contain many wrinkles, with sharply-bent tips and dislocations revealed by XTEM, yielding insights on the growth and buckling processes of the GTF. Measurements on mm-scale back-gated transistor devices fabricated from the transferred GTF show ambipolar field effect with resistance modulation ~50% and carrier mobilities reaching ~2000 cm^2/Vs. We also demonstrate quantum transport of carriers with phase coherence length over 0.2 $\mu$m from the observation of 2D weak localization in low temperature magneto-transport measurements. Our results show that despite the non-uniformity and surface roughness, such large-scale, flexible thin films can have electronic properties promising for device applications.Comment: This version (as published) contains additional data, such as cross sectional TEM image