Modeling the architecture of depolymerase-containing receptor binding proteins in Klebsiella phages

Klebsiella pneumoniae carries a thick polysaccharide capsule. This highly variable chemical structure plays an important role in its virulence. Many Klebsiella bacteriophages recognize this capsule with a receptor binding protein (RBP) that contains a depolymerase domain. This domain degrades the capsule to initiate phage infection. RBPs are highly specific and thus largely determine the host spectrum of the phage. A majority of known Klebsiella phages have only one or two RBPs, but phages with up to 11 RBPs with depolymerase activity and a broad host spectrum have been identified. A detailed bioinformatic analysis shows that similar RBP domains repeatedly occur in K. pneumoniae phages with structural RBP domains for attachment of an RBP to the phage tail (anchor domain) or for branching of RBPs (T4gp10-like domain). Structural domains determining the RBP architecture are located at the N-terminus, while the depolymerase is located in the center of protein. Occasionally, the RBP is complemented with an autocleavable chaperone domain at the distal end serving for folding and multimerization. The enzymatic domain is subjected to an intense horizontal transfer to rapidly shift the phage host spectrum without affecting the RBP architecture. These analyses allowed to model a set of conserved RBP architectures, indicating evolutionary linkages

A scoping review of prevalence, incidence and risk factors for HIV infection amongst young people in Brazil

Background Despite young people being a key population for HIV prevention, the HIV epidemic amongst young Brazilians is perceived to be growing. We therefore reviewed all published literature on HIV prevalence and risk factors for HIV infection amongst 10-25 year olds in Brazil. Methods We searched Embase, LILACS, Proquest, PsycINFO, PubMed, Scopus and Web of Science for studies published up to March 2017 and analyzed reference lists of relevant studies. We included published studies from any time in the HIV epidemic which provided estimates specific to ages 10-25 (or some subset of this age range) for Brazilians on either: (a) HIV prevalence or incidence; or (b) the association between HIV and socio-demographic or behavioral risk factors. Results Forty eight publications met the inclusion criteria: 44 cross-sectional, two case-control, two cohort. Four studies analysed national data. Forty seven studies provided HIV prevalence estimates, largely for six population subgroups: Counselling and Testing Center attendees; blood donors; pregnant women; institutional individuals; men-who-have-sex-with-men (MSM) and female sex workers (FSW); four provided HIV incidence estimates. Twelve studies showed HIV status to be associated with a wide range of risk factors, including age, sexual and reproductive history, infection history, substance use, geography, marital status, mental health and socioeconomic status. Conclusions Few published studies have examined HIV amongst young people in Brazil, and those published have been largely cross-sectional and focused on traditional risk groups and the south of the country. Despite these limitations, the literature shows raised HIV prevalence amongst MSM and FSW, as well as amongst those using drugs. Time trends are harder to identify, although rates appear to be falling for pregnant women, possibly reversing an earlier de-masculinization of the epidemic. Improved surveillance of HIV incidence, prevalence and risk factors is a key component of efforts to eliminate HIV in Brazil

Low-Cost Compact Integrated Rectenna for Implantable Medical Receivers

This work describes a novel fully integrated rectenna circuit using tunnelling-based devices for implanted medical devices. An ASPAT (Asymmetric Spacer Layer Tunnel Diode) was used as the active rectifier due to its high non-linearity and temperature insensitivity features. A miniaturized geometry rectenna ( 1×5 mm 2 ) with improved matching characteristics was demonstrated, by integrating a Cockcroft-Walton rectifier with an L-shaped planar folded antenna structure operating at ISM frequency bands. The circuit performance was experimentally explored at various separation distance between transmitter and receiver units. For a 5cm transmission set-up, the rectenna with a single-stage rectifier delivered 0.8V output at 20dBm transmit power. An extended doubler configuration exhibited enhanced performance when multiple stages are used, is predicted to reach 0.24mW output power at 23dBm transmit power and yielding ~1.6V output voltage with an efficiency of 0.12%. These findings can assist in compensating for the degraded antenna gain attributed to the extremely small effective-radiating area of 0.04λ . Furthermore, the ability of controlling the antenna input impedance helps in circumventing the requirement for a matching circuitry thereby offering further reduction in chip size.UWIPOM2 project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 857654

Miniaturized Folded Antenna with Improved Matching Characteristic for mm-wave Detections

UCMMT 2021 - UK-Europe-China Work. Millimetre-Waves Terahertz Technol., Sep. 2021UWIPOM2 project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 857654

Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages

Pseudomonas virus vB_PaeM_PA5oct is proposed as a model jumbo bacteriophage to investigate phage-bacteria interactions and is a candidate for phage therapy applications. Combining hybrid sequencing, RNA-Seq and mass spectrometry allowed us to accurately annotate its 286,783 bp genome with 461 coding regions including four non-coding RNAs (ncRNAs) and 93 virion-associated proteins. PA5oct relies on the host RNA polymerase for the infection cycle and RNA-Seq revealed a gradual take-over of the total cell transcriptome from 21% in early infection to 93% in late infection. PA5oct is not organized into strictly contiguous regions of temporal transcription, but some genomic regions transcribed in early, middle and late phases of infection can be discriminated. Interestingly, we observe regions showing limited transcription activity throughout the infection cycle. We show that PA5oct upregulates specific bacterial operons during infection including operons pncA-pncB1-nadE involved in NAD biosynthesis, psl for exopolysaccharide biosynthesis and nap for periplasmic nitrate reductase production. We also observe a downregulation of T4P gene products suggesting mechanisms of superinfection exclusion. We used the proteome of PA5oct to position our isolate amongst other phages using a gene-sharing network. This integrative omics study illustrates the molecular diversity of jumbo viruses and raises new questions towards cellular regulation and phage-encoded hijacking mechanisms

An Inversion Analysis of Recent Variability in Natural CO2 Fluxes Using GOSAT and In Situ Observations

About one-half of the global CO2 emissions from fossil fuel combustion and deforestation accumulates in the atmosphere, where it contributes to global warming. The rest is taken up by vegetation and the ocean. The precise contribution of the two sinks, and their location and year-to-year variability are, however, not well understood. We use two different approaches, batch Bayesian synthesis inversion and variational data assimilation, to deduce the global spatiotemporal distributions of CO2 fluxes during 2009-2010. One of our objectives is to assess different sources of uncertainties in inferred fluxes, including uncertainties in prior flux estimates and observations, and differences in inversion techniques. For prior constraints, we utilize fluxes and uncertainties from the CASA-GFED model of the terrestrial biosphere and biomass burning driven by satellite observations and interannually varying meteorology. We also use measurement-based ocean flux estimates and two sets of fixed fossil CO2 emissions. Here, our inversions incorporate column CO2 measurements from the GOSAT satellite (ACOS retrieval, filtered and bias-corrected) and in situ observations (individual flask and afternoon-average continuous observations) to estimate fluxes in 108 regions over 8-day intervals for the batch inversion and at 3 x 3.75 weekly for the variational system. Relationships between fluxes and atmospheric concentrations are derived consistently for the two inversion systems using the PCTM atmospheric transport model driven by meteorology from the MERRA reanalysis. We compare the posterior fluxes and uncertainties derived using different data sets and the two inversion approaches, and evaluate the posterior atmospheric concentrations against independent data including aircraft measurements. The optimized fluxes generally resemble those from other studies. For example, the results indicate that the terrestrial biosphere is a net CO2 sink, and a GOSAT-only inversion suggests a shift in the global sink from the tropics south to the north relative to the prior and to an in-situ-only inversion. We also find a smaller terrestrial sink in higher-latitude northern regions in boreal summer of 2010 relative to 2009

Concentration dependent structural, thermal, and optical features of Pr 3+-doped multicomponent tellurite glasses

Tuning the structural, thermal, and optical properties of low phonon energy glasses such as tellurite glasses (phonon energy ∼750 cm−1) with suitable rare earth dopants is a key issue in the fabrication of solid state lasers and optical amplifiers. In this work, (70-x) TeO2-10 WO3-10 ZnO-5 TiO2-5 Na2O-(x) Pr2O3 (x = 1.0–5.0 mol %) glasses were synthesized with high optical quality and characterized using X-ray diffraction (XRD), Scanning electron microscopy and Energy dispersive X-ray analysis (SEM-EDAX), Attenuated total reflectance-Fourier transform infrared (ATR-FTIR), Raman spectroscopy, Thermo-gravimetric analysis (TGA), Differential scanning calorimetry (DSC), optical absorption and luminescence techniques. The XRD and SEM measurements reveal the amorphous nature of all the prepared glasses and EDAX confirms all the elements present in the respective glasses. The presence of various functional groups such as stretching vibrations of Te[single bond]–O bonds in the [TeO4] trigonal bi-pyramid units, symmetrical stretching or bending vibrations of Te[single bond]–O[single bond]–Te or O[single bond]–Te[single bond]–O linkages at corner sharing sites along the chains of TeO4, TeO3 and TeO3+1, stretching vibrations of W[single bond]–O– and W[double bond; length as m-dash]═O bonds in WO4 tetragonal or WO6 octagonal units, vibrations of Zn[single bond]–O bonds from ZnO4 groups, including non-hygroscopic nature of the glasses are confirmed by ATR-FTIR and Raman spectra, respectively. For Pr3+-doped glasses, from the DSC profiles the glass transition temperature (Tg), onset crystallization temperature (Tx), crystallization temperature (Tc), and melting temperature (Tm) are identified and the evaluated thermal stability values varied in the temperature range of 169–220 °C with increasing Pr3+ doping concentration. Further, the Pr3+ -doped tellurite glasses demonstrate excellent glass stability with higher criterion of Hruby's value (HR) between 1.9 and 3.9. From the measured optical absorption spectrum, experimental oscillator strengths are calculated and used to evaluate three phenomenological Judd-Ofelt (J-O) intensity parameters Ω_λ_ (_λ_ = 2, 4 and 6) and respective radiative properties such as radiative transition probabilities (AR), the branching ratios (βR), and the radiative lifetime (τR) of metastable states for 1.0 mol % Pr3+-doped glass. Five main emission transitions at 3P0 → 3H5 (530 nm; green) with a shoulder at 543 nm, a weak band at 1D2 → 3H4 (592 nm; orange), 3P0 → 3H6 (615 nm; orange), 3P0 → 3F2 (649 nm; red), and 3P0 → 3F3 (686 nm; red) upon exciting at 486 nm (3H4 → 3P0) wavelength are observed from the luminescence spectra of Pr3+-doped tellurite glasses. Following the energy level diagram, Pr3+ ion concentration quenching on the luminescence intensity has been explained by a non-radiative energy transfer between the ions through cross-relaxation and energy migration processes. The concentration dependent structural, thermal, and optical behaviors of Pr 3+-doped tellurite glasses are understood and our systematic analysis could contribute towards the development of suitable optical devices fabrication. Raman spectra of all the synthesized glasses

Simulation Studies of Satellite Laser CO2 Mission Concepts

Results of mission simulation studies are presented for a laser-based atmospheric CO2 sounder. The simulations are based on real-time carbon cycle process modeling and data analysis. The mission concept corresponds to ASCENDS as recommended by the US National Academy of Sciences Decadal Survey. Compared to passive sensors, active (lidar) sensing of CO2 from space has several potentially significant advantages that hold promise to advance CO2 measurement capability in the next decade. Although the precision and accuracy requirements remain at unprecedented levels of stringency, analysis of possible instrument technology indicates that such sensors are more than feasible. Radiative transfer model calculations, an instrument model with representative errors, and a simple retrieval approach complete the cycle from "nature" run to "pseudodata" CO2. Several mission and instrument configuration options are examined, and the sensitivity to key design variables is shown. Examples are also shown of how the resulting pseudo-measurements might be used to address key carbon cycle science questions

Sensitivity of CO2 Simulation in a GCM to the Convective Transport Algorithms

Convection plays an important role in the transport of heat, moisture and trace gases. In this study, we simulated CO2 concentrations with an atmospheric general circulation model (GCM). Three different convective transport algorithms were used. One is a modified Arakawa-Shubert scheme that was native to the GCM; two others used in two off-line chemical transport models (CTMs) were added to the GCM here for comparison purposes. Advanced CO2 surfaced fluxes were used for the simulations. The results were compared to a large quantity of CO2 observation data. We find that the simulation results are sensitive to the convective transport algorithms. Overall, the three simulations are quite realistic and similar to each other in the remote marine regions, but are significantly different in some land regions with strong fluxes such as Amazon and Siberia during the convection seasons. Large biases against CO2 measurements are found in these regions in the control run, which uses the original GCM. The simulation with the simple diffusive algorithm is better. The difference of the two simulations is related to the very different convective transport speed

Comparing Global Atmospheric CO2 Flux and Transport Models with Remote Sensing (and Other) Observations

We report recent progress derived from comparison of global CO2 flux and transport models with new remote sensing and other sources of CO2 data including those from satellite. The overall objective of this activity is to improve the process models that represent our understanding of the workings of the atmospheric carbon cycle. Model estimates of CO2 surface flux and atmospheric transport processes are required for initial constraints on inverse analyses, to connect atmospheric observations to the location of surface sources and sinks, to provide the basic framework for carbon data assimilation, and ultimately for future projections of carbon-climate interactions. Models can also be used to test consistency within and between CO2 data sets under varying geophysical states. Here we focus on simulated CO2 fluxes from terrestrial vegetation and atmospheric transport mutually constrained by analyzed meteorological fields from the Goddard Modeling and Assimilation Office for the period 2000 through 2009. Use of assimilated meteorological data enables direct model comparison to observations across a wide range of scales of variability. The biospheric fluxes are produced by the CASA model at 1x1 degrees on a monthly mean basis, modulated hourly with analyzed temperature and sunlight. Both physiological and biomass burning fluxes are derived using satellite observations of vegetation, burned area (as in GFED-3), and analyzed meteorology. For the purposes of comparison to CO2 data, fossil fuel and ocean fluxes are also included in the transport simulations. In this presentation we evaluate the model's ability to simulate CO2 flux and mixing ratio variability in comparison to remote sensing observations from TCCON, GOSAT, and AIRS as well as relevant in situ observations. Examples of the influence of key process representations are shown from both forward and inverse model comparisons. We find that the model can resolve much of the synoptic, seasonal, and interannual variability in the observations, although reasons for persistent discrepancies in northern hemisphere vegetation uptake are examined. At this time, we do not find any serious shortcomings in the model transport representation, but this is still the subject of close scrutiny. In general, the fidelity of these simulations leads us to anticipate incorporation of real-time, highly resolved remote sensing and other observations into quantitative analyses that will reduce uncertainty in CO2 fluxes and revolutionize our understanding of the key processes controlling atmospheric CO2 and its evolution with time