Intraspecific competition replaces interspecific facilitation as abiotic stress decreases: The shifting nature of plant–plant interactions

Plant–plant interactions change depending on environmental conditions, shifting from competition to facilitation when the stress is high. In addition to these changes, the relevance of intraspecific compared to interspecific interactions may also shift as abiotic stress does. We inferred intra- and interspecific plant–plant interactions of the cushion plant Hormathophylla spinosa as related to the dominant shrub Juniperus sabina in two sites with contrasting abiotic conditions (a slope with high-stress conditions vs. a valley bottom with milder conditions) in a Mediterranean high mountain. Specifically, we studied the spatial patterns and several variables related to plant performance (plant size and form, non-structural carbohydrate – NSC – concentrations and radial growth) of H. spinosa.The spatial pattern varied depending on site conditions. H. spinosa plants were positively associated with juniper in the high-stress slope site, probably through higher establishment rates due to the amelioration of soil conditions. In contrast, in the milder valley site H. spinosa establishment occurred mostly in open areas. Age structure, inferred from annual rings, reflected a massive establishment event in the whole study area which occurred 30–50 years ago. Canopy variables and radial growth were density dependent: both were negatively affected by the high density of H. spinosa individuals in the valley, but favoured by junipers on the slope. Interestingly, NSCs showed the opposite pattern, suggesting lower investment in growth by H. spinosa plants in the valley than on the slope.Our results reinforce the strong links existing between intra- and interspecific relationships and the need to include both when studying the influence of abiotic conditions on plant–plant interactions. This approach enabled us to detect that the direction and intensity of plant–plant interactions may shift at different ecological levels. Particularly interesting was the finding that optimal sites at the population level may not necessarily be the sites showing maximum individual performance.     

Balearic insular isolation and large continental spread framed the phylogeography of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae)

Recent Quaternary geological and climate events have shaped the evolutionary histories of plant species in the Mediterranean basin, one of the most important hotspots of biodiversity. Genetic analyses of the western Mediterranean Cheirolophus intybaceus s.l. (Asteraceae) based on AFLP were conducted to establish the relationships between its close species and populations, to reconstruct the phylogeography of the group and to analyse potential unidirectional versus bidirectional dispersals between the Ibero‐Provençal belt and the Balearic Islands. AFLP data revealed two main genetic groups, one constituted by the Balearic populations and Garraf (NE Iberia) and the other formed by the remaining mainland populations that were further sub‐structured into two geographically separated subgroups (SE + E Iberia and NE Iberia + SW France). Genetic diversity and spatial structure analyses suggested a mid‐Pleistocene scenario for the origin of C. intybaceus in southern Iberia, followed by dispersal to the north and a single colonisation event of the Balearic archipelago from the near Dianic NE Iberian area. This hypothesis was supported by paleogeographic data, which showed the existence of terrestrial connections between the continent and the islands during the Middle–Late Pleistocene marine regressions, whereas the more recent single back‐colonisation of the mainland from Mallorca might be explained by several hypotheses, such as long‐distance dispersal mediated by migratory marine birds or sea currents.     

Environmental and socio‐economic factors related to urban bird communities

Urban fauna communities may be strongly influenced by environmental and socio‐economic factors, but the relative importance of these factors is poorly known. Most research on urban fauna has been conducted in large cities and it is unclear if the patterns found in these locations coincide with those from smaller human settlements. We examined the relative importance of environmental and socio‐economic factors in explaining variation in urban bird communities across 72 neighbourhoods in 18 regional towns in south‐eastern Australia. Native bird species richness varied from 6 to 32 across neighbourhoods and was higher in neighbourhoods with more nectar‐rich plants. Variation in bird species diversity across neighbourhoods was also strongly positively related to the density of nectar‐rich plants, but was higher also in neighbourhoods with higher socio‐economic status (reflecting higher levels of disposal income, education and home ownership). The density of native birds across neighbourhoods per season varied from 1 to 15 birds per hectare and was lower in neighbourhoods with a greater cover of impervious surfaces. The density of exotic birds (introduced to Australia) per season also varied across neighbourhoods (0–13 birds per hectare) and was lower in neighbourhoods with more nectar‐rich plants and higher in neighbourhoods with greater impervious surface cover. Our results demonstrated that the vegetation characteristics of household gardens, along streetscapes and in urban parklands had a strong influence on the richness and diversity of urban bird communities. The density of native and exotic birds varied primarily in response to changes in the built environment (measured through impervious surface cover). Socio‐economic factors had relatively little direct influence on urban birds, but neighbourhood socio‐economics may influence bird communities indirectly through the positive relationship between socio‐economic status and vegetation cover recorded in our study area.     

Rehabilitation of former Snowy Scheme sites in Kosciuszko National Park

Ten years of restoration work at 200 sites within Kosciuszko National Park – sites damaged during the construction of Australia's most iconic hydroelectric scheme – is showing substantial progress and is contributing to the protection of the park's internationally significant ecosystems.     

Does the presence of grassy strips and landscape grain affect the spatial distribution of aphids and their carabid predators?

• 1 We investigated, over the course of 2 years, the spatial distribution and abundance of two species of aphid, Metopolophium dirhodum and Sitobion avenae, and predatory species of carabid. This was undertaken in 24 wheat fields in ‘coarse‐grain’ and ‘fine‐grain’ landscapes in western France. A greater percentage of the latter landscape was covered by hedgerows and grassland and the total area covered by fields and the average size of the fields were smaller.
• 2 The effects on aphid abundance of the distance from field margins, the presence of grassy strips and carabid abundance were determined in both landscapes.
• 3 Both aphid species were more abundant in the ‘fine‐grain’ landscape, which may have been a result of the higher density of semi‐natural elements. In both types of landscape, the total numbers of aphids were negatively correlated with the distance from the field margin. This may have been because aphids were dispersing from overwintering sites in field margins. The abundance of M. dirhodum was strongly negatively correlated with the presence of grassy strips in the ‘coarse‐grain’ landscape, although there were no such significant correlations for either of the aphid species in the ‘fine‐grain’ landscape.
• 4 Aphid and carabid abundances were negatively correlated in the ‘fine‐grain’ and positively in ‘coarse‐grain’ landscape.
• 5 The results obtained in the present study emphasize the importance of semi‐natural areas in agricultural landscapes in shaping the spatial distribution of aphids and carabid beetles, their natural enemies, at different spatial scales.

     

Lorentz force in water: evidence that hydronium cyclotron resonance enhances polymorphism

Abstract

There is an ongoing question regarding the structure forming capabilities of water at ambient temperatures. To probe for different structures, we studied effects in pure water following magnetic field exposures corresponding to the ion cyclotron resonance of H₃O⁺. Included were measurements of conductivity and pH. We find that under ion cyclotron resonance (ICR) stimulation, water undergoes a transition to a form that is hydroxonium-like, with the subsequent emission of a transient 48.5?Hz magnetic signal, in the absence of any other measurable field. Our results indicate that hydronium resonance stimulation alters the structure of water, enhancing the concentration of EZ-water. These results are not only consistent with Del Giudice's model of electromagnetically coherent domains, but they can also be interpreted to show that these domains exist in quantized spin states.     

Scale matters

During meiosis in many organisms, homologous chromosomes engage in numerous recombination events initiated by DNA double-strand breaks (DSBs) formed by the Spo11 protein. DSBs are distributed nonrandomly, which governs how recombination influences inheritance and genome evolution. The chromosomal features that shape DSB distribution are not well understood. In the budding yeast Saccharomyces cerevisiae, trimethylation of lysine 4 of histone H3 (H3K4me3) has been suggested to play a causal role in targeting Spo11 activity to small regions of preferred DSB formation called hotspots. The link between H3K4me3 and DSBs is supported in part by a genome-wide spatial correlation between the two. However, this correlation has only been evaluated using relatively low-resolution maps of DSBs, H3K4me3 or both. These maps illuminate chromosomal features that influence DSB distributions on a large scale (several kb and greater) but do not adequately resolve features, such as chromatin structure, that act on finer scales (kb and shorter). Using recent nucleotide-resolution maps of DSBs and meiotic chromatin structure, we find that the previously described spatial correlation between H3K4me3 and DSB hotspots is principally attributable to coincident localization of both to gene promoters. Once proximity to the nucleosome-depleted regions in promoters is accounted for, H3K4me3 status has only modest predictive power for determining DSB frequency or location. This analysis provides a cautionary tale about the importance of scale in genome-wide analyses of DSB and recombination patterns.     

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy.NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner.     

Monoclonal antibodies in neuro-oncology

Monoclonal antibodies (mAbs) are used with increasing success against many tumors but, for brain tumors, the blood-brain barrier (BBB) is a special concern. The BBB prevents antibody entry to the normal brain; however, its role in brain tumor therapy is more complex. The BBB is closest to normal at micro-tumor sites; its properties and importance change as the tumor grows. In this review, evolving insight into the role of the BBB is balanced against other factors that affect efficacy or interpretation when mAbs are used against brain tumor targets. As specific examples, glioblastoma multiforme (GBM), primary central nervous system lymphoma (PCNSL) and blood-borne metastases from breast cancer are discussed in the context of treatment, respectively, with the mAbs bevacizumab, rituximab, and trastuzumab, each of which is already widely used against tumor outside the brain. It is suggested that success against brain tumors will require getting past the BBB in two senses: physically, to better attack brain tumor targets and conceptually, to give equal attention to problems that are shared with other tumor sites.     

Prediction of methionine oxidation risk in monoclonal antibodies using a machine learning method

ABSTRACT

Monoclonal antibodies (mAbs) have become a major class of protein therapeutics that target a spectrum of diseases ranging from cancers to infectious diseases. Similar to any protein molecule, mAbs are susceptible to chemical modifications during the manufacturing process, long-term storage, and in vivo circulation that can impair their potency. One such modification is the oxidation of methionine residues. Chemical modifications that occur in the complementarity-determining regions (CDRs) of mAbs can lead to the abrogation of antigen binding and reduce the drug’s potency and efficacy. Thus, it is highly desirable to identify and eliminate any chemically unstable residues in the CDRs during the therapeutic antibody discovery process. To provide increased throughput over experimental methods, we extracted features from the mAbs’ sequences, structures, and dynamics, used random forests to identify important features and develop a quantitative and highly predictive in silico methionine oxidation model.