Morphology of Three Imported Aphthona Flea Beetles Used as Biological Control Agents of Leafy Spurge

The following morphological study of the three imported Aphtona flea beetles supplies a detailed description of selected structures that will distinguish each of the three imported species and will separate them from a common native fle beetle (Glyptina atriventris) found at South Dakota release sites

CATH functional families predict functional sites in proteins

MOTIVATION: Identification of functional sites in proteins is essential for functional characterization, variant interpretation and drug design. Several methods are available for predicting either a generic functional site, or specific types of functional site. Here, we present FunSite, a machine learning predictor that identifies catalytic, ligand-binding and protein-protein interaction functional sites using features derived from protein sequence and structure, and evolutionary data from CATH functional families (FunFams). RESULTS: FunSite's prediction performance was rigorously benchmarked using cross-validation and a holdout dataset. FunSite outperformed other publicly-available functional site prediction methods. We show that conserved residues in FunFams are enriched in functional sites. We found FunSite's performance depends greatly on the quality of functional site annotations and the information content of FunFams in the training data. Finally, we analyse which structural and evolutionary features are most predictive for functional sites. AVAILABILITY: https://github.com/UCL/cath-funsite-predictor. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Ab-Initio Calculation of Molecular Aggregation Effects: a Coumarin-343 Case Study

We present time-dependent density functional theory (TDDFT) calculations for single and dimerized Coumarin-343 molecules in order to investigate the quantum mechanical effects of chromophore aggregation in extended systems designed to function as a new generation of sensors and light-harvesting devices. Using the single-chromophore results, we describe the construction of effective Hamiltonians to predict the excitonic properties of aggregate systems. We compare the electronic coupling properties predicted by such effective Hamiltonians to those obtained from TDDFT calculations of dimers, and to the coupling predicted by the transition density cube (TDC) method. We determine the accuracy of the dipole-dipole approximation and TDC with respect to the separation distance and orientation of the dimers. In particular, we investigate the effects of including Coulomb coupling terms ignored in the typical tight-binding effective Hamiltonian. We also examine effects of orbital relaxation which cannot be captured by either of these models

Exploring the protonation properties of photosynthetic phycobiliprotein pigments from molecular modeling and spectral line shapes

In photosynthesis, specialized light harvesting pigment- protein complexes (PPCs) are used to capture incident sunlight and funnel its energy to the reaction center. In Cryptophyte algae these complexes are suspended in the lumen, where the pH ranges between ~5-7, depending on the prolongation of the incident sunlight. However, the pKa of the several kinds of bilin chromophores encountered in these complexes and the effect of its protonation state on the energy transfer process is still unknown. Here, we combine quantum chemical and continuum solvent calculations to estimate the intrinsic aqueous pKas of different bilin pigments. We then use Propka and APBS classical electrostatic calculations to estimate the change in protonation free energies when the bilins are embedded inside five different phycobiliproteins (PE545, PC577, PC612, PC630 and PC645), and critically asses our results by analysis of the changes in the absorption spectral line shapes measured within a pH range from 4.0 to 9.4. Our results suggest that each individual protein environment strongly impacts the intrinsic pKa of the different chomophores, being the final responsible of their protonation state

Drivers of inter-annual variability in Net Ecosystem Exchange in a semi-arid savanna ecosystem, South Africa

Inter-annual variability in primary production and ecosystem respiration was explored using eddy-covariance data at a semi-arid savanna site in the Kruger Park, South Africa. New methods of extrapolating night-time respiration to the entire day and filling gaps in eddy-covariance data in semi-arid systems were developed. Net ecosystem exchange (NEE) in these systems occurs as pulses associated with rainfall events, a pattern not well-represented in current standard gap-filling procedures developed primarily for temperate flux sites. They furthermore do not take into account the decrease in respiration at high soil temperatures. An artificial neural network (ANN) model incorporating these features predicted measured fluxes accurately (MAE 0.42 gC/m<sup>2</sup>/day), and was able to represent the seasonal patterns of photosynthesis and respiration at the site. The amount of green leaf area (indexed using satellite-derived estimates of fractional interception of photosynthetically active radiation <i>f</i><sub>APAR</sub>), and the timing and magnitude of rainfall events, were the two most important predictors used in the ANN model. These drivers were also identified by multiple linear regressions (MLR), with strong interactive effects. The annual integral of the filled NEE data was found to range from −138 to +155 g C/m<sup>2</sup>/y over the 5 year eddy covariance measurement period. When applied to a 25 year time series of meteorological data, the ANN model predicts an annual mean NEE of 75(±105) g C/m<sup>2</sup>/y. The main correlates of this inter-annual variability were found to be variation in the amount of absorbed photosynthetically active radiation (APAR), length of the growing season, and number of days in the year when moisture was available in the soil

Modifiable risk factors for 9-year mortality in older English and Brazilian adults: The ELSA and SIGa-Bagé ageing cohorts

To quantify and compare 9-year all-cause mortality risk attributable to modifiable risk factors among older English and Brazilian adults. We used data for participants aged 60 years and older from the English Longitudinal Study of Ageing (ELSA) and the Bagé Cohort Study of Ageing (SIGa-Bagé). The five modifiable risk factors assessed at baseline were smoking, hypertension, diabetes, obesity and physical inactivity. Deaths were identified through linkage to mortality registers. For each risk factor, estimated all-cause mortality hazard ratios (HR) and population attributable fractions (PAF) were adjusted by age, sex, all other risk factors and socioeconomic position (wealth) using Cox proportional hazards modelling. We also quantified the risk factor adjusted wealth gradients in mortality, by age and sex. Among the participants, 659 (ELSA) and 638 (SIGa-Bagé) died during the 9-year follow-up. Mortality rates were higher in SIGa-Bagé. HRs and PAFs showed more similarities than differences, with physical inactivity (PAF 16.5% ELSA; 16.7% SIGa-Bagé) and current smoking (PAF 4.9% for both cohorts) having the strongest association. A clear graded relationship existed between the number of risk factors and subsequent mortality. Wealth gradients in mortality were apparent in both cohorts after full adjustment, especially among men aged 60-74 in ELSA. A different pattern was found among older women, especially in SIGa-Bagé. These findings call attention for the challenge to health systems to prevent and modify the major risk factors related to non-communicable diseases, especially physical inactivity and smoking. Furthermore, wealth inequalities in mortality persist among older adults

Role of the coordinating histidine in altering the mixed valency of CuA: An electron nuclear double resonance-electron paramagnetic resonance investigation

The binuclear CuA site engineered into Pseudomonas aeruginosa azurin has provided a CuA-azurin with a well-defined crystal structure and a CuSSCu core having two equatorial histidine ligands, His120 and His46. The mutations His120Asn and His120Gly were made at the equatorial His120 ligand to understand the histidine-related modulation to CuA, notably to the valence delocalization over the CuSSCu core. For these His120 mutants Q-band electron nuclear double resonance (ENDOR) and multifrequency electron paramagnetic resonance (EPR) (X, C, and S-band), all carried out under comparable cryogenic conditions, have provided markedly different electronic measures of the mutation-induced change. Q-band ENDOR of cysteine Cβ protons, of weakly dipolar-coupled protons, and of the remaining His46 nitrogen ligand provided hyperfine couplings that were like those of other binuclear mixed-valence CuA systems and were essentially unperturbed by the mutation at His120. The ENDOR findings imply that the CuA core electronic structure remains unchanged by the His120 mutation. On the other hand, multifrequency EPR indicated that the H120N and H120G mutations had changed the EPR hyperfine signature from a 7-line to a 4-line pattern, consistent with trapped-valence, Type 1 mononuclear copper. The multifrequency EPR data imply that the electron spin had become localized on one copper by the His120 mutation. To reconcile the EPR and ENDOR findings for the His120 mutants requires that either: if valence localization to one copper has occurred, the spin density on the cysteine sulfurs and the remaining histidine (His46) must remain as it was for a delocalized binuclear CuA center, or if valence delocalization persists, the hyperfine coupling for one copper must markedly diminish while the overall spin distribution on the CuSSCu core is preserved