Cognate peptide-receptor ligand mapping by directed phage display

BACKGROUND: A rapid phage display method for the elucidation of cognate peptide specific ligand for receptors is described. The approach may be readily integrated into the interface of genomic and proteomic studies to identify biologically relevant ligands. METHODS: A gene fragment library from influenza coat protein haemagglutinin (HA) gene was constructed by treating HA cDNA with DNAse I to create 50 – 100 bp fragments. These fragments were cloned into plasmid pORFES IV and in-frame inserts were selected. These in-frame fragment inserts were subsequently cloned into a filamentous phage display vector JC-M13-88 for surface display as fusions to a synthetic copy of gene VIII. Two well characterized antibodies, mAb 12CA5 and pAb 07431, directed against distinct known regions of HA were used to pan the library. RESULTS: Two linear epitopes, HA peptide 112 – 126 and 162–173, recognized by mAb 12CA5 and pAb 07431, respectively, were identified as the cognate epitopes. CONCLUSION: This approach is a useful alternative to conventional methods such as screening of overlapping synthetic peptide libraries or gene fragment expression libraries when searching for precise peptide protein interactions, and may be applied to functional proteomics

The ProkaBioDen database, a global database of benthic prokaryotic biomasses and densities in the marine realm

Benthic prokaryotes include Bacteria and Archaea and dominate densities of marine benthos. They play major roles in element cycles and heterotrophic, chemoautotrophic, and phototrophic carbon production. To understand how anthropogenic disturbances and climate change might affect these processes, better estimates of prokaryotic biomasses and densities are required. Hence, I developed the ProkaBioDen database, the largest open-access database of benthic prokaryotic biomasses and densities in marine surface sediments. In total, the database comprises 1,089 georeferenced benthic prokaryotic biomass and 1,875 density records extracted from 85 and 112 studies, respectively. I identified all references applying the procedures for systematic reviews and meta analyses and report prokaryotic biomasses as g C cm(-3) sediment, g C g(-1) sediment, and g C m(-2). Density records are presented as cell cm(-3) sediment, cell g(-1) sediment/ sulfide/ vent precipitate, and cell m(-2). This database should serve as reference to close sampling gaps in the future

Hydration increases the lifetime of HSO5 and enhances its ability to act as a nucleation precursor – a computational study

Recent experimental findings indicate that HSO5 radicals may play a key role in the nucleation of atmospheric SO2 oxidation products. HSO5 radicals are metastable intermediates formed in the SO2 oxidation process, and their stability and lifetime are, at present, highly uncertain. Previous high-level computational studies have predicted rather low stabilities for HSO5 with respect to dissociation into SO3+HO2, and have predicted the net reaction HSO3+OH→SO3+HO2 to be slightly exothermal. However, these studies have not accounted for hydration of HSO5 or its precursor HSO3. In this study, we have estimated the effect of hydration on the stability and lifetime of HSO5 using the advanced quantum chemical methods CCSD(T) and G3B3. We have computed formation energies and free energies for mono- and dihydrates of OH, HSO3, HSO5, SO3 and HO2, and also reanalyzed the individual steps of the HSO3+O2→HSO5→SO3+HO2 reaction at a higher level of theory than previously published. Our results indicate that hydration is likely to significantly prolong the lifetime of the HSO5 intermediate in atmospheric conditions, thus increasing the probability of reactions that form products with more than one sulfur atom. Kinetic modeling indicates that these results may help explain the experimental observations that a mixture of sulfur-containing products formed from SO2 oxidation by OH radicals nucleates much more effectively than sulfuric acid taken from a liquid reservoir

Modelling Ag-particle activation and growth in a TSI WCPC model 3785

In this work, we modelled activation and growth of silver particles in the water-operated TSI model 3785 water condensation particle counter (WCPC). Our objective was to investigate theoretically how various effects influence the counting efficiency of this CPC. Coupled fluid and particle dynamic processes were modelled with the computational fluid dynamics (CFD) code FLUENT in combination with the Fine Particle Model (FPM) to obtain profiles of temperature, vapour concentration, nucleation rate, and particle size. We found that the counting efficiency of the TSI 3785 for small particles might be affected by the presence of larger particles. Moreover, homogeneous nucleation processes can significantly influence counting efficiency

Modelling Ag-particle activation and growth in a TSI WCPC model 3785

In this work, we modelled activation and growth of silver particles in the water-operated TSI model 3785 water condensation particle counter (WCPC). Our objective was to investigate theoretically how various effects influence the counting efficiency of this CPC. Coupled fluid and particle dynamic processes were modelled with the computational fluid dynamics (CFD) code FLUENT in combination with the Fine Particle Model (FPM) to obtain profiles of temperature, vapour concentration, nucleation rate, and particle size. We found that the counting efficiency of the TSI 3785 for small particles might be affected by the presence of larger particles. Moreover, homogeneous nucleation processes can significantly influence counting efficiency

Surface roughness during depositional growth and sublimation of ice crystals

Full version of an earlier discussion paper (Chou et al. 2018)Ice surface properties can modify the scattering properties of atmospheric ice crystals and therefore affect the radiative properties of mixed-phase and cirrus clouds. The Ice Roughness Investigation System (IRIS) is a new laboratory setup designed to investigate the conditions under which roughness develops on single ice crystals, based on their size, morphology and growth conditions (relative humidity and temperature). Ice roughness is quantified through the analysis of speckle in 2-D light-scattering patterns. Characterization of the setup shows that a supersaturation of 20 % with respect to ice and a temperature at the sample position as low as-40 °C could be achieved within IRIS. Investigations of the influence of humidity show that higher supersaturations with respect to ice lead to enhanced roughness and irregularities of ice crystal surfaces. Moreover, relative humidity oscillations lead to gradual ratcheting-up of roughness and irregularities, as the crystals undergo repeated growth-sublimation cycles. This memory effect also appears to result in reduced growth rates in later cycles. Thus, growth history, as well as supersaturation and temperature, influences ice crystal growth and properties, and future atmospheric models may benefit from its inclusion in the cloud evolution process and allow more accurate representation of not just roughness but crystal size too, and possibly also electrification properties.Peer reviewe

Has phytodetritus processing by an abyssal soft-sediment community recovered 26 years after an experimental disturbance?

The potential harvest of polymetallic nodules will heavily impact the abyssal, soft sediment ecosystem by removing sediment, hard substrate, and associated fauna inside mined areas. It is therefore important to know whether the ecosystem can recover from this disturbance and if so at which rate. The first objective of this study was to measure recovery of phytodetritus processing by the benthic food web from a sediment disturbance experiment in 1989. The second objective was to determine the role of holothurians in the uptake of fresh phytodetritus by the benthic food web. To meet both objectives, large benthic incubation chambers (CUBEs; 50 × 50 × 50 cm) were deployed inside plow tracks (with and without holothurian presence) and at a reference site (holothurian presence, only) at 4100 m water depth. Shortly after deployment, 13C- and 15N-labeled phytodetritus was injected in the incubation chambers and during the subsequent 3-day incubation period, water samples were taken five times to measure the production of 13C-dissolved inorganic carbon over time. At the end of the incubation, holothurians and sediment samples were taken to determine biomass, densities and incorporation of 13C and 15N into bacteria, nematodes, macrofauna, and holothurians. For the first objective, the results showed that biomass of bacteria, nematodes and macrofauna did not differ between reference sites and plow track sites when holothurians were present. Additionally, meiofauna and macrofauna taxonomic composition was not significantly different between the sites. In contrast, total 13C uptake by bacteria, nematodes and holothurians was significantly lower at plow track sites compared to reference sites, though the number of replicates was low. This result suggests that important ecosystem functions such as organic matter processing have not fully recovered from the disturbance that occurred 26 years prior to our study. For the second objective, the analysis indicated that holothurians incorporated 2.16 × 10−3 mmol labile phytodetritus C m−2 d−1 into their biomass, which is one order of magnitude less as compared to bacteria, but 1.3 times higher than macrofauna and one order of magnitude higher than nematodes. Additionally, holothurians incorporated more phytodetritus carbon per unit biomass than macrofauna and meiofauna, suggesting a size-dependence in phytodetritus carbon uptake

Comparison of numerical solutions for Q^2 evolution equations

Q^2 evolution equations are important not only for describing hadron reactions in accelerator experiments but also for investigating ultrahigh-energy cosmic rays. The standard ones are called DGLAP evolution equations, which are integrodifferential equations. There are methods for solving the Q^2 evolution equations for parton-distribution and fragmentation functions. Because the equations cannot be solved analytically, various methods have been developed for the numerical solution. We compare brute-force, Laguerre-polynomial, and Mellin-transformation methods particularly by focusing on the numerical accuracy and computational efficiency. An efficient solution could be used, for example, in the studies of a top-down scenario for the ultrahigh-energy cosmic rays.Comment: 12 pages, LaTeX, 13 eps files, Journal of Computational Physics in press, http://hs.phys.saga-u.ac.j

Heterogeneous ice nucleation: exploring the transition from stochastic to singular freezing behavior

Heterogeneous ice nucleation, a primary pathway for ice formation in the atmosphere, has been described alternately as being stochastic, in direct analogy with homogeneous nucleation, or singular, with ice nuclei initiating freezing at deterministic temperatures. We present an idealized, conceptual model to explore the transition between stochastic and singular ice nucleation. This "soccer ball" model treats particles as being covered with surface sites (patches of finite area) characterized by different nucleation barriers, but with each surface site following the stochastic nature of ice embryo formation. The model provides a phenomenological explanation for seemingly contradictory experimental results obtained in our research groups. Even with ice nucleation treated fundamentally as a stochastic process this process can be masked by the heterogeneity of surface properties, as might be typical for realistic atmospheric particle populations. Full evaluation of the model findings will require experiments with well characterized ice nucleating particles and the ability to vary both temperature and waiting time for freezing

Hygroscopic growth and activation of HULIS particles: experimental data and a new iterative parameterization scheme for complex aerosol particles

International audienceThe hygroscopic growth and activation of two HULIS and one Aerosol-Water-Extract sample, prepared from urban-type aerosol, were investigated. All samples were extracted from filters, redissolved in water and atomized for the investigations presented here. The hygroscopic growth measurements were done using LACIS (Leipzig Aerosol Cloud Interaction Simulator) together with a HH-TDMA (High Humidity Tandem Differential Mobility Analyzer). Hygroscopic growth was determined for relative humidities up to 99.75%. The critical diameters for activation were measured using LACIS for supersaturations between 2 and 10 per mill. All three samples showed a similar hygroscopic growth behaviour, and the two HULIS samples also were similar in their activation behavior, while the Aerosol-Water-Extract turned out to be more CCN active than the HULIS samples. The experimental data was used to derive parameterizations for the hygroscopic growth and activation of HULIS particles. The concept of ?ion (Wex et al., 2007a) and the Szyszkowski-equation (Szyszkowski, 1908; Facchini et al., 1999) were used for parameterizing the Raoult and the Kelvin (surface tension) terms of the Köhler equation, respectively. This concept proved to be very successful for the HULIS samples in the saturation range from relative humidities larger than 98% up to activation. However it failed for the Aerosol-Water extract