Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements

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Measuring avian specialization

Measuring the extent to which a species is specialized is a major challenge in ecology, with important repercussions for fundamental research as well as for applied ecology and conservation. Here, we develop a multidimensional index of specialization based on five sets of ecological characteristics of breeding bird species. We used two recent databases of species traits of European birds based on foraging ecology, habitat, and breeding characteristics. The indices of specialization were calculated by applying the Gini coefficient, an index of inequality. The Gini coefficient is a measure of statistical dispersion on a scale between 0 and 1, reflecting a gradient from low to high specialization, respectively. Finally, we tested the strength of the phylogenetic signal of each specialization index to understand how the variance of such indices is shared throughout the phylogeny. The methods for constructing and evaluating a multidimensional index of bird specialization could also be applied to other taxa and regions, offering a simple but useful tool, particularly suited for global or biogeographic studies, as a contribution to comparative estimates of the degree of specialization of species.     

Comparative analysis of the methods used for finding surface energy to investigate protein interaction behavior on chromatographic supports

Hydrophobic interaction chromatography, an important and effective purification strategy, is generally used for the purification of variety of biomolecules. A basic understanding of the protein interaction behavior is required to effectively separate these biomolecules. A colloidal type extended Derjaguin, Landau, Verwey, and Overbeek calculations were utilized to study the interactions behavior of model proteins to commercially available hydrophobic chromatographic materials that is, Toyopearl Phenyl 650C and Toyopearl Butyl 650C. Physicochemical properties of selected model proteins were achieved by contact angle and zeta potential measurements. The contact angle of chromatographic materials used was achieved through sessile drop method on disrupted beads and capillary penetration method (CPM) on intact beads. The surface properties were further used to calculate the interactions of the proteins to chromatographic supports. The calculated secondary energy minimum of the proteins with the chromatographic materials (from the contact angle values determined through both methods can be correlated with the retention volumes from the real chromatography. The secondary energy minimum values are higher for each protein to the chromatographic materials calculated from the inputs derived through sessile drop method compared to CPM. For instance, immunoglobulin G has secondary energy minimum value of 0.17 kT compared to 0.11 kT, obtained through sessile drop method and CPM, respectively. Average relative values of the energy minimum calculated for all proteins are as 1.51 kT and 1.29 kT for Toyopearl Butyl 650C and Toyopearl Phenyl 650C, respectively, as a conversion factor for estimation of secondary energy minimum for both methods.     

Determination of community structure through deconvolution of PLFA-FAME signature of mixed population

Phospholipid fatty acids (PLFAs) as biomarkers are well established in the literature. A general method based on least square approximation (LSA) was developed for the estimation of community structure from the PLFA signature of a mixed population where biomarker PLFA signatures of the component species were known. Fatty acid methyl ester (FAME) standards were used as species analogs and mixture of the standards as representative of the mixed population. The PLFA/FAME signatures were analyzed by gas chromatographic separation, followed by detection in flame ionization detector (GC-FID). The PLFAs in the signature were quantified as relative weight percent of the total PLFA. The PLFA signatures were analyzed by the models to predict community structure of the mixture. The LSA model results were compared with the existing "functional group" approach. Both successfully predicted community structure of mixed population containing completely unrelated species with uncommon PLFAs. For slightest intersection in PLFA signatures of component species, the LSA model produced better results. This was mainly due to inability of the "functional group" approach to distinguish the relative amounts of the common PLFA coming from more than one species. The performance of the LSA model was influenced by errors in the chromatographic analyses. Suppression (or enhancement) of a component's PLFA signature in chromatographic analysis of the mixture, led to underestimation (or overestimation) of the component's proportion in the mixture by the model. In mixtures of closely related species with common PLFAs, the errors in the common components were adjusted across the species by the model.     

2020年邳州市草地贪夜蛾初迁虫源的迁入路径及气象背景

2020年江苏省邳州市于3月31日发现草地贪夜蛾Spodoptera frugiperda成虫,远早于该地区2019年草地贪夜蛾的始见期6月份。为明确该地区草地贪夜蛾种群性质,利用昆虫轨迹分析方法,模拟分析了2020年江苏省邳州市早期发现的草地贪夜蛾的迁飞路径及天气背景场。结果表明：邳州市2019年12月-2020年2月温度低,草地贪夜蛾无法在此地越冬存活,2020年3月31日所诱捕的草地贪夜蛾为外地迁入,其虫源来自广西和广东西部的周年繁殖区;虽然邳州市3月份常年盛行北风和西北风,西南风发生概率低导致草地贪夜蛾迁入邳州市概率较小,但2020年3月底850 hPa的强西南气流为草地贪夜蛾从我国华南地区迁入邳州市提供了条件。本研究结果阐明了在极端条件下草地贪夜蛾从华南地区迁入江苏省的可能性,丰富了江苏省草地贪夜蛾春季早期迁入的理论依据。     

Using root traits to understand temporal changes in biodiversity effects in grassland mixtures

Biodiversity–ecosystem functioning (BEF) studies typically show that species richness enhances community biomass, but the underlying mechanisms remain debated. Here, we combine metrics from BEF research that distinguish the contribution of dominant species (selection effects, SE) from those due to positive interactions such as resource partitioning (complementarity effects, CE) with a functional trait approach in an attempt to reveal the functional characteristics of species that drive community biomass in species mixtures. In a biodiversity experiment with 16 plant species in monocultures, 4‐species and 16‐species mixtures, we used aboveground biomass to determine the relative contributions of CE and SE to biomass production in mixtures in the second, dry year of the experiment. We also measured root traits (specific root length, root length density, root tissue density and the deep root fraction) of each species in monocultures and linked the calculated community weighted mean (CWM) trait values and trait diversity of mixtures to CE and SE. In the second year of the experiment, community biomass, CE and SE increased compared to the first year. The contribution of SE to this positive effect was greater than that of CE. The increased contribution of SE was associated with root traits: SE increased most in communities with high abundance of species with deep, thick and dense roots. In contrast, changes in CE were not related to trait diversity or CWM trait values. Together, these results suggest that increased positive effects of species richness on community biomass in a dry year were mainly driven by increased dominance of deep‐rooting species, supporting the insurance hypothesis of biodiversity. Positive CE indicates that other positive interactions did occur, but we could not find evidence that belowground resource partitioning or facilitation via root trait diversity was important for community productivity in our biodiversity experiment.     

Designing an immunoinformatic vaccine for peri-implantitis using a structural biology approach

ObjectivesPeri-implantitis is a destructive inflammatory process that affects the soft and hard tissues around dental implants. porphyromonas gingivalis, an anaerobic gram-negative bacterium, appears to be the main culprit. Since there is no efficient and specific vaccine to treat peri-implantitis, the goal of our research has been to develop a multi-epitope vaccination utilizing an immunoinformatics approach that targeted P. gingivalis type I fim A.Materials and methodsP. gingivalis peptides 6JKZ and 6KMF are suitable for vaccine development. B- and T-cell epitopes from 6KMF and 6JKZ were detected and evaluated based on critical factors to produce a multi-epitope vaccine construct. It was assessed based on allergenicity, antigenicity, stability. The vaccine's dual major histocompatibility complex (MHC-I and MHC-II) binding epitopes allowed it to reach a larger population. P. gingivalis fimbriae induce immune subversion through TLR -CXCR4 receptor complex pathway. The ClusPro 2.0 server was used to do the molecular docking using TLR2 - CXCR4 and vaccine epitopes as receptor and ligand respectively.ResultsThe designed vaccine was non-allergenic and had a high antigenicity, solubility, and stability. The 3D structure of the vaccine revealed strong interaction with CXCR4(TLR2) using molecular docking. The vaccine-CXCR4 interface was more consistent, possibly because the vaccination has a higher affinity for the CXCR4-TLR2 complex.ConclusionThis study details the vaccine's distinct and sustained interaction with the CXCR4(TLR2) immunological receptor and its consistent and effective utterance in the bacterial system. As a result, our vaccine formulation will evoke a significant memory response and induce an adaptive immune response against P. gingivalis.     

Dynamical systems analysis of arterial blood pressure signals in relation to heart rate fluctuations in chick embryos

We attempted a new approach based on a modern dynamical system theory to reconstruct the arterial blood pressure signals in relation to heart rate fluctuations of developing chick embryos. The dynamical systems approach in general is to model a phenomenon that is presented by a single time series record and approximate the dynamical property (e.g. heart rate fluctuations) of a system based only on information contained in a single-variable (arterial blood pressure) of the system. The time-series data of the arterial blood pressure was reconstructed in 3-dimensional space to draw characteristic orbits. Since the reconstructed orbits of the blood pressure should retain information contained in the pressure signals, we attempted to derive instantaneous heart rate (IHR) from the reconstructed orbits. The derived IHR presenting HR fluctuations coincided well with the IHR obtained conventionally from the peak-to-peak time intervals of the maximum blood pressure. Movements of the reconstructed orbits of the arterial blood pressure in 3-dimensional space reflected HR fluctuations (i.e. transient decelerations and accelerations).     

Cell balance equation for chemotactic bacteria with a biphasic tumbling frequency

Alts three-dimensional cell balance equation characterizing the chemotactic bacteria was analyzed under the presence of one-dimensional spatial chemoattractant gradients. Our work differs from that of others who have developed rather general models for chemotaxis in the use of a non-smooth anisotropic tumbling frequency function that responds biphasically to the combined temporal and spatial chemoattractant gradients. General three-dimensional expressions for the bacterial transport parameters were derived for chemotactic bacteria, followed by a perturbation analysis under the planar geometry. The bacterial random motility and chemotaxis were summarized by a motility tensor and a chemotactic velocity vector, respectively. The consequence of invoking the diffusion-approximation assumption and using intrinsic one-dimensional models with modified cellular swimming speeds was investigated by numerical simulations. Characterizing the bacterial random orientation after tumbles by a turn angle probability distribution function, we found that only the first-order angular moment of this turn angle probability distribution is important in influencing the bacterial long-term transport. Mathematics Subject Classification (2000):60G05, 60J60, 82A70