Abundance In Mixture Research Articles

PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data.

Determination of serotypes of Streptococcus pneumoniae is essential for monitoring current vaccine programmes. Since October 2017, pneumococcal serotypes in England have been derived from whole genome sequencing (WGS) data using our bioinformatic tool PneumoCaT. That tool was designed for serotype determination from pure cultures in a reference laboratory. To help determine multiple serotypes in pneumococcal carriage samples, we developed a new software tool named PneumoKITy (Pneumococcal K-mer Integrated Typing) that uses the powerful Mash k-mer screening method for pneumococcal serotyping. Mash k-mer screening is more sequence specific and much faster than the mapping method used in PneumoCaT and can determine 54 (58.1 %) of the 93 serotypes in the SSI Diagnostica phenotypical serotyping scheme to type level with the remainder called to serogroup or subgroup level (e.g., 11A/D). PneumoKITy can be run on both FastQ and assembly input, requiring up to 11× less memory and running up to 29× faster than the current version of PneumoCaT (1.2.1) on FastQ files. PneumoKITy can be used as a rapid, flexible serotype screening method which adds sensitive detection of mixed serotypes, e.g., for nasopharyngeal carriage studies where the presence of multiple serotypes is common. PneumoKITy's ability to function from assembly file, for pure culture serotype detection, increases its speed. This speed potentially enables the software to be run using low infrastructure overhead via web-based platforms. PneumoKITy could be used as a fast initial screening method with other tools used for those serotypes that could not be fully determined to type level if necessary. PneumoKITy was found to be highly accurate and sensitive when run on a panel of FastQ files derived from mixed cultures with all serotypes in 47/51 (92.2 %) of samples being accurately detected. PneumoKITy was also able to accurately estimate the relative abundance of serotypes in the same sample. Estimates being within a mean relative abundance of 1.5 % of the expected abundance in mixtures with known concentrations. PneumoKITy was able to detect minor serotypes with expected abundance of 1 % in the known mixture serotypes. PneumoKITy is a rapid, flexible tool with wide-ranging applications outside of the pure-culture, reference laboratory serotyping remit of PneumoCaT.

Forest edges, tree diversity and tree identity change leaf miner diversity in a temperate forest

Abstract In forests, besides tree diversity, tree identity can determine herbivore species diversity. Herbivore species diversity can also depend on spatial factors, such as edge effects; however, empirical evidence for this remains scarce. Furthermore, patterns in herbivore diversity may differ between forest stand level and responses at individual tree species. It is therefore important to disentangle stand‐level patterns from associational responses specific to certain host species. We studied the effects of edge distance, tree diversity and tree species composition on leaf miner abundance, richness and diversity in temperate forests. We disentangled leaf miners’ responses at stand level from those of miners associated with each of three individual tree species: Quercus robur L., Quercus rubra L. and Fagus sylvatica L. We found that tree diversity increased stand‐level leaf miner richness and diversity. Fagus sylvatica and stand‐level leaf miner abundance increased closer to edges. This was suppressed at stand level in more diverse mixtures. Underlying tree diversity effects, stand‐level leaf miner metrics are strongly associated with tree species composition, due to many unique species found on F. sylvatica and Q. robur. Additionally, F. sylvatica experienced associational susceptibility to abundance in mixtures with Q. robur. Quercus robur experienced association susceptibility to miner richness in the mixture with Q. rubra. Studying the herbivore community at different spatial scales is a first step towards better understanding tree identity effects underlying tree diversity effects. Our findings emphasise context dependency of positive diversity effects on herbivores in terms of edge effects and tree species composition.

Spectral variability of plagioclase–mafic mixtures (3): Quantitative analysis applying the MGM algorithm

Among the techniques to detect planet’s mineralogical composition remote sensing, visible and near-infrared (VNIR) reflectance spectroscopy is a powerful tool, because crystal field absorption bands are related to particular transitional metals in well-defined crystal structures, e.g., Fe2+ in M1 and M2 sites of olivine (OL) or pyroxene (PX). Although OL, PX and their mixtures have been widely studied, plagioclase (PL), considered a spectroscopically transparent mineral, has been poorly analyzed.In this work we quantitatively investigate the influence of plagioclase absorption band on the absorption bands of Fe, Mg minerals using the Modified Gaussian Model – MGM (Sunshine, J.M. et al. [1990]. J. Geophys. Res. 95, 6955–6966). We consider three plagioclase compositions of varying FeO wt.% contents and five mafic end-members (1) 56% orthopyroxene and 44% clinopyroxene, (2) 28% olivine and 72% orthopyroxene, (3) 30% orthopyroxene and 70% olivine, (4) 100% olivine and (5) 100% orthopyroxene, at two different particle sizes. The spectral parameters considered here are: band depth, band center, band width, c0 (the continuum intercept) and c1 (the continuum offset). In particular, we show the variation of the plagioclase and composite (plagioclase–olivine) band spectral parameters versus the volumetric iron content related to the plagioclase abundance in mixtures. Generally, increasing the vol. FeO% due to the PL: (1) 1250nm band deepens with linear trend in mixtures with pyroxenes, while it decreases in mixtures with olivine, with trend shifting from parabolic to linear increasing the olivine content in end-member; (2) 1250nm band center moves towards longer wavelengths with linear trend in pyroxene-rich mixtures and parabolic trend in olivine-rich mixtures; and (3) 1250nm band clearly widens with linear trend in olivine-free mixtures, while the widening is only slight in olivine-rich mixtures. We also outline how spectral parameters can be ambiguous leading to an incorrect mineralogical interpretation. Furthermore, we show the presence of an asymmetry of the plagioclase band towards the IR region, resolvable adding a Gaussian in the 1600–1800nm spectral region.

Systematic T1 improvement for hyperpolarized 129xenon

The spin–lattice relaxation time T1 of hyperpolarized (HP)-129Xe was improved at typical storage conditions (i.e. low and homogeneous magnetic fields). Very long wall relaxation times T1wall of about 18h were observed in uncoated, spherical GE180 glass cells of ∅=10cm which were free of rubidium and not permanently sealed but attached to a standard glass stopcock. An “aging” process of the wall relaxation was identified by repeating measurements on the same cell. This effect could be easily removed by repeating the initial cleaning procedure. In this way, a constant wall relaxation was ensured. The Xe nuclear spin-relaxation rate 1/T1Xe–Xe due to van der Waals molecules was investigated too, by admixing three different buffer gases (N2, SF6 and CO2). Especially CO2 exhibited an unexpected high efficiency (r) in shortening the lifetime of the Xe–Xe dimers and hence prolonging the total T1 relaxation even further. These measurements also yielded an improved accuracy for the van der Waals relaxation for pure Xe (with 85% 129Xe) of T1Xe–Xe=(4.6±0.1)h. Repeating the measurements with HP 129Xe in natural abundance in mixtures with SF6, a strong dependence of T1Xe–Xe and r on the isotopic enrichment was observed, uncovering a shorter T1Xe–Xe relaxation for the 129Xe in natural composition as compared to the 85% isotopically enriched gas.

Reflectance spectroscopy of plagioclase-dominated mineral mixtures: Implications for characterizing lunar anorthosites remotely

Anorthositic rocks dominate the Moon’s upper crust. As remnants of the lunar magma ocean (LMO), small variations in the mineralogy of these rocks may hold key information about the homogeneity of LMO composition and solidification processes. Orbital near-infrared (NIR) sensors are sensitive to mineralogy, but technologic advances have only recently enabled detection of the plagioclase component in crustal rocks based on an absorption band centered near 1250 nm. Anorthosites occupy a unique mineralogic range that is well suited for NIR studies: the highly transparent component, plagioclase, is present in high abundances while the spectrally dominant mafic or oxide minerals are present in only minor abundance. As a result, spectra of anorthosites are more likely than many other rock types to contain visually discernable signatures from more than one mineral component, facilitating their identification and characterization in NIR data. In support of new NIR measurements for the Moon, we present laboratory spectral analyses of well-controlled plagioclase-dominated mineral mixtures. We focus on the spectral effects of varying mafic and oxide composition and abundance in mixtures with a common plagioclase end-member. The results demonstrate that plagioclase can be a significant contributor to reflectance spectra when strongly absorbing minerals are present in low abundance. We show that the contribution of plagioclase is more pronounced in mixtures with pyroxenes and certain spinels, but more easily masked in mixtures containing small amounts of olivine. Differences in minor mineral composition are clearly expressed in bulk spectra. Modeling of mixtures using a Hapke nonlinear approach accurately estimates mineral abundances in laboratory spectra to within 5 vol% for mixtures with ≥90 vol% plagioclase. Together, these results imply that not only should orbital NIR data sets be able to discern the presence of plagioclase in anorthositic crustal exposures, but also that detailed information about anorthosite mineral assemblages can be reliably accessed in reflectance spectra.

Simple plant traits explain functional group diversity decline in novel grassland communities of Texas

Previous research has found that plant diversity declines more quickly in exotic than native grassland plots, which offers a model system for testing whether diversity decline is associated with specific plant traits. In a common garden experiment in the Southern Great Plains in central Texas, USA, we studied monocultures and 9-species mixtures of either all exotic or all native grassland species. A total of 36 native and exotic species were paired by phylogeny and functional group. We used community-level measures (relative abundance in mixture) and whole-plant (height, aboveground biomass, and light capture) and leaf-level traits (area, specific leaf area, and C:N ratio) to determine whether trait differences explained native-exotic differences in functional group diversity. Increases in species’ relative abundance in mixture were correlated with high biomass, height, and light capture in both native and exotic communities. However, increasing exotic species were all C4 grasses, whereas, increasing native species included forb, C3 grass and C4 grass species. Exotic C4 grasses had traits associated with relatively high resource capture: greater leaf area, specific leaf area, height, biomass, and light capture, but similar leaf C:N ratios compared to native C4 grasses. Leaf C:N was consistently higher for native than exotic C3 species, implying that resource use efficiency was greater in natives than exotics. Our results suggest that functional diversity will differ between grasslands restored to native assemblages and those dominated by novel collections of exotic species, and that simple plant traits can help to explain diversity decline.

Atomic pair distribution functions analysis of disordered low-Z materials

Results of high-energy X-ray diffraction experiments coupled to atomic pair distribution function analysis of disordered low-Z materials are presented. Several scientifically and technologically important classes of disordered low-Z materials such as small and large organic molecules, graphitic powders, polymers and liquids are intentionally explored to certify the technique's performance. Results clearly show that disordered low-Z materials can be well characterized in terms of material's phase identity, relative abundance in mixtures and atomic-scale structure. The demonstrated efficiency of the technique provides the scientific community with much needed confidence to apply it more often than now.

Low target strength fish in mixed species assemblages: the case of orange roughy

AbstractUse of acoustics to estimate biomass remains problematic for mixed species assemblages, and the problem is particularlydifficult where the main species of interest has low acoustic target strength, as is the case for orange roughy. Despite their size andrelative abundance in mixtures, orange roughy have low acoustic backscatter due to their oil-filled swimbladder. Trawl catchesand acoustic target strength—length relationships at 38kHz were combined to estimate the species-specific area backscatteringcoefficients from a mixture of species on the flat areas around the North West Hills on the Chatham Rise to the east of NewZealand. Orange roughy constituted a large proportion (¯ x =48%) by weight in trawl catches, but their contribution to the areabackscattering coefficient was very low (<1%). Robust cardinalfish (30.1%), three species of rattails (White rattail=17.4%,Notable rattail=13.8% and Serrulate rattail=9.7%) and Johnson’s cod (10.8%) made much larger contributions to the areabackscattering coefficient ( values in brackets ) despite their relatively low catch rates (totaling an average of 7.6% of the catch byweight). We calculated the effect of changing the mean density of orange roughy on the backscattering coefficient by simulatingorder of magnitude increases or decreases in orange roughy densities. Increasing the density of orange roughy by a factor of10 times would only increase the area backscattering coefficient from the fish community by 3%. We conclude that changesin orange roughy density of this order are not likely to be detectable in acoustic backscatter using echo integration data. Thisdoes not mean that orange roughy cannot be separated from mixtures, but to detect them it will be necessary to use single-targetdiscrimination techniques such as the phase difference- TS methods [Barr, R., Coombs, R.F., Macaulay, G., 2000. Can wediscriminate between different deepwater fishes using a standard acoustics target strength ping? In: Proceedings of the 2000Conference on International Society for Acoustic Remote Sensing, Sydney, Australia, pp. 77–80].© 2004 Elsevier B.V. All rights reserved.

Does disturbance favour weak competitors? Mechanisms of changing plant abundance after flooding

Question: Does disturbance reduce competition intensity and thus favour weak competitors that are presumably less affected by disturbance than strong competitors? Methods: We used a single flooding event with increasing duration to simulate disturbance with increasing intensity. Six flood-plain grass species, typical of different flood regimes were grown in monocultures and in an additive species mixture. Flooding took place early in the first growing season and changes were monitored until the end of the second growing season. Results: Longer flooding durations initially decreased competition, but only a single species (Agrostis) increased its abundance in mixtures after flooding. The two weakest competitors in our selection (Poa trivialis and Elytrigia repens) failed to benefit from flooding because direct losses from flooding exceeded gains from reduced competition. Accordingly, we found no trade-off between flooding tolerance and competitive ability indicating that floods affect strong and weak competitors equally, although some species tolerated floods better than others. Conclusions: Since competition is only temporarily weakened after disturbance, increased competitive ability relative to other species may provide a more effective strategy for persistence in flood-disturbed sites. Above-ground runners seem an important prerequisite for enhanced competitive ability of clonal species in flood-disturbed sites.

Overyielding in grassland communities: testing the sampling effect hypothesis with replicated biodiversity experiments

We derive and test some assumptions and predictions of the Sampling Effect Hypothesis (SEH) by examining the relationship between the traits of species in monoculture and their relative abundance in mixture, and by comparing polyculture performance with single‐species plots. Although we found a positive relationship between production in monoculture and dominance in mixtures as predicted by the SEH, the relationship had low explanatory power. Counter to predictions, the species with the highest monoculture biomass were not able to strongly dominate all mixtures; instead the dominance of these species decreased with increasing species richness. On average, polycultures did not achieve greater biomass than (transgressively overyield) the species in each mixture, or at each site, that was most productive in monoculture. However, mixture yields did transgressively overyield both the monoculture biomass of the dominant species in the mixtures, and the weighted average of all monocultures (non‐transgressive overyielding), both of which were positively related to increasing species richness. The varying responses of different overyielding tests resulted because resource partitioning and positive interactions were often counter‐balanced by selection for species with lower biomass than the highest‐yielding monocultures. Judging whether or not mixtures overyield therefore depends in part upon which species is the basis for comparison. We present a new general framework for overyielding analysis where every monoculture provides a potential comparison and from which the most relevant tests can be selected.

Formation of submicron colloidal particles from marine bacteria by viral infection

Formation of submicron colloidal particles from marine bacteria by viral infection