FluShuffle and FluResort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry

Background: Influenza is one of the oldest and deadliest infectious diseases known to man. Reassorted strains of the virus pose the greatest risk to both human and animal health and have been associated with all pandemics of the past century, with the possible exception of the 1918 pandemic, resulting in tens of millions of deaths. We have developed and tested new computer algorithms, FluShuffle and FluResort, which enable reassorted viruses to be identified by the most rapid and direct means possible. These algorithms enable reassorted influenza, and other, viruses to be rapidly identified to allow prevention strategies and treatments to be more efficiently implemented.Results: The FluShuffle and FluResort algorithms were tested with both experimental and simulated mass spectra of whole virus digests. FluShuffle considers different combinations of viral protein identities that match the mass spectral data using a Gibbs sampling algorithm employing a mixed protein Markov chain Monte Carlo (MCMC) method. FluResort utilizes those identities to calculate the weighted distance of each across two or more different phylogenetic trees constructed through viral protein sequence alignments. Each weighted mean distance value is normalized by conversion to a Z-score to establish a reassorted strain.Conclusions: The new FluShuffle and FluResort algorithms can correctly identify the origins of influenza viral proteins and the number of reassortment events required to produce the strains from the high resolution mass spectral data of whole virus proteolytic digestions. This has been demonstrated in the case of constructed vaccine strains as well as common human seasonal strains of the virus. The algorithms significantly improve the capability of the proteotyping approach to identify reassorted viruses that pose the greatest pandemic risk. © 2012 Lun et al.; licensee BioMed Central Ltd.Link_to_subscribed_fulltex

Spatial and Temporal Variation in Brackish Wetland Seedbanks: Implications for Wetland Restoration Following \u3ci\u3ePhragmites\u3c/i\u3e Control

Chesapeake Bay tidal wetlands are experiencing a broad-scale, aggressive invasion by the non-native, clonal grass Phragmites australis. The grass is often managed with herbicides in efforts to restore native plant communities and wildlife habitat. Management efforts, however, can act as a disturbance, resulting in increased light availability, potentially fostering reinvasion from soil seedbanks. If native vegetation establishes quickly from seedbanks, the site should have greater resiliency against invasion, while disturbed sites where native plants do not rapidly establish may be rapidly colonized by P. australis. We surveyed the soil seedbank of three vegetation cover types in five Chesapeake Bay subestuaries: areas where P. australis had been removed, where P. australis was left intact, and with native, reference vegetation. We determined the total germination, the proportion of the seedbank that was attributable to invasive species, the richness, the functional diversity, and the overall composition of the seedbanks in each of the cover types (i.e., plots). After 2 years of herbicide treatment in the P. australis removal plots, vegetation cover type impacted the total germination or the proportion of invasive species in the seedbank. In contrast, we also found that seedbank functional composition in tidal brackish wetlands was not influenced by vegetation cover type in most cases. Instead, plots within a subestuary had similar seedbank functional composition across the years and were composed of diverse functional groups. Based on these findings, we conclude that plant community recovery following P. australis removal is not seed-limited, and any lack of native vegetation recruitment is likely the result of yet-to-be-determined abiotic factors. These diverse seedbanks could lead to resilient wetland communities that could resist invasions. However, due to the prevalence of undesirable species in the seedbank, passive revegetation following invasive plant removal may speed up their re-establishment. The need for active revegetation will need to be assessed on a case-by-case basis to ensure restoration goals are achieved

Ion Mobility-Mass Spectrometry with a Radial Opposed Migration Ion and Aerosol Classifier (ROMIAC)

The first application of a novel differential mobility analyzer, the radial opposed migration ion and aerosol classifier (ROMIAC), is demonstrated. The ROMIAC uses antiparallel forces from an electric field and a cross-flow gas to both scan ion mobilities and continuously transmit target mobility ions with 100% duty cycle. In the ROMIAC, diffusive losses are minimized, and resolution of ions, with collisional cross-sections of 200–2000 Å^2, is achieved near the nondispersive resolution of ~20. Higher resolution is theoretically possible with greater cross-flow rates. The ROMIAC was coupled to a linear trap quadrupole mass spectrometer and used to classify electrosprayed C2–C12 tetra-alkyl ammonium ions, bradykinin, angiotensin I, angiotensin II, bovine ubiquitin, and two pairs of model peptide isomers. Instrument and mobility calibrations of the ROMIAC show that it exhibits linear responses to changes in electrode potential, making the ROMIAC suitable for mobility and cross-section measurements. The high resolution of the ROMIAC facilitates separation of isobaric isomeric peptides. Monitoring distinct dissociation pathways associated with peptide isomers fully resolves overlapping peaks in the ion mobility data. The ability of the ROMIAC to operate at atmospheric pressure and serve as a front-end analyzer to continuously transmit ions with a particular mobility facilitates extensive studies of target molecules using a variety of mass spectrometric methods

A longitudinal study of Sin Nombre virus prevalence in rodents, southeastern Arizona.

We determined the prevalence of Sin Nombre virus antibodies in small mammals in southeastern Arizona. Of 1,234 rodents (from 13 species) captured each month from May through December 1995, only mice in the genus Peromyscus were seropositive. Antibody prevalence was 14.3% in 21 white-footed mice (P. leucopus), 13.3% in 98 brush mice (P. boylii), 0.8% in 118 cactus mice (P. eremicus), and 0% in 2 deer mice (P. maniculatus). Most antibody-positive mice were adult male Peromyscus captured close to one another early in the study. Population dynamics of brush mice suggest a correlation between population size and hantavirus-antibody prevalence

Project Freebird: An orbital transfer vehicle

Freebird is a space-based orbital transfer vehicle designed to repair and deorbit orbital assets. Freebird is based at International Space Station Alpha (ISSA) at an inclination of 51.6 deg and is capable of three types of missions: crewed and teleoperated LEO missions, and extended robotic missions. In a crewed local configuration, the vehicle can visit inclinations between 30.8 deg and 72.4 deg at altitudes close to 390 km. Adding extra fuel tanks extends this range of inclination up to 84.9 deg and down to 18.3 deg. Furthermore, removing the crew module, using the vehicle in a teleoperated manner, and operating with extra fuel tanks allows missions to polar and geosynchronous orbits. To allow for mission flexibility, the vehicle was designed in a semimodular configuration. The major system components include a crew module, a 'smart box' (which contains command, communications, guidance, and navigation equipment), a propulsion pack, extra fuel tanks, and a vehicle storage facility (VSF) for storage purposes. To minimize risk as well as development time and cost, the vehicle was designed using only proven technology or technology which is expected to be flight-qualified in time for the intended launch date of 2002. And, because Freebird carries crew and operates near the space station, it must meet or exceed the NASA reliability standard of 0.994, as well as other standard requirements for such vehicles. The Freebird program was conceived and designed as a way to provide important and currently unavailable satellite repair and replacement services of a value equal to or exceeding operational costs

Chiral Heterocyclic Ligands. XI. Self-assembly and X-Ray Crystal Structures of Chiral Silver Coordination Polymers of (S)-(-)-Nicotine

Three chiral coordination polymers have been prepared by reaction of (S)-(-)-nicotine with silver(I) salts. X-Ray crystal structure determinations revealed that these all contain polymer chains in which the nicotine molecule acts as a bridging ligand between four-coordinate silver atoms. In one case additional bridging by nitrate anions leads to a three-dimensional network structure

Boron-doped diamond dual-plate deep-microtrench device for generator-collector sulfide sensing

International audienceA BDD-BDD dual-plate microtrench electrode with 6 μm inter-electrode spacing is investigated using generator-collector electrochemistry and shown to give microtrench depth-dependent sulfide detection down to the μM levels. The effect of the microtrench depth is compared for a “shallow” 44 μm and a “deep” 180 μm microtrench and linked to the reduction of oxygen to hydrogen peroxide which interferes with sulfide redox cycling. With a deeper microtrench and a fixed collector potential at −1.4 V vs. SCE, two distinct redox cycling potential domains are observed at 0.0 V vs. SCE (2-electron) and at 1.1 V vs. SCE (6-electron)

Experimental investigation of ion-ion recombination under atmospheric conditions

We present the results of laboratory measurements of the ion–ion recombination coefficient at different temperatures, relative humidities and concentrations of ozone and sulfur dioxide. The experiments were carried out using the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber at CERN, the walls of which are made of conductive material, making it possible to measure small ions. We produced ions in the chamber using a 3.5 GeV c−1 beam of positively charged pions (π+) generated by the CERN Proton Synchrotron (PS). When the PS was switched off, galactic cosmic rays were the only ionization source in the chamber. The range of the ion production rate varied from 2 to 100 cm−3 s−1, covering the typical range of ionization throughout the troposphere. The temperature ranged from −55 to 20 °C, the relative humidity (RH) from 0 to 70 %, the SO2 concentration from 0 to 40 ppb, and the ozone concentration from 200 to 700 ppb. The best agreement of the retrieved ion–ion recombination coefficient with the commonly used literature value of 1.6 × 10−6 cm3 s−1 was found at a temperature of 5 °C and a RH of 40 % (1.5 ± 0.6) × 10−6 cm3 s−1. At 20 °C and 40 % RH, the retrieved ion–ion recombination coefficient was instead (2.3 ± 0.7) × 10−6 cm3 s−1. We observed no dependency of the ion–ion recombination coefficient on ozone concentration and a weak variation with sulfur dioxide concentration. However, we observed a more than fourfold increase in the ion–ion recombination coefficient with decreasing temperature. We compared our results with three different models and found an overall agreement for temperatures above 0 °C, but a disagreement at lower temperatures. We observed a strong increase in the recombination coefficient for decreasing relative humidities, which has not been reported previously

Cellobiose Dehydrogenase Aryl Diazonium Modified Single Walled Carbon Nanotubes: Enhanced Direct Electron Transfer through a Positively Charged Surface

One of the challenges in the field of biosensors and biofuel cells is to establish a highly efficient electron transfer rate between the active site of redox enzymes and electrodes to fully access the catalytic potential of the biocatalyst and achieve high current densities. We report on very efficient direct electron transfer (DET) between cellobiose dehydrogenase (CDH) from Phanerochaete sordida (PsCDH) and surface modified single walled carbon nanotubes (SWCNT). Sonicated SWCNTs were adsorbed on the top of glassy carbon electrodes and modified with aryl diazonium salts generated in situ from p-aminobenzoic acid and p-phenylenediamine, thus featuring at acidic pH (3.5 and 4.5) negative or positive surface charges. After adsorption of PsCDH, both electrode types showed excellent long-term stability and very efficient DET. The modified electrode presenting p-aminophenyl groups produced a DET current density of 500,mu A cm(-2) at 200 mV vs normal hydrogen reference electrode (NHE) in a 5 mM lactose solution buffered at pH 3.5. This is the highest reported DET value so far using a CDH modified electrode and comes close to electrodes using mediated electron transfer. Moreover, the onset of the electrocatalytic current for lactose oxidation started at 70 mV vs NHE, a potential which is 50 mV lower compared to when unmodified SWCNTs were used. This effect potentially reduces the interference by oxidizable matrix components in biosensors and increases the open circuit potential in biofuel cells. The stability of the electrode was greatly increased compared with unmodified but cross-linked SWCNTs electrodes and lost only 15% of the initial current after 50 h of constant potential scanning